niryuu/sni-each-converted huggingface dataset:
Background. The newly emerged influenza A(H1N1) virus (new H1N1 virus) is causing the first influenza pandemic of this century. Three influenza pandemics of the previous century caused variable mortality, which largely depended on the development of severe pneumonia. However, the ability of the new H1N1 virus to cause pneumonia is poorly understood. Methods. The new H1N1 virus was inoculated intratracheally into ferrets. Its ability to cause pneumonia was compared with that of seasonal influenza H1N1 virus and highly pathogenic avian influenza (HPAI) H5N1 virus by using clinical, virological, and pathological analyses. Results. Our results showed that the new H1N1 virus causes pneumonia in ferrets intermediate in severity between that caused by seasonal H1N1 virus and by HPAI H5N1 virus. The new H1N1 virus replicated well throughout the lower respiratory tract and more extensively than did both seasonal H1N1 virus (which replicated mainly in the bronchi) and HPAI H5N1 virus (which replicated mainly in the alveoli). High loads of new H1N1 virus in lung tissue were associated with diffuse alveolar damage and mortality. Conclusions. The new H1N1 virus may be intrinsically more pathogenic for humans than is seasonal H1N1 virus. A new influenza A virus of the subtype H1N1 (new H1N1 virus) that first emerged in Mexico at the beginning of 2009 is the first pandemic human influenza virus of the 21st century. Studies have concluded that this virus probably originated from a domestic swine reservoir on the basis of its genetic signature [1, 2]. On 11 June 2009, the World Health Organization declared phase 6 of the global pandemic alert level [3] .
Output: Severity of Pneumonia Due to New H1N1 Influenza Virus in Ferrets Is Intermediate between That Due to Seasonal H1N1 Virus and Highly Pathogenic Avian Influenza H5N1 Virus
Background. Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus transmission in living-donor kidney transplantation. Methods. Living kidney donors and their corresponding recipients were enrolled at the time of transplantation. Follow-up study visits for recipients were scheduled 4-6 weeks and 1 year thereafter. At each visit, plasma and urine samples were collected and transplant recipients were evaluated for signs of infection or other transplant-related complications. For metagenomic analysis, samples were enriched for viruses, amplified by anchored random polymerase chain reaction (PCR), and sequenced using high-throughput metagenomic sequencing. Viruses detected by sequencing were confirmed using real-time PCR. Results. We analyzed a total of 30 living kidney donor and recipient pairs, with a follow-up of at least 1 year. In addition to viruses commonly detected during routine post-transplant virus monitoring, metagenomic sequencing detected JC polyomavirus (JCPyV) in the urine of 7 donors and their corresponding recipients. Phylogenetic analysis confirmed infection with the donor strain in 6 cases, suggesting transmission from the transplant donor to the recipient, despite recipient seropositivity for JCPyV at the time of transplantation. Conclusions. Metagenomic sequencing identified frequent transmission of JCPyV from kidney transplant donors to recipients. Considering the high incidence rate, future studies within larger cohorts are needed to define the relevance of JCPyV infection and the donor's virome for transplant outcomes.
Output: Clinical Infectious Diseases Metagenomic Virome Sequencing in Living Donor and Recipient Kidney Transplant Pairs Revealed JC Polyomavirus Transmission
Background: Local health departments are the backbone of public health emergency (PHE) response plans. The front line of emergency response preparedness is people. Role perceptions of individual staff members of a given organization strongly affect response probability and performance. Therefore, the aim of this study was to determine local public health employees' perceptions of emergency response responsibilities, identify factors that influence their perception, and indicate the challenges and bottlenecks of PHE response in the Health Inspection Institution (HII) after its separation from China's multiple Centers for Disease Control and Prevention (CDC). Methods: We used a stratified randomized sample survey to examine HII workers' knowledge of their own duties concerning PHE response in 17 facilities in Heilongjiang, a province in northeastern China. Data were collected from May to July 2010 using a 9-item combined question inquiring about the workers' statutory duties. Results: Of 348 administered surveys, 309 were returned for an overall response rate of 88.8 %. Overall, the correct recognition rate of PHE responsibilities was low. Some HII workers were confused about their responsibilities required by law, regulations, and emergency response plans. A quarter of all the respondents had the lowest knowledge for PHE responsibilities. Factors influencing their perceptions of responsibilities were department, work experience in a CDC, and PHE response experience. Conclusions: To improve preparedness for a PHE, efforts are needed to train, support, and monitor the workers' knowledge and competencies in PHEs as part of an organizational change; the worker's knowledge of their responsibilities should be measured and used as an indicator of preparedness for a PHE, and training should be undertaken where there are deficiencies. Management should also encourage workers in the departments of food hygiene/school health surveillance to be more involved in PHE preparedness and response issues. International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
Output: Determinants of emergency response responsibility perceptions in the local public health workforce after China's health sector restructuring
Background: Clinical diagnosis of Japanese encephalitis is usually difficult due to non-specific signs at the early and acute stages of the infection. Virus isolation from peripheral blood is also not possible because of the short period and low level of transient viremia even in the acute stage of the disease. It is thus urgent to develop a feasible and convenient method for laboratory diagnosis of the infection. Objectives: To establish a newly designed molecular approach that can be used to detect intracellular Japanese encephalitis viral RNA in host cells. Study design: The method was firstly established and then was carried out to test its efficacy in cultured BHK-21 cells, subsequently in peripheral blood mononuclear cells (PBMCs) isolated from mice that have been inoculated with JE virus suspension. Results: In this study, in situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) was established; which combines merits of recently developed loop-mediated isothermal amplification (LAMP) and in situ reverse-transcriptase polymerase chain reaction (in situ RT-PCR). Conclusions: The newly designed method can detect viral RNAs in peripheral blood mononuclear cells (PBMCs) in a short time with high sensitivity and efficiency. (W.-J. Chen). a These authors contributed equally to this study.
Output: In situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) for detection of Japanese encephalitis viral RNA in host cells
We review a sequence of strategic planning efforts over time in the United States, all involving processes to prioritize new vaccine candidates. The Institute of Medicine of the National Academies of Sciences, Engineering, and Medicine has been involved in three priority setting processes, each using different metrics and methodologies: infant mortality equivalents (1985)(1986), cost-effectiveness (2000), and more recently, the implementation of a software system based on a broader multi-criteria systems approach that can include either of the earlier metrics among other various considerations (2015). The systems approach offers users the flexibility to select, combine, rank, weigh and evaluate different attributes representing their perspectives, assumptions, and particular needs. This approach also overcomes concerns relating to the previous single-metric ranking approaches that yielded lists that, once published, were static, and could not readily accommodate new information about emerging pathogens, new scientific advances, or changes in the costs and performance features of interventions. We discuss the rationale and reasoning behind the design of this multi-criteria decision support approach, stakeholder feedback about the tool, and highlight the potential advantages from using this expanded approach to better inform and support vaccine policies.
Output: Planning and priority setting for vaccine development and immunization q
Quickly detecting harmful cascades in networks can allow us to analyze the causes and prevent further spreading of destructive influence. Since it is often impossible to observe the state of all nodes in a network, a common method is to detect harmful cascades from sparsely placed sensors. However, the harmful cascades are usually dynamic (e.g., the cascade initiators and diffusion trajectories can change over the time), which can severely destroy the robustness of selected sensors. Meanwhile the large scale of current networks greatly increases the time complexity of sensor selection. Motivated by the observation, in this paper we investigate the scalable sensor selection problem for early detection of dynamic harmful cascades in networks. Specifically, we first put forward a dynamic susceptible-infected model to describe harmful cascades, and formally define a detection time minimization (DTM) problem which focuses on effective sensors placement for early detection of dynamic cascades. We prove that it is #P-hard to calculate the objective function exactly and propose two Monte-Carlo methods to estimate it efficiently. We prove the NP-hardness of DTM problem and design a corresponding greedy algorithm. Based on that, we propose an efficient upper bound based greedy (UBG) algorithm with the theoretical performance guarantee reserved. To further meet different types of large-scale networks, we propose two accelerations of UBG: Quickest-Path-UBG for sparse networks and Local-Reduction-UBG for dense networks to improve the time complexity. The experimental results on synthetic and real-world social networks demonstrate the practicality of our approaches.
Output: Early detection of dynamic harmful cascades in large-scale networks ଝ
Background: Coronavirus causes respiratory infections in humans. To determine the prevalence of human coronavirus (HCoV) infection among patients with influenza-like illness, 5833 clinical samples from nasopharyngeal swabs and aspirates collected between January 2012 and December 2013 were examined. Results: HCoV was found in 46 (0.79 %) samples. There were 19 (0.32 %) HCoV-HKU1, 19 (0.32 %) HCoV-NL63, 5 (0.09 %) HCoV-229E, and 3 (0.05 %) HCoV-OC43. None of the sample tested positive for MERS-CoV. The majority (54 %) of the HCoV-positive patients were between the ages of 0 and 5 years. HCoV was detected throughout the 2-year period and generally peaked from May to October, which coincided with the rainy season. Phylogenetic trees based on the alignment of the spike (S) gene sequences suggest an emergence of a new clade for HCoV-229E. The data in this study provide an insight into the prevalence of the recent circulating HCoVs in the region.
Output: Molecular epidemiology and characterization of human coronavirus
Background: In HIV-infected patients, prediction of Cytomegalovirus (CMV) disease remains difficult. A protective role of mannan-binding lectin (MBL) and ficolins against CMV disease has been reported after transplantation, but the impact in HIV-infected patients is unclear. Methods: In a case-control study nested within the Swiss HIV Cohort Study, we investigated associations between plasma levels of MBL/ficolins and CMV disease. We compared HIV-infected patients with CMV disease (cases) to CMV-seropositive patients without CMV disease (controls) matched for CD4 T-cells, sampling time, and use of combination antiretroviral therapy. MBL and M-ficolin, L-ficolin, and H-ficolin were quantified using ELISA. Results: We analysed 105 cases and 105 matched controls. CMV disease was neither associated with MBL (odds ratio [OR] 1.03 per log 10 ng/mL increase (95% CI 0.73-1.45)) nor with ficolins (OR per log 10 ng/mL increase 0.66 (95% CI 0.28-1.52), 2.34 (95% CI 0.44-12.36), and 0.89 (95% CI 0.26-3.03) for M-ficolin, L-ficolin, and H-ficolin, respectively). We found no evidence of a greater association between MBL and CMV disease in patients with low CD4 counts; however in the multivariable analysis, CMV disease was more likely in patients with an increased HIV RNA (OR 1.53 per log 10 copies/mL; 95% CI 1.08-2.16), or a shorter duration of HIV-infection (OR 0.91 per year; 95% CI 0.84-0.98).
Output: Low Levels of Mannan-Binding Lectin or Ficolins Are Not Associated with an Increased Risk of Cytomegalovirus Disease in HIV-Infected Patients
Background: Feline leukemia virus (FeLV) is an exogenous gammaretrovirus of domestic cats (Felis catus) and some wild felids. The outcomes of FeLV infection in domestic cats vary according to host susceptibility, virus strain, and infectious challenge dose. Jaguarundis (Puma yagouaroundi) are small wild felids from South and Central America. We previously reported on FeLV infections in jaguarundis. We hypothesized here that the outcomes of FeLV infection in P. yagouaroundi mimic those observed in domestic cats. The aim of this study was to investigate the population of jaguarundis at Fundação Parque Zoológico de São Paulo for natural FeLV infection and resulting outcomes. Methods: We investigated the jaguarundis using serological and molecular methods and monitored them for FeLV-related diseases for 5 years. We retrieved relevant biological and clinical information for the entire population of 23 jaguarundis held at zoo. Post-mortem findings from necropsies were recorded and histopathological and immunohistopathological analyses were performed. Sequencing and phylogenetic analyses were performed for FeLV-positive samples. For sample prevalence, 95% confidence intervals (CI) were calculated. Fisher's exact test was used to compare frequencies between infected and uninfected animals. P-values <0.05 were considered significant. Results: In total, we detected evidence of FeLV exposure in four out of 23 animals (17%; 95% CI 5-39%). No endogenous FeLV (enFeLV) sequences were detected. An intestinal B-cell lymphoma in one jaguarundi was not associated with FeLV. Two jaguarundis presented FeLV test results consistent with an abortive FeLV infection with seroconversion, and two other jaguarundis had results consistent with a progressive infection and potentially FeLV-associated clinical disorders and post-mortem changes. Phylogenetic analysis of env revealed the presence of FeLV-A, a common origin of the virus in both animals (100% identity) and the closest similarity to FeLV-FAIDS and FeLV-3281 (98.4% identity), originally isolated from cats in the USA. Conclusions: We found evidence of progressive and abortive FeLV infection outcomes in jaguarundis, and domestic cats were probably the source of infection in these jaguarundis.
Output: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi)
Although winter dysentery (WD), which is caused by the bovine coronavirus (BCoV) is characterized by the sudden onset of diarrhea in many adult cattle in a herd, the pathogenesis of the WD-BCoV is not completely understood. In this study, colostrumdeprived calves were experimentally infected with a Korean WD-BCoV strain and examined for viremia, enteric and nasal virus shedding as well as for viral antigen expression and virus-associated lesions in the small and large intestines and the upper and lower respiratory tract from 1 to 8 days after an oral infection. The WD-BCoV-inoculated calves showed gradual villous atrophy in the small intestine and a gradual increase in the crypt depth of the large intestine. The WD-BCoV-infected animals showed epithelial damage in nasal turbinates, trachea and lungs, and interstitial pneumonia. The WD-BCoV antigen was detected in the epithelium of the small and large intestines, nasal turbinates, trachea and lungs. WD-BCoV RNA was detected in the serum from post-inoculation day 3. These results show that the WD-BCoV has dual tropism and induces pathological changes in both the digestive and respiratory tracts of calves. To our knowledge, this is the first detailed report of dual enteric and respiratory tropisms of WD-BCoV in calves. Comprehensive studies of the dual tissue pathogenesis of the BCoV might contribute to an increased understanding of similar pneumoenteric CoV infections in humans.
Output: Dual enteric and respiratory tropisms of winter dysentery bovine coronavirus in calves
The SARS-CoV-2 pandemic demonstrates the need for accurate and convenient approaches to 2 diagnose and therapeutically monitor respiratory viral infections. We demonstrated that self-3 sampling with foam swabs is well-tolerated and provides quantitative viral output concordant 4 with flocked swabs. Using longitudinal home-based self-sampling, we demonstrate nasal 5 cytokine levels correlate and cluster according to immune cell of origin. Periods of stable viral 6 loads are followed by rapid elimination, which could be coupled with cytokine expansion and 7 contraction using mathematical models. Nasal foam swab self-sampling at home provides a 8 precise, mechanistic readout of respiratory virus shedding and local immune responses. 9 . CC-BY-ND 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: Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics
 Searches related to COVID-19 and face masks in Taiwan increased rapidly, following the announcements of Taiwan' first imported case and reached its peak as local cases were reported.  Searches for handwashing were gradually increased in period of face masks shortage in Taiwan.  Google Trends provides information on the most common knowledge needed by users and location of searches.  In response to the ongoing outbreak, our results demonstrated that Google Trends could potentially define the proper timing and location for practicing appropriate risk communication strategies to the affected population. Objective: An emerging outbreak of COVID-19 has been detected in at least 26 countries worldwide. Given this pandemic situation, robust risk communication is urgently needed particularly in affected countries. Therefore, this study explored the potential use of Google Trends (GT) to monitor public restlessness toward COVID-19 epidemic infection in Taiwan. We retrieved GT data for the specific locations of Taiwan nationwide and subregions using defined search terms related to coronavirus, handwashing, and face masks. Results: Searches related to COVID-19 and face masks in Taiwan increased rapidly, following the announcements of Taiwan' first imported case and reached its peak as local cases were reported. However, searches for handwashing were gradually increased in period of face masks shortage. Moreover, high to moderate correlations between Google relative search volume (RSV) and COVID-19 cases were found in Taipei (lag-3), New Taipei (lag-2), Taoyuan (lag-2), Tainan (lag-1), Taichung (lag0), and Kaohsiung (lag0). In response to the ongoing outbreak, our results demonstrated that GT could potentially define the proper timing and location for practicing appropriate risk communication strategies to the affected population.
Output: Journal Pre-proof Applications of google search trends for risk communication in infectious disease management: A case study of COVID-19 outbreak in Taiwan Applications of Google Search Trends for Risk Communication in Infectious Disease Management: a Case Study of COVID-19 Outbreak in Taiwan
The appearance of the novel betacoronavirus SARS-CoV-2 represents a major threat to human health, and its diffusion around the world is causing dramatic consequences. The knowledge of the 3D structures of SARS-CoV-2 proteins can facilitate the development of therapeutic and diagnostic molecules. Specifically, comparative analyses of the structures of SARS-CoV-2 proteins and homologous proteins from previously characterized viruses, such as SARS-CoV, can reveal the common and/or distinctive traits that underlie the mechanisms of recognition of cell receptors and of molecules of the immune system. Herein, we apply our recently developed energy-based methods for the prediction of antibodybinding epitopes and protein-protein interaction regions to the Receptor Binding Domain (RBD) of the Spike proteins from SARS-CoV-2 and SARS-CoV. Our analysis focusses only on the study of the structure of RBDs in isolation, without making use of any previous knowledge of binding properties. Importantly, our results highlight structural and sequence differences among the regions that are predicted to be immunoreactive and bind/elicit antibodies. These results provide a rational basis to the observation that several SARS-CoV RDB-specific monoclonal antibodies fail to appreciably bind the SARS-CoV-2 counterpart. Furthermore, we correctly identify the region of SARS-CoV-2 RBD that is engaged by the cell receptor ACE2 during viral entry into host cells. The data, sequences and structures we present here can be useful for the development of novel therapeutic and diagnostic interventions.
Output: Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and
Infrared thermography (IRT), one of the most valuable tools, is used for noncontact, noninvasive, and rapid monitoring of body temperature; this has been used for mass screening of febrile travelers at places such as airport quarantine stations for over 10 years after the 2003 severe acute respiratory syndrome (SARS) outbreak. The usefulness of thermography for mass screening has been evaluated in many recent studies; its sensitivity varies from 40 to 89.4% under various circumstances. In this chapter, we perform IRT evaluations for detecting febrile international travelers entering Japan at Nagoya Airport, immediately after the SARS epidemic, . The correlation of body surface temperature measured via thermography with the axillary temperature was significant. Through IRT, febrile individuals were detected with good accuracy and the detection accuracy was improved by corroborating surveillance with self-reporting questionnaires. However, there are several limitations associated with the use of IRT for fever screening. For instance, taking antifebrile medications results in rapid modification of the body temperature and directly affects the efficiency of IRT. To solve this unreliability and obtain higher accuracy in mass screening, we have developed a novel infection screening system using multisensor data, i.e., heart and respiration rates are determined by microwave radar in noncontact manner and facial skin temperature is monitored through IRT. The detection accuracy of the system improved, which is notably higher compared to the conventional screening method using only IRT.
Output: Applications of Infrared Thermography for Noncontact and Noninvasive Mass Screening of Febrile International Travelers at Airport Quarantine Stations
So what's the point of reading about health care challenges in developing countries? How does it help us practise better medicine and lead better lives? Our answer is that medicine cannot be practised in isolation. As the world becomes smaller, health care around the world has more, not less, in common. All health care systems struggle with the challenges of limited resources and growing demand. As well as providing clinically practical, we think the BMJ has a role in presenting an international perspective on health care [1].
Output: The World Federation: Enhancing Global Critical Care Practice and Performance
Background: Pneumonia is a leading cause of morbidity and mortality in children worldwide; however, its diagnosis can be challenging, especially in settings where skilled clinicians or standard imaging are unavailable. We sought to determine the diagnostic accuracy of lung ultrasound when compared to radiographically-confirmed clinical pediatric pneumonia. Methods: Between January 2012 and September 2013, we consecutively enrolled children aged 2e59 months with primary respiratory complaints at the outpatient clinics, emergency department, and inpatient wards of the Instituto Nacional de Salud del Niño in Lima, Peru. All participants underwent clinical evaluation by a pediatrician and lung ultrasonography by one of three general practitioners. We also consecutively enrolled children without respiratory symptoms. Children with respiratory symptoms had a chest radiograph. We obtained ancillary laboratory testing in a subset. Results: Final clinical diagnoses included 453 children with pneumonia, 133 with asthma, 103 with bronchiolitis, and 143 with upper respiratory infections. In total, CXR confirmed the diagnosis in 191 (42%) of 453 children with clinical pneumonia. A consolidation on lung ultrasound, which is our primary endpoint for pneumonia, had a sensitivity of 88.5%, specificity of 100%, and an area under-the-curve of 0.94 (95% CI 0.92e0.97) when compared to radiographically-confirmed clinical pneumonia. When any abnormality on lung ultrasound was compared to radiographically-confirmed clinical pneumonia the sensitivity increased to 92.2% and the specificity decreased to 95.2%, with an area under-the-curve of 0.94 (95% CI 0.91e0.96). Conclusions: Lung ultrasound had high diagnostic accuracy for the diagnosis of radiographicallyconfirmed pneumonia. Added benefits of lung ultrasound include rapid testing and high inter-rater agreement. Lung ultrasound may serve as an alternative tool for the diagnosis of pediatric pneumonia.
Output: Lung ultrasound as a diagnostic tool for radiographically-confirmed pneumonia in low resource settings
Despite the fact that most emerging diseases stem from the transmission of pathogenic agents from animals to humans, the factors that mediate this process are still ill defined. What is known, however, is that the interface between humans and animals is of paramount importance in the process. This review will discuss the importance of the human-animal interface to the disease emergence process. We also provide an overview of factors that are believed to contribute to the origin and global spread of emerging infectious diseases and offer suggestions that may serve as future prevention strategies, such as social mobilization, public health education, behavioral change, and communication strategies. Because there exists no comprehensive global surveillance system to monitor zoonotic disease emergence, the intervention measures discussed herein may prove effective temporary alternatives. of this interface will be crucial to future pandemic prevention efforts.
Output: The Origin and Prevention of Pandemics
The safe disposal of effluents can present a major problem to large urban communities because of their inevitable content of potentially pathogenic enteric viruses. At least one hundred types of virus may be present although many of these are difficult or even impossible to characterise under these conditions. Wastewater treatment does not greatly effect the survival of many enteric viruses and some survive well even after effluent disposal. The use of disinfectants for the inactivation of virus in effluent is practicable but requires careful manipulation in order to avoid the disemination of byproducts toxic to man or capable of interferring with the ecology of the receiving waters or soils. No one system is likely to be either universally acceptable because of the variable quality of effluents and much research remains to be done before guidelines can be recommended or established.
Output: Virus Removal by Disinfection of Effluents
Influenza C virus (ICV) is a common yet under-recognized cause of acute respiratory illness. ICV seropositivity has been found to be as high as 90% by 7-10 years of age, suggesting that most people are exposed to ICV at least once during childhood. Due to difficulty detecting ICV by cell culture, epidemiologic studies of ICV likely have underestimated the burden of ICV infection and disease. Recent development of highly sensitive RT-PCR has facilitated epidemiologic studies that provide further insights into the prevalence, seasonality, and course of ICV infection. In this review, we summarize the epidemiology and clinical characteristics of ICV.
Output: viruses Epidemiology and Clinical Characteristics of Influenza C Virus
Streptococcus pneumoniae is the main cause of diseases such as meningitis, pneumoniae and sepsis, especially in children and old people. Due to costly antibiotic treatment, and increasing resistance of pneumococcus, developing high-efficient protective vaccine against this pathogen is an urgent need. Although the pneumoniae polysaccharide vaccine (PPV) and pneumonia conjugate vaccines (PCV) are the efficient pneumococcal vaccine in children and adult groups, but the serotype replacement of S. pneumoniae strains causes the reduction in efficacy of such vaccines. For overcoming the aforesaid drawbacks epitope-based vaccines are introduced as the relevant alternative. In our previous research, the epitope vaccine was designed based on immunodominant epitopes from PspA, CbpA antigens as cellular stimulants and PhtD, PiuA as humoral stimulants. Because the low immunogenicity is the main disadvantage of epitope vaccine, in the current study, we applied coiled-coil selfassembled structures for developing our vaccine. Recently, self-assembled peptide nanoparticles (SAPNs) have gained much attention in the field of vaccine development due to their multivalency, self-adjuvanticity, biocompatibility, and size similarity to pathogen. In this regard, the final designed vaccine is comprised of cytotoxic T lymphocytes (CTL) epitopes from PspA and CbpA, helper T lymphocytes (HTL) epitopes from PhtD and PiuA, the pentamer and trimmer oligomeric domains form 5-stranded and 3-stranded coiled-coils as self-assembled scaffold, Diphtheria toxoids (DTD) as a universal T-helper, which fused to each other with appropriate linkers. The four different arrangements based on the order of above-mentioned compartments were constructed, and each of them were modeled, and validated to find the 3D structure. The structural, physicochemical, and immunoinformatics analyses of final vaccine construct represented that our vaccine could stimulate potent immune response against S. pneumoniae; however, the potency of that should be approved via various in vivo and in vitro immunological tests.
Output: Designing self-assembled peptide nanovaccine against Streptococcus pneumoniae: An in silico strategy
Lower respiratory infections remain one of the top global causes of death and the emergence of new diseases continues to be a concern. In the first two decades of the 21st century, we have born witness to the emergence of newly recognized coronaviruses that have rapidly spread around the globe, including severe acute respiratory syndrome virus (SARS) and Middle Eastern respiratory syndrome virus (MERS). We have also experienced the emergence of a novel H1N1 pandemic influenza strain in 2009 that caused substantial morbidity and mortality around the world and has transitioned into a seasonal strain. Although we perhaps most frequently think of viruses when discussing emerging respiratory infections, bacteria have not been left out of the mix, as we have witnessed an increase in the number of infections from Legionella spp. since the organisms' initial discovery in 1976. Here, we explore the basic epidemiology, clinical presentation, histopathology, and clinical laboratory diagnosis of these four pathogens and emphasize themes in humans' evolving relationship with our natural environment that have contributed to the infectious burden. Histology alone is rarely diagnostic for these infections, but has been crucial to bettering our understanding of these diseases. Together, we rely on the diagnostic acumen of pathologists to identify the clinicopathologic features that raise the suspicion of these diseases and lead to the early control of the spread in our populations. (A. Bryan). Pathology 36 (2019) 152-159 0740-2570/
Output: Emerging respiratory infections: The infectious disease pathology of SARS, MERS, pandemic influenza, and Legionella
In recent years, porcine epidemic diarrhea virus (PEDv) has caused major epidemics, which has been a burden to North America's swine industry. Low infectious dose and high viability in the environment are major challenges in eradication of this virus. To further understand the viability of PEDv in the infected manure, we longitudinally monitored survivability and infectivity of PEDv in two open earthen manure storages (EMS; previously referred to as lagoon) from two different infected swine farms identified in the province of Manitoba, Canada. Our study revealed that PEDv could survive up to 9 months in the infected EMS after the initial outbreak in the farm. The viral load varied among different layers of the EMS with an average of 1.1 × 10 5 copies/ml of EMS, independent of EMS temperature and pH. In both studied EMS, the evidence of viral replication was observed through increased viral load in the later weeks of the samplings while there was no new influx of infected manure into the EMS, which was suggestive of presence of potential alternative hosts for PEDv within the EMS. Decreasing infectivity of virus over time irrespective of increased viral load suggested the possibility of PEDv evolution within the EMS and perhaps in the new host that negatively impacted virus infectivity. Viral load in the top layer of the EMS was low and mostly non-infective suggesting that environmental factors, such as UV and sunlight, could diminish the replicability and infectivity of the virus. Thus, frequent agitation of the EMS that could expose virus to UV and sunlight might be a potential strategy for reduction of PEDv load and infectivity in the infected EMS.
Output: Monitoring Survivability and Infectivity of Porcine Epidemic Diarrhea Virus (PEDv) in the Infected On-Farm Earthen Manure Storages (EMS)
Background: The mass media are often criticized for oversimplifying the causes of suicide and overlooking some of the risk factors. However, there is a lack of empirical evidence to support this assertion. The study aims to examine the accuracy of news reports in Hong Kong (HK) and in particular whether or not such reports stereotype victims according to gender and suicide method. Methods: Data from a case-control psychological autopsy (PA) study of 150 HK suicides were utilized. The reports of the PA cases from five major HK newspapers were collected and reviewed to identify whether or not there was a match in terms of the cases' profile and risk factors. Results: The age, gender, and method of the suicides were largely reported correctly (>70%) but accounts of risk factors were seldom accurate (b 46%). No significant difference was found between tabloid-and non-tabloid-type newspapers' accuracy. Media stereotyping of genderspecific suicide and charcoal-burning suicide was identified. Limitations: The study was based on a HK sample so the findings are not necessarily applicable elsewhere. The HK mass media generally demonstrated poor accuracy in reporting suicide risk factors. Their reporting was also problematic in terms of stereotyping gender-and methodspecific suicides. Clinical practitioners should be alerted to these findings when working with the media. They can also adopt this novel usage of PA data to extract further information from other PA studies and thereby broaden the investigation of reporting accuracy and stereotyping of suicide to more diverse social contexts.
Output: Suicide news reporting accuracy and stereotyping in Hong Kong
Background. Recent data suggest that human coronavirus (HCoV) pneumonia is associated with significant mortality in hematopoietic cell transplant (HCT) recipients. Investigation of risk factors for prolonged shedding and intrahost genome evolution may provide critical information for development of novel therapeutics. Methods. We retrospectively reviewed HCT recipients with HCoV detected in nasal samples by polymerase chain reaction (PCR). HCoV strains were identified using strain-specific PCR. Shedding duration was defined as time between first positive and first negative sample. Logistic regression analyses were performed to evaluate factors for prolonged shedding (≥21 days). Metagenomic next-generation sequencing (mNGS) was conducted when ≥4 samples with cycle threshold values of <28 were available. Results. Seventeen of 44 patients had prolonged shedding. Among 31 available samples, 35% were OC43, 32% were NL63, 19% were HKU1, and 13% were 229E; median shedding duration was similar between strains (P = .79). Bivariable logistic regression analyses suggested that high viral load, receipt of high-dose steroids, and myeloablative conditioning were associated with prolonged shedding. mNGS among 5 subjects showed single-nucleotide polymorphisms from OC43 and NL63 starting 1 month following onset of shedding. Conclusions. High viral load, high-dose steroids, and myeloablative conditioning were associated with prolonged shedding of HCoV in HCT recipients. Genome changes were consistent with the expected molecular clock of HCoV.
Output: Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution
We developed a panel of monoclonal antibodies (MAb) against chicken b2-microglobulin (chb2M) by fusions between SP2/0 myeloma cells and spleen cells from mice immunized with a synthesized peptide corresponding to positions 91-119 of the COOH domain of chb2M. Two of them, 6E7 and 3D1, identified as IgG1/k, could react with chb2M protein from avian macrophage HD11 cells and human 293T cells transfected with pcDNA3.1-chb2M in immunofluorescence assays. Only a 12 kDa protein band of chb2M could be detected in the HD11 and 293T/chb2M cell lysates by Western blot analysis. Chicken b2M in serum and plasma could be found in Western blot by MAb 3D1. Moreover, MAb 3D1 also recognized the chb2M antigen on the cell membranes in flow cytometry. Immunohistochemical staining with these MAbs revealed that chb2M was present in chicken thymus, spleen, and bursa. These MAbs will be good tools for analyzing the mechanism of the chicken immune system.
Output: Monoclonal Antibodies Directed Against Chicken b2-Microglobulin Developed With a Synthesized Peptide
Interferon-inducible transmembrane proteins 1, 2, and 3 (IFITM 1,2, and 3) are viral restriction factors that mediate cellular resistance to several viruses. We have genotyped a possible splice-site altering single-nucleotide polymorphism (rs12252) in the IFITM3 gene in 34 patients with H1N1 influenza and severe pneumonia, and >5000 individuals comprising patients with community-acquired mild lower respiratory tract infection and matched controls of Caucasian ancestry. We found evidence of an association between rs12252 rare allele homozygotes and susceptibility to mild influenza (in patients attending primary care) but could not confirm a previously reported association between this single-nucleotide polymorphism and susceptibility to severe H1N1 infection.
Output: IFITM3 and Susceptibility to Respiratory Viral Infections in the Community
In this study, we investigated the presence of canine bocaviruses (CBoVs) in fecal samples from 105 cats with diarrhea and 92 asymptomatic cats in northeast China. One fecal sample, 17CC0312, collected from an asymptomatic cat, was found to be positive for canine bocavirus 1 (CBoV1). The nearly complete genome of this virus was cloned and sequenced. The viral genome was 5,069 nucleotides (nt) in length and combined four open reading frames (ORFs) in the order 5′-NS1-ORF4-NP1-VP1/VP2-3′. The 17CC0312 virus shared more than 90.3% nucleotide sequence identity with CBoV1 reference sequences and was placed within the CBoV1 group in a phylogenetic tree based on complete genome sequences. Further phylogenetic analysis based on the deduced amino acid sequence of the VP2 gene showed that this feline CBoV1 strain belongs to CBoV1 lineage 3. These data provide the first molecular evidence of the presence of CBoV1 in a domestic cat and suggest that cats might be carriers of CBoV1.
Output: Complete genome sequence analysis of canine bocavirus 1 identified for the first time in domestic cats
Recently, it was shown that aminopeptidase N (E.C. 3.4.11.2, CD13) is up-regulated during mitogenic stimulation of peripheral T-cells. In this study, we demonstrate that the half-life of APN mRNA was considerably prolonged in these cells leading to a 2.7-fold increase of APN transcript level. The apparent halflife time of the APN transcript was investigated by the RNA synthesis inhibitor-chase method using actinomycin D. The steady-state APN mRNA levels was determined by a competitive promoter activity as well. These studies suggest a control of APN gene expression at the post-transcriptional level in addition to promoter-mediated regulation. © 1997 Federation of European Biochemical Societies.
Output: The activation-dependent induction of APN-(CD13) in T-cells is controlled at different levels of gene expression
publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. J. Dairy Sci. 96 :981-992 http://dx. Farmers attempting to reduce first-calving age (FCA) need to understand which rearing management factors influence FCA and first-lactation milk production (FLP). Reduced FCA might be associated with lower FLP. This study describes the association between herd FCA, FLP, and several herd-level health and rearing management variables and describes the association between FCA and FLP at the cow level. It uses data from a 2010 survey of 100 Dutch dairy farms about general management, colostrum and milk feeding, housing, cleanliness, healthcare, disease, and breeding. It also used available data on FCA and 305-d FLP at both cow and herd level. The associations between median FCA and median FLP of the herd and herd-level health and rearing management variables were determined using multivariate regression analysis. The median FCA was associated with minimum age of first insemination, feeding of waste milk, and the amount of milk given preweaning. The median FLP was associated with median FCA and vaccination status for bovine respiratory syncytial virus. The association between FCA and FLP (based on 8,454 heifers) was analyzed with a single-effect linear mixed model, where the dependent variable was either FCA or relative FCA (defined as the difference between FCA of the heifer and median FCA of the herd to which they belonged). Heifers having an FCA of 24 mo produced, on average, 7,164 kg of milk per 305 d, and calving 1 mo earlier gave 143 kg less milk per 305 d. When FCA did not deviate from the median herd FCA, heifers produced, on average, 7,272 kg of milk per 305 d. From the median FCA of the herd, heifers calving 1 mo earlier produced 90 kg of milk per 305 d less, and heifers calving 1 mo later produced 86 kg per 305 d more. This is the first study that explained FLP using relative FCA. It assumes that heifers raised within the same farm have similar development because they are similarly managed. Similar management is reflected by the median FCA of the herd, with a deviation of the heifer's FCA from median FCA reflecting the heifer's development relative to the herd's average. The advantage of using relative FCA was that it accounts for between-farm differences in rearing management. It showed that earlier insemination without adjusting management to ensure sufficient development lowers FLP. An economic optimum exists between rearing costs, FCA, and FLP and, as a consequence, decisions with regard to young stock management should be made with care.
Output: First-calving age and first-lactation milk production on Dutch dairy farms
Chemotherapy; Non-small-cell lung cancer (NSCLC); Severe acute respiratory syndrome (SARS) Summary Our aim was to describe the impact of severe acute respiratory syndrome (SARS) on the status and chemotherapy of non-small-cell lung cancer (NSCLC) patients who had entered clinical trials, and to review how to differentiate the signs and symptoms of SARS from lung cancer and its treatment-related toxicities. A prospective case series involving 79 NSCLC patients who were enrolled in clinical trials undergoing chemotherapy at Taipei Veterans General Hospital, between April 1 and July 15, 2003, was studied. Whether or not there existed a delay, omission, or refusal of scheduled chemotherapy, was recorded. Whether or not our patients had been suspected of or treated as having SARS, was recorded. The patients filled out questionnaires regarding lung cancer treatment and the risk of getting SARS from the hospital. Among these patients, five were placed in an isolation unit to rule out SARS infection during this period of time, and no patient was documented to have suffered from a SARS infection after examinations. Of 373 scheduled chemotherapy injections in 79 patients, a delay in treatment occurred only 10 times. Three patients refused further chemotherapy because of a fear of getting SARS if they visited the hospital. Fifty-eight patients responded to our questionnaires. Thirty-seven patients (63.8%) were afraid of visiting hospital during this SARS infection period. Twenty-one patients (36.2%) felt that a SARS infection was more severe and fatal than their lung cancer. In conclusion, SARS is a new disease entity that is highly contagious. Its clinical manifestations overlap with the signs and symptoms of lung cancer. Thus, a clear differentiation between the two conditions is needed, especially for those patients who are under active anti-cancer treatment.
Output: Impact of severe acute respiratory syndrome on the status of lung cancer chemotherapy patients and a correlation of the signs and symptoms
An antifungal peptide with a defensin-like sequence and exhibiting a molecular mass of 7.3 kDa was purified from dried seeds of Phaseolus vulgaris 'Cloud Bean'. The isolation procedure entailed anion exchange chromatography on DEAE-cellulose, affinity chromatography an Affi-gel blue gel, cation exchange chromatography on SP-Sepharose, and gel filtration by fast protein liquid chromatography on Superdex 75. Although the antifungal peptide was unadsorbed on DEAE-cellulose, it was adsorbed on both Affi-gel blue gel and SP-Sepharose. The antifungal peptide exerted antifungal activity against Mycosphaerella arachidicola with an IC 50 value of 1.8 M. It was also active against Fusarium oxysporum with an IC 50 value of 2.2 M. It had no inhibitory effect on HIV-1 reverse transcriptase when tested up to 100 M. Proliferation of L1210 mouse leukemia cells and MBL2 lymphoma cells was inhibited by the antifungal peptide with an IC 50 of 10 M and 40 M, respectively.
Output: An antifungal defensin from Phaseolus vulgaris cv. 'Cloud Bean'