niryuu/sni-each-converted huggingface dataset:
Post-translational modifications (PTMs), including phosphorylation, ubiquitylation and acetylation, of signal transduction proteins involved in the pathways engaged downstream of virus sensing are crucial to reach a fine-tuned regulation of the innate immune response 27 . In light of the very well documented importance of phosphorylation PTMs in the regulation of the antiviral response, the protein phosphatases negatively regulating the signaling events have started to be identified. The exact role of the Ser/Thr protein phosphatase 1 (PP1) in the antiviral response remains elusive as PP1α and PP1γ were found to dephosphorylate MDA-5 and RIG-I leading to their activation 28 , while they were also described to be responsible for the dephosphorylation of key C-terminal phosphoresidues of IRF3 leading to its inhibition 29 . Most . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . doi: bioRxiv preprint 15 Clement, J. F. et al. Phosphorylation of IRF-3 on Ser 339 generates a hyperactive form of IRF-3 through regulation of dimerization and CBP association.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - finding, 7 - background, 8 - other, 9 - background, 10 - other, 11 - other, 12 - other
Porphyromonas gulae is a major periodontal pathogen in dogs, which can be transmitted to their owners. A major virulence factor of P. gulae consists of a 41-kDa filamentous appendage (FimA) on the cell surface, which is classified into three genotypes: A, B, and C. Thus far, inhibition of periodontal disease in dogs remains difficult. The present study assessed the inhibitory effects of a combination of clindamycin and interferon alpha (IFN-α) formulation against P. gulae and periodontal disease. Growth of P. gulae was significantly inhibited by clindamycin; this inhibition had a greater effect on type C P. gulae than on type A and B isolates. In contrast, the IFN-α formulation inhibited the expression of IL-1β and COX-2 elicited by type A and B isolates, but not that elicited by type C isolates. Furthermore, periodontal recovery was promoted by the administration of both clindamycin and ifn-α formulation to dogs undergoing periodontal treatment; moreover, this combined treatment reduced the number of fimA genotypes in oral specimens from treated dogs. these results suggest that a combination of clindamycin and ifn-α formulation inhibit P. gulae virulence and thus may be effective for the prevention of periodontal disease induced by P. gulae.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - purpose, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding
Background: Respiratory protection effi ciency of facemasks is critically important in the battle against communicable respiratory infections such as infl uenza and severe acute respiratory syndrome (SARS). We studied the spatial distributions of simulated virus-laden respiratory droplets when human subjects wore facemasks and were exposed to regulatory viral droplets by conducting in vivo experiments in facemask use. Methods: Transmission pathway of aerosols of Fluorescein-KCl solution through facemasks and protective effi ciency of facemasks were examined by using normal surgical facemasks and two facemasks with exhaust valves (Facemask A) and exhaust holes (Facemask B) covered with the same surgical fi lters situated at the back of the facemasks. Fluorescein-KCl solution was sprayed onto the faces of participants wearing the facemasks and performing intermittent exercises on a treadmill in a climatic chamber. Results: Experimental results showed that when droplets spread onto a person face-to-face over short distances, 92.3% to 99.5% of droplets were blocked by the front surface of the facemask, whereas only 0.5% to 7.7% of droplets reached the back of the facemask. Both facemasks A and B had near or over 99% protection effi ciency, compared with that of 95.5% to 97% of surgical facemasks. Using the same fi lters as normal surgical masks, facemasks A and B provided more effective respiratory protection against communicable respiratory infections such as infl uenza and SARS by the location of the breathing pathway to the back of the facemasks. Conclusions: Separating the breathing pathway from the virus-contaminated area in facemasks can provide more effective protection against communicable respiratory infections such as infl uenza and SARS.
Output: 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
Direct-acting antivirals are effective tools to control viral infections. SARS-CoV-2 is a coronavirus associated with the epidemiological outbreak in late 2019. Previous reports showed that HIV-1 protease inhibitors could block SARS-CoV main protease. Based on that and using an in silico approach, we evaluated SARS-CoV-2 main protease as a target for HIV-1 protease inhibitors to reveal the structural features related to their antiviral effect. Our results showed that several HIV inhibitors such as lopinavir, ritonavir, and saquinavir produce strong interaction with the active site of SARS-CoV-2 main protease. Furthermore, broad library protease inhibitors obtained from PubChem and ZINC (www.zinc.docking.org) were evaluated. Our analysis revealed 20 compounds that could be clustered into three groups based on their chemical features. Then, these structures could serve as leading compounds to develop a series of derivatives optimizing their activity against SARS-CoV-2 and other coronaviruses. Altogether, the results presented in this work contribute to gain a deep understanding of the molecular pharmacology of SARS-CoV-2 treatment and validate the use of protease inhibitors against SARS-CoV-2.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding
www.ajpmonline.org
Output: 1 - other
Over the past few decades, global metapopulation epidemic simulations built with worldwide air-transportation data have been the main tool for studying how epidemics spread from the origin to other parts of the world (e.g., for pandemic influenza, SARS, and Ebola). However, it remains unclear how disease epidemiology and the air-transportation network structure determine epidemic arrivals for different populations around the globe. Here, we fill this knowledge gap by developing and validating an analytical framework that requires only basic analytics from stochastic processes. We apply this framework retrospectively to the 2009 influenza pandemic and 2014 Ebola epidemic to show that key epidemic parameters could be robustly estimated in real-time from public data on local and global spread at very low computational cost. Our framework not only elucidates the dynamics underlying global spread of epidemics but also advances our capability in nowcasting and forecasting epidemics.
