niryuu/sni-each-converted huggingface dataset:
Background: 3D domain swapping is a novel structural phenomenon observed in diverse set of protein structures in oligomeric conformations. A distinct structural feature, where structural segments in a protein dimer or higher oligomer were shared between two or more chains of a protein structure, characterizes 3D domain swapping. 3D domain swapping was observed as a key mediator of numerous functional mechanisms and play pathogenic role in various diseases including conformational diseases like amyloidosis, Alzheimer's disease, Parkinson's disease and prion diseases. We report the first study with a focus on identifying functional classes, pathways and diseases mediated by 3D domain swapping in the human proteome. Methods: We used a panel of four enrichment tools with two different ontologies and two annotations database to derive biological and clinical relevant information associated with 3D domain swapping. Protein domain enrichment analysis followed by Gene Ontology (GO) term enrichment analysis revealed the functional repertoire of proteins involved in swapping. Pathway analysis using KEGG annotations revealed diverse pathway associations of human proteins involved in 3D domain swapping. Disease Ontology was used to find statistically significant associations with proteins in swapped conformation and various disease categories (P-value < 0.05). Results: We report meta-analysis results of a literature-curated dataset of human gene products involved in 3D domain swapping and discuss new insights about the functional repertoire, pathway associations and disease implications of proteins involved in 3D domain swapping. Conclusions: Our integrated bioinformatics pipeline comprising of four different enrichment tools, two ontologies and two annotations revealed new insights into the functional and disease correlations with 3D domain swapping. GO term enrichment were used to infer terms associated with three different GO categories. Protein domain enrichment was used to identify conserved domains enriched in swapped proteins. Pathway enrichment analysis using KEGG annotations revealed that proteins with swapped conformations are present in all six classes of KEGG BRITE hierarchy and significantly enriched KEGG pathways were observed in five classes. Five major classes of disease were found to be associated with 3D domain swapping using functional disease ontology based enrichment analysis. Five classes of human diseases: cancer, diseases of the respiratory or pulmonary system, degenerative diseases of the central nervous system, vascular disease and encephalitis were found to be significant. In conclusion, our study shows that bioinformatics based analytical approaches using curated data can enhance the understanding of functional and disease implications of 3D domain swapping.
Output: Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome
Strategies that can improve health and maximize growth in the preweaning period should improve the subsequent production and longevity of replacement animals. Few data are available that quantify feed and water consumption, as well as growth, in healthy versus non-healthy calves-the objective of this study. A database of Holstein calves (<1 wk of age; n = 313) was developed to compare calves that developed diarrhea in the first 21 d after arrival from commercial farms to the research facility versus calves that remained healthy. Individual calf data from 4 experiments included daily intake of milk replacer, free water, electrolyte solution, and starter grain, as well as weekly body weight (BW) and frame measures for 21 d after arrival. Calves with a fecal score of >2 for ≥3 consecutive days over the first 21 d of each experiment were retrospectively classified as diarrheic (DIA; n = 96); the remainder were classified as healthy (HEA; n = 217). Other health issues were minimal. The likelihood of elevated fecal score occurrence and the cumulative number of days with an elevated score were greater for DIA calves than for HEA calves. The initial total protein concentration in blood did not differ between classifications. Cumulative milk replacer dry matter intake (DMI) and water consumed from milk replacer were significantly less for DIA calves than for HEA calves, because DIA calves were more likely to refuse milk replacer. Cumulative starter DMI was decreased for DIA versus HEA calves. As a result, cumulative total DMI was significantly less for DIA calves than for HEA calves. Cumulative free water intake did not differ between classifications. The DIA calves were more likely to receive electrolyte solution and have more days given electrolyte solution than HEA calves. As a result, total cumulative intake of electrolyte solution was greater in DIA calves than in HEA calves. Cumulative total water intake did not differ between classifications. Initial BW did not differ between classifications; however, a classification × time interaction for BW indicated that HEA calves were heavier than DIA calves and had greater ADG. Significant classification × time interactions for hip height and heart girth revealed that HEA calves had a larger frame size. Gain-feed ratios for both milk replacer intake and total DMI differed between classifications: DIA calves were less feed-efficient than HEA calves. In conclusion, diarrhea in young calves decreases DMI, BW gain, and feed efficiency relative to HEA calves within 21 d of arrival.
