niryuu/sni-each-converted huggingface dataset:
As expected, cats from endemic areas produce IFN-γ after ex vivo blood stimulation with LSA and therefore are able to activate a cell-mediated adaptive immune response against the parasite that is variably associated with antibody or blood PCR positivity. The association of this assay to serological and molecular tests provides a better estimate of cat exposure to L. infantum.
Output: 1 - finding, 2 - finding
Background. Kawasaki disease (KD) is characterized by systemic vasculitis of unknown etiology. Our previous studies showed expression of CD40 ligand on CD4+ T cells correlated to the coronary artery lesion (CAL) and disease progress in KD. Other studies from Japan suggested the role of CD40L in the pathogenesis of CAL, and this might help explain the excessive number of males affected with KD but cannot be reproduced by Taiwanese population. This study was conducted to investigate the CD40 polymorphism in KD and CAL formation. Methods. A total of 950 subjects (381 KD patients and 569 controls) were investigated to identify 2 tagging single-nucleotide polymorphisms (tSNPs) of CD40 (rs4810485 and rs1535045) by using the TaqMan allelic discrimination assay. Results. A significant association was noted with regards to CD40 tSNPs (rs1535045) between controls and KD patients (P = 0.0405, dominant model). In KD patients, polymorphisms of CD40 (rs4810485) showed significant association with CAL formation (P = 0.0436, recessive model). Haplotype analysis did not yield more significant results between polymorphisms of CD40 and susceptibility/disease activity of KD. Conclusions. This study showed for the first time that polymorphisms of CD40 are associated with susceptibility to KD and CAL formation, in the Taiwanese population.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding
Rationale: After lung transplantation, insults to the allograft generally result in one of four histopathologic patterns of injury: (1) acute rejection, (2) lymphocytic bronchiolitis, (3) organizing pneumonia, and (4) diffuse alveolar damage (DAD). We hypothesized that DAD, the most severe form of acute lung injury, would lead to the highest risk of chronic lung allograft dysfunction (CLAD) and that a type I immune response would mediate this process. Objectives: Determine whether DAD is associated with CLAD and explore the potential role of CXCR3/ligand biology. Methods: Transbronchial biopsies from all lung transplant recipients were reviewed. The association between the four injury patterns and subsequent outcomes were evaluated using proportional hazards models with time-dependent covariates. Bronchoalveolar lavage (BAL) concentrations of the CXCR3 ligands (CXCL9/MIG, CXCL10/ IP10, and CXCL11/ITAC) were compared between allograft injury patterns and "healthy" biopsies using linear mixed-effects models. The effect of these chemokine alterations on CLAD risk was assessed using Cox models with serial BAL measurements as time-dependent covariates. Measurements and Main Results: There were 1,585 biopsies from 441 recipients with 62 episodes of DAD. An episode of DAD was associated with increased risk of CLAD (hazard ratio, 3.0; 95% confidence interval, 1.9-4.7) and death (hazard ratio, 2.3; 95% confidence interval, 1.7-3.0). There were marked elevations in BAL CXCR3 ligand concentrations during DAD. Furthermore, prolonged elevation of these chemokines in serial BAL fluid measurements predicted the development of CLAD. Conclusions: DAD is associated with marked increases in the risk of CLAD and death after lung transplantation. This association may be mediated in part by an aberrant type I immune response involving CXCR3/ligands.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding
Understanding how disease affects commercial production is imperative for pig producers to quantify its full impact on pig performance, carcass quality, and net returns. The objective of this experiment was to assess the productivity and economic importance of naturally occurring health challenges (HC) under commercial conditions. Three 1,000 pig grow-finish facilities received 936 pigs each. The experimental period started approximately 34 d post placement at an average start BW of 13.1 ± 0.2 kg.
Output: 1 - background, 2 - background, 3 - purpose, 4 - method, 5 - method
This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.
Output: 1 - finding, 2 - finding
Citation Yuan S. 2015. Statins may decrease the fatality rate of Middle East respiratory syndrome infection. mBio 6(4):e01120-15.
Output: 1 - other, 2 - finding, 3 - other
Cereal commodities are frequently contaminated with mycotoxins produced by the secondary metabolism of fungal infection. Among these contaminants, deoxynivalenol (DON), also known as vomitoxin, is the most prevalent type B trichothecene mycotoxin worldwide. Pigs are very sensitive to the toxic effects of DON and are frequently exposed to naturally contaminated feed. Recently, DON naturally contaminated feed has been shown to decrease porcine reproductive and respiratory syndrome virus (PRRSV) specific antibody responses following experimental infection. The objective of this study was to determine the impact of DON naturally contaminated feed on the immune response generated following vaccination with PRRSV live attenuated vaccine. Eighteen pigs were randomly divided into three experimental groups of 6 animals based on DON content of the diets (0, 2.5 and 3.5 mg DON/kg). They were fed these rations one week prior to the vaccination and for all the duration of the immune response evaluation. All pigs were vaccinated intra-muscularly with one dose of Ingelvac ® PRRSV modified live vaccine (MLV). Blood samples were collected at day −1, 6, 13, 20, 27 and 35 post vaccination (pv) and tested for PRRSV RNA by RT-qPCR and for virus specific antibodies by ELISA. Results showed that ingestion of DON-contaminated diets significantly decreased PRRSV viremia. All pigs fed control diet were viremic while only 1 (17%) and 3 (50%) out of 6 pigs were viremic in the groups receiving 3.5 and 2.5 mg of DON/kg, respectively. Subsequently, all pigs fed control diet developed PRRSV specific antibodies while only viremic pigs that were fed contaminated diets have developed PRRSV specific antibodies. These results suggest that feeding pigs with DON-contaminated diet could inhibit vaccination efficiency of PRRSV MLV by severely impairing viral replication.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding
Fresh demyelinating lesions could be demonstrated in paralyzed animals. Viral antigen was demonstrated and infectious JHM virus could be recovered from one animal which developed clinical signs at 3 months a.i. In one animal with clinical onset of 8 months a.i., completely remyelinated areas as well as recent demyelinating lesions were observed, suggesting a recurrence of the disease process. Remyelinated areas were also found in 40 ~ of clinically silent animals. The morphology of the late onset of the demyelination was similar to that occurring in SDE. Remyelination consisted of both CNS and PNS-type. This animal model offers the possibility to investigate the virus-host relationship which is responsible for the induction of a demyelinating process after a long incubation period.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding
PRRSV PEDV Antiviral inhibitor Broad-spectrum 3C-like serine/3C-like protease A B S T R A C T Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are highly virulent and contagious porcine pathogens that cause tremendous economic losses to the swine industry worldwide. Currently, there is no effective treatment for PRRSV and PEDV, and commercial vaccines do not induce sterilizing immunity. In this study, we screened a library of 1000 compounds and identified two specific inhibitors, designated compounds 2 and 3, which target the PRRSV 3C-like serine protease (3CLSP). First, we evaluated the inhibitory effects of compounds 2 and 3 on PRRSV 3CLSP activity. Next, we determined the anti-PRRSV capacity of compounds 2 and 3 in MARC-145 cells and obtained EC 50 and CC 50 values of 57 μM (CC 50 = 479.9 μM) and 56.8 μM (CC 50 = 482.8 μM), respectively. Importantly, compounds 2 and 3 also targeted the PEDV 3C-like protease (3CL protease) and inhibited PEDV replication, showing EC 50 and CC 50 values of 100 μM (CC 50 = 533.8 μM) and 57.9 μM (CC 50 = 522.3 μM), respectively. Finally, our results indicated that the active sites (His39 in 3CLSP and His41 in 3CL protease) were conservative, and contacted compounds 2 and 3 via hydrogen bonds and hydrophobic forces in the putative substrate-binding models. In summary, compounds 2 and 3 exhibit broad-spectrum antiviral activity and may facilitate the development of antiviral drugs against PRRSV and PEDV.
Output: 1 - background, 2 - background, 3 - background, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding
The diagnostic performance of porcine epidemic diarrhea virus (PEDV) IgG and IgA ELISAs was evaluated using paired serum and meat juice samples collected from PEDV-negative (n = 50) and PEDV-inoculated pigs (n = 87). Serum samples were tested by PEDV (IgG, IgA) ELISAs using a procedure performed routinely at the Iowa State University-Veterinary Diagnostic Laboratory (ISU-VDL). Serum samples were tested using PEDV serum IgG and IgA ELISA procedures as routinely performed at the Iowa State University-Veterinary Diagnostic Laboratory (ISU-VDL). Serum samples were diluted 1:50 and conjugate concentrations were 1/20,000 for IgG and 1/3000 for IgA. Meat juice samples were tested using the serum PEDV IgG and IgA ELISAs, with modifications, i.e., meat juice samples were diluted 1:25 and conjugate concentrations were 1/40,000 for IgG and 1/10,000 for IgA. Receiver operator characteristic (ROC) curve analyses were used to estimate diagnostic sensitivities and specificities over a range of sample-to-positive (S/P) cutoffs. Consistent with previous reports, this study showed that the PEDV IgG and IgA meat juice ELISAs provided excellent diagnostic performance and suggest that meat juice recovered from samples collected at slaughter could be used in routine PEDV surveillance.
Output: 1 - background, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding
The experiment results show that IILLS achieves the AUC values of 0.8675 and 0.9061 with the 10-fold cross validation and leave-one-out cross validation (LOOCV), respectively, which illustrates that IILLS is superior to the competing methods. In addition, the case studies also further indicate that the IILLS method is effective for the virus-receptor interaction prediction.
Output: 1 - finding, 2 - finding, 3 - finding
Method: This is a cohort study designed to investigate psychiatric complications among SARS survivors treated in the United Christian Hospital 30 months after the SARS outbreak. Psychiatric morbidities were assessed by the Structured Clinical Interview for DSM-IV, the Impact of Events Scale-Revised and the Hospital Anxiety and Depression Scale. Functional outcomes were assessed by the Medical Outcomes Study 36-Item Short-Form Health Survey. Results: Ninety subjects were recruited, yielding a response rate of 96.8%. Post-SARS cumulative incidence of DSM-IV psychiatric disorders was 58.9%. Current prevalence for any psychiatric disorder at 30 months post-SARS was 33.3%. One-fourth of the patients had post-traumatic stress disorder (PTSD), and 15.6% had depressive disorders. Conclusion: The outbreak of SARS can be regarded as a mental health catastrophe. PTSD was the most prevalent long-term psychiatric condition, followed by depressive disorders. Our results highlight the need to enhance preparedness and competence of health care professionals in detecting and managing the psychological sequelae of future comparable infectious disease outbreaks.
Output: 1 - method, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding
Citation Stenglein MD, et al. 2012. Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease. mBio 3(4):e00180-12.
Output: 1 - finding, 2 - finding, 3 - other
Objectives: 1) To compare the 2-year completed suicide and reattempt rates in a preintervention group of Hong Kong Chinese suicide attempters (aged 65 years and older) who received standard care and a postintervention group enrolled in a regional elderly suicide prevention program (ESPP) that adopts a two-tiered multifaceted care management model and 2) to examine the trend of suicide rates in older adults aged 65 years and older in the pre-and postintervention periods. Design: The first part is an observational cohort study with baseline, follow-up, and outcome data being identified from a clinical electronic registry. The second part examines changes in suicide rates from official mortality statistics. Setting: A government-funded suicide intervention program serving catchment population (852,796 people aged 65 years and older) in Hong Kong, China. Participants: Suicide attempters (aged 65 years and older) presenting to old-age psychiatric service in the pre-and postintervention phases. Measurements: 1) Two-year rates of completed suicide and suicide reattempt and 2) changes in population suicide rates in the pre-and postintervention periods. Results: The 2-year completed suicide rate was 7.58% in the preintervention group (N = 66) and 1.99% in the ESPP group (N = 351) χ 2 = 6.192; p value: 0.028; df = 1). Reattempt rates were not different. At a population level, suicide rate dropped significantly only in women aged 85 years and older, relative to the preintervention period. Conclusions: The ESPP was associated with a reduced rate of completed suicide in old-age suicide attempters and might have contributed to a fall of suicide rate in women aged 85 years and older. (Am J Geriatr Psychiatry 2011; 19:1-12) 
Output: 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - other
A polysaccharide microarray platform was prepared by immobilizing Burkholderia pseudomallei and Burkholderia mallei polysaccharides. This polysaccharide array was tested with success for detecting B. pseudomallei and B. mallei serum (human and animal) antibodies. The advantages of this microarray technology over the current serodiagnosis of the above bacterial infections were discussed. D
Output: 1 - background, 2 - background, 3 - finding, 4 - other
The estimated costs and TAT were 8.2€ and 2 h for DFA, 31.8€ and 1.5 h for Simplexa™ and 55€ and 3 h for TAC testing. Conclusions: Performing the Simplexa™ test 24 h a day/7 days a week instead of DFA would considerably improve the overall sensitivity and time-to-result, albeit at a higher cost generated in the laboratory. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding
The term is derived from the Greek word for "alternative"-para and for "mucus"-myxo. 2. Syncytium A syncytium (pl., syncytia) refers to a multinucleated cell that can result from multiple cell fusions of uninuclear cells. The term is derived from the Greek word for "together"-syn and for "box (cell)"-kytos.
Output: 1 - background, 2 - other, 3 - background, 4 - background
FilmArray Respiratory Panel (RP) (Idaho Technology, Inc., Salt Lake City, UT, USA) performance was retrospectively evaluated in respiratory samples collected from neonates in 2 reference neonatology units. Using the FilmArray RP assay, 121/152 (79.6%) samples were positive for at least 1 respiratory virus, while 31/ 152 (20.4%) were negative. FilmArray RP results were concordant in 68/72 (94.4%) respiratory samples tested with laboratory-developed real-time PCR assays, while in 4/72 (5.6%) samples, the FilmArray RP assay detected an additional virus (2 human rhinovirus/enterovirus and 2 bocavirus). In addition, FilmArray RP results for 70 of 80 (87.5%) respiratory samples tested were concordant with the Seegene Seeplex RV15® detection assay (Seegene, Inc., Seoul, South Korea), while 10/80 (12.5%) were discordant. The advantages of the FilmArray RP are the rapid detection of respiratory viruses (1 hour), the wide number of pathogens detectable in a single assay, and the reduced hands-on time.
Output: 1 - method, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
The role of rhinovirus asymptomatic infections in the transmission among close contacts subjects is unknown. We tested health care workers, a pair of one child and a family member and immunocompromised patients (n =191). HRV were detected on 22.9% symptomatic and 3.6% asymptomatic cases suggesting lower transmission among contacts. Rhinovirus infections are among the most frequent causes of the common colds (18). It is the most common etiology of viral respiratory infections among diverse populations, including adults, children and more recent studies have linked HRVs to more severe lower respiratory illnesses in otherwise healthy young children (11-12), immunocompromised (4,6), and elderly patients. (5,13, 23). In Brazil, there are few HRV studies, Arruda et.al. (1991), realized the first Brazilian study detecting a 45.5% rate on symptomatic children in Fortaleza -CE. Another study realized in Salvador -BA also showed a high prevalence (48.5%) (Souza ,2003). The only study
Output: 1 - background, 2 - method, 3 - method, 4 - finding, 5 - background, 6 - background, 7 - background, 8 - background, 9 - other, 10 - background, 11 - finding, 12 - finding, 13 - other
TCR Vβ CDR3 repertoire diversity in human peripheral blood; spectratype; immune reconstitution; hematopoietic stem cell transplantation Corresponding author: Sarfraz A. Memon, M.D., Experimental Transplantation and Immunology Branch,
Output: 1 - other, 2 - other
Here we aim to investigate the importance of spillover transmission for explaining the number and the size of outbreaks. We propose a simple stochastic Susceptible-Infected-Recovered model with a recurrent infection of an incidental host from a reservoir (e.g. humans by a zoonotic species), considering two
Output: 1 - purpose, 2 - method
Conclusions: Preliminary results show that there is significant air motion associated with a cough (on the order of 0.5 m/s) as far away as 1 m from the mouth of the healthy person who coughs. The results from this pilot study provide the framework for a more extensive participant recruitment campaign that will encompass a statisticallysignificant cohort.
Output: 1 - finding, 2 - finding
Bovine respiratory disease (BRD) often occurs when active respiratory virus infections (BHV-1, etc.) impair resistance to Mannheimia haemolytica infection in the lower respiratory tract. The interactions that occur when the respiratory epithelium encounters these viral and bacterial pathogens are poorly understood. We used Agilent bovine gene microarray chips containing 44,000 transcripts to elucidate bovine bronchial epithelial cell (BBEC) responses following in vitro exposure to BHV-1 alone, M. haemolytica alone, or both BHV-1 and M. haemolytica. Microarray analysis revealed differential regulation (>2-fold) of 978 transcripts by BHV-1 alone, 2040 transcripts by M. haemolytica alone, and 2189 genes by BHV-1 and M. haemolytica in combination. M. haemolytica treatment produced significantly greater inductions (>10-fold) of several inflammation associated genes, such as CXCL2, IL-6, IL-1␣, e-selectin, and IL-8, than to BHV-1 alone. Functional analysis of the microarray data revealed a significant upregulation of genes involved in important biological processes such as inflammation (TNF-␣, IL-8, Tlr-2, IL-1, CXCL2, CSF2), vascular functions (VEGF, EDN2) and leukocyte migration (ICAM1, IL-16) during a co-infection with BHV-1 and M. haemolytica compared to either pathogen alone. This study provides evidence to support that lung epithelial cells are a source of mediators that may promote inflammatory changes observed during bovine respiratory disease.
Output: 1 - background, 2 - background, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding
Published: xx xx xxxx OPEN www.nature.com/scientificreports/
Output: 1 - other
A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9-97.9% and 83.6-96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.
Output: 1 - method, 2 - method, 3 - finding, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding
Maternally-derived antibody to enterotropic mouse hepatitis virus (MHV) strain Y was transferred to pups by both intrauterine (IgG) and lactogenic (IgA and IgG) routes. Antibody present in the gastric whey of pups suckling immune dams dropped to undetectable levels by weaning age (21 days post partum). MHV-specific IgG was found in the serum of passively immune pups up to 10 weeks of age. Immune dams transferred equal levels of antibody to 3 consecutive litters of pups, without evidence of decline. Immunoblots showed that IgA and IgG in whey and serum were directed against nucleoprotein N and glycoprotein S. MHV-specific IgM was not detected in any sample.
Output: 1 - background, 2 - finding, 3 - finding, 4 - finding, 5 - finding
Statistics. Statistical analyses were conducted using SPSS software (version 20 SPSS, Inc., Chicago, IL). For normally distributed variables, Student's t-test and one-way ANOVA were used for comparisons, and the data are presented as the mean ± SE. The Mann-Whitney U and Kruskal-Wallis tests were used for comparisons of variables that were not normally distributed. Correlations were assessed with Pearson's correlation coefficient for parametric distributions. Statistical significance was set at P < 0.05.
Output: 1 - method, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding
Patients of all ages were recruited to the study. The patients with agreed diagnosis (diagnosed patients; n=794) included more pediatric (≤18 years) than adult (>18 years) patients (445 patients [56%] vs 349 [44%]). The age distribution was relatively uniform for patients aged 20-80 years and peaked at <4 years of age for pediatric patients (Fig.  S2) . The observed age distribution for pediatric patients is consistent with that expected and represents the background distribution in the inpatient setting [4] (e.g., the emergency department [ED], pediatrics departments, and internal departments). Patients of both genders were recruited to the study. The patient population was balanced in respect to gender distribution (47% females, 53% males).
Output: 1 - method, 2 - method, 3 - method, 4 - other, 5 - finding, 6 - finding, 7 - finding, 8 - finding
T h e ne w e ngl a nd jou r na l o f m e dicine n engl j med 382;13 nejm.org March 26, 2020 WHO -HEO -RDBlueprint%28nCoV%29 -2020 .1 -eng .pdf).
Output: 1 - other, 2 - other, 3 - other
Homogenates obtained by a Dounce homogeniser of oligodendrocyte and whole brain from 2-day-old rats were suspended in Published by Elsevier Science Publishers B. V.
Output: 1 - method
Acute respiratory distress syndrome (28.36%), acute cardiac injury (7.89%) and acute kidney 35 injury (7.60%) were the most common complications recorded. 36 37 Conclusions: Clinical and epidemiological characteristics of COVID-19 patients were mostly 38 heterogeneous and non-specific. This is the most comprehensive report of the characteristics of 39
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding
Repurposing antimalarials as dengue antivirals Chloroquine Primaquine Stable replicon cell lines for dengue and West Nile viruses Inhibition of dengue virus replication and infectivity Amodiaquine therapeutic index a b s t r a c t Dengue virus serotypes 1-4 (DENV1-4) are transmitted by mosquitoes which cause most frequent arboviral infections in the world resulting in $390 million cases with $25,000 deaths annually. There is no vaccine or antiviral drug currently available for human use. Compounds containing quinoline scaffold were shown to inhibit flavivirus NS2B-NS3 protease (NS2B-NS3pro) with good potencies. In this study, we screened quinoline derivatives, which are known antimalarial drugs for inhibition of DENV2 and West Nile virus (WNV) replication using the corresponding replicon expressing cell-based assays. Amodiaquine (AQ), one of the 4-aminoquinoline drugs, inhibited DENV2 infectivity measured by plaque assays, with EC 50 and EC 90 values of 1.08 ± 0.09 lM and 2.69 ± 0.47 lM, respectively, and DENV2 RNA replication measured by Renilla luciferase reporter assay, with EC 50 value of 7.41 ± 1.09 lM in the replicon expressing cells. Cytotoxic concentration (CC 50 ) in BHK-21 cells was 52.09 ± 4.25 lM. The replication inhibition was confirmed by plaque assay of the extracellular virions as well as by qRT-PCR of the intracellular and extracellular viral RNA levels. AQ was stable for at least 96 h and had minor inhibitory effect on entry, translation, and post-replication stages in the viral life cycle. DENV protease, 5 0 -methyltransferase, and RNA-dependent RNA polymerase do not seem to be targets of AQ. Both p-hydroxyanilino and diethylaminomethyl moieties are important for AQ to inhibit DENV2 replication and infectivity. Our results support AQ as a promising candidate for anti-flaviviral therapy.
Output: 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding
A prospective cohort study was undertaken to determine calf-level factors that affected calf health status between birth and 6 months of age. A convenience sample of approximately 3300 female Holstein calves born in 1991 on two large Florida dairy farms was used for the study. Data collected on each calf at birth included farm of origin, weight, height at the pelvis, birth date, and serum total protein (a measure of colostral immunoglobulin absorption). Birth season was dichotomized into summer and winter using meteorological data collected by University of Florida Agricultural Research Stations. Health data including date of initial treatment and number of treatments were collected for the diseases diarrhea, omphalitis, septicemia and pneumonia. All calves were followed for 6 months. Cumulative incidences of mortality and occurrence of diarrhea, omphalitis, septicemia and pneumonia were 0.12, 0.35, 0.11, 0.24 and 0.21, respectively. Serum total protein (TP) was a significant risk factor for mortality. The association of TP and mortality was quadratic and showed a dramatic decrease in mortality as TP increased from 4.0 to 5.0 g/dl, a small improvement from 5.0 to 6.0 g/d1 and virtually no improvement in mortality rates as TP increased over 6.0 g/dl. The hazard mortality ratio was constant from birth to six months, indicating that the increased risk of mortality associated with low levels of TP was evident through six months of age. No interactions between TP, farm, season, or birth weight were found in these analyses. Serum total protein concentration was a significant risk factor for the 32 G. A. Donovan et al. /Preventive Veterinary Medicine 34 (1998) 31-46 occurrences, age of onset and severity of septicemia and pneumonia. The association between TP and septicemia was linear and an interaction with birth season was found. The association between TP and pneumonia was quadratic, and in contrast to the TP-and-septicemia relationship, the morbidity hazard ratio for pneumonia was not constant over the time measured; that is, colostral immunity protected the calf from developing pneumonia early in life, but this effect disappeared as the calf got older. Total protein was not a significant risk factor for diarrhea or omphalitis. 0 1998 Elsevier Science B.V.
Output: 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding, 25 - finding, 26 - finding, 27 - finding, 28 - finding, 29 - other
Equivalently, for each detected case there are at least 1.8 (95% CI 0.5-3.4) undetected cases. If the model is correct, this is an upper bound on the detection frequency because (1) Singapore's detection is probably not 100% efficient. Singapore had as of 12 February 2020 eight
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding
Infectious bronchitis virus (IBV), the first coronavirus described, has been a continuing problem in poultry for more than 70 years. IBV, causing a highly contagious respiratory disease in chickens, resembles the recently described severe acute respiratory syndrome virus in pathogenesis and genome organization. While previous studies demonstrated that effector and memory CD8 C T lymphocytes are critical in controlling acute IBV infection and disease in chickens, here chicken anti-IBV antibody (IgG) secreting cells (ASC) in both peripheral blood mononuclear cells (PBMC) and spleens collected following IBV Gray infection were evaluated using an ELISPOT assay. The ASC in peripheral blood and spleens can be detected from 3 to 7 days post-infection (p.i.), which is 3-7 days earlier than anti-IBV IgG detected in the serum. The ASC frequency reached a maximum at 7-10 days p.i., and decreased more than 90% in the spleen and 70% in PBMC by 14 days p.i. The ASC levels in the PBMC then decreased gradually to 0.5 ASC/10 6 over the next 8 weeks. The higher concentration of about 20 ASC/10 6 cells in spleens may, at least partially, account for the presence of antibody in the serum although bone marrow ASC were not determined. In vitro stimulation of PBMC and splenocytes with IBV antigen demonstrated that memory B cells can be activated to secrete antibody by 3 weeks p.i. ELISPOT detection of primary B cells could be useful in the early detection of infection following infection with respiratory coronaviruses. q
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - other
Quantification of physiologic defensin concentrations in vivo is complex, as defensins are present at high local concentrations within specific cell types or upon release from cells into confined anatomical niches (e.g., crypts of the small intestine) but can become diluted in extracellular fluids. For the myeloid -defensins, Daher et al. estimated ~3 mM (10 mg/ml) HNPs in neutrophils, with even higher local concentrations in the azurophilic granules in which they are stored 1 . For the enteric -defensins, Ayabe et al. estimated concentrations of ≥3.5 mM (15-100 mg/ml) in the crypt lumen, the site of Paneth cell degranulation 31 . These concentrations are likely similar in the human small intestine, where HD5 expression exceeds that of HD6 by 6-fold 32 . In healthy patients, epithelial lining fluid of the lung contains 31-79 nM HNP1-3, nasal fluid contains ~2.7 M HNP1-3, saliva contains 0.3-3 M HNP1-3, and vaginal secretions contain ~1.5 M HNPs and 0.3-14 M HD5 23; 33; 34; 35; 36; 37; 38 . For the -defensins, 5-10 nM HBD2 has been measured in nasal fluid 37; 39 . However, in certain disease states defensin levels can be highly elevated. For example, 57 M to 2.4 mM concentrations of HNP1 have been found in epithelial lining fluid of cystic fibrosis patients 36 . Overall, the concentrations of defensins present in vivo are generally within the range that is needed for direct antiviral activity by -defensins and generally below the concentrations required for direct antiviral activity by -defensins. Wilson et al. 
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - other
Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 1212 |
Output: 1 - other
www.thelancet.com/respiratory Vol
Output: 1 - other
Acute otitis media (AOM) is an inflammatory response to microbes in the middle ear, sometimes associated with rupture of the tympanic membrane. Human leukocytes produce different patterns of inflammatory mediators in vitro when stimulated with Gram-positive and Gram-negative bacteria, respectively. Here, we investigated the cytokine and prostaglandin E 2 (PGE 2 ) responses in middle ear fluids (MEFs) from children with spontaneously perforated AOM, and related the mediator levels to the presence of pathogens detected by culture (live) or PCR (live or dead). Furthermore, the in vivo cytokine pattern was compared with that induced in leukocytes stimulated by dead bacteria in vitro. MEFs with culturable pathogenic bacteria contained more interleukin (IL)-1b (median: 110 lg/L vs. <7.5 lg/L), tumour necrosis factor (TNF) (6.3 lg/L vs. <2.5 lg/L), IL-8 (410 lg/L vs. 38 lg/L) and IL-10 (0.48 lg/L vs. <0.30 lg/L) than culture-negative fluids, irrespective of PCR findings. IL-6 and PGE 2 were equally abundant (69-110 lg/L) in effusions with live, dead or undetectable bacteria. Cytokine levels were unrelated to bacterial species and to the presence or absence of virus. Similar levels of TNF and IL-6 as found in the MEFs were obtained by in vitro stimulation of leukocytes, whereas 11 times more IL-1b and 3.5 times more IL-8 were produced in vivo, and 22 times more IL-10 was produced in vitro. Vigorous production of proinflammatory cytokines accompanies AOM with membrane rupture, regardless of the causative agent, but the production seems to cease rapidly once the bacteria are killed and fragmented. IL-6 and PGE 2 , however, remain after bacterial disintegration, and may play a role in the resolution phase.
Output: 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - purpose, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding
We thank Héctor R. Morbidoni for critical reading of this manuscript and Paola Gallo for English revisions.
Output: 1 - background
Attaching and effacing Escherichia coli are involved in diarrhea in 2 to 8-week old calves. The virulence factors of these bacteria include: (i) the secretion of proteins (i.e. EspB) involved in microvilli effacement, (ii) the production of the intimin, a 94 kDa outer membrane protein encoded by the eaeA gene and involved in the intimate attachment of bacteria to epithelial cell and (iii) the production of verotoxins: VT1 and/or VT2. We investigated the presence and the pathotype of these strains in several calf populations by colony hybridization or by genetic amplification. Using the colony hybridization method we showed first that only 5% of calves who died from diarrhea presented EaeA E. coli strains and secondly that 19% of healthy calves showed an asymptomatic carriage. However, using colony hybridization and genetic amplification, we identified EaeA strains in 91% of calves living in farms with recurrent diarrhea problems. In 66% of the calves, there was a correlation between the presence of AEEC and diarrhea. At the pathotype level, most of the EaeA isolates were negative for VT probes. In VT bacteria, the majority were VT1. The number of VT positive bacteria was significantly higher in calves who died from diarrhea than in healthy or sick calves. This underlined the aggravating role of verotoxins in the disease. Moreover, only 25% of the bovine AEEC were positive with the EaeB probe. Surprisingly, the proportion of EaeB strains was significantly higher in healthy calves than in other populations. # 1998 Elsevier Science B.V. All rights reserved.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding
hemorrhagic fever in humans. The geographic range of human CCHF cases largely reflects the presence of ticks. However, highly similar CCHFV lineages occur in geographically distant regions. Tick-infested migratory birds have been suggested, but not confirmed, to contribute to the dispersal. Bats have recently been shown to carry nairoviruses distinct from CCHFV. In order to assess the presence of CCHFV in a wide range of bat species over a wide geographic range, we analyzed 1,135 sera from 16 different bat species collected in Congo, Gabon, Ghana, Germany, and Panama. Using a CCHFV glycoproteinbased indirect immunofluorescence test (IIFT), we identified reactive antibodies in 10.0% (114/1,135) of tested bats, pertaining to 12/16 tested species. Depending on the species, 3.6%-42.9% of cave-dwelling bats and 0.6%-7.1% of foliage-living bats were seropositive (two-tailed t-test, p = 0.0447 cave versus foliage). 11/30 IIFT-reactive sera from 10 different African bat species had neutralizing activity in a viruslike particle assay. Neutralization of full CCHFV was confirmed in 5 of 7 sera. Widespread infection of cave-dwelling bats may indicate a role for bats in the life cycle and geographic dispersal of CCHFV.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - purpose, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding
Several studies have demonstrated that administration of EBOV GP-specific antibodies protects nonhuman primates from lethal EBOV infection and may constitute a leading treatment option for EVD in humans [12] [13] [14] [15] [16] . During the West African EVD outbreak, EBOV GP-specific monoclonal antibody (MAb) cocktails (e.g., ZMapp) 12 , were used to treat several patients 17-20 . However, most of characterized therapeutic MAbs to date are EBOV GP-specific and cross-neutralizing activity against any other ebolavirus species (e.g., SUDV and
Output: 1 - background, 2 - background, 3 - finding, 4 - background, 5 - background
Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n = 29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - finding, 10 - finding, 11 - finding, 12 - finding
The average accuracy based on leave-one-out (LOO) cross validation of a Bayesian classifier generated from 143 amyloidogenic sequences is 60.84%. This is consistent with the average accuracy of 61.15% for a holdout test set comprised of 103 AM and 28 non-amyloidogenic sequences. The LOO cross validation accuracy increases to 81.08% when the training set is augmented by the holdout test set. In comparison, the average classification accuracy for the holdout test set obtained using a decision tree is 78.64%. Non-amyloidogenic sequences are predicted with average LOO cross validation accuracies between 74.05% and 77.24% using the Bayesian classifier, depending on the training set size. The accuracy for the holdout test set was 89%. For the decision tree, the nonamyloidogenic prediction accuracy is 75.00%. Conclusions: This exploratory study indicates that both classification methods may be promising in providing straightforward predictions on the amyloidogenicity of a sequence. Nevertheless, the number of available sequences that satisfy the premises of this study are limited, and are consequently smaller than the ideal training set size. Increasing the size of the training set clearly increases the accuracy, and the expansion of the training set to include not only more derivatives, but more alignments, would make the method more sound. The accuracy of the classifiers may also be improved when additional factors, such as structural and physico-chemical data, are considered. The development of this type of classifier has significant applications in evaluating engineered antibodies, and may be adapted for evaluating engineered proteins in general.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding
Background: Data for predicting which patients with pandemic influenza A (H1N1) infection are likely to run a complicated course are sparse. We retrospectively studied whether the admission serum C-reactive protein (CRP) levels can serve as a predictor of illness severity. Methods: Included were all consecutive adult patients who presented to the emergency department (ED) between May-December, 2009 with a flu-like illness, a confirmed diagnosis of pandemic influenza A (H1N1) infection and a serum CRP level measured within 24 hours of presentation. Patients with a proven additional concurrent acute illness (e.g., bacteremia) were excluded. We used the ROC curve analysis, Kaplan-Meier curves and the Cox proportional hazard model to evaluate the predictive ability of CRP as a prognostic factor. Results: Seventeen (9%) of the 191 enrolled patients were admitted to the intensive care unit (ICU), of whom eight (4%) required mechanical ventilation and three (2%) died. The median admission serum CRP levels were significantly higher among patients who required subsequent ICU care and mechanical ventilation than among patients who did not (123 mg/L and 112 mg/L vs. 40 mg/L, p < .001 and 43 mg/L, p = .017, respectively). A Cox proportional hazard model identified admission serum CRP levels and auscultatory findings over the lungs as independent prognostic factors for ICU admission. Admission serum CRP levels were the only independent prognostic factor for mechanical ventilation. Thirty days after presenting to the ED, none of the patients with admission serum CRP level <28 mg/L (lower tertile) required either ICU admission or mechanical ventilation. At the same time point, 19% of the patients with admission serum CRP level ≥70 mg/L (upper tertile) needed to be admitted to the ICU and 8% of the same upper tertile group required mechanical ventilation. The differences in the rates between the lower vs. upper tertile groups were significant (Log-Rank p < .001 for ICU and p < .024 for mechanical ventilation). Conclusions: In our study group, serum CRP levels obtained in the early ED admission stage from patients presenting with pandemic H1N1 influenza A infection were found to serve as a useful gauge for predicting disease course and assisting in patient management.
Output: 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding
Discussion: While several pathogens from the highest priority group already have a high profile in national and international health policy documents, high scores for other pathogens (e.g., Helicobacter pylori, Respiratory syncytial virus or Hantavirus) indicate a possible under-recognised importance within the current German public health framework. A process to strengthen respective surveillance systems and research has been started. The prioritization methodology has worked well; its modular structure makes it potentially useful for other settings.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding
The video component of this article can be found at jove 15, 23 . The qRT-PCR-based assay described here can detect attachment events using as few as 20 plaque forming units (PFUs) of virus, which translates into an MOI of 0.0004 for a 48-well plate. Therefore, the strong sensitivity of the assay overcomes the requirement for high MOI as well as any virus labeling or concentration steps. Further, the assay can be i) adapted to measure virion endocytosis Journal of Visualized Experiments
Output: 1 - other, 2 - finding, 3 - finding, 4 - finding, 5 - finding