Output: 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - method, 6 - finding
This paper assesses the impact of the September 11 terrorist attacks and its after-effects on U.S. airline demand. Using monthly time-series data from 1986 to 2003, we find that September 11 resulted in both a negative transitory shock of over 30% and an ongoing negative demand shock amounting to roughly 7.4% of pre-September 11 demand. This ongoing demand shock has yet to dissipate (as of November 2003) and cannot be explained by economic, seasonal, or other factors.
Output: 1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding
No highlights are required as this is not a research article
Output: 1 - other
Conclusions: Normal cough produced a turbulent jet about 0.7 m towards the end of the bed from the recumbent subject. N95 mask was more effective than surgical mask in preventing expelled air leakage during coughing but there was still significant sideway leakage.
Output: 1 - finding, 2 - finding
Streptococcus mutans is a bacterial cause of dental caries that is resistant to bacitracin. The aim of this study was to elucidate the mbrABCD-related bacitracin resistance mechanism of S. mutans. Transcriptome data demonstrated that the expression levels of 33 genes were induced more than twofold by bacitracin. Fourteen genes were selected from the upregulated genes, and defective mutants of these genes were constructed for measurement of their sensitivity to bacitracin. Among the mutants, only the mbrA-or mbrB-deficient mutants exhibited 100-to 121-fold greater sensitivity to bacitracin when compared with the wild-type strain. Moreover, knockout of the mbrC and mbrD genes abolished the bacitracin-induced mbrAB upregulation. These results suggest that both mbrC and mbrD are required for mbrAB upregulation that confers the bacitracinresistant phenotype on S. mutans.
Output: 1 - background, 2 - purpose, 3 - finding, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding
www.nature.com/reviews/molcellbio
Output: 1 - other
Abbreviations: B16M -B16 melanoma; ELISA -enzyme-linked immunosorbent assay; IL-18 -interleukin-18; i.p.intraperitoneal; LPS -lipopolysaccharide; MHV -Mouse Hepatitis Virus; TNF-a -tumor necrosis factor a
Output: 1 - finding
We found that the sensitivities of 3 rapid influenza antigen tests for pandemic influenza A/H1N1 virus were low to moderate: BD Directigen EZ Flu A+B test (Becton Dickinson), 46.7%; BinaxNOW Influenza A&B (Inverness Medical), 38.3%; and QuickVue Influenza A+B Test (Quidel), 53.3%. A patient with influenza-like illness who has a negative rapid antigen test result should undergo further testing using reverse-transcription polymerase chain reaction.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding
Background: Despite current knowledge of mutations in 45 genes that can cause nonsyndromic sensorineural hearing loss (SNHL), no unified clinical test has been developed that can comprehensively detect mutations in multiple genes. We therefore designed Affymetrix resequencing microarrays capable of resequencing 13 genes mutated in SNHL (GJB2, GJB6, CDH23, KCNE1, KCNQ1, MYO7A, OTOF, PDS, MYO6, SLC26A5, TMIE, TMPRSS3, USH1C). We present results from hearing loss arrays developed in two different research facilities and highlight some of the approaches we adopted to enhance the applicability of resequencing arrays in a clinical setting. Results: We leveraged sequence and intensity pattern features responsible for diminished coverage and accuracy and developed a novel algorithm, sPROFILER, which resolved >80% of no-calls from GSEQ and allowed 99.6% (range: 99.2-99.8%) of sequence to be called, while maintaining overall accuracy at >99.8% based upon dideoxy sequencing comparison. Conclusions: Together, these findings provide insight into critical issues for disease-centered resequencing protocols suitable for clinical application and support the use of array-based resequencing technology as a valuable molecular diagnostic tool for pediatric SNHL and other genetic diseases with substantial genetic heterogeneity.