Output: Intake and growth in transported Holstein calves classified as diarrheic or healthy within the first 21 days after arrival in a retrospective observational study
Gestational trophoblastic disease includes choriocarcinoma, a frankly malignant tumor, and hydatidiform mole (HM), which often leads to the development of persistent gestational trophoblastic neoplasia and requires chemotherapy. NANOG is an important transcription factor that is crucial for maintaining embryonic stem cell self-renewal and pluripotency. We postulated that NANOG is involved in the pathogenesis of gestational trophoblastic disease. In this study, significantly higher NANOG mRNA and protein expression levels, by quantitative PCR and immunoblotting, respectively, were demonstrated in HMs, particularly those that developed persistent disease, when compared with normal placentas. In addition, significantly increased nuclear NANOG immunoreactivity was found by immunohistochemistry in HMs (P < 0.001) and choriocarcinoma (P ‫؍‬ 0.002). Higher NANOG expression levels were demonstrated in HMs that developed persistent disease, as compared with those that regressed (P ‫؍‬ 0.025). Nuclear localization of NANOG was confirmed by confocal microscopy and immunoblotting in choriocarcinoma cell lines. There was a significant inverse correlation between NANOG immunoreactivity and apoptotic index assessed by M30 CytoDeath antibody (P ‫؍‬ 0.012). After stable knockdown of NANOG in the choriocarcinoma cell line JEG-3 by an shRNA approach, increased apoptosis was observed in relation to with enhanced caspases and poly(ADP-ribose) polymerase activities. NANOG knockdown was also associated with decreased mobility and invasion of JEG-3 and downregulation of matrix metalloproteases 2 and 9. These findings suggest that NANOG is involved in the pathogenesis and clinical progress of gestational trophoblastic disease , likely through its effect on apoptosis , cell migration , and invasion.
Output: Tumorigenesis and Neoplastic Progression Overexpression of NANOG in Gestational Trophoblastic Diseases Effect on Apoptosis, Cell Invasion, and Clinical Outcome
Objectives: We compared the expelled air dispersion distances during coughing from a human patient simulator (HPS) lying at 45u with and without wearing a surgical mask or N95 mask in a negative pressure isolation room. Methods: Airflow was marked with intrapulmonary smoke. Coughing bouts were generated by short bursts of oxygen flow at 650, 320, and 220L/min to simulate normal, mild and poor coughing efforts, respectively. The coughing jet was revealed by laser light-sheet and images were captured by high definition video. Smoke concentration in the plume was estimated from the light scattered by smoke particles. Significant exposure was arbitrarily defined where there was $ 20% of normalized smoke concentration. Results: During normal cough, expelled air dispersion distances were 68, 30 and 15 cm along the median sagittal plane when the HPS wore no mask, a surgical mask and a N95 mask, respectively. In moderate lung injury, the corresponding air dispersion distances for mild coughing efforts were reduced to 55, 27 and 14 cm, respectively, p , 0.001. The distances were reduced to 30, 24 and 12 cm, respectively during poor coughing effort as in severe lung injury. Lateral dispersion distances during normal cough were 0, 28 and 15 cm when the HPS wore no mask, a surgical mask and a N95 mask, respectively. 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: Exhaled Air Dispersion during Coughing with and without Wearing a Surgical or N95 Mask
Aim: To compare the performances of molecular and non-molecular tests to diagnose respiratory viral infections and to evaluate the pros and contras of each technique. Methods: Two hundred ninety-nine respiratory samples were prospectively explored using multiplex molecular techniques (FilmArray Respiratory Panel, Clart Pneumovir), immunological techniques (direct fluorescent assay, lateral flow chromatography) and cell cultures. Findings: Molecular techniques permitted the recovery of up to 50% more respiratory pathogens in comparison to non-molecular methods. FilmArray detected at least 30% more pathogens than Clart Pneumovir which could be explained by the differences in their technical designs. The turnaround time under 2 hours for the FilmArray permitted delivery of results when patients were still in the emergency room. ⁎ Corresponding author at: LHUB-ULB -Microbiology,
Output: Prospective evaluation of diagnostic tools for respiratory viruses in children and adults
The SARS outbreak in 2003 provides a unique opportunity for the study of human responses to a novel virus. We have previously reported that dendritic cells (DCs) might be involved in the immune escape mechanisms for SARS-CoV. In this study, we focussed on the gene expression of toll-like receptors (TLRs), chemokine receptors (CCRs) and death receptor ligands in SARS-CoV infected DCs. We also compared adult and cord blood (CB) DCs to find a possible explanation for the age-dependent severity of SARS. Our results demonstrates that SARS-CoV did not modulate TLR-1 to TLR-10 gene expression but significantly induced the expression of CCR-1, CCR-3, and CCR-5. There was also strong induction of TNF-related apoptosis-inducing ligand (TRAIL), but not Fas ligand gene expression in SARS-CoV infected DCs. Interestingly, the expressions of most genes studied were higher in CB DCs than adult DCs. The upregulation of chemokines and CCRs may facilitate DC migration from the infection site to the lymph nodes, whereas the increase of TRAIL may induce lymphocyte apoptosis. These findings may explain the increased lung infiltrations and lymphoid depletion in SARS patients. Further explorations of the biological significance of these findings are warranted.
Output: BMC Immunology Toll-like receptors, chemokine receptors and death receptor ligands responses in SARS coronavirus infected human monocyte derived dendritic cells
of the novel 2009 influenza A H1N1 virus in California led to an evaluation of hospital respiratory protection programs (RPPs) and practices by the California Department of Public Health during the 2009-2010 influenza season. Methods-Onsite evaluation of 16 hospitals consisted of interviews with managers and health care workers about RPPs and practices, review of written RPPs, and limited observations of personnel using respirators. Data were analyzed using descriptive statistics. Results-All hospitals had implemented policies requiring the minimum use of N95 filtering facepiece respirators when working with patients with H1N1 virus infection; 95.5% of health care workers (n = 199) reported they would wear at least this level of protection when in close contact with a patient with confirmed or suspected H1N1 virus infection. However, evaluation of written RPPs indicated deficiencies in required areas, most commonly in recordkeeping, designation of a program administrator, program evaluation, employee training, and fit testing procedures. Conclusions-Health care workers were aware of respiratory protection required when providing care for patients with confirmed or suspected H1N1 virus infection. Hospitals should improve written RPPs, fully implement written procedures, and conduct periodic program evaluation to ensure effectiveness of respirator use for health care worker protection. Increased accessibility of resources tailored for hospital respirator program administrators may be helpful. * In allotment, suppliers allow hospitals to order only a certain number of respirators, based on their order quantities in the past. Beckman et al.
Output: Evaluation of respiratory protection programs and practices in California hospitals during the 2009-2010 H1N1 influenza pandemic
Despite the significant role of seasonal influenza vaccination in preventing and minimizing the serious complications of influenza infection in type 2 diabetes mellitus (T2DM) patients, unsatisfactory compliance still exists for vaccination. Study objectives were to explore the vaccination status and determinants in T2DM patients in southwestern Saudi Arabia. A cross-sectional study on a representative sample of T2DM patients in Abha city, southwestern Saudi Arabia, was conducted. Data for sociodemographic characteristics, clinical criteria, vaccination status, vaccination motivators and barriers and seasonal influenza knowledge were collected. Out of 353 T2DM patients included in the study, seasonal influenza vaccination coverage was 61% in year 2017. A significant factors associated with non-vaccination were; poor influenza and its vaccine knowledge (OR = 4.31, 95% CI: 2.73-6.80), illiteracy (OR = 1.93, 95% CI: 1.11-3.37), and more than 10 years disease duration (OR = 2.07, 95% CI: 1.11-3.87). Presence of family history of DM and ischemic heart comorbidity minimized the possibility of non-vaccination (OR = 0.54 and 0.28 respectively). Healthcare givers' advice was the most reported vaccination motivator (84.7%) while; fear of vaccine side effects was the most stated barrier (73%). In conclusion, influenza vaccination rate among T2DM in the present study is less than the recommended level. Continuous primary health care center-based educational programs should be implemented to aware and encourage influenza vaccination among T2DM patients.
Output: Influenza Vaccination in Type 2 Diabetes Patients: Coverage Status and Its Determinants in Southwestern Saudi Arabia
Objective: To analyse the clinical features of COVID-19 parturients, and to compare anaesthetic regimen and clinical outcomes in parturients with or without COVID-19 undergoing cesarean delivery. Methods: Data were extracted from the electronic medical record of 3 medical institutions in Hubei Province, China, from June 1, 2019 to March 20, 2020 according to inclusion and exclusion criteria. After propensity score matching with demographics, the clinical and laboratory characteristics of parturients with or without COVID-19 were analysed. The anaesthetic regimen and clinical outcomes of themselves and their infants were compared in these two groups of parturients. Results: A total of 1,588 patients without SARS-CoV-2 infection undergoing cesarean delivery were retrospectively included. After achieving a balanced cohort through propensity score matching, 89 patients (COVID-19 group), who were diagnosed with COVID-19 by SARS-CoV-2 nucleic acid test and CT scan matched with 173 patients without COVID-19 (Control group). The SARS-CoV-2 infected parturients in the early stages of COVID-19 outbreak was much more than during the later stage. The main clinical characteristics of parturients with COVID-19 were fever (34.8%), cough (33.7%), an increased plasma CRP (52.8%) and a decreased lymphocyte counting (33.7%). A high rate of emergency and a high incidence of anaesthesia-related complications, such as pharyngalgia, multiple puncture, intraoperative hypotension, nausea, vomiting, vertigo and chills in the COVID-19 parturients. In addition, the parturients with COVID-19 had a long duration of operation and hospital stay, and an increased intraoperative oxytocin utilization and postoperative oxygen therapy. The newborns from the SARS-CoV-2 infected mothers, who received general anaesthesia, had a high risk of Apgar score ≤ 8 at 1 and 5 minutes after delivery and a higher rate of neonatal intensive care unit (NICU) admission. Conclusions: Anaesthesia-related complications occur more frequently in the COVID-19 parturients and their newborns have a high risk of distress.
Output: Anaesthetic managment and clinical outcomes of parturients with COVID-19: a multicentre, retrospective, propensity score matched cohort study Short Title: Obstetric anaesthesia for parturients with COVID-19
Bats are reservoirs for emerging zoonotic viruses that can have a profound impact on human and animal health, including lyssaviruses, filoviruses, paramyxoviruses, and severe acute respiratory syndrome coronaviruses (SARS-CoVs). In the course of a project focused on pathogen discovery in contexts where human-bat contact might facilitate more efficient interspecies transmission of viruses, we surveyed gastrointestinal tissue obtained from bats collected in caves in Nigeria that are frequented by humans. , et al. 2010. Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria. mBio 1(4): Coronavirus consensus PCR and unbiased high-throughput pyrosequencing revealed the presence of coronavirus sequences related to those of SARS-CoV in a Commerson's leaf-nosed bat (Hipposideros commersoni). Additional genomic sequencing indicated that this virus, unlike subgroup 2b CoVs, which includes SARS-CoV, is unique, comprising three overlapping open reading frames between the M and N genes and two conserved stem-loop II motifs. Phylogenetic analyses in conjunction with these features suggest that this virus represents a new subgroup within group 2 CoVs. IMPORTANCE Bats (order Chiroptera, suborders Megachiroptera and Microchiroptera) are reservoirs for a wide range of viruses that cause diseases in humans and livestock, including the severe acute respiratory syndrome coronavirus (SARS-CoV), responsible for the global SARS outbreak in 2003. The diversity of viruses harbored by bats is only just beginning to be understood because of expanded wildlife surveillance and the development and application of new tools for pathogen discovery. This paper describes a new coronavirus, one with a distinctive genomic organization that may provide insights into coronavirus evolution and biology.
Output: Identification of a Severe Acute Respiratory Syndrome Coronavirus- Like Virus in a Leaf-Nosed Bat in Nigeria
Using immunohistochemical techniques, we examined major histocompatibility complex (MHC) antigen expression on astrocytes, oligodendrocytes, and macrophages-microglia derived from surgically resected tissue from young adults and maintained in dissociated cell cultures supplemented with either fetal calf or human AB serum. The majority of these cells in culture expressed class I MHC antigens. MHC class II expression was observed on only a restricted proportion of astrocytes either under basal or induction conditions (,/-interferon, activated lymphocyte supernatants), on the majority of macrophagesmicroglia under inducing conditions, and not on oligodendrocytes. MHC class II expression on astrocytes in culture did not correlate with the extent of in situ gliosis or with in vitro cell morphology. MHC antigen expression was not detected in situ immunohistochemically. These data extend observations on the dissociation of in vivo and in vitro expression of MHC antigens on glial cells. The apparent greater expression of MHC class II antigens on macrophages-microgha compared to astrocytes raises the issue of the relative roles of each of these cell types in promoting immune reactivity under pathologic conditions. mechanisms contribute to lesion formation in some chronic demyelinating diseases of the CNS induced by viral infection in animals, and are postulated to participate in the pathogenesis of the human chronic demyelinating disease, multiple sclerosis (MS). The above pathologic conditions are characterized by accumulation of lymphocytes, macrophages-microglia, and reactive astrocytes in the region of demyelination. The contribution of each of the cell types present in the region of these lesions to promoting ongoing immune reactivg~y remains under active study. A major consideration with regard to specific cell types either promoting antigen-specific immune reactivity or becoming targets of antigen-0165-5728/89/$03.50
Output: Immunohistochemical studies of adult human glial cells
Twenty years ago (1992), a landmark Institute of Medicine report entitled "Emerging Infections: Microbial Threats to Health in the United States" underscored the important but often underappreciated concept of emerging infectious diseases (EIDs). A review of the progress made and setbacks experienced over the past 2 decades suggests that even though many new diseases have emerged, such as SARS (severe acute respiratory syndrome) and the 2009 pandemic influenza, significant advances have occurred in EID control, prevention, and treatment. Among many elements of the increase in the capacity to control EIDs are genomics-associated advances in microbial detection and treatment, improved disease surveillance, and greater awareness of EIDs and the complicated variables that underlie emergence. In looking back over the past 20 years, it is apparent that we are in a time of great change in which both the challenge of EIDs and our responses to them are being transformed. Recent advances support guarded optimism that further breakthroughs lie ahead.
Output: Emerging Infectious Diseases in 2012: 20 Years after the Institute of Medicine Report
The aim of this study was to quantify and compare interferon-c (IFN-c) concentrations in the serum of clinically normal cats infected with feline coronavirus (FCoV) with its concentration in the sera and effusions of cats with feline infectious peritonitis (FIP), a disease associated with infection with a mutated form of FCoV. Clinically normal FCoV-infected cats living in catteries with a high prevalence of FIP had the highest serum IFN-c concentrations. The serum concentration of IFN-c was not significantly different in cats with FIP compared with clinically normal FCoV-infected animals living in catteries with a low prevalence of the disease. Moreover, the concentration of IFN-c was significantly higher in the effusions than in the serum of cats with FIP, probably due to IFN-c production within lesions. These findings support the hypothesis that there is a strong, 'systemic' cell mediated immune response in clinically normal, FCoV-infected cats and that a similar process, albeit at a tissue level, is involved in the pathogenesis of FIP.
Output: Interferon-c in the serum and effusions of cats with feline coronavirus infection The Veterinary Journal
Keywords: interferon, interferon-stimulated genes, tumor necrosis factor-related apoptosis-inducing ligand, acute lung injury, innate immunity, influenza, respiratory syncytial virus, coronavirus FiGURe 1 | PRRs and their downstream signaling pathways in virus-induced iFN induction. In viral infection, type I IFNs are induced by TLR, RLR, CLR, and cytosolic nucleic acid sensors. Cell membrane-located TLRs ligate to viral envelope proteins (e.g., TLR2/herpes simplex virus), upon which they recruit MyD88. MyD88 interacts with IRAK kinase (IRAK-1, -2, or -4) that either directly activate IRF1 or interact with TRAF6, which induces IRF7 or assembles with TAK1. TAK1 forms a complex with TAB-1/-2 and -3 and subsequently either activates the MAPK kinases p38 and JNK, leading to AP-1 phosphorylation and nuclear translocation, or induces ubiquitination of NEMO followed by IκB degradation and NFκB activation. Endosomal TLRs recognizing viral nucleic acid and signal via the adaptor protein MyD88 (for TLR7/8/9) or interact with TRIF (for TLR3) followed by TRAF3, TANK, and TBK1 activation. TBK1 and IKKε then phosphorylate and activate IRF3 and IRF7. Additionally, TRIF can interact with TRAF6 to initiate TAK1 signaling. Both RLRs, RIG-I and MDA-5, recognize nucleic acid contents in the cytoplasm and stimulate the mitochondrial anchored IPS-1 for dimerization followed by TRADD recruitment that acts via TRAF3 on IRF3 and IRF7. Additionally, IPS-1 can interact with FADD and RIP1 to activate NFκB via IKK activated by caspase-8 and -10. Also PKR signaling results in NFκB activation and nuclear translocation. The dsDNA sensor cGAS produces cGAMP that activates ER-located STING that via TBK1 induces IRF3 translocation and type I IFN production. CLRs play a minor role in viral recognition; however, DC-SIGN activates the small GTPase Ras and Raf protein kinase, followed by NFκB activation. Type III IFN are induced by TLR3, TLR9, and via RIG-I and peroxisomal-resident IPS-1. Especially IRF1, but also NFκB, IRF3, and IRF7 are implicated in IFN-λ production, with the latter being stabilized by Med23.
Output: The impact of the interferon/TNF- Related Apoptosis-inducing Ligand Signaling Axis on Disease Progression in Respiratory viral infection and Beyond
Background: During the last decade, conflict or natural disasters have displaced unprecedented numbers of persons. This leads to conditions prone to outbreaks that imperil the health of displaced persons and threaten global health security. Past literature has minimally examined the association of communicable disease outbreaks with complex emergencies (CEs) and natural disasters (NDs). Methods: To examine this association, we identified CEs and NDs using publicly available datasets from the Center for Research on the Epidemiology of Disasters and United Nations Flash and Consolidated Appeals archive for 2005-2014. We identified outbreaks from World Health Organization archives. We compared findings to identify overlap of outbreaks, including their types (whether or not of a vaccine-preventable disease), and emergency event types (CE, ND, or Both) by country and year using descriptive statistics and measure of association. Results: There were 167 CEs, 912 NDs, 118 events linked to 'Both' types of emergencies, and 384 outbreaks. Of CEs, 43% were associated with an outbreak; 24% NDs were associated with an outbreak; and 36% of 'Both' types of emergencies were associated with an outbreak. Africa was disproportionately affected, where 67% of total CEs, 67% of 'Both' events (CE and ND), and 46% of all outbreaks occurred for the study period. The odds ratio of a vaccine-preventable outbreak occurring in a CE versus an ND was 4.14 (95% confidence limits 1.9, 9.4). Conclusions: CEs had greater odds of being associated with outbreaks compared with NDs. Moreover, CEs had high odds of a vaccine-preventable disease causing that outbreak. Focusing on better vaccine coverage could reduce CE-associated morbidity and mortality by preventing outbreaks from spreading.
Output: Public health implications of complex emergencies and natural disasters
Background: As the COVID-19 epidemic is spreading, incoming data allows us to quantify values of key variables that determine the transmission and the effort required to control the epidemic. We determine the incubation period and serial interval distribution for transmission clusters in Singapore and in Tianjin. We infer the basic reproduction number and identify the extent of pre-symptomatic transmission. Methods: We collected outbreak information from Singapore and Tianjin, China, reported from Jan.19-Feb.26 and Jan.21-Feb.27, respectively. We estimated incubation periods and serial intervals in both populations. Results: The mean incubation period was 7.1 (6.13, 8.25) days for Singapore and 9 (7.92, 10.2) days for Tianjin. Both datasets had shorter incubation periods for earlier-occurring cases. The mean serial interval was 4.56 (2.69, 6.42) days for Singapore and 4.22 (3.43, 5.01) for Tianjin. We inferred that early in the outbreaks, infection was transmitted on average 2.55 and 2.89 days before symptom onset (Singapore, Tianjin). The estimated basic reproduction number for Singapore was 1.97 (1.45, 2.48) secondary cases per infective; for Tianjin it was 1.87 (1.65, 2.09) secondary cases per infective. Conclusions: Estimated serial intervals are shorter than incubation periods in both Singapore and Tianjin, suggesting that pre-symptomatic transmission is occurring. Shorter serial intervals lead to lower estimates of R0, which suggest that half of all secondary infections should be prevented to control spread.
Output: Transmission interval estimates suggest pre-symptomatic spread of COVID-19
Respiratory droplet characteristics are key to determine the droplet-bornepathogen transmission, which provide scientific basis for formulating the disease prevention from droplet transmission and control measures. Through studying the data information from existing documents, this paper gives the respiratory droplet characteristics, like size, concentration, velocity, etc. Meanwhile, droplet evaporation,droplet-bornepathogen activity and their transmission are discussed. The droplet size is no significant difference with human health level, gender and age. The size of droplets produced by health people is between 0.1 and 10μm, it produced by patientsis between 0.05 and 10μm, and the patients' dropletconcentration is higher. The coughed droplet concentrations change with the size into a peak rule. The velocity of the cough droplets is the biggest, the range of 10 to 25m/s, the transmission distance is more than 2m.
Output: -NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer-review under responsibility of the organizing committee of ISHVAC-COBEE 2015 ScienceDirect Documentary Research of Human Respiratory Droplet Characteristics
We examined associations between single-nucleotide polymorphisms (SNPs) of IFITM3, TLR3, and CD55 genes and influenza clinical outcomes in Chinese. A multicenter study was conducted on 275 adult cases of avian (H7N9) and pandemic (H1N1 pdm09 ) influenza. Host DNA was extracted from diagnostic respiratory samples; IFITM3 rs12252, TLR3 rs5743313, CD55 rs2564978, and TLR4 rs4986790/4986791 were targeted for genotyping (Sanger sequencing). The primary outcome analyzed was death. Results. IFITM3 and TLR3 SNPs were in Hardy-Weinberg equilibrium; their allele frequencies (IFITM3/C-allele 0.56, TLR3/Callele 0.88) were comparable to 1000 Genomes Han Chinese data. We found over-representation of homozygous IFITM3 CC (54.5% vs 33.2%; P = .02) and TLR3 CC (93.3% vs 76.9%; P = .04) genotypes among fatal cases. Recessive genetic models showed their significant independent associations with higher death risks (adjusted hazard ratio [aHR] 2.78, 95% confidence interval [CI] 1.29-6.02, and aHR 4.85, 95% CI 1.11−21.06, respectively). Cumulative effects were found (aHR 3.53, 95% CI 1.64−7.59 per risk genotype; aHR 9.99, 95% CI 1.27−78.59 with both). Results were consistent for each influenza subtype and other severity indicators. The CD55 TT genotype was linked to severity. TLR4 was nonpolymorphic. Conclusions. Host genetic factors may influence clinical outcomes of avian and pandemic influenza infections. Such findings have important implications on disease burden and patient care in at-risk populations.
Output: IFITM3, TLR3, and CD55 Gene SNPs and Cumulative Genetic Risks for Severe Outcomes in Chinese Patients With H7N9/H1N1 pdm09 Influenza
The pathogenesis of dengue virus (DENV) infection is not completely understood. Endothelial cells may act as a target of the virus and be involved in disease pathogenesis. Therefore, the identification of host cell components involved in DENV replication would provide useful information for better understanding DENV infection. In this study, a significantly decreased level of miR-223 was found in DENV2-infected EAhy926 cells, a human endothelial-like cell line, whereas miR-223 overexpression inhibited DENV2 replication. Furthermore, we identified that miR-223 directly targeted the 3 0 untranslated region (3 0 UTR) of the messenger RNA (mRNA) for microtubule-destabilizing protein stathmin 1 (STMN1), thereby reducing its mRNA and protein levels. The depletion of miR-223 or overexpression of STMN1 enhanced DENV2 replication, whereas the opposite (increased miR-223 or decreased STMN1) suppressed DENV2 replication, indicating that miR-223 downregulates STMN1 expression by targeting the 3 0 UTR of the STMN1 gene to inhibit DENV2 replication. Finally, we demonstrated that two transcription factors, C/EBPa and E2F1, are involved in the regulation of miR-223 levels after DENV2 infection in EAhy926 cells. Collectively, our results suggest that miR-223 may act as a novel antiviral factor, which may open an avenue to limit DENV infection.
Output: miR-223 inhibits dengue virus replication by negatively regulating the microtubule-destabilizing protein STMN1 in EAhy926 cells
Community-acquired pneumonia is still a significant cause of morbidity and mortality and is often misdiagnosed and inappropriately treated. Although it can be caused by a wide variety of micro-organisms, the pneumococcus, atypicals, such as Mycoplasma pneumoniae and Chlamydophila pneumoniae, Staphylococcus aureus and certain Gram-negative rods are the usual pathogens encountered. The site-of-care decision is critical in determining the site and type of care as well as the extent of diagnostic workup. Antimicrobial therapy should be started as soon as possible particularly in those requiring admission to hospital, but typically the physician does not know with any degree of certainty the identity of the etiologic pathogen. A number of national guidelines have been published to help the physician with this choice. The initial drug(s) can be modified if necessary if the pathogen and its antimicrobial susceptibility pattern becomes known. Adjunctive therapy such as pressors and fluid replacement are of value and macrolides appear to help as well, likely secondary to their immunomodulatory effects. Recent data also suggest a role for steroids.
Output: Community-acquired pneumonia: An overview
Infectious bronchitis (IB) is one of the major economically important poultry diseases distributed worldwide. It is caused by infectious bronchitis virus (IBV) and affects both galliform and nongalliform birds. Its economic impact includes decreased egg production and poor egg quality in layers, stunted growth, poor carcass weight, and mortality in broiler chickens. Although primarily affecting the respiratory tract, IBV demonstrates a wide range of tissues tropism, including the renal and reproductive systems. Thus, disease outcome may be influenced by the organ or tissue involved as well as pathotypes or strain of the infecting virus. Knowledge on the epidemiology of the prevalent IBV strains in a particular region is therefore important to guide control and preventions. Meanwhile previous diagnostic methods such as serology and virus isolations are less sensitive and time consuming, respectively; current methods, such as reverse transcription polymerase chain reaction (RT-PCR), Restriction Fragment Length Polymorphism (RFLP), and sequencing, offer highly sensitive, rapid, and accurate diagnostic results, thus enabling the genotyping of new viral strains within the shortest possible time. This review discusses aspects on pathogenesis and diagnostic methods for IBV infection.
Output: Pathogenesis and Diagnostic Approaches of Avian Infectious Bronchitis
The aldehyde inhibitor Z-Ala-Ala-Phe-CHO has been synthesized and shown by 13 C-NMR to react with the active site serine hydroxyl group of alpha-chymotrypsin to form two diastereomeric hemiacetals. For both hemiacetals oxyanion formation occurs with a pK a value of~7 showing that chymotrypsin reduces the oxyanion pK a values bỹ 5.6 pK a units and stabilizes the oxyanions of both diastereoisomers by~32 kJ mol −1 . As pH has only a small effect on binding we conclude that oxyanion formation does not have a significant effect on binding the aldehyde inhibitor. By comparing the binding of Z-Ala-Ala-Phe-CHO with that of Z-Ala-Ala-Phe-H we estimate that the aldehyde group increases binding~100 fold. At pH 7.2 the effective molarity of the active site serine hydroxy group is~6000 which is~7× less effective than with the corresponding glyoxal inhibitor. Using 1 H-NMR we have shown that at both 4 and 25°C the histidine pK a is~7.3 in free chymotrypsin and it is raised to~8 when Z-Ala-Ala-Phe-CHO is bound. We conclude that oxyanion formation only has a minor role in raising the histidine pK a and that the aldehyde hydrogen must be replaced by a larger group to raise the histidine pK a N 10 and give stereospecific formation of tetrahedral intermediates. The results show that a large increase in the pK a of the active site histidine is not needed for the active site serine hydroxyl group to have an effective molarity of 6000.
Output: Hemiacetal stabilization in a chymotrypsin inhibitor complex and the reactivity of the hydroxyl group of the catalytic serine residue of chymotrypsin
This study analysed the consequences of deviation from the WHO case definition for the assessment of patients with suspected severe acute respiratory syndrome (SARS) in The Netherlands during 2003. Between 17 March and 7 July 2003, as a result of dilemmas in balancing sensitivity and specificity, five different case definitions were used. The patients referred for SARS assessment were analysed from a public health perspective. None of the patients referred had SARS, based on serological and virological criteria. Nevertheless, all 72 patients required thorough assessment and, depending on the results of the assessment, institution of appropriate prevention and control measures. Changing case definitions caused confusion in classifying cases. A centralised assessment of the reported cases by a team with clinical and public health expertise (epidemiological and geographical risk assessment) is a practical solution for addressing differences in applying case definitions. The burden of managing non-cases is an important issue when allocating public health resources, and should be taken into account during the preparation phase, rather than during an outbreak. This applies not only to SARS, but also to other public health threats, such as pandemic influenza or a bioterrorist episode.
Output: Public health implications of using various case definitions in The Netherlands during the worldwide SARS outbreak
Vaccines have been the single most significant advancement in public health, preventing morbidity and mortality in millions of people annually. Vaccine development has traditionally focused on whole organism vaccines, either live attenuated or inactivated vaccines. While successful for many different infectious diseases whole organisms are expensive to produce, require culture of the infectious agent, and have the potential to cause vaccine associated disease in hosts. With advancing technology and a desire to develop safe, cost effective vaccine candidates, the field began to focus on the development of recombinantly expressed antigens known as subunit vaccines. While more tolerable, subunit vaccines tend to be less immunogenic. Attempts have been made to increase immunogenicity with the addition adjuvants, either immunostimulatory molecules or an antigen delivery system that increases immune responses to vaccines. An area of extreme interest has been the application of nanotechnology to vaccine development, which allows for antigens to be expressed on a particulate delivery system. One of the most exciting examples of nanovaccines are rationally designed protein nanoparticles. These nanoparticles use some of the basic tenants of structural biology, biophysical chemistry, and vaccinology to develop protective, safe, and easily manufactured vaccines. Rationally developed nanoparticle vaccines are one of the most promising candidates for the future of vaccine development.
