Carrel name: journal-medicine-cord Creating study carrel named journal-medicine-cord Initializing database file: cache/cord-298183-cisrvghj.json key: cord-298183-cisrvghj authors: Fredricks, David N; Relman, David A title: The infectious aetiology of disease: the search for new agents date: 2005-03-01 journal: Medicine DOI: 10.1383/medc.33.3.37.61122 sha: doc_id: 298183 cord_uid: cisrvghj file: cache/cord-252266-8o4kte9i.json key: cord-252266-8o4kte9i authors: Beeching, Nick title: Fever in the returning traveller date: 2005-07-01 journal: Medicine DOI: 10.1383/medc.2005.33.7.3 sha: doc_id: 252266 cord_uid: 8o4kte9i file: cache/cord-324301-bzrh2fni.json key: cord-324301-bzrh2fni authors: Zambon, Maria title: Influenza, respiratory syncytial virus and SARS date: 2005-05-01 journal: Medicine DOI: 10.1383/medc.33.5.130.64960 sha: doc_id: 324301 cord_uid: bzrh2fni file: cache/cord-256610-0njpw3zz.json key: cord-256610-0njpw3zz authors: Ferguson, Neil M title: Mathematical prediction in infection date: 2005-03-01 journal: Medicine DOI: 10.1383/medc.33.3.1.61124 sha: doc_id: 256610 cord_uid: 0njpw3zz Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-medicine-cord === file2bib.sh === id: cord-298183-cisrvghj author: Fredricks, David N title: The infectious aetiology of disease: the search for new agents date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-298183-cisrvghj.txt cache: ./cache/cord-298183-cisrvghj.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-298183-cisrvghj.txt' === file2bib.sh === id: cord-256610-0njpw3zz author: Ferguson, Neil M title: Mathematical prediction in infection date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-256610-0njpw3zz.txt cache: ./cache/cord-256610-0njpw3zz.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-256610-0njpw3zz.txt' === file2bib.sh === id: cord-324301-bzrh2fni author: Zambon, Maria title: Influenza, respiratory syncytial virus and SARS date: 2005-05-01 pages: extension: .txt txt: ./txt/cord-324301-bzrh2fni.txt cache: ./cache/cord-324301-bzrh2fni.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-324301-bzrh2fni.txt' === file2bib.sh === id: cord-252266-8o4kte9i author: Beeching, Nick title: Fever in the returning traveller date: 2005-07-01 pages: extension: .txt txt: ./txt/cord-252266-8o4kte9i.txt cache: ./cache/cord-252266-8o4kte9i.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-252266-8o4kte9i.txt' Que is empty; done journal-medicine-cord === reduce.pl bib === id = cord-298183-cisrvghj author = Fredricks, David N title = The infectious aetiology of disease: the search for new agents date = 2005-03-01 pages = extension = .txt mime = text/plain words = 1311 sentences = 84 flesch = 42 summary = The hypothesis that a disease has an infectious cause is supported by: clinical features (similar to those of known infectious diseases, e.g. fever, leucocytosis), epidemiology (case clustering in time or location), histology (inflammation of affected tissues, e.g. granulomata) or characteristic microbial structures, treatment (clinical response to antimicrobial treatment), and prevention of disease by vaccines targeting microbial antigens. Many of the recently discovered microbial pathogens were identified by detecting their unique nucleic acid sequences in tissues. A unique 16S rDNA sequence was detected in the tissues of three patients with bacillary angiomatosis but not in control tissues, identifying a bacterium in the Bartonella genus as a cause of a the disease. Several sequence-based approaches to pathogen discovery have yielded novel microbes that cause human disease. Future attempts to identify novel microbes associated with human disease may use other sequence-based approaches. Future attempts to identify novel microbes associated with human disease may use other sequence-based approaches. cache = ./cache/cord-298183-cisrvghj.txt txt = ./txt/cord-298183-cisrvghj.txt === reduce.pl bib === id = cord-252266-8o4kte9i author = Beeching, Nick title = Fever in the returning traveller date = 2005-07-01 pages = extension = .txt mime = text/plain words = 1769 sentences = 102 flesch = 44 summary = The quality of pre-travel advice and vaccinations, adherence to chemoprophylaxis against malaria, avoidance of insect bites and general behaviour abroad (including sexual history) are also important. Initial investigations should include adequate malaria films (supplemented by quick antigen detection tests in many laboratories) and blood count, repeated as necessary, blood, urine and faecal cultures, serum biochemistry, chest radiography and other imaging (e.g. liver ultrasonography) as indicated. Worldwide, but mainly tropics Persistent fever, right upper Neutrophil leucocytosis, abdominal pain and tenderness, ultrasonography of liver, serology signs at right lung base African trypanosomiasis Visitors to African game parks, Chancre at bite site, tachycardia, Hypoglycaemia, thrombocytopenia, tsetse fly lymphadenopathy, splenomegaly, thick blood films, serology, consider transient oedema, variable rashes CSF examination only after obtaining expert advice Falciparum malaria must be excluded, and is the diagnosis in 65-75% of patients hospitalized after visiting Sub-Saharan Africa, compared with 15-25% of those returning from Asia, who are more likely to have dengue fever. cache = ./cache/cord-252266-8o4kte9i.txt txt = ./txt/cord-252266-8o4kte9i.txt === reduce.pl bib === id = cord-324301-bzrh2fni author = Zambon, Maria title = Influenza, respiratory syncytial virus and SARS date = 2005-05-01 pages = extension = .txt mime = text/plain words = 2978 sentences = 178 flesch = 43 summary = The recent emergence of the SARS coronavirus in the human population in 2003, with an ensuing global epidemic affecting more than 8000 individuals with a case fatality of about 10%, underlines the fact that respiratory viral infections of humans may originate in animals, and that many different influenza A viruses also occur naturally in animal reservoirs, representing a constant threat of zoonotic infections of humans and ensuing global pandemics. About 30-50% of acute LRTIs are viral in origin; of these, influenza and respiratory syncytial virus (RSV) are associated with the greatest disease burden in humans. About 30-50% of acute LRTIs are viral in origin; of these, influenza and respiratory syncytial virus (RSV) are associated with the greatest disease burden in humans. Seasonal illness, epidemics and pandemics -influenza viruses circulating in humans (A H1N1, H3N2, B and C) cause respiratory tract disease. cache = ./cache/cord-324301-bzrh2fni.txt txt = ./txt/cord-324301-bzrh2fni.txt === reduce.pl bib === id = cord-256610-0njpw3zz author = Ferguson, Neil M title = Mathematical prediction in infection date = 2005-03-01 pages = extension = .txt mime = text/plain words = 1606 sentences = 84 flesch = 39 summary = The contribution concludes with a brief review of the recent application of mathematical models to emerging human and animal epidemics, notably the spread of HIV in Africa, the variant Creutzfeldt-Jakob disease epidemic in the UK and its relationship to bovine spongiform encephalitis in cattle, the 2001 foot and mouth epidemic in UK livestock, bioterrorism threats such as smallpox, and the SARS epidemics in 2003. Epidemics can be described and sometimes predicted by mathematical models because they involve relatively simple processes occurring within large populations of individuals. From the definition of R 0 , this occurs when 1/R 0 of an individual's contacts are susceptible at any point in time, and thus R 0 not only determines the epidemic growth rate, but also the proportion of the population that are infected by the disease, and the steady-state incidence of infection. cache = ./cache/cord-256610-0njpw3zz.txt txt = ./txt/cord-256610-0njpw3zz.txt ===== Reducing email addresses Creating transaction Updating adr table ===== Reducing keywords cord-252266-8o4kte9i cord-324301-bzrh2fni cord-298183-cisrvghj cord-256610-0njpw3zz Creating transaction Updating wrd table ===== Reducing urls Creating transaction Updating url table ===== Reducing named entities cord-298183-cisrvghj cord-252266-8o4kte9i cord-324301-bzrh2fni cord-256610-0njpw3zz Creating transaction Updating ent table ===== Reducing parts of speech cord-298183-cisrvghj cord-256610-0njpw3zz cord-252266-8o4kte9i cord-324301-bzrh2fni Creating transaction Updating pos table Building ./etc/reader.txt /data-disk/reader-compute/reader-cord/bin/email-patron.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/email-patron.sh: fork: retry: No child processes cord-324301-bzrh2fni cord-298183-cisrvghj cord-256610-0njpw3zz cord-324301-bzrh2fni cord-298183-cisrvghj cord-256610-0njpw3zz number of items: 4 sum of words: 7,664 average size in words: 1,916 average readability score: 42 nouns: disease; influenza; infection; virus; fever; malaria; infections; illness; patients; humans; risk; children; viruses; diseases; blood; years; treatment; microbes; infants; diagnosis; cause; vaccines; transmission; pneumonia; dna; days; syndrome; individuals; hospital; films; age; vaccination; tract; tests; liver; host; tissues; serology; sequences; sequence; patient; features; drugs; symptoms; subtypes; pathogens; identification; history; examination; coronavirus verbs: use; causes; include; identify; suggested; associated; occur; known; infect; detect; based; returning; requires; excluding; develop; contains; presenting; neutralizing; make; consider; circulating; think; preventing; arise; allow; suspected; see; lead; lasting; increasing; imported; find; cultivate; borne; affected; transmitted; targeting; shown; repeated; related; reduce; raise; limiting; improve; ensuing; emerged; described; control; conferred; become adjectives: respiratory; viral; severe; microbial; human; novel; clinical; acute; high; infectious; likely; nucleic; many; bacterial; pre; immunocompromised; elderly; early; unique; several; major; last; immune; domestic; different; characteristic; upper; syncytial; persistent; negative; little; general; difficult; common; antiviral; zoonotic; useful; thin; thick; small; rare; positive; non; lower; infected; important; greatest; global; existing; congenital adverbs: also; usually; particularly; later; less; recently; often; however; yet; worldwide; severely; primarily; frequently; commonly; always; almost; seldom; regularly; probably; previously; possibly; overseas; now; newly; naturally; mainly; long; least; just; highly; generally; first; directly; abroad; widely; well; vividly; typically; therefore; thereafter; strongly; still; sometimes; slightly; simultaneously; significantly; separately; selectively; reverse; relatively pronouns: it; they; its; we; their; our; them; you; us; she; he proper nouns: RSV; •; Africa; SARS; East; Asia; bacillary; angiomatosis; UK; South; Leucopenia; HIV; B.; PCR; Fever; C; sha; RNA; DOI; CoV; Bartonella; America; Abstract; A; sera; leucocytosis; henselae; haemagglutinin; granulomata; dysplasia; Worldwide; Whipple; Thrombocytopenia; TB; Plasmodium; P.; Neuraminidase; National; Middle; LRTIs; Kaposi; Figure; Eosinophilia; David; Central; B; 16S; zanamivir; www.promedmail.org/; whipplei keywords: rsv; malaria; influenza; infection; fever; dna one topic; one dimension: disease file(s): https://doi.org/10.1383/medc.33.3.37.61122 titles(s): The infectious aetiology of disease: the search for new agents three topics; one dimension: fever; influenza; epidemic file(s): https://www.ncbi.nlm.nih.gov/pubmed/32308535/, https://www.sciencedirect.com/science/article/pii/S1357303906002015, https://api.elsevier.com/content/article/pii/S1357303906001769 titles(s): Fever in the returning traveller | Influenza, respiratory syncytial virus and SARS | Mathematical prediction in infection five topics; three dimensions: fever malaria disease; influenza rsv respiratory; epidemic disease infected; understanding genetic variability; understanding genetic variability file(s): https://www.ncbi.nlm.nih.gov/pubmed/32308535/, https://www.sciencedirect.com/science/article/pii/S1357303906002015, https://api.elsevier.com/content/article/pii/S1357303906001769, https://doi.org/10.1383/medc.33.3.37.61122, https://doi.org/10.1383/medc.33.3.37.61122 titles(s): Fever in the returning traveller | Influenza, respiratory syncytial virus and SARS | Mathematical prediction in infection | The infectious aetiology of disease: the search for new agents | The infectious aetiology of disease: the search for new agents Type: cord title: journal-medicine-cord date: 2021-05-30 time: 15:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Medicine" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-252266-8o4kte9i author: Beeching, Nick title: Fever in the returning traveller date: 2005-07-01 words: 1769 sentences: 102 pages: flesch: 44 cache: ./cache/cord-252266-8o4kte9i.txt txt: ./txt/cord-252266-8o4kte9i.txt summary: The quality of pre-travel advice and vaccinations, adherence to chemoprophylaxis against malaria, avoidance of insect bites and general behaviour abroad (including sexual history) are also important. Initial investigations should include adequate malaria films (supplemented by quick antigen detection tests in many laboratories) and blood count, repeated as necessary, blood, urine and faecal cultures, serum biochemistry, chest radiography and other imaging (e.g. liver ultrasonography) as indicated. Worldwide, but mainly tropics Persistent fever, right upper Neutrophil leucocytosis, abdominal pain and tenderness, ultrasonography of liver, serology signs at right lung base African trypanosomiasis Visitors to African game parks, Chancre at bite site, tachycardia, Hypoglycaemia, thrombocytopenia, tsetse fly lymphadenopathy, splenomegaly, thick blood films, serology, consider transient oedema, variable rashes CSF examination only after obtaining expert advice Falciparum malaria must be excluded, and is the diagnosis in 65-75% of patients hospitalized after visiting Sub-Saharan Africa, compared with 15-25% of those returning from Asia, who are more likely to have dengue fever. abstract: Abstract Fever is a common reason for acute hospital admission for tropical illness in UK referral units. A sensible working diagnosis can usually be formulated from a careful history and examination and initial simple investigations. The history should include details of exactly where the patient has been, what conditions he or she was living in, and the exact dates of arrival and departure. The quality of pre-travel advice and vaccinations, adherence to chemoprophylaxis against malaria, avoidance of insect bites and general behaviour abroad (including sexual history) are also important. Localizing features of the illness should be sought on examination. Maintain a high index of suspicion for underlying HIV. The most important illness to consider and exclude is malaria (about 40% of cases), and most of the remainder have cosmopolitan viral infections or imported infections such as an arbovirus (dengue), enteric fever or viral hepatitis. Rarer causes are usually evident from the history and examination, which presupposes a good knowledge of geographical medicine. Initial investigations should include adequate malaria films (supplemented by quick antigen detection tests in many laboratories) and blood count, repeated as necessary, blood, urine and faecal cultures, serum biochemistry, chest radiography and other imaging (e.g. liver ultrasonography) as indicated. In patients in whom malaria is suspected despite negative films, the combination of thrombocytopenia and splenomegaly is supportive but not diagnostic of malaria. url: https://www.ncbi.nlm.nih.gov/pubmed/32308535/ doi: 10.1383/medc.2005.33.7.3 id: cord-256610-0njpw3zz author: Ferguson, Neil M title: Mathematical prediction in infection date: 2005-03-01 words: 1606 sentences: 84 pages: flesch: 39 cache: ./cache/cord-256610-0njpw3zz.txt txt: ./txt/cord-256610-0njpw3zz.txt summary: The contribution concludes with a brief review of the recent application of mathematical models to emerging human and animal epidemics, notably the spread of HIV in Africa, the variant Creutzfeldt-Jakob disease epidemic in the UK and its relationship to bovine spongiform encephalitis in cattle, the 2001 foot and mouth epidemic in UK livestock, bioterrorism threats such as smallpox, and the SARS epidemics in 2003. Epidemics can be described and sometimes predicted by mathematical models because they involve relatively simple processes occurring within large populations of individuals. From the definition of R 0 , this occurs when 1/R 0 of an individual''s contacts are susceptible at any point in time, and thus R 0 not only determines the epidemic growth rate, but also the proportion of the population that are infected by the disease, and the steady-state incidence of infection. abstract: Abstract It is now increasingly common for infectious disease epidemics to be analysed with mathematical models. Modelling is possible because epidemics involve relatively simple processes occurring within large populations of individuals. Modelling aims to explain and predict trends in disease incidence, prevalence, morbidity or mortality. Models give important insight into the development of epidemics. Following disease establishment, epidemic growth is approximately exponential. The rate of growth in this phase is primarily determined by the basic reproduction number (R0), the number of secondary cases per primary case when the population is susceptible. R0 also determines the ease with which control policies can control epidemics. Once a significant proportion of the population has been infected, not all contacts of an infected individual will be with susceptible people. Infection can now continue only because new births replenish the susceptible population. Eventually, an endemic equilibrium is reached whereby every infected person infects one other individual on average. Heterogeneity in host susceptibility, infectiousness, human contact patterns and the genetic composition of pathogen populations introduces substantial additional complexity into the models required to model real diseases realistically. The contribution concludes with a brief review of the recent application of mathematical models to emerging human and animal epidemics, notably the spread of HIV in Africa, the variant Creutzfeldt-Jakob disease epidemic in the UK and its relationship to bovine spongiform encephalitis in cattle, the 2001 foot and mouth epidemic in UK livestock, bioterrorism threats such as smallpox, and the SARS epidemics in 2003. url: https://api.elsevier.com/content/article/pii/S1357303906001769 doi: 10.1383/medc.33.3.1.61124 id: cord-298183-cisrvghj author: Fredricks, David N title: The infectious aetiology of disease: the search for new agents date: 2005-03-01 words: 1311 sentences: 84 pages: flesch: 42 cache: ./cache/cord-298183-cisrvghj.txt txt: ./txt/cord-298183-cisrvghj.txt summary: The hypothesis that a disease has an infectious cause is supported by: clinical features (similar to those of known infectious diseases, e.g. fever, leucocytosis), epidemiology (case clustering in time or location), histology (inflammation of affected tissues, e.g. granulomata) or characteristic microbial structures, treatment (clinical response to antimicrobial treatment), and prevention of disease by vaccines targeting microbial antigens. Many of the recently discovered microbial pathogens were identified by detecting their unique nucleic acid sequences in tissues. A unique 16S rDNA sequence was detected in the tissues of three patients with bacillary angiomatosis but not in control tissues, identifying a bacterium in the Bartonella genus as a cause of a the disease. Several sequence-based approaches to pathogen discovery have yielded novel microbes that cause human disease. Future attempts to identify novel microbes associated with human disease may use other sequence-based approaches. Future attempts to identify novel microbes associated with human disease may use other sequence-based approaches. abstract: Abstract There are many diseases for which a microbial aetiology is suspected. The hypothesis that a disease has an infectious cause is supported by: clinical features (similar to those of known infectious diseases, e.g. fever, leucocytosis), epidemiology (case clustering in time or location), histology (inflammation of affected tissues, e.g. granulomata) or characteristic microbial structures, treatment (clinical response to antimicrobial treatment), and prevention of disease by vaccines targeting microbial antigens. Proof that a microbe causes a disease requires more rigorous evidence. Future attempts to identify novel microbes associated with human disease may use sequence-based approaches. High-throughput sequencing may allow identification of unique microbial nucleic acid sequences in a background of host DNA. The complete sequencing of the human genome and multiple microbial genomes make this approach more feasible. DNA microarrays are also likely to be used in the search for novel pathogens. url: https://doi.org/10.1383/medc.33.3.37.61122 doi: 10.1383/medc.33.3.37.61122 id: cord-324301-bzrh2fni author: Zambon, Maria title: Influenza, respiratory syncytial virus and SARS date: 2005-05-01 words: 2978 sentences: 178 pages: flesch: 43 cache: ./cache/cord-324301-bzrh2fni.txt txt: ./txt/cord-324301-bzrh2fni.txt summary: The recent emergence of the SARS coronavirus in the human population in 2003, with an ensuing global epidemic affecting more than 8000 individuals with a case fatality of about 10%, underlines the fact that respiratory viral infections of humans may originate in animals, and that many different influenza A viruses also occur naturally in animal reservoirs, representing a constant threat of zoonotic infections of humans and ensuing global pandemics. About 30-50% of acute LRTIs are viral in origin; of these, influenza and respiratory syncytial virus (RSV) are associated with the greatest disease burden in humans. About 30-50% of acute LRTIs are viral in origin; of these, influenza and respiratory syncytial virus (RSV) are associated with the greatest disease burden in humans. Seasonal illness, epidemics and pandemics -influenza viruses circulating in humans (A H1N1, H3N2, B and C) cause respiratory tract disease. abstract: Abstract Acute lower respiratory tract infections (LRTIs) are a major worldwide health problem, particularly in childhood, and are ranked first among the conditions contributing to the global burden of disease. About 30–50% of acute LRTIs are viral in origin; of these, influenza and respiratory syncytial virus (RSV) are associated with the greatest disease burden in humans. Vaccination against circulating human influenza strains and the use of neuraminidase inhibitor drugs have improved the options for control of influenza, but as yet there are no successful vaccines or antiviral drugs for use against RSV infection. The recent emergence of the SARS coronavirus in the human population in 2003, with an ensuing global epidemic affecting more than 8000 individuals with a case fatality of about 10%, underlines the fact that respiratory viral infections of humans may originate in animals, and that many different influenza A viruses also occur naturally in animal reservoirs, representing a constant threat of zoonotic infections of humans and ensuing global pandemics. Avian influenza viruses have transmitted directly to humans from domestic poultry on several occasions in the last decade, and the current extensive burden of disease from avian influenza in South East Asia provides a real possibility for the emergence of a novel influenza virus pathogenic in humans. url: https://www.sciencedirect.com/science/article/pii/S1357303906002015 doi: 10.1383/medc.33.5.130.64960 ==== 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