Output: 1 - background, 2 - background, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding
Pandemic growth rates from sequences E. de Silva et al. 1807 
Output: 1 - other
This study aimed to determine the aetiology of community-acquired pneumonia (CAP) by adding polymerase chain reaction (PCR) to conventional methods and to describe the clinical and laboratory features between patients with bacterial pneumonia (BP) and viral pneumonia (VP). Adults with CAP admitted from November 2009 to October 2010 were included. Demographics, comorbidities, severity and clinical features were recorded. Conventional microbiological methods included blood and sputum cultures, acute and convalescent serologic samples, and antigen urinary detection. New methods included multiplex PCR for Mycoplasma pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae, Bordetella pertussis and 15 respiratory viruses. A total of 169 patients were included. Using conventional methods, we identified a pathogen in 51 % of cases. With PCR, up to 70 % of cases had an aetiological diagnosis. Fortyfive patients had BP (34 %), 22 had VP (17 %) and 25 (19 %) had co-infection (BP and VP). Pneumococci and respiratory syncytial virus (RSV) were the most frequently identified pathogens. Procalcitonin (PCT) and C-reactive protein (CRP) median values were significantly higher in BP than in VP patients. Shaking chills, higher CURB score and shock were significantly more frequent in BP. A viral infection was identified in more than one-third of patients with CAP. Clinical and laboratory features could help to differentiate between VP and BP and to guide empirical therapy. A. Sangil : E. Calbo : S. Benet : M. E. Viladot : V. Pascual :
Output: 1 - purpose, 2 - method, 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
MERS-coronavirus infection is currently responsible for considerable morbidity and mortality in Saudi Arabia. Understanding its burden, as an emerging infectious disease, is vital for devising appropriate control strategies. In this study, the burden of MERS-CoV was estimated over 31 months period from June 6, 2012 to January 5, 2015. The total number of patients was 835; 528 (63.2%) patients were male, 771 (92.3%) patients were ≥25 years of age, and 210 (25.1%) patients were healthcare workers. A total of 751 (89.9%) patients required hospitalization. The median duration between onset of illness and hospitalization was 2 days (interquartile range, 0-5). The median length of hospital stay was 14 days (IQR, 6-27). The overall case fatality rate was 43.1%. Basic reproductive number was 0.9. Being Saudi, non-healthcare workers, and age ≥65 years were significantly associated with higher mortality. In conclusion, MERS-CoV infection caused a substantial health burden in Saudi Arabia.
Output: 1 - background, 2 - background, 3 - background, 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
The optimal template for homology modeling of the E protein of SARS-CoV-2 was the E protein of SARS(PDB ID: 5x29.1), with the sequence identity of 91.38% and author/funder. All rights reserved. No reuse allowed without permission.
Output: 1 - finding, 2 - finding, 3 - other, 4 - other
In particular, 63% (12 of 19) of fecal samples from Miniopterus pusillus were positive for the virus. These findings suggest that this virus might be commonly circulating in M. pusillus in Hong Kong.
Output: 1 - finding, 2 - finding
Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 12503 |
Output: 1 - other
Public Health jo urnal homepage: www .e lse vi er.co m/ pu he p u b l i c h e a l t h 1 5 0 ( 2 0 1 7 ) 1 4 9 e1 5 1.
Output: 1 - other, 2 - other
Hepatocytes are key effector cells in anti-Coxsackievirus immunity PLOS Pathogens.
Output: 1 - other
Mannheimia haemolytica is the most important bacterial agent associated with the bovine respiratory disease complex (BRDC), which causes worldwide economic losses to the cattle industry. M. haemolytica cells initially colonize the tonsillar crypts in the upper respiratory tract of cattle, from where they can subsequently descend into the lungs to cause disease. Many bacteria exist as biofilms inside their hosts. We hypothesize that M. haemolytica colonization of cattle during its commensal state may include biofilm formation. To begin to assess this possibility, we developed an in vitro system to study biofilm formation directly on bovine respiratory epithelial cells. Using fixed primary bovine bronchial epithelial cells, we observed M. haemolytica biofilm formation after a 48 h incubation period at 37 C. Addition of mucin, the main component of mucus present in the upper respiratory tract, decreased M. haemolytica biofilm formation on bovine epithelial cells. We investigated the effects of prior viral infection of the epithelial cells on subsequent biofilm formation by M. haemolytica and found negligible effects. Utilization of this model system will provide new insights into the potential role of biofilm formation by M. haemolytica in the pathogenesis of BRDC.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding
License, which permits unrestricted use, provided the original author and source are credited.
Output: 1 - other, 2 - other
Citation Chan JM, Rabadan R. 2013. Quantifying pathogen surveillance using temporal genomic data. mBio 4(1):e00524-12.
Output: 1 - other, 2 - other, 3 - other
WIDER IMPLICATIONS: This is the first comprehensive review of rodent models of both infectious and autoimmune disease of testis/ epididymis, and their clinical implications, i.e. their importance in understanding male infertility related to infectious and non-infectious/ autoimmune disease of the reproductive organs.
Output: 1 - finding, 2 - finding
The objective of this study was to develop a symptom scoring system for use in clinical studies that differentiates children with cold symptoms who have an identifiable viral etiology for their upper respiratory tract infection (URI) from those in whom no virus is detected. Nasal swabs for PCR testing for identification of respiratory viruses were obtained on children aged 2-11 y at baseline and when parents thought their child was developing a cold. Parentalrecorded severity of specific symptoms in children with and without a documented viral URI were compared. Nasal swabs were obtained on 108 children whose parents reported their child was developing a cold. A viral etiology was identified in 62 of 108 (57.4%) samples. Symptom measures that best differentiated children with a viral etiology from those without were significant runny nose and significant cough on days 1-4 of the illness. A URI symptom score was developed based on these symptoms, with a sensitivity of 81.4%, specificity of 61.9%, and accuracy of 73.3%. Parental impression is only a moderately accurate predictor of viral URI in children. Our URI symptom score provided a more accurate method for identifying children with viral URIs for clinical studies. (Pediatr Res 68: 252-257, 2010)
Output: 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - other
within the receptor binding domain (RBD) of the MERS-CoV S protein. We used a complex consisting of the epitope peptide of the MERS-CoV S protein and CpG-DNA encapsulated in liposome complex to immunize mice, and produced the monoclonal antibodies 506-2G10G5 and 492-1G10E4E2. The western blotting data showed that both monoclonal antibodies detected the S protein and immunoprecipitated the native form of the S protein. Indirect immunofluorescence and confocal analysis suggested strong reactivity of the antibodies towards the S protein of MERS-CoV virus infected Vero cells. Furthermore, the 506-2G10G5 monoclonal antibody significantly reduced plaque formation in MERS-CoV infected Vero cells compared to normal mouse IgG and 492-1G10E4E2. Thus, we successfully produced a monoclonal antibody directed against the RBD domain of the S protein which could be used in the development of diagnostics and therapeutic applications in the future. [BMB Reports 2019; 52(6): 397-402] BMB Rep. 2019; 52(6): 397-402 www.bmbreports.org
Output: 1 - background, 2 - method, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - other
Mis-secreted glycoproteins (LGI1, reelin) are emerging causes of epilepsy. LMAN2L belongs to a glycoprotein secretion chaperone family. One recessive LMAN2L missense mutation predicted to impair the chaperone's interaction with glycoproteins was reported in a family with intellectual disability (ID) and remitting epilepsy. We describe four members of a family with autosomal dominant inheritance of a similar phenotype. We show that they segregate a NM_001142292.1:c.1073delT mutation that eliminates LMAN2L's endoplasmic reticulum retention signal and mislocalizes the protein from that compartment to the plasma membrane. LMAN2L mislocalization, like impaired glycoprotein interaction, disturbs brain development, including generation of developmentally restricted epilepsy.
Output: 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - finding, 6 - finding, 7 - finding
Citation Peng X, et al. 2011. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. mBio 2(6):e00198-11.
Output: 1 - finding, 2 - finding, 3 - other
Musk of musk deer has been one of the most precious traditional medicinal materials for treatment of stroke, but trading is prohibited. Musk of muskrat, Ondatra zibethicus, is an accessible substitute for musk of musk deer. However, neuroprotective effects of the musk of muskrat on stroke model are so far unclear. Aim of the study is to determine neuroprotective effects of the musk of muskrat on focal cerebral ischemia. The protective effects against focal cerebral ischemia were evaluated using a model of middle cerebral artery occlusion (90-minute occlusion followed by 24-hour reperfusion). Musk of muskrat was collected from scent bag of muskrat and orally administered at doses of 100 and 300 mg/kg twice at times of 0 and 90 min after occlusion. The effects on sensorimotor dysfunction were investigated by using balance beam test and rotarod test after brain ischemia. The expression of cyclooxygenase-2 (COX-2) was investigated by immunohistochemistry. Oral administration of musk at 300 mg/kg significantly reduced (p<0.001) the infarct volume by 32.4% compared with a vehicle-treated group. Oral administration of musk at 300 mg/kg also ameliorated ischemia-induced spontaneous and vestibule sensorimotor dysfunction in balance beam test and rotarod test compared with control group and COX-2 upregulation. Musk of muskrat may have neuroprotective effects against transient focal cerebral ischemia with recovery of sensorimotor dysfunction. Regarding the immunohistochemistry, the effects of muskrat may be due to anti-inflammatory properties through inhibition of COX-2 expressions.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - finding, 12 - finding, 13 - finding
The copyright holder for this preprint (which was not peer-reviewed) is . 1101 updating the predictions with the use of fresh data and using more complicated mathematical models.
Output: 1 - other, 2 - other, 3 - other
Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.
Output: 1 - background, 2 - method, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding
Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 12226 |
Output: 1 - other
A total of 123 community paediatricians and 23 microbiology laboratories studied the clinical and bacteriological efficacy of treatment of group A streptococcal pharyngitis in Italy. Of 1065 patients, from whom Streptococcus pyogenes was isolated, 723 returned to follow up and of these 138 (19%) still had a positive throat culture. The erythromycin resistance (ER) rate was 23.7% with resistance phenotype distribution of: 31.7% constitutive (CR), 26.6% inducible (IR) and 41.7% efflux pump (M) resistance phenotype. All strains were susceptible to the b-lactam agents tested. CR strains were highly resistant to all 14, 15 and 16 membered macrolides with the exception of rokitamycin which showed activity against 37.8% of isolates. All phenotype M and some IR isolates were susceptible to clindamycin, rokitamycin, josamycin and spiramycin; clarithromycin was active against a small percentage of strains belonging to the IR and M phenotype. Bacterial eradication was found in 85.5, 78.7 and 75.8% of the penicillin, macrolide and cephalosporin treated groups. Genotyping of strains showed that 8.7% of the 19% of cases classified as 'failed bacterial eradication' were due to recolonization with a different isolate, observed exclusively among b-lactams treated patients. Clinical cure was achieved in a high percentage of cases, irrespective of the antibiotic prescribed, with the best clinical efficacy being found following therapy with amoxycillin and clarithromycin (90.9%).
Output: 1 - method, 2 - method, 3 - method, 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
Fig. 6. Input mzML/mzXML les were processed with OpenMS 34 and low-quality MS/MS spectra .
Output: 1 - method, 2 - other
News exposure and collective attention during epidemics PLOS Computational Biology.
Output: 1 - finding
In an effort to rapidly discover lead compounds targeting M pro , two compounds (11a and 11b) were designed and synthesized, both of which exhibited excellent inhibitory activity with an IC 50 value of 0.05 μ M and 0.04 μ M respectively. Significantly, both compounds exhibited potent anti-SARS-CoV-2 infection activity in a cell-based assay with an EC 50 value of 0.42 μ M and 0.33 μ M, respectively. The X-ray crystal structures of SARS-CoV-2 M pro in complex with 11a and 11b were determined at 1.5 Å resolution, respectively. The crystal structures showed that 11a and 11b are covalent inhibitors, the aldehyde groups of which are bound covalently to Cys145 of M pro . Both compounds showed good PK properties in vivo, and 11a also exhibited low toxicity which is promising drug leads with clinical potential that merits further studies.
Output: 1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding
Objectives of this study were to determine prevalence of infection in feral cats in Northern Florida with a select group of infectious organisms and to determine risk factors for infection. Blood samples or sera from 553 cats were tested with a panel of antibody, antigen or PCR assays. Male cats were at higher risk for FIV, Mycoplasma haemofelis, and M. haemominutum. Infection with either FeLV or FIV was associated with increased risk for coinfection with the other retrovirus, M. haemofelis, or M. haemominutum. Bartonella henselae had the highest prevalence and was the only organism that did not have any associated risk for coinfection with other organisms. Feral cats in this study had similar or lower prevalence rates of infections than those published for pet cats in the United States. Thus, feral cats assessed in this study appear to be of no greater risk to human beings or other cats than pet cats.
Output: 1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding
Bordetella bronchiseptica isolate KM22 has been used in experimental infections of swine as a model of clinical B. bronchiseptica infection and to study host-to-host transmission. The draft genome sequence of KM22 was reported in 2014. Here, we report the complete genome sequence of KM22.
Output: 1 - background, 2 - background, 3 - purpose
Define the space of probability distributions on the action space (0 ≤ a i ≤ 1) [0, 1] as ([0, 1]). A mixed strategy profile σ (·) is a function that maps the state s ∈ {0, 1} n to the space of probability distributions on the actions space, i.e., σ i : {0, 1} n → ([0, 1]). The definition of a mixed MMPE strategy profile σ * := {σ * i : {0, 1} n → [0, 1]} is a distribution on the action space that satisfies the following, for all t = 1, 2, . . . , and i ∈ N ,
Output: 1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method
Design, synthesis and biological evaluation of a series of 5-chloropyridine ester-derived severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors is described. Position of the carboxylate functionality is critical to potency. Inhibitor 10 with a 5-chloropyridinyl ester at position 4 of the indole ring is the most potent inhibitor with a SARS 3Clpro IC 50 value of 30 nM and antiviral EC 50 value of 6.9 μM. Molecular Docking studies have provided possible binding modes of these inhibitors.
Output: 1 - background, 2 - background, 3 - background, 4 - finding
The AsiaFluCap Simulator is freely available software (www.cdprg.org) which can be used by policy makers, policy advisors, donors and other stakeholders involved in preparedness for providing evidence based and illustrative information on health care resource capacities during future pandemics. The tool can inform both preparedness plans and simulation exercises and can help increase the general understanding of dynamics in resource capacities during a pandemic. The combination of a mathematical model with multiple resources and the linkage to GIS for creating maps makes the tool unique compared to other available software.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding
publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. Comment 544 www.thelancet.com/infection Vol 14 July 2014 5 Lowe R, Barcellos C, Coelho C, et al. Dengue outlook for the World Cup in Brazil: an early warning model framework driven by real-time seasonal climate forecasts. Lancet Infect Dis 2014; published online May 17.
Output: 1 - background, 2 - other, 3 - other, 4 - other, 5 - background, 6 - other, 7 - other
Citation Perlman S, Zhao J. 2013. Human coronavirus EMC is not the same as severe acute respiratory syndrome coronavirus. mBio 4(1):e00002-13.
Output: 1 - other, 2 - finding, 3 - other
Glycyrrhiza glabra L. has become an endangered medicinal plant due to the unabated extraction of glycyrrhizin. Glycyrrhizin is a triterpenoid saponin that is a root centric secondary metabolite having numerous pharmacological properties, such as anti-inflammatory, immunomodulatory, antiallergic, antiulcer, and is found to be effective even against HIV. Harvesting of the roots for high value glycyrrhizin destroys the whole plant causing existential threat to the plant itself and consequent damage to biodiversity. The present study establishes that hairy root cultures of G. glabra, using an optimized elicitor, can dramatically enhance focused production of glycyrrhizin at a much faster pace year-round without causing destruction of the plant. Hairy root cultures of G. glabra were developed using the Agrobacterium rhizogenes A4 strain. The glycyrrhizin content was enhanced using different biotic and abiotic elicitors, for example, PEG (polyethylene glycol), CdCl 2 , cellulase, and mannan at different concentrations and durations. PEG at 1% concentration enhanced the yield of glycyrrhizin up to 5.4fold after 24 h of exposure, whereas 200 µg mL −1 cellulase enhanced glycyrrhizin yield to 8.6-fold after 7 days of treatment. Mannan at 10 mg L −1 concentration enhanced the production of glycyrrhizin up to 7.8-fold after 10 days of stress. Among different antioxidant enzymes, SOD activity was significantly enhanced under drought, cellulase and mannan stress. This identification of elicitors can result in abundant supply of valuable glycyrrhizin to meet broad spectrum demand through commercial production without endangering G. glabra L.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - purpose, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding
Background: Emerging viral diseases, most of which are caused by the transmission of viruses from animals to humans, pose a threat to public health. Discovering pathogenic viruses through surveillance is the key to preparedness for this potential threat. Next generation sequencing (NGS) helps us to identify viruses without the design of a specific PCR primer. The major task in NGS data analysis is taxonomic identification for vast numbers of sequences. However, taxonomic identification via a BLAST search against all the known sequences is a computational bottleneck. Description: Here we propose an enhanced lowest-common-ancestor based method (ELM) to effectively identify viruses from massive sequence data. To reduce the computational cost, ELM uses a customized database composed only of viral sequences for the BLAST search. At the same time, ELM adopts a novel criterion to suppress the rise in false positive assignments caused by the small database. As a result, identification by ELM is more than 1,000 times faster than the conventional methods without loss of accuracy. Conclusions: We anticipate that ELM will contribute to direct diagnosis of viral infections. The web server and the customized viral database are freely available.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding
Respiratory viruses are frequently detected in association with chronic tonsillar hypertrophy in the absence of symptoms of acute respiratory infection (ARI). The present analysis was done in follow-up to a previous clinical study done by this same group. Nasopharyngeal washes (NPWs) were obtained from 83 of 120 individuals at variable times post adenotonsillectomy, in the absence of ARI symptoms. A look back at virus detection results in NPWs from the same 83 individuals at the time of tonsillectomy revealed that 73.5% (61/83) were positive for one or more viruses. The overall frequency of respiratory virus detection in posttonsillectomy NPWs was 58.8%. Rhinovirus (RV) was the agent most frequently detected, in 38 of 83 subjects (45.8%), followed by enterovirus in 7 (8.4%), human metapneumovirus in 6 (7.2%), human respiratory syncytial virus in 3 (3.6%) and human coronavirus in 1 (1.2%). Remarkably, there was no detection of adenovirus (HAdV) or human bocavirus (HBoV) in asymptomatic individuals in follow-up of adenotonsillectomy. In keeping with persistence of respiratory DNA viruses in human tonsils, tonsillectomy significantly reduces asymptomatic shedding of HAdV and HBoV in NPWs.
Output: 1 - background, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding
Conclusions Infection immunity to a recent human H3N2 virus confers minimal cross-protection against a European swine H3N2 virus. We discuss our findings with regard to the recent zoonotic infections of humans in the United States with a swine-origin H3N2 variant virus. Please cite this paper as: Qiu et al. (2013) Prior infection of pigs with a recent human H3N2 influenza virus confers minimal cross-protection against a European swine H3N2 virus.
Output: 1 - finding, 2 - finding, 3 - finding
Results: High prices of medicinal plants are widely considered to reflect resource scarcity. Real-time market prices for three of the four very different TCM species we studied all showed major price fluctuations. The exception was P. polyphylla, whose wild populations are widely known to be increasingly scarce, where there was a steady increase in price, with few fluctuations in the upward price trend. The three other species showed significant price fluctuations. These were driven by multiple factors. Ecological and biogeographic factors that influence abundance or scarcity of supply certainly played a role. But other factors were also influential. These included both national and global economic factors (the influence of the Global Financial Crisis (GFC)), national policy changes that in turn influenced businessmen giving expensive gifts (that included O. sinensis)), climate change (influencing fruiting success of S. sphenanthera), price speculation by traders and lack of information (e.g: reduction in G. gecko prices due to traders incorrectly believing that domestication would increase supplies). Conclusions: Price fluctuations in the four TCM species we examined are influenced by many factors and not just resource scarcity. And the situation is more complex than the trajectory based on Homma's (1992) model, where he predicted that higher prices would result in a shift to cultivation, thus replacing wild harvest. In case of both O. sinensis and P. polyphylla, Homma (1992 Homma ( , 1996 was right in terms of scarcity and high prices stimulating a major investment in cultivation (P. polyphylla) and artificial production (O. sinensis). But in both cases, intensive production through cultivation or artificial propagation do not yet occur on a large enough scale to reduce harvest of wild stocks. Substitution and adulteration occur with all four species. Improving information to doi.
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 - finding, 20 - finding, 21 - finding, 22 - other
The heptad repeats (HR1 and HR2) of the spike protein of SARS-CoV are highly conserved regions forming a critical 6-helix bundle during the fusion step of virus entry and are attractive targets of entry inhibitors. In this study, we report that a minimal HR2 peptide, P6 of 23-mer, can block the fusion of SARS-CoV with an IC 50 of 1.04 ± 0.22 M. This finding supports the structural prediction of the deep groove of HR1 trimer as a target for fusion inhibitors, and suggests P6 as a potential lead peptide for future drug development. Moreover, combination of an HR-1 peptide, N46, and its mutated version, N46eg, shows synergistic inhibition with an IC 50 of 1.39 ± 0.05 M and combination index of 0.75 ± 0.15, suggesting a common strategy to achieve promising inhibition by HR1 peptide for other class I envelope viruses.
Output: 1 - background, 2 - purpose, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding
After 3-day acclimation, pigs in the challenged group were inoculated with a prototype US PEDV isolate US/Iowa/18984/ 2013 (GenBank accession #KF804028) (Hoang et al., 2013), 10 3 plaque-forming units/pig, via oro-gastric gavage as previously described (Madson et al., 2014). Pigs in the control group received virus-free cell culture media. Some of these pigs were inoculated again with the same strain in the identical manner at day 56 post-inoculation (PI).
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding
Viral channel forming proteins (VCPs) have been discovered in the late 70s and are found in many viruses to date. Usually they are small and have to assemble to form channels which depolarize the lipid membrane of the host cells. Structural information is just about to emerge for just some of them. Thus, computational methods play a pivotal role in generating plausible structures which can be used in the drug development process. In this review the accumulation of structural data is introduced from a historical perspective. Computational performances and their predictive power are reported guided by biological questions such as the assembly, mechanism of function and drug-protein interaction of VCPs. An outlook of how coarse grained simulations can contribute to yet unexplored issues of these proteins is given. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding
Trial registration: UKCRN ID number 19086, registered May 2015; as well as registration at www.trialregister.nl under the acronym 'BreathDx' with trial ID number NTR 6114 (retrospectively registered on 28 October 2016).
Output: 1 - finding, 2 - finding
The dynamics of H5N1 influenza virus pathogenesis are multifaceted and can be seen as an emergent property that cannot be comprehended without looking at the system as a whole. In past years, most of the high-throughput studies on H5N1-host interactions have focused on the host transcriptomic response, at the cellular or the lung tissue level. These studies pointed out that the dynamics and magnitude of the innate immune response and immune cell infiltration is critical to H5N1 pathogenesis. However, viral-host interactions are multidimensional and advances in technologies are creating new possibilities to systematically measure additional levels of 'omic data (e.g. proteomic, metabolomic, and RNA profiling) at each temporal and spatial scale (from the single cell to the organism) of the host response. Natural host genetic variation represents another dimension of the host response that determines pathogenesis. Systems biology models of H5N1 disease aim at understanding and predicting pathogenesis through integration of these different dimensions by using intensive computational modeling. In this review, we describe the importance of 'omic studies for providing a more comprehensive view of infection and mathematical models that are being developed to integrate these data. This review provides a roadmap for what needs to be done in the future and what computational strategies should be used to build a global model of H5N1 pathogenesis. It is time for systems biology of H5N1 pathogenesis to take center stage as the field moves towards a more comprehensive view of virushost interactions.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - finding, 10 - finding
Porcine epidemic diarrhea virus (PEDV) is a coronavirus which causes severe diarrhea and fatal dehydration in piglets. In general, probiotic supplements could enhance recovery and protect piglets against enteric pathogens. Seven local lactic acid bacteria (LAB), (Ent. faecium 79N and 40N, Lact. plantarum 22F, 25F and 31F, Ped. acidilactici 72N and Ped. pentosaceus 77F) from pig feces were well-characterized as high potential probiotics. Cell-free supernatants (CFS) and live LAB were evaluated for antiviral activities by coincubation on Vero cells and challenged with a pandemic strain of PEDV isolated from pigs in Thailand. Cell survival and viral inhibition were determined by cytopathic effect (CPE) reduction assay and confirmed by immunofluorescence. At 1:16, CFS dilution (pH 6.3-6.8) showed no cytotoxicity in Vero cells and was therefore used as the dilution for antiviral assays. The diluted CFS of all Lact. plantarum showed the antiviral effect against PEDV; however, the same antiviral effect could not be observed in Ent. faecium and Pediococcus strains. In competitive experiment, only live Lact. plantarum 25F and Ped. pentosaceus 77F showed CPE reduction in the viral infected cells to <50% observed field area. This study concluded that the CFS of all tested lactobacilli, and live Lact. plantarum (22F and 25F) and Pediococcus strains 72N and 77F could reduce infectivity of the pandemic strain of PEDV from pigs in Thailand on the target Vero cells.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - method, 9 - method, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding
The present work was conducted to investigate the antioxidant activity and neuroprotective effects of Tripterygium regelii extract (TRE) on H 2 O 2 -induced apoptosis in human dopaminergic cells, SH-SY5Y. TRE possessed considerable amounts of phenolics (282.73 mg tannic acid equivalents/g of extract) and flavonoids (101.43 mg naringin equivalents/g of extract). IC 50 values for reducing power and DPPH radical scavenging activity were 52.51 and 47.83 lg, respectively. The H 2 O 2 scavenging capacity of TRE was found to be 57.68 lM 9 lg -1 min -1 . By examining the effects of TRE on SH-SY5Y cells injured by H 2 O 2 , we found that after incubation of cells with TRE prior to H 2 O 2 exposure, the H 2 O 2 induced cytotoxicity was significantly reversed and the apoptotic features such as change in cellular morphology, nuclear condensation and DNA fragmentation was inhibited. Moreover, TRE was very effective attenuating the disruption of mitochondrial membrane potential and apoptotic cell death induced by H 2 O 2 . TRE extract effectively suppressed the up-regulation of Bax, Caspase-3 and -9, and down-regulation of Bcl-2. Moreover, TRE pretreatment evidently increased the tyrosine hydroxylase (TH) and brain-derived neurotrophic factor (BDNF) in SH-SY5Y cells. These findings demonstrate that TRE protects SH-SY5Y cells against H 2 O 2 -induced injury and antioxidant properties may account for its neuroprotective actions and suggest that TRE might potentially serve as an agent for prevention of neurodegenerative disease associated with oxidative stress.
Output: 1 - purpose, 2 - finding, 3 - finding, 4 - finding, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding
The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of São Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. No repeatable, characteristic amino acid motifs for regions of the PCV2 capsid protein seemed to be associated with abortion in sows.
Output: 1 - finding, 2 - finding
Flies were transferred to plates of Escherichia coli or Pseudomonas aeruginosa and allowed to walk on the bacteria for a total of 5 min. After the flies were contaminated, they were either immediately collected to quantify bacteria or were placed onto sterile plates to clean for 5 or 10 min. After cleaning, flies were placed into tubes with 1 ml of sterile 0.85% saline and were gently shaken for 1 min to remove bacteria. A serial dilution was made and 50-ml spot titers were plated. Cleaning behavior was also monitored and scored for a period of 5 min. Results demonstrate a bacterial reduction for both bacteria on all three fly species. Sarcophaga bullata and D. virilis both showed a significant reduction of both bacteria within 10 min, whereas M. domestica only showed a significant reduction in P. aeruginosa. Cleaning behavior increased significantly in flies that were exposed to bacteria compared to flies that were not exposed to bacteria. This study is important, as it demonstrates that fly cleaning could affect mechanical transmission of disease, and additional studies should look at flies' abilities to remove other types of microorganisms.
Output: 1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding