niryuu/sni-each-converted huggingface dataset:
The RNA guanylyltransferase (GTase) is involved in the synthesis of the m7 Gppp-RNA cap structure found at the 59 end of eukaryotic mRNAs. GTases are members of the covalent nucleotidyl transferase superfamily, which also includes DNA and RNA ligases. GTases catalyze a two-step reaction in which they initially utilize GTP as a substrate to form a covalent enzyme-GMP intermediate. The GMP moiety is then transferred to the diphosphate end of the RNA transcript in the second step of the reaction to form the Gppp-RNA structure. In the current study, we used a combination of virtual database screening, homology modeling, and biochemical assays to search for novel GTase inhibitors. Using this approach, we demonstrate that mycophenolic acid (MPA) can inhibit the GTase reaction by preventing the catalytic transfer of the GMP moiety onto an acceptor RNA. As such, MPA represents a novel type of inhibitor against RNA guanylyltransferases that inhibits the second step of the catalytic reaction. Moreover, we show that the addition of MPA to S. cerevisiae cells leads to a reduction of capped mRNAs. Finally, biochemical assays also demonstrate that MPA can inhibit DNA ligases through inhibition of the second step of the reaction. The biological implications of these findings for the MPA-mediated inhibition of members of the covalent nucleotidyl superfamily are discussed. Citation: Tremblay-Létourneau M, Despins S, Bougie I, Bisaillon M (2011) Virtual High-Throughput Screening Identifies Mycophenolic Acid as a Novel RNA Capping Inhibitor. PLoS ONE 6(9): e24806.
Output: Virtual High-Throughput Screening Identifies Mycophenolic Acid as a Novel RNA Capping Inhibitor
Middle East respiratory syndrome coronavirus MERS Healthcare-associated outbreaks S U M M A R Y Middle East respiratory syndrome coronavirus (MERS-CoV) is capable of causing acute respiratory illness. Laboratory-confirmed MERS-CoV cases may be asymptomatic, have mild disease, or have a life-threatening infection with a high case fatality rate. There are three patterns of transmission: sporadic community cases from presumed non-human exposure, family clusters arising from contact with an infected family index case, and healthcareacquired infections among patients and from patients to healthcare workers. Healthcareacquired MERS infection has become a well-known characteristic of the disease and a leading means of spread. The main factors contributing to healthcare-associated outbreaks include delayed recognition, inadequate infection control measures, inadequate triaging and isolation of suspected MERS or other respiratory illness patients, crowding, and patients remaining in the emergency department for many days. A review of the literature suggests that effective control of hospital outbreaks was accomplished in most instances by the application of proper infection control procedures. Prompt recognition, isolation and management of suspected cases are key factors for prevention of the spread of MERS. Repeated assessments of infection control and monitoring of corrective measures contribute to changing the course of an outbreak. Limiting the number of contacts and hospital visits are also important factors to decrease the spread of infection.
Output: Healthcare-associated infections: the hallmark of Middle East respiratory syndrome coronavirus with review of the literature
Human coronaviruses are one of the main causes of upper respiratory tract infections in humans. While more often responsible for mild illness, they have been associated with illnesses that require hospitalization. In this study, an assay for one of the human coronaviruses, OC43, was developed using a truncated recombinant nucleocapsid (N) protein antigen in an enzyme immunosorbent assay (ELISA) and evaluated using serum collected from HCoV-OC43-infected patients, healthy adults, and patients with other respiratory virus infections. Results showed that the diagnostic sensitivity and specificity of the assay were 90.9% (10/11) and 82.9% (39/47), respectively. To evaluate the clinical utility of the ELISA, serum samples collected from patients during an outbreak of HCoV-OC43 infection and previously identified as positive by HCoV-OC43 whole N ELISA were screened resulting in 100% diagnosis agreement between the testing methods. These results suggest that this assay offers a reliable method to detect HCoV-OC43 infection and may be a useful tool in coronavirus seroepidemiological studies. Published by Elsevier B.V. 0166-0934/$ -see front matter Published by Elsevier B.V.
Output: Development of a recombinant truncated nucleocapsid protein based immunoassay for detection of antibodies against human coronavirus OC43 ଝ
Objective: To evaluate the scientific basis for the use of Kang 601 heji (K-601) as an anti-inflammatory and antipyretic agent using appropriate animal models. Methods: Carrageenan-induced rat paw and xylene-induced ear oedemas were models used to investigate anti-inflammatory actions of K-601. Lipopolysaccharide-induced pyrexia model was used to evaluate antipyretic activity in Wistar rats. The antiinflammatory and antipyretic mechanisms were evaluated by detecting prostaglandins E 2 , nitric oxide, interleukin-1b and tumour necrosis factor-a levels using appropriate reagents and ELISA kits. Results: The results revealed that K-601 reduced the level of inflammations in both antiinflammatory models in a dose-dependent manner. The same was true for the antipyretic model. The possible mechanisms of actions were through the inhibition of prostaglandins E 2 , interleukin-1b, tumour necrosis factor-a and nitric oxide. Conclusions: K-601 has proven anti-inflammatory and antipyretic actions. The findings provide a scientific basis for the use of K-601 as anti-inflammatory and antipyretic agent in traditional Chinese medicinal practice.
Output: Anti-inflammatory and antipyretic properties of Kang 601 heji, a traditional Chinese oral liquid dosage form
Viral exacerbations continue to represent the major burden in terms of morbidity, mortality and health care costs associated with asthma. Those at greatest risk for acute asthma are those with more severe airways disease and poor asthma control. It is this group with established asthma in whom acute exacerbations triggered by virus infections remain a serious cause of increased morbidity. A range of novel therapies are emerging to treat asthma and in particular target this group with poor disease control, and in most cases their efficacy is now being judged by their ability to reduce the frequency of acute exacerbations. Critical for the development of new treatment approaches is an improved understanding of virus-host interaction in the context of the asthmatic airway. This requires research into the virology of the disease in physiological models in conjunction with detailed phenotypic characterisation of asthma patients to identify targets amenable to therapeutic intervention. ARTICLE HISTORY
Output: Advances in the treatment of virus-induced asthma
Backgrounds: Up to February 16, 2020, 355 cases have been confirmed as having COVID-19 infection on the Diamond Princess cruise ship. It is of crucial importance to estimate the reproductive number (R0) of the novel virus in the early stage of outbreak and make a prediction of daily new cases on the ship. Method: We fitted the reported serial interval (mean and standard deviation) with a gamma distribution and applied "earlyR" package in R to estimate the R0 in the early stage of COVID-19 outbreak. We applied "projections" package in R to simulate the plausible cumulative epidemic trajectories and future daily incidence by fitting the data of existing daily incidence, a serial interval distribution, and the estimated R0 into a model based on the assumption that daily incidence obeys approximately Poisson distribution determined by daily infectiousness. Results: The Maximum-Likelihood (ML) value of R0 was 2.28 for COVID-19 outbreak at the early stage on the ship. The median with 95% confidence interval (CI) of R0 values was 2.28 (2.06-2.52) estimated by the bootstrap resampling method. The probable number of new cases for the next ten days would gradually increase, and the estimated cumulative cases would reach 1514 (1384-1656) at the tenth day in the future. However, if R0 value was reduced by 25% and 50%, the estimated total number of cumulative cases would be reduced to 1081 (981-1177) and 758 (697-817), respectively. Conclusion: The median with 95% CI of R0 of COVID-19 was about 2.28 (2.06-2.52) during the early stage experienced on the Diamond Princess cruise ship. The future daily incidence and probable outbreak size is largely dependent on the change of R0. Unless strict infection management and control are taken, our findings indicate the potential of COVID-19 to cause greater outbreak on the ship.
Output: Estimation of the reproductive number of novel coronavirus (COVID-19) and the probable outbreak size on the Diamond Princess cruise ship: A data-driven analysis
Bovine coronavirus (BCoV) is a viral enteric pathogen associated with calf diarrhea worldwide being, in Argentina, mostly detected in dairy husbandry systems. The aim of the present work was to study if maternal IgG1 antibodies (Abs) to BCoV acquired by colostrum intake modulate the development of BCoV infection in calves reared in a dairy farm in Argentina. Thirty Holstein calves were monitored during their first 60 days of age. Animals were classified into two groups depending on their initial BCoV IgG1 Ab titers. The ''failure of passive transfer'' (FPT) group had significantly lower IgG1 Abs to BCoV than the ''acceptable passive transfer'' (APT) group of calves (log10 1.98 vs. 3.38 respectively) (p < 0.0001). These differences were also observed when the total protein levels in both groups were compared (p = 0.0081). Moreover, 71% (5/7) of calves from the FPT group showed IgG1 seroconversion to BCoV compared to 29.4% (5/17) of animals from the APT group. Regarding viral circulation, BCoV was detected in 10% (3/30) of all calves and BCoV IgG1 Ab seroconversion was detected in 42% of the total animals showing that almost half of the calves were infected with BCoV. In conclusion, calves with high titers of specific BCoV IgG1 (≥1024) were mostly protected against viral infection, while animals with low titers of IgG1 (<1024) were mostly infected with BCoV. IgG1 Abs from colostrum origin are critical for prevention of BCoV infection. BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). mostró. Con respecto a la circulación viral, se detectó BCoV en el 10% (3/30) de los terneros así como también seroconversión de IgG1 en el 42% del total de los animales, lo que evidencia que aproximadamente la mitad de los terneros se infectaron con BCoV. Este estudio mostró que los terneros con altos títulos de IgG1 específica (≥ 1.024) estuvieron mayormente protegidos contra la infección con BCoV, mientras que los animales con títulos bajos de IgG1 (< 1.024) estuvieron predispuestos a la infección. Esto confirma que los anticuerpos IgG1 calostrales son críticos para la prevención de la infección por este agente viral.
Output: M I C R O B I O L O G Í A Passive immunity to control Bovine coronavirus diarrhea in a dairy herd in Argentina PALABRAS CLAVE bajo la licencia CC BY-NC-ND (http://creativecommons.org/licenses/by- nc-nd/4.0/)
3C-like protease (3CL pro ) plays pivotal roles in the life cycle of severe acute respiratory syndrome coronavirus (SARS-CoV) and only the dimeric protease is proposed as the functional form. Guided by the crystal structure and molecular dynamics simulations, we performed systematic mutation analyses to identify residues critical for 3CL pro dimerization and activity in this study. Seven residues on the dimer interface were selected for evaluating their contributions to dimer stability and catalytic activity by biophysical and biochemical methods. These residues are involved in dimerization through hydrogen bonding and broadly located in the N-terminal finger, the a-helix A 0 of domain I, and the oxyanion loop near the S1 substrate-binding subsite in domain II. We revealed that all seven single mutated proteases still have the dimeric species but the monomer-dimer equilibria of these mutants vary from each other, implying that these residues might contribute differently to the dimer stability. Such a conclusion could be further verified by the results that the proteolytic activities of these mutants also decrease to varying degrees. The present study would help us better understand the dimerizationactivity relationship of SARS-CoV 3CL pro and afford potential information for designing anti-viral compounds targeting the dimer interface of the protease.
Output: Residues on the Dimer Interface of SARS Coronavirus 3C-like Protease: Dimer Stability Characterization and Enzyme Catalytic Activity Analysis
Background: Morbidity and mortality rates of low birth weight (LBW) newborns at term are higher than rates in normal birth weight (NBW) newborns. LBW newborns are at greater risk to acquire recurrent bacterial and viral infections during their first few weeks of life possibly as an outcome of compromised innate immune functions. As adaptive immunity is in a naive state, increased risk of infection of LBW as compared to NBW newborns may reflect impairments in innate immunity. Methodology: To characterize the increased susceptibility to infections in LBW newborns we used microarray technology to identify differences in gene expression in LBW newborns (n = 8) compared to NBW newborns (n = 4) using cord blood. The results obtained from the microarray study were validated on a larger number of samples using real time RT-PCR (LBW = 22, NBW = 18) and western blotting (LBW = 12, NBW = 12). The Interferome database was used to identify interferon (IFN) signature genes and ingenuity pathway analysis identified canonical pathways and biological functions associated with the differentially expressed genes in LBW newborns. ELISAs for IFNs and bactericidal/permeability-increasing protein were performed in both LBW and NBW newborns and in adults (LBW = 18, NBW = 18, Adults = 8). Principal Findings: Upon microarray analysis, we identified 1,391 differentially expressed genes, of which, 1,065 genes were down-regulated and 326 genes were up-regulated in the LBW compared to NBW newborns. Of note, 70 IFN-signature genes were found to be significantly down-regulated in LBW compared to NBW newborns. Ingenuity pathway analysis revealed pattern recognition receptors signaling including Toll-Like Receptors (TLRs) -1, -5, and -8 genes and IFN signaling as the most significantly impacted pathways. Respiratory infectious diseases were the most significantly affected bio-functions in LBW newborns. Conclusion and Significance: Diminished PRRs, IFN-signature, and BPI gene expression raises the possibility that impairments in these pathways contribute to the susceptibility of LBW term infants to infection.
Output: Decreased Pattern Recognition Receptor Signaling, Interferon-Signature, and Bactericidal/Permeability- Increasing Protein Gene Expression in Cord Blood of Term Low Birth Weight Human Newborns
Coronavirus disease-2019 (COVID-19) is a rapidly escalating epidemic caused by SARS-CoV-2. Identification of a simple and effective indicator to assess disease severity and prognosis is urgently needed. Dynamic changes of blood lymphocyte percentage (LYM%) in 15 death cases, 15 severe cases as well as 40 moderate cases of COVID-19 patients were retrospectively analyzed. A Time-LYM% model (TLM) was established according to the descriptive studies and was validated in 92 hospitalized cases. Results from death and severe cases showed that LYM% in blood tests were inversely associated with the severity and prognosis of COVID-19. LYM% in moderate type of patients with COVID-19 remained higher than 20% 10-12 days after symptom onset. In contrast, LYM% was lower than 20% in severe cases. However, LYM% in severe cases was higher than 5% 17-19 days after the onset of the disease, while it fell below 5% in death cases. Accordingly, we established a Time-LYM% model (TLM), which was validated as an independent criterion of disease classification in another 92 hospitalized patients with COVID-19. Lymphopenia can be used as an indicator of disease severity and prognosis of COVID-19 patients. TLM is worth of application in the clinical practice.
Output: Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study Summary Background
2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase), a membraneassociated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the β5-α7 loop is observed. The role of the N terminus of helix α7-unique for CNPase in the 2H family-during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating that the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms.
Output: Crystallographic Analysis of the Reaction Cycle of 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family
Saffold virus (SAFV), a picornavirus, is occasionally detected in children with acute flaccid paralysis, meningitis, and cerebellitis; however, the neuropathogenicity of SAFV remains undetermined. The virulence of two clinical isolates of SAFV type 3 (SAFV-3) obtained from a patient with aseptic meningitis (AM strain) and acute upper respiratory inflammation (UR strain) was analyzed in neonatal and young mice utilizing virological, pathological, and immunological methods. The polyproteins of the strains differed in eight amino acids. Both clinical isolates were infective, exhibited neurotropism, and were mildly neurovirulent in neonatal ddY mice. Both strains pathologically infected neural progenitor cells and glial cells, but not large neurons, with the UR strain also infecting epithelial cells. UR infection resulted in longer inflammation in the brain and spinal cord because of demyelination, while the AM strain showed more infectivity in the cerebellum in neonatal ddY mice. Additionally, young BALB/c mice seroconverted following mucosal inoculation with the UR, but not the AM, strain. Both SAFV-3 isolates had neurotropism and mild neurovirulence but showed different cell tropisms in both neonatal and young mouse models. This animal model has the potential to recapitulate the potential neuropathogenicity of SAFV-3.
Output: Neuropathogenicity of Two Saffold Virus Type 3 Isolates in Mouse Models
Purpose: The aim of the study was to identify characteristic clinical features and outcomes of critically ill patients with confirmed severe acute respiratory syndrome (SARS). Materials and Methods: This retrospective study enrolled all patients admitted to a 12-bed SARS intensive care unit (ICU) in a tertiary care medical center in Taipei between May 15 and July 17, 2003. Patients with positive results of either reverse transcriptase-polymerase chain reaction or antibody to SARS coronavirus were defined as SARS cases and others with negative results as control cases. Results: Of the 50 patients, 14 had confirmed SARS. Demographics were similar between the 2 groups. The highest leukocyte and neutrophil counts, lactate dehydrogenase, and creatine kinase; positive endexpiratory pressure; and use of corticosteroids, ribavirin, and intravenous immunoglobulin were higher in the SARS group. In contrast, the lowest lymphocyte count and the ratio of PaO 2 to the fraction of inspired oxygen were lower in the SARS group. Of the 15 deaths in the control group, 12 (80%) occurred during the first 2 weeks after ICU admission. However, in the confirmed SARS group, 5 (55.6%) of the 9 deaths occurred within the third or fourth week. This difference in timing between these 2 groups was significant (P = .004). Conclusions: In a SARS ICU, patients with a confirmed diagnosis of SARS had significantly different clinical features and timing of mortality from those of the control group.
Output: Characteristic features and outcomes of severe acute respiratory syndrome found in severe acute respiratory syndrome intensive care unit patients
Partetravirus is a recently described group of animal parvoviruses which include the human partetravirus, bovine partetravirus and porcine partetravirus (previously known as human parvovirus 4, bovine hokovirus and porcine hokovirus respectively). In this report, we describe the discovery and genomic characterization of partetraviruses in bovine and ovine samples from China. These partetraviruses were detected by PCR in 1.8% of bovine liver samples, 66.7% of ovine liver samples and 71.4% of ovine spleen samples. One of the bovine partetraviruses detected in the present samples is phylogenetically distinct from previously reported bovine partetraviruses and likely represents a novel genotype. The ovine partetravirus is a novel partetravirus and phylogenetically most related to the bovine partetraviruses. The genome organization is conserved amongst these viruses, including the presence of a putative transmembrane protein encoded by an overlapping reading frame in ORF2. Results from the present study provide further support to the classification of partetraviruses as a separate genus in Parvovirinae.
Output: Discovery and Genomic Characterization of a Novel Ovine Partetravirus and a New Genotype of Bovine Partetravirus
Numerous reviews on dog zonoses address long-lasting lists of zoonotic infections, observed worldwide or very specifically in certain regions only. Here we describe the average family dog in the Western hemisphere owned by an average family without sufficient knowledge about potential hazards their pet might transmit to family members. This chapter is based on semi quantitative risk analysis in order to rank potential health risk transmitted from family dogs to human. Surprisingly every day risk is different from the generally expected potential risk according to traditional ranking of hazards (zoonoses) in dogs in general. Attention is given to human behavior regarding the family dog and responsible dog ownership. Modern trends include pet travel or pet import from endemic to non-endemic areas, without sufficient knowledge amongst pet owners or public health institutes. Of great value is information provided by ESCCAP (www.esccap.org) with information for European countries (veterinarians and pet-owners) on prevalences and prevention of parasitic infections in dogs and cats in the major languages of Europe. Eventually attention is paid to new trends in dog feed such as feeding bones and raw meat. This may have serious consequences for the spread of ordinary zoonoses like Salmonella and parasitic infections not only between dogs, but also to family members. A last point of attention is the prevention of attracting wild life zoonoses via dogs to family members (eg. Echinococcus multilocularis and Baylisascaris spp.). Authorities responsible for public health should be encouraged to pay more attention, not only in providing more regulations, but primary in enforcement of existing rules and stimulating responsible pet-ownership. Companion animal veterinarians and (local) public health authorities, including physicians, should contribute equally in zoonoses prevention programs ('One health' approach). 575 
Output: Dogs and Transmission of Infection to Man, "Respected Member of the Family?"
Graphical Abstract Highlights d DENV NS4B induces mitochondria elongation during viral infection d Elongated mitochondria and virus-induced convoluted membranes are physically linked d NS4B inhibits activation of the mitochondrial fission factor DRP1 d Mitochondria elongation alleviates DENV-induced RIG-Idependent innate immunity SUMMARY With no antiviral drugs or widely available vaccines, Dengue virus (DENV) constitutes a public health concern. DENV replicates at ER-derived cytoplasmic structures that include substructures called convoluted membranes (CMs); however, the purpose of these membrane alterations remains unclear. We determine that DENV nonstructural protein (NS)4B, a promising drug target with unknown function, associates with mitochondrial proteins and alters mitochondria morphology to promote infection. During infection, NS4B induces elongation of mitochondria, which physically contact CMs. This restructuring compromises the integrity of mitochondria-associated membranes, sites of ER-mitochondria interface critical for innate immune signaling. The spatio-temporal parameters of CM biogenesis and mitochondria elongation are linked to loss of activation of the fission factor Dynamin-Related Protein-1. Mitochondria elongation promotes DENV replication and alleviates RIG-I-dependent activation of interferon responses. As Zika virus infection induces similar mitochondria elongation, this perturbation may protect DENV and related viruses from innate immunity and create a favorable replicative environment.
Output: Dengue Virus Perturbs Mitochondrial Morphodynamics to Dampen Innate Immune Responses Article Dengue Virus Perturbs Mitochondrial Morphodynamics to Dampen Innate Immune Responses
Bovine coronavirus (BCoV) is an economically signifi cant cause of enteric and respiratory diseases in cattle throughout the world. BCoV is a known cause of neonatal calf diarrhea, winter dysentery in adult cattle, and respiratory disorders in cattle of all ages. In this chapter, we describe a simple and effi cient protocol for total nucleic acids extraction to be used in conventional RT-PCR assay. This is a technique used routinely in our virology laboratory to detect BCoV from stool and nasopharyngeal samples of cattle.
Output: Detection of Bovine Coronavirus by Conventional Reverse Transcription Polymerase Chain Reaction
Note: this report is a pre-print and has not yet been peer-reviewed. As the number of novel coronavirus cases grows both inside and outside of China, public health authorities require evidence on the effectiveness of control measures such as thermal screening of arrivals at airports. We evaluated the effectiveness of exit and entry screening for 2019-nCoV infection. In our baseline scenario, we estimated that 46.5% (95%CI: 35.9 to 57.7) of infected travellers would not be detected, depending on the incubation period, sensitivity of exit and entry screening, and the proportion of cases which are asymptomatic. Airport screening is unlikely to detect a sufficient proportion of 2019-nCoV infected travellers to avoid entry of infected travellers. We developed an online tool so that results can be updated as new information becomes available. As of 29 Jan 2019, 5,997 confirmed and 9,239 suspected cases of 2019-nCoV have been reported from China with 132 deaths confirmed so far 1 . There were cases in at least 15 other countries, identified due to symptoms plus recent travel history to Hubei province, China, which strongly suggests that the reported cases constitute only a small fraction of the actual number of infected individuals in China 2 . While the most affected region, Hubei province, has now ceased air travel and closed major public transport routes 3 it is unlikely that these measures will fully contain the outbreak. Despite limited evidence for its effectiveness 4,5 , airport screening is frequently implemented to limit the probability of infected cases entering other regions or countries. Here we use the available evidence to evaluate the effectiveness of exit and entry screening for detecting travellers with 2019-nCoV. We also provide an online app so that results can be updated as new information becomes available. . CC-BY 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint .
Output: Effectiveness of airport screening at detecting travellers infected with 2019-nCoV
Since the identification and imprisonment of "Typhoid Mary," a woman who infected at least 47 people with typhoid in the early 1900s, epidemiologists have recognized that 'superspreading' hosts play a key role in disease epidemics. Such variability in transmission also exists among species within a community (amplification hosts) and among habitat patches across a landscape (disease 'hotspots'), underscoring the need for an integrative framework for studying transmission heterogeneity. Here, we synthesize literature on human, plant, and animal diseases to evaluate the relative contributions of host, pathogen, and environmental factors in driving transmission heterogeneity across hosts and space. We show that host and spatial heterogeneity are closely linked and that quantitatively assessing the contribution of infectious individuals, species, or environmental patches to overall transmission can aid management strategies. We conclude by posing hypotheses regarding how pathogen natural history influences transmission heterogeneity and highlight emerging frontiers in the study of transmission heterogeneity.
Output: From superspreaders to disease hotspots: linking transmission across hosts and space
Previously, fusion of established T cell lines or clones has been claimed to be difficult. We now report our experiences in the fusion of both long term cultures of rat T cell clones and mouse T cell lines to rat W/Fu (C58NT)D. Upon fusion of rat T cell clones the hybrids obtained expressed antigen specificities identical to those of the parent clones. In addition, C58 was used for interspecies hybridisation of murine T cell lines. The specificity of intra-and inter-species hybrids was maintained by subcloning. We conclude that the C58 cell line can be used to generate continuously growing monoclonal T-cell reagents of sufficient stability using both intra-and inter-species hybridisation.
Output: CD4 rat X rat and mouse x rat T cell hybridomas produced by fusion of established T cell lines and clones to W/Fu (C58NT)D
This research explores perceived importance of safety and security measures from the perspectives of tourists and service providers. Use of face-to-face-semi structured interviews with supply side providers in Thailand results in recognizing safety measures to ask tourists about, other than those found in the literature. Researchers collected questionnaire data from international leisure and business tourists to Thailand on importance of safety and security measures. Analysis of the importance of 23 safety and security measures show a six factor pattern in thinking about measures. However, the most important measure is not in a factor. Therefore, the study considers analysis method issues and raises questions about the value of structured data and merits of the recognition of if-then conditions by research methods such as long interviews. Examination of practical, theoretical and methodological values of findings includes considering research needed and the utility of safety measure information in business decision making.
Output: Perceptions of importance and what safety is enough ☆
Molecular diagnostics of infectious diseases, in particular, nucleic-acid-based methods, are the fastest growing field in clinical laboratory diagnostics. These applications are stepwise replacing or complementing culture-based, biochemical, and immunological assays in microbiology laboratories. The first-generation nucleic acid assays were monoparametric such as conventional tests, determining only a single parameter. Improvements and new approaches in technology now open the possibility for the development of multiparameter assays using microarrays, multiplex nucleic acid amplification techniques, or mass spectrometry, while the introduction of closed-tube systems has resulted in rapid microbial diagnostics with a subsequently reduced contamination risk. Whereas the first assays were focused on the detection and identification of microbial pathogens, these new technologies paved the way for the parallel determination of multiple antibiotic resistance determinants or to perform microbial epidemiology and surveillance on a genetic level. Phenotype-based methods One of the oldest but still very important methods in clinical bacteriology is the detection of human pathogens by direct microscopic examination of the specimen. Many
Output: Current applications and future trends of molecular diagnostics in clinical bacteriology
To develop a more effective vaccination strategy for reducing the impact of respiratory syncytial virus (RSV) infection, especially in young infants (<6 months old), it is necessary to understand the transmission dynamics of RSV. Methods. We conducted a community-based prospective cohort study from 2014 to 2016 in Biliran Province, the Philippines, on children <5 years old. We collected nasopharyngeal swabs from symptomatic children with acute respiratory infection (ARI) during household visits and at health facilities. In households (n = 181) with RSV-positive ARI cases (RSV-ARI), we also identified ARI episodes among other children <5 years old in the same household. In addition, we determined the serial interval to estimate the basic reproduction number (R 0 ), the average number of secondary cases generated by a single primary case. Results. In the 181 households analyzed, we found 212 RSV-ARI in 152 households with a single case and 29 households with multiple cases, which included 29 1st RSV-ARI and 31 2nd RSV-ARI. We also found possible index cases among children <5 years old in the same household for 29.0% (18 of 62) of young infants with RSV-ARI. The estimated mean serial interval was 3.2 days, and R 0 was estimated to be 0.92-1.33 for RSV-A and 1.04-1.76 for RSV-B, which varied between different times (2014 and 2015) and places. Conclusions. Young infants are likely to acquire RSV infection from older children in the same household. Therefore, vaccination targeting older children might protect infants from RSV infection.
Output: Open Forum Infectious Diseases Transmission of Respiratory Syncytial Virus Among Children Under 5 Years in Households of Rural Communities, the Philippines
NICEATM and ICCVAM convened an international workshop to review the state of the science of human and veterinary vaccine potency and safety testing methods and to identify opportunities to advance new and improved methods that can further reduce, refine, and replace animal use. Six topics were addressed in detail by speakers and workshop participants and are reported in a series of six reports. This workshop report, the second in the series, provides recommendations for current and future use of nonanimal methods and strategies for veterinary vaccine potency testing. Workshop participants recommended that future efforts to replace animal use give priority to vaccines (1) that use large numbers of animals per test and for which many serials are produced annually, (2) that involve significant animal pain and distress during procedures, (3) for which the functional protective antigen has been identified, (4) that involve foreign animal/zoonotic organisms that are dangerous to humans, and (5) that involve pathogens that can be easily spread to wildlife populations. Vaccines identified as the highest priorities were those for rabies, Leptospira spp., Clostridium spp., Erysipelas, foreign animal diseases (FAD), poultry diseases, and fish diseases. Further research on the identification, purification, and characterization of vaccine protective antigens in veterinary vaccines was also identified as a priority. critical knowledge and data gaps, including opportunities to apply new science and technology. Recommendations included (1) investigations into the relative impact of various adjuvants on antigen quantification assays, (2) investigations into extraction methods that could be used for vaccines containing adjuvants that can interfere with antigen assays, and (3) review of the current status of rabies and tetanus human vaccine in vitro potency methods for their potential application to the corresponding veterinary vaccines. Workshop participants recommended enhanced international harmonization and cooperation and closer collaborations between human and veterinary researchers to expedite progress. Implementation of the workshop recommendations is expected to advance alternative in vitro methods for veterinary vaccine potency testing that will benefit animal welfare and replace animal use while ensuring continued protection of human and animal health.
Output: NICEATM-ICCVAM # International Workshop on Alternative Methods to Reduce, Refine, and Replace the Use of Animals in Vaccine Potency and Safety Testing: Non-animal replacement methods for veterinary vaccine potency testing: state of the science and future directions peer-review under responsibility of the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM). peer-review under responsibility of the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM)
The search for new biomarkers for diagnosis, prognosis and therapeutic monitoring of diseases continues in earnest despite dwindling success at finding novel reliable markers. Some of the current markers in clinical use do not provide optimal sensitivity and specificity, with the prostate cancer antigen (PSA) being one of many such examples. The emergence of proteomic techniques and systems approaches to study disease pathophysiology has rekindled the quest for new biomarkers. In particular the use of protein microarrays has surged as a powerful tool for large scale testing of biological samples. Approximately half the reports on protein microarrays have been published in the last two years especially in the area of biomarker discovery. In this review, we will discuss the application of protein microarray technologies that offer unique opportunities to find novel biomarkers.
Output: Applications of protein microarrays for biomarker discovery
a b s t r a c t N-7 and 2 0 -O methylation of host cell mRNA occurs in the nucleus and results in the generation of cap structures (cap 0, m 7 GpppN; cap 1, m 7 GpppNm) that control gene expression by modulating nuclear export, splicing, turnover, and protein synthesis. Remarkably, RNA cap modification also contributes to mammalian cell host defense as viral RNA lacking 2 0 -O methylation is sensed and inhibited by IFIT1, an interferon (IFN) stimulated gene (ISG). Accordingly, pathogenic viruses that replicate in the cytoplasm have evolved mechanisms to circumvent IFIT1 restriction and facilitate infection of mammalian cells. These include: (a) generating cap 1 structures on their RNA through cap-snatching or virally-encoded 2 0 -O methyltransferases, (b) using cap-independent means of translation, or (c) using RNA secondary structural motifs to antagonize IFIT1 binding. This review will discuss new insights as to how specific modifications at the 5 0 -end of viral RNA modulate host pathogen recognition responses to promote infection and disease.
Output: Innate immune restriction and antagonism of viral RNA lacking 2'-O methylation
Epizootic Epitheliotropic Disease Virus (EEDV; Salmonid Herpesvirus-3) causes a serious disease hatchery-reared lake trout (Salvelinus namaycush), threatening restoration efforts of this species in North America. The current inability to replicate EEDV in vitro necessitates the search for a reproducible, sensitive, and specific assay that allows for its detection and quantitation in a time-and cost-effective manner. Herein, we describe a loopmediated isothermal amplification (LAMP) assay that was developed for the quantitative detection of EEDV in infected fish tissues. The newly developed LAMP reaction was optimized in the presence of calcein, and the best results were produced using 2 mM MgCl 2 , 1.8 mM dNTPs and at an incubation temperature of 67.1°C. This method was highly specific to EEDV, as it showed no cross-reactivity with several fish viruses, including Salmonid Herpesvirus -1 , -2, -4, and -5, Infectious Pancreatic Necrosis Virus, Spring Viremia of Carp Virus, Infectious Hematopoietic Necrosis Virus, Golden Shiner Reovirus, Fathead Minnow Nidovirus, and Viral Hemorrhagic Septicemia Virus. The analytical sensitivity of the EEDV-LAMP method was estimated to be as low as 16 copies of plasmid per reaction. When infected fish tissue was used, a positive reaction could be obtained when an infected gill tissue sample that contained 430 viral copies/μg was diluted up to five orders of magnitude. The sensitivity and specificity of the newly developed LAMP assay compared to the SYBR Green qPCR assay were 84.3% and 93.3%, respectively. The quantitative LAMP for EEDV had a correlation coefficient (R 2 = 0.980), and did not differ significantly from the SYBR Green quantitative PCR assay (p > 0.05). Given its cost-and time-effectiveness, this quantitative LAMP assay is suitable for screening lake trout populations and for the initial diagnosis of clinical cases.
Output: Development of a loop-mediated isothermal amplification assay for the detection and quantification of epizootic epitheliotropic disease virus (salmonid herpesvirus-3)
The need for novel therapeutic options to fight herpesvirus infections still persists. Herein we report the design, synthesis and antiviral evaluation of a new family of non-nucleoside antivirals, derived from 1-[x-(4-bromophenoxy)alkyl]uracil derivatives -previously reported inhibitors of human cytomegalovirus (HCMV). Introduction of the N-(4-phenoxyphenyl)acetamide side chain at N 3 increased their potency and widened activity spectrum. The most active compounds in the series exhibit submicromolar activity against different viral strains of HCMV and varicella zoster virus (VZV) replication in HEL cell cultures. Inactivity against other DNA and RNA viruses, including herpes simplex virus 1/2, points to a novel mechanism of antiviral action.
Output: Toward the discovery of dual HCMV-VZV inhibitors: Synthesis, structure activity relationship analysis, and cytotoxicity studies of long chained 2-uracil-3-yl-N-(4-phenoxyphenyl)acetamides
During th e pas t thre e decades , ther e ha s bee n a growin g realizatio n tha t breast-feeding no t only provides the nutritional requirements of the infant , but als o supplie s a hos t o f defens e factor s fo r th e protectio n o f th e recipient and/o r th e mammar y gland . Th e stud y o f thi s remarkabl e defense syste m in huma n mil k ha s bee n difficult , however , becaus e o f it s biochemical complexities , th e smal l concentration s o f certai n ver y poten t agents i n huma n milk , th e nee d t o develo p specia l method s t o quantif y certain factor s becaus e o f thei r particula r form s i n huma n milk , th e compartmentalization o f some of the agents, and the dynamic effects o f th e length o f lactatio n an d othe r materna l factor s upo n th e concentration s o r functions o f th e component s o f th e system . I n thi s chapter, w e summariz e the current information concernin g the molecular forms, concentrations i n milk durin g th e severa l phase s o f lactation , biologica l activities , fat e i n th e recipient infant, an d in vivo functions o f the defense agent s in human milk . (2 ) mos t component s of th e immunologi c syste m i n huma n mil k ar e produce d throughou t lactation an d durin g gradua l weaning ; (3 ) th e factor s ar e usuall y commo n to othe r mucosa l sites ; (4 ) the y ar e adapte d t o resis t digestio n i n th e gastrointestinal trac t of th e recipien t infant ; (5 ) they protec t b y noninflammatory mechanisms ; an d (6 ) th e agent s ac t synergisticall y wit h eac h othe r or with defense agent s produced b y the recipient. Representativ e example s of solubl e defens e agent s ar e liste d i n Tabl e I .
Output: Defense Agents in Milk A. Defens e Agent s i n Huma n Mil k A. Factors with Nonnutrltive Functions In Human Milk The defens e agent s i n huma n milk , thoug h biochemicall y diverse , shar e certain features : (1 ) ther e i s ofte n a n invers e relationshi p betwee n th e 728 Armon
Multiplex PCR has become the test of choice for the detection of multiple respiratory viruses in clinical specimens. However, there are few direct comparisons of different PCR assays. This study compares 4 different multiplex PCR assays for the recovery of common respiratory viruses. We tested 213 respiratory specimens using four different multiplex PCR assays: the xTAG respiratory viral panel fast (Abbott Molecular Laboratories), Fast-track Respiratory Pathogen assay (Fast-track Diagnostics), Easyplex respiratory pathogen 12 kit (Ausdiagnostics), and an in-house multiplex real-time PCR assay. The performance of the four assays was very similar, with 93-100% agreement for all comparisons. Other issues, such as through-put, technical requirements and cost, are likely to be as important for making a decision about which of these assays to use given their comparative performance.
Output: Comparison of four multiplex PCR assays for the detection of viral pathogens in respiratory specimens
The genome of bacteriophage q~6 is composed of three unique segments of double-stranded RNA packaged within a procapsid. One segment can recombine with another in regions that share little sequence similarity. Although the recombination is therefore heterologous, the crossover points usually consist of two to six identical nucleotides. The frequency of recombinants is enhanced by conditions that prevent or hinder the minus strand synthesis of a single plus strand segment. Recombination serves as a repair system as well as a means of changing the genetic structure of the virus. The reaction can be studied in an in-vitro packaging and replication system involving purified procapsids and ssRNA. Although there are striking differences in the mechanisms of recombination in RNA viruses, there are also strong similarities. All seem to use a copy-choice template switching action for recombination. The q~ 6 system is a useful model for the recombination of other segmented double-stranded RNA viruses such as the Reoviridae.
Output: Heterologous recombination in the segmented dsRNA genome of bacteriophage (I)6 General background of viral RNA recombination