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M.; Cremer, Olaf L. title: Cytomegalovirus reactivation and mortality in patients with acute respiratory distress syndrome date: 2016-03-01 journal: Intensive Care Med DOI: 10.1007/s00134-015-4071-z sha: doc_id: 1938 cord_uid: n2d5fw2f file: cache/cord-001690-cn21fgug.json key: cord-001690-cn21fgug authors: Franceschi, Valentina; Parker, Scott; Jacca, Sarah; Crump, Ryan W.; Doronin, Konstantin; Hembrador, Edguardo; Pompilio, Daniela; Tebaldi, Giulia; Estep, Ryan D.; Wong, Scott W.; Buller, Mark R.; Donofrio, Gaetano title: BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1((-/-)) Mice from Monkeypoxvirus Lethal Challenge date: 2015-06-18 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0003850 sha: doc_id: 1690 cord_uid: cn21fgug file: cache/cord-010130-28bt3x25.json key: cord-010130-28bt3x25 authors: Crocchiolo, R.; Bramanti, S.; Vai, A.; Sarina, B.; Mineri, R.; Casari, E.; Tordato, F.; Mauro, E.; Timofeeva, I.; Lugli, E.; Mavilio, D.; Carlo‐Stella, C.; Santoro, A.; Castagna, L. title: Infections after T‐replete haploidentical transplantation and high‐dose cyclophosphamide as graft‐versus‐host disease prophylaxis date: 2015-03-26 journal: Transpl Infect Dis DOI: 10.1111/tid.12365 sha: doc_id: 10130 cord_uid: 28bt3x25 file: cache/cord-003376-2qi4aibx.json key: cord-003376-2qi4aibx authors: van de Groep, Kirsten; Nierkens, Stefan; Cremer, Olaf L.; Peelen, Linda M.; Klein Klouwenberg, Peter M. C.; Schultz, Marcus J.; Hack, C. Erik; van der Poll, Tom; Bonten, Marc J. M.; Ong, David S. Y. title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date: 2018-12-18 journal: Crit Care DOI: 10.1186/s13054-018-2261-0 sha: doc_id: 3376 cord_uid: 2qi4aibx file: cache/cord-006713-io9yp1y2.json key: cord-006713-io9yp1y2 authors: Wrede, C. E.; Holler, E. title: Intensivmedizinische Betreuung von Patienten nach Stammzelltransplantation date: 2007 journal: Intensivmed Notfallmed DOI: 10.1007/s00390-007-0774-x sha: doc_id: 6713 cord_uid: io9yp1y2 file: cache/cord-016478-gpl0zbvd.json key: cord-016478-gpl0zbvd authors: Barry, Maura; Chandra, Sunandana; Hymes, Kenneth B. title: Cytopenias in Transplant Patients date: 2018-12-08 journal: Principles and Practice of Transplant Infectious Diseases DOI: 10.1007/978-1-4939-9034-4_10 sha: doc_id: 16478 cord_uid: gpl0zbvd file: cache/cord-004591-2hchnlwb.json key: cord-004591-2hchnlwb authors: Wicker, S.; Friedrichs, I.; Rabenau, H.F. title: Seroprävalenz von Antikörpern gegen schwangerschaftsrelevante virale Infektionserreger bei Mitarbeiterinnen im Gesundheitswesen date: 2012-07-25 journal: Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz DOI: 10.1007/s00103-012-1509-0 sha: doc_id: 4591 cord_uid: 2hchnlwb file: cache/cord-006841-3u56erru.json key: cord-006841-3u56erru authors: Einsele, Hermann; Bertz, Hartmut; Beyer, Jörg; Kiehl, Michael G.; Runde, Volker; Kolb, Hans-Jochen; Holler, Ernst; Beck, Robert; Schwerdfeger, Rainer; Schumacher, Ulrike; Hebart, Holger; Martin, Hans; Kienast, Joachim; Ullmann, Andrew J.; Maschmeyer, Georg; Krüger, William; Niederwieser, Dietger; Link, Hartmut; Schmidt, Christian A.; Oettle, Helmut; Klingebiel, Thomas title: Infectious complications after allogeneic stem cell transplantation: epidemiology and interventional therapy strategies: Guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncology (DGHO) date: 2003-09-10 journal: Ann Hematol DOI: 10.1007/s00277-003-0772-4 sha: doc_id: 6841 cord_uid: 3u56erru file: cache/cord-007575-5ekgabx5.json key: cord-007575-5ekgabx5 authors: Luby, James P. title: Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date: 2016-01-14 journal: Am J Med Sci DOI: 10.1097/00000441-198707000-00007 sha: doc_id: 7575 cord_uid: 5ekgabx5 file: cache/cord-004059-furt6xcn.json key: cord-004059-furt6xcn authors: Hraiech, Sami; Bonnardel, Eline; Guervilly, Christophe; Fabre, Cyprien; Loundou, Anderson; Forel, Jean-Marie; Adda, Mélanie; Parzy, Gabriel; Cavaille, Guilhem; Coiffard, Benjamin; Roch, Antoine; Papazian, Laurent title: Herpes simplex virus and Cytomegalovirus reactivation among severe ARDS patients under veno-venous ECMO date: 2019-12-23 journal: Ann Intensive Care DOI: 10.1186/s13613-019-0616-6 sha: doc_id: 4059 cord_uid: furt6xcn file: cache/cord-016267-idrc1sdh.json key: cord-016267-idrc1sdh authors: Ljungman, Per title: Viral Infections in Hematopoietic Stem Cell Transplant Recipients date: 2009-11-27 journal: Allogeneic Stem Cell Transplantation DOI: 10.1007/978-1-59745-478-0_29 sha: doc_id: 16267 cord_uid: idrc1sdh file: cache/cord-015922-5wwy0m2k.json key: cord-015922-5wwy0m2k authors: Marty, Francisco M.; Baden, Lindsey R. title: Infection in the Hematopoietic Stem Cell Transplant Recipient date: 2008 journal: Hematopoietic Stem Cell Transplantation DOI: 10.1007/978-1-59745-438-4_19 sha: doc_id: 15922 cord_uid: 5wwy0m2k file: cache/cord-001079-v01vwu00.json key: cord-001079-v01vwu00 authors: Thoden, J.; Potthoff, A.; Bogner, J. R.; Brockmeyer, N. H.; Esser, S.; Grabmeier-Pfistershammer, K.; Haas, B.; Hahn, K.; Härter, G.; Hartmann, M.; Herzmann, C.; Hutterer, J.; Jordan, A. R.; Lange, C.; Mauss, S.; Meyer-Olson, D.; Mosthaf, F.; Oette, M.; Reuter, S.; Rieger, A.; Rosenkranz, T.; Ruhnke, M.; Schaaf, B.; Schwarze, S.; Stellbrink, H. 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M.; d'Arienzo, P.; Jovine, E.; Grazi, G. L.; Mazziotti, A.; Maffei, M.; Muzzi, C.; Tancioni, S.; Sama, C.; Cavallari, A.; Gavelli, G. title: Pulmonary complications of liver transplantation: radiological appearance and statistical evaluation of risk factors in 300 cases date: 2000 journal: Eur Radiol DOI: 10.1007/s003309900268 sha: doc_id: 6586 cord_uid: 49btg9w7 file: cache/cord-023854-w8kx5n8k.json key: cord-023854-w8kx5n8k authors: Schuster, V.; Kreth, H. 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Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2018-04-23 journal: J Clin Immunol DOI: 10.1007/s10875-018-0485-z sha: doc_id: 6466 cord_uid: e1phpqes file: cache/cord-009567-osstpum6.json key: cord-009567-osstpum6 authors: nan title: Abstracts Oral date: 2008-04-23 journal: Am J Transplant DOI: 10.1111/j.1600-6143.2008.02254.x sha: doc_id: 9567 cord_uid: osstpum6 file: cache/cord-022888-dnsdg04n.json key: cord-022888-dnsdg04n authors: nan title: Poster Sessions date: 2009-08-19 journal: Eur J Immunol DOI: 10.1002/eji.200990224 sha: doc_id: 22888 cord_uid: dnsdg04n file: cache/cord-005460-ezrn8cva.json key: cord-005460-ezrn8cva authors: nan title: Physicians – Poster Session date: 2017-07-28 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2017.134 sha: doc_id: 5460 cord_uid: ezrn8cva file: cache/cord-005453-4057qib7.json key: cord-005453-4057qib7 authors: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 journal: Bone Marrow Transplant DOI: 10.1038/s41409-019-0559-4 sha: doc_id: 5453 cord_uid: 4057qib7 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-cmv-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39913 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38539 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39203 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39426 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40699 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41206 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41616 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40150 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40718 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41592 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39163 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41334 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41655 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45032 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42765 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38869 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41027 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 44328 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45451 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45892 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-004591-2hchnlwb author: Wicker, S. title: Seroprävalenz von Antikörpern gegen schwangerschaftsrelevante virale Infektionserreger bei Mitarbeiterinnen im Gesundheitswesen date: 2012-07-25 pages: extension: .txt txt: ./txt/cord-004591-2hchnlwb.txt cache: ./cache/cord-004591-2hchnlwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004591-2hchnlwb.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43152 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47387 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43594 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45769 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47702 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46354 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47265 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47250 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47904 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47444 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47967 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47887 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === Traceback (most recent call last): File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-193356-hqbstgg7' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/file2bib.py", line 64, in if ( bibliographics.loc[ escape ,'author'] ) : author = bibliographics.loc[ escape,'author'] File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1762, in __getitem__ return self._getitem_tuple(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1272, in _getitem_tuple return self._getitem_lowerdim(tup) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1389, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1965, in _getitem_axis return self._get_label(key, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 625, in _get_label return self.obj._xs(label, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/generic.py", line 3537, in xs loc = self.index.get_loc(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-193356-hqbstgg7' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48121 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45355 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46169 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48704 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46922 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46003 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-003376-2qi4aibx author: van de Groep, Kirsten title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date: 2018-12-18 pages: extension: .txt txt: ./txt/cord-003376-2qi4aibx.txt cache: ./cache/cord-003376-2qi4aibx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003376-2qi4aibx.txt' === file2bib.sh === id: cord-001938-n2d5fw2f author: Ong, David S. Y. title: Cytomegalovirus reactivation and mortality in patients with acute respiratory distress syndrome date: 2016-03-01 pages: extension: .txt txt: ./txt/cord-001938-n2d5fw2f.txt cache: ./cache/cord-001938-n2d5fw2f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001938-n2d5fw2f.txt' === file2bib.sh === id: cord-010130-28bt3x25 author: Crocchiolo, R. title: Infections after T‐replete haploidentical transplantation and high‐dose cyclophosphamide as graft‐versus‐host disease prophylaxis date: 2015-03-26 pages: extension: .txt txt: ./txt/cord-010130-28bt3x25.txt cache: ./cache/cord-010130-28bt3x25.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010130-28bt3x25.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49007 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47176 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46522 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47982 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-004059-furt6xcn author: Hraiech, Sami title: Herpes simplex virus and Cytomegalovirus reactivation among severe ARDS patients under veno-venous ECMO date: 2019-12-23 pages: extension: .txt txt: ./txt/cord-004059-furt6xcn.txt cache: ./cache/cord-004059-furt6xcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004059-furt6xcn.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49888 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49281 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48842 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-006841-3u56erru author: Einsele, Hermann title: Infectious complications after allogeneic stem cell transplantation: epidemiology and interventional therapy strategies: Guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncology (DGHO) date: 2003-09-10 pages: extension: .txt txt: ./txt/cord-006841-3u56erru.txt cache: ./cache/cord-006841-3u56erru.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006841-3u56erru.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48106 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-016478-gpl0zbvd author: Barry, Maura title: Cytopenias in Transplant Patients date: 2018-12-08 pages: extension: .txt txt: ./txt/cord-016478-gpl0zbvd.txt cache: ./cache/cord-016478-gpl0zbvd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016478-gpl0zbvd.txt' === file2bib.sh === id: cord-006713-io9yp1y2 author: Wrede, C. E. title: Intensivmedizinische Betreuung von Patienten nach Stammzelltransplantation date: 2007 pages: extension: .txt txt: ./txt/cord-006713-io9yp1y2.txt cache: ./cache/cord-006713-io9yp1y2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006713-io9yp1y2.txt' === file2bib.sh === id: cord-015139-s7ox0h4f author: Stockschläder, M. title: Atemwegsinfektionen bei immunsupprimierten Personen date: 2003 pages: extension: .txt txt: ./txt/cord-015139-s7ox0h4f.txt cache: ./cache/cord-015139-s7ox0h4f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015139-s7ox0h4f.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49357 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47688 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-288721-3bv3aak6 author: Schneider, Annika title: Single organelle analysis to characterize mitochondrial function and crosstalk during viral infection date: 2019-06-11 pages: extension: .txt txt: ./txt/cord-288721-3bv3aak6.txt cache: ./cache/cord-288721-3bv3aak6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288721-3bv3aak6.txt' === file2bib.sh === id: cord-001690-cn21fgug author: Franceschi, Valentina title: BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1((-/-)) Mice from Monkeypoxvirus Lethal Challenge date: 2015-06-18 pages: extension: .txt txt: ./txt/cord-001690-cn21fgug.txt cache: ./cache/cord-001690-cn21fgug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001690-cn21fgug.txt' === file2bib.sh === id: cord-311505-akcc9oms author: Geisen, Will R. title: Cytomegalovirus Enterocolitis secondary to experimental COVID-19 therapy date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-311505-akcc9oms.txt cache: ./cache/cord-311505-akcc9oms.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311505-akcc9oms.txt' === file2bib.sh === id: cord-340228-mvqoyror author: Al-Herz, Waleed title: Spectrum of Viral Infections Among Primary Immunodeficient Children: Report From a National Registry date: 2019-05-29 pages: extension: .txt txt: ./txt/cord-340228-mvqoyror.txt cache: ./cache/cord-340228-mvqoyror.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340228-mvqoyror.txt' === file2bib.sh === id: cord-004643-uu4uipfy author: Hasan, Mohammad Rubayet title: Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report date: 2020-03-20 pages: extension: .txt txt: ./txt/cord-004643-uu4uipfy.txt cache: ./cache/cord-004643-uu4uipfy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004643-uu4uipfy.txt' === file2bib.sh === id: cord-016267-idrc1sdh author: Ljungman, Per title: Viral Infections in Hematopoietic Stem Cell Transplant Recipients date: 2009-11-27 pages: extension: .txt txt: ./txt/cord-016267-idrc1sdh.txt cache: ./cache/cord-016267-idrc1sdh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016267-idrc1sdh.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40393 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-348547-wmvqvbqi author: Desmons, Aurore title: Post-mortem diagnosis, of cytomegalovirus and varicella zoster virus co-infection by combined histology and tissue molecular biology, in a sudden unexplained infant death date: 2013-10-31 pages: extension: .txt txt: ./txt/cord-348547-wmvqvbqi.txt cache: ./cache/cord-348547-wmvqvbqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348547-wmvqvbqi.txt' === file2bib.sh === id: cord-282618-tjvjlyn9 author: Luke, J M title: Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers date: 2010-11-25 pages: extension: .txt txt: ./txt/cord-282618-tjvjlyn9.txt cache: ./cache/cord-282618-tjvjlyn9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282618-tjvjlyn9.txt' === file2bib.sh === id: cord-323691-5s5almd2 author: Mishin, Vasiliy P title: A ‘minimal’ approach in design of flavivirus infectious DNA date: 2001-12-04 pages: extension: .txt txt: ./txt/cord-323691-5s5almd2.txt cache: ./cache/cord-323691-5s5almd2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323691-5s5almd2.txt' === file2bib.sh === id: cord-315304-pge45105 author: Kotton, C.N. title: Organ Transplantation, Risks date: 2015-03-06 pages: extension: .txt txt: ./txt/cord-315304-pge45105.txt cache: ./cache/cord-315304-pge45105.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315304-pge45105.txt' === file2bib.sh === id: cord-279638-jr1mbh7s author: Calore, Elisabetta title: Treatment of Acute Graft-versus-Host Disease in Childhood with Extracorporeal Photochemotherapy/Photopheresis: The Padova Experience date: 2015-07-14 pages: extension: .txt txt: ./txt/cord-279638-jr1mbh7s.txt cache: ./cache/cord-279638-jr1mbh7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279638-jr1mbh7s.txt' === file2bib.sh === id: cord-019009-3ngfv96u author: Gea-Banacloche, Juan title: Risks and Epidemiology of Infections After Hematopoietic Stem Cell Transplantation date: 2016-02-15 pages: extension: .txt txt: ./txt/cord-019009-3ngfv96u.txt cache: ./cache/cord-019009-3ngfv96u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-019009-3ngfv96u.txt' === file2bib.sh === id: cord-023854-w8kx5n8k author: Schuster, V. title: Virusinfektionen date: 2019 pages: extension: .txt txt: ./txt/cord-023854-w8kx5n8k.txt cache: ./cache/cord-023854-w8kx5n8k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-023854-w8kx5n8k.txt' === file2bib.sh === id: cord-018785-tcr5xlf8 author: Nambiar, Puja title: Infection in Kidney Transplantation date: 2018-06-27 pages: extension: .txt txt: ./txt/cord-018785-tcr5xlf8.txt cache: ./cache/cord-018785-tcr5xlf8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018785-tcr5xlf8.txt' === file2bib.sh === id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-269194-b1wlr3t7.txt cache: ./cache/cord-269194-b1wlr3t7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269194-b1wlr3t7.txt' === file2bib.sh === id: cord-023669-3ataw6gy author: Masur, Henry title: Critically Ill Immunosuppressed Host date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-023669-3ataw6gy.txt cache: ./cache/cord-023669-3ataw6gy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023669-3ataw6gy.txt' === file2bib.sh === id: cord-348130-t9tysvr8 author: Cho, Sung-Yeon title: Infectious complications after hematopoietic stem cell transplantation: current status and future perspectives in Korea date: 2018-02-27 pages: extension: .txt txt: ./txt/cord-348130-t9tysvr8.txt cache: ./cache/cord-348130-t9tysvr8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-348130-t9tysvr8.txt' === file2bib.sh === id: cord-296402-rd5clf8h author: José Castón, Juan title: Efectos de la infección viral en el paciente trasplantado date: 2007-10-31 pages: extension: .txt txt: ./txt/cord-296402-rd5clf8h.txt cache: ./cache/cord-296402-rd5clf8h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296402-rd5clf8h.txt' === file2bib.sh === id: cord-017030-tzuyo6tx author: Henao-Martínez, Andrés F. title: Infections in Heart, Lung, and Heart-Lung Transplantation date: 2018-12-08 pages: extension: .txt txt: ./txt/cord-017030-tzuyo6tx.txt cache: ./cache/cord-017030-tzuyo6tx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017030-tzuyo6tx.txt' === file2bib.sh === id: cord-103297-4stnx8dw author: Widrich, Michael title: Modern Hopfield Networks and Attention for Immune Repertoire Classification date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-103297-4stnx8dw.txt cache: ./cache/cord-103297-4stnx8dw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103297-4stnx8dw.txt' === file2bib.sh === id: cord-016990-ot1wi3xi author: Zaki, Sherif R. title: Viral Infections of the Lung date: 2008 pages: extension: .txt txt: ./txt/cord-016990-ot1wi3xi.txt cache: ./cache/cord-016990-ot1wi3xi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016990-ot1wi3xi.txt' === file2bib.sh === id: cord-015389-vwgai4k9 author: nan title: Publication only date: 2009-03-25 pages: extension: .txt txt: ./txt/cord-015389-vwgai4k9.txt cache: ./cache/cord-015389-vwgai4k9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015389-vwgai4k9.txt' === file2bib.sh === id: cord-015365-iqdi99pd author: nan title: 25th Annual Meeting of the Austrian Society of Transplantation, Transfusion and Genetics Graz, October 19–21, 2011 date: 2011 pages: extension: .txt txt: ./txt/cord-015365-iqdi99pd.txt cache: ./cache/cord-015365-iqdi99pd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-015365-iqdi99pd.txt' === file2bib.sh === id: cord-006856-b1w25ob5 author: nan title: 19th Meeting of the Austrian Society of Transplantation, Transfusion, and Genetics, October 26–28, 2005 date: 2005 pages: extension: .txt txt: ./txt/cord-006856-b1w25ob5.txt cache: ./cache/cord-006856-b1w25ob5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-006856-b1w25ob5.txt' === file2bib.sh === id: cord-014462-11ggaqf1 author: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 pages: extension: .txt txt: ./txt/cord-014462-11ggaqf1.txt cache: ./cache/cord-014462-11ggaqf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-014462-11ggaqf1.txt' === file2bib.sh === id: cord-018393-5jlqn7wq author: Finke, Ernst-Jürgen title: Bioterrorismus, infektiologische Aspekte date: 2011-12-14 pages: extension: .txt txt: ./txt/cord-018393-5jlqn7wq.txt cache: ./cache/cord-018393-5jlqn7wq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-018393-5jlqn7wq.txt' === file2bib.sh === id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 pages: extension: .txt txt: ./txt/cord-340489-yo3cp5vs.txt cache: ./cache/cord-340489-yo3cp5vs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-340489-yo3cp5vs.txt' === file2bib.sh === id: cord-022752-bdve1ydv author: Knuf, Markus title: Infektiologie date: 2019-08-09 pages: extension: .txt txt: ./txt/cord-022752-bdve1ydv.txt cache: ./cache/cord-022752-bdve1ydv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022752-bdve1ydv.txt' === file2bib.sh === id: cord-305085-bv7udg9k author: Lawrence, Robert M. title: Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date: 2011-12-31 pages: extension: .txt txt: ./txt/cord-305085-bv7udg9k.txt cache: ./cache/cord-305085-bv7udg9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-305085-bv7udg9k.txt' === file2bib.sh === id: cord-313474-1gux1gsi author: nan title: Physicians Abstracts date: 2015-03-20 pages: extension: .txt txt: ./txt/cord-313474-1gux1gsi.txt cache: ./cache/cord-313474-1gux1gsi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-313474-1gux1gsi.txt' === file2bib.sh === id: cord-005487-vac061r8 author: nan title: Physicians Abstracts: EBMT 2010 date: 2010-04-07 pages: extension: .txt txt: ./txt/cord-005487-vac061r8.txt cache: ./cache/cord-005487-vac061r8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-005487-vac061r8.txt' === file2bib.sh === id: cord-005478-5iu38pr6 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-005478-5iu38pr6.txt cache: ./cache/cord-005478-5iu38pr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-005478-5iu38pr6.txt' === file2bib.sh === id: cord-005480-yg7salqt author: nan title: Oral Sessions and Working Party date: 2008-03-26 pages: extension: .txt txt: ./txt/cord-005480-yg7salqt.txt cache: ./cache/cord-005480-yg7salqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-005480-yg7salqt.txt' === file2bib.sh === id: cord-004675-n8mlxe7p author: nan title: 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2019-02-26 pages: extension: .txt txt: ./txt/cord-004675-n8mlxe7p.txt cache: ./cache/cord-004675-n8mlxe7p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-004675-n8mlxe7p.txt' === file2bib.sh === id: cord-006466-e1phpqes author: nan title: 2018 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2018-04-23 pages: extension: .txt txt: ./txt/cord-006466-e1phpqes.txt cache: ./cache/cord-006466-e1phpqes.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-006466-e1phpqes.txt' === file2bib.sh === id: cord-009567-osstpum6 author: nan title: Abstracts Oral date: 2008-04-23 pages: extension: .txt txt: ./txt/cord-009567-osstpum6.txt cache: ./cache/cord-009567-osstpum6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-009567-osstpum6.txt' === file2bib.sh === id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 pages: extension: .txt txt: ./txt/cord-022888-dnsdg04n.txt cache: ./cache/cord-022888-dnsdg04n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 13 resourceName b'cord-022888-dnsdg04n.txt' === file2bib.sh === id: cord-005453-4057qib7 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-005453-4057qib7.txt cache: ./cache/cord-005453-4057qib7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 31 resourceName b'cord-005453-4057qib7.txt' === file2bib.sh === id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 pages: extension: .txt txt: ./txt/cord-005460-ezrn8cva.txt cache: ./cache/cord-005460-ezrn8cva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 38 resourceName b'cord-005460-ezrn8cva.txt' Que is empty; done keyword-cmv-cord === reduce.pl bib === id = cord-001938-n2d5fw2f author = Ong, David S. Y. title = Cytomegalovirus reactivation and mortality in patients with acute respiratory distress syndrome date = 2016-03-01 pages = extension = .txt mime = text/plain words = 4483 sentences = 200 flesch = 36 summary = Furthermore, CMV reactivation in critically ill patients has been associated with a prolonged duration of mechanical ventilation [2, 4, [9] [10] [11] [12] [13] , an increased length of stay in the ICU [3, 5, 9, 10, 13] , and excess mortality [2, 4, [7] [8] [9] . Nevertheless, it remains uncertain whether these findings imply that CMV reactivation is a truly independent risk factor with respect to these observed poor clinical outcomes because most studies that have assessed these associations did not adequately account for all possible sources of bias. Possible confounders that were screened included all patient characteristics and therapeutic interventions listed in Table 1 , and some markers of disease severity: Acute Physiology and Chronic Health Evaluation APACHE Acute Physiology and Chronic Health Evaluation, ARDS acute respiratory distress syndrome, COPD chronic obstructive pulmonary disease, ICU intensive care unit, PEEP positive end expiratory pressure, P/F partial pressure of oxygen in arterial blood to fraction of inspired oxygen ratio (APACHE) IV score, presence of septic shock, partial pressure of oxygen in arterial blood to fraction of inspired oxygen ratio, and positive end expiratory pressure (PEEP) setting. cache = ./cache/cord-001938-n2d5fw2f.txt txt = ./txt/cord-001938-n2d5fw2f.txt === reduce.pl bib === id = cord-001690-cn21fgug author = Franceschi, Valentina title = BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1((-/-)) Mice from Monkeypoxvirus Lethal Challenge date = 2015-06-18 pages = extension = .txt mime = text/plain words = 6710 sentences = 334 flesch = 53 summary = In the present study, a new vaccination strategy approach based on three recombinant bovine herpesvirus 4 (BoHV-4) vectors, each expressing different MPXV glycoproteins, A29L, M1R and B6R were investigated in terms of protection from a lethal MPXV challenge in STAT1 knockout mice. In vivo efficacy testing of BoHV-4-A-CMV-A29LgD 106 ΔTK, BoHV-4-A-EF1α-M1RgD 106 ΔTK and BoHV-4-A-EF1α-B6RgD 106 ΔTK To test the efficacy of the vectors in vivo, we sought to determine if they could protect mice against a lethal challenge with MPXV. Since the purpose of this study was to determine the capability of BoHV-4-based viral vectors to protect STAT1 (-/-) mice against a lethal MPXV infection, the first concern was the generation of optimized expression cassettes to be integrated into the BAC-BoHV-4-A genome that were able to efficiently express A29L, M1R and B6R antigens. In summary, our findings have demonstrated that BoHV-4 based vectors can be used as vaccines to protect against a lethal MPXV challenge in mice. cache = ./cache/cord-001690-cn21fgug.txt txt = ./txt/cord-001690-cn21fgug.txt === reduce.pl bib === id = cord-010130-28bt3x25 author = Crocchiolo, R. title = Infections after T‐replete haploidentical transplantation and high‐dose cyclophosphamide as graft‐versus‐host disease prophylaxis date = 2015-03-26 pages = extension = .txt mime = text/plain words = 3519 sentences = 175 flesch = 46 summary = RESULTS: After a median follow‐up of 23 months, cumulative incidence of viral infections was 70% (95% confidence interval [CI] 59–81) at 100 days and 77% (95% CI 67–87) at 1 year; 35 of 65 patients at risk had CMV reactivation (54%) and the rate of polyomavirus‐virus‐associated cystitis was 19% (13/70). In the present analysis, we described infectious complications after unmanipulated, T-cell replete haplo-HSCT using post-transplant Cy in 70 consecutive patients and found, aside from a high incidence of viral infections/reactivations, especially in the early posttransplant period, a quite low incidence of late bacterial infections, together with a very low incidence of IFIs after day +180 (2 events in the overall 11 observed). In conclusion, the present single-center data on 70 consecutive patients receiving T-cell replete haplo-HSCT with post-transplant Cy confirm a high rate of viral infections before day +100 and a lower incidence of infections afterward, suggesting a satisfactory although non-optimal immune reconstitution after this type of transplantation. cache = ./cache/cord-010130-28bt3x25.txt txt = ./txt/cord-010130-28bt3x25.txt === reduce.pl bib === id = cord-003376-2qi4aibx author = van de Groep, Kirsten title = Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date = 2018-12-18 pages = extension = .txt mime = text/plain words = 3889 sentences = 191 flesch = 42 summary = title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study Cytomegalovirus (CMV) reactivation is observed in 14-41% of intensive care unit (ICU) patients without known prior immune deficiency [1] [2] [3] and is associated with increased morbidity and mortality [4] [5] [6] . Therefore, this longitudinal study aimed to investigate whether the temporal course of seven host response biomarkers, including both pro-and anti-inflammatory cytokines, in previously immunocompetent ICU patients with sepsis differs between patients with and without CMV reactivation. Time trends of various markers within patients were described by symmetric percentage differences relative to their levels 2 days prior to CMV viremia onset (Fig. 2 for primary comparison, Additional file 1: Figure S1 for secondary comparison). We performed an explorative study to compare time trends of host response biomarkers in patients with reactivation that were matched to non-reactivating control patients who were either seropositive or seronegative for CMV. cache = ./cache/cord-003376-2qi4aibx.txt txt = ./txt/cord-003376-2qi4aibx.txt === reduce.pl bib === id = cord-006713-io9yp1y2 author = Wrede, C. E. title = Intensivmedizinische Betreuung von Patienten nach Stammzelltransplantation date = 2007 pages = extension = .txt mime = text/plain words = 5253 sentences = 608 flesch = 34 summary = Auf der anderen Seite haben diese Entwicklungen aber auch dazu geführt, dass sich das Spektrum der zur intensivmedizinischen Behandlung führenden Komplikationen verändert hat: Sie treten heute weniger in der Akutphase im ersten Monat nach Transplantation, sondern häufiger im weiteren Verlauf Monate und Jahre nach SZT bei Auftreten der GvHD oder nach erneuter adoptiver Zelltherapie mit Retransplantation auf. Während in der neutropenischen Pre-engraftment Phase die neutropenische Enterocolitis (siehe Kapitel Infektionen nach Stammzelltransplantation) im Vordergund steht, stellen vor allem bei allogener Transplantation nach dem Engraftment Enteritiden eine häufige Komplikation dar: Hier ist die exakte Erregerdiagnose wichtig, neben Clostridium difficile können eine Vielzahl viraler Erreger (CMV, HHV6, VZV, Adenovirus, aber auch typische Enteroviren wie Rotaviren und Noroviren) zu schweren und lang anhaltenden Enteritiden führen. Eine adäquate Diagnostik und Therapie von Komplikationen nach SZT ist für die intensivmedizinische Behandlung dieser Patienten essentiell, und kann zu einer Verbesserung der Prognose führen. cache = ./cache/cord-006713-io9yp1y2.txt txt = ./txt/cord-006713-io9yp1y2.txt === reduce.pl bib === id = cord-016478-gpl0zbvd author = Barry, Maura title = Cytopenias in Transplant Patients date = 2018-12-08 pages = extension = .txt mime = text/plain words = 5636 sentences = 259 flesch = 32 summary = The differential diagnosis for anemia after solid organ transplant includes hemolysis, drug toxicities, iron deficiency, infection, posttransplant lymphoproliferative disorder, graft-vs.-host disease, and hemophagocytic syndrome. Sirolimus and calcineurin inhibitors such as tacrolimus and cyclosporine have been shown in renal and lung transplant recipients to cause hemolytic anemia, thrombotic thrombocytopenic purpura, and atypical hemolytic uremic syndrome [15] [16] [17] . While this etiology is more often identified as a drug-related phenomenon, particularly due to the immunosuppressants required to prevent organ rejection (see next section), there have been multiple case reports associating CMV infection as a trigger of TMA in the posttransplant setting [53, 54] . When this is identified, numerous case studies in multiple different organ systems (lung, liver, kidney solid organ transplant) have reported that changing from one CI to another (tacrolimus to cyclosporine or vice versa) or to another class of medication such as sirolimus or mycophenolate mofetil can prevent further episodes of TMA from occurring [61] [62] [63] [64] . cache = ./cache/cord-016478-gpl0zbvd.txt txt = ./txt/cord-016478-gpl0zbvd.txt === reduce.pl bib === id = cord-006841-3u56erru author = Einsele, Hermann title = Infectious complications after allogeneic stem cell transplantation: epidemiology and interventional therapy strategies: Guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncology (DGHO) date = 2003-09-10 pages = extension = .txt mime = text/plain words = 5273 sentences = 281 flesch = 34 summary = The number of stem cells in the graft and the type of GvHD prophylaxis are factors which determine the rate of hematopoeitic reconstitution and may therefore also influence incidence and severity of infections during the early post-transplantation period. Modification of empiric antimicrobial regimens in patients with neutropenic fever after allogeneic stem cell transplantation When the causative agent of an infection has been identified, antibacterial therapy should be adapted according to the resistance pattern of the pathogen. If fever occurs in a patient later than 100 days after allogeneic stem cell transplantation, the upper and lower respiratory tract (bronchitis, pneumonia, sinusitis), and bacteremias have to be considered as specific foci of infections. Clinical manifestations of adenovirus infections in patients after allogeneic stem cell transplantation that have been reported so far include pneumonia, hepatitis, cystitis, diarrhea, and also disseminated disease (for diagnostic procedures see Table 3 ). cache = ./cache/cord-006841-3u56erru.txt txt = ./txt/cord-006841-3u56erru.txt === reduce.pl bib === id = cord-004591-2hchnlwb author = Wicker, S. title = Seroprävalenz von Antikörpern gegen schwangerschaftsrelevante virale Infektionserreger bei Mitarbeiterinnen im Gesundheitswesen date = 2012-07-25 pages = extension = .txt mime = text/plain words = 2010 sentences = 260 flesch = 54 summary = In den vergangenen Jahren sind in Deutschland wiederholt behördliche Be schäftigungsverbote für schwangere Mit arbeiterinnen ausgesprochen worden, so fern diese in der Kinderbetreuung oder im Gesundheitswesen tätig und gegenüber schwangerschaftsrelevanten Infektionen (z. Im Hinblick auf eine potenzielle Infek tionsgefährdung dürfen nach § 4 Abs. 2 Nr. 6 des MuSchG werdende Mütter nicht "mit Arbeiten, bei denen sie infol ge ihrer Schwangerschaft in besonderem Maße der Gefahr, an einer Berufskrank heit zu erkranken, ausgesetzt sind oder bei denen durch das Risiko der Entste hung einer Berufskrankheit eine erhöh te Gefährdung für die werdende Mutter oder eine Gefahr für die Leibesfrucht be steht" beschäftigt werden. Healthcare workers · Maternity protection law · Pregnancy · Occupationally acquired infections gezeigt werden, dass Patienten und medi zinisches Personal sowohl Auslöser von Infektionsketten sein als auch an solchen Infektionen erkranken und versterben können [25] . Occupational risk of human cytomegalovirus and parvovirus B19 infection in female day care personnel in the Netherlands: a study based on seroprevalence Occupational risk for primary cytomegalovirus infection among pediatric health-care workers cache = ./cache/cord-004591-2hchnlwb.txt txt = ./txt/cord-004591-2hchnlwb.txt === reduce.pl bib === === reduce.pl bib === id = cord-004059-furt6xcn author = Hraiech, Sami title = Herpes simplex virus and Cytomegalovirus reactivation among severe ARDS patients under veno-venous ECMO date = 2019-12-23 pages = extension = .txt mime = text/plain words = 3388 sentences = 187 flesch = 43 summary = However, little is known about herpes simplex virus (HSV) and Cytomegalovirus (CMV) reactivation occurring in patients with severe ARDS under veno-venous extracorporeal membrane oxygenation (ECMO). The following data were retrospectively recorded from the patients' medical file: age, sex, Simplified Acute Physiologic Score II (SAPS II) [21] , Sequential Organ Failure Assessment (SOFA) score [22] , presence of co-morbidities, presence of previous immunosuppression, cause of ARDS, date of MV initiation, date of ECMO implementation, other organ failure associated with ARDS during ICU stay (in particular need for catecholamines or renal replacement therapy), blood transfusion, post-aggressive pulmonary fibrosis (defined by an alveolar procollagen III higher than 9 µg/l) [23] , time of HSV/CMV reactivation, delay between MV and HSV/CMV reactivation, delay between ECMO and HSV/CMV reactivation, duration of MV (from the day of intubation to the day of MV weaning), ECMO duration (from the day of ECMO implementation to its removal or death), ECMO-free days at day 28, ventilator-free days (VFD) at day 28, ICU length of stay [from the day of ICU admission (in the first ICU if the patient was referred from another hospital) to discharge], hospital length of stay [from the admission to hospital (in the original hospital if the patient was referred from another hospital) to discharge to home or to rehabilitation ward], ICU and hospital mortality, acyclovir or ganciclovir treatment after reactivation under ECMO. cache = ./cache/cord-004059-furt6xcn.txt txt = ./txt/cord-004059-furt6xcn.txt === reduce.pl bib === id = cord-016267-idrc1sdh author = Ljungman, Per title = Viral Infections in Hematopoietic Stem Cell Transplant Recipients date = 2009-11-27 pages = extension = .txt mime = text/plain words = 7092 sentences = 366 flesch = 34 summary = As early identification of patients at risk for developing viral disease reduces virus-related morbidity and mortality, monitoring with sensitive techniques such as antigenemia or quantitative PCR is indicated in all allogeneic SCT patients. Although the incidence of EBV-PTLD is generally lower than 2% following allogeneic SCT, it may increase up to 20% in patients with risk factors such as mismatched donor SCT, the use of an EBV positive donor to an EBV negative recipient, T-cell depletion, ATG therapy, and other forms of intensified immunosuppression for prevention and treatment of GVHD [92, 93] . Prevention of Epstein-Barr virus-lymphoproliferative disease by molecular monitoring and preemptive rituximab in high-risk patients after allogeneic stem cell transplantation Epstein-Barr virus (EBV) load in bone marrow transplant recipients at risk to develop posttransplant lymphoproliferative disease: prophylactic infusion of EBV-specific cytotoxic T cells BK virus infection in hematopoietic stem cell transplant recipients: frequency, risk factors, and association with postengraftment hemorrhagic cystitis cache = ./cache/cord-016267-idrc1sdh.txt txt = ./txt/cord-016267-idrc1sdh.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-015139-s7ox0h4f author = Stockschläder, M. title = Atemwegsinfektionen bei immunsupprimierten Personen date = 2003 pages = extension = .txt mime = text/plain words = 3915 sentences = 461 flesch = 33 summary = Pul monale Veränderungen finden sich häufig bei immunsupprimierten Patienten und können durch die Grunderkrankung, deren Behandlung, Infektionen, Tumoren oder Kombinationen dieser Ursachen bedingt sein. Bei CMV-Infektionen findet man häufig eine Kombinationen von milchglasartiger, interstitieller Verschattung mit später disseminierten fleckförmigen Knötchen, wobei die Unter-und Mittelfelder betont betroffen sind [5] . Die Therapiestrategien "universelle Prophylaxe" und "preemptive treatment" der CMV-Erkrankung gelten auch für Patienten mit iatrogener Immunsuppression nach Organtransplantation. B. die CMV-Retinitis, bei 85% der AIDS-oder HIV-infizierten Patienten mit geringer CD4-Zahl beobachtet werden [57] . Zusammenfassend kann festge-stellt werden,dass für allogen stammzelltransplantierte Patienten und Hochrisikopatienten, die sich einer autologen BSZT unterziehen, eine Prophylaxe mit Fluconazol (400 mg/Tag) empfohlen wird [63] .Aspergillusinfektionen werden hierdurch allerdings nicht mit erfasst. Bei Patienten mit Lungeninfiltraten in der febrilen Neutropenie ist jedoch wegen fehlender Aspergilluswirksamkeit von Fluconazol bereits initial konventionelles oder liposomales Amphotericin B zu empfehlen. cache = ./cache/cord-015139-s7ox0h4f.txt txt = ./txt/cord-015139-s7ox0h4f.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-288721-3bv3aak6 author = Schneider, Annika title = Single organelle analysis to characterize mitochondrial function and crosstalk during viral infection date = 2019-06-11 pages = extension = .txt mime = text/plain words = 5604 sentences = 309 flesch = 39 summary = Thus, single-organelle and multi-parameter resolution allows to explore altered energy metabolism and antiviral defence by tagged mitochondria selectively in virus-infected cells and will be instrumental to identify viral immune escape and to develop and monitor novel mitochondrial-targeted therapies. When challenged with high concentrations of calcium (100 µM), mitochondria isolated from virus-infected livers are much more fragile shown by time-dependent loss of membrane potential and change of their morphology indicated by decrease in side-scatter (Fig. 2F ). Number of viable mitochondria detected per second by flow-cytometry declined after calcium challenge, consistent with loss of mitochondrial integrity, and did so much faster in samples from virus-infected livers (Fig. 2F ). In order to further evaluate mitochondrial functionality, we challenged mitochondria with Ca 2+ as stress test and performed time kinetic measurements of DilC 1 (5) fluorescence and side-scatter of mito-DsRed + and mito-DsRed − mitochondria isolated from Ad-CMV-mitoRL infected livers. cache = ./cache/cord-288721-3bv3aak6.txt txt = ./txt/cord-288721-3bv3aak6.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-269194-b1wlr3t7 author = Engstrom-Melnyk, Julia title = Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date = 2015-12-31 pages = extension = .txt mime = text/plain words = 12542 sentences = 501 flesch = 36 summary = Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. cache = ./cache/cord-269194-b1wlr3t7.txt txt = ./txt/cord-269194-b1wlr3t7.txt === reduce.pl bib === id = cord-016990-ot1wi3xi author = Zaki, Sherif R. title = Viral Infections of the Lung date = 2008 pages = extension = .txt mime = text/plain words = 19585 sentences = 1132 flesch = 36 summary = 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. cache = ./cache/cord-016990-ot1wi3xi.txt txt = ./txt/cord-016990-ot1wi3xi.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-023854-w8kx5n8k author = Schuster, V. title = Virusinfektionen date = 2019 pages = extension = .txt mime = text/plain words = 8437 sentences = 1326 flesch = 48 summary = Anschließend dringt das Virus in die Nervenendigungen von peripheren sensorischen Nerven ein und wandert in ihnen retrograd bis zu den spinalen Hinterstrangganglien (bei HSV-1 meist Ganglion des N. Schleimhaut (Dermatom), wo es zur lokalen Virusvermehrung und Ausbildung von Bläschen kommt: Herpes zoster bei VZV, Herpes labialis oder genitalis bei HSV Die Infektion beginnt mit unspezifischen Symptomen (Fieber, Kopfschmerzen, Krankheitsgefühl) . VZV kann bei nachlassender zellulärer Immunität sowie durch noch unbekannte Mechanismen jederzeit reaktiviert werden: VZV wandert nun entlang der sensorischen peripheren Nerven anterograd an die Hautoberfläche, wo es im Bereich der betroffenen Dermatome zur Virusvermehrung mit Bläschenbildung (Herpes zoster) kommt. Inwieweit diese Komplikationen tatsächlich ursächlich nur durch HHV-6, oder möglicherweise erst in Verbindung mit zusätzlichen Infektionen (HIV, CMV und andere Herpesviren) hervorgerufen werden, ist derzeit nicht bekannt. Die Entwicklung eines Hydrops fetalis nach einer mütterlichen (und fetalen) Parvovirus-B19-Infektion ist insgesamt selten, sie liegt bei ca. cache = ./cache/cord-023854-w8kx5n8k.txt txt = ./txt/cord-023854-w8kx5n8k.txt === reduce.pl bib === id = cord-004643-uu4uipfy author = Hasan, Mohammad Rubayet title = Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report date = 2020-03-20 pages = extension = .txt mime = text/plain words = 3015 sentences = 151 flesch = 35 summary = Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics. Ganciclovir resistance was confirmed by the presence of the A594V mutation in UL97 [6] What was unique in our patient compared to other reported CMV-associated HLH cases was the overwhelming infection with MDROs. On hospital admission, the patient was found to be colonized with multiple MDROs including VRE, and carbapenamase-producing Enterobacteriaceae, which may have been acquired during his previous hospital course in India. cache = ./cache/cord-004643-uu4uipfy.txt txt = ./txt/cord-004643-uu4uipfy.txt === reduce.pl bib === === reduce.pl bib === id = cord-019009-3ngfv96u author = Gea-Banacloche, Juan title = Risks and Epidemiology of Infections After Hematopoietic Stem Cell Transplantation date = 2016-02-15 pages = extension = .txt mime = text/plain words = 8485 sentences = 401 flesch = 32 summary = Several characteristics of the transplant infl uence the risk of infection: the conditioning preparative regimen, the source of stem cells, the degree of HLA identity between donor and recipient, and the prophylactic strategy adopted to prevent GVHD (use of T cell depletion or immunosuppressive medications). These factors may result in increased risk of infections associated with T cell immunodefi ciency, like CMV, Pneumocystis jirovecii pneumonia (PCP), and Epstein-Barr virus (EBV)-related posttransplant lymphoproliferative disorder (PTLD). Risk factors for recurrence of invasive fungal infection during secondary antifungal prophylaxis in allogeneic hematopoietic stem cell transplant recipients Impact of the intensity of the pretransplantation conditioning regimen in patients with prior invasive aspergillosis undergoing allogeneic hematopoietic stem cell transplantation: a retrospective survey of the infectious diseases working party of the european group for blood and marrow transplantation Infl iximab use in patients with severe graftversus-host disease and other emerging risk factors of noncandida invasive fungal infections in allogeneic hematopoietic stem cell transplant recipients: a cohort study cache = ./cache/cord-019009-3ngfv96u.txt txt = ./txt/cord-019009-3ngfv96u.txt === reduce.pl bib === id = cord-023669-3ataw6gy author = Masur, Henry title = Critically Ill Immunosuppressed Host date = 2009-05-15 pages = extension = .txt mime = text/plain words = 11194 sentences = 576 flesch = 34 summary = As the population of patients with cancer, organ transplants, vasculitides, and human immunodefi ciency virus (HIV) infection has grown, intensivists are seeing more and more patients with altered immunity. For instance, if a patient presents with severe hypoxemia and diffuse pulmonary infi ltrates, a health care provider who recognizes a prior splenectomy as the major predisposition to infection would focus the diagnostic evaluation and the empiric therapy on Streptococcus pneumoniae and Haemophilus infl uenzae. Patients with HIV infection develop clinical disease as a result of three basic processes: the direct effect of HIV on specifi c organs (e.g., cardiomyopathy, enteropathy, dementia); immunologically mediated processes (e.g., glomerulonephritis, thrombocytopenia); or opportunistic infections and tumors that are enabled by HIV-induced immunosuppression. For instance, if a patient with HIV infection and a CD4+ T lymphocyte count of 700 cells/µL presents with diffuse pulmonary infi ltrates, the diagnostic evaluation and empiric antimicrobial regimen should focus on S. cache = ./cache/cord-023669-3ataw6gy.txt txt = ./txt/cord-023669-3ataw6gy.txt === reduce.pl bib === === reduce.pl bib === id = cord-015365-iqdi99pd author = nan title = 25th Annual Meeting of the Austrian Society of Transplantation, Transfusion and Genetics Graz, October 19–21, 2011 date = 2011 pages = extension = .txt mime = text/plain words = 30685 sentences = 2517 flesch = 50 summary = Retrospective study to test ferritin serum levels as biomarker for graft-versus-host disease-associated non-infectious inflammatory reaction in 117 children after hematopoietic stem cell transplantation Background. One hundred seventy-eight patients (85 males, 93 females) with a median age of 40 years alive on day þ 100 after HCT with myeloablative (n ¼ 110) or reduced-intensity (n ¼ 68) conditioning and a related (n ¼ 37) or unrelated (n ¼ 141) stem cell donor were enrolled into the study. Using a non-myeloablative conditioning regimen followed by donor bone marrow (DBM) transplantation, we observed successful production of mixed chimerism in non-human primate renal allograft recipients, followed by normal kidney function with no evidence of chronic rejection for periods as long as thirteen years after discontinuing all I.S. In vitro studies of these recipients as well as of humans suggest that both central (clonal deletion) and peripheral (regulatory cells) mechanisms are involved. cache = ./cache/cord-015365-iqdi99pd.txt txt = ./txt/cord-015365-iqdi99pd.txt === reduce.pl bib === id = cord-018785-tcr5xlf8 author = Nambiar, Puja title = Infection in Kidney Transplantation date = 2018-06-27 pages = extension = .txt mime = text/plain words = 9364 sentences = 506 flesch = 36 summary = The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The risk factors for development of CMV disease include donor seropositivity/recipient seronegativity(Dþ/RÀ), use of induction immunosuppression (antilymphocyte antibodies), donor age >60 years, simultaneous kidney-pancreas transplantation, treatment for acute rejection, impaired transplant function, and concurrent infection from other viruses (like EBV and HHV-6 and 7) (De Keyzer et al. The risk factors for PTLD include EBV naïve recipients who receive EBV seropositive organs, active primary EBV infection, younger recipient, coinfection by CMV and other viruses, prior splenectomy, second transplant, acute or chronic graft versus host disease, immunosuppressive drug regimen (OKT3 or polyclonal antilymphocyte antibody), and the type of organ transplanted. cache = ./cache/cord-018785-tcr5xlf8.txt txt = ./txt/cord-018785-tcr5xlf8.txt === reduce.pl bib === === reduce.pl bib === id = cord-006856-b1w25ob5 author = nan title = 19th Meeting of the Austrian Society of Transplantation, Transfusion, and Genetics, October 26–28, 2005 date = 2005 pages = extension = .txt mime = text/plain words = 29625 sentences = 1983 flesch = 52 summary = Egr-1 and hypoxia-inducible factor-1 (HIF-1) gene expression was examined in left ventricular biopsies of explanted failing hearts in 28 ICM and 42 DCM patients, as well as in 12 donor grafts before reperfusion (control), at 10, 30, 60 minutes after reperfusion, and at 1, 2, 3, 4, 6, 12 posttransplant weeks, using real-time RT-PCR. The risk of transplant-related mortality (TRM) due to graft-versushost disease (GvHD) is higher in male recipients of female stem cells compared with female patients receiving a graft from a female donor. We therefore analyzed a single-center cohort of 72 high-risk patients transplanted with a related or unrelated stem cell graft after nonmyeloablative conditioning for outcome (acute and chronic GvHD, TRM, relapse, and survival). Four patients between the age of 34 and 44 years underwent allogeneic peripheral blood stem cell (PBSC) transplantation (SCT) from HLA-identical sibling or unrelated donors at our institution. cache = ./cache/cord-006856-b1w25ob5.txt txt = ./txt/cord-006856-b1w25ob5.txt === reduce.pl bib === id = cord-015389-vwgai4k9 author = nan title = Publication only date = 2009-03-25 pages = extension = .txt mime = text/plain words = 23868 sentences = 1465 flesch = 57 summary = This study evaluates the safety of this approach, in terms of infusion-related toxicity and hematopoietic reconstitution, in 385 consecutive autologous transplantations performed from 4/97 to 9/08 in 348 patients (median age 46; underlying disease: lymphoma in 178, myeloma in 131, acute leukaemia in 17, breast cancer in 22). Patients and methods: Eight pts after allogeneic hematopoetic stem cell transplantation (HSCT) underwent MSCs infusions (median age of pts was 11 years, male/female: 6/2) between 2006 and 2009. Akiyama Tokyo Metropolitan Komagome Hospital (Tokyo, JP) Acute graft-versus-host disease (GVHD) is one of the major factors that have infl uence on the outcomes of allogeneic hematopoietic stem cell transplantation (HSCT). Material and methods: during a 8 years period we have performed 144 stem cells transplantation in 134 patients with different hematological malignancies(AML: 74; ALL: 6; CML: 7; CLL: 1, NHL: 13; Hodgkin Diseases: 16; Multiple myelomas: 24; Aplastic anaemia: 1;Myelofi brosis:1 Ewing Sarcoma: 1; Male:78 Female 66. cache = ./cache/cord-015389-vwgai4k9.txt txt = ./txt/cord-015389-vwgai4k9.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-282618-tjvjlyn9 author = Luke, J M title = Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers date = 2010-11-25 pages = extension = .txt mime = text/plain words = 6241 sentences = 336 flesch = 43 summary = To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. A neomycin resistance gene (NeoR) without an upstream Kozak sequence was cloned downstream of an enhanced green fluorescent protein (EGFP) transgene in different configurations similar to that used with PREs. Quantifiable neoR translation products were present in all tested configurations, as was biologically active neoR protein after plasmid transfection into both HEK293 and CHO cell lines (Supplementary Table S1 ). The assay was in the same format as in (a), except for the fact that Pol III inhibitor-treated cells were transfected with EGFP plasmids containing the CMV-HTLV-I R promoter with or without VA1; (c) Inhibition of PKR, not of adenosine deaminase acting on RNA (ADAR) or RNA interference (RNAI), was required for VA1 expression enhancement effect. cache = ./cache/cord-282618-tjvjlyn9.txt txt = ./txt/cord-282618-tjvjlyn9.txt === reduce.pl bib === === reduce.pl bib === id = cord-022752-bdve1ydv author = Knuf, Markus title = Infektiologie date = 2019-08-09 pages = extension = .txt mime = text/plain words = 25995 sentences = 3963 flesch = 43 summary = Zu den primär durch eine Blickdiagnose zu diagnostizierenden Infektionskrankheiten gehören auch die Windpocken (Varizellen) (› Abb. 10.5) mit kurz vor Exanthemausbruch bestehendem Fieber sowie Kopf-und Gliederschmerzen. Expositionsanamnese / Grundkrankheit (Disposition) Bei Kenntnis von zwei der drei genannten Faktoren kann auf den dritten geschlossen und eine kalkulierte antiinfektive Therapie begonnen werden. Wichtig für den klinischen Alltag sind nicht so sehr die Sensitivität und Spezifität eines Testverfahrens (Qualitätsmerkmale des Testverfahrens), sondern vor allem der positive bzw. Patienten mit einer Immundefizienz können abhängig von der vorliegenden Funktionsstörung oft auf Impfungen nicht adäquat reagieren und werden durch Lebendimpfstoffe u. Da der übermäßige Antibiotikaverbrauch zur Resistenzentwicklung beiträgt und Antibiotika Nebenwirkungen verursachen, ist eine möglichst zielgerechte Therapie für Patienten mit AOM, die wirklich davon profitieren, anzustreben. Da die normale Mundflora aus vielen verschiedenen Bakterienspezies besteht, wobei sowohl grampositive Erreger (grüne Streptokokken, β-hämolysierende Streptokokken) als auch Anaerobier und Actinomyzeten besonders häufig vorkommen, kann sich bei Prädisposition leicht eine Infektion entwickeln. cache = ./cache/cord-022752-bdve1ydv.txt txt = ./txt/cord-022752-bdve1ydv.txt === reduce.pl bib === id = cord-014462-11ggaqf1 author = nan title = Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date = 2011-04-21 pages = extension = .txt mime = text/plain words = 35453 sentences = 1711 flesch = 49 summary = Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. cache = ./cache/cord-014462-11ggaqf1.txt txt = ./txt/cord-014462-11ggaqf1.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-340228-mvqoyror author = Al-Herz, Waleed title = Spectrum of Viral Infections Among Primary Immunodeficient Children: Report From a National Registry date = 2019-05-29 pages = extension = .txt mime = text/plain words = 2930 sentences = 170 flesch = 42 summary = Results: A total of 274 PID children were registered in KNPIDR during the study period with predominance of immunodeficiencies affecting cellular and humoral immunity, followed by combined immunodeficiencies with associated syndromic features and diseases of immune dysregulation. CMV and parainfluenza infections were more common in the group of immunodeficiencies affecting cellular and humoral immunity while EBV and human papilloma virus (HPV) were more common in the immune dysregulation group and combined immunodeficiencies with associated syndromic features, respectively. The distribution of these patients according to PID categories is: immunodeficiencies affecting cellular and humoral immunity, 97 patients (35.4%); combined immunodeficiencies with associated syndromic features, 67 patients (24.5%); predominantly antibody deficiencies, 34 patients (12.4%); diseases of immune dysregulation, 47 patients (17.2%); congenital defects of phagocyte number or function, 17 patients (6.2%); autoinflammatory disorders, 1 patient (0.3%); and complement deficiencies, 11 patients (4%). cache = ./cache/cord-340228-mvqoyror.txt txt = ./txt/cord-340228-mvqoyror.txt === reduce.pl bib === === reduce.pl bib === id = cord-103297-4stnx8dw author = Widrich, Michael title = Modern Hopfield Networks and Attention for Immune Repertoire Classification date = 2020-08-17 pages = extension = .txt mime = text/plain words = 14093 sentences = 926 flesch = 57 summary = In this work, we present our novel method DeepRC that integrates transformer-like attention, or equivalently modern Hopfield networks, into deep learning architectures for massive MIL such as immune repertoire classification. DeepRC sets out to avoid the above-mentioned constraints of current methods by (a) applying transformer-like attention-pooling instead of max-pooling and learning a classifier on the repertoire rather than on the sequence-representation, (b) pooling learned representations rather than predictions, and (c) using less rigid feature extractors, such as 1D convolutions or LSTMs. In this work, we contribute the following: We demonstrate that continuous generalizations of binary modern Hopfield-networks (Krotov & Hopfield, 2016 Demircigil et al., 2017) have an update rule that is known as the attention mechanisms in the transformer. We evaluate the predictive performance of DeepRC and other machine learning approaches for the classification of immune repertoires in a large comparative study (Section "Experimental Results") Exponential storage capacity of continuous state modern Hopfield networks with transformer attention as update rule cache = ./cache/cord-103297-4stnx8dw.txt txt = ./txt/cord-103297-4stnx8dw.txt === reduce.pl bib === === reduce.pl bib === id = cord-005487-vac061r8 author = nan title = Physicians Abstracts: EBMT 2010 date = 2010-04-07 pages = extension = .txt mime = text/plain words = 58975 sentences = 3128 flesch = 58 summary = We retrospectively analyzed 1257 patients (pts), 755 children (age≤18) and 502 adults, receiving fi rst single (n = 1080) or double UCBT (n = 177) in EBMT centers, between 1995 and 2009 , for malignant and non-malignant diseases, who survived at least 100 days from transplantation with neutrophils recovery and without relapse or autologous reconstitution. Prochymal® improves response rates in patients with steroid-refractory acute graft-versus-host disease involving the liver and gut: results of a randomized, placebo-controlled, multicentre phase III trial in GvHD P.J. Martin (1) , J.P. Uberti (2) Background and methods: Steroid-refractory acute GVHD (SR-GVHD) remains a signifi cant and life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). A. Nagler (1) Background: Allogeneic transplantation of hematopoietic stem cells (allo-SCT) from an HLA-matched related (MRD) or unrelated donor (URD) is a curative option for patients (pts) with high-risk hematological disease (HRHD). cache = ./cache/cord-005487-vac061r8.txt txt = ./txt/cord-005487-vac061r8.txt === reduce.pl bib === id = cord-017030-tzuyo6tx author = Henao-Martínez, Andrés F. title = Infections in Heart, Lung, and Heart-Lung Transplantation date = 2018-12-08 pages = extension = .txt mime = text/plain words = 11531 sentences = 740 flesch = 32 summary = There are several factors predisposing thoracic transplant recipients to infections: (A) factors present before transplantation: age, presence of comorbidities (e.g., chronic kidney disease, diabetes mellitus, cancer, etc.), nutrition status, latent infections, colonization with healthcare-associated organisms, and occult community-acquired infections; (B) factors during the surgery: duration of the transplant procedure, graft injury including ischemic time, colonization or latent infection of the graft, surgical instrumentation (e.g., mechanical ventilation, invasive devices such as catheters, drains, Foley catheters, etc.), ICU stay, and need for re-interventions; and (C) factors present after transplant: degree of immunosuppression, CMV infection, and rejections ( Mechanical ventilation (MV) for >5 days immediately following transplant surgery and isolation of Staphylococcus aureus (SA) from airway cultures in the recipient were considered risk factors for invasive SA infections in a retrospective study of patients with lung and heart-lung transplants [20] . cache = ./cache/cord-017030-tzuyo6tx.txt txt = ./txt/cord-017030-tzuyo6tx.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-311505-akcc9oms author = Geisen, Will R. title = Cytomegalovirus Enterocolitis secondary to experimental COVID-19 therapy date = 2020-09-22 pages = extension = .txt mime = text/plain words = 1354 sentences = 82 flesch = 38 summary = Additionally, this case validates colonoscopy as a mode to rule out concurrent infectious etiologies causing diarrhea in COVID-19-positive patients. Additionally, this case validates colonoscopy as a mode to rule out concurrent infectious etiologies causing diarrhea in COVID-19-positive patients. The novel 2019 coronavirus (COVID-19), a form of severe acute respiratory syndrome (SARS-CoV-2), has caused a pandemic of historical proportions. Due to its worldwide distribution, a paucity of clinical trial data, and a high mortality rate, the COVID pandemic has led to widespread implementation of experimental therapies with varying levels of success and, in some instances, poor outcomes (3, 4, 5) . We present a patient who was treated with experimental therapies and subsequently developed severe gastrointestinal pathology that was diagnosed by colonoscopy. The report describes a patient with SARS-CoV-2 pneumonia who was treated with experimental immunomodulating therapies and, subsequently, developed cytomegalovirus (CMV) colitis. cache = ./cache/cord-311505-akcc9oms.txt txt = ./txt/cord-311505-akcc9oms.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-018393-5jlqn7wq author = Finke, Ernst-Jürgen title = Bioterrorismus, infektiologische Aspekte date = 2011-12-14 pages = extension = .txt mime = text/plain words = 25008 sentences = 3876 flesch = 44 summary = Wenn sie sich jedoch verstärkt, kann man sie leicht erkennen, aber nur schwer heilen." (Nicolo Macchiavelli, 1449 -1527 Es ist wenig wahrscheinlich, dass biologische Anschläge rechtzeitig als solche erkannt werden, sofern kein automatisches Monitoring mit einem zuverlässigen Echtzeit-Nachweis von B-Agenzien existiert. B. Enzephalitiden viraler Genese sowie die Frühstadien von nvCJD und möglicherweise auch die Frühsymptomatik der Alzheimer-Krankheit; außerdem die Borreliose-Infektion (Neuroborreliose), bei der ein heterogenes Symptomenbild angenommen wird, das sich wenig mit der Ausprägung einer (BDV-spezifischen) Dysfunktion im limbischen System deckt. Unklar ist jedoch, wie häufig sich aus initial milden Infektionen der oberen Luftwege eine Bronchitis oder eine Pneumonie entwickelt und was die auslösenden Faktoren dafür sind. Beim Nachweis hoch positiver (häufig mit anderen Chlamydienspezies kreuzreagierender) Antikörper ist bei entsprechender klinischer Symptomatik die gezielte Erhebung der Anamnese hinsichtlich einer möglichen Exposition des Patienten gegenüber den natürlichen Wirten diagnostisch wegweisend. Aus Patientenseren wurden Cyclospora-spezifische Antikörper isoliert, jedoch sind die Vorgänge der Immunantwort auf Cyclospora noch nicht vollständig geklärt und ob sich eine Immunität entwickelt, ist fraglich. cache = ./cache/cord-018393-5jlqn7wq.txt txt = ./txt/cord-018393-5jlqn7wq.txt === reduce.pl bib === id = cord-279638-jr1mbh7s author = Calore, Elisabetta title = Treatment of Acute Graft-versus-Host Disease in Childhood with Extracorporeal Photochemotherapy/Photopheresis: The Padova Experience date = 2015-07-14 pages = extension = .txt mime = text/plain words = 5592 sentences = 279 flesch = 57 summary = Acute graft-versus-host disease (aGVHD) is the major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Update on the mechanism of action and on clinical efficacy of extracorporeal photopheresis in the treatment of acute and chronic graft versus host disease in children Extracorporeal photopheresis (photochemotherapy) in the treatment of acute and chronic graft versus host disease: immunological mechanisms and the results from clinical studies Role of extracorporeal photopheresis (ECP) in treatment of steroid-refractory acute graft-versus-host disease Extracorporeal Photopheresis for the treatment of acute and chronic graft-versus-host disease in adults and children: best practice recommendations from an Italian Society of Hemapheresis and Cell Manipulation (SIdEM) and Italian Group for Bone Marrow Transplantation (GITMO) consensus process Extracorporeal photopheresis for steroid resistant graft versus host disease in pediatric patients: a pilot single institution report Extracorporeal photochemotherapy in graft-versus-host disease: a longitudinal study on factors influencing the response and survival in pediatric patients cache = ./cache/cord-279638-jr1mbh7s.txt txt = ./txt/cord-279638-jr1mbh7s.txt === reduce.pl bib === id = cord-296402-rd5clf8h author = José Castón, Juan title = Efectos de la infección viral en el paciente trasplantado date = 2007-10-31 pages = extension = .txt mime = text/plain words = 11020 sentences = 998 flesch = 52 summary = Respecto al citomegalovirus (CMV), tanto la reactivación como la infección adquirida en período peritrasplante, suelen producirse entre el primero y el cuarto mes postrasplante, aunque en la actualidad se describen cada Las infecciones virales continúan siendo una importante causa de morbimortalidad en los pacientes trasplantados. Igualmente, en otro ensayo que comparó valganciclovir con ganciclovir oral en Castón profilaxis durante 90 días en receptores de TOS (hepático, cardíaco, renal y páncreas y riñón) en situación D+/R-, se observó cómo en ambos grupos todos los casos de enfermedad por CMV aparecieron después de los primeros 6 meses postrasplante 18 . De esta forma, los receptores seronegativos que reciben órganos de donantes seropositivos presentan entre 10 y 50 veces mayor riesgo de ELPT como consecuencia del desarrollo de infección primaria por VEB 27 . cache = ./cache/cord-296402-rd5clf8h.txt txt = ./txt/cord-296402-rd5clf8h.txt === reduce.pl bib === id = cord-348130-t9tysvr8 author = Cho, Sung-Yeon title = Infectious complications after hematopoietic stem cell transplantation: current status and future perspectives in Korea date = 2018-02-27 pages = extension = .txt mime = text/plain words = 9707 sentences = 506 flesch = 34 summary = In addition, the types and risk factors of infectious complications differ according to the stem cell source, donor type, conditioning intensity, region, prophylaxis strategy, and comorbidities, such as graft-versushost disease and invasive fungal infection. Bacteria: consider fluoroquinolone a Fungus: consider prophylaxis during neutropenia, consider PCP prophylaxis Virus: during neutropenia or longer depending on risks HSCT, hematopoietic stem cell transplantation; PCP, Pneumocystis jirovecii pneumonia; GVHD, graft-versus-host disease; TNF-α, tumor necrosis factor-α. In a systematic review and meta-analysis of non-HIV immunocompromised hosts (patients with acute leukemia and recipients of HSCT and solid organ transplant), the incidence of PCP was reduced by 91% (relative risk [RR], 0.09) in trimethoprim/sulfamethoxazole prophylaxis group compared with placebo [69, 70] . Epidemiology and risk factors for invasive fungal diseases among allogeneic hematopoietic stem cell transplant recipients in Korea: results of cache = ./cache/cord-348130-t9tysvr8.txt txt = ./txt/cord-348130-t9tysvr8.txt === reduce.pl bib === id = cord-315304-pge45105 author = Kotton, C.N. title = Organ Transplantation, Risks date = 2015-03-06 pages = extension = .txt mime = text/plain words = 4211 sentences = 206 flesch = 29 summary = Viral infection is associated with both direct (invasive disease) and indirect (immune modulation) effects affecting susceptibility to other infections and promoting allograft rejection. The risk for viral infection is a function of the intensity of exposure and virulence of the specific virus, the intensity of immune suppression used to prevent graft rejection or graft-versus-host disease, underlying immune deficits, and factors affecting host susceptibility. Multiple factors contribute to viral reactivation after transplantation, including graft rejection and therapy, immune suppression (especially reduction of T-cell mediated, cytotoxic immunity), inflammation, and tissue injury. The clinical presentation of CMV (HHV-5) can range from a 'CMV syndrome' including fever, malaise, leukopenia, to a 'flu-like' illness with myalgias and fatigue, to a more significant end-organ disease with pneumonitis, colitis, encephalitis, hepatitis, or chorioretinitis. The treatment of viral infections in the renal transplantation recipient includes: the reduction of immunosuppression, antiviral therapy, diagnosis and treatment of co-infections (such as CMV, EBV, HHV-6, or À7), and use of adjunctive therapies such as immunoglobulins or colony stimulating factors. cache = ./cache/cord-315304-pge45105.txt txt = ./txt/cord-315304-pge45105.txt === reduce.pl bib === === reduce.pl bib === id = cord-323691-5s5almd2 author = Mishin, Vasiliy P title = A ‘minimal’ approach in design of flavivirus infectious DNA date = 2001-12-04 pages = extension = .txt mime = text/plain words = 5060 sentences = 255 flesch = 49 summary = Abstract The 'infectious DNA' approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Substantial difficulties, however, were encountered in design of flavivirus 'infectious DNA', requiring either modification of the viral genome cassette (Yamshchikov et al., 2001) to prevent unwanted expression of viral genome segments encoding toxic for Escherichia coli products, or deletion of the structural protein region (Varnavski et al., 2000) . For this reason we sought to investigate if the stability of constructs containing an unmodified virus genome cassette can be improved by preventing its deleterious expression at the transcriptional level, i.e. by minimizing spurious transcription from eukaryotic promoters in E. cache = ./cache/cord-323691-5s5almd2.txt txt = ./txt/cord-323691-5s5almd2.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-305085-bv7udg9k author = Lawrence, Robert M. title = Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date = 2011-12-31 pages = extension = .txt mime = text/plain words = 45849 sentences = 2358 flesch = 45 summary = Postnatal exposure of susceptible infants to CMV, including premature infants without passively acquired maternal antibodies against CMV, infants born to CMV-seronegative mothers, and immunodeficient infants, can cause significant clinical illness (pneumonitis, hepatitis, thrombocytopenia).* In one study of premature infants followed up to 12 months, Vochem et al 430 found CMV transmission in 17 of 29 infants (59%) exposed to CMV virolactia and breastfed compared with no infants infected of 27 exposed to breast milk without CMV. 38, 104, 121 Laboratory reports demonstrate the presence of cell-free virus and cell-associated virus in breast milk as well as various immunologic factors that could block or limit infection.* A dose-response relationship has been observed, correlating the HIV viral load in human milk as well as a mother' s plasma viral load with an increased transmission risk for the breastfed infant. 76 No case of transmission of yellow fever virus from an infected mother to her infant via breastfeeding or breast milk has been reported. cache = ./cache/cord-305085-bv7udg9k.txt txt = ./txt/cord-305085-bv7udg9k.txt === reduce.pl bib === === reduce.pl bib === id = cord-348547-wmvqvbqi author = Desmons, Aurore title = Post-mortem diagnosis, of cytomegalovirus and varicella zoster virus co-infection by combined histology and tissue molecular biology, in a sudden unexplained infant death date = 2013-10-31 pages = extension = .txt mime = text/plain words = 2317 sentences = 130 flesch = 45 summary = title: Post-mortem diagnosis, of cytomegalovirus and varicella zoster virus co-infection by combined histology and tissue molecular biology, in a sudden unexplained infant death Objectives To describe post-mortem combined histological and tissue molecular biological techniques for the diagnosis of cytomegalovirus and varicella zoster virus co-infection as a cause of death. Study design Real-time quantitative PCR and RT-PCR assays for Herpesviruses, respiratory viruses, Adenovirus, Enterovirus and Parvovirus B19 were performed on multi-organ frozen samples and paraffin-embedded tissues in combination with histology. Conclusions This case shows that thorough quantitative virological investigations on frozen tissues must be performed in combination with histology and immunohistochemistry for the determination of the cause of a sudden unexplained infant death. Post-mortem virological quantitative molecular analyses performed on frozen tissue samples revealed cytomegalovirus (CMV) and varicella zoster virus (VZV), mainly in the lungs. However, pulmonary necrotizing inflammatory lesions, immunohistochemistry, and molecular detection of CMV and VZV in multi-organs samples demonstrated the role of the co-infection in the death. cache = ./cache/cord-348547-wmvqvbqi.txt txt = ./txt/cord-348547-wmvqvbqi.txt === reduce.pl bib === id = cord-005478-5iu38pr6 author = nan title = The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date = 2019-07-03 pages = extension = .txt mime = text/plain words = 63350 sentences = 3869 flesch = 58 summary = There were some differences among groups: patients in group-1 were younger (median age 46 years, p< 0.02) were transplanted in more recent year (2015, p< 0.001), received more frequently a regimen based on TBF (thiotepa, fludarabine and busulfan) (83%, p< 0.001) and bone marrow (BM) as source of stem cells (77%, p< 0.001), with no ATG (100%, p< 0.001). Clinical Trial Registry: NCT01217723 Disclosure: None of the Authors have any conflicts of interest to declare O105 Immune reconstitution -based score at diagnosis of CGVHD predicts GVHD severity and overall-survival: A novel prognostication tool for GVHD treatment tailoring Background: Allogeneic stem cell transplantation (HSCT) survivors are at a relevant risk of developing chronic GvHD (cGvHD), which importantly affects quality of life and increases morbidity and mortality. cache = ./cache/cord-005478-5iu38pr6.txt txt = ./txt/cord-005478-5iu38pr6.txt === reduce.pl bib === id = cord-340489-yo3cp5vs author = nan title = KAPITEL 13 Infektionskrankheiten date = 2008-12-31 pages = extension = .txt mime = text/plain words = 26536 sentences = 3917 flesch = 45 summary = Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. cache = ./cache/cord-340489-yo3cp5vs.txt txt = ./txt/cord-340489-yo3cp5vs.txt === reduce.pl bib === === reduce.pl bib === id = cord-313474-1gux1gsi author = nan title = Physicians Abstracts date = 2015-03-20 pages = extension = .txt mime = text/plain words = 51420 sentences = 2890 flesch = 57 summary = Materials (or patients) and methods: We performed a multicenter, multinational, open-label, randomized study comparing anti-lymphocyte globulin (ATG-Fresenius s ) 10 mg/kg on day -3, -2 and -1 with no ATG in patients with AML (n ¼ 110) or ALL (n ¼ 45) in 1 st complete remission (CR; n ¼ 139) or 2 nd CR (n ¼ 16) who received peripheral blood stem cells from their HLA-identical sibling after standard TBI (12 Gy)/Ccclophosphamide (120 mg/kg) or busulfan (16 mg/ kg)/Cy (120 mg/kg) based myeloablative conditioning regimen. After allo-HSCT, detection of positive WT1 was followed by immunomodulatory therapeutic interventions according to the time from transplant, the presence of active graft-versus-host disease (GvHD) and the general clinical conditions: tapering and/or discontinuation of immunosuppressive drugs (IS), donor lymphocytes infusions (DLI), administration of hypomethylating agents. Introduction: Haploidentical hematopoietic stem cell transplantation(Haplo-HSCT)is feasible option for patients with acute leukemia(AL)at high risk of relapse who do not have HLA-matched related or unrelated donors. cache = ./cache/cord-313474-1gux1gsi.txt txt = ./txt/cord-313474-1gux1gsi.txt === reduce.pl bib === id = cord-005480-yg7salqt author = nan title = Oral Sessions and Working Party date = 2008-03-26 pages = extension = .txt mime = text/plain words = 72626 sentences = 3873 flesch = 55 summary = Standard NIH or Eurolupus cyclophosphamide (CY) protocols and mycophenolate Mofetil (MMF) as induction therapy in severe BILAG A SLE is still associated with 20 % failure, 50% relapse and 10% to 15 % death at 10 years In the absence of a single standard treatment worldwide for refractory SLE, phase I-II studies analysed the use of: a) rituximab (anti CD20 mAb) in more than 1 000 patients showing complete to partial early response around 100% with relapse in 50 to 60% of the cases; b) autologous Hematopoietic Stem Cell Transplantation (HSCT) since 1997 under the auspices of the joined EBMT-EULAR working party, reporting durable remission with reduced or no immunosuppressive drug requirement in 66%, one-third of whom later relapsed to some degree with a 74 ± 7% (n= 62/79) overall survival at 5 years for SLE among the 863 HSCT procedures registered: in 2007 in the EBMT data base. cache = ./cache/cord-005480-yg7salqt.txt txt = ./txt/cord-005480-yg7salqt.txt === reduce.pl bib === id = cord-004675-n8mlxe7p author = nan title = 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date = 2019-02-26 pages = extension = .txt mime = text/plain words = 86427 sentences = 5050 flesch = 46 summary = However, the mean infusion rate per site was similar between patients aged <18 years ( XMEN disease (X-linked Immunodeficency with Magnesium defect, Epstein-Barr virus infection and Neoplasia) is a primary immune deficiency caused by mutations in MAGT1 and characterized by chronic infection with Epstein-Barr virus (EBV), EBV-driven lymphoma, CD4 T-cell lymphopenia, and dysgammaglobulinemia. We present the case of a 1-year old Hispanic infant with a pathogenic variant in MAGT1 gene that clinically manifested with early Pneumocystis jirovecii and cytomegalovirus (CMV) interstitial pneumonia, and EBV chronic infection with good response to intravenous immunoglobulins supplementation without hematopoietic stem cell transplantation or gene therapy. Chief, Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD, USA Hypomorphic Recombination Activating Gene 1 (RAG1) mutations result in residual T-and B-cell development in both humans and mice and have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI). cache = ./cache/cord-004675-n8mlxe7p.txt txt = ./txt/cord-004675-n8mlxe7p.txt === reduce.pl bib === id = cord-006466-e1phpqes author = nan title = 2018 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date = 2018-04-23 pages = extension = .txt mime = text/plain words = 92230 sentences = 5516 flesch = 46 summary = Whole exome sequencing revealed a heterozygous mutation, previously reported (c.1425+1G>T) Conclusions: In summary, this report emphasizes the suspicion of a combined immunodeficiency in the presence of multiple abscesses by Mycoplasma, the usefulness of rDNA 16s in order to achieve proper Objectives: We describe a 15-year-old male patient with novel heterozygous mutation of EP300 gene; his first manifestations were initially characterized by infections, cytopenia and hypogammaglobulinemia suggesting a Common Variable Immunodeficiency (CVID), but later on, persisting lymphopenia was suggestive of a combined immunodeficiency. Conclusions: Close monitoring of immune function in early life for patients with CHH and CID as well as the availability of suitable donors assists in determining management, including HSCT Introduction/Background: Leukocyte Adhesion Deficiency (LAD) represents a group of distinct inherited disorders, which inhibit the normal extravasation of neutrophils and their recruitment to sites of infection or inflammation. cache = ./cache/cord-006466-e1phpqes.txt txt = ./txt/cord-006466-e1phpqes.txt === reduce.pl bib === id = cord-009567-osstpum6 author = nan title = Abstracts Oral date = 2008-04-23 pages = extension = .txt mime = text/plain words = 131214 sentences = 7728 flesch = 53 summary = Introduction: Previously, it has been demonstrated that FOXP3, a gene required for the development and function of regulatory T cells, was highly expressed in the graft during cardiac rejection, suggesting infiltration of regulatory T cells in the transplanted organ during an allogeneic response. Efficacy and safety parameters assessed at follow-up included: acute rejection; patient and graft survival; renal function, vital signs, basic lab results and immunosuppressive regimen for the patients 10 years after completion of the original study. We analyzed, for the first time, the expression of TLR4 in PBMC from kidney recipients with contrasted situations: operational tolerance and chronic immune-mediated rejection (Banff 2005), compared to patients with normal histology and stable graft function, non transplant patients with renal failure and healthy volunteers. cache = ./cache/cord-009567-osstpum6.txt txt = ./txt/cord-009567-osstpum6.txt === reduce.pl bib === id = cord-022888-dnsdg04n author = nan title = Poster Sessions date = 2009-08-19 pages = extension = .txt mime = text/plain words = 188640 sentences = 9313 flesch = 45 summary = Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. cache = ./cache/cord-022888-dnsdg04n.txt txt = ./txt/cord-022888-dnsdg04n.txt === reduce.pl bib === id = cord-005460-ezrn8cva author = nan title = Physicians – Poster Session date = 2017-07-28 pages = extension = .txt mime = text/plain words = 287105 sentences = 15681 flesch = 56 summary = Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . cache = ./cache/cord-005460-ezrn8cva.txt txt = ./txt/cord-005460-ezrn8cva.txt === reduce.pl bib === id = cord-005453-4057qib7 author = nan title = The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date = 2019-07-03 pages = extension = .txt mime = text/plain words = 275771 sentences = 16876 flesch = 56 summary = To compare the safety and efficacy of prophylactic DLI for prevention of relapse after allogeneic peripheral blood stem cell transplantation from haploidentical donors (HID-SCT) and matched-sibling donors (MSD-SCT) in patients with very high-risk acute myeloid leukemia (AML), we performed a retrospective, observational cohort study enrolled in 21 HID-SCT and 13 MSD-SCT recipients. The aim of this study is to identify the prognostic impact of pre-transplant TIM3 levels on early and late transplant related complications as well as post-transplant relapse and survival Methods: A total of 177 hematopoietic stem cell transplantation (HSCT) recipients with an initial diagnosis of acute leukemia [median age: 36(16-66) years; male/ female: 111/66] were included in the study. cache = ./cache/cord-005453-4057qib7.txt txt = ./txt/cord-005453-4057qib7.txt ===== Reducing email addresses cord-016903-z2vqfq98 cord-018393-5jlqn7wq Creating transaction Updating adr table ===== Reducing keywords cord-001938-n2d5fw2f cord-001690-cn21fgug cord-010130-28bt3x25 cord-006713-io9yp1y2 cord-003376-2qi4aibx cord-016478-gpl0zbvd cord-007575-5ekgabx5 cord-004059-furt6xcn cord-004591-2hchnlwb cord-006841-3u56erru cord-016267-idrc1sdh cord-001079-v01vwu00 cord-015922-5wwy0m2k cord-015139-s7ox0h4f cord-018331-ovmtz4sb cord-016903-z2vqfq98 cord-003085-7krf1yxz cord-018659-rxzy6k3b 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cord-335692-5uxtua9o cord-311505-akcc9oms cord-259194-9zllvfqb cord-017782-dtveihrj cord-347064-ljd121no cord-274012-56i4sikj cord-283826-lgyc3sro cord-021977-yu0hrg6h cord-296402-rd5clf8h cord-018393-5jlqn7wq cord-279638-jr1mbh7s cord-348130-t9tysvr8 cord-315304-pge45105 cord-323691-5s5almd2 cord-350807-qdq96723 cord-290976-dhwlr2ui cord-276343-sb3vd7fq cord-193356-hqbstgg7 cord-305085-bv7udg9k cord-347761-wgodcsav cord-354325-r73datur cord-348547-wmvqvbqi cord-005478-5iu38pr6 cord-340489-yo3cp5vs cord-313474-1gux1gsi cord-005480-yg7salqt cord-004675-n8mlxe7p cord-006466-e1phpqes cord-009567-osstpum6 cord-022888-dnsdg04n cord-354374-rtgjjglc cord-005453-4057qib7 cord-005460-ezrn8cva Creating transaction Updating wrd table ===== Reducing urls cord-001938-n2d5fw2f cord-001690-cn21fgug cord-010130-28bt3x25 cord-001079-v01vwu00 cord-288721-3bv3aak6 cord-267269-05mezubh cord-004643-uu4uipfy cord-022752-bdve1ydv cord-103297-4stnx8dw cord-272835-6nx4f8ss cord-018545-fk17n2bx cord-348130-t9tysvr8 cord-018393-5jlqn7wq cord-193356-hqbstgg7 cord-350807-qdq96723 cord-005478-5iu38pr6 cord-022888-dnsdg04n cord-005460-ezrn8cva cord-005453-4057qib7 cord-005480-yg7salqt Creating transaction Updating url table ===== Reducing named entities cord-001938-n2d5fw2f cord-010130-28bt3x25 cord-001690-cn21fgug cord-003376-2qi4aibx cord-006713-io9yp1y2 cord-016478-gpl0zbvd cord-004591-2hchnlwb cord-006841-3u56erru cord-004059-furt6xcn cord-007575-5ekgabx5 cord-016267-idrc1sdh cord-015139-s7ox0h4f cord-001079-v01vwu00 cord-015922-5wwy0m2k cord-018331-ovmtz4sb cord-016903-z2vqfq98 cord-018659-rxzy6k3b cord-003085-7krf1yxz cord-005225-7uuilki4 cord-288721-3bv3aak6 cord-018943-5zf0eya3 cord-006393-jcj9nqfu cord-267269-05mezubh cord-004986-en7taikk cord-017012-yl0vanuh cord-005794-3u4iu41r cord-023729-dipjubn7 cord-022472-q2qtl26d cord-269194-b1wlr3t7 cord-016932-bej10xbf cord-006586-49btg9w7 cord-016990-ot1wi3xi cord-004643-uu4uipfy cord-011030-o4jn5883 cord-023854-w8kx5n8k cord-019009-3ngfv96u cord-023669-3ataw6gy cord-263276-keyu60in cord-018785-tcr5xlf8 cord-285433-ehnu83qe cord-016998-6n662amh cord-291960-1is0rv6c cord-015365-iqdi99pd cord-006856-b1w25ob5 cord-015389-vwgai4k9 cord-282618-tjvjlyn9 cord-011197-bmigh2rs cord-016255-kkko1xne cord-293886-gbv1ipmn cord-307016-4hdsb5oq cord-280374-yj0r4rwt cord-340228-mvqoyror cord-257114-pxmflm2c cord-014462-11ggaqf1 cord-022752-bdve1ydv cord-103297-4stnx8dw cord-288945-c9ow1q5c cord-272835-6nx4f8ss cord-017030-tzuyo6tx cord-342000-h4jo2bir cord-335692-5uxtua9o cord-266218-r6xg9zts cord-304066-rirbdhz3 cord-018545-fk17n2bx cord-311505-akcc9oms cord-259194-9zllvfqb cord-005487-vac061r8 cord-017782-dtveihrj cord-347064-ljd121no cord-274012-56i4sikj cord-283826-lgyc3sro cord-021977-yu0hrg6h cord-310217-p9nqcz5d cord-296402-rd5clf8h cord-279638-jr1mbh7s cord-348130-t9tysvr8 cord-315304-pge45105 cord-323691-5s5almd2 cord-350807-qdq96723 cord-276343-sb3vd7fq cord-193356-hqbstgg7 cord-018393-5jlqn7wq cord-347761-wgodcsav cord-348547-wmvqvbqi cord-354325-r73datur cord-290976-dhwlr2ui cord-305085-bv7udg9k cord-354374-rtgjjglc cord-340489-yo3cp5vs cord-313474-1gux1gsi cord-005478-5iu38pr6 cord-005480-yg7salqt cord-006466-e1phpqes cord-004675-n8mlxe7p cord-009567-osstpum6 cord-022888-dnsdg04n cord-005453-4057qib7 cord-005460-ezrn8cva Creating transaction Updating ent table ===== Reducing parts of speech cord-001938-n2d5fw2f cord-010130-28bt3x25 cord-003376-2qi4aibx cord-004591-2hchnlwb cord-001690-cn21fgug cord-006713-io9yp1y2 cord-016478-gpl0zbvd cord-006841-3u56erru cord-004059-furt6xcn cord-015139-s7ox0h4f cord-018331-ovmtz4sb cord-018943-5zf0eya3 cord-016267-idrc1sdh cord-003085-7krf1yxz cord-018659-rxzy6k3b cord-016903-z2vqfq98 cord-007575-5ekgabx5 cord-015922-5wwy0m2k cord-288721-3bv3aak6 cord-005225-7uuilki4 cord-006393-jcj9nqfu cord-004986-en7taikk cord-005794-3u4iu41r cord-023729-dipjubn7 cord-004643-uu4uipfy cord-001079-v01vwu00 cord-267269-05mezubh cord-006586-49btg9w7 cord-022472-q2qtl26d cord-016932-bej10xbf cord-263276-keyu60in cord-023854-w8kx5n8k cord-285433-ehnu83qe cord-011030-o4jn5883 cord-019009-3ngfv96u cord-269194-b1wlr3t7 cord-011197-bmigh2rs cord-023669-3ataw6gy cord-291960-1is0rv6c cord-293886-gbv1ipmn cord-018785-tcr5xlf8 cord-280374-yj0r4rwt cord-016998-6n662amh cord-340228-mvqoyror cord-342000-h4jo2bir cord-282618-tjvjlyn9 cord-017012-yl0vanuh cord-016990-ot1wi3xi cord-307016-4hdsb5oq cord-016255-kkko1xne cord-288945-c9ow1q5c cord-335692-5uxtua9o cord-310217-p9nqcz5d cord-304066-rirbdhz3 cord-311505-akcc9oms cord-266218-r6xg9zts cord-347064-ljd121no cord-257114-pxmflm2c cord-259194-9zllvfqb cord-017030-tzuyo6tx cord-272835-6nx4f8ss cord-017782-dtveihrj cord-315304-pge45105 cord-276343-sb3vd7fq cord-274012-56i4sikj cord-015389-vwgai4k9 cord-283826-lgyc3sro cord-021977-yu0hrg6h cord-350807-qdq96723 cord-018545-fk17n2bx cord-279638-jr1mbh7s cord-323691-5s5almd2 cord-354374-rtgjjglc cord-348130-t9tysvr8 cord-296402-rd5clf8h cord-347761-wgodcsav cord-290976-dhwlr2ui cord-348547-wmvqvbqi cord-022752-bdve1ydv cord-006856-b1w25ob5 cord-015365-iqdi99pd cord-354325-r73datur cord-014462-11ggaqf1 cord-103297-4stnx8dw cord-018393-5jlqn7wq cord-193356-hqbstgg7 cord-340489-yo3cp5vs cord-305085-bv7udg9k cord-005487-vac061r8 cord-313474-1gux1gsi cord-005478-5iu38pr6 cord-005480-yg7salqt cord-004675-n8mlxe7p cord-006466-e1phpqes cord-009567-osstpum6 cord-022888-dnsdg04n cord-005453-4057qib7 cord-005460-ezrn8cva Creating transaction Updating pos table Building ./etc/reader.txt cord-005453-4057qib7 cord-022888-dnsdg04n cord-005460-ezrn8cva cord-005453-4057qib7 cord-005460-ezrn8cva cord-005480-yg7salqt number of items: 97 sum of words: 1,754,227 average size in words: 36,546 average readability score: 44 nouns: patients; cells; cell; disease; infection; transplantation; transplant; treatment; results; risk; donor; study; years; therapy; infections; days; months; virus; stem; group; patient; time; survival; recipients; age; blood; day; graft; analysis; response; data; methods; pts; cases; diagnosis; expression; conditioning; mortality; incidence; levels; dose; relapse; prophylaxis; donors; children; range; number; use; marrow; studies verbs: used; dying; received; showed; included; associated; compared; following; increased; developed; treating; performed; reported; occurs; based; reduced; observed; found; related; identified; underwent; cause; induced; presented; suggest; remains; evaluate; analyzed; require; demonstrated; considered; resulted; led; given; matched; detected; improve; diagnosed; determined; see; described; providing; expressed; decreased; assessed; achieve; indicated; reveal; transplanted; affected adjectives: median; high; clinical; acute; immune; viral; severe; specific; significant; non; human; first; chronic; higher; positive; low; anti; hematopoietic; primary; renal; different; early; respiratory; overall; negative; peripheral; common; post; unrelated; lower; normal; important; single; autologous; long; second; free; infectious; pre; multiple; similar; complete; effective; inflammatory; major; present; new; pulmonary; total; several adverbs: also; respectively; however; significantly; well; previously; therefore; often; prior; still; even; highly; especially; usually; currently; recently; furthermore; less; particularly; commonly; retrospectively; frequently; later; alone; clinically; moreover; statistically; now; mainly; early; potentially; approximately; generally; successfully; finally; additionally; together; interestingly; subsequently; relatively; first; already; least; fully; directly; overall; daily; almost; typically; initially pronouns: we; our; it; their; i; its; they; he; them; she; his; her; us; one; itself; themselves; you; him; mg; your; bohv-4; my; me; itma; r348; herself; ourselves; ours; n40np; interleukin-15; il-12r1; igmcic; igg4; himself; esat-6; e2f2-/-mice; e.g.•; crx-527; ≥65; αat; yourself; wel; u; trl2x4; tdcs; stat1; sdc‐sign; s382; s; rab3b proper nouns: CMV; HSCT; T; der; GVHD; mg; HLA; von; SCT; CD4; HIV; mit; PCR; bei; OS; EBV; AML; eine; B; und; CD8; werden; GvHD; CD34; ATG; C; NK; CI; zu; II; einer; kg; IV; ASCT; sind; HCT; oder; G; IFN; durch; University; RIC; CR; A; ist; den; auf; aGVHD; DC; el keywords: cmv; patient; infection; cell; hsct; hiv; ebv; gvhd; cd4; transplant; hla; transplantation; dna; pcr; patienten; hct; die; cd8; und; der; aml; virus; therapie; rna; ric; result; recipient; nrm; hcv; day; atg; von; hsv; disease; cd34; aids; university; tbi; mit; lung; ivig; infektion; icu; graft; ebmt; background; asct; werden; vod; trm one topic; one dimension: patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747999/ titles(s): Cytomegalovirus reactivation and mortality in patients with acute respiratory distress syndrome three topics; one dimension: patients; infection; der file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/, https://api.elsevier.com/content/article/pii/B9781437707885100136, https://api.elsevier.com/content/article/pii/B9783437428319100130 titles(s): Physicians – Poster Session | Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding | KAPITEL 13 Infektionskrankheiten five topics; three dimensions: patients cell cells; infection cmv patients; cells cell il; patients cells cell; der die und file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/, https://api.elsevier.com/content/article/pii/B9781437707885100136, https://doi.org/10.1101/2020.04.12.038158, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639731/, https://api.elsevier.com/content/article/pii/B9783437428319100130 titles(s): Physicians – Poster Session | Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding | Modern Hopfield Networks and Attention for Immune Repertoire Classification | Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh | KAPITEL 13 Infektionskrankheiten Type: cord title: keyword-cmv-cord date: 2021-05-24 time: 22:41 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:cmv ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-342000-h4jo2bir author: Aggarwal, Ashim title: Early Cardiac Allograft Vasculopathy: Are the Viruses to Blame? date: 2012-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This paper describes a case of early (7 months after transplant) cardiac allograft vasculopathy. This-43-year-old (CMV positive, EBV negative) female patient underwent an orthotopic heart transplant with a (CMV negative, EBV positive) donor heart. She had a history of herpes zoster infection and postherpetic neuralgia in the past. The patient's panel reactive antibodies had been almost undetectable on routine surveillance testing, and her surveillance endomyocardial biopsies apart from a few episodes of mild-to-moderate acute cellular rejection (treated adequately with steroids) never showed any evidence of humoral rejection. The postoperative course was complicated by multiple admissions for upper respiratory symptoms, and the patient tested positive for entero, rhino, and coronaviruses serologies. During her last admission (seven months postoperatively) the patient developed mild left ventricular dysfunction with an ejection fraction of 40%. The patient's endomyocardial biopsy done at that time revealed concentric intimal proliferation and inflammation resulting in near-total luminal occlusion in the epicardial and the intramyocardial coronary vessels, suggestive of graft vasculopathy with no evidence of rejection, and the patient had a fatal ventricular arrhythmia. url: https://doi.org/10.1155/2012/734074 doi: 10.1155/2012/734074 id: cord-340228-mvqoyror author: Al-Herz, Waleed title: Spectrum of Viral Infections Among Primary Immunodeficient Children: Report From a National Registry date: 2019-05-29 words: 2930.0 sentences: 170.0 pages: flesch: 42.0 cache: ./cache/cord-340228-mvqoyror.txt txt: ./txt/cord-340228-mvqoyror.txt summary: Results: A total of 274 PID children were registered in KNPIDR during the study period with predominance of immunodeficiencies affecting cellular and humoral immunity, followed by combined immunodeficiencies with associated syndromic features and diseases of immune dysregulation. CMV and parainfluenza infections were more common in the group of immunodeficiencies affecting cellular and humoral immunity while EBV and human papilloma virus (HPV) were more common in the immune dysregulation group and combined immunodeficiencies with associated syndromic features, respectively. The distribution of these patients according to PID categories is: immunodeficiencies affecting cellular and humoral immunity, 97 patients (35.4%); combined immunodeficiencies with associated syndromic features, 67 patients (24.5%); predominantly antibody deficiencies, 34 patients (12.4%); diseases of immune dysregulation, 47 patients (17.2%); congenital defects of phagocyte number or function, 17 patients (6.2%); autoinflammatory disorders, 1 patient (0.3%); and complement deficiencies, 11 patients (4%). abstract: Objective: To present the frequency and spectrum of viral infections in primary immunodeficient children. Methods: The data was obtained from the Kuwait National Primary Immunodeficiency Disorders (PIDs) Registry during the period of 2004-2018. Results: A total of 274 PID children were registered in KNPIDR during the study period with predominance of immunodeficiencies affecting cellular and humoral immunity, followed by combined immunodeficiencies with associated syndromic features and diseases of immune dysregulation. Overall infectious complications affected 82.4% of the patients, and viral infections affected 31.7% of the registered patients. Forty-five patients (16.4%) developed viral infections caused by at least 2 organisms, among those 20 patients were affected by three or more viral infections. There was a statistically significant association between viral infections and PID category. However, there was no statistically significant association between viral infections and gender or the patients' onset age. There was a total of 170 viral infections during the study period and the causes of these infections were predominated by CMV (22.2%), adenovirus (11.7%), EBV (11.1%), and enteroviruses (7.4%). CMV and parainfluenza infections were more common in the group of immunodeficiencies affecting cellular and humoral immunity while EBV and human papilloma virus (HPV) were more common in the immune dysregulation group and combined immunodeficiencies with associated syndromic features, respectively. The most common presentation was viremia (28.8%) followed by pneumonia (28.2%) and skin infections (17.6%). The most common causes of viremia were CMV followed by adenovirus and EBV, while the most common organisms causing pneumonia were CMV followed by rhinovirus and parainfluenza. There were 80 deaths among the registered patients, 10% were caused by viral infections. Conclusions: Viral infections are common in PIDs and result into a wide-range of clinical manifestations causing significant morbidity and mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/31191561/ doi: 10.3389/fimmu.2019.01231 id: cord-307016-4hdsb5oq author: Allen, Upton title: Prevention and Treatment of Infectious Complications After Solid Organ Transplantation in Children date: 2010-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Effective prevention, diagnosis, and treatment of infectious diseases after transplantation are key factors contributing to the success of organ transplantation. Most transplant patients experience different kinds of infections during the first year after transplantation. Children are at particular risk of developing some types of infections by virtue of lack of immunity although they may be at risk for other types due the effect of immunosuppressive regimens necessary to prevent rejection. Direct consequences of infections result in syndromes such as mononucleosis, pneumonia, gastroenteritis, hepatitis, among other entities. Indirect consequences are mediated through cytokines, chemokines, and growth factors elaborated by the transplant recipient in response to microbial replication and invasion, which contribute to the net state of immunosuppression among other effects. This review summarizes the major infections that occur after pediatric organ transplantation, highlighting the current treatment and prevention strategies, based on the available data and/or consensus. url: https://doi.org/10.1016/j.pcl.2010.01.005 doi: 10.1016/j.pcl.2010.01.005 id: cord-257114-pxmflm2c author: BURGUETE, SERGIO R. title: Lung transplant infection date: 2012-12-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lung transplantation has become an accepted therapeutic procedure for the treatment of end‐stage pulmonary parenchymal and vascular disease. Despite improved survival rates over the decades, lung transplant recipients have lower survival rates than other solid organ transplant recipients. The morbidity and mortality following lung transplantation is largely due to infection‐ and rejection‐related complications. This article will review the common infections that develop in the lung transplant recipient, including the general risk factors for infection in this population, and the most frequent bacterial, viral, fungal and other less frequent opportunistic infections. The epidemiology, diagnosis, prophylaxis, treatment and outcomes for the different microbial pathogens will be reviewed. The effects of infection on lung transplant rejection will also be discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/22591266/ doi: 10.1111/j.1440-1843.2012.02196.x id: cord-016478-gpl0zbvd author: Barry, Maura title: Cytopenias in Transplant Patients date: 2018-12-08 words: 5636.0 sentences: 259.0 pages: flesch: 32.0 cache: ./cache/cord-016478-gpl0zbvd.txt txt: ./txt/cord-016478-gpl0zbvd.txt summary: The differential diagnosis for anemia after solid organ transplant includes hemolysis, drug toxicities, iron deficiency, infection, posttransplant lymphoproliferative disorder, graft-vs.-host disease, and hemophagocytic syndrome. Sirolimus and calcineurin inhibitors such as tacrolimus and cyclosporine have been shown in renal and lung transplant recipients to cause hemolytic anemia, thrombotic thrombocytopenic purpura, and atypical hemolytic uremic syndrome [15] [16] [17] . While this etiology is more often identified as a drug-related phenomenon, particularly due to the immunosuppressants required to prevent organ rejection (see next section), there have been multiple case reports associating CMV infection as a trigger of TMA in the posttransplant setting [53, 54] . When this is identified, numerous case studies in multiple different organ systems (lung, liver, kidney solid organ transplant) have reported that changing from one CI to another (tacrolimus to cyclosporine or vice versa) or to another class of medication such as sirolimus or mycophenolate mofetil can prevent further episodes of TMA from occurring [61] [62] [63] [64] . abstract: Anemia, leukopenia, thrombocytopenia, as well as pancytopenias can be seen following solid organ transplant. Varying patterns of cytopenia can be seen based on the drugs used in the posttransplant period, infections encountered by the individual, as well as the individual’s immune response and bone marrow function. The chapter discusses the main causes of anemia, leukopenia/neutropenia, and thrombocytopenia. The differential diagnosis for anemia after solid organ transplant includes hemolysis, drug toxicities, iron deficiency, infection, posttransplant lymphoproliferative disorder, graft-vs.-host disease, and hemophagocytic syndrome. Etiologies for leukopenia and neutropenia include drug toxicities and infection, and etiologies for thrombocytopenia include drug toxicities, infections, autoimmune events such as immune thrombocytopenic purpura, and underlying causes such as persistent portal hypertension and splenomegaly. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120766/ doi: 10.1007/978-1-4939-9034-4_10 id: cord-354325-r73datur author: Berger, Mitchell title: Therapeutic Applications of Monoclonal Antibodies date: 2002-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: ABSTRACT Researchers have sought therapeutic applications for monoclonal antibodies since their development in 1975. However, murine-derived monoclonal antibodies may cause an immunogenic response in human patients, reducing their therapeutic efficacy. Chimeric and humanized antibodies have been developed that are less likely to provoke an immune reaction in human patients than are murine-derived antibodies. Antibody fragments, bispecific antibodies, and antibodies produced through the use of phage display systems and genetically modified plants and animals may aid researchers in developing new uses for monoclonal antibodies in the treatment of disease. Monoclonal antibodies may have a number of promising potential therapeutic applications in the treatment of asthma, autoimmune diseases, cancer, poisoning, septicemia, substance abuse, viral infections, and other diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/12120821/ doi: 10.1097/00000441-200207000-00004 id: cord-005794-3u4iu41r author: Berner, Michel E. title: High frequency oscillatory ventilation for respiratory failure due to RSV bronchiolitis date: 2008-05-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To describe the time course of high frequency oscillatory ventilation (HFOV) in respiratory syncytial virus (RSV) bronchiolitis. DESIGN: Retrospective charts review. SETTING: A tertiary paediatric intensive care unit. PATIENTS AND PARTICIPANTS: Infants with respiratory failure due to RSV infection. INTERVENTION: HFOV. MEASUREMENTS AND RESULTS: Pattern of lung disease, ventilatory settings, blood gases, infant’s vital parameters, sedation and analgesia during the periods of conventional mechanical ventilation (CMV, 6 infants), after initiation of HFOV (HFOVi, 9 infants), in the middle of its course (HFOVm), at the end (HFOVe) and after extubation (Post-Extub) were compared. All infants showed a predominant overexpanded lung pattern. Mean airway pressure was raised from a mean (SD) 12.5 (2.0) during CMV to 18.9 (2.7) cmH(2)O during HFOVi (P < 0.05), then decreased to 11.1(1.3) at HFOVe (P < 0.05). Mean FiO(2) was reduced from 0.68 (0.18) (CMV) to 0.59 (0.14) (HFOVi) then to 0.29 (0.06) (P < 0.05) at HFOVe and mean peak to peak pressure from 44.9 (12.4) cmH(2)O (HFOVi) to 21.1 (7.7) P < 0.05 (HFOVe) while mean (SD) PaCO(2) showed a trend to decrease from 72 (22) (CMV) to 47 (8) mmHg (HFVOe) and mean infants respiratory rate a trend to increase from 20 (11) (HFOVi) to 34 (14) (HFOVe) breaths/min. With usual doses of sedatives and opiates, no infant was paralysed and all were extubated to CPAP or supplemental oxygen after a mean of 120 h. CONCLUSION: RSV induced respiratory failure with hypercapnia can be managed with HFOV using high mean airway pressure and large pressure swings while preserving spontaneous breathing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095463/ doi: 10.1007/s00134-008-1151-3 id: cord-354374-rtgjjglc author: C.G. Pollok, Richard title: Enteric viruses in HIV-related diarrhoea date: 2000-12-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: HIV-related diarrhoea is an important cause of morbidity and mortality in HIV infection. Cytomegalovirus is a well-established cause of diarrhoea, but the role of other enteric viruses is less clear and will be discussed here. The clinical manifestations, disease mechanisms, diagnostic techniques and current treatments for the management of these infections are reviewed. url: https://api.elsevier.com/content/article/pii/S1357431000018165 doi: 10.1016/s1357-4310(00)01816-5 id: cord-279638-jr1mbh7s author: Calore, Elisabetta title: Treatment of Acute Graft-versus-Host Disease in Childhood with Extracorporeal Photochemotherapy/Photopheresis: The Padova Experience date: 2015-07-14 words: 5592.0 sentences: 279.0 pages: flesch: 57.0 cache: ./cache/cord-279638-jr1mbh7s.txt txt: ./txt/cord-279638-jr1mbh7s.txt summary: Acute graft-versus-host disease (aGVHD) is the major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Update on the mechanism of action and on clinical efficacy of extracorporeal photopheresis in the treatment of acute and chronic graft versus host disease in children Extracorporeal photopheresis (photochemotherapy) in the treatment of acute and chronic graft versus host disease: immunological mechanisms and the results from clinical studies Role of extracorporeal photopheresis (ECP) in treatment of steroid-refractory acute graft-versus-host disease Extracorporeal Photopheresis for the treatment of acute and chronic graft-versus-host disease in adults and children: best practice recommendations from an Italian Society of Hemapheresis and Cell Manipulation (SIdEM) and Italian Group for Bone Marrow Transplantation (GITMO) consensus process Extracorporeal photopheresis for steroid resistant graft versus host disease in pediatric patients: a pilot single institution report Extracorporeal photochemotherapy in graft-versus-host disease: a longitudinal study on factors influencing the response and survival in pediatric patients abstract: Acute graft-versus-host disease (aGVHD) is the major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Systemic steroid treatment represents the first-line therapy for aGVHD and is associated with a response rate of 30% to 60%. Steroid-resistant patients have a poor prognosis with high transplantation-related mortality (TRM). Several second-line therapies have been proposed for the management of unresponsive aGVHD, without proven beneficial effects on patients' outcome or overall long-term survival. For these reasons, extracorporeal photochemotherapy/photopheresis (ECP), a cell-based approach to control GVHD that spares generalized immunosuppression, seems to be promising. In this study, we report the outcome of 72 consecutive pediatric patients treated with ECP between 1997 and 2013 for aGVHD. Among them, 21 patients had steroid-resistant aGVHD, 42 had steroid-dependent aGVHD, and 9 did not receive steroid as first-line therapy because of clinical contraindications. A complete response was obtained in 72% of patients, a partial response was observed in 11%, and there was no response in 17% of patients. At day +180, TRM was 4% in the whole cohort; TRM was 3% and 20% among responders and nonresponders to ECP, respectively (P < .0001). The 5-year overall survival was 71%, showing a difference between responders and nonresponders of 78% and 30%, respectively (P = .0004). The 5-year time to progression of primary disease was 81%, without any significant difference between the 2 groups. Moreover, the 5-year progression-free survival of primary disease was 72%, with a significant difference (P = .0007) between responders (79%) and nonresponders (30%) to ECP. In conclusion, this study demonstrates that ECP is highly effective in aGVHD without a negative impact on primary disease. url: https://doi.org/10.1016/j.bbmt.2015.07.007 doi: 10.1016/j.bbmt.2015.07.007 id: cord-347761-wgodcsav author: Cant, Andrew title: Infections in the Immunocompromised date: 2009-10-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infections in the immunocompromised differ significantly from those in the immunocompetent. They can be more serious, more often life threatening, more difficult to diagnose and are caused by more unusual organisms. Children can be immunocompromised for a variety of reasons and the numbers, worldwide, are growing. url: https://www.ncbi.nlm.nih.gov/pubmed/20204751/ doi: 10.1007/978-1-4419-0981-7_1 id: cord-348130-t9tysvr8 author: Cho, Sung-Yeon title: Infectious complications after hematopoietic stem cell transplantation: current status and future perspectives in Korea date: 2018-02-27 words: 9707.0 sentences: 506.0 pages: flesch: 34.0 cache: ./cache/cord-348130-t9tysvr8.txt txt: ./txt/cord-348130-t9tysvr8.txt summary: In addition, the types and risk factors of infectious complications differ according to the stem cell source, donor type, conditioning intensity, region, prophylaxis strategy, and comorbidities, such as graft-versushost disease and invasive fungal infection. Bacteria: consider fluoroquinolone a Fungus: consider prophylaxis during neutropenia, consider PCP prophylaxis Virus: during neutropenia or longer depending on risks HSCT, hematopoietic stem cell transplantation; PCP, Pneumocystis jirovecii pneumonia; GVHD, graft-versus-host disease; TNF-α, tumor necrosis factor-α. In a systematic review and meta-analysis of non-HIV immunocompromised hosts (patients with acute leukemia and recipients of HSCT and solid organ transplant), the incidence of PCP was reduced by 91% (relative risk [RR], 0.09) in trimethoprim/sulfamethoxazole prophylaxis group compared with placebo [69, 70] . Epidemiology and risk factors for invasive fungal diseases among allogeneic hematopoietic stem cell transplant recipients in Korea: results of abstract: Hematopoietic stem cell transplantation (HSCT) is a treatment for hematologic malignancies, immune deficiencies, or genetic diseases, ect. Recently, the number of HSCTs performed in Korea has increased and the outcomes have improved. However, infectious complications account for most of the morbidity and mortality after HSCT. Post-HSCT infectious complications are usually classified according to the time after HSCT: pre-engraftment, immediate post-engraftment, and late post-engraftment period. In addition, the types and risk factors of infectious complications differ according to the stem cell source, donor type, conditioning intensity, region, prophylaxis strategy, and comorbidities, such as graft-versushost disease and invasive fungal infection. In this review, we summarize infectious complications after HSCT, focusing on the Korean perspectives. url: https://doi.org/10.3904/kjim.2018.036 doi: 10.3904/kjim.2018.036 id: cord-010130-28bt3x25 author: Crocchiolo, R. title: Infections after T‐replete haploidentical transplantation and high‐dose cyclophosphamide as graft‐versus‐host disease prophylaxis date: 2015-03-26 words: 3519.0 sentences: 175.0 pages: flesch: 46.0 cache: ./cache/cord-010130-28bt3x25.txt txt: ./txt/cord-010130-28bt3x25.txt summary: RESULTS: After a median follow‐up of 23 months, cumulative incidence of viral infections was 70% (95% confidence interval [CI] 59–81) at 100 days and 77% (95% CI 67–87) at 1 year; 35 of 65 patients at risk had CMV reactivation (54%) and the rate of polyomavirus‐virus‐associated cystitis was 19% (13/70). In the present analysis, we described infectious complications after unmanipulated, T-cell replete haplo-HSCT using post-transplant Cy in 70 consecutive patients and found, aside from a high incidence of viral infections/reactivations, especially in the early posttransplant period, a quite low incidence of late bacterial infections, together with a very low incidence of IFIs after day +180 (2 events in the overall 11 observed). In conclusion, the present single-center data on 70 consecutive patients receiving T-cell replete haplo-HSCT with post-transplant Cy confirm a high rate of viral infections before day +100 and a lower incidence of infections afterward, suggesting a satisfactory although non-optimal immune reconstitution after this type of transplantation. abstract: BACKGROUND: Recently, a platform of T‐cell replete haploidentical hematopoietic stem cell transplantation (haplo‐HSCT) using post‐transplant cyclophosphamide (Cy) has shown high reproducibility and acceptable safety profile. METHOD: This prospective cohort analysis allowed us to collect data on infections among 70 consecutive recipients of haplo‐HSCT affected by various hematologic malignancies. RESULTS: After a median follow‐up of 23 months, cumulative incidence of viral infections was 70% (95% confidence interval [CI] 59–81) at 100 days and 77% (95% CI 67–87) at 1 year; 35 of 65 patients at risk had CMV reactivation (54%) and the rate of polyomavirus‐virus‐associated cystitis was 19% (13/70). Cumulative incidence of bacterial and fungal infections at 1 year were 63% (95% CI 51–75) and 12% (95% CI 4–19), respectively. Of note, only 1 invasive fungal infection occurred beyond 1 year after transplant (day +739). CONCLUSION: In conclusion, despite a high rate of viral infections in the early period, present data suggest a satisfactory infectious profile after T‐cell replete haplo‐HSCT using post‐transplant Cy. These results may help clinicians to improve both prophylactic and therapeutic antimicrobial strategies in this emerging haploidentical setting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169814/ doi: 10.1111/tid.12365 id: cord-293886-gbv1ipmn author: Cunha, Burke A. title: Severe cytomegalovirus (CMV) community-acquired pneumonia (CAP) in a nonimmunocompromised host date: 2008-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Community-acquired pneumonia (CAP) in an immunocompetent host may be severe because of a variety or combination of host and microbial factors. In patients with severe cardiopulmonary dysfunction, even relatively avirulent pathogens, that is, Mycoplasma pneumoniae, Moraxella catarrhalis, may compromise borderline cardiac/heart function and present clinically as severe CAP. Alternately, patients with Streptococcus pneumoniae and impaired humoral immunity/splenic dysfunction may present as severe CAP. With the exception of Legionnaire's disease, influenza, and adenovirus, pathogen virulence is not a key determinant of CAP severity. METHODS: Diagnostically, patients with severe CAP may be approached based on the pattern of infiltrates on chest x-ray together with the severity of hypoxemia (ie, increased A-a gradient: >35). RESULTS: We present the case of an immunocompetent adult who presented with severe CAP during peak influenza season. Direct fluorescent antibody testing of his respiratory secretions was negative for influenza, adenovirus, and other respiratory viruses. Diagnostic bronchoscopy was negative for bacterial and fungal pathogens. The only clues to the cause of his severe CAP was the presence of relative lymphopenia, atypical lymphocytosis and elevated serum transaminases. After influenza and adenovirus were ruled out, cytomegalovirus (CMV) CAP was considered. The diagnosis of CMV CAP was made serologically by demonstrating highly elevated IgM CMV titers. Because the diagnosis was made during the patient's recovery late in hospitalization, he did not receive CMV antiviral therapy. CONCLUSION: This case should remind clinicians that influenza and adenovirus are diagnostic considerations in patients presenting with severe CAP with diffuse bilateral interstitial infiltrates accompanied by severe hypoxemia in normal hosts. If influenza and adenovirus are ruled out, then CMV CAP, although rare, should be considered, particularly when viral CAP is accompanied by relative lymphopenia, atypical lymphocytosis and increased serum transaminases. url: https://api.elsevier.com/content/article/pii/S0147956308001039 doi: 10.1016/j.hrtlng.2008.05.008 id: cord-259194-9zllvfqb author: Cupples, Sandra A. title: Transplant Infectious Disease: Implications for Critical Care Nurses date: 2011-11-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infection is an important issue for critical care nurses as they care for patients throughout all phases of the transplant continuum: potential organ donors, transplant candidates, and transplant recipients. This article has reviewed salient issues relative to infections in each of these patient populations, including patients with VADs, and has highlighted key points pertaining to bacterial, viral, and fungal infections. url: https://api.elsevier.com/content/article/pii/S0899588511000293 doi: 10.1016/j.ccell.2011.08.001 id: cord-018331-ovmtz4sb author: Dancygier, Henryk title: Viral Infections by Nonhepatotropic Viruses date: 2010 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123179/ doi: 10.1007/978-3-642-04519-6_10 id: cord-018659-rxzy6k3b author: Danziger-Isakov, Lara title: Posttransplant Complications and Comorbidities date: 2018-01-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious complications cause significant acute morbidity and mortality after pediatric lung transplantation. With the lung graft in direct communication with the environment, it is susceptible to a variety of bacterial, fungal, and viral pathogens. Appreciation for pretransplant risk factors in addition to perioperative and posttransplant exposures is necessary to anticipate, diagnose, and treat infections in this population. Further, epidemiologic associations between infection and chronic allograft dysfunction have been reported and suggest consequences of infectious events may have substantial impact. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123596/ doi: 10.1007/978-3-319-07284-5_71 id: cord-348547-wmvqvbqi author: Desmons, Aurore title: Post-mortem diagnosis, of cytomegalovirus and varicella zoster virus co-infection by combined histology and tissue molecular biology, in a sudden unexplained infant death date: 2013-10-31 words: 2317.0 sentences: 130.0 pages: flesch: 45.0 cache: ./cache/cord-348547-wmvqvbqi.txt txt: ./txt/cord-348547-wmvqvbqi.txt summary: title: Post-mortem diagnosis, of cytomegalovirus and varicella zoster virus co-infection by combined histology and tissue molecular biology, in a sudden unexplained infant death Objectives To describe post-mortem combined histological and tissue molecular biological techniques for the diagnosis of cytomegalovirus and varicella zoster virus co-infection as a cause of death. Study design Real-time quantitative PCR and RT-PCR assays for Herpesviruses, respiratory viruses, Adenovirus, Enterovirus and Parvovirus B19 were performed on multi-organ frozen samples and paraffin-embedded tissues in combination with histology. Conclusions This case shows that thorough quantitative virological investigations on frozen tissues must be performed in combination with histology and immunohistochemistry for the determination of the cause of a sudden unexplained infant death. Post-mortem virological quantitative molecular analyses performed on frozen tissue samples revealed cytomegalovirus (CMV) and varicella zoster virus (VZV), mainly in the lungs. However, pulmonary necrotizing inflammatory lesions, immunohistochemistry, and molecular detection of CMV and VZV in multi-organs samples demonstrated the role of the co-infection in the death. abstract: Abstract Background An autopsy case of a two-month-old male infant who suddenly and unexpectedly died during his sleep, eight days after the onset of benign varicella. Objectives To describe post-mortem combined histological and tissue molecular biological techniques for the diagnosis of cytomegalovirus and varicella zoster virus co-infection as a cause of death. Study design Real-time quantitative PCR and RT-PCR assays for Herpesviruses, respiratory viruses, Adenovirus, Enterovirus and Parvovirus B19 were performed on multi-organ frozen samples and paraffin-embedded tissues in combination with histology. Results Cytomegalovirus and varicella zoster virus were detected by molecular biology with highest viral loads detected in the lungs (4.6×107 and 1.9×105 genome copies per million of cells, respectively). Pulmonary extensive necrotizing inflammation and immunohistochemistry correlated to virological data. Virological molecular biology was negative on paraffin-embedded tissues. Conclusions This case shows that thorough quantitative virological investigations on frozen tissues must be performed in combination with histology and immunohistochemistry for the determination of the cause of a sudden unexplained infant death. url: https://doi.org/10.1016/j.jcv.2013.08.007 doi: 10.1016/j.jcv.2013.08.007 id: cord-018545-fk17n2bx author: Dorofaeff, Tavey title: Infections in the PICU date: 2012 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123446/ doi: 10.1007/978-3-642-02202-9_268 id: cord-006841-3u56erru author: Einsele, Hermann title: Infectious complications after allogeneic stem cell transplantation: epidemiology and interventional therapy strategies: Guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncology (DGHO) date: 2003-09-10 words: 5273.0 sentences: 281.0 pages: flesch: 34.0 cache: ./cache/cord-006841-3u56erru.txt txt: ./txt/cord-006841-3u56erru.txt summary: The number of stem cells in the graft and the type of GvHD prophylaxis are factors which determine the rate of hematopoeitic reconstitution and may therefore also influence incidence and severity of infections during the early post-transplantation period. Modification of empiric antimicrobial regimens in patients with neutropenic fever after allogeneic stem cell transplantation When the causative agent of an infection has been identified, antibacterial therapy should be adapted according to the resistance pattern of the pathogen. If fever occurs in a patient later than 100 days after allogeneic stem cell transplantation, the upper and lower respiratory tract (bronchitis, pneumonia, sinusitis), and bacteremias have to be considered as specific foci of infections. Clinical manifestations of adenovirus infections in patients after allogeneic stem cell transplantation that have been reported so far include pneumonia, hepatitis, cystitis, diarrhea, and also disseminated disease (for diagnostic procedures see Table 3 ). abstract: The risk of infection after allogeneic stem cell transplantation is determined by the underlying disease, the intensity of previous treatments and complications that may have occurred during that time, but above all, the risk of infection is determined by the selected transplantation modality (e.g. HLA-match between the stem cell donor and recipient, T cell depletion of the graft, and others). In comparison with patients treated with high-dose chemotherapy and autologous stem cell transplantation, patients undergoing allogeneic stem cell transplantation are at a much higher risk of infection even after hematopoietic reconstitution, due to the delayed recovery of T and B cell functions. The rate at which immune function recovers after hematopoietic reconstitution greatly influences the incidence and type of post-transplant infectious complications. Infection-associated mortality, for example, is significantly higher following engraftment than during the short neutropenic period that immediately follows transplantation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103165/ doi: 10.1007/s00277-003-0772-4 id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 words: 12542.0 sentences: 501.0 pages: flesch: 36.0 cache: ./cache/cord-269194-b1wlr3t7.txt txt: ./txt/cord-269194-b1wlr3t7.txt summary: Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. abstract: Abstract Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. url: https://api.elsevier.com/content/article/pii/S0580951715000069 doi: 10.1016/bs.mim.2015.04.005 id: cord-018393-5jlqn7wq author: Finke, Ernst-Jürgen title: Bioterrorismus, infektiologische Aspekte date: 2011-12-14 words: 25008.0 sentences: 3876.0 pages: flesch: 44.0 cache: ./cache/cord-018393-5jlqn7wq.txt txt: ./txt/cord-018393-5jlqn7wq.txt summary: Wenn sie sich jedoch verstärkt, kann man sie leicht erkennen, aber nur schwer heilen." (Nicolo Macchiavelli, 1449 -1527 Es ist wenig wahrscheinlich, dass biologische Anschläge rechtzeitig als solche erkannt werden, sofern kein automatisches Monitoring mit einem zuverlässigen Echtzeit-Nachweis von B-Agenzien existiert. B. Enzephalitiden viraler Genese sowie die Frühstadien von nvCJD und möglicherweise auch die Frühsymptomatik der Alzheimer-Krankheit; außerdem die Borreliose-Infektion (Neuroborreliose), bei der ein heterogenes Symptomenbild angenommen wird, das sich wenig mit der Ausprägung einer (BDV-spezifischen) Dysfunktion im limbischen System deckt. Unklar ist jedoch, wie häufig sich aus initial milden Infektionen der oberen Luftwege eine Bronchitis oder eine Pneumonie entwickelt und was die auslösenden Faktoren dafür sind. Beim Nachweis hoch positiver (häufig mit anderen Chlamydienspezies kreuzreagierender) Antikörper ist bei entsprechender klinischer Symptomatik die gezielte Erhebung der Anamnese hinsichtlich einer möglichen Exposition des Patienten gegenüber den natürlichen Wirten diagnostisch wegweisend. Aus Patientenseren wurden Cyclospora-spezifische Antikörper isoliert, jedoch sind die Vorgänge der Immunantwort auf Cyclospora noch nicht vollständig geklärt und ob sich eine Immunität entwickelt, ist fraglich. abstract: Infektionskrankheiten sind ständige Begleiter und gefürchtete Geißeln der Menschheit. Pest und Pocken versetzen als todbringende Seuchen die Menschen nicht erst seit dem Altertum in Schrecken (lat.: terror). Archaische Ängste und vor allem eine hohe Medienaufmerksamkeit sorgen immer wieder für Panik und irrationale Reaktionen: Im indischen Surat setzte im Herbst 1994 während eines ungewöhnlichen Pestausbruchs eine Massenflucht ein, nachdem die Presse den Verdacht auf Lungenpest und terroristische Anschläge verbreitet hatte. Über 800.000 Menschen, darunter auch zahlreiche Ärzte und Pflegekräfte, verließen daraufhin ihre Arbeitsplätze und Wohnorte. Allein die drastischen Flug- und Handelsbeschränkungen brachten Indien einen ökonomischen Schaden von etwa 3 Milliarden US $. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123253/ doi: 10.1007/978-3-642-17158-1_3 id: cord-022472-q2qtl26d author: Fishman, Jay A. title: Infection in Renal Transplant Recipients date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155736/ doi: 10.1016/b978-1-4160-0158-4.50041-0 id: cord-017782-dtveihrj author: Fong, I. W. title: Litigations for HIV Related Complications date: 2010-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In 1992, a 27-year-old male with same sex exposure requested human immuno-deficiency virus (HIV) testing anonymously at a walk-in clinic. He was advised that the test (HIV serology) was positive and he requested a repeat test (anonymously) 1 month later, which was also reported as being positive. About 2 years later, he was assessed by a general practitioner for symptoms of depression and continued medical care. At that time, investigations revealed a CD4 T-cell count of about 700 cells/uL. Sometime in 1996 a repeat blood test revealed a CD4 cell count just <500 cells/uL. No consultation to an infectious diseases specialist or HIV clinic was made. The GP(general practitioner) then initiated a regimen consisting of didanosine, lamivudine, and saquinavir for HIV infection. At that time, testing for HIV viral load was not generally available to the medical community, but became procurable in 1997. Initially, the patient tolerated the regimen well and over the next 3 years his CD4 cell count was maintained above 600–700 cells/uL and the HIV viral load remained undetectable (<50 copies). However, the patient started to show morphologic changes of moderate facial and peripheral lipoatrophy, developed mild sensory peripheral neuropathy, and increased liver enzymes attributable to fatty liver, and elevations of the fasting serum glucose. In the summer of 2000, although the CD4 cell count remained stable, the HIV viral load was reported as being over 7,000 copies/uL. At this time, the patient was referred to a university hospital HIV clinic. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122441/ doi: 10.1007/978-1-4419-8053-3_13 id: cord-001690-cn21fgug author: Franceschi, Valentina title: BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1((-/-)) Mice from Monkeypoxvirus Lethal Challenge date: 2015-06-18 words: 6710.0 sentences: 334.0 pages: flesch: 53.0 cache: ./cache/cord-001690-cn21fgug.txt txt: ./txt/cord-001690-cn21fgug.txt summary: In the present study, a new vaccination strategy approach based on three recombinant bovine herpesvirus 4 (BoHV-4) vectors, each expressing different MPXV glycoproteins, A29L, M1R and B6R were investigated in terms of protection from a lethal MPXV challenge in STAT1 knockout mice. In vivo efficacy testing of BoHV-4-A-CMV-A29LgD 106 ΔTK, BoHV-4-A-EF1α-M1RgD 106 ΔTK and BoHV-4-A-EF1α-B6RgD 106 ΔTK To test the efficacy of the vectors in vivo, we sought to determine if they could protect mice against a lethal challenge with MPXV. Since the purpose of this study was to determine the capability of BoHV-4-based viral vectors to protect STAT1 (-/-) mice against a lethal MPXV infection, the first concern was the generation of optimized expression cassettes to be integrated into the BAC-BoHV-4-A genome that were able to efficiently express A29L, M1R and B6R antigens. In summary, our findings have demonstrated that BoHV-4 based vectors can be used as vaccines to protect against a lethal MPXV challenge in mice. abstract: Monkeypox virus (MPXV) is the etiological agent of human (MPX). It is an emerging orthopoxvirus zoonosis in the tropical rain forest of Africa and is endemic in the Congo-basin and sporadic in West Africa; it remains a tropical neglected disease of persons in impoverished rural areas. Interaction of the human population with wildlife increases human infection with MPX virus (MPXV), and infection from human to human is possible. Smallpox vaccination provides good cross-protection against MPX; however, the vaccination campaign ended in Africa in 1980, meaning that a large proportion of the population is currently unprotected against MPXV infection. Disease control hinges on deterring zoonotic exposure to the virus and, barring that, interrupting person-to-person spread. However, there are no FDA-approved therapies against MPX, and current vaccines are limited due to safety concerns. For this reason, new studies on pathogenesis, prophylaxis and therapeutics are still of great interest, not only for the scientific community but also for the governments concerned that MPXV could be used as a bioterror agent. In the present study, a new vaccination strategy approach based on three recombinant bovine herpesvirus 4 (BoHV-4) vectors, each expressing different MPXV glycoproteins, A29L, M1R and B6R were investigated in terms of protection from a lethal MPXV challenge in STAT1 knockout mice. BoHV-4-A-CMV-A29LgD(106)ΔTK, BoHV-4-A-EF1α-M1RgD(106)ΔTK and BoHV-4-A-EF1α-B6RgD(106)ΔTK were successfully constructed by recombineering, and their capacity to express their transgene was demonstrated. A small challenge study was performed, and all three recombinant BoHV-4 appeared safe (no weight-loss or obvious adverse events) following intraperitoneal administration. Further, BoHV-4-A-EF1α-M1RgD(106)ΔTK alone or in combination with BoHV-4-A-CMV-A29LgD(106)ΔTK and BoHV-4-A-EF1α-B6RgD(106)ΔTK, was shown to be able to protect, 100% alone and 80% in combination, STAT1((-/-)) mice against mortality and morbidity. This work demonstrated the efficacy of BoHV-4 based vectors and the use of BoHV-4 as a vaccine-vector platform. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4473039/ doi: 10.1371/journal.pntd.0003850 id: cord-274012-56i4sikj author: Gavaldà, Joan title: Infección en el trasplante de pulmón date: 2007-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Actualmente, el trasplante de pulmón se considera un tratamiento válido para un buen número de pacientes con insuficiencia respiratoria grave. De todas formas, las complicaciones son muy frecuentes y pueden llevar a fracaso del injerto a medio y largo plazo y menor supervivencia. De acuerdo con el registro de la International Society for Heart and Lung Transplantation, las tasas de supervivencia al primer, segundo y quinto año fueron, en 2006, del 74, 65 y 47%, respectivamente. El principal obstáculo para el éxito a largo plazo del trasplante de pulmón es el rechazo crónico, caracterizado histológicamente como bronquiolitis obliterante, que acontece en cerca de dos terceras partes de los pacientes. Uno de los factores más importantes para el desarrollo de bronquiolitis obliterante, además del número de rechazos agudos, es la infección y la enfermedad por citomegalovirus (CMV). Recientemente, se ha destacado el papel de la infección por diferentes virus respiratorios como factores de riesgo para el desarrollo de rechazo crónico en receptores de un trasplante de pulmón. Las complicaciones infecciosas son una causa frecuente de morbimortalidad en este tipo de pacientes, y la causa de muerte de cerca de la mitad de ellos. La infección bacteriana es la complicación más frecuente de un receptor de un trasplante de pulmón. Del total, el 35-66% son bacterianas y el 50-85% de los pacientes presentan como mínimo un episodio de infección bacteriana. La segunda causa más frecuente de infección, después de la bacteriana, es la infección por CMV. A pesar de utilizar diferentes estrategias de prevención, la incidencia sigue siendo elevada, y se sitúa alrededor del 7% el primer año postrasplante. Es el único tipo de trasplante de órgano sólido en el cual la etiología más frecuente de la infección fúngica es Aspergillus spp., a diferencia del resto, en que típicamente se deben a Candida spp. La incidencia de aspergilosis invasora se cifra en alrededor del 4%. Lung transplantation is now considered an established therapeutic option for patients with severe respiratory failure. Nevertheless, complications are frequent and can lead to intermediate- or long-term graft dysfunction and decreased survival. According to the registry of the International Society for Heart and Lung Transplantation, survival rates in these patients at one, two, and five years are 74%, 65%, and 47%, respectively. The main obstacle to long-term success of lung transplantation, however, is chronic rejection, which is characterized histologically as bronchiolitis obliterans and occurs in up to two-thirds of patients. One of the most important risk factors for the development of bronchiolitis obliterans, in addition to the number of previous acute rejection episodes and the incidence of persistent rejection, is cytomegalovirus infection and disease. Moreover, recent evidence has indicated a role for respiratory viruses as risk factors for the development of chronic rejection in lung transplant recipients. Infectious complications are a frequent cause of morbidity and mortality in these patients and are the cause of death in nearly half of them. Bacterial infection is the most frequent infectious complication in lung transplant patients. Among the total of infections, 35%-66% are bacterial and 50%-85% of patients present at least one episode. CMV is the second most frequent cause of infectious complications following lung transplantation. Despite the use of various preventive strategies, the risk of developing CMV disease in lung transplant recipients is over 5% during the first year. This is the only type of solid organ transplant in which the etiology of fungal infection is characteristically Aspergillus spp., in contrast to others in which infection by Candida spp. is most common. The incidence of invasive aspergillosis is about 4%. url: https://api.elsevier.com/content/article/pii/S0213005X07743732 doi: 10.1157/13112940 id: cord-019009-3ngfv96u author: Gea-Banacloche, Juan title: Risks and Epidemiology of Infections After Hematopoietic Stem Cell Transplantation date: 2016-02-15 words: 8485.0 sentences: 401.0 pages: flesch: 32.0 cache: ./cache/cord-019009-3ngfv96u.txt txt: ./txt/cord-019009-3ngfv96u.txt summary: Several characteristics of the transplant infl uence the risk of infection: the conditioning preparative regimen, the source of stem cells, the degree of HLA identity between donor and recipient, and the prophylactic strategy adopted to prevent GVHD (use of T cell depletion or immunosuppressive medications). These factors may result in increased risk of infections associated with T cell immunodefi ciency, like CMV, Pneumocystis jirovecii pneumonia (PCP), and Epstein-Barr virus (EBV)-related posttransplant lymphoproliferative disorder (PTLD). Risk factors for recurrence of invasive fungal infection during secondary antifungal prophylaxis in allogeneic hematopoietic stem cell transplant recipients Impact of the intensity of the pretransplantation conditioning regimen in patients with prior invasive aspergillosis undergoing allogeneic hematopoietic stem cell transplantation: a retrospective survey of the infectious diseases working party of the european group for blood and marrow transplantation Infl iximab use in patients with severe graftversus-host disease and other emerging risk factors of noncandida invasive fungal infections in allogeneic hematopoietic stem cell transplant recipients: a cohort study abstract: Infections following HCT are frequently related to risk factors caused by the procedure itself. Neutropenia and mucositis predispose to bacterial infections. Prolonged neutropenia increases the likelihood of invasive fungal infection. GVHD and its treatment create the most important easily identifiable risk period for a variety of infectious complications, particularly mold infections. Profound, prolonged T cell immunodeficiency, present after T cell-depleted or cord blood transplants, is the main risk factor for viral problems like disseminated adenovirus disease or EBV-related posttransplant lymphoproliferative disorder. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124050/ doi: 10.1007/978-3-319-28797-3_6 id: cord-311505-akcc9oms author: Geisen, Will R. title: Cytomegalovirus Enterocolitis secondary to experimental COVID-19 therapy date: 2020-09-22 words: 1354.0 sentences: 82.0 pages: flesch: 38.0 cache: ./cache/cord-311505-akcc9oms.txt txt: ./txt/cord-311505-akcc9oms.txt summary: Additionally, this case validates colonoscopy as a mode to rule out concurrent infectious etiologies causing diarrhea in COVID-19-positive patients. Additionally, this case validates colonoscopy as a mode to rule out concurrent infectious etiologies causing diarrhea in COVID-19-positive patients. The novel 2019 coronavirus (COVID-19), a form of severe acute respiratory syndrome (SARS-CoV-2), has caused a pandemic of historical proportions. Due to its worldwide distribution, a paucity of clinical trial data, and a high mortality rate, the COVID pandemic has led to widespread implementation of experimental therapies with varying levels of success and, in some instances, poor outcomes (3, 4, 5) . We present a patient who was treated with experimental therapies and subsequently developed severe gastrointestinal pathology that was diagnosed by colonoscopy. The report describes a patient with SARS-CoV-2 pneumonia who was treated with experimental immunomodulating therapies and, subsequently, developed cytomegalovirus (CMV) colitis. abstract: The novel coronavirus-2019 (COVID-19) has caused a global pandemic of historical proportions, infecting millions of people worldwide. Due to its high mortality rate and a paucity of clinical data, experimental therapies have been utilized with uncertain success and, unfortunately, poor outcomes. We describe a gentleman who was treated with experimental therapies and subsequently developed cytomegalovirus colitis and hypovolemic shock. Additionally, this case validates colonoscopy as a mode to rule out concurrent infectious etiologies causing diarrhea in COVID-19-positive patients. url: https://api.elsevier.com/content/article/pii/S2214250920302705 doi: 10.1016/j.idcr.2020.e00962 id: cord-006586-49btg9w7 author: Golfieri, R. title: Pulmonary complications of liver transplantation: radiological appearance and statistical evaluation of risk factors in 300 cases date: 2000 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The aim of this study was to evaluate the incidence, radiographic appearance, time of onset, outcome and risk factors of non-infectious and infectious pulmonary complications following liver transplantation. Chest X-ray features of 300 consecutive patients who had undergone 333 liver transplants over an 11-year period were analysed: the type of pulmonary complication, the infecting pathogens and the mean time of their occurrence are described. The main risk factors for lung infections were quantified through univariate and multivariate statistical analysis. Non-infectious pulmonary abnormalities (atelectasis and/or pleural effusion: 86.7 %) and pulmonary oedema (44.7 %) appeared during the first postoperative week. Infectious pneumonia was observed in 13.7 %, with a mortality of 36.6 %. Bacterial and viral pneumonia made up the bulk of infections (63.4 and 29.3 %, respectively) followed by fungal infiltrates (24.4 %). A fairly good correlation between radiological chest X-ray pattern, time of onset and the cultured microorganisms has been observed in all cases. In multivariate analysis, persistent non-infectious abnormalities and pulmonary oedema were identified as the major independent predictors of posttransplant pneumonia, followed by prolonged assisted mechanical ventilation and traditional caval anastomosis. A “pneumonia-risk score” was calculated: low-risk score ( < 2.25) predicts 2.7 % of probability of the onset of infections compared with 28.7 % of high-risk ( > 3.30) population. The “pneumonia-risk score” identifies a specific group of patients in whom closer radiographic monitoring is recommended. In addition, a highly significant correlation (p < 0.001) was observed between pneumonia-risk score and the expected survival, thus confirming pulmonary infections as a major cause of death in OLT recipients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102073/ doi: 10.1007/s003309900268 id: cord-011030-o4jn5883 author: Hakki, Morgan title: Moving Past Ganciclovir and Foscarnet: Advances in CMV Therapy date: 2020-01-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PURPOSE OF REVIEW: CMV DNA polymerase inhibitors such as ganciclovir and foscarnet have dramatically reduced the burden of CMV infection in the HCT recipient. However, their use is often limited by toxicities and resistance. Agents with novel mechanisms and favorable toxicity profiles are critically needed. We review recent developments in CMV antivirals and immune-based approaches to mitigating CMV infection. RECENT FINDINGS: Letermovir, an inhibitor of the CMV terminase complex, was approved in 2017 for primary CMV prophylaxis in adult seropositive allogeneic HCT recipients. Maribavir, an inhibitor of the CMV UL97 kinase, is currently in two phase 3 treatment studies. Adoptive immunotherapy using third-party T cells has proven safe and effective in preliminary studies. Vaccine development continues, with several promising candidates currently under study. SUMMARY: No longer limited to DNA polymerase inhibitors, the prevention and treatment of CMV infections in the HCT recipient is a rapidly evolving field which should translate into improvements in CMV-related outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223398/ doi: 10.1007/s11899-020-00557-6 id: cord-004643-uu4uipfy author: Hasan, Mohammad Rubayet title: Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report date: 2020-03-20 words: 3015.0 sentences: 151.0 pages: flesch: 35.0 cache: ./cache/cord-004643-uu4uipfy.txt txt: ./txt/cord-004643-uu4uipfy.txt summary: Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics. Ganciclovir resistance was confirmed by the presence of the A594V mutation in UL97 [6] What was unique in our patient compared to other reported CMV-associated HLH cases was the overwhelming infection with MDROs. On hospital admission, the patient was found to be colonized with multiple MDROs including VRE, and carbapenamase-producing Enterobacteriaceae, which may have been acquired during his previous hospital course in India. abstract: BACKGROUND: Infections with multidrug-resistant organisms (MDRO) pose a serious threat to patients with dysregulated immunity such as in hemophagocytic lymphohistiocytosis (HLH), but such infections have rarely been comprehensively characterized. Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria. CASE PRESENTATION: A previously healthy, six-year-old boy presented with a 45-day history of fever prior to a diagnosis of hemophagocytic lymphohistiocytosis and hemorrhagic colitis, both associated with CMV. On hospital admission, the patient was found to be colonized with multiple, multidrug-resistant (MDR) bacteria including vancomycin-resistant enterococci (VRE) and carbapenamase-producing organisms (CPO). He eventually developed respiratory, urine and bloodstream infections with highly drug-resistant, including pandrug-resistant bacteria, which could not be controlled by antibiotic treatment. Antiviral therapy also failed to contain his CMV infection and the patient succumbed to overwhelming bacterial and viral infection. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics. CONCLUSIONS: The case highlights both the risk of acquiring MDR superbugs and the severity of these infections in HLH patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083060/ doi: 10.1186/s12879-020-04966-z id: cord-017030-tzuyo6tx author: Henao-Martínez, Andrés F. title: Infections in Heart, Lung, and Heart-Lung Transplantation date: 2018-12-08 words: 11531.0 sentences: 740.0 pages: flesch: 32.0 cache: ./cache/cord-017030-tzuyo6tx.txt txt: ./txt/cord-017030-tzuyo6tx.txt summary: There are several factors predisposing thoracic transplant recipients to infections: (A) factors present before transplantation: age, presence of comorbidities (e.g., chronic kidney disease, diabetes mellitus, cancer, etc.), nutrition status, latent infections, colonization with healthcare-associated organisms, and occult community-acquired infections; (B) factors during the surgery: duration of the transplant procedure, graft injury including ischemic time, colonization or latent infection of the graft, surgical instrumentation (e.g., mechanical ventilation, invasive devices such as catheters, drains, Foley catheters, etc.), ICU stay, and need for re-interventions; and (C) factors present after transplant: degree of immunosuppression, CMV infection, and rejections ( Mechanical ventilation (MV) for >5 days immediately following transplant surgery and isolation of Staphylococcus aureus (SA) from airway cultures in the recipient were considered risk factors for invasive SA infections in a retrospective study of patients with lung and heart-lung transplants [20] . abstract: Half a century has passed since the first orthotopic heart transplant took place. Surgical innovations allowed for heart, lung, and heart-lung transplantation to save lives of patients with incurable chronic cardiopulmonary conditions. The complexity of the surgical interventions, chronic host health conditions, and antirejection immunosuppressive medications makes infectious complications common. Infections have remained one of the main barriers for successful transplantation and a source of significant morbidity and mortality. Recognition of infections and its management in this setting require outstanding clinical skills since transplant recipients may not exhibit classic signs or symptoms of disease, and laboratory work has some pitfalls. The prevention, identification, and management of infectious diseases complications in this population are a priority to undertake to improve the medical outcomes of transplantation. Herein, we reviewed the historical aspects, epidemiology, and prophylaxis of infections in heart, lung, and heart-lung transplantation. We also discuss the most prevalent organisms affecting the host and the organ systems involved. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121494/ doi: 10.1007/978-1-4939-9034-4_2 id: cord-017012-yl0vanuh author: Herberg, Jethro title: Infectious Diseases and the Kidney date: 2009 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The kidney is involved in a wide range of bacterial, viral, fungal, and parasitic diseases. In most systemic infections, renal involvement is a minor component of the illness, but in some, renal failure may be the presenting feature and the major problem in management. Although individual infectious processes may have a predilection to involve the renal vasculature, glomeruli, interstitium, or collecting systems, a purely anatomic approach to the classification of infectious diseases affecting the kidney is rarely helpful because most infections may involve several different aspects of renal function. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121468/ doi: 10.1007/978-3-540-76341-3_52 id: cord-016903-z2vqfq98 author: Herndler-Brandstetter, Dietmar title: The Efficacy of Vaccines to Prevent Infectious Diseases in the Elderly date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious diseases still represent a major challenge to human progress and survival. Especially elderly persons are more frequently and severely affected by infectious diseases and they display distinct features with respect to clinical presentation and treatment. Although vaccinations are considered a vital medical procedure for preventing morbidity and mortality caused by infectious diseases, the protective effect of vaccinations is abrogated in elderly persons. This is due to a decline in the functions of the immune system referred to as immunosenescence. The first part of this chapter will therefore summarize the status quo of the efficacy of vaccines in preventing morbidity and mortality caused by typical infectious diseases in the elderly, such as influenza, pneumonia and tuberculosis. The second part will then elucidate the underlying age-related mechanisms which may contribute to the decreased efficacy of vaccines. Based on the complex mechanisms involved in immunosenescence, strategies will be outlined which may be succesfful in enhancing protective immune responses following vaccination in elderly persons. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121339/ doi: 10.1007/978-0-387-76842-7_10 id: cord-004059-furt6xcn author: Hraiech, Sami title: Herpes simplex virus and Cytomegalovirus reactivation among severe ARDS patients under veno-venous ECMO date: 2019-12-23 words: 3388.0 sentences: 187.0 pages: flesch: 43.0 cache: ./cache/cord-004059-furt6xcn.txt txt: ./txt/cord-004059-furt6xcn.txt summary: However, little is known about herpes simplex virus (HSV) and Cytomegalovirus (CMV) reactivation occurring in patients with severe ARDS under veno-venous extracorporeal membrane oxygenation (ECMO). The following data were retrospectively recorded from the patients'' medical file: age, sex, Simplified Acute Physiologic Score II (SAPS II) [21] , Sequential Organ Failure Assessment (SOFA) score [22] , presence of co-morbidities, presence of previous immunosuppression, cause of ARDS, date of MV initiation, date of ECMO implementation, other organ failure associated with ARDS during ICU stay (in particular need for catecholamines or renal replacement therapy), blood transfusion, post-aggressive pulmonary fibrosis (defined by an alveolar procollagen III higher than 9 µg/l) [23] , time of HSV/CMV reactivation, delay between MV and HSV/CMV reactivation, delay between ECMO and HSV/CMV reactivation, duration of MV (from the day of intubation to the day of MV weaning), ECMO duration (from the day of ECMO implementation to its removal or death), ECMO-free days at day 28, ventilator-free days (VFD) at day 28, ICU length of stay [from the day of ICU admission (in the first ICU if the patient was referred from another hospital) to discharge], hospital length of stay [from the admission to hospital (in the original hospital if the patient was referred from another hospital) to discharge to home or to rehabilitation ward], ICU and hospital mortality, acyclovir or ganciclovir treatment after reactivation under ECMO. abstract: BACKGROUND: Herpesviridae reactivation among non-immunocompromised critically ill patients is associated with impaired prognosis, especially during acute respiratory distress syndrome (ARDS). However, little is known about herpes simplex virus (HSV) and Cytomegalovirus (CMV) reactivation occurring in patients with severe ARDS under veno-venous extracorporeal membrane oxygenation (ECMO). We tried to determine the frequency of Herpesviridae reactivation and its impact on patients’ prognosis during ECMO for severe ARDS. RESULTS: During a 5-year period, 123 non-immunocompromised patients with a severe ARDS requiring a veno-venous ECMO were included. Sixty-seven patients (54%) experienced HSV and/or CMV reactivation during ECMO course (20 viral co-infection, 40 HSV alone, and 7 CMV alone). HSV reactivation occurred earlier than CMV after the beginning of MV [(6–15) vs. 19 (13–29) days; p < 0.01] and after ECMO implementation [(2–8) vs. 14 (10–20) days; p < 0.01]. In univariate analysis, HSV/CMV reactivation was associated with a longer duration of mechanical ventilation [(22–52.5) vs. 17.5 (9–28) days; p < 0.01], a longer duration of ECMO [15 (10–22.5) vs. 9 (5–14) days; p < 0.01], and a prolonged ICU [29 (19.5–47.5) vs. 16 (9–30) days; p < 0.01] and hospital stay [44 (29–63.5) vs. 24 (11–43) days; p < 0.01] as compared to non-reactivated patients. However, in multivariate analysis, viral reactivation remained associated with prolonged MV only. When considered separately, both HSV and CMV reactivation were associated with a longer duration of MV as compared to non-reactivation patients [29 (19.5–41) and 28 (20.5–37), respectively, vs. 17.5 (9–28) days; p < 0.05]. Co-reactivation patients had a longer duration of MV [58.5 (38–72.3); p < 0.05] and ICU stay [51.5 (32.5–69) vs. 27.5 (17.75–35.5) and 29 (20–30.5), respectively] as compared to patients with HSV or CMV reactivation alone. In multivariate analysis, HSV reactivation remained independently associated with a longer duration of MV and hospital length of stay. CONCLUSIONS: Herpesviridae reactivation is frequent among patients with severe ARDS under veno-venous ECMO and is associated with a longer duration of mechanical ventilation. The direct causative link between HSV and CMV reactivation and respiratory function worsening under ECMO remains to be confirmed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6928167/ doi: 10.1186/s13613-019-0616-6 id: cord-276343-sb3vd7fq author: Humar, Atul title: Assessment of Adenovirus Infection in Adult Lung Transplant Recipients Using Molecular Surveillance date: 2006-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background Little is known about adenovirus infections in adult lung transplant recipients. Because the virus can establish latency, re-activation may be relatively common after transplantation. Methods We assessed adenovirus infection in 80 adult lung transplant recipients. Adenovirus polymerase chain reaction (real-time PCR assay; limit of detection ∼25 copies/ml plasma) was done on plasma samples collected at regular intervals until 1 year post-transplant. Results Adenovirus DNA was detected in 18 of 80 patients (22.5%) and in 19 of 595 (3.4%) plasma samples up to 12 months post-transplant. Median time to detection of viremia was 134 days post-transplant (range 1 to 370 days). Median viral load was 180 copies/ml plasma (range 50 to 360 copies/ml). Symptoms were evaluated at the time of adenovirus detection: 14 of 18 (78%) patients were asymptomatic; 4 of 18 (22%) patients had otherwise unexplained febrile/flu-like illness that resolved spontaneously. Adenovirus was not found to be a trigger for acute rejection. No detrimental effect on pulmonary function was seen immediately after adenovirus infection. Conclusions Adenovirus viremia is common in adult lung transplant recipients. In contrast to findings on adenoviral pneumonitis in lung transplant recipients, isolated episodes of low-level viremia are self-limited and do not trigger acute rejection or a decline in pulmonary function. url: https://www.ncbi.nlm.nih.gov/pubmed/17178339/ doi: 10.1016/j.healun.2006.09.015 id: cord-280374-yj0r4rwt author: Jain, Richa title: Hepatic sinusoidal-obstruction syndrome and busulfan-induced lung injury in a post-autologous stem cell transplant recipient date: 2018-01-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Veno-occlusive disease of the liver is mostly encountered as a complication of hematopoietic stem cell transplantation with myeloablative regimens with an incidence estimated to be 13.7%. It is clinically characterized by tender hepatomegaly, jaundice, weight gain and ascites. Strong clinical suspicion and an early recognition of clinical signs are essential to establish the diagnosis and institute effective regimen. Another complication of cytotoxic drugs given for cancers, is development of busulfan-induced lung injury. A strong index of suspicion is needed for its diagnosis, especially in setting where opportunistic fungal and viral infections manifest similarly. We illustrate the clinical and autopsy finings in a 2½-year-old boy who received autologous stem-cell transplantation following resection of stage IV neuroblastoma. He subsequently developed both hepatic veno-occlusive disease and busulfan-induced lung injury. The autopsy findings are remarkable for their rarity. url: https://www.ncbi.nlm.nih.gov/pubmed/28984258/ doi: 10.1007/s13312-017-1172-5 id: cord-296402-rd5clf8h author: José Castón, Juan title: Efectos de la infección viral en el paciente trasplantado date: 2007-10-31 words: 11020.0 sentences: 998.0 pages: flesch: 52.0 cache: ./cache/cord-296402-rd5clf8h.txt txt: ./txt/cord-296402-rd5clf8h.txt summary: Respecto al citomegalovirus (CMV), tanto la reactivación como la infección adquirida en período peritrasplante, suelen producirse entre el primero y el cuarto mes postrasplante, aunque en la actualidad se describen cada Las infecciones virales continúan siendo una importante causa de morbimortalidad en los pacientes trasplantados. Igualmente, en otro ensayo que comparó valganciclovir con ganciclovir oral en Castón profilaxis durante 90 días en receptores de TOS (hepático, cardíaco, renal y páncreas y riñón) en situación D+/R-, se observó cómo en ambos grupos todos los casos de enfermedad por CMV aparecieron después de los primeros 6 meses postrasplante 18 . De esta forma, los receptores seronegativos que reciben órganos de donantes seropositivos presentan entre 10 y 50 veces mayor riesgo de ELPT como consecuencia del desarrollo de infección primaria por VEB 27 . abstract: Las infecciones virales continúan siendo una importante causa de morbimortalidad en los pacientes trasplantados. En estos pacientes, el riesgo de infección viral depende de varios factores como el tipo de trasplante, la intensidad de la inmunosupresión y la susceptibilidad del receptor. Además de efectos directos, la infección viral puede causar efectos indirectos derivados del efecto inmunomodulador de algunos virus como citomegalovirus o herpesvirus 6. Entre estos efectos se encuentran un mayor riesgo de replicación de otros virus, de rechazo, de otras infecciones oportunistas y de otras entidades específicas en cada tipo de trasplante. Los tests moleculares cuantitativos han reemplazado en la mayoría de las ocasiones a los métodos serológicos y al cultivo para el diagnóstico de estas infecciones, especialmente en el caso de citomegalovirus, virus de Epstein-Barr, y los virus de la hepatitis B y C. Sin embargo, estos avances diagnósticos no se han acompañado del desarrollo de antivirales específicos o de vacunas eficaces, por lo que las medidas de prevención continúan siendo fundamentales en estos pacientes. Viral infection remains an important cause of morbidity and mortality in transplant recipients. The risk of viral infection in these patients depends on several factors, such as the type of organ transplanted, the intensity of immunosuppression, and the recipient's susceptibility. In additional to direct effects, viral infection cause indirect effects, including greater risk of replication of other viruses, graft rejection, opportunistic infections and other specific entities for each type of transplant. These indirect effects result from the immunomodulatory activity of some viruses, such as cytomegalovirus and human herpes virus-6. For the most part, quantitative molecular tests have replaced serologic testing and in vitro culture for diagnosing infection. This approach is particularly prominent for cytomegalovirus, Epstein-Barr virus, hepatitis B virus, and hepatitis C virus. Despite these diagnostic advances, the development of specific antiviral agents and effective antiviral vaccines is limited. Thus, prophylactic strategies are still essential in transplant recipients. url: https://www.sciencedirect.com/science/article/pii/S0213005X07743471 doi: 10.1157/13109990 id: cord-347064-ljd121no author: José, Ricardo J. title: Opportunistic bacterial, viral and fungal infections of the lung date: 2016-05-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Opportunistic infections are a major cause of morbidity and mortality in severely immunocompromised patients, such as those receiving chemotherapy or biological therapies, patients with haematological malignancy, aplastic anaemia or HIV infection, and recipients of solid-organ or stem cell transplants. The type and degree of the immune defect dictate the profile of potential opportunistic pathogens; T-cell-mediated defects increase the risk of viral (cytomegalovirus, respiratory viruses) and Pneumocystis jirovecii infections, whereas neutrophil defects are associated with bacterial pneumonia and invasive aspergillosis. However, patients often have combinations of immune defects, and a wide range of other opportunistic infections can cause pneumonia. Importantly, conventional non-opportunistic pathogens are frequently encountered in immunocompromised hosts and should not be overlooked. The radiological pattern of disease (best assessed by computed tomography) and speed of onset help to identify the likely pathogen(s); radiological imaging can subsequently be supported by targeted investigation including the early use of bronchoscopy in selected patients. Rapid and expert clinical assessment can identify the most likely pathogens, which can then be treated aggressively, providing the best opportunity for a positive clinical outcome. url: https://www.sciencedirect.com/science/article/pii/S1357303916300159 doi: 10.1016/j.mpmed.2016.03.015 id: cord-335692-5uxtua9o author: Kilic, A. title: Evaluation of the performance of DiaSorin molecular Pneumocystis jirovecii-CMV multiplex real-time PCR assay from bronchoalveolar lavage samples date: 2020-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The aim of this study was to evaluate the performance of the DiaSorin Molecular PJ-CMV multiplex real-time PCR (PJ-CMV PCR) assay (DiaSorin Molecular LLC, USA) in bronchoalveolar lavage (BAL) samples compared to direct immunofluorescence assay (IFA) for the detection of Pneumocystis jirovecii and assess CMV and P. jirovecii co-infection rate in immunosuppressed patients with suspected pneumonia. A total of 125 BAL samples from immunosuppressed patients submitted for PJP-IFA were tested. Surplus samples were saved and further tested by using the PJ-CMV PCR assay. Among the 125 samples, P. jirovecii was detected in 31.2% (39/125) and in 40% (50/125) of the specimens using IFA and PJ-CMV PCR respectively. Eleven of the PJ-CMV PCR positive samples were negative by direct IFA for P. jirovecii. All samples positive by direct IFA were also positive by PJ-CMV PCR. Using the direct IFA as a gold standard, the PJ-CMV PCR sensitivity, specificity, positive predictive value and negative predictive value for detection of P. jirovecii were 100%, 87.2%, 78% and 100%, respectively. However, after reviewing the clinical diagnosis, the specificity and PPV increased to 100%. Of the 50 P. jirovecii samples positive by PJ-CMV PCR, 18 (36%) were also positive for CMV by the PJ-CMV PCR. The co-infection rate was found to be 37.5% (6/16) and 35.2% (12/34) in HIV infected and non-HIV infected patients. This study indicated that the DiaSorin Molecular PJ-CMV multiplex real-time PCR assay has higher sensitivity than direct IFA for detection of P. jirovecii and provides rapid detection of PJ and CMV infection in BAL samples. url: https://www.sciencedirect.com/science/article/pii/S1156523319303488 doi: 10.1016/j.mycmed.2020.100936 id: cord-022752-bdve1ydv author: Knuf, Markus title: Infektiologie date: 2019-08-09 words: 25995.0 sentences: 3963.0 pages: flesch: 43.0 cache: ./cache/cord-022752-bdve1ydv.txt txt: ./txt/cord-022752-bdve1ydv.txt summary: Zu den primär durch eine Blickdiagnose zu diagnostizierenden Infektionskrankheiten gehören auch die Windpocken (Varizellen) (› Abb. 10.5) mit kurz vor Exanthemausbruch bestehendem Fieber sowie Kopf-und Gliederschmerzen. Expositionsanamnese / Grundkrankheit (Disposition) Bei Kenntnis von zwei der drei genannten Faktoren kann auf den dritten geschlossen und eine kalkulierte antiinfektive Therapie begonnen werden. Wichtig für den klinischen Alltag sind nicht so sehr die Sensitivität und Spezifität eines Testverfahrens (Qualitätsmerkmale des Testverfahrens), sondern vor allem der positive bzw. Patienten mit einer Immundefizienz können abhängig von der vorliegenden Funktionsstörung oft auf Impfungen nicht adäquat reagieren und werden durch Lebendimpfstoffe u. Da der übermäßige Antibiotikaverbrauch zur Resistenzentwicklung beiträgt und Antibiotika Nebenwirkungen verursachen, ist eine möglichst zielgerechte Therapie für Patienten mit AOM, die wirklich davon profitieren, anzustreben. Da die normale Mundflora aus vielen verschiedenen Bakterienspezies besteht, wobei sowohl grampositive Erreger (grüne Streptokokken, β-hämolysierende Streptokokken) als auch Anaerobier und Actinomyzeten besonders häufig vorkommen, kann sich bei Prädisposition leicht eine Infektion entwickeln. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161407/ doi: 10.1016/b978-3-437-21661-9.00010-8 id: cord-315304-pge45105 author: Kotton, C.N. title: Organ Transplantation, Risks date: 2015-03-06 words: 4211.0 sentences: 206.0 pages: flesch: 29.0 cache: ./cache/cord-315304-pge45105.txt txt: ./txt/cord-315304-pge45105.txt summary: Viral infection is associated with both direct (invasive disease) and indirect (immune modulation) effects affecting susceptibility to other infections and promoting allograft rejection. The risk for viral infection is a function of the intensity of exposure and virulence of the specific virus, the intensity of immune suppression used to prevent graft rejection or graft-versus-host disease, underlying immune deficits, and factors affecting host susceptibility. Multiple factors contribute to viral reactivation after transplantation, including graft rejection and therapy, immune suppression (especially reduction of T-cell mediated, cytotoxic immunity), inflammation, and tissue injury. The clinical presentation of CMV (HHV-5) can range from a ''CMV syndrome'' including fever, malaise, leukopenia, to a ''flu-like'' illness with myalgias and fatigue, to a more significant end-organ disease with pneumonitis, colitis, encephalitis, hepatitis, or chorioretinitis. The treatment of viral infections in the renal transplantation recipient includes: the reduction of immunosuppression, antiviral therapy, diagnosis and treatment of co-infections (such as CMV, EBV, HHV-6, or À7), and use of adjunctive therapies such as immunoglobulins or colony stimulating factors. abstract: Viruses are among the most common causes of opportunistic infection after solid organ and hematopoietic stem cell transplantation (SOT and HSCT). Viral infection is associated with both direct (invasive disease) and indirect (immune modulation) effects affecting susceptibility to other infections and promoting allograft rejection. The transplantation recipient is susceptible to a broad array of viral pathogens. Some may be transmitted with the allograft as donor-derived infections, while others result from exposure, either soon after the transplant or from more distant exposures when infection is latent and reactivates in the setting of immune suppression. Simultaneous infections with multiple viral or viral and nonviral pathogens are common. The risk for viral infection is a function of the intensity of exposure and virulence of the specific virus, the intensity of immune suppression used to prevent graft rejection or graft-versus-host disease, underlying immune deficits, and factors affecting host susceptibility. Studies of viral latency, reactivation, and of the cellular effects of viral infection will provide clues for future strategies in prevention and treatment of viral infections. This article covers specific issues relating to viral infection in SOT and HSCT; additional details regarding these viral infections are also found elsewhere in this text. url: https://www.sciencedirect.com/science/article/pii/B9780128012383026295 doi: 10.1016/b978-0-12-801238-3.02629-5 id: cord-266218-r6xg9zts author: Law, Arjun Datt title: Reduced-Intensity Conditioning and Dual T Lymphocyte Suppression with Antithymocyte Globulin and Post-Transplant Cyclophosphamide as Graft-versus-Host Disease Prophylaxis in Haploidentical Hematopoietic Stem Cell Transplants for Hematological Malignancies date: 2018-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Haploidentical hematopoietic stem cell transplantation (haploHSCT) with conditioning regimens using post-transplant cyclophosphamide (PTCy) for peripheral blood stem cell (PBSC) grafts is limited by comparably higher rates of acute and chronic graft-versus-host disease (GVHD). Antithymocyte globulin (ATG) may mitigate this risk. We evaluated haploHSCT after reduced-intensity conditioning (RIC) with ATG, PTCy, and cyclosporine to prevent rejection and GVHD. Fifty adults underwent haploHSCT from August 2016 to February 2018. RIC included fludarabine (30 mg/m(2)/day on days –5 to –2), busulfan (3.2 mg/m(2)/day on days –3 and –2), and total body irradiation (200 cGy) on day –1. Unmanipulated PBSCs were infused on day 0. GVHD prophylaxis included ATG (4.5 mg/kg over days –3 to –1), PTCy (50 mg/kg/day on days +3 and +4), and cyclosporine from day +5. Median age was 56 years (range, 22 to 70 years); 25 (73.5%) patients were in first complete remission (CR1), 5 (14.7%) were in second complete remission (CR2), and 8 (23.5%) had active disease. Median time to neutrophil engraftment was 16 days (range, 8 to 43 days). At day +100, the cumulative incidence of acute GVHD of any grade, and grades III to IV was 38.3% and 5.2%, respectively. Mild chronic GVHD was seen in 15.5%. Cytomegalovirus (CMV) reactivation occurred in 37 (74%) cases and CMV disease occurred in 4 (11.5%) cases. Epstein-Barr virus (EBV) reactivation occurred in 21 (61.8%) patients. The incidence of histologically confirmed post-transplantation lymphoproliferative disorder (PTLD) was 5.8%. Four patients received rituximab. There were no CMV, EBV, or PTLD-related deaths. Six-month and 1-year overall survival (OS), cumulative incidence of relapse (CIR), and nonrelapse mortality (NRM) were 73.9%, 10.2%, and 19.4%, respectively, and 48.1%, 16% and 38.2%, respectively. Infection was the most common cause of death (18%). Unmanipulated haploidentical PBSC transplantation following RIC with ATG, PTCy, and cyclosporine as a GVHD prevention strategy results in low rates of acute and chronic GVHD. url: https://api.elsevier.com/content/article/pii/S1083879118303951 doi: 10.1016/j.bbmt.2018.07.008 id: cord-305085-bv7udg9k author: Lawrence, Robert M. title: Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date: 2011-12-31 words: 45849.0 sentences: 2358.0 pages: flesch: 45.0 cache: ./cache/cord-305085-bv7udg9k.txt txt: ./txt/cord-305085-bv7udg9k.txt summary: Postnatal exposure of susceptible infants to CMV, including premature infants without passively acquired maternal antibodies against CMV, infants born to CMV-seronegative mothers, and immunodeficient infants, can cause significant clinical illness (pneumonitis, hepatitis, thrombocytopenia).* In one study of premature infants followed up to 12 months, Vochem et al 430 found CMV transmission in 17 of 29 infants (59%) exposed to CMV virolactia and breastfed compared with no infants infected of 27 exposed to breast milk without CMV. 38, 104, 121 Laboratory reports demonstrate the presence of cell-free virus and cell-associated virus in breast milk as well as various immunologic factors that could block or limit infection.* A dose-response relationship has been observed, correlating the HIV viral load in human milk as well as a mother'' s plasma viral load with an increased transmission risk for the breastfed infant. 76 No case of transmission of yellow fever virus from an infected mother to her infant via breastfeeding or breast milk has been reported. abstract: nan url: https://api.elsevier.com/content/article/pii/B9781437707885100136 doi: 10.1016/b978-1-4377-0788-5.10013-6 id: cord-290976-dhwlr2ui author: Lednicky, John A title: Isolation and genetic characterization of human coronavirus NL63 in primary human renal proximal tubular epithelial cells obtained from a commercial supplier, and confirmation of its replication in two different types of human primary kidney cells date: 2013-06-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Cryopreserved primary human renal proximal tubule epithelial cells (RPTEC) were obtained from a commercial supplier for studies of Simian virus 40 (SV40). Within twelve hrs after cell cultures were initiated, cytoplasmic vacuoles appeared in many of the RPTEC. The RPTEC henceforth deteriorated rapidly. Since SV40 induces the formation of cytoplasmic vacuoles, this batch of RPTEC was rejected for the SV40 study. Nevertheless, we sought the likely cause(s) of the deterioration of the RPTEC as part of our technology development efforts. METHODS: Adventitious viruses in the RPTEC were isolated and/or detected and identified by isolation in various indicator cell lines, observation of cytopathology, an immunoflurorescence assay, electron microscopy, PCR, and sequencing. RESULTS: Cytomegalovirus (CMV) was detected in some RPTEC by cytology, an immunofluorescence assay, and PCR. Human Herpesvirus 6B was detected by PCR of DNA extracted from the RPTEC, but was not isolated. Human coronavirus NL63 was isolated and identified by RT-PCR and sequencing, and its replication in a fresh batch of RPTEC and another type of primary human kidney cells was confirmed. CONCLUSIONS: At least 3 different adventitious viruses were present in the batch of contaminated RPTEC. Whereas we are unable to determine whether the original RPTEC were pre-infected prior to their separation from other kidney cells, or had gotten contaminated with HCoV-NL63 from an ill laboratory worker during their preparation for commercial sale, our findings are a reminder that human-derived biologicals should always be considered as potential sources of infectious agents. Importantly, HCoV-NL63 replicates to high titers in some primary human kidney cells. url: https://doi.org/10.1186/1743-422x-10-213 doi: 10.1186/1743-422x-10-213 id: cord-003085-7krf1yxz author: Li, Xi title: Cytomegalovirus infection and outcome in immunocompetent patients in the intensive care unit: a systematic review and meta-analysis date: 2018-06-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Cytomegalovirus (CMV) infection is common in immunocompetent patients in intensive care units (ICUs). However, whether CMV infection or CMV reactivation contributes to mortality of immunocompetent patients remains unclear. METHODS: A literature search was conducted for relevant studies published before May 30, 2016. Studies reporting on CMV infection in immunocompetent patients in ICUs and containing 2 × 2 tables on CMV results and all-cause mortality were included. RESULTS: Eighteen studies involving 2398 immunocompetent patients admitted to ICUs were included in the meta-analysis. The overall rate of CMV infection was 27% (95%CI 22–34%, I(2) = 89%, n = 2398) and the CMV reactivation was 31% (95%CI 24–39%, I(2) = 74%, n = 666). The odds ratio (OR) for all-cause mortality among patients with CMV infection, compared with those without infection, was 2.16 (95%CI 1.70–2.74, I(2) = 10%, n = 2239). Moreover, upon exclusion of studies in which antiviral treatment was possibly or definitely provided to some patients, the association of mortality rate with CMV infection was also statistically significant (OR: 1.69, 95%CI 1.01–2.83, I(2) = 37%, n = 912,). For CMV seropositive patients, the OR for mortality in patients with CMV reactivation as compared with patients without CMV reactivation was 1.72 (95%CI 1.04–2.85, I(2) = 29%, n = 664). Patients with CMV infection required significantly longer mechanical ventilation (mean difference (MD): 9 days (95% CI 5–14, I(2) = 81%, n = 875)) and longer duration of ICU stay (MD: 12 days (95% CI 7–17, I(2) = 70%, n = 949)) than patients without CMV infection. When analysis was limited to detection in blood, CMV infection without antiviral drug treatment or reactivation was not significantly associated with higher mortality (OR: 1.69, 95%CI 0.81–3.54, I(2) = 52%, n = 722; OR: 1.49, I(2) = 63%, n = 469). CONCLUSION: Critically ill patients without immunosuppression admitted to ICUs show a high rate of CMV infection. CMV infection during the natural unaltered course or reactivation in critically ill patients is associated with increased mortality, but have no effect on mortality when CMV in blood. More studies are needed to clarify the impact of CMV infection on clinical outcomes in those patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3195-5) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027797/ doi: 10.1186/s12879-018-3195-5 id: cord-016267-idrc1sdh author: Ljungman, Per title: Viral Infections in Hematopoietic Stem Cell Transplant Recipients date: 2009-11-27 words: 7092.0 sentences: 366.0 pages: flesch: 34.0 cache: ./cache/cord-016267-idrc1sdh.txt txt: ./txt/cord-016267-idrc1sdh.txt summary: As early identification of patients at risk for developing viral disease reduces virus-related morbidity and mortality, monitoring with sensitive techniques such as antigenemia or quantitative PCR is indicated in all allogeneic SCT patients. Although the incidence of EBV-PTLD is generally lower than 2% following allogeneic SCT, it may increase up to 20% in patients with risk factors such as mismatched donor SCT, the use of an EBV positive donor to an EBV negative recipient, T-cell depletion, ATG therapy, and other forms of intensified immunosuppression for prevention and treatment of GVHD [92, 93] . Prevention of Epstein-Barr virus-lymphoproliferative disease by molecular monitoring and preemptive rituximab in high-risk patients after allogeneic stem cell transplantation Epstein-Barr virus (EBV) load in bone marrow transplant recipients at risk to develop posttransplant lymphoproliferative disease: prophylactic infusion of EBV-specific cytotoxic T cells BK virus infection in hematopoietic stem cell transplant recipients: frequency, risk factors, and association with postengraftment hemorrhagic cystitis abstract: Viral infections are important as causes of morbidity and mortality after allogeneic stem cell transplantation (SCT). Severe viral infections are more common after unrelated and mismatched donor SCT and in particular after haploidentical SCT. B-cell function and specific antibodies are the main defense mechanisms against infection with exogenous viruses, thus reducing the risk for reinfection in already seropositive individuals. On the other hand, T-cell function in particular cytotoxic T-cell function is the main mechanism for preventing severe viral disease and also for the control of viruses such as herpesviruses that can cause latency and thus reactivate in an immunocompromised individual. The immune defects in SCT-patients are frequently complex with defects in cytotoxic T-lymphocyte, helper T-lymphocyte, NK-cell, and B-lymphocyte functions. T-cell dysfunction is usually most important early after SCT while deficient B-cell reconstitution can remain for many years after SCT. Furthermore, since loss of specific antibodies occurs frequently over time after allogeneic SCT, this will also increase the risk for reinfections with previously encountered viruses such as measles or varicella-zoster virus (VZV) and allow reactivation of viruses controlled by antibodies such as hepatitis B virus (HBV) [1, 2]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120500/ doi: 10.1007/978-1-59745-478-0_29 id: cord-007575-5ekgabx5 author: Luby, James P. title: Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date: 2016-01-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pneumonias in adults due to mycoplasma, chlamydiae, and viruses are a common clinical problem. These microorganisms contribute to the etiologies in 6–35% of all cases of pneumonia and are the sole pathogens in 1–17% of hospitalized cases. Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. Developments in the rapid diagnosis and therapy of respiratory syncytial virus infections with an aerosolized antiviral drug in children may pave the way for comparable advances in difficult pneumonias in adult patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119385/ doi: 10.1097/00000441-198707000-00007 id: cord-282618-tjvjlyn9 author: Luke, J M title: Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers date: 2010-11-25 words: 6241.0 sentences: 336.0 pages: flesch: 43.0 cache: ./cache/cord-282618-tjvjlyn9.txt txt: ./txt/cord-282618-tjvjlyn9.txt summary: To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. A neomycin resistance gene (NeoR) without an upstream Kozak sequence was cloned downstream of an enhanced green fluorescent protein (EGFP) transgene in different configurations similar to that used with PREs. Quantifiable neoR translation products were present in all tested configurations, as was biologically active neoR protein after plasmid transfection into both HEK293 and CHO cell lines (Supplementary Table S1 ). The assay was in the same format as in (a), except for the fact that Pol III inhibitor-treated cells were transfected with EGFP plasmids containing the CMV-HTLV-I R promoter with or without VA1; (c) Inhibition of PKR, not of adenosine deaminase acting on RNA (ADAR) or RNA interference (RNAI), was required for VA1 expression enhancement effect. abstract: Methods to improve plasmid-mediated transgene expression are needed for gene medicine and gene vaccination applications. To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. We report herein the development of potent minimal, antibiotic-free, high-manufacturing-yield mammalian expression vectors incorporating rationally designed additive combinations of expression enhancers. The SV40 72 bp enhancer incorporated upstream of the cytomegalovirus (CMV) enhancer selectively improved extrachromosomal transgene expression. The human T-lymphotropic virus type I (HTLV-I) R region, incorporated downstream of the CMV promoter, dramatically increased mRNA translation efficiency, but not overall mRNA levels, after transient transfection. A similar mRNA translation efficiency increase was observed with plasmid vectors incorporating and expressing the protein kinase R-inhibiting adenoviral viral associated (VA)1 RNA. Strikingly, HTLV-I R and VA1 did not increase transgene expression or mRNA translation efficiency from plasmid DNA after genomic integration. The vector platform, when combined with electroporation delivery, further increased transgene expression and improved HIV-1 gp120 DNA vaccine-induced neutralizing antibody titers in rabbits. These antibiotic-free vectors incorporating transient expression enhancers are safer, more potent alternatives to improve transgene expression for DNA therapy or vaccination. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/gt.2010.149) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/21107439/ doi: 10.1038/gt.2010.149 id: cord-016932-bej10xbf author: Lum, Lawrence G. title: Specific Adoptive T-Cell Therapy for Viral and Fungal Infections date: 2018-06-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite advances in anti-infective agents, viral and fungal infections after hematopoietic stem cell transplantation (HSCT) continue to cause life-threatening complications that limit the success of HSCT. Early adoptive T-cell immunotherapy studies showed that administration of allogeneic virus-specific cytotoxic T lymphocytes (vCTL) can prevent and control viral infections and reconstitute antiviral immunity to cytomegalovirus (CMV) and Epstein-Barr virus (EBV). Advances in immunobiology, in vitro culture technology, and current good manufacturing practice (cGMP) have provided opportunities for advancing adoptive cell therapy for viral infections: (1) T cells have been expanded targeting multiple pathogens; (2) vCTL production no longer requires viral infection or viral vector transduction of antigen-presenting cells (APCs); (3) the source of lymphocytes is no longer restricted to donors who are immune to the pathogens; (4) naive T cells have been redirected with chimeric antigen receptor T cells (CARTs) or armed with bispecific antibody-armed T cells (BATs) to mediate vCTL activity; (5) these technologies could be combined to targeted multiple viral or fungal pathogens; and (6) pathogen-specific T-cell products manufactured from third parties and banked for “off-the-shelf” use post-HSCT may soon become a reality. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121368/ doi: 10.1007/978-3-319-77674-3_20 id: cord-015922-5wwy0m2k author: Marty, Francisco M. title: Infection in the Hematopoietic Stem Cell Transplant Recipient date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120030/ doi: 10.1007/978-1-59745-438-4_19 id: cord-023669-3ataw6gy author: Masur, Henry title: Critically Ill Immunosuppressed Host date: 2009-05-15 words: 11194.0 sentences: 576.0 pages: flesch: 34.0 cache: ./cache/cord-023669-3ataw6gy.txt txt: ./txt/cord-023669-3ataw6gy.txt summary: As the population of patients with cancer, organ transplants, vasculitides, and human immunodefi ciency virus (HIV) infection has grown, intensivists are seeing more and more patients with altered immunity. For instance, if a patient presents with severe hypoxemia and diffuse pulmonary infi ltrates, a health care provider who recognizes a prior splenectomy as the major predisposition to infection would focus the diagnostic evaluation and the empiric therapy on Streptococcus pneumoniae and Haemophilus infl uenzae. Patients with HIV infection develop clinical disease as a result of three basic processes: the direct effect of HIV on specifi c organs (e.g., cardiomyopathy, enteropathy, dementia); immunologically mediated processes (e.g., glomerulonephritis, thrombocytopenia); or opportunistic infections and tumors that are enabled by HIV-induced immunosuppression. For instance, if a patient with HIV infection and a CD4+ T lymphocyte count of 700 cells/µL presents with diffuse pulmonary infi ltrates, the diagnostic evaluation and empiric antimicrobial regimen should focus on S. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173421/ doi: 10.1016/b978-032304841-5.50056-x id: cord-018943-5zf0eya3 author: Michels, Guido title: Transplantationsmedizin in der Intensivmedizin date: 2011-09-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Die postoperative intensivmedizinische Behandlung von Patienten nach Herztransplantation basiert häufig auf Erfahrung und deren Weitergabe zwischen den Transplantationszentren (hohe Variabilität). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123958/ doi: 10.1007/978-3-642-16841-3_24 id: cord-323691-5s5almd2 author: Mishin, Vasiliy P title: A ‘minimal’ approach in design of flavivirus infectious DNA date: 2001-12-04 words: 5060.0 sentences: 255.0 pages: flesch: 49.0 cache: ./cache/cord-323691-5s5almd2.txt txt: ./txt/cord-323691-5s5almd2.txt summary: Abstract The ''infectious DNA'' approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Substantial difficulties, however, were encountered in design of flavivirus ''infectious DNA'', requiring either modification of the viral genome cassette (Yamshchikov et al., 2001) to prevent unwanted expression of viral genome segments encoding toxic for Escherichia coli products, or deletion of the structural protein region (Varnavski et al., 2000) . For this reason we sought to investigate if the stability of constructs containing an unmodified virus genome cassette can be improved by preventing its deleterious expression at the transcriptional level, i.e. by minimizing spurious transcription from eukaryotic promoters in E. abstract: Abstract The ‘infectious DNA’ approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Its use, however, is often limited by the instability of plasmids due to a transcriptional activity of eukaryotic promoters in Escherichia coli resulting in synthesis of products toxic for the bacterial host. Using a highly unstable representative infectious clone of Japanese encephalitis (JE) flavivirus, we tested a new approach in design of such problematic ‘infectious DNA’ constructs, which is based on minimizing unwanted transcription in the bacterial host. A plasmid containing full genome size JE cDNA under control of the minimal cytomegalovirus (CMV) promoter can be propagated in E. coli with growth and stability characteristics similar to that of constructs controlled by the T7 promoter. Transfection of this plasmid into susceptible cells leads to the establishment of a productive infectious cycle. Reinsertion of the CMV enhancer at the 3′-end of the JE cassette substantially increased the specific infectivity without affecting the stability and growth characteristics of the construct. This approach can be useful when stabilization of infectious clones by modification of a viral cDNA cassette is not the feasible or suitable alternative. url: https://www.ncbi.nlm.nih.gov/pubmed/11682130/ doi: 10.1016/s0168-1702(01)00371-9 id: cord-004986-en7taikk author: Nagy, Nathalie title: Infections gastro-intestinales chez le patient immunocompromis date: 2002 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The gastrointestinal tract is frequently involved in immunocompromised hosts. The most common digestive manifestations are dysphagia, odynophagia and diarrhea. These diseases are more frequent in patients with acquired immunodeficiency virus (AIDS). These GI diseases are of several categories: HIV related inflammatory conditions (HIV related enteropathy, idiopathic esophageal ulceration), infections due to germs also commonly present in immunocompetent patients (Salmonellosis, shigellosis,…), opportunistic infections (CMV, Mucormycosis,Cryptosporidium, Mycobacterium, Isospora belli,…). The prevalence, pathogenesis, clinical manifestation, gross pathological findings and microscopic features are discussed for each entity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087899/ doi: 10.1007/bf03016656 id: cord-018785-tcr5xlf8 author: Nambiar, Puja title: Infection in Kidney Transplantation date: 2018-06-27 words: 9364.0 sentences: 506.0 pages: flesch: 36.0 cache: ./cache/cord-018785-tcr5xlf8.txt txt: ./txt/cord-018785-tcr5xlf8.txt summary: The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The risk factors for development of CMV disease include donor seropositivity/recipient seronegativity(Dþ/RÀ), use of induction immunosuppression (antilymphocyte antibodies), donor age >60 years, simultaneous kidney-pancreas transplantation, treatment for acute rejection, impaired transplant function, and concurrent infection from other viruses (like EBV and HHV-6 and 7) (De Keyzer et al. The risk factors for PTLD include EBV naïve recipients who receive EBV seropositive organs, active primary EBV infection, younger recipient, coinfection by CMV and other viruses, prior splenectomy, second transplant, acute or chronic graft versus host disease, immunosuppressive drug regimen (OKT3 or polyclonal antilymphocyte antibody), and the type of organ transplanted. abstract: Infection is an important cause of morbidity and mortality after kidney transplantation. It has been estimated that 70% of kidney transplant recipients will experience an infection episode within the first 3 years after transplantation (Dharnidharka et al. 2007). After cardiovascular disease, infection is the second leading cause of death in recipients with allograft function (Snyder et al. 2009). The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. Pretransplant screening, immunizations, and optimal antibacterial and antiviral prophylaxis can help to reduce the impact of infection. Awareness of the approach to infection in the transplant recipient including diagnostic and management strategies is essential to optimizing outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123753/ doi: 10.1007/978-3-319-19617-6_22 id: cord-310217-p9nqcz5d author: Nikolina, Basic-Jukic title: Can hyperimmune anti-CMV globuline substitute for convalescent plasma for treatment of COVID-19? date: 2020-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Information on treatment of COVID-19 infection in renal transplant recipients is scarce, especially in symptomatic patients and patients with recent major clinical events. This group of patients suffers from different opportunistic infections which may coexist with COVID-19. Currently available expert opinions suggest reduction of immunosuppression therapy for renal transplant recipients with symptomatic COVID-19 infection with either antiviral drugs, hydroxychloroquine and/or azithromycin. Inspired by our experience in treatment of CMV pneumonia and literature data on the potential benefit of convalescent plasma for treatment of different viral diseases we suggest use of the hyperimmune anti-CMV gamma globulins in addition to other available therapies. Besides the immunosuppression reduction which is supposed to be beneficial, immunoglobulins with their immunomodulatory effects and possible antiviral role, may increase a possibility for favorable outcome. url: https://doi.org/10.1016/j.mehy.2020.109903 doi: 10.1016/j.mehy.2020.109903 id: cord-001938-n2d5fw2f author: Ong, David S. Y. title: Cytomegalovirus reactivation and mortality in patients with acute respiratory distress syndrome date: 2016-03-01 words: 4483.0 sentences: 200.0 pages: flesch: 36.0 cache: ./cache/cord-001938-n2d5fw2f.txt txt: ./txt/cord-001938-n2d5fw2f.txt summary: Furthermore, CMV reactivation in critically ill patients has been associated with a prolonged duration of mechanical ventilation [2, 4, [9] [10] [11] [12] [13] , an increased length of stay in the ICU [3, 5, 9, 10, 13] , and excess mortality [2, 4, [7] [8] [9] . Nevertheless, it remains uncertain whether these findings imply that CMV reactivation is a truly independent risk factor with respect to these observed poor clinical outcomes because most studies that have assessed these associations did not adequately account for all possible sources of bias. Possible confounders that were screened included all patient characteristics and therapeutic interventions listed in Table 1 , and some markers of disease severity: Acute Physiology and Chronic Health Evaluation APACHE Acute Physiology and Chronic Health Evaluation, ARDS acute respiratory distress syndrome, COPD chronic obstructive pulmonary disease, ICU intensive care unit, PEEP positive end expiratory pressure, P/F partial pressure of oxygen in arterial blood to fraction of inspired oxygen ratio (APACHE) IV score, presence of septic shock, partial pressure of oxygen in arterial blood to fraction of inspired oxygen ratio, and positive end expiratory pressure (PEEP) setting. abstract: PURPOSE: Cytomegalovirus (CMV) reactivation occurs frequently in patients with the acute respiratory distress syndrome (ARDS) and has been associated with increased mortality. However, it remains unknown whether this association represents an independent risk for poor outcome. We aimed to estimate the attributable effect of CMV reactivation on mortality in immunocompetent ARDS patients. METHODS: We prospectively studied immunocompetent ARDS patients who tested seropositive for CMV and remained mechanically ventilated beyond day 4 in two tertiary intensive care units in the Netherlands from 2011 to 2013. CMV loads were determined in plasma weekly. Competing risks Cox regression was used with CMV reactivation status as a time-dependent exposure variable. Subsequently, in sensitivity analyses we adjusted for the evolution of disease severity until onset of reactivation using marginal structural modeling. RESULTS: Of 399 ARDS patients, 271 (68 %) were CMV seropositive and reactivation occurred in 74 (27 %) of them. After adjustment for confounding and competing risks, CMV reactivation was associated with overall increased ICU mortality (adjusted subdistribution hazard ratio (SHR) 2.74, 95 % CI 1.51–4.97), which resulted from the joint action of trends toward an increased mortality rate (direct effect; cause specific hazard ratio (HR) 1.58, 95 % CI 0.86–2.90) and a reduced successful weaning rate (indirect effect; cause specific HR 0.83, 95 % CI 0.58–1.18). These associations remained in sensitivity analyses. The population-attributable fraction of ICU mortality was 23 % (95 % CI 6–41) by day 30 (risk difference 4.4, 95 % CI 1.1–7.9). CONCLUSION: CMV reactivation is independently associated with increased case fatality in immunocompetent ARDS patients who are CMV seropositive. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00134-015-4071-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747999/ doi: 10.1007/s00134-015-4071-z id: cord-005225-7uuilki4 author: Paduch, Darius A. title: Viral lower urinary tract infections date: 2008-03-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lower urinary tract infections (UTIs) are common among the general population and are most often caused by bacterial pathogens. Viruses are an uncommon cause of UTIs in an immunocompetent host; however, viruses are increasingly recognized as the cause of lower UTI, especially hemorrhagic cystitis, among immunocompromised patients. BK virus, adenovirus, and cytomegalovirus are predominant pathogens involved in hemorrhagic cystitis after stem cell and solid organ transplantation, and their early diagnosis and treatment may prevent significant morbidity of hemorrhagic cystitis. The diagnosis of viral lower UTI is based on molecular techniques, and real-time polymerase chain reaction is often the method of choice because it allows for quantification of viral load. Cidofovir is becoming a drug of choice in viral UTIs because it is active against the most common viral pathogens. This review discusses the epidemiology, pitfalls in diagnosis, and current treatment of viral UTIs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089127/ doi: 10.1007/s11934-007-0080-y id: cord-272835-6nx4f8ss author: Paulsen, Grant C. title: Respiratory Viral Infections in Solid Organ and Hematopoietic Stem Cell Transplantation date: 2017-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory viruses are common in solid organ and hematopoietic stem cell transplant recipients and a recognized cause of significant morbidity and mortality. Epidemiology, risk factors, and attributable mortality in both populations are reviewed. In addition, virus-specific prevention and treatment options, including emerging investigational therapies, are discussed for respiratory syncytial virus, influenza, adenovirus, parainfluenza, and other respiratory viruses. url: https://www.sciencedirect.com/science/article/pii/S0272523117300783 doi: 10.1016/j.ccm.2017.07.012 id: cord-021977-yu0hrg6h author: Pham, Phuong-Thu T. title: Medical Management of the Kidney Transplant Recipient: Infections and Malignant Neoplasms date: 2010-12-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152293/ doi: 10.1016/b978-0-323-05876-6.00101-5 id: cord-291960-1is0rv6c author: Piñana, José Luis title: Pulmonary cytomegalovirus (CMV) DNA shedding in allogeneic hematopoietic stem cell transplant recipients: Implications for the diagnosis of CMV pneumonia date: 2019-02-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To date no definitive cut-off value for cytomegalovirus (CMV) DNA load in bronchoalveolar lavage (BAL) fluid specimens has been established to discriminate between CMV pneumonia and pulmonary CMV DNA shedding in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients. METHODS: The current retrospective study is aimed at assessing the range of CMV DNA loads quantified in BAL fluid specimens from allo-HSCT patients with pneumonia in which different microorganisms were causally involved. RESULTS: A total of 144 BAL specimens from 123 patients were included. CMV DNA was detected in 56 out of 144 BAL fluid specimens and the median CMV DNA load from patients in whom CMV pneumonia was unlikely or could be tentatively ruled out was 1210 (31–68, 920) IU/ml. The frequency of CMV DNA detection and median CMV DNA loads were comparable, irrespective of the attributable cause of pneumonia. Detection of CMV DNA loads in BAL fluid specimens >500 IU/ml was independently associated with pneumonia-attributable mortality. CONCLUSIONS: The current study highlights the difficulty in establishing universal CMV DNA load thresholds in BAL fluid specimens for distinguishing between CMV pneumonia and pulmonary CMV DNA shedding, and suggests that the presence of CMV DNA in BAL fluid specimens beyond a certain level may have a deleterious impact on patient outcome. url: https://api.elsevier.com/content/article/pii/S0163445319300581 doi: 10.1016/j.jinf.2019.02.009 id: cord-267269-05mezubh author: Plazolles, N. title: Pivotal Advance: The promotion of soluble DC‐SIGN release by inflammatory signals and its enhancement of cytomegalovirus‐mediated cis‐infection of myeloid dendritic cells date: 2010-10-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: DC‐SIGN is a member of the C‐type lectin family. Mainly expressed by myeloid DCs, it is involved in the capture and internalization of pathogens, including human CMV. Several transcripts have been identified, some of which code for putative soluble proteins. However, little is known about the regulation and the functional properties of such putative sDC‐SIGN variants. To better understand how sDC‐SIGN could be involved in CMV infection, we set out to characterize biochemical and functional properties of rDC‐SIGN as well as naturally occurring sDC‐SIGN. We first developed a specific, quantitative ELISA and then used it to detect the presence sDC‐SIGN in in vitro‐generated DC culture supernatants as cell‐free secreted tetramers. Next, in correlation with their inflammatory status, we demonstrated the presence of sDC‐SIGN in several human body fluids, including serum, joint fluids, and BALs. CMV infection of human tissues was also shown to promote sDC‐SIGN release. Based on the analysis of the cytokine/chemokine content of sDC‐SIGN culture supernatants, we identified IFN‐γ and CXCL8/IL‐8 as inducers of sDC‐SIGN production by MoDC. Finally, we demonstrated that sDC‐SIGN was able to interact with CMV gB under native conditions, leading to a significant increase in MoDC CMV infection. Overall, our results confirm that sDC‐SIGN, like its well‐known, counterpart mDC‐SIGN, may play a pivotal role in CMV‐mediated pathogenesis. url: https://doi.org/10.1189/jlb.0710386 doi: 10.1189/jlb.0710386 id: cord-350807-qdq96723 author: Reckziegel, Maria title: Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection date: 2020-05-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory tract infections (RTI) can take a serious course under immunosuppression. Data on the impact of the underlying pathogens are still controversial. Samples from the upper (n = 322) and lower RT (n = 169) were collected from 136 children and 355 adults; 225 among them have been immunocompromised patients. Exclusion criteria were presence of relevant cultivable microorganisms, C-reactive protein > 20 mg/dl, or procalcitonin > 2.0 ng/ml. Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Viral/bacterial genome equivalents were detected in more than two-thirds of specimens. Under immunosuppression, herpesviruses (EBV 30.9%/14.6%, p < 0.001; CMV 19.6%/7.9%, p < 0.001; HSV-1: 14.2%/7.1%, p = 0.012) were frequently observed, mainly through their reactivation in adults. Immunocompromised adults tended to present a higher RSV prevalence (6.4%/2.4%, p = 0.078). Immunocompetent patients were more frequently tested positive for IV (15.0%/5.8%, p = 0.001) and M.p. (6.4%/0.4%, p < 0.001), probably biased due to the influenza pandemic of 2009 and an M.p. epidemic in 2011. About 41.8% of samples were positive for a single pathogen, and among them EBV (19.9%) was most prevalent followed by HRV (18.2%) and IV (16.6%). HSV-2 and C.p. were not found. Marked seasonal effects were observed for HRV, IV, and RSV. Differences in pathogen prevalence were demonstrated between immunocompetent and immunocompromised patients. The exact contribution of some herpesviruses to the development of RTI remains unclear. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-03878-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32462500/ doi: 10.1007/s10096-020-03878-9 id: cord-304066-rirbdhz3 author: Reddehase, Matthias J. title: Adverse immunological imprinting by cytomegalovirus sensitizing for allergic airway disease date: 2019-05-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Cytomegalovirus (CMV) infection has a profound impact on the host’s immune system. Immunological imprinting by CMV is not restricted to immunity against CMV itself, but can affect immunity against other viral or non-viral infectious agents and also immunopathological responses. One category is heterologous immunity based on molecular mimicry, where antigen recognition receptors specific for a CMV antigen with broad avidity distribution also bind with some avidity to unrelated antigens and exert effector functions against target structures other than those linked to CMV. Another category is induction of cytokines by CMV infection that inhibit or drive immune responses to bystander antigens unrelated to CMV, and a third category is the activation of antigen-presenting cells by CMV from which unrelated antigens profit as “stowaways”. A striking example of the “stowaway” category, actually one that is of medical importance, has been published recently and will be discussed here for the more general reader. Specifically, in a murine model, CMV airway infection and inhaled environmental antigen of poor intrinsic allergenic potential were found to sensitize for allergic airway disease (AAD) only when combined. As to the mechanism, viral activation of CD11b(+) conventional dendritic cells (CD11b(+) cDC) that localize to airway mucosa facilitates uptake and processing of inhaled antigen. Thus, CMV serves as a “door opener” for otherwise harmless environmental antigens that have no intrinsic property to activate DC. Antigen-laden CD11b(+) cDC migrate selectively to the airway draining lymph nodes, where they prime type-2 CD4(+) T helper (Th-2) cells. Upon airway re-exposure to the inhaled antigen, Th-2 cells secrete interleukins (IL-4, IL-5, IL-9, and IL-25) known to induce goblet cell metaplasia, the lead histopathological manifestation of AAD that is characterized by thickening of airway epithelia and increased numbers of mucus-producing goblet cells, resulting in enhanced mucus secretion and airflow obstruction. url: https://doi.org/10.1007/s00430-019-00610-z doi: 10.1007/s00430-019-00610-z id: cord-288721-3bv3aak6 author: Schneider, Annika title: Single organelle analysis to characterize mitochondrial function and crosstalk during viral infection date: 2019-06-11 words: 5604.0 sentences: 309.0 pages: flesch: 39.0 cache: ./cache/cord-288721-3bv3aak6.txt txt: ./txt/cord-288721-3bv3aak6.txt summary: Thus, single-organelle and multi-parameter resolution allows to explore altered energy metabolism and antiviral defence by tagged mitochondria selectively in virus-infected cells and will be instrumental to identify viral immune escape and to develop and monitor novel mitochondrial-targeted therapies. When challenged with high concentrations of calcium (100 µM), mitochondria isolated from virus-infected livers are much more fragile shown by time-dependent loss of membrane potential and change of their morphology indicated by decrease in side-scatter (Fig. 2F ). Number of viable mitochondria detected per second by flow-cytometry declined after calcium challenge, consistent with loss of mitochondrial integrity, and did so much faster in samples from virus-infected livers (Fig. 2F ). In order to further evaluate mitochondrial functionality, we challenged mitochondria with Ca 2+ as stress test and performed time kinetic measurements of DilC 1 (5) fluorescence and side-scatter of mito-DsRed + and mito-DsRed − mitochondria isolated from Ad-CMV-mitoRL infected livers. abstract: Mitochondria are key for cellular metabolism and signalling processes during viral infection. We report a methodology to analyse mitochondrial properties at the single-organelle level during viral infection using a recombinant adenovirus coding for a mitochondrial tracer protein for tagging and detection by multispectral flow cytometry. Resolution at the level of tagged individual mitochondria revealed changes in mitochondrial size, membrane potential and displayed a fragile phenotype during viral infection of cells. Thus, single-organelle and multi-parameter resolution allows to explore altered energy metabolism and antiviral defence by tagged mitochondria selectively in virus-infected cells and will be instrumental to identify viral immune escape and to develop and monitor novel mitochondrial-targeted therapies. url: https://www.ncbi.nlm.nih.gov/pubmed/31186476/ doi: 10.1038/s41598-019-44922-9 id: cord-023854-w8kx5n8k author: Schuster, V. title: Virusinfektionen date: 2019 words: 8437.0 sentences: 1326.0 pages: flesch: 48.0 cache: ./cache/cord-023854-w8kx5n8k.txt txt: ./txt/cord-023854-w8kx5n8k.txt summary: Anschließend dringt das Virus in die Nervenendigungen von peripheren sensorischen Nerven ein und wandert in ihnen retrograd bis zu den spinalen Hinterstrangganglien (bei HSV-1 meist Ganglion des N. Schleimhaut (Dermatom), wo es zur lokalen Virusvermehrung und Ausbildung von Bläschen kommt: Herpes zoster bei VZV, Herpes labialis oder genitalis bei HSV Die Infektion beginnt mit unspezifischen Symptomen (Fieber, Kopfschmerzen, Krankheitsgefühl) . VZV kann bei nachlassender zellulärer Immunität sowie durch noch unbekannte Mechanismen jederzeit reaktiviert werden: VZV wandert nun entlang der sensorischen peripheren Nerven anterograd an die Hautoberfläche, wo es im Bereich der betroffenen Dermatome zur Virusvermehrung mit Bläschenbildung (Herpes zoster) kommt. Inwieweit diese Komplikationen tatsächlich ursächlich nur durch HHV-6, oder möglicherweise erst in Verbindung mit zusätzlichen Infektionen (HIV, CMV und andere Herpesviren) hervorgerufen werden, ist derzeit nicht bekannt. Die Entwicklung eines Hydrops fetalis nach einer mütterlichen (und fetalen) Parvovirus-B19-Infektion ist insgesamt selten, sie liegt bei ca. abstract: Dieses Kapitel behandelt Klinik, Komplikationen, Diagnostik, Prophylaxe und Therapie der wesentlichen Virusinfektionen im Kindes- und Jugendlichenalter, u. a. Virusinfektionen der Herpes-Gruppe (HSV1 und 2 [u. a. schwere neonatale Infektionen, Herpesenzephalitis]), VZV [u. a. neonatale VZV-Infektionen, Herpes-Zoster], EBV, CMV, HHV6–7 [Dreitagefieber], HHV8 [Kaposi-Sarkom]. Unter den Virushepatititiden spielen bei Kindern die Hepatitis A, B (chronische Hepatitis B) sowie C (chronische Hepatitis B) die größte Rolle. Weitere bedeutsame Viren sind Parvovirus-B19 (Ursache der Ringelröteln, einer aplastischen Krise oder eines Hydrops fetalis), humane Papillomaviren (bedeutsam v. a. Genitalwarzen, Larynxpapillome und Karzinome), Rotaviren (bedeutsame Gastroenteritiserreger), FSME, HIV sowie die „typischen Kinderkrankheiten“ Masern, Mumps und Röteln. Häufige Erreger des oberen und unteren Respirationstrakts sind Rhinoviren, das RS-Virus, das humane Metapneumovirus (hMPV), das humane Bocavirus (hBoV), das humane Coronavirus (HCoV) sowie Influenza- und Parainfluenzaviren. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176200/ doi: 10.1007/978-3-662-57295-5_14 id: cord-023729-dipjubn7 author: Serlin, Michael H. title: Gastrointestinal Disorders in HIV date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173545/ doi: 10.1016/b978-1-4160-2882-6.50027-7 id: cord-288945-c9ow1q5c author: Spengler, Ulrich title: Liver Disease Associated with Non-Hepatitis Viruses date: 2019-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Hepatitis is commonly associated with certain viruses labeled as “Hepatitis” viruses. However, many other viral infections can also affect the liver ranging from mild asymptomatic elevations of aminotransferases to fulminant hepatic failure. This article will provide a brief overview on a variety of different viral infections that may be associated with significant liver pathology at least under certain conditions, for example, immunosuppression. This overview discusses key virological features, clinical presentation of associated liver disease and provides some information on diagnosis and an outline of treatment options. Thus, the overview can provide first orientation when infectious hepatitis is encountered in a patient that cannot be explained by the usual hepatitis viruses. url: https://www.sciencedirect.com/science/article/pii/B9780128012383657823 doi: 10.1016/b978-0-12-801238-3.65782-3 id: cord-283826-lgyc3sro author: Stiehm, E. Richard title: Therapeutic Use of Immunoglobulins date: 2010-11-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S006531011000006X doi: 10.1016/j.yapd.2010.08.005 id: cord-015139-s7ox0h4f author: Stockschläder, M. title: Atemwegsinfektionen bei immunsupprimierten Personen date: 2003 words: 3915.0 sentences: 461.0 pages: flesch: 33.0 cache: ./cache/cord-015139-s7ox0h4f.txt txt: ./txt/cord-015139-s7ox0h4f.txt summary: Pul monale Veränderungen finden sich häufig bei immunsupprimierten Patienten und können durch die Grunderkrankung, deren Behandlung, Infektionen, Tumoren oder Kombinationen dieser Ursachen bedingt sein. Bei CMV-Infektionen findet man häufig eine Kombinationen von milchglasartiger, interstitieller Verschattung mit später disseminierten fleckförmigen Knötchen, wobei die Unter-und Mittelfelder betont betroffen sind [5] . Die Therapiestrategien "universelle Prophylaxe" und "preemptive treatment" der CMV-Erkrankung gelten auch für Patienten mit iatrogener Immunsuppression nach Organtransplantation. B. die CMV-Retinitis, bei 85% der AIDS-oder HIV-infizierten Patienten mit geringer CD4-Zahl beobachtet werden [57] . Zusammenfassend kann festge-stellt werden,dass für allogen stammzelltransplantierte Patienten und Hochrisikopatienten, die sich einer autologen BSZT unterziehen, eine Prophylaxe mit Fluconazol (400 mg/Tag) empfohlen wird [63] .Aspergillusinfektionen werden hierdurch allerdings nicht mit erfasst. Bei Patienten mit Lungeninfiltraten in der febrilen Neutropenie ist jedoch wegen fehlender Aspergilluswirksamkeit von Fluconazol bereits initial konventionelles oder liposomales Amphotericin B zu empfehlen. abstract: Pulmonary infections in immunocompromised patients remain a diagnostic and therapeutic challenge.New methods for the early detection of fungal and viral diseases might allow an immediate and specific therapy, thereby lowering the high mortality associated with such infections.The development of new drugs will hopefully lead to more effective treatment while decreasing the incidence of adverse effects. Interdisciplinary team work between internal medicine, radiology, surgery, microbiology, and virology is essential for the successful management of these patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095897/ doi: 10.1007/s00103-002-0536-7 id: cord-285433-ehnu83qe author: Sun, Hongliu title: Detection of Cytomegalovirus Antibodies Using a Biosensor Based on Imaging Ellipsometry date: 2015-08-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Cytomegalovirus (CMV) is the most common infectious cause of mental disability in newborns in developed countries. There is an urgent need to establish an early detection and high-throughput screening method for CMV infection using portable detection devices. METHODS: An antibody analysis method is reported for the detection and identification of CMV antibodies in serum using a biosensor based on high spatial resolution imaging ellipsometry (BIE). CMV antigen (CMV-3A) was immobilized on silicon wafers and used to capture CMV antibodies in serum. An antibody against human immunoglobulin G (anti-IgG) was used to confirm the IgG antibody against CMV captured by the CMV-3A. RESULTS: Our results show that this assay is rapid and specific for the identification of IgG antibody against CMV. Further, patient serum was quantitatively assessed using the standard curve method, and the quantitative results were in agreement with the enzyme-linked immunosorbent assay. The CMV antibody detection sensitivity of BIE reached 0.01 IU/mL. CONCLUSIONS: This novel biosensor may be a valuable diagnostic tool for analysis of IgG antibody against CMV during CMV infection screening. url: https://doi.org/10.1371/journal.pone.0136253 doi: 10.1371/journal.pone.0136253 id: cord-001079-v01vwu00 author: Thoden, J. title: Therapy and prophylaxis of opportunistic infections in HIV-infected patients: a guideline by the German and Austrian AIDS societies (DAIG/ÖAG) (AWMF 055/066) date: 2013-09-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: There was a growing need for practical guidelines for the most common OIs in Germany and Austria under consideration of the local epidemiological conditions. MATERIALS AND METHODS: The German and Austrian AIDS societies developed these guidelines between March 2010 and November 2011. A structured Medline research was performed for 12 diseases, namely Immune reconstitution inflammatory syndrome, Pneumocystis jiroveci pneumonia, cerebral toxoplasmosis, cytomegalovirus manifestations, candidiasis, herpes simplex virus infections, varizella zoster virus infections, progressive multifocal leucencephalopathy, cryptosporidiosis, cryptococcosis, nontuberculosis mycobacteria infections and tuberculosis. Due to the lack of evidence by randomized controlled trials, part of the guidelines reflects expert opinions. The German version was accepted by the German and Austrian AIDS Societies and was previously published by the Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften (AWMF; German Association of the Scientific Medical Societies). CONCLUSION: The review presented here is a translation of a short version of the German–Austrian Guidelines of opportunistic infections in HIV patients. These guidelines are well-accepted in a clinical setting in both Germany and Austria. They lead to a similar treatment of a heterogeneous group of patients in these countries. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776256/ doi: 10.1007/s15010-013-0504-1 id: cord-006393-jcj9nqfu author: Tutschka, Peter J. title: The use of immunoglobulin in bone marrow transplantation date: 1990 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The role of bone marrow transplantation is to restore lymphohematopoietic function of a recipient whose marrow has been destroyed, either by disease or by the preparative therapy employed in an attempt to eradicate the patient's lymphohematopoietic malignancy. The restoration of lymphohematopoietic function through the donor graft occurs in stages, requires several months, and is often not completed until 1 to 2 years after transplantation. These sequential steps of immuno-reconstitution are associated with a number of definable and predictable immune deficiencies and seem to be responsible for the pattern of complications that emerges after transplantation. Most of these complications are either the result of, or associated with, infections that also occur in an almost predictable pattern. In the various phases of immune deficiency following sequentially after transplantation, the humoral immune system is greatly affected, thus raising the possibility that passively administered antibodies in the form of immune globulin therapy might be beneficial in all phases of the marrow transplant procedure. This paper attempts to summarize the use of immune globulin preparations in clinical bone marrow transplantation, showing the rationale for and some of the results of therapeutic immune globulin administration. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101739/ doi: 10.1007/bf00918696 id: cord-004591-2hchnlwb author: Wicker, S. title: Seroprävalenz von Antikörpern gegen schwangerschaftsrelevante virale Infektionserreger bei Mitarbeiterinnen im Gesundheitswesen date: 2012-07-25 words: 2010.0 sentences: 260.0 pages: flesch: 54.0 cache: ./cache/cord-004591-2hchnlwb.txt txt: ./txt/cord-004591-2hchnlwb.txt summary: In den vergangenen Jahren sind in Deutschland wiederholt behördliche Be schäftigungsverbote für schwangere Mit arbeiterinnen ausgesprochen worden, so fern diese in der Kinderbetreuung oder im Gesundheitswesen tätig und gegenüber schwangerschaftsrelevanten Infektionen (z. Im Hinblick auf eine potenzielle Infek tionsgefährdung dürfen nach § 4 Abs. 2 Nr. 6 des MuSchG werdende Mütter nicht "mit Arbeiten, bei denen sie infol ge ihrer Schwangerschaft in besonderem Maße der Gefahr, an einer Berufskrank heit zu erkranken, ausgesetzt sind oder bei denen durch das Risiko der Entste hung einer Berufskrankheit eine erhöh te Gefährdung für die werdende Mutter oder eine Gefahr für die Leibesfrucht be steht" beschäftigt werden. Healthcare workers · Maternity protection law · Pregnancy · Occupationally acquired infections gezeigt werden, dass Patienten und medi zinisches Personal sowohl Auslöser von Infektionsketten sein als auch an solchen Infektionen erkranken und versterben können [25] . Occupational risk of human cytomegalovirus and parvovirus B19 infection in female day care personnel in the Netherlands: a study based on seroprevalence Occupational risk for primary cytomegalovirus infection among pediatric health-care workers abstract: Healthcare workers (HCWs) are exposed to infectious diseases throughout the course of their work. The concerns of pregnant HCWs are considerable because certain otherwise mild infections may affect fetal development. We studied 424 pregnant HCWs at the University Hospital Frankfurt between March 2007 and July 2011. Serological tests were carried out for varicella zoster virus (VZV), measles, mumps, rubella (MMR), cytomegalovirus (CMV) and parvovirus B19. Our overall seroprevalence data with regard to VZV, MMR, CMV and parvovirus B 19 corresponded to the general population. However, physicians demonstrated lower seroprevalence towards the two non-vaccine-preventable diseases (CMV: 37.5% [KI 27.4–48.5]; parvovirus B19: 69.3% [KI 58.6–78.7]) compared with nurses (CMV: 53.4% [KI 46.1–60.6], parvovirus B19: 75.1% [68.4–81.1]). It was striking that, only one in five of the study population showed IgG antibodies against all of the six pregnant-relevant viral diseases tested, of the physicians as few as one in six. A routine exclusion from the workplace due to non-immunity would mean that it would not be possible to employ the majority of pregnant staff in healthcare and childcare. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080042/ doi: 10.1007/s00103-012-1509-0 id: cord-103297-4stnx8dw author: Widrich, Michael title: Modern Hopfield Networks and Attention for Immune Repertoire Classification date: 2020-08-17 words: 14093.0 sentences: 926.0 pages: flesch: 57.0 cache: ./cache/cord-103297-4stnx8dw.txt txt: ./txt/cord-103297-4stnx8dw.txt summary: In this work, we present our novel method DeepRC that integrates transformer-like attention, or equivalently modern Hopfield networks, into deep learning architectures for massive MIL such as immune repertoire classification. DeepRC sets out to avoid the above-mentioned constraints of current methods by (a) applying transformer-like attention-pooling instead of max-pooling and learning a classifier on the repertoire rather than on the sequence-representation, (b) pooling learned representations rather than predictions, and (c) using less rigid feature extractors, such as 1D convolutions or LSTMs. In this work, we contribute the following: We demonstrate that continuous generalizations of binary modern Hopfield-networks (Krotov & Hopfield, 2016 Demircigil et al., 2017) have an update rule that is known as the attention mechanisms in the transformer. We evaluate the predictive performance of DeepRC and other machine learning approaches for the classification of immune repertoires in a large comparative study (Section "Experimental Results") Exponential storage capacity of continuous state modern Hopfield networks with transformer attention as update rule abstract: A central mechanism in machine learning is to identify, store, and recognize patterns. How to learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent transformer architectures. We show that the attention mechanism of transformer architectures is actually the update rule of modern Hop-field networks that can store exponentially many patterns. We exploit this high storage capacity of modern Hopfield networks to solve a challenging multiple instance learning (MIL) problem in computational biology: immune repertoire classification. Accurate and interpretable machine learning methods solving this problem could pave the way towards new vaccines and therapies, which is currently a very relevant research topic intensified by the COVID-19 crisis. Immune repertoire classification based on the vast number of immunosequences of an individual is a MIL problem with an unprecedentedly massive number of instances, two orders of magnitude larger than currently considered problems, and with an extremely low witness rate. In this work, we present our novel method DeepRC that integrates transformer-like attention, or equivalently modern Hopfield networks, into deep learning architectures for massive MIL such as immune repertoire classification. We demonstrate that DeepRC outperforms all other methods with respect to predictive performance on large-scale experiments, including simulated and real-world virus infection data, and enables the extraction of sequence motifs that are connected to a given disease class. Source code and datasets: https://github.com/ml-jku/DeepRC url: https://doi.org/10.1101/2020.04.12.038158 doi: 10.1101/2020.04.12.038158 id: cord-006713-io9yp1y2 author: Wrede, C. E. title: Intensivmedizinische Betreuung von Patienten nach Stammzelltransplantation date: 2007 words: 5253.0 sentences: 608.0 pages: flesch: 34.0 cache: ./cache/cord-006713-io9yp1y2.txt txt: ./txt/cord-006713-io9yp1y2.txt summary: Auf der anderen Seite haben diese Entwicklungen aber auch dazu geführt, dass sich das Spektrum der zur intensivmedizinischen Behandlung führenden Komplikationen verändert hat: Sie treten heute weniger in der Akutphase im ersten Monat nach Transplantation, sondern häufiger im weiteren Verlauf Monate und Jahre nach SZT bei Auftreten der GvHD oder nach erneuter adoptiver Zelltherapie mit Retransplantation auf. Während in der neutropenischen Pre-engraftment Phase die neutropenische Enterocolitis (siehe Kapitel Infektionen nach Stammzelltransplantation) im Vordergund steht, stellen vor allem bei allogener Transplantation nach dem Engraftment Enteritiden eine häufige Komplikation dar: Hier ist die exakte Erregerdiagnose wichtig, neben Clostridium difficile können eine Vielzahl viraler Erreger (CMV, HHV6, VZV, Adenovirus, aber auch typische Enteroviren wie Rotaviren und Noroviren) zu schweren und lang anhaltenden Enteritiden führen. Eine adäquate Diagnostik und Therapie von Komplikationen nach SZT ist für die intensivmedizinische Behandlung dieser Patienten essentiell, und kann zu einer Verbesserung der Prognose führen. abstract: Within the hematologic therapy procedures, stem cell transplantation (SCT) represents the most extensive and invasive intervention. Those patients have certain risks for several bacterial, viral, as well as fungal infections during the different stages of transplantation. Especially in allogenic transplantation, discrimination of non-infectious, mostly immunologic complications like graft-versus-host reactions or VOD (veno-occlusive disease) is crucial, and often represents a therapeutic challenge. An adequate intensive care therapy of these patients can only be achieved with the knowledge of the specific complications of SCT. This review starts with an overview of the SCT stages with their corresponding infectious and noninfectious complications, followed by the discussion of organ specific pulmonary, renal, cardiac, gastrointestinal, hepatic and neurological complications of stem cell transplantation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102276/ doi: 10.1007/s00390-007-0774-x id: cord-011197-bmigh2rs author: Yener, Nazik title: Airway Pressure Release Ventilation as a Rescue Therapy in Pediatric Acute Respiratory Distress Syndrome date: 2020-03-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To describe experience with airway pressure release ventilation (APRV) in children with severe acute respiratory distress syndrome (ARDS) refractory to conventional low tidal volume ventilation. METHODS: This retrospective observational study was performed in an 11-bed, level 3 pediatric intensive care unit. Evaluation was made of 30 pediatric patients receiving airway pressure release ventilation as rescue therapy for severe ARDS. RESULTS: Patients were switched to APRV on an average 3.2 ± 2.6 d following intubation. When changed from conventional mechanical ventilation (CMV) to APRV, there was an expected increase in the SpO(2)/FiO(2) ratio (165.1 ± 13.6 vs. 131.7 ± 10.2; p = 0.035). Mean peak inspiratory pressure was significantly lower during APRV (25.4 ± 1.26 vs. 29.8 ± 0.60, p < 0.001) compared to CMV prior to APRV but mean airway pressure (P(aw)) was significantly higher during APRV (19.1 ± 0.9 vs. 15.3 ± 1.3, p < 0.001). Hospital mortality in this study group was 16.6%. CONCLUSIONS: The results of this study support the hypothesis that APRV may offer potential clinical advantages for ventilatory management and may be considered as an alternative rescue mechanical ventilation mode in pediatric ARDS patients refractory to conventional ventilation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223785/ doi: 10.1007/s12098-020-03235-w id: cord-016990-ot1wi3xi author: Zaki, Sherif R. title: Viral Infections of the Lung date: 2008 words: 19585.0 sentences: 1132.0 pages: flesch: 36.0 cache: ./cache/cord-016990-ot1wi3xi.txt txt: ./txt/cord-016990-ot1wi3xi.txt summary: 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. abstract: The lungs are among the most vulnerable to microbial assault of all organs in the body. From a contemporary vantage, lower respiratory tract infections are the greatest cause of infection-related mortality in the United States, and rank seventh among all causes of deaths in the United States.2,3 From a global and historic perspective, the scope and scale of lower respiratory tract infection is greater than any other infectious syndrome, and viral pneumonias have proven to be some of the most lethal and dramatic of human diseases. The 1918–1919 influenza pandemic, perhaps the most devastating infectious disease pandemic in recorded history, resulted in an estimated 40 million deaths worldwide, including 700,000 deaths in the U.S.4 The global outbreak of severe acute respiratory syndrome (SARS) during 2003, although considerably smaller in scale, resulted in 8098 cases and 774 deaths5 and is a dramatic contemporary example of the ability of viral pneumonias to rapidly disseminate and cause severe disease in human populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121437/ doi: 10.1007/978-0-387-68792-6_11 id: cord-263276-keyu60in author: Zhou, Weimin title: Prevalence of Herpes and Respiratory Viruses in Induced Sputum among Hospitalized Children with Non Typical Bacterial Community-Acquired Pneumonia date: 2013-11-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: Few comprehensive studies have searched for viruses in infants and young children with community-acquired pneumonia (CAP) in China. The aim of this study was to investigate the roles of human herpes viruses (HHVs) and other respiratory viruses in CAP not caused by typical bacterial infection and to determine their prevalence and clinical significance. METHODS: Induced sputum (IS) samples were collected from 354 hospitalised patients (infants, n = 205; children, n = 149) with respiratory illness (CAP or non-CAP) admitted to Wenling Hospital of China. We tested for HHVs and respiratory viruses using PCR-based assays. The epidemiological profiles were also analysed. RESULTS: High rate of virus detection (more than 98%) and co-infection (more than 80%) were found among IS samples from 354 hospitalised infants and children with respiratory illness in this study. Of 273 CAP samples tested, CMV (91.6%), HHV-6 (50.9%), RSV (37.4%), EBV (35.5%), HBoV (28.2%), HHV-7 (18.3%) and rhinovirus (17.2%) were the most commonly detected viruses. Of 81 non- CAP samples tested, CMV (63%), RSV (49.4%), HHV-6 (42%), EBV (24.7%), HHV-7 (13.6%) and HBoV (8.6%) were the dominant viruses detected. The prevalence of several viral agents (rhinovirus, bocavirus, adenovirus and CMV) among IS samples of CAP were significantly higher than that of non-CAP control group. We also found the prevalence of RSV coinfection with HHVs was also higher among CAP group than that of non-CAP control. CONCLUSIONS: With sensitive molecular detection techniques and IS samples, high rates of viral identification were achieved in infants and young children with respiratory illness in a rural area of China. The clinical significance of rhinovirus, bocavirus, adenovirus and HHV (especially CMV) infections should receive greater attention in future treatment and prevention studies of CAP in infants and children. url: https://www.ncbi.nlm.nih.gov/pubmed/24260230/ doi: 10.1371/journal.pone.0079477 id: cord-004675-n8mlxe7p author: nan title: 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2019-02-26 words: 86427.0 sentences: 5050.0 pages: flesch: 46.0 cache: ./cache/cord-004675-n8mlxe7p.txt txt: ./txt/cord-004675-n8mlxe7p.txt summary: However, the mean infusion rate per site was similar between patients aged <18 years ( XMEN disease (X-linked Immunodeficency with Magnesium defect, Epstein-Barr virus infection and Neoplasia) is a primary immune deficiency caused by mutations in MAGT1 and characterized by chronic infection with Epstein-Barr virus (EBV), EBV-driven lymphoma, CD4 T-cell lymphopenia, and dysgammaglobulinemia. We present the case of a 1-year old Hispanic infant with a pathogenic variant in MAGT1 gene that clinically manifested with early Pneumocystis jirovecii and cytomegalovirus (CMV) interstitial pneumonia, and EBV chronic infection with good response to intravenous immunoglobulins supplementation without hematopoietic stem cell transplantation or gene therapy. Chief, Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD, USA Hypomorphic Recombination Activating Gene 1 (RAG1) mutations result in residual T-and B-cell development in both humans and mice and have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086569/ doi: 10.1007/s10875-019-00597-5 id: cord-005453-4057qib7 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 words: 275771.0 sentences: 16876.0 pages: flesch: 56.0 cache: ./cache/cord-005453-4057qib7.txt txt: ./txt/cord-005453-4057qib7.txt summary: To compare the safety and efficacy of prophylactic DLI for prevention of relapse after allogeneic peripheral blood stem cell transplantation from haploidentical donors (HID-SCT) and matched-sibling donors (MSD-SCT) in patients with very high-risk acute myeloid leukemia (AML), we performed a retrospective, observational cohort study enrolled in 21 HID-SCT and 13 MSD-SCT recipients. The aim of this study is to identify the prognostic impact of pre-transplant TIM3 levels on early and late transplant related complications as well as post-transplant relapse and survival Methods: A total of 177 hematopoietic stem cell transplantation (HSCT) recipients with an initial diagnosis of acute leukemia [median age: 36(16-66) years; male/ female: 111/66] were included in the study. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091813/ doi: 10.1038/s41409-019-0559-4 id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 words: 287105.0 sentences: 15681.0 pages: flesch: 56.0 cache: ./cache/cord-005460-ezrn8cva.txt txt: ./txt/cord-005460-ezrn8cva.txt summary: Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/ doi: 10.1038/bmt.2017.134 id: cord-005478-5iu38pr6 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date: 2019-07-03 words: 63350.0 sentences: 3869.0 pages: flesch: 58.0 cache: ./cache/cord-005478-5iu38pr6.txt txt: ./txt/cord-005478-5iu38pr6.txt summary: There were some differences among groups: patients in group-1 were younger (median age 46 years, p< 0.02) were transplanted in more recent year (2015, p< 0.001), received more frequently a regimen based on TBF (thiotepa, fludarabine and busulfan) (83%, p< 0.001) and bone marrow (BM) as source of stem cells (77%, p< 0.001), with no ATG (100%, p< 0.001). Clinical Trial Registry: NCT01217723 Disclosure: None of the Authors have any conflicts of interest to declare O105 Immune reconstitution -based score at diagnosis of CGVHD predicts GVHD severity and overall-survival: A novel prognostication tool for GVHD treatment tailoring Background: Allogeneic stem cell transplantation (HSCT) survivors are at a relevant risk of developing chronic GvHD (cGvHD), which importantly affects quality of life and increases morbidity and mortality. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092200/ doi: 10.1038/s41409-019-0562-9 id: cord-005480-yg7salqt author: nan title: Oral Sessions and Working Party date: 2008-03-26 words: 72626.0 sentences: 3873.0 pages: flesch: 55.0 cache: ./cache/cord-005480-yg7salqt.txt txt: ./txt/cord-005480-yg7salqt.txt summary: Standard NIH or Eurolupus cyclophosphamide (CY) protocols and mycophenolate Mofetil (MMF) as induction therapy in severe BILAG A SLE is still associated with 20 % failure, 50% relapse and 10% to 15 % death at 10 years In the absence of a single standard treatment worldwide for refractory SLE, phase I-II studies analysed the use of: a) rituximab (anti CD20 mAb) in more than 1 000 patients showing complete to partial early response around 100% with relapse in 50 to 60% of the cases; b) autologous Hematopoietic Stem Cell Transplantation (HSCT) since 1997 under the auspices of the joined EBMT-EULAR working party, reporting durable remission with reduced or no immunosuppressive drug requirement in 66%, one-third of whom later relapsed to some degree with a 74 ± 7% (n= 62/79) overall survival at 5 years for SLE among the 863 HSCT procedures registered: in 2007 in the EBMT data base. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092258/ doi: 10.1038/bmt.2008.30 id: cord-005487-vac061r8 author: nan title: Physicians Abstracts: EBMT 2010 date: 2010-04-07 words: 58975.0 sentences: 3128.0 pages: flesch: 58.0 cache: ./cache/cord-005487-vac061r8.txt txt: ./txt/cord-005487-vac061r8.txt summary: We retrospectively analyzed 1257 patients (pts), 755 children (age≤18) and 502 adults, receiving fi rst single (n = 1080) or double UCBT (n = 177) in EBMT centers, between 1995 and 2009 , for malignant and non-malignant diseases, who survived at least 100 days from transplantation with neutrophils recovery and without relapse or autologous reconstitution. Prochymal® improves response rates in patients with steroid-refractory acute graft-versus-host disease involving the liver and gut: results of a randomized, placebo-controlled, multicentre phase III trial in GvHD P.J. Martin (1) , J.P. Uberti (2) Background and methods: Steroid-refractory acute GVHD (SR-GVHD) remains a signifi cant and life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). A. Nagler (1) Background: Allogeneic transplantation of hematopoietic stem cells (allo-SCT) from an HLA-matched related (MRD) or unrelated donor (URD) is a curative option for patients (pts) with high-risk hematological disease (HRHD). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092333/ doi: 10.1038/bmt.2010.40 id: cord-006466-e1phpqes author: nan title: 2018 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2018-04-23 words: 92230.0 sentences: 5516.0 pages: flesch: 46.0 cache: ./cache/cord-006466-e1phpqes.txt txt: ./txt/cord-006466-e1phpqes.txt summary: Whole exome sequencing revealed a heterozygous mutation, previously reported (c.1425+1G>T) Conclusions: In summary, this report emphasizes the suspicion of a combined immunodeficiency in the presence of multiple abscesses by Mycoplasma, the usefulness of rDNA 16s in order to achieve proper Objectives: We describe a 15-year-old male patient with novel heterozygous mutation of EP300 gene; his first manifestations were initially characterized by infections, cytopenia and hypogammaglobulinemia suggesting a Common Variable Immunodeficiency (CVID), but later on, persisting lymphopenia was suggestive of a combined immunodeficiency. Conclusions: Close monitoring of immune function in early life for patients with CHH and CID as well as the availability of suitable donors assists in determining management, including HSCT Introduction/Background: Leukocyte Adhesion Deficiency (LAD) represents a group of distinct inherited disorders, which inhibit the normal extravasation of neutrophils and their recruitment to sites of infection or inflammation. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101862/ doi: 10.1007/s10875-018-0485-z id: cord-006856-b1w25ob5 author: nan title: 19th Meeting of the Austrian Society of Transplantation, Transfusion, and Genetics, October 26–28, 2005 date: 2005 words: 29625.0 sentences: 1983.0 pages: flesch: 52.0 cache: ./cache/cord-006856-b1w25ob5.txt txt: ./txt/cord-006856-b1w25ob5.txt summary: Egr-1 and hypoxia-inducible factor-1 (HIF-1) gene expression was examined in left ventricular biopsies of explanted failing hearts in 28 ICM and 42 DCM patients, as well as in 12 donor grafts before reperfusion (control), at 10, 30, 60 minutes after reperfusion, and at 1, 2, 3, 4, 6, 12 posttransplant weeks, using real-time RT-PCR. The risk of transplant-related mortality (TRM) due to graft-versushost disease (GvHD) is higher in male recipients of female stem cells compared with female patients receiving a graft from a female donor. We therefore analyzed a single-center cohort of 72 high-risk patients transplanted with a related or unrelated stem cell graft after nonmyeloablative conditioning for outcome (acute and chronic GvHD, TRM, relapse, and survival). Four patients between the age of 34 and 44 years underwent allogeneic peripheral blood stem cell (PBSC) transplantation (SCT) from HLA-identical sibling or unrelated donors at our institution. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103192/ doi: 10.1007/s10353-005-0216-6 id: cord-009567-osstpum6 author: nan title: Abstracts Oral date: 2008-04-23 words: 131214.0 sentences: 7728.0 pages: flesch: 53.0 cache: ./cache/cord-009567-osstpum6.txt txt: ./txt/cord-009567-osstpum6.txt summary: Introduction: Previously, it has been demonstrated that FOXP3, a gene required for the development and function of regulatory T cells, was highly expressed in the graft during cardiac rejection, suggesting infiltration of regulatory T cells in the transplanted organ during an allogeneic response. Efficacy and safety parameters assessed at follow-up included: acute rejection; patient and graft survival; renal function, vital signs, basic lab results and immunosuppressive regimen for the patients 10 years after completion of the original study. We analyzed, for the first time, the expression of TLR4 in PBMC from kidney recipients with contrasted situations: operational tolerance and chronic immune-mediated rejection (Banff 2005), compared to patients with normal histology and stable graft function, non transplant patients with renal failure and healthy volunteers. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159651/ doi: 10.1111/j.1600-6143.2008.02254.x id: cord-014462-11ggaqf1 author: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 words: 35453.0 sentences: 1711.0 pages: flesch: 49.0 cache: ./cache/cord-014462-11ggaqf1.txt txt: ./txt/cord-014462-11ggaqf1.txt summary: Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639731/ doi: 10.1007/s13337-011-0027-2 id: cord-015365-iqdi99pd author: nan title: 25th Annual Meeting of the Austrian Society of Transplantation, Transfusion and Genetics Graz, October 19–21, 2011 date: 2011 words: 30685.0 sentences: 2517.0 pages: flesch: 50.0 cache: ./cache/cord-015365-iqdi99pd.txt txt: ./txt/cord-015365-iqdi99pd.txt summary: Retrospective study to test ferritin serum levels as biomarker for graft-versus-host disease-associated non-infectious inflammatory reaction in 117 children after hematopoietic stem cell transplantation Background. One hundred seventy-eight patients (85 males, 93 females) with a median age of 40 years alive on day þ 100 after HCT with myeloablative (n ¼ 110) or reduced-intensity (n ¼ 68) conditioning and a related (n ¼ 37) or unrelated (n ¼ 141) stem cell donor were enrolled into the study. Using a non-myeloablative conditioning regimen followed by donor bone marrow (DBM) transplantation, we observed successful production of mixed chimerism in non-human primate renal allograft recipients, followed by normal kidney function with no evidence of chronic rejection for periods as long as thirteen years after discontinuing all I.S. In vitro studies of these recipients as well as of humans suggest that both central (clonal deletion) and peripheral (regulatory cells) mechanisms are involved. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103185/ doi: 10.1007/s10353-011-0041-z id: cord-015389-vwgai4k9 author: nan title: Publication only date: 2009-03-25 words: 23868.0 sentences: 1465.0 pages: flesch: 57.0 cache: ./cache/cord-015389-vwgai4k9.txt txt: ./txt/cord-015389-vwgai4k9.txt summary: This study evaluates the safety of this approach, in terms of infusion-related toxicity and hematopoietic reconstitution, in 385 consecutive autologous transplantations performed from 4/97 to 9/08 in 348 patients (median age 46; underlying disease: lymphoma in 178, myeloma in 131, acute leukaemia in 17, breast cancer in 22). Patients and methods: Eight pts after allogeneic hematopoetic stem cell transplantation (HSCT) underwent MSCs infusions (median age of pts was 11 years, male/female: 6/2) between 2006 and 2009. Akiyama Tokyo Metropolitan Komagome Hospital (Tokyo, JP) Acute graft-versus-host disease (GVHD) is one of the major factors that have infl uence on the outcomes of allogeneic hematopoietic stem cell transplantation (HSCT). Material and methods: during a 8 years period we have performed 144 stem cells transplantation in 134 patients with different hematological malignancies(AML: 74; ALL: 6; CML: 7; CLL: 1, NHL: 13; Hodgkin Diseases: 16; Multiple myelomas: 24; Aplastic anaemia: 1;Myelofi brosis:1 Ewing Sarcoma: 1; Male:78 Female 66. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104434/ doi: 10.1038/bmt.2009.50 id: cord-016998-6n662amh author: nan title: Nierentransplantation date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Die Nierentransplantation ist die effektivste Behandlungsmethode der chronischen terminalen Niereninsuffizienz. Seit den 1960er Jahren entwickelte sie sich zu einer Standardtherapie. Wichtige Voraussetzungen waren die Entdeckung des HLA-Systems, die Entwicklung der Immunsuppressiva sowie die technische Perfektionierung des Organerhaltes außerhalb eines lebenden Körpers. Die 5-Jahres-Überlebensrate für Allotransplantate beträgt etwa 65%, diejenige von Lebendspenden 79%. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121448/ doi: 10.1007/978-3-540-48556-8_13 id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 words: 188640.0 sentences: 9313.0 pages: flesch: 45.0 cache: ./cache/cord-022888-dnsdg04n.txt txt: ./txt/cord-022888-dnsdg04n.txt summary: Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. abstract: No Abtract url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163517/ doi: 10.1002/eji.200990224 id: cord-313474-1gux1gsi author: nan title: Physicians Abstracts date: 2015-03-20 words: 51420.0 sentences: 2890.0 pages: flesch: 57.0 cache: ./cache/cord-313474-1gux1gsi.txt txt: ./txt/cord-313474-1gux1gsi.txt summary: Materials (or patients) and methods: We performed a multicenter, multinational, open-label, randomized study comparing anti-lymphocyte globulin (ATG-Fresenius s ) 10 mg/kg on day -3, -2 and -1 with no ATG in patients with AML (n ¼ 110) or ALL (n ¼ 45) in 1 st complete remission (CR; n ¼ 139) or 2 nd CR (n ¼ 16) who received peripheral blood stem cells from their HLA-identical sibling after standard TBI (12 Gy)/Ccclophosphamide (120 mg/kg) or busulfan (16 mg/ kg)/Cy (120 mg/kg) based myeloablative conditioning regimen. After allo-HSCT, detection of positive WT1 was followed by immunomodulatory therapeutic interventions according to the time from transplant, the presence of active graft-versus-host disease (GvHD) and the general clinical conditions: tapering and/or discontinuation of immunosuppressive drugs (IS), donor lymphocytes infusions (DLI), administration of hypomethylating agents. Introduction: Haploidentical hematopoietic stem cell transplantation(Haplo-HSCT)is feasible option for patients with acute leukemia(AL)at high risk of relapse who do not have HLA-matched related or unrelated donors. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25794251/ doi: 10.1038/bmt.2015.27 id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 words: 26536.0 sentences: 3917.0 pages: flesch: 45.0 cache: ./cache/cord-340489-yo3cp5vs.txt txt: ./txt/cord-340489-yo3cp5vs.txt summary: Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. abstract: Zur Orientierung Infektionskrankheiten werden durch Pathogene verursacht, die sich im Wirt vermehren: Ektoparasiten, Helminthen, Protozoen, Pilze, Bakterien, Viren, Prionen. Infektionskrankheiten können alle Organe bzw. Organsysteme befallen. Entstehung und Verlauf werden durch Faktoren beeinflusst, die sich grob einteilen lassen in Erreger- und Wirtsfaktoren. Die Kenntnis und richtige Einschätzung dieser Faktoren sind entscheidend für Diagnostik und Therapie dieser Erkrankungen. url: https://api.elsevier.com/content/article/pii/B9783437428319100130 doi: 10.1016/b978-3-437-42831-9.10013-0 id: cord-003376-2qi4aibx author: van de Groep, Kirsten title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date: 2018-12-18 words: 3889.0 sentences: 191.0 pages: flesch: 42.0 cache: ./cache/cord-003376-2qi4aibx.txt txt: ./txt/cord-003376-2qi4aibx.txt summary: title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study Cytomegalovirus (CMV) reactivation is observed in 14-41% of intensive care unit (ICU) patients without known prior immune deficiency [1] [2] [3] and is associated with increased morbidity and mortality [4] [5] [6] . Therefore, this longitudinal study aimed to investigate whether the temporal course of seven host response biomarkers, including both pro-and anti-inflammatory cytokines, in previously immunocompetent ICU patients with sepsis differs between patients with and without CMV reactivation. Time trends of various markers within patients were described by symmetric percentage differences relative to their levels 2 days prior to CMV viremia onset (Fig. 2 for primary comparison, Additional file 1: Figure S1 for secondary comparison). We performed an explorative study to compare time trends of host response biomarkers in patients with reactivation that were matched to non-reactivating control patients who were either seropositive or seronegative for CMV. abstract: BACKGROUND: Cytomegalovirus (CMV) reactivation in previously immunocompetent critically ill patients is associated with increased mortality, which has been hypothesized to result from virus-induced immunomodulation. Therefore, we studied the effects of CMV reactivation on the temporal course of host response biomarkers in patients with sepsis. METHODS: In this matched cohort study, each sepsis patient developing CMV reactivation between day 3 and 17 (CMV+) was compared with one CMV seropositive patient without reactivation (CMVs+) and one CMV seronegative patient (CMVs−). CMV serostatus and plasma loads were determined by enzyme-linked immunoassays and real-time polymerase chain reaction, respectively. Systemic interleukin-6 (IL-6), IL-8, IL-18, interferon-gamma–induced protein-10 (IP-10), neutrophilic elastase, IL-1 receptor antagonist (RA), and IL-10 were measured at five time points by multiplex immunoassay. The effects of CMV reactivation on sequential concentrations of these biomarkers were assessed in multivariable mixed models. RESULTS: Among 64 CMV+ patients, 45 could be matched to CMVs+ or CMVs− controls or both. The two baseline characteristics and host response biomarker levels at viremia onset were similar between groups. CMV+ patients had increased IP-10 on day 7 after viremia onset (symmetric percentage difference +44% versus −15% when compared with CMVs+ and +37% versus +4% when compared with CMVs−) and decreased IL-1RA (−41% versus 0% and −49% versus +10%, respectively). However, multivariable analyses did not show an independent association between CMV reactivation and time trends of IL-6, IP-10, IL-10, or IL-1RA. CONCLUSION: CMV reactivation was not independently associated with changes in the temporal trends of host response biomarkers in comparison with non-reactivating patients. Therefore, these markers should not be used as surrogate clinical endpoints for interventional studies evaluating anti-CMV therapy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13054-018-2261-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299562/ doi: 10.1186/s13054-018-2261-0 id: cord-016255-kkko1xne author: van der Meer, J.T.M. title: 14 Intravasale infecties en sepsis date: 2011 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infecties in het hart en de bloedbaan worden intravasale of endovasculaire infecties genoemd. De circulatie van bloed door het hart is essentieel voor de aanvoer van zuurstof en voedingstoffen naar weefsel en organen en voor de afvoer van afvalstoffen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120488/ doi: 10.1007/978-90-313-7944-6_14 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel