# ent

id: cord-026595-imn2jxcu
type: EVENT
entity:
  Final Year Turkish Dental Students Knowledge Attitude and Self Perceived Competency towards Preventive Dentistry Appreciation


id: cord-001566-kkaxha7d
type: ORG
entity:
  the Institute of Basic Medical Sciences of Chinese Academy of Medical Sciences Shanghai Cancer Institute


id: cord-299552-rgrm8dil
type: WORK_OF_ART
entity:
  The Global Spread of 2019 NCoV A Molecular Evolutionary Analysis Structure Function and Antigenicity of the SARS CoV 2 Spike Glycoprotein Cryo EM Structure of the


id: cord-279528-41atidai
type: DNA
entity:
  Species ID Length 1 Gorilla CAA43421 121 2 Chimp CAA26204 125 3 Human AAA16334 147 4 Rat CAA29887 147 5 Mouse CAA24101 147 6 Gutta ACH46399 147 7 Duck CAA33756 147 8 Gallus CAA23700 147 9 Opossum AAA30976 147 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 pigmy chimpanzee common chimpanzee human and gorilla ND5 protein sequences


id: cord-306411-dutbxfl4
type: DNA
entity:
  human coronavirus 229E HCoV 229E human coronavirus NL63 HCoV NL63 human coronavirus OC43 HCoV OC43 human parainfluenza virus 1 PIV 1 human parainfluenza virus 2 PIV 2 human parainfluenza virus 3 PIV 3 human parainfluenza virus 4 PIV 4 human rhinovirus HRV human enterovirus HEV


id: cord-306411-dutbxfl4
type: DISEASE
entity:
  human coronavirus 229E HCoV 229E human coronavirus NL63 HCoV NL63 human coronavirus OC43 HCoV OC43 human parainfluenza virus 1 PIV 1 human parainfluenza virus 2 PIV 2 human parainfluenza virus 3 PIV 3 human parainfluenza virus 4 PIV 4 human rhinovirus HRV human enterovirus HEV and human bocavirus HBoV Coinfections


id: cord-352190-1987sfyz
type: CHEMICAL
entity:
  N gene primer pair N1 and N2 was used 14 To amplify the 7b gene the previously designed primer pair 7b F1 and 7b R1 was used 3 All PCR reactions


id: cord-283092-t3yqsac3
type: WORK_OF_ART
entity:
  A Mathematical Model in the Time of Covid 19 a Preprint Fractional Differential Equations Mathematics in Science and Engineering Theory of Fractional Dynamic Systems Applications of Fractional Calculus in Physics Applications


id: cord-321953-yql6gpd3
type: WORK_OF_ART
entity:
  Tracking the Origin and Deciphering the Phylogenetic Relationship of Porcine Epidemic Diarrhea Virus


id: cord-321953-yql6gpd3
type: ORG
entity:
  Department of Veterinary Population Medicine College of Veterinary Medicine University of Minnesota St


id: cord-321953-yql6gpd3
type: WORK_OF_ART
entity:
  the Role of Potentially Contaminated Feed as a Source of the First Detected Outbreaks of Porcine Epidemic Diarrhea


id: cord-311625-d7iycdyh
type: DNA
entity:
  5 untranslated region 5 UTR Open Reading Frames ORFs 1a and 1b and 3 untranslated region 3 UTR Table 1


id: cord-001572-ap4ro5me
type: PROTEIN
entity:
  AdvisoryCommittees CommitteesMeetingMaterials Blood VaccinesandOtherBiologics VaccinesandRelatedBiological


id: cord-001572-ap4ro5me
type: CELL_LINE
entity:
  human acute monocytic leukemia cell line THP 1 A human coronavirus responsible for the common cold massively kills dendritic cells


id: cord-001572-ap4ro5me
type: CHEMICAL
entity:
  rubella 3 4 5 Diploid cell lines have a finite lifespan and in these cell lines the chromosomes are paired Often these cells retain many characteristics of the cell types from which they originate The disadvantage of diploid cell lines lies


id: cord-303978-z3888e3g
type: DNA
entity:
  5 benzylaminocarbonyl dU BndU 5 naphthylmethylaminocarbonyl dU NapdU 5 tryptaminocarbonyl dU TrpdU 5 phenylethyl 1 aminocarbonyl PEdU 5 tyrosylaminocarbonyl dU TyrdU or 5 2 naphthylmethyl aminocarbonyl 2NapdU


id: cord-303978-z3888e3g
type: CHEMICAL
entity:
  5 benzylaminocarbonyl dU BndU 5 naphthylmethylaminocarbonyl dU NapdU 5 tryptaminocarbonyl dU TrpdU 5 phenylethyl 1 aminocarbonyl


id: cord-004269-g6ki6vyy
type: ORG
entity:
  Israel European Centre for Disease Prevention and Control Public Health Emergency Preparedness for Cases of Viral Haemorrhagic Fever Ebola


id: cord-259823-ia1g5dt4
type: DNA
entity:
  human metapneumovirus hMPV human coronavirus or bocavirus 10 Molecular techniques are more sensitive and capable of diagnosing more viruses 11 Prompt


id: cord-335620-xqokfg3l
type: PROTEIN
entity:
  duck TM1 CIL TM2 CTD IFITM1 IFITM1 IFITM1 IFITM1 IFITM1 IFITM3 IFITM3 IFITM3 IFITM3 IFITM3 IFITM1 IFITM1 IFITM1 IFITM1 IFITM1 IFITM3 IFITM3 IFITM3 IFITM3 IFITM3 53 52 51 82 70 74 74


id: cord-335620-xqokfg3l
type: GGP
entity:
  CIL TM2 CTD IFITM1 IFITM1 IFITM1 IFITM1 IFITM1 IFITM3 IFITM3 IFITM3 IFITM3 IFITM3 IFITM1 IFITM1 IFITM1 IFITM1 IFITM1 IFITM3 IFITM3 IFITM3 IFITM3 IFITM3


id: cord-296033-5zyoddl7
type: ORG
entity:
  the Centre of Virus Resource and Information Wuhan Institute of Virology Chinese Academy of Sciences Plasmids


id: cord-319635-kh99n7q2
type: DNA
entity:
  primer pair 10 36F 5 CTGTGTGAACTT C T T G G C T T A G T A T C G 3 and 850 877R 5 CAGTTTTCATGAGATATCGTGTGTGGC 3 Fragments 868 bp


id: cord-319635-kh99n7q2
type: CELL_LINE
entity:
  plant RNA viruses Western equine encephalitis virus is a recombinant virus Evidence for recombination in natural populations


id: cord-319635-kh99n7q2
type: CELL_LINE
entity:
  Hepatitis C virus RNA recombination of hepatitis delta virus in natural mixed genotype infection and transfected cultured cells


id: cord-265260-n6wm54wz
type: WORK_OF_ART
entity:
  Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 SARS CoV 2


id: cord-330602-g0xaonxv
type: DISEASE
entity:
  influenza A H1N1 virus Impact of influenza during the post pandemic season epidemiological picture from syndromic and virological surveillance Rhinovirus infections


# bib

id: cord-001313-f72hl6du
author: Toncheva, D.
date: 2014-05-15
txt: ./txt/cord-001313-f72hl6du.txt
cache: ./cache/cord-001313-f72hl6du.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052113/
doi: 10.1155/2014/920723
summary:
  Balkan endemic nephropathy (BEN) is a familial chronic tubulointerstitial disease with insidious onset and slow progression leading to terminal renal failure. Mutant genes (CELA1, HSPG2, and KCNK5) in BEN patients encode proteins involved in basement membrane/extracellular matrix and vascular tone, tightly connected to process of angiogenesis. Balkan endemic nephropathy (BEN) is a familial chronic tubulointerstitial disease with insidious onset and slow progression to terminal renal failure. In the present study we aimed to perform exome sequencing of 22 000 genes with the Illumina Nextera Exome Enrichment Kit using NGS technology in order to find specific mutations for BEN. have intensively studied the pathological changes in the kidneys of BEN patients and presented evidence that renal vascular changes occur early in Balkan nephropathy [30] . MDR1 haplotypes modify BEN disease risk: a study in Bulgarian patients with Balkan endemic nephropathy compared to healthy controls

title:
  NGS Nominated CELA1, HSPG2, and KCNK5 as Candidate Genes for Predisposition to Balkan Endemic Nephropathy

abstract:
  Balkan endemic nephropathy (BEN) is a familial chronic tubulointerstitial disease with insidious onset and slow progression leading to terminal renal failure. The results of molecular biological investigations propose that BEN is a multifactorial disease with genetic predisposition to environmental risk agents. Exome sequencing of 22 000 genes with Illumina Nextera Exome Enrichment Kit was performed on 22 DNA samples (11 Bulgarian patients and 11 Serbian patients). Software analysis was performed via NextGene, Provean, and PolyPhen. The frequency of all annotated genetic variants with deleterious/damaging effect was compared with those of European populations. Then we focused on nonannotated variants (with no data available about them and not found in healthy Bulgarian controls). There is no statistically significant difference between annotated variants in BEN patients and European populations. From nonannotated variants with more than 40% frequency in both patients' groups, we nominated 3 genes with possible deleterious/damaging variants—CELA1, HSPG2, and KCNK5. Mutant genes (CELA1, HSPG2, and KCNK5) in BEN patients encode proteins involved in basement membrane/extracellular matrix and vascular tone, tightly connected to process of angiogenesis. We suggest that an abnormal process of angiogenesis plays a key role in the molecular pathogenesis of BEN.


id: cord-001525-b7kbyp3s
author: Zadrazilova, Iveta
date: 2015-01-15
txt: ./txt/cord-001525-b7kbyp3s.txt
cache: ./cache/cord-001525-b7kbyp3s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321674/
doi: 10.1155/2015/349534
summary:
  The aim of the current study was to assess the overall in vitro bactericidal activity of nine newly synthesized diamides in dependence on time and concentration against clinical isolates of MRSA as representatives of multidrug-resistant bacteria. The MBC was defined as the lowest concentration of substance, which produced ≥99.9% killing Table 1 : Chemical structures and in vitro MIC and MBC [ g/mL] values of tested 5-and 4-chloro-2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides (bactericidal effect of individual compounds against particular strains marked in bold). In the present study the series of nine newly synthesized diamides was evaluated as prospective bactericidal agents against representatives of multidrugresistant bacteria, three clinical isolates of MRSA, and Staphylococcus aureus ATCC 29213 (methicillin-susceptible) as the reference and quality control strain. It is of note that based on time-kill assays in the present study, all tested diamides (particularly compound 1f exhibiting rapid bactericidal concentration-dependent effect even at 2x MIC) were most effective against isolate MRSA 63718, which is the strain with elevated vancomycin MIC of 2 g/mL.

title:
  In Vitro Bactericidal Activity of 4- and 5-Chloro-2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides against MRSA

abstract:
  A series of nine substituted 2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides was assessed as prospective bactericidal agents against three clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and S. aureus ATCC 29213 as the reference and quality control strain. The minimum bactericidal concentration was determined by subculturing aliquots from MIC determination onto substance-free agar plates. The bactericidal kinetics of compounds 5-chloro-2-hydroxy-N-[(2S)-3-methyl-1-oxo-1-{[4-(trifluoromethyl)phenyl]amino}butan-2-yl]benzamide (1f), N-{(2S)-1-[(4-bromophenyl)amino]-3-methyl-1-oxobutan-2-yl}-4-chloro-2-hydroxybenzamide (1g), and 4-chloro-N-{(2S)-1-[(3,4-dichlorophenyl)amino]-3-methyl-1-oxobutan-2-yl}-2-hydroxybenzamide (1h) was established by time-kill assay with a final concentration of the compound equal to 1x, 2x, and 4x MIC; aliquots were removed at 0, 4, 6, 8, and 24 h time points. The most potent bactericidal agent was compound 1f exhibiting remarkable rapid concentration-dependent bactericidal effect even at 2x MIC at 4, 6, and 8 h (with a reduction in bacterial count ranging from 3.08 to 3.75 log(10) CFU/mL) and at 4x MIC at 4, 6, 8, and 24 h (5.30 log(10) CFU/mL reduction in bacterial count) after incubation against MRSA 63718. Reliable bactericidal effect against other strains was maintained at 4x MIC at 24 h.


id: cord-001566-kkaxha7d
title: Development of Monoclonal Antibodies in China: Overview and Prospects
author: Zhang, Mao-Yu
date: 2015-02-25
txt: ./txt/cord-001566-kkaxha7d.txt
cache: ./cache/cord-001566-kkaxha7d.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355554/
doi: 10.1155/2015/168935
summary:
  This paper aims to provide a comprehensive review of mAbs development in China through systematic analysis of drug registry, patent applications, clinical trials, academic publication, and ongoing R&D projects. Over the past three decades, monoclonal antibodies (mAbs) have achieved a dramatic development from scientific tools to powerful human therapeutic agents [1] (see Figure 1 ). Development of this class of therapeutic agents started as early as 1980s but achieved no clinical or commercial success until 2002 when adalimumab became the first human mAb approved by the US Food and Drug Administration (FDA) [14] . R&D of mAbs in China began in the 1980s [16] and the first mAb therapeutic agent (Murine Monoclonal Antibody against Human CD3 Antigen of T Lymphocyte for Injection) was introduced in 1999 [17] . This paper aims to provide a comprehensive review of mAb development in China through systematic analysis of product registry, patent application, clinical trials, academic publication, and ongoing R&D projects.

abstract:
  Monoclonal antibodies (mAbs) have become increasingly important as human therapeutic agents. Yet, current research concentrates on technology itself and pays attention to developed countries. This paper aims to provide a comprehensive review of mAbs development in China through systematic analysis of drug registry, patent applications, clinical trials, academic publication, and ongoing R&D projects. The trends in therapeutic areas and industrialization process are also highlighted. Development and research trends of mAbs are analyzed to provide a future perspective of mAbs as therapeutic agents in China.


id: cord-001572-ap4ro5me
title: Hematopoietic Cancer Cell Lines Can Support Replication of Sabin Poliovirus Type 1
author: Oosterhoff, Dinja
date: 2015-02-28
txt: ./txt/cord-001572-ap4ro5me.txt
cache: ./cache/cord-001572-ap4ro5me.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359862/
doi: 10.1155/2015/358462
summary:
  To determine replication kinetics, the susceptible tumor cell lines were infected with Sabin poliovirus type 1 from the parental virus or virus that was passaged for 5 times on the hematopoietic cell lines at MOI 1 or MOI 0.01, and samples of the supernatant and cellular lysates were harvested at different time points. To determine whether hematopoietic cell lines can support replication of Sabin poliovirus type 1, cells were infected with an MOI of 1 and cells together with supernatant were harvested at day 3 (for all virus passages in Vero cells and for passages 3-5 on U937 cells) or day 6 after infection. In the supernatant of all cell lines tested, at day 4, a high virus titer, comparable to Sabin poliovirus type 1 replicated in Vero cells, was observed in the culture medium, indicating that virus replication was efficient during multiple rounds of replication.

abstract:
  Viral vaccines can be produced in adherent or in suspension cells. The objective of this work was to screen human suspension cell lines for the capacity to support viral replication. As the first step, it was investigated whether poliovirus can replicate in such cell lines. Sabin poliovirus type 1 was serially passaged on five human cell lines, HL60, K562, KG1, THP-1, and U937. Sabin type 1 was capable of efficiently replicating in three cell lines (K562, KG1, and U937), yielding high viral titers after replication. Expression of CD155, the poliovirus receptor, did not explain susceptibility to replication, since all cell lines expressed CD155. Furthermore, we showed that passaged virus replicated more efficiently than parental virus in KG1 cells, yielding higher virus titers in the supernatant early after infection. Infection of cell lines at an MOI of 0.01 resulted in high viral titers in the supernatant at day 4. Infection of K562 with passaged Sabin type 1 in a bioreactor system yielded high viral titers in the supernatant. Altogether, these data suggest that K562, KG1, and U937 cell lines are useful for propagation of poliovirus.


id: cord-004269-g6ki6vyy
title: Qualitative Research: Institutional Preparedness During Threats of Infectious Disease Outbreaks
author: de Rooij, Doret
date: 2020-01-23
txt: ./txt/cord-004269-g6ki6vyy.txt
cache: ./cache/cord-004269-g6ki6vyy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6998699/
doi: 10.1155/2020/5861894
summary:
  BACKGROUND: As demonstrated during the global Ebola crisis of 2014–2016, healthcare institutions in high resource settings need support concerning preparedness during threats of infectious disease outbreaks. Second, these triggers informed the design of a phased preparedness system which was tested in a focus group discussion ( RESULTS: Four preparedness phases were identified: preparedness phase green is a situation without the presence of the infectious disease threat that requires centralized care, anywhere in the world. Use of this system by both curative healthcare institutions and the (municipal) public health service, could help to effectively communicate and align preparedness activities during future threats of severe infectious diseases. In the second phase of the focus group, preparedness activities identified in step 1 were presented to representatives of each type of healthcare institution separately. While specific preparedness activities differ between types of healthcare institutions and threat phases, in this study, a uniform enhanced preparedness system has been developed.

abstract:
  BACKGROUND: As demonstrated during the global Ebola crisis of 2014–2016, healthcare institutions in high resource settings need support concerning preparedness during threats of infectious disease outbreaks. This study aimed to exploratively develop a standardized preparedness system to use during unfolding threats of severe infectious diseases. METHODS: A qualitative three-step study among infectious disease prevention and control experts was performed. First, interviews (n = 5) were conducted to identify which factors trigger preparedness activities during an unfolding threat. Second, these triggers informed the design of a phased preparedness system which was tested in a focus group discussion (n = 5) were conducted to identify which factors trigger preparedness activities during an unfolding threat. Second, these triggers informed the design of a phased preparedness system which was tested in a focus group discussion (n = 5) were conducted to identify which factors trigger preparedness activities during an unfolding threat. Second, these triggers informed the design of a phased preparedness system which was tested in a focus group discussion ( RESULTS: Four preparedness phases were identified: preparedness phase green is a situation without the presence of the infectious disease threat that requires centralized care, anywhere in the world. Phase yellow is an outbreak in the world with some likelihood of imported cases. Phase orange is a realistic chance of an unexpected case within the country, or unrest developing among population or staff; phase red is cases admitted to hospitals in the country, potentially causing a shortage of resources. Specific preparedness activities included infection prevention, diagnostics, patient care, staff, and communication. Consensus was reached on the need for the development of a preparedness system and national coordination during threats. CONCLUSIONS: In this study, we developed a standardized system to support institutional preparedness during an increasing threat. Use of this system by both curative healthcare institutions and the (municipal) public health service, could help to effectively communicate and align preparedness activities during future threats of severe infectious diseases.


id: cord-026595-imn2jxcu
author: Qamar, Mariam Khan
date: 2020-06-01
txt: ./txt/cord-026595-imn2jxcu.txt
cache: ./cache/cord-026595-imn2jxcu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285392/
doi: 10.1155/2020/3413087
summary:
  Several studies have been conducted to assess the practices and knowledge of dental students and have demonstrated poor compliance of the students to infection control measures. A study conducted in India to assess the infection control practices among dental students showed that only one-tenth of the respondents adhere to the infection control measures [1] . Similar studies have been conducted worldwide to investigate the knowledge and practices of dental students on infection control [6] [7] [8] [9] [10] [11] [12] [13] [14] , and a general consensus is that students need awareness and must be protected in the unsafe environment. Knowledge, attitudes, and practice regarding infection control measures among dental students in Central India Knowledge, attitudes, and practice of infection control among dental students at Sana''a University Knowledge, attitude and practices about hepatitis B and infection control measures among dental students in Patiala

title:
  What Do the Dental Students Know about Infection Control? A Cross-Sectional Study in a Teaching Hospital, Rawalpindi, Pakistan

abstract:
  BACKGROUND: Dental students are exposed to various infections and infective sources during their training, and on this aspect, their level of knowledge is suboptimal and practices are risky. Therefore, improving their knowledge and practices would contribute significantly to infection control. OBJECTIVE: To ascertain the level of understanding of senior dental students regarding the infection control in the dental practice. METHODS: A cross-sectional study was conducted among dental students (3rd year and 4th year) of the Foundation University Dental College, Pakistan. The sample consisted of 100 third year dental students and 88 fourth year students. A self-administrated questionnaire was used for data collection which consisted of fourteen close-ended items. Frequencies of knowledge, attitudes, and practice were calculated separately by using SPSS 21.0 software. RESULTS: Almost half of the students would not use any antiseptic for sterilizing their hands, and only two-third would ask their patient to use an oral mouth rinse before starting the treatment. Many students did not the optimal temperature of the autoclave for sterilization of the instruments. Only one-third would wear the personal protective equipment during a procedure. Around one-third of the study participants reported that ineffective sterilization during clinical practice can transmit infection from one patient to another. CONCLUSION: Knowledge on infection control among the dental students is though weak, practices are not as per standards but attitudes are positive and encouraging for taking steps and complying with measures on infection control.


id: cord-031416-ytbs95wi
title: A System Biology-Based Approach for Designing Combination Therapy in Cancer Precision Medicine
author: Sabzpoushan, S. H.
date: 2020-08-26
txt: ./txt/cord-031416-ytbs95wi.txt
cache: ./cache/cord-031416-ytbs95wi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7471815/
doi: 10.1155/2020/5072697
summary:
  In this paper, we have used an agent-based stochastic tumor growth model and presented a mathematical and theoretical perspective to cancer therapy. Where precision medicine will allow researchers to predict more accurately which therapies will work better in which groups of people, combination therapy is a keystone of cancer therapy and potentially reduces drug resistance, while simultaneously providing therapeutic anticancer benefits, such as reducing tumor growth and metastatic potential, arresting mitotically active cells, reducing cancer stem cell populations, and inducing apoptosis. In this research, we have used our previously proposed ABSM model [28] as a cancer system, i.e., we may fit it to a given patient and use it for demonstrating our system biology-based approach for designing combination therapy in cancer precision medicine.

abstract:
  In this paper, we have used an agent-based stochastic tumor growth model and presented a mathematical and theoretical perspective to cancer therapy. This perspective can be used to theoretical study of precision medicine and combination therapy in individuals. We have conducted a series of in silico combination therapy experiments. Based on cancer drugs and new findings of cancer biology, we hypothesize relationships between model parameters which in some cases represent individual genome characteristics and cancer drugs, i.e., in our approach, therapy players are delegated by biologically reasonable parameters. In silico experiments showed that combined therapies are more effective when players affect tumor via different mechanisms and have different physical dimensions. This research presents for the first time an algorithm as a theoretical viewpoint for the prediction of effectiveness and classification of therapy sets.


id: cord-259823-ia1g5dt4
author: Gowin, Ewelina
date: 2017-01-15
txt: ./txt/cord-259823-ia1g5dt4.txt
cache: ./cache/cord-259823-ia1g5dt4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28182108/
doi: 10.1155/2017/8037963
summary:
  British, American, and Polish guidelines state that, in children hospitalized due to pneumonia, microbiological examinations should include blood cultures, the detection of the presence of viruses with the use of PCR (Polymerase Chain Reaction) or immunofluorescence in material collected from the nasopharynx (smear or upper respiratory aspirate), the assessment of antibodies against Mycoplasma and Chlamydophila in classes IgM and IgG, and the comparison of antibody levels in the acute phase of the disease and during convalescence [4] [5] [6] . achieved positive results of multiplex real-time PCR tests detecting only viral factors in 76% of cases in a group of children below the age of six with symptoms of respiratory tract infection and the dominant pathogen was RSV [12] .

title:
  Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience

abstract:
  The aim of the study was assessment of the usefulness of multiplex real-time PCR tests in the diagnostic and therapeutic process in children hospitalized due to pneumonia and burdened with comorbidities. Methods. The study group included 97 children hospitalized due to pneumonia at the Karol Jonscher Teaching Hospital in Poznań, in whom multiplex real-time PCR tests (FTD respiratory pathogens 33; fast-track diagnostics) were used. Results. Positive test results of the test were achieved in 74 patients (76.3%). The average age in the group was 56 months. Viruses were detected in 61 samples (82% of all positive results); bacterial factors were found in 29 samples (39% of all positive results). The presence of comorbidities was established in 90 children (92.78%). On the basis of the obtained results, 5 groups of patients were established: viral etiology of infection, 34 patients; bacterial etiology, 7 patients; mixed etiology, 23 patients; pneumocystis, 9 patients; and no etiology diagnosed, 24 patients. Conclusions. Our analysis demonstrated that the participation of viruses in causing severe lung infections is significant in children with comorbidities. Multiplex real-time PCR tests proved to be more useful in establishing the etiology of pneumonia in hospitalized children than the traditional microbiological examinations.


id: cord-261633-r4qlbnc5
title: Defensins and Sepsis
author: Xie, Guo-Hao
date: 2014-08-19
txt: ./txt/cord-261633-r4qlbnc5.txt
cache: ./cache/cord-261633-r4qlbnc5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25210703/
doi: 10.1155/2014/180109
summary:
  The impact of -defensin-2 on the inflammatory response (e.g., the level of ICAM-1 expression), the severity of lung injury, and the sepsis outcome (7-day survival rate) were observed and evaluated. Previous studies showed that single nucleotide polymorphism (SNP) of -defensin-1 gene (DEFB1) correlates with chronic obstructive pulmonary disease, asthma, genetic allergy, HIV infection, and pseudomonas species infection in oral mucosa [38] [39] [40] [41] [42] . Distribution of alleles, gene types, and haplotypes associating with these loci were studied and compared between septic patients and controls, as well as between survivals and victims of severe sepsis. The authors found that patients with high copy number of DEFA1/DEFA3 were predisposed to severe sepsis and tended to have lower level of plasma HNP1-3 as well as cytokines such as TNF-, IL-6, and IL-10.

abstract:
  Sepsis is a leading cause of mortality and morbidity in the critical illness. Multiple immune inflammatory processes take part in the pathogenesis of sepsis. Defensins are endogenous antimicrobial peptides with three disulphide bonds created by six cysteine residues. Besides the intrinsic microbicidal properties, defensins are active players which modulate both innate and adaptive immunity against various infections. Defensins can recruit neutrophils, enhance phagocytosis, chemoattract T cells and dendritic cells, promote complement activation, and induce IL-1β production and pyrotosis. Previous publications have documented that defensins play important roles in a series of immune inflammatory diseases including sepsis. This review aims to briefly summarize in vitro, in vivo, and genetic studies on defensins' effects as well as corresponding mechanisms within sepsis and highlights their promising findings which may be potential targets in future therapies of sepsis.


id: cord-262468-7ddgegb2
author: Deng, Jianqing
date: 2020-07-28
txt: ./txt/cord-262468-7ddgegb2.txt
cache: ./cache/cord-262468-7ddgegb2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32775423/
doi: 10.1155/2020/4691026
summary:
  Furthermore, the multivariate logistic regression models indicated that participants with HHcy had a 2.14-fold higher risk of TAAAs than those with a normal serum tHcy level (adjusted odds ratio (OR), 2.14; 95% confidence interval, 1.00–4.56). Hyperhomocysteinemia (HHcy), defined as an elevated serum total homocysteine (tHcy) level, is associated with atherosclerotic diseases and intracranial aneurysms as well as abdominal aortic aneurysms (AAAs) [7] [8] [9] [10] [11] [12] [13] . Next, we performed a univariable logistic regression analysis to detect the relationship between TAAAs and conventional risk factors including age, sex, smoking and drinking habit, diabetes, hypertension, CAD, ischemic stroke, hyperlipidemia, eGFR, and BMI. After adjustment for confounders, the serum tHcy level was independently associated with the risk of TAAAs in different multivariate logistic regression models (as either a categorical variable or continuous variable).

title:
  The Association between Hyperhomocysteinemia and Thoracoabdominal Aortic Aneurysms in Chinese Population

abstract:
  OBJECTIVE: To shed light on the association between hyperhomocysteinemia (HHcy) and thoracoabdominal aortic aneurysms (TAAAs). METHODS: From July 2013 to March 2017, we conducted a matched case–control study involving individuals who presented to the Chinese People's Liberation Army General Hospital and underwent thoracoabdominal magnetic resonance angiography or computed tomography angiography. A total of 73 patients with TAAAs were enrolled in the case group, and 219 sex-matched subjects without TAAAs were included in the control group. We then examined the relationship between HHcy and TAAAs by logistic regression models and subgroup as well as interaction analyses. RESULTS: Serum total homocysteine (tHcy) concentrations and the proportion of HHcy were significantly higher in the patients with TAAAs than in those without TAAAs (P < 0.001). Furthermore, the multivariate logistic regression models indicated that participants with HHcy had a 2.14-fold higher risk of TAAAs than those with a normal serum tHcy level (adjusted odds ratio (OR), 2.14; 95% confidence interval, 1.00–4.56). Similarly, each 1 μmol/L increase in the serum tHcy concentration was associated with a 4% higher risk of TAAAs (adjusted OR, 1.04; 95% confidence interval, 1.00–1.07). Subgroup analyses indicated that HHcy tended to be associated with a greater risk of TAAAs in all stratified subgroups (adjusted ORs > 1). Furthermore, the interaction analyses revealed no interactive role in the association between HHcy and TAAAs. CONCLUSIONS: The present case–control study suggests that HHcy is an independent risk factor for TAAAs. Larger prospective cohort studies are warranted to validate these findings.


id: cord-265260-n6wm54wz
author: Cuong, Hoang Quoc
date: 2020-09-25
txt: ./txt/cord-265260-n6wm54wz.txt
cache: ./cache/cord-265260-n6wm54wz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2020/7610678
doi: 10.1155/2020/7610678
summary:
  RESULTS: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. CONCLUSIONS: Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. In this study, the assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master showed positive results from a single reaction of triplicate in the three days of 4.8 copies/reaction ( Table 3) . In this study, we reported the comparative analysis of laboratory screening for SARS-CoV-2 among three primer-probe sets in two different master mixes (Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master).

title:
  Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

abstract:
  BACKGROUND: There is a shortage of chemical reagents for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis and a surge of SARS-CoV-2 cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary. METHODS: We compared the ability to screen SARS-CoV-2 among three primer-probe sets in two different master mixes, Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master. RESULTS: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. R squared and amplification efficiency were 0.97 and ranged from 107 to 108%, respectively. CONCLUSIONS: Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. There is a need to consider the combination of these reagent sets as a new strategy to increase the testing capacity of screening programs for COVID-19.


id: cord-271106-srym2kh4
author: De Rosa, Nicoletta
date: 2019-04-11
txt: ./txt/cord-271106-srym2kh4.txt
cache: ./cache/cord-271106-srym2kh4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31111049/
doi: 10.1155/2019/3548396
summary:
  title: Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study In conclusion, the presence of a latent infection causes condylomatosis relapse; in order to reduce the relapse risk an induction of a protective immune response seems to be essential to allow rapid viral clearance from genital areas surrounding lesion and treatment zones. EP and EA dry root extracts seem to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis. Therapy with HPVADL18 is effective in reducing relapse incidence of lesions in patients treated for genital condylomatosis. In conclusion, HPVADL185 seems to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis.

title:
  Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study

abstract:
  Introduction. HPV infection is a highly infectious disease; about 65% of partners of individuals with genital warts will develop genital condylomatosis. Only in 20-30% it regresses spontaneously and relapse rates range deeply (9-80%). Echinacea extracts possess antiviral and immunomodulator activities. The aim of this study was to evaluate the efficacy of the therapy, using a formulation based on HPVADL18® (on dry extracts of 200 mg Echinacea Purpurea (EP) roots plus E. Angustifolia (EA)), on the posttreatment relapse incidence of genital condylomatosis. Materials and Methods. It is a prospective single-arm study. Patients with a satisfactory and positive vulvoscopy, colposcopy, or peniscopy for genital condylomatosis were divided into two random groups and subjected to destructive therapy with Co2 Laser. Group A (N=64) immediately after the laser therapy started a 4-month treatment with oral HPVADL18®; Group B (N=61) did not undergo any additional therapy. Patients were subjected to a follow-up after 1, 6, and 12 months. Differences in relapse incidence between the two groups during follow-up controls were evaluated by χ2-test; the groups were stratified by age, gender, and condylomatosis extension degree. Results and Discussion. Gender, age, and condyloma lesions' extension degree showed no statistically significant differences between the two trial groups. The relapse incidence differs statistically between the two studied groups and progressively decreases during the 12 months after treatment in both groups. Statistically significant reduction of relapse rates has been shown in Group A in patients over 25 years old. This difference is significant for both men and women. The relapse incidence is superior in case of extended condylomatosis. Conclusions. In conclusion, the presence of a latent infection causes condylomatosis relapse; in order to reduce the relapse risk an induction of a protective immune response seems to be essential to allow rapid viral clearance from genital areas surrounding lesion and treatment zones. Echinacea promotes this process. EP and EA dry root extracts seem to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis.


id: cord-274056-9t3kneoo
author: Abd Elwahaab, Marwa A.
date: 2019-05-08
txt: ./txt/cord-274056-9t3kneoo.txt
cache: ./cache/cord-274056-9t3kneoo.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2019/8702968
doi: 10.1155/2019/8702968
summary:
  title: A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector For beta globin protein sequences, seven species are selected in our sample set: human, chimpanzee, gorilla, mouse, rat, gallus, and opossum, as illustrated in Table 1 . The similarity/dissimilarity vectors that are corresponding to beta globin, ND5, and spike protein sequences are illustrated in Tables 9, 10, and 11, respectively, based on the two methods discussed before. The results in Table 10 show that both the magnitude ( 5 ) and the angle ( 5 ) can measure similarity/dissimilarity degree well among ND5 protein sequences as shown in Figure 2 . The similarity/dissimilarity analysis among the seven beta globin sequences measured according to ( 5 ) is illustrated in Table 12 and shown in Figure 4 . The similarity/dissimilarity analysis among the beta globin sequences measured according to (GR spike ) is illustrated in Table 14 and shown in Figure 6 .

title:
  A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector

abstract:
  Similarity/dissimilarity analysis is a key way of understanding the biology of an organism by knowing the origin of the new genes/sequences. Sequence data are grouped in terms of biological relationships. The number of sequences related to any group is susceptible to be increased every day. All the present alignment-free methods approve the utility of their approaches by producing a similarity/dissimilarity matrix. Although this matrix is clear, it measures the degree of similarity among sequences individually. In our work, a representative of each of three groups of protein sequences is introduced. A similarity/dissimilarity vector is evaluated instead of the ordinary similarity/dissimilarity matrix based on the group representative. The approach is applied on three selected groups of protein sequences: beta globin, NADH dehydrogenase subunit 5 (ND5), and spike protein sequences. A cross-grouping comparison is produced to ensure the singularity of each group. A qualitative comparison between our approach, previous articles, and the phylogenetic tree of these protein sequences proved the utility of our approach.


id: cord-279528-41atidai
title: Measuring Similarity among Protein Sequences Using a New Descriptor
author: Abo-Elkhier, Mervat M.
date: 2019-11-22
txt: ./txt/cord-279528-41atidai.txt
cache: ./cache/cord-279528-41atidai.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31886192/
doi: 10.1155/2019/2796971
summary:
  Each amino acid in the protein sequence is represented by a number, and a new 2D graphical representation is suggested. A new descriptor is introduced, comprising a vector composed of the mean and standard deviation of the total numbers of each protein sequence (A t , SA t ). e 2D graphical representation for human, chimpanzee, and opossum beta globin protein sequences is illustrated in e 2D graphical representation of TGEVG from class I and GD03T0013 from SARS_CoV protein sequences is illustrated in Figures 4(a) and 4(b) respectively. A new descriptor for protein sequences is suggested, which is a vector composed of the arithmetic mean A t and standard deviation SA t of the combined intensity level value A t (i) of the protein sequence. F-Curve, a graphical representation of protein sequences for similarity analysis based on physicochemical properties of amino acids

abstract:
  The comparison of protein sequences according to similarity is a fundamental aspect of today's biomedical research. With the developments of sequencing technologies, a large number of protein sequences increase exponentially in the public databases. Famous sequences' comparison methods are alignment based. They generally give excellent results when the sequences under study are closely related and they are time consuming. Herein, a new alignment-free method is introduced. Our technique depends on a new graphical representation and descriptor. The graphical representation of protein sequence is a simple way to visualize protein sequences. The descriptor compresses the primary sequence into a single vector composed of only two values. Our approach gives good results with both short and long sequences within a little computation time. It is applied on nine beta globin, nine ND5 (NADH dehydrogenase subunit 5), and 24 spike protein sequences. Correlation and significance analyses are also introduced to compare our similarity/dissimilarity results with others' approaches, results, and sequence homology.


id: cord-280908-o1z4ka3r
author: Vieira, Sandra E.
date: 2017-05-24
txt: ./txt/cord-280908-o1z4ka3r.txt
cache: ./cache/cord-280908-o1z4ka3r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28626754/
doi: 10.1155/2017/3459785
summary:
  To our knowledge, this is the first report to perform an analysis of the association between clinical features and genotypes in infections caused by HRSV A ON1 in the southeast region of Brazil. The comparative clinical analyses included 32 infants with a HRSV single infection (22 AON1 and 10 other genotypes) and showed no significant differences between these subgroups (Table 1 ). The present study showed the strong predominance of HRSV infections in infants hospitalized with bronchiolitis, predominance of the HRSVA ON1 genotype, and occurrence of the NA1 and NA2 genotypes, previously unidentified in southeast region of Brazil. These results need to be confirmed by more extensive analyses but are consistent with a previous German study that found no clinical differences between infections by other HRSV genotypes [17] . Genetic variability of human respiratory syncytial virus a strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication

title:
  Infections Caused by HRSV A ON1 Are Predominant among Hospitalized Infants with Bronchiolitis in São Paulo City

abstract:
  Human respiratory syncytial virus is the main cause of respiratory infections in infants. Several HRSV genotypes have been described. Goals. To describe the main genotypes that caused infections in São Paulo (2013–2015) and to analyze their clinical/epidemiological features. Methods. 94 infants (0–6 months) with bronchiolitis were studied. Clinical/epidemiological information was collected; a search for 16 viruses in nasopharyngeal secretion (PCR-real-time and conventional, sequencing, and phylogenetic analyses) was performed. Results. The mean age was 2.4 m; 48% were male. The mean length of hospital stay was 4.4 d (14% in the Intensive Care Unit). The positive rate of respiratory virus was 98.9%; 73 cases (77.6%) were HRSV (76,7% HRSVA). HRSVA formed three clusters: ON1 (n = 34), NA1 (n = 1), and NA2 (n = 4). All HRSVB were found to cluster in the BA genotype (BA9-n = 10; BA10-n = 3). Clinical analyses showed no significant differences between the genotype AON1 and other genotypes. Conclusion. This study showed a high rate of HRSV detection in bronchiolitis. HRSVA ON1, which has recently been described in other countries and has not been identified in previous studies in the southeast region of Brazil, was predominant. The clinical characteristics of the infants that were infected with AON1 were similar to infants with infections by other genotypes.


id: cord-283092-t3yqsac3
title: Qualitative Analysis of a Mathematical Model in the Time of COVID-19
author: Shah, Kamal
date: 2020-05-25
txt: ./txt/cord-283092-t3yqsac3.txt
cache: ./cache/cord-283092-t3yqsac3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32596319/
doi: 10.1155/2020/5098598
summary:
  In this article, a qualitative analysis of the mathematical model of novel corona virus named COVID-19 under nonsingular derivative of fractional order is considered. Under the new nonsingular derivative, we, first of all, establish some sufficient conditions for existence and uniqueness of solution to the model under consideration. For the semianalytical results, we extend the usual Laplace transform coupled with Adomian decomposition method to obtain the approximate solutions for the corresponding compartments of the considered model. From Figure 1 , we see that at when the rate of healthy immigrants is zero, it means that protection rate is increasing and hence the population of infected class is decreasing while the population of healthy class is increasing at different rates due to fractional order derivative by evaluating the solution up to twenty terms via using MATAB.

abstract:
  In this article, a qualitative analysis of the mathematical model of novel corona virus named COVID-19 under nonsingular derivative of fractional order is considered. The concerned model is composed of two compartments, namely, healthy and infected. Under the new nonsingular derivative, we, first of all, establish some sufficient conditions for existence and uniqueness of solution to the model under consideration. Because of the dynamics of the phenomenon when described by a mathematical model, its existence must be guaranteed. Therefore, via using the classical fixed point theory, we establish the required results. Also, we present the results of stability of Ulam's type by using the tools of nonlinear analysis. For the semianalytical results, we extend the usual Laplace transform coupled with Adomian decomposition method to obtain the approximate solutions for the corresponding compartments of the considered model. Finally, in order to support our study, graphical interpretations are provided to illustrate the results by using some numerical values for the corresponding parameters of the model.


id: cord-293503-e7be12qb
title: CT Findings in a Novel Coronavirus Disease (COVID-19) Pneumonia at Initial Presentation
author: Xiang, Chao
date: 2020-08-15
txt: ./txt/cord-293503-e7be12qb.txt
cache: ./cache/cord-293503-e7be12qb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32851078/
doi: 10.1155/2020/5436025
summary:
  COVID-19 leads to respiratory infections similar to those of SARS and MERS, causing pneumonia, severe acute respiratory syndrome, kidney failure, and even death. The CT image characteristics were recorded as follows: (a) lesion''s location (segment), (b) morphology (patchy, nodular, and linear), (c) distribution (single or multiple, peripheral or/and central), (d) type (ground-glass opacity, consolidation, and linear opacity), (e) pattern (reticulation, parenchymal bands, crazy-paving, and interlobular thickening), (f) atelectasis, (g) cavitation, (h) pleural effusion, (i) hilar or mediastinal lymphadenopathy, (j) bronchiectasis, and (k) air bronchogram. Although a patient with exposure history may be asymptomatic and obtained negative results of CT findings and viral nucleic acid test at initial presentation, the potential infection cannot be totally excluded, and performing repeating CT scan and coronavirus RNA test is needed. Ground-glass opacity and consolidation with multiple, bilateral, and lower lobe distribution are the main features of COVID-19 pneumonia at initial CT scan.

abstract:
  BACKGROUND: COVID-19 first broke out in China and spread rapidly over the world. OBJECTIVES: To describe the CT features of COVID-19 pneumonia and to share our experience at initial diagnoses. Patients and Methods. Data from 53 patients (31 men, 22 women; mean age, 53 years; age range, 16-83 years) with confirmed COVID-19 pneumonia were collected. Their complete clinical data was reviewed, and their CT features were recorded and analyzed. RESULTS: The average time between onset of illness and the initial CT scan was six days (range, 1-42 days). A total of 399 segments were involved and distributed bilaterally (left lung: 186 segments [46.6%], right lung: 213 segments [53.4%]) and peripherally (38 [71.7%] patients). Multiple lobes (45 [84.9%]) and bilateral lower lobes (left lower lobe: 104 [26.1%], right lower lobe: 107 [26.8%], and total: 211 [52.9%]) were the most commonly involved. Ground-glass opacity with consolidation (24 [45.3%]) and pure ground-glass opacity (28 [52.8%]) were the main findings. The other findings were crazy-paving (14 [26.4%]), bronchiectasis (12 [22.6%]), atelectasis (7 [13.2%]), parenchymal bands (6 [11.3%]), air bronchogram (6 [11.3%]), interlobular thickening (5 [9.4%]), reticular pattern (1 [1.9%]), and pleural effusion (1 [1.9%]). CONCLUSIONS: Most COVID-19 pneumonia patients had abnormalities on chest CT images at initial presentation. Imaging features combined with patient's exposure history and onset symptoms could facilitate the identification of the suspected patient for further examinations.


id: cord-296033-5zyoddl7
author: Hu, Xiaoliang
date: 2017-10-23
txt: ./txt/cord-296033-5zyoddl7.txt
cache: ./cache/cord-296033-5zyoddl7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2017/7089091
doi: 10.1155/2017/7089091
summary:
  Coronaviruses (CoVs), such as human coronavirus NL63 (HCoV-NL63), severe acute respiratory syndrome CoV (SARS-CoV), murine hepatitis virus (MHV), porcine epidemic diarrhea virus (PEDV), and Middle East Respiratory Syndrome Coronavirus (MERS-CoV), encode papain-like (PL) proteases that inhibit Sendai virus(SeV-) induced interferon (IFN-β) production. Furthermore, TGEV PL1 exerted deubiquitinase (DUB) activity which strongly inhibited the retinoic acid-induced gene I(RIG-1-) and stimulator of interferon gene(STING-) dependent IFN expression. In the present study, we found that TGEV PL1 encoded by the replicase gene could suppress the IFN-expression and inhibit the nuclear translocation of interferon regulatory factor 3 (IRF3) and exerted deubiquitinase (DUB) activity which strongly inhibited the retinoic acid-induced gene I-(RIG-1-) and stimulator of interferon gene-(STING-) dependent IFN expression. We observed the inhibition of SeV-induced IFN-promoter activation in the presence of PL1, similar to the antagonistic function of NL63 PLP2 and porcine epidemic diarrhea virus (PEDV) PLP2, clearly indicating that TGEV PL1 could act as an interferon antagonist.

title:
  Transmissible Gastroenteritis Virus Papain-Like Protease 1 Antagonizes Production of Interferon-β through Its Deubiquitinase Activity

abstract:
  Coronaviruses (CoVs), such as human coronavirus NL63 (HCoV-NL63), severe acute respiratory syndrome CoV (SARS-CoV), murine hepatitis virus (MHV), porcine epidemic diarrhea virus (PEDV), and Middle East Respiratory Syndrome Coronavirus (MERS-CoV), encode papain-like (PL) proteases that inhibit Sendai virus- (SeV-) induced interferon (IFN-β) production. Recently, the crystal structure of transmissible gastroenteritis virus (TGEV) PL1 has been solved, which was similar to that of SARS-CoV PL2(pro), which may antagonize host innate immunity. However, very little is known about whether TGEV PL1 can antagonize host innate immune response. Here, we presented evidence that TGEV PL1 encoded by the replicase gene could suppress the IFN-β expression and inhibit the nuclear translocation of interferon regulatory factor 3 (IRF3). The ability to antagonize IFN-β production was dependent on the intact catalytic activity of PL1. Furthermore, TGEV PL1 exerted deubiquitinase (DUB) activity which strongly inhibited the retinoic acid-induced gene I- (RIG-1-) and stimulator of interferon gene- (STING-) dependent IFN expression. Our data collectively suggest that TGEV PL1 can inhibit the IFN-β expression and interfere with RIG-1- and STING-mediated signaling through a viral DUB activity. Our study has yielded strong evidence for the TGEV PL1 mechanisms that counteract the host innate immunity.


id: cord-296682-ugffeegr
title: A Comprehensive Review of Cutaneous Manifestations Associated with COVID-19
author: Rahimi, Hoda
date: 2020-07-05
txt: ./txt/cord-296682-ugffeegr.txt
cache: ./cache/cord-296682-ugffeegr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32724793/
doi: 10.1155/2020/1236520
summary:
  In this article, all reported cases to date were collected and classified under 6 major groups: maculopapular rash, urticaria, chilblain, vesicular lesions, livedo reticularis, and petechiae. All articles including case reports and original articles from the emergence of the disease (31 December 2019) to the submission of the article (9 May 2020) were included except for one article in which all 6 cases had neither positive PCR test nor common symptoms of COVID-19, and the authors presumed that their cutaneous manifestations may be related to SARS-CoV-2 without any documented evidence [6] . Although the appearance of skin rash in the prodromal phase or asymptomatic carriers was scarce, it is of great importance for all clinicians to keep in mind that cutaneous lesions might be the only symptom of COVID-19, as it would contribute to sooner diagnosis and management of the patients/carriers and better control of the disease spreading.

abstract:
  The novel coronavirus (SARS-CoV-2), the cause of coronavirus 2019 disease (COVID-19) pandemic, is associated with some cutaneous manifestations. Although the cutaneous presentations of COVID-19 are infrequent, it is of great importance for all clinicians to be aware of these manifestations, as it may contribute to sooner and better diagnosis and management of the disease, even in asymptomatic or paucisymptomatic patients. The reported cutaneous manifestations of COVID-19 are various, dispersed, and sometimes confusing. In this article, all reported cases to date were collected and classified under 6 major groups: maculopapular rash, urticaria, chilblain, vesicular lesions, livedo reticularis, and petechiae. Different characteristics of each group were discussed in detail as well.


id: cord-298185-w37nvorf
author: Cao, Kai
date: 2020-10-24
txt: ./txt/cord-298185-w37nvorf.txt
cache: ./cache/cord-298185-w37nvorf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33134387/
doi: 10.1155/2020/7605453
summary:
  OBJECTIVE: To estimate the prevalence rate of ocular symptoms and the positive rate of conjunctival swab samples of patients diagnosed with 2019 Novel Coronavirus Disease (COVID-19). Most importantly, we extracted the number of events of ocular symptoms (conjunctivitis/conjunctival congestion, foreign body sensation, increased secretion, and eye itching) and the number of positive viral RNA detections in conjunctival swab samples. The pooled prevalence rates of ocular symptoms, such as conjunctivitis/conjunctival congestion, were expressed using proportions with 95% confidence intervals (CIs) estimated from either a fixed-effect model or a random-effect model. The strength of our study is that it is the first meta-analysis to summarize the rapidly emerging yet controversial publications reporting the prevalence rates of ocular symptoms and the positive rate of conjunctival swab samples in COVID-19 patients.

title:
  Current Evidence of 2019 Novel Coronavirus Disease (COVID-19) Ocular Transmission: A Systematic Review and Meta-Analysis

abstract:
  OBJECTIVE: To estimate the prevalence rate of ocular symptoms and the positive rate of conjunctival swab samples of patients diagnosed with 2019 Novel Coronavirus Disease (COVID-19). METHODS: We performed a systematic review and meta-analysis. A comprehensive literature search was done based on PubMed, Embase, MedRxiv, and the Cochrane Library. The primary outcomes are the prevalence rate of conjunctivitis/conjunctival congestion and the positive rate of conjunctival swab samples. Rates were expressed as proportions with 95% confidence intervals (CIs). RESULTS: A total of 12 studies with 1930 participants were included for meta-analysis. The pooled prevalence rate of conjunctivitis/conjunctival congestion was 8% (95% CI: 5%-12%). 1% (95% CI: 1%-4%) of COVID-19 patients were diagnosed with conjunctivitis/conjunctival congestion as the initial symptom. The pooled positive rate of conjunctival swab samples was 3% (95% CI: 2%-5%). We also assessed other ocular symptoms reported in the 12 studies, including foreign body sensation, increased secretion, and eye itching. The pooled prevalence rates were 6% (95% CI: 3%-10%), 10% (95% CI: 8%-12%), and 9% (95% CI: 7%-10%), respectively. CONCLUSIONS: The evidence on the positive rate of conjunctival swab samples and the prevalence rates of ocular symptoms indicated that COVID-19 ocular transmission was possible but less likely.


id: cord-299552-rgrm8dil
title: Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics?
author: Bianchi, Martina
date: 2020-05-30
txt: ./txt/cord-299552-rgrm8dil.txt
cache: ./cache/cord-299552-rgrm8dil.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32596311/
doi: 10.1155/2020/4389089
summary:
  In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. In this report, a structural comparison between the Sars-CoV-2 surface proteins from different isolates with homologous proteins from closely related viruses such as those from Bat and Pangolin is described. Sars-CoV-2 E sequences differ from the homologous proteins also at positions 55-56, where the dyad Ser-Phe replaces Thr-Val (except in Bat coronavirus isolate BtKY72, accession code KY352407). In this paper, E and M proteins from 797 Sars-CoV-2 genomes have been compared to the counterparts taken from the most closely related virus also to evaluate the potential role of amino acid mutations in the epizootic origin of COVID-19.

abstract:
  The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. The analyses here reported show the high structural similarity of Envelope and Membrane proteins to the counterparts from Pangolin and Bat coronavirus isolates. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. Structural modelling has been applied to map the variant sites onto the predicted three-dimensional structure of the Envelope and Membrane proteins.


id: cord-300944-c57impca
author: Huang, Xiaolan
date: 2013-11-04
txt: ./txt/cord-300944-c57impca.txt
cache: ./cache/cord-300944-c57impca.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2013/984028
doi: 10.1155/2013/984028
summary:
  Programmed −1 ribosomal frameshifting (PRF) and stop codon readthrough are two translational recoding mechanisms utilized by some RNA viruses to express their structural and enzymatic proteins at a defined ratio. Among the 31 detected pseudoknots, the established −1 frameshift stimulating pseudoknot at the gag-pro junction [25, 43] is identified as the most stable pseudoknot as BioMed Research International 5 judged by the lowest calculated free energy of −33.7 kcal/mol (Table 1) . While pseudoknots were detected shortly downstream from the frame-shift or read-through sites in most of the viral sequences using the default ranges of stem and loop lengths, the default search did miss some known cases, such as the frameshift stimulator pseudoknot in human coronavirus 229E that has a 164 nt L2. "Rank" indicates the relative ranking (according to the calculated free energy of the stems) of the frameshift/readthrough stimulating pseudoknots among all possible pseudoknots detected within the full-length genomic RNAs.

title:
  A Genome-Wide Analysis of RNA Pseudoknots That Stimulate Efficient −1 Ribosomal Frameshifting or Readthrough in Animal Viruses

abstract:
  Programmed −1 ribosomal frameshifting (PRF) and stop codon readthrough are two translational recoding mechanisms utilized by some RNA viruses to express their structural and enzymatic proteins at a defined ratio. Efficient recoding usually requires an RNA pseudoknot located several nucleotides downstream from the recoding site. To assess the strategic importance of the recoding pseudoknots, we have carried out a large scale genome-wide analysis in which we used an in-house developed program to detect all possible H-type pseudoknots within the genomic mRNAs of 81 animal viruses. Pseudoknots are detected downstream from ~85% of the recoding sites, including many previously unknown pseudoknots. ~78% of the recoding pseudoknots are the most stable pseudoknot within the viral genomes. However, they are not as strong as some designed pseudoknots that exhibit roadblocking effect on the translating ribosome. Strong roadblocking pseudoknots are not detected within the viral genomes. These results indicate that the decoding pseudoknots have evolved to possess optimal stability for efficient recoding. We also found that the sequence at the gag-pol frameshift junction of HIV1 harbors potential elaborated pseudoknots encompassing the frameshift site. A novel mechanism is proposed for possible involvement of the elaborated pseudoknots in the HIV1 PRF event.


id: cord-303978-z3888e3g
author: Hong, Ka Lok
date: 2015-06-23
txt: ./txt/cord-303978-z3888e3g.txt
cache: ./cache/cord-303978-z3888e3g.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2015/419318
doi: 10.1155/2015/419318
summary:
  Multiple virulent strains of the gram-negative bacteria, Escherichia coli, have been chosen as targets for the selection of specific ssDNA MREs due to their enterotoxigenic effects and the potential of contaminating food and water [39] . They also developed a sandwich detection system, in which biotinylated antibodies targeting the K88 strain were immobilized on magnetic beads as the capturing element and the 5 FITC labeled ssDNA library from round 13 selection served as the reporter in a fluorescent assay. In their later study, the affinities of selected candidate MREs were improved with reported values of in the nanomolar range and were specific for the target bacteria at different growth phases [57] . Acetamiprid Immobilization free 4.98 M -[27] Fluorescence plate based cross-binding assay showed the ssDNA MRE was approximately two to five times more selective on the alpha toxin than negative targets.

title:
  Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications

abstract:
  Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed.


id: cord-306411-dutbxfl4
author: Eifan, Saleh A.
date: 2017-11-21
txt: ./txt/cord-306411-dutbxfl4.txt
cache: ./cache/cord-306411-dutbxfl4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29359144/
doi: 10.1155/2017/1928795
summary:
  title: Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital This retrospective cohort study aimed to determine the etiological agents responsible for respiratory tract infections by Anyplex II RV16 detection kit (RV16, Seegene), involving 2266 pediatric patients with respiratory infections admitted to the Department of Pediatrics at King Abdul-Aziz Medical City, Ministry of National Guard, Riyadh, from July 2014 to June 2015. Different studies reported the detection of viruses like human respiratory syncytial virus A (RSV A), human respiratory syncytial virus B (RSV B), human adenovirus (AdV), Human metapneumovirus (HMPV), human coronavirus, and human parainfluenza virus (PIV). This study aimed to determine the distribution of 16 different viruses causing respiratory infections in children, by using RV16, and to compare data on demographic characteristics, symptoms, and single infections or coinfections.

title:
  Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital

abstract:
  Respiratory infections are caused by an array of viruses, and limited information is available about viral coexistence, comparative symptoms, and the burden of illness. This retrospective cohort study aimed to determine the etiological agents responsible for respiratory tract infections by Anyplex II RV16 detection kit (RV16, Seegene), involving 2266 pediatric patients with respiratory infections admitted to the Department of Pediatrics at King Abdul-Aziz Medical City, Ministry of National Guard, Riyadh, from July 2014 to June 2015. The most frequent respiratory infections were recorded in the 1 to 5 year age group (44.7%). Rhinovirus (32.5%), Adenovirus (16.9%), and Respiratory syncytial virus (RSV) B (10.4%) were most common. In single viral infections, Rhinovirus (41.2%), Metapneumovirus (15.3%), and Bocavirus (13.7%) were most frequent. In multiple viral infections, Rhinovirus (36.7%), Adenovirus (35.2%), Bocavirus (11.2), RSV B (7.8%), and RSV A (6.7%) were most frequent. No significant difference was observed in clinical presentations; however, rhinorrhea and hypodynamia were significantly associated with viral respiratory infections. Most respiratory viral pathogens peaked during December, January, March, and April. Rhinovirus, Adenovirus, and Bocavirus circulations were detected throughout the year. Winter peaks were recorded for Rhinovirus, RSV B, Adenovirus, and RSV A, whereas the Metapneumovirus, and the Bocavirus peaked in March and April. These findings enhance understanding of viral etiology and distribution to improve respiratory infection management and treatment.


id: cord-309319-si5c14e8
title: Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China
author: Cao, Chunxiang
date: 2016-08-15
txt: ./txt/cord-309319-si5c14e8.txt
cache: ./cache/cord-309319-si5c14e8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27597972/
doi: 10.1155/2016/7247983
summary:
  Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The Bayesian Maximum Entropy (BME) approach of modern geostatistics incorporates higher-order statistical estimation for space-time epidemic phenomena and has shown more accurate mapping results than those derived from linear kriging geostatistics [19] . BME provides an effective stochastic method, based on a cogent theoretical and technological strategy, to analyze relationships of SARS outbreaks in the composite space-time domain. (2) BME considers spatial heterogeneity in SARS outbreaks, which broadens the traditional epidemic research field from the temporal to space-time domain. In the case of the SARS outbreaks, we used the observations to explore general structural characteristics of the SARS S/TRF, that is, the existence of mean (or surface) trends in the space-time domain, and to explore the underlying temporal and spatial structure of the S/TRF with suitable covariance functions.

abstract:
  Severe acute respiratory syndrome (SARS) is one of the most severe emerging infectious diseases of the 21st century so far. SARS caused a pandemic that spread throughout mainland China for 7 months, infecting 5318 persons in 194 administrative regions. Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The BME reveals that SARS outbreaks show autocorrelation within certain spatial and temporal distances. We use BME to fit a theoretical covariance model that has a sine hole spatial component and exponential temporal component and obtain the weights of geographical and temporal autocorrelation factors. Using the covariance model, SARS dynamics were estimated and simulated under the most probable conditions. Our study suggests that SARS transmission varies in its epidemiological characteristics and SARS outbreak distributions exhibit palpable clusters on both spatial and temporal scales. In addition, the BME modelling demonstrates that SARS transmission features are affected by spatial heterogeneity, so we analyze potential causes. This may benefit epidemiological control of pandemic infectious diseases.


id: cord-311625-d7iycdyh
author: Choong, Oi Kuan
date: 2014-02-20
txt: ./txt/cord-311625-d7iycdyh.txt
cache: ./cache/cord-311625-d7iycdyh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24707494/
doi: 10.1155/2014/654712
summary:
  The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log(10) from 10(14) in the virus-inoculated cells to 10(9) in the circular TFO RNAs-transfected cells. The data analyzed by one-way ANOVA, Tukey post hoc test showed significant high viral RNA genome copy number of 4.03 × 10 14 for virus inoculated cells as compared to circular TFO1, TFO3, TFO4, and TFO5 treatments ( ≤ 0.05). In this study, circular Triple Helix Forming Oligonucleotide (TFO) RNAs, specifically targeting the short regions of viral genome for triplex formation, were designed and evaluated.

title:
  In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication

abstract:
  Feline Infectious Peritonitis (FIP) is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV), a virulent mutant strain of Feline Enteric Coronavirus (FECV). Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log(10) from 10(14) in the virus-inoculated cells to 10(9) in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection.


id: cord-316181-ccauw70y
title: Radix Bupleuri: A Review of Traditional Uses, Botany, Phytochemistry, Pharmacology, and Toxicology
author: Yang, Fude
date: 2017-05-16
txt: ./txt/cord-316181-ccauw70y.txt
cache: ./cache/cord-316181-ccauw70y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28593176/
doi: 10.1155/2017/7597596
summary:
  Crude extracts and pure compounds isolated from Radix Bupleuri exhibited various biological activities, such as anti-inflammatory, anticancer, antipyretic, antimicrobial, antiviral, hepatoprotective, neuroprotective, and immunomodulatory effects. Pharmacokinetic studies have demonstrated that the major bioactive compounds (saikosaponins a, b(2), c, and d) were absorbed rapidly in rats after oral administration of the extract of Radix Bupleuri. Triterpenoid saponins are the main active components of Radix Bupleuri, which exhibit a broad spectrum of biological and pharmacological effects, including analgesic, immunomodulatory, hepatoprotective, immunomodulatory, anti-inflammatory, antitumor, and antiviral activities [3, [41] [42] [43] . reported that saikosaponins from Radix Bupleuri exhibited anti-inflammatory activity on inflammatory processes including inhibition of inflammatory exudation, capillary permeability, inflammatory mediators release, migration of white cells, connective tissue hyperplasia, and a variety of allergic inflammation [67] . Saponins isolated from Radix Bupleuri also exhibited significantly anti-proliferative activity in human non-small cell lung cancer A549 cells through Fas-dependent apoptotic pathway [80] .

abstract:
  Radix Bupleuri (Chaihu) has been used as a traditional medicine for more than 2000 years in China, Japan, Korea, and other Asian countries. Phytochemical studies demonstrated that this plant contains essential oils, triterpenoid saponins, polyacetylenes, flavonoids, lignans, fatty acids, and sterols. Crude extracts and pure compounds isolated from Radix Bupleuri exhibited various biological activities, such as anti-inflammatory, anticancer, antipyretic, antimicrobial, antiviral, hepatoprotective, neuroprotective, and immunomodulatory effects. However, Radix Bupleuri could also lead to hepatotoxicity, particularly in high doses and with long-term use. Pharmacokinetic studies have demonstrated that the major bioactive compounds (saikosaponins a, b(2), c, and d) were absorbed rapidly in rats after oral administration of the extract of Radix Bupleuri. This review aims to comprehensively summarize the traditional uses, botany, phytochemistry, pharmacology, toxicology, and pharmacokinetics of Radix Bupleuri reported to date with an emphasis on its biological properties and mechanisms of action.


id: cord-319635-kh99n7q2
title: Cell Type-Dependent RNA Recombination Frequency in the Japanese Encephalitis Virus
author: Chiang, Wei-Wei
date: 2014-07-22
txt: ./txt/cord-319635-kh99n7q2.txt
cache: ./cache/cord-319635-kh99n7q2.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2014/471323
doi: 10.1155/2014/471323
summary:
  Such cleaved small RNA fragments may be further degraded through an RNA interference pathway triggered by viral double-stranded RNA during replication in mosquito cells, resulting in a lower frequency of RNA recombination in mosquito cells compared to that which occurs in mammalian cells. Yates'' chi-square test was used to assess the frequency of RNA recombination in cells coinfected by two virus strains or transfected by viral RNA fragments. Two and one recombinant form(s) were, respectively, identified in selected samples from BHK-21 and C6/36 cells, when they were coinfected with the T1P1-S1 and CJN-S1 strains of the Japanese encephalitis virus. As in our previous report, different strains of the JEV can coinfect host cells derived from mosquitoes or mammals [25] , which actually generates recombinant forms of the virus [30] . In this study, we infected host cells with Nakayama strains of the JEV, followed by transfection of the (+)5 3 -UTR-I RNA fragment.

abstract:
  Japanese encephalitis virus (JEV) is one of approximately 70 flaviviruses, frequently causing symptoms involving the central nervous system. Mutations of its genomic RNA frequently occur during viral replication, which is believed to be a force contributing to viral evolution. Nevertheless, accumulating evidences show that some JEV strains may have actually arisen from RNA recombination between genetically different populations of the virus. We have demonstrated that RNA recombination in JEV occurs unequally in different cell types. In the present study, viral RNA fragments transfected into as well as viral RNAs synthesized in mosquito cells were shown not to be stable, especially in the early phase of infection possibly via cleavage by exoribonuclease. Such cleaved small RNA fragments may be further degraded through an RNA interference pathway triggered by viral double-stranded RNA during replication in mosquito cells, resulting in a lower frequency of RNA recombination in mosquito cells compared to that which occurs in mammalian cells. In fact, adjustment of viral RNA to an appropriately lower level in mosquito cells prevents overgrowth of the virus and is beneficial for cells to survive the infection. Our findings may also account for the slower evolution of arboviruses as reported previously.


id: cord-321953-yql6gpd3
author: Barrera, Maritza
date: 2017-12-12
txt: ./txt/cord-321953-yql6gpd3.txt
cache: ./cache/cord-321953-yql6gpd3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29379796/
doi: 10.1155/2017/2978718
summary:
  Therefore, this report was conducted using the complete sequence of the S gene and powerful Bayesian phylogeographic reconstructions to clarify the putative origin of PEDV in Ecuador, revealing the wide expansion of the emergent PEDV strains, which caused the first PEDV outbreak in this country. To perform sequence comparison analyses and to establish the phylogenetic relationships of PEDV sequence from Ecuador, alignments using the consensus sequence of complete S gene available at GenBank database (Supplementary Information Table S1 ) were conducted by the algorithm ClustalW included in the program BioEdit Sequence Alignment Editor [33] . The phylogeographic study revealed the emergence of the Chinese PEDV strains followed by spreading to US in 2013 (Figures 3(a) and 3(b), Supplementary Material Video S1). Complete genome sequence of a porcine epidemic diarrhea S gene indel strain isolated in France in

title:
  Tracking the Origin and Deciphering the Phylogenetic Relationship of Porcine Epidemic Diarrhea Virus in Ecuador

abstract:
  In 2010, new Chinese strains of porcine epidemic diarrhea virus (PEDV), clinically more severe than the classical strains, emerged. These strains were spread to United States in 2013 through an intercontinental transmission from China with further spreading across the world, evidencing the emergent nature of these strains. In the present study, an analysis of PEDV field sequences from Ecuador was conducted by comparing all the PEDV S gene sequences available in the GenBank database. Phylogenetic comparisons and Bayesian phylogeographic inference based on complete S gene sequences were also conducted to track the origin and putative route of PEDV. The sequence from the PED-outbreak in Ecuador was grouped into the clade II of PEDV genogroup 2a together with other sequences of isolates from Mexico, Canada, and United States. The phylogeographic study revealed the emergence of the Chinese PEDV strains, followed by spreading to US in 2013, from US to Korea, and later the introduction of PEDV to Canada, Mexico, and Ecuador directly from the US. The sources of imports of live swine in Ecuador in 2014 were mainly from Chile and US. Thus, this movement of pigs is suggested as the main way for introducing PEDV to Ecuador.


id: cord-330276-qvmhuid3
author: Giorgi, Gabriele
date: 2020-06-19
txt: ./txt/cord-330276-qvmhuid3.txt
cache: ./cache/cord-330276-qvmhuid3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32685446/
doi: 10.1155/2020/1863153
abstract: nan
summary:
  [1] , trauma and diseases related to stress and mental health that originate in the workplace may have a different pattern of development or require an organization-centered treatment approach, including field and intervention studies. With regard to promoting safe and secure working environments to create a decent work for all, some papers published in this special issue introduce advances in measuring psychosocial risk factors, mental health, and work-related issues. They found that ward type predicted the level of work arduousness beyond other factors such as age or gender, suggesting that trauma and diseases related to stress and mental health that originate in the workplace may have a different pattern of development or require an organizationcentered treatment approach that complements the personcentered approach derived from research conducted in clinical and psychiatric contexts. Addressing risks: mental health, work-related stress, and occupational disease management to enhance wellbeing

title:
  Addressing Risks: Mental Health, Work-Related Stress, and Occupational Disease Management to Enhance Well-Being 2019


id: cord-330602-g0xaonxv
author: Sugiura, Hiroaki
date: 2013-02-07
txt: ./txt/cord-330602-g0xaonxv.txt
cache: ./cache/cord-330602-g0xaonxv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2013/746053
doi: 10.1155/2013/746053
summary:
  Japanese traditional surveillance is based on definitive diagnosis and is enforced by the infection control laws in Japan for the early detection of agents of bioterrorism and outbreaks of emerging infectious diseases. The purpose of the present study was to evaluate whether the PCR method triggered by the results of the prescription surveillance system can rapidly and accurately identify causative pathogens of local outbreaks of infection. Between October 4 and 28, 2011, 50 patients were included in the present study who either presented at a single clinic with a chief complaint of respiratory symptoms or fever or were suspected of having respiratory tract infections after being identified through the syndromic prescription surveillance system. Here, we examined a combination of syndromic surveillance and PCR testing and showed the potential to identify pathogens during the early stage of an outbreak of respiratory infections.

title:
  Prescription Surveillance and Polymerase Chain Reaction Testing to Identify Pathogens during Outbreaks of Infection

abstract:
  Syndromic surveillance, including prescription surveillance, offers a rapid method for the early detection of agents of bioterrorism and emerging infectious diseases. However, it has the disadvantage of not considering definitive diagnoses. Here, we attempted to definitively diagnose pathogens using polymerase chain reaction (PCR) immediately after the prescription surveillance system detected an outbreak. Specimens were collected from 50 patients with respiratory infections. PCR was used to identify the pathogens, which included 14 types of common respiratory viruses and Mycoplasma pneumoniae. Infectious agents including M. pneumoniae, respiratory syncytial virus (RSV), rhinovirus, enterovirus, and parainfluenza virus were detected in 54% of patients. For the rapid RSV diagnosis kit, sensitivity was 80% and specificity was 85%. For the rapid adenovirus diagnosis kit, no positive results were obtained; therefore, sensitivity could not be calculated and specificity was 100%. Many patients were found to be treated for upper respiratory tract infections without the diagnosis of a specific pathogen. In Japan, an outbreak of M. pneumoniae infection began in 2011, and our results suggested that this outbreak may have included false-positive cases. By combining syndromic surveillance and PCR, we were able to rapidly and accurately identify causative pathogens during a recent respiratory infection outbreak.


id: cord-335620-xqokfg3l
author: Wang, Anqi
date: 2017-03-13
txt: ./txt/cord-335620-xqokfg3l.txt
cache: ./cache/cord-335620-xqokfg3l.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2017/5149062
doi: 10.1155/2017/5149062
summary:
  Goose IFITM1 and IFITM3 are most closely related to their respective orthologs in ducks; these proteins exhibited high mRNA transcript levels in immune-related tissues, including the thymus, bursa of Fabricius, and Harderian gland, compared to other tissues. Furthermore, goose IFITM3 was activated in goose peripheral blood mononuclear cells (PBMCs) infected with Tembusu virus (TMUV) or treated with Toll-like receptors (TLRs) agonists, while only the R848 and Poly (I:C) agonists induced significant upregulation of goose IFITM1. To evaluate the tissue expression profiles of IFITM1 and IFITM3, various tissues, including the brain, bursa of Fabricius, cecum, cecal tonsil, gizzard, heart, Harderian gland, kidney, liver, lung, muscle, pancreas, proventriculus, small intestine, skin, spleen, thymus, and trachea, were collected from two-week-old gosling and adult goose. Notably, high expression levels of goose IFITM3 were observed in respiratory tract tissues (lung and trachea), the target tissues of infection with influenza A viruses, compared to the other tissues, which might contribute to the inhibition of influenza A virus replication [43] .

title:
  Identification of IFITM1 and IFITM3 in Goose: Gene Structure, Expression Patterns, and Immune Reponses against Tembusu Virus Infection

abstract:
  As interferon-stimulated genes (ISGs), interferon-inducible transmembrane proteins 1 and 3 (IFITM1 and IFITM3) can effectively inhibit the replication of multiple viruses. Here, goose IFITM1 and IFITM3 were cloned and identified for the first time. The two proteins share the same topological structure and several important sites critical for the antiviral functions in other species are conserved in the goose. Goose IFITM1 and IFITM3 are most closely related to their respective orthologs in ducks; these proteins exhibited high mRNA transcript levels in immune-related tissues, including the thymus, bursa of Fabricius, and Harderian gland, compared to other tissues. Moreover, goose IFITM1 was highly constitutively expressed in gastrointestinal tract tissues, while goose IFITM3 was expressed in respiratory organs. Furthermore, goose IFITM3 was activated in goose peripheral blood mononuclear cells (PBMCs) infected with Tembusu virus (TMUV) or treated with Toll-like receptors (TLRs) agonists, while only the R848 and Poly (I:C) agonists induced significant upregulation of goose IFITM1. Furthermore, goose IFITM1 and IFITM3 were upregulated in the sampled tissues, to some extent, after TMUV infection. Notably, significant upregulation of goose IFITM1 and IFITM3 was detected in the cecum and cecal tonsil, where TMUV was primarily distributed. These data provide new insights into the immune effectors in geese and promote our understanding of the role of IFITM1 and IFITM3 in the defense against TMUV.


id: cord-336177-p7b7yw28
author: Selvi, Valeria
date: 2020-09-22
txt: ./txt/cord-336177-p7b7yw28.txt
cache: ./cache/cord-336177-p7b7yw28.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2020/2606058
doi: 10.1155/2020/2606058
summary:
  Regarding the pandemic 2009 influenza A H1N1, the results from the prospective cohort study by Hung and colleagues showed that plasma treatment reduced mortality (the patients involved in the study were seriously ill and required intensive care); no adverse events were observed [4, 8, 20] . A meta-analysis by Mair-Jenkins and colleagues, including 32 studies of SARS coronavirus and severe influenza, reported that convalescent plasma reduced mortality and it was safe (no relevant adverse events or complications after treatment were reported). Based on the evidence from past experience in passive immunization, the BRN explained that there was a considerable possibility that the application of whole blood (as well as plasma, serum, or immunoglobulin concentrates) from convalescent persons could be effective in the treatment/prevention of infectious disease. Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection

title:
  Convalescent Plasma: A Challenging Tool to Treat COVID-19 Patients—A Lesson from the Past and New Perspectives

abstract:
  On March 11(th), 2020, the World Health Organization declared COVID-19 infection as a pandemic. Since it is a novel virus, there are basically no proven drugs or therapies; although many laboratories in different countries are working to develop a vaccine, it will take time to make it available. Passive immunization is the therapy born from the intuition of Behring and Kisato in the late 19(th) century. It was widely used for the treatment of bacterial infections until the discovery of antibiotics, as well as during the viral pandemics of the 20(th) century and of the beginning of the 21(st); it still has clinical applications (e.g., tetanus prevention). This paper summarizes the basic principles of passive immunization, with particular reference to convalescent plasma. The literature concerning its use during past epidemics and the results of the first clinical studies concerning its use during the current pandemic are discussed too. A large section is dedicated to the analysis of the possible, although rare, side effects. Recently, in 2017, the WHO Blood Regulators Network (BRN) published a position paper, recommending convalescent plasma as the first-choice treatment to be tested in the absence of authorized drugs; however, this strategy has not been followed. In the current epidemic, the principle of passive immunization through convalescent plasma has been applied in several circumstances and particularly in patients with serious complications. The first reported results are encouraging and confirm the effectiveness of plasma therapy and its safety. Also, the FDA has proposed plasma treatment in order to face the increasingly complex situation and manage patients with serious or immediately life-threatening COVID-19 disease. Several studies and clinical programs are still ongoing.


id: cord-344061-gsl84nv6
author: Pariani, Elena
date: 2014-06-12
txt: ./txt/cord-344061-gsl84nv6.txt
cache: ./cache/cord-344061-gsl84nv6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25013770/
doi: 10.1155/2014/241298
summary:
  We evaluated the proportion of SARI/ARDS cases and deaths due to influenza A(H1N1)pdm09 infection and the impact of other respiratory viruses during pandemic and postpandemic period (2009–2011) in northern Italy; additionally we searched for unknown viruses in those cases for which diagnosis remained negative. 206 respiratory samples were collected from SARI/ARDS cases and analyzed by real-time RT-PCR/PCR to investigate influenza viruses and other common respiratory pathogens; also, a virus discovery technique (VIDISCA-454) was applied on those samples tested negative to all pathogens. This study aimed at evaluating the proportion of SARI/ARDS cases and deaths due to A(H1N1)pdm09 infection and assessing the impact of other respiratory pathogens during pandemic and postpandemic period (2009) (2010) (2011) in northern Italy as well as searching for unknown viruses in those cases for which diagnosis remained negative. During pandemic and postpandemic period, several pathogens cocirculated and were associated to severe respiratory infections; however, influenza A(H1N1)pdm09 virus had the greatest impact (58.3%) in our SARI/ARDS series.

title:
  Influenza and Other Respiratory Viruses Involved in Severe Acute Respiratory Disease in Northern Italy during the Pandemic and Postpandemic Period (2009–2011)

abstract:
  Since 2009 pandemic, international health authorities recommended monitoring severe and complicated cases of respiratory disease, that is, severe acute respiratory infection (SARI) and acute respiratory distress syndrome (ARDS). We evaluated the proportion of SARI/ARDS cases and deaths due to influenza A(H1N1)pdm09 infection and the impact of other respiratory viruses during pandemic and postpandemic period (2009–2011) in northern Italy; additionally we searched for unknown viruses in those cases for which diagnosis remained negative. 206 respiratory samples were collected from SARI/ARDS cases and analyzed by real-time RT-PCR/PCR to investigate influenza viruses and other common respiratory pathogens; also, a virus discovery technique (VIDISCA-454) was applied on those samples tested negative to all pathogens. Influenza A(H1N1)pdm09 virus was detected in 58.3% of specimens, with a case fatality rate of 11.3%. The impact of other respiratory viruses was 19.4%, and the most commonly detected viruses were human rhinovirus/enterovirus and influenza A(H3N2). VIDISCA-454 enabled the identification of one previously undiagnosed measles infection. Nearly 22% of SARI/ARDS cases did not obtain a definite diagnosis. In clinical practice, great efforts should be dedicated to improving the diagnosis of severe respiratory disease; the introduction of innovative molecular technologies, as VIDISCA-454, will certainly help in reducing such “diagnostic gap.”


id: cord-347200-dtwhd6zy
title: NK Cells in Mucosal Defense against Infection
author: Ivanova, Daria
date: 2014-08-14
txt: ./txt/cord-347200-dtwhd6zy.txt
cache: ./cache/cord-347200-dtwhd6zy.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2014/413982
doi: 10.1155/2014/413982
summary:
  Mucosal NK cells play a pivotal role in early protection through their cytolytic function and IFNγ production against bacteria, fungi, viruses, and parasitic infections. Since NK precursors and other ILC populations in secondary lymphoid tissues express varying levels of this integrin, it may be possible that an NK-DC interaction is a requirement for immature NK cells to be signaled to home to mucosal sites. During mucosal infections of humans and mice, NK cells are recruited to sites of infection and play an important role in immune defense [6, 48] . Therefore the cytokine milieu present in the different mucosal tissues in addition to activating signals stimulated that by diverse pathogens help NK cells respond to infection. NK cells in humans are also important for innate control of gut mucosal infections. During infection, resident mucosal tissue NK cells respond primarily through IFN production, which contributes directly to early control of pathogens.

abstract:
  Conventional natural killer cells (NK cells) provide continual surveillance for cancer and rapid responses to infection. They develop in the bone marrow, emerge as either NK precursor cells, immature, or mature cells, and disperse throughout the body. In the periphery NK cells provide critical defense against pathogens and cancer and are noted to develop features of adaptive immune responses. In the tightly regulated and dynamic mucosal tissues, they set up residency via unknown mechanisms and from sources that are yet to be defined. Once resident, they appear to have the ability to functionally mature dependent on the mucosal tissue microenvironment. Mucosal NK cells play a pivotal role in early protection through their cytolytic function and IFNγ production against bacteria, fungi, viruses, and parasitic infections. This review presents what is known about NK cell development and phenotypes of mucosal tissue resident conventional NK cells. The question of how they come to reside in their tissues and published data on their function against pathogens during mucosal infection are discussed. Dissecting major questions highlighted in this review will be important to the further understanding of NK cell homing and functional diversity and improve rational design of NK cell based therapies against mucosal infection.


id: cord-351685-n70tkf38
author: Altamimi, Asmaa
date: 2020-02-19
txt: ./txt/cord-351685-n70tkf38.txt
cache: ./cache/cord-351685-n70tkf38.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2020/9629747
doi: 10.1155/2020/9629747
summary:
  title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory METHODS: It was a surveillance system-based study, for which data from a total of 23,646 suspected patients in Riyadh and Al Qassim regions were analyzed from January 2017 until December 2017 to estimate the prevalence of MERS-CoV among suspected cases and to determine potential demographic risk factors related to the confirmation of the diagnosis. During the study period, i.e., the year 2017, only 119 confirmed cases were reported, which means that the number of MERS-CoV infection cases has decreased in Riyadh and Al-Qassim regions in comparison to that of the last three years. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study

title:
  Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory

abstract:
  Introduction. Middle East respiratory syndrome coronavirus was first recognized in September 2012 in Saudi Arabia. The clinical presentations of MERS and non-MERS SARI are often similar. Therefore, the identification of suspected cases that may have higher chances of being diagnosed as cases of MERS-CoV is essential. However, the real challenge is to flag these patients through some demographic markers. The nature of these markers has not previously been investigated in Saudi Arabia, and hence, this study aims to identify them. METHODS: It was a surveillance system-based study, for which data from a total of 23,646 suspected patients in Riyadh and Al Qassim regions were analyzed from January 2017 until December 2017 to estimate the prevalence of MERS-CoV among suspected cases and to determine potential demographic risk factors related to the confirmation of the diagnosis. RESULTS: Of 23,646 suspected cases, 119 (0.5%) were confirmed by laboratory results. These confirmed cases (67.2% of which were males) had a mean age of 43.23 years (SD ± 22.8). Around 42.2% of the confirmed cases were aged between 41 and 60 years and about 47% of confirmed cases had their suspected specimen tested in the summer. The study identified three significant and independent predictors for confirmation of the disease: an age between 41 and 60 years, male gender, and summer season admission. CONCLUSION: The study provides evidence that the MERS-CoV epidemic in the subject regions has specific characteristics that might help future plans for the prevention and management of such a contagious disease. Future studies should aim to confirm such findings in other regions of Saudi Arabia as well and explore potential preventable risk factors.


id: cord-352190-1987sfyz
title: Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis
author: Xia, Hongyue
date: 2020-08-13
txt: ./txt/cord-352190-1987sfyz.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32923488/
doi: 10.1155/2020/9089768
summary:
  PURPOSE: We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. The goal of our study is to increase the sampling of FCoV in China and to also examine the selective pressures acting on the genes of these viruses isolated from different parts of the world. To detect the presence of positive selection in the FCoV sequences from the different countries, we applied the branch, site, and branch-site tests from the PAML suit [18] . By analyzing the selective pressure experienced by genes in the FCoV genome involved in replication, entry, and virulence, we have identified a few sites that potentially experienced adaptive evolution.

abstract:
  PURPOSE: We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. METHODS: Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms. RESULTS: Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified. CONCLUSION: Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the sites showing evidence of positive selection might be associated with the more severe pathology of FIPV or help these viruses survive other harmful conditions.


id: cord-352231-awkkper2
author: Bakri, Faris Ghalib
date: 2018-04-11
txt: ./txt/cord-352231-awkkper2.txt
cache: ./cache/cord-352231-awkkper2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29850587/
doi: 10.1155/2018/9291326
summary:
  In 1987, Garfield listed the "top 100" best cited articles ever published in JAMA and named them "citation classics" [8] , and these classics represent the highest impact work in a given field [9] . We analyzed the papers according to number of citations, publication year, authors, journal impact factor, country of origin, and article type (basic science, observational study, interventional clinical trial, and review) [21] . We also observed the lack of papers on brucellosis in animal health and for this we suggest two explanations: (a) journals in the categories of agriculture and food sciences receive fewer citations than those in basic and clinical sciences as evidenced by the impact factor in these categories. Despite these limitations, the study provides a picture for the main cited articles in brucellosis research publications since the discovery of Brucella 130 years ago.

title:
  The Highest Cited Papers in Brucellosis: Identification Using Two Databases and Review of the Papers'' Major Findings

abstract:
  Citation classics represent the highest impact work in a given field. We aim to identify and analyze the most frequently cited papers on brucellosis. We used the databases Scopus and Web of Science to determine the most frequently cited papers. The most cited fifty papers in each database were identified. We then ranked the papers according to the highest citation count recorded from any of the two databases. The most frequently cited paper received 964 citations and was by DelVecchio VG et al. reporting the complete genomic sequencing of Brucella melitensis. The papers were published in 30 journals led by the “Infection and Immunity” journal and the “Veterinary Microbiology” journal (each had 7 papers). Citation classics in brucellosis were all in English except one in French and were mostly of basic science type. In addition, we noticed that 12 articles that were identified among the highest fifty articles in one database were missed by the other database and vice versa. Therefore, we suggest that searching in more than one database would detect additional citation classics.


id: cord-354730-hfau2odb
author: Wang, Rong
date: 2014-07-03
txt: ./txt/cord-354730-hfau2odb.txt
cache: ./cache/cord-354730-hfau2odb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25101271/
doi: 10.1155/2014/315470
summary:
  PRRSV interplays with host IFN production and IFN-activated signaling, which may contribute to the delayed onset and low level of neutralizing antibodies, as well as weak cell-mediated immune response in infected pigs. This review summarizes the recent advances in the research of PRRSV interference with IFN-mediated innate immunity, the viral proteins involved, and their molecular mechanisms, as well as diverse effects by different strains and in different cell types. These transcription activation factors translocate into the nucleus and result in induction of type I IFNs and expression of inflammatory cytokines, which not only lead to an antiviral state of the neighboring uninfected cells, but also serve as key regulators to evoke adaptive immune response. Porcine reproductive and respiratory syndrome virus nonstructural protein 1 modulates host innate immune response by antagonizing IRF3 activation Porcine reproductive and respiratory syndrome virus inhibits type I interferon signaling by blocking STAT1/STAT2 nuclear translocation

title:
  Antagonizing Interferon-Mediated Immune Response by Porcine Reproductive and Respiratory Syndrome Virus

abstract:
  Interferons (IFNs) are important components in innate immunity involved in the first line of defense to protect host against viral infection. Porcine reproductive and respiratory syndrome virus (PRRSV) leads to severe economic losses for swine industry since being first identified in early 1990s. PRRSV interplays with host IFN production and IFN-activated signaling, which may contribute to the delayed onset and low level of neutralizing antibodies, as well as weak cell-mediated immune response in infected pigs. PRRSV encodes several proteins that act as antagonists for the IFN signaling. In this review, we summarized the various strategies used by PRRSV to antagonize IFN production and thwart IFN-activated antiviral signaling, as well as the variable interference with IFN-mediated immune response by different PRRSV strains. Thorough understanding of the interaction between PRRSV and host innate immune response will facilitate elucidation of PRRSV pathogenesis and development of a better strategy to control PRRS.