Output: Vaccine Technologies: From Whole Organisms to Rationally Designed Protein Assemblies HHS Public Access Author manuscript
The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable.
Output: An empirical test of the midpoint rooting method
Ebola virus (EBOV) causes severe outbreaks of viral hemorrhagic fever in humans. While virus-host interactions are promising targets for antivirals, there is only limited knowledge regarding the interactions of EBOV with cellular host factors. Recently, we performed a genome-wide siRNA screen that identified the nuclear RNA export factor 1 (NXF1) as an important host factor for the EBOV life cycle. NXF1 is a major component of the nuclear mRNA export pathway that is usurped by many viruses whose life cycles include nuclear stages. However, the role of NXF1 in the life cycle of EBOV, a virus replicating in cytoplasmic inclusion bodies, remains unknown. In order to better understand the role of NXF1 in the EBOV life cycle, we performed a combination of co-immunoprecipitation and double immunofluorescence assays to characterize the interactions of NXF1 with viral proteins and RNAs. Additionally, using siRNA-mediated knockdown of NXF1 together with functional assays, we analyzed the role of NXF1 in individual aspects of the virus life cycle. With this approach we identified the EBOV nucleoprotein (NP) as a viral interaction partner of NXF1. Further studies revealed that NP interacts with the RNA-binding domain of NXF1 and competes with RNA for this interaction. Co-localization studies showed that RNA binding-deficient, but not wildtype NXF1, accumulates in NP-derived inclusion bodies, and knockdown experiments demonstrated that NXF1 is necessary for viral protein expression, but not for viral RNA synthesis. Finally, our results showed that NXF1 interacts with viral mRNAs, but not with viral genomic RNAs. Based on these results we suggest a model whereby NXF1 is recruited into inclusion bodies to promote the export of viral mRNA:NXF1 complexes from these sites. This would represent a novel function for NXF1 in the life cycle of cytoplasmically replicating viruses, and may provide a basis for new therapeutic approaches against EBOV, and possibly other emerging viruses.
Output: The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression
Chemical modification of the proteins bovine serum albumin, ␣-lactalbumin, ␤-lactoglobulin and chicken lysozyme by 3-hydroxyphthalic anhydride (3-HP) yielded compounds which exerted antiviral activity in vitro as compared with the native unmodified proteins. Of the three enveloped viruses tested, human herpes simplex virus type 1 (HSV-1), bovine parainfluenza virus type 3 and porcine respiratory corona virus, only HSV-1 proved sensitive to the 3-HP-proteins. All of the chemically modified proteins presented antiviral activity against HSV-1 when assayed before, during or after infection. However, to achieve HSV-1 inhibition, significantly higher concentrations of the modified proteins were required if present before infection as compared to during or after infection. Our results suggest that multiple mechanisms are involved in the inhibition of HSV-1 infection. Proteolytical digestion of albumin, ␣-lactalbumin, ␤-lactoglobulin and lysozyme by trypsin, chymotrypsin and pepsin yielded several peptide fragments with antiherpetic activity. Chemical modification of these peptide fragments by 3-HP generated peptides with antiviral activity, however, this was almost always combined with a cytotoxic effect on the Vero cells. Overall, our results suggest that targeted chemical modification of some natural products might provide compounds effective against HSV-1 infection.
Output: The antiviral activity of naturally occurring proteins and their peptide fragments after chemical modification
The RNA-dependent RNA polymerases (RdRPs) encoded by the RNA viruses are a unique class of nucleic acid polymerases. Each viral RdRP contains a 500-600 residue catalytic module with palm, fingers, and thumb domains forming an encircled human right hand architecture. Seven polymerase catalytic motifs are located in the RdRP palm and fingers domains, comprising the most conserved parts of the RdRP and are responsible for the RNA-only specificity in catalysis. Functional regions are often found fused to the RdRP catalytic module, resulting in a high level of diversity in RdRP global structure and regulatory mechanism. In this review, we surveyed all 46 RdRP-sequence available virus families of the positive-strand RNA viruses listed in the 2018b collection of the International Committee on Virus Taxonomy (ICTV) and chose a total of 49 RdRPs as representatives. By locating hallmark residues in RdRP catalytic motifs and by referencing structural and functional information in the literature, we were able to estimate the N-and C-terminal boundaries of the catalytic module in these RdRPs, which in turn serve as reference points to predict additional functional regions beyond the catalytic module. Interestingly, a large number of virus families may have additional regions fused to the RdRP N-terminus, while only a few of them have such regions on the C-terminal side of the RdRP. The current knowledge on these additional regions, either in three-dimensional (3D) structure or in function, is quite limited. In the five RdRP-structure available virus families in the positive-strand RNA viruses, only the Flaviviridae family has the 3D structural information resolved for such regions. Hence, future efforts to solve full-length RdRP structures containing these regions and to dissect the functional contribution of them are necessary to improve the overall understanding of the RdRP proteins as an evolutionarily integrated group, and our analyses here may serve as a guideline for selecting representative RdRP systems in these studies.
Output: A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses