cord-001313-f72hl6du	2014	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
cord-001525-b7kbyp3s	2015	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.
cord-001566-kkaxha7d	2015	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.
cord-001572-ap4ro5me	2015	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.
cord-004269-g6ki6vyy	2020	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.
cord-026595-imn2jxcu	2020	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
cord-031416-ytbs95wi	2020	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.
cord-259823-ia1g5dt4	2017	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] .
cord-261633-r4qlbnc5	2014	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.
cord-262468-7ddgegb2	2020	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).
cord-265260-n6wm54wz	2020	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).
cord-271106-srym2kh4	2019	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.
cord-274056-9t3kneoo	2019	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 .
cord-279528-41atidai	2019	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
cord-280908-o1z4ka3r	2017	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
cord-283092-t3yqsac3	2020	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.
cord-293503-e7be12qb	2020	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.
cord-296033-5zyoddl7	2017	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.
cord-296682-ugffeegr	2020	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.
cord-298185-w37nvorf	2020	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.
cord-299552-rgrm8dil	2020	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.
cord-300944-c57impca	2013	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.
cord-303978-z3888e3g	2015	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.
cord-306411-dutbxfl4	2017	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.
cord-309319-si5c14e8	2016	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.
cord-311625-d7iycdyh	2014	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.
cord-316181-ccauw70y	2017	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] .
cord-319635-kh99n7q2	2014	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.
cord-321953-yql6gpd3	2017	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
cord-330276-qvmhuid3	2020	[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
cord-330602-g0xaonxv	2013	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.
cord-335620-xqokfg3l	2017	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] .
cord-336177-p7b7yw28	2020	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
cord-344061-gsl84nv6	2014	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.
cord-347200-dtwhd6zy	2014	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.
cord-351685-n70tkf38	2020	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
cord-352190-1987sfyz	2020	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.
cord-352231-awkkper2	2018	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.
cord-354730-hfau2odb	2014	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