niryuu/sni-each-converted huggingface dataset:
From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals. We investigated two patients who developed acute respiratory syndromes after independent contact history with this market. The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration. Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF). It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced). The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus. Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/ 4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21. Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.
Output: RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak
Stress Granules (SGs) are dynamic ribonucleoprotein aggregates, which have been observed in cells subjected to environmental stresses, such as oxidative stress and heat shock (HS). Although pluripotent stem cells (PSCs) are highly sensitive to oxidative stress, the role of SGs in regulating PSC self-renewal and differentiation has not been fully elucidated. Here we found that sodium arsenite (SA) and HS, but not hydrogen peroxide (H 2 O 2 ), induce SG formation in human induced (hi) PSCs. Particularly, we found that these granules contain the well-known SG proteins (G3BP, TIAR, eIF4E, eIF4A, eIF3B, eIF4G, and PABP), were found in juxtaposition to processing bodies (PBs), and were disassembled after the removal of the stress. Moreover, we showed that SA and HS, but not H 2 O 2 , promote eIF2α phosphorylation in hiPSCs forming SGs. Analysis of pluripotent protein expression showed that HS significantly reduced all tested markers (OCT4, SOX2, NANOG, KLF4, L1TD1, and LIN28A), while SA selectively reduced the expression levels of NANOG and L1TD1. Finally, in addition to LIN28A and L1TD1, we identified DPPA5 (pluripotent protein marker) as a novel component of SGs. Collectively, these results provide new insights into the molecular cues of hiPSCs responses to environmental insults.
Output: Effects of oxidative and thermal stresses on stress granule formation in human induced pluripotent stem cells
This paper presents the results of investigations whose aim was to describe the influence of the pressure difference level on the ability of contaminants migration between neighbouring rooms in dynamic conditions associated with door swing. The analysis was based on airflow visualization made with cold smoke, which simulated the heavy contaminants. The test room was pressurized to a specific level and then the door was opened to observe the trail of the smoke plume in the plane of the door. The door was opened in both directions: to the positively and negatively pressurized room. This study focuses on the visualization of smoke plume discharge and an uncertainty analysis is not applicable. Unlike other studies which focus on the analysis of pressure difference, the present study looks at the contaminants which are heavier than air and on "pumping out" the contaminants by means of door swing. Setting the proper level of pressure difference between the contaminated room and the neighbouring rooms can prove instrumental in ensuring protection against toxic contaminants migration. This study helped to establish the threshold of pressure difference necessary to reduce migration of heavy contaminants to neighbouring rooms.
Output: Influence of the Pressure Difference and Door Swing on Heavy Contaminants Migration between Rooms
Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify novel coronavirus (2019-nCoV) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for 2019-nCoV. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines.
Output: Title: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes Short title: Automated tool for phylogenetic and mutational analysis of coronaviruses genomes
The development of high-throughput DNA sequencing technologies has enabled large-scale characterization of functional antibody repertoires, a new method of understanding protective and pathogenic immune responses. Important parameters to consider when sequencing antibody repertoires include the methodology, the B-cell population and clinical characteristics of the individuals analysed, and the bioinformatic analysis. Although focused sequencing of immunoglobulin heavy chains or complement determining regions can be utilized to monitor particular immune responses and B-cell malignancies, high-fidelity analysis of the full-length paired heavy and light chains expressed by individual B cells is critical for characterizing functional antibody repertoires. Bioinformatic identification of clonal antibody families and recombinant expression of representative members produces recombinant antibodies that can be used to identify the antigen targets of functional immune responses and to investigate the mechanisms of their protective or pathogenic functions. Integrated analysis of coexpressed functional genes provides the potential to further pinpoint the most important antibodies and clonal families generated during an immune response. Sequencing antibody repertoires is transforming our understanding of immune responses to autoimmunity, vaccination, infection and cancer. We anticipate that antibody repertoire sequencing will provide next-generation biomarkers, diagnostic tools and therapeutic antibodies for a spectrum of diseases, including rheumatic diseases.
Output: Sequencing the functional antibody repertoire-diagnostic and therapeutic discovery
The protein sequence-structure gap results from the contrast between rapid, low-cost deep sequencing, and slow, expensive experimental structure determination techniques. Comparative homology modelling may have the potential to close this gap by predicting protein structure in target sequences using existing experimentally solved structures as templates. This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. Homology modelling was then carried out for targettemplate pairs in different species, different genera and different families, and model quality assessed using several metrics. Reconstructed ancestral RdRP sequences for individual genera were also used as templates for the production of ancestral RdRP homology models. High quality ancestral RdRP models were consistently produced, as were good quality models for target-template pairs in the same genus. Homology modelling between genera in the same family produced mixed results and inter-family modelling was unreliable. We present a protocol for the production of optimal RdRP homology models for use in further experiments, e.g. docking to discover novel anti-viral compounds. (219 words)
Output: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling
Consultation-liaison psychiatry (CLP) was first established in China after liberation in 1949. It has developed more rapidly over the last two decades but, despite major regional differences in the level of CLP, the overall practice of CLP in the country remains quite basic, largely limited to case-based consultation with other medical departments. There is little ongoing collaboration between departments of psychiatry and other departments, and medical students and nonpsychiatric clinicians rarely get training in CLP.
Output: Consultation-liaison psychiatry in China
When Severe Acute Respiratory Syndrome (SARS) spread in Vietnam in March 2003, Bach Mai Hospital (BMH) contributed greatly to putting SARS under control by conducting strict nosocomial infection control. At BMH, technical guidance on nosocomial infection control had been implemented by Japanese experts since 2000. In addition, after the SARS outbreak, the Japan Disaster Relief Team was dispatched to assist in SARS control at BMH. SARS control in Vietnam was reviewed in reference to this technical guidance to investigate effective control measures. Major subjects of the technical guidance included the establishment of a control system, development of manuals and teaching materials, training of medical staff, and supplying protective attire. BMH provided medical care for 35 SARS cases; however, no nosocomial infection cases occurred leading to SARS containment. A swift reaction, effective nosocomial infection control, proper advice by the Ministry of Health and other elements are considered important factors in the success of SARS containment at BMH. In addition, the fruit of technical cooperation conducted under the project is regarded, to no small extent, as having formed the basis for this. Nosocomial infection control is a crucial factor in achieving high-quality medical care, as well as SARS control at the hospital level. D
Output: Contribution of technical guidance on nosocomial infection control to the containment of Severe Acute Respiratory Syndrome in Vietnam
Demyelination in the central nervous system induced by neurovirulent strains of Mouse Hepatitis Virus (MHV) is mediated by the viral spike glycoprotein, but it is not clear whether the mechanism of this disease pathology involves direct viral infection of oligodendrocytes. Detailed studies of glial cell tropism of MHV are presented, demonstrating that direct MHV infection of oligodendrocytes differs between demyelinating (RSA59) and non-demyelinating (RSMHV2) viral strains both in vitro and in vivo. Our results indicate that direct injury of mature oligodendrocytes is an important mechanism of virus-induced demyelination. In vivo, RSA59 infection was identified in spinal cord gray and white matter, but infected oligodendrocytes were restricted to white matter. In contrast, RSMHV2 infection was restricted to gray matter neurons and was not localized to oligodendrocytes. In vitro, RSA59 can infect both oligodendrocyte precursors and differentiated oligodendrocytes, whereas RSMHV2 can infect oligodendrocyte precursors but not differentiated oligodendrocytes. Viral spreading through axonal means to white matter and release of the demyelinating strain MHV at the nerve end is critical for oligodendrocytes infection and subsequent demyelination. Understanding the mechanisms by which known viruses effect demyelination in this animal model has important therapeutic implications in the treatment of human demyelinating disease.
Output: Gliopathy of Demyelinating and Non-Demyelinating Strains of Mouse Hepatitis Virus
A recombinant transmissible gastroenteritis coronavirus (rTGEV) in which E gene was deleted (rTGEV-ΔE) has been engineered. This deletion mutant only grows in cells expressing E protein (E + cells) indicating that E was an essential gene for TGEV replication. Electron microscopy studies of rTGEV-ΔE infected BHK-pAPN-E − cells showed that only immature intracellular virions were assembled. These virions were non-infectious and not secreted to the extracellular medium in BHK-pAPN-E − cells. RNA and protein composition analysis by RNase-gold and immunoelectron microscopy showed that rTGEV-ΔE virions contained RNA and also all the structural TGEV proteins, except the deleted E protein. Nevertheless, full virion maturation was blocked. Studies of the rTGEV-ΔE subcellular localization by confocal and immunoelectron microscopy in infected E − cells showed that in the absence of E protein virus trafficking was arrested in the intermediate compartment. Therefore, the absence of E protein in TGEV resulted in two actions, a blockade of virus trafficking in the membranes of the secretory pathway, and prevention of full virus maturation.
Output: Absence of E protein arrests transmissible gastroenteritis coronavirus maturation in the secretory pathway
To extend the frontier of genome editing and enable the radical redesign of mammalian genomes, we developed a set of dead-Cas9 base editor (dBE) variants that allow editing at tens of thousands of loci per cell by overcoming the cell death associated with DNA double-strand breaks (DSBs) and single-strand breaks (SSBs). We used a set of gRNAs targeting repetitive elementsranging in target copy number from about 31 to 124,000 per cell. dBEs enabled survival after 5 large-scale base editing, allowing targeted mutations at up to ~13,200 and ~2610 loci in 293T and human induced pluripotent stem cells (hiPSCs), respectively, three orders of magnitude greater than previously recorded. These dBEs can overcome current on-target mutation and toxicity barriers that prevent cell survival after large-scale genome engineering. One Sentence Summary: Base editing with reduced DNA nicking allows for the simultaneous 10
Output: Enabling large-scale genome editing by reducing DNA nicking
We developed a novel concept that allows to considerably improve the performance of conventionally used ÿltering-facepiece respirators against ÿne and ultraÿne aerosols including airborne viral and bacterial agents. The concept is based on the continuous emission of unipolar ions. The e ect was evaluated through the real-time monitoring of the concentration and size distribution of ÿne and ultraÿne aerosol particles. The measurements were conducted inside and outside of a respiratory mask that was face sealed on a breathing manikin. A commonly used Type N95 respirator and surgical mask were utilized for the tests. The manikin was placed in a 24.3-m 3 indoor test chamber and exposed to polydisperse surrogate aerosols simulating viral and bacterial particles with respect to the aerodynamic size. The particle penetration through the mask was found to decrease by one-to-two orders of magnitude as a result of continuous unipolar ion emission in the chamber. The ux of air ions migrated to the breathing zone and imparted electrical charges of the same polarity to the aerosol particles and the respirator ÿlter surface. This created an electrostatic shield along the external surface of the ÿlter, thus enhancing the protection characteristics provided by the respirator. The above performance enhancement e ect is crucial for minimizing the infectious risk in the cases when the conventional ÿltering-facepiece respirators are not able to provide an adequate protection against airborne viruses and bacteria. ?
Output: Unipolar ion emission enhances respiratory protection against ÿne and ultraÿne particles
The uncertainties of healthcare payment and delivery reform on income and care process have created a sense of foreboding, concern, and fear that a career in medicine is not what it used to be and that a career in infectious diseases in particular may no longer be viable. Fears have been raised that the need for infectious diseases consultation and management will be curtailed because we provide cognitive services that are not perceived as being needed in a health system filled with intensivists, hospitalists, and skilled nursing facility physicians. Now is the time for us to reframe our role in the health system that is evolving to a process of care focused on population health and patient safety that pays providers for value they bring to achieve those goals. Specific suggestions are made to enhance the infectious diseases physician's profile with the intent of encouraging debate, discussion, and action.
Output: The Infectious Diseases Physician in the Future of Healthcare: Not Only About Antibiotic Prescribing
Purpose Thymic stromal lymphopoietin (TSLP) is released by intestinal epithelial cells (IECs), and TSLPconditioned dendritic cells appear to be involved in immune homeostasis of intestine and immunoglobulin A (IgA) class-switching in the physiological condition. In contrast, TSLP activates dendritic cells to induce strong T-cell proliferation and is involved in inflammatory T helper (Th) 2 responses in human allergic diseases. However, it is not clear how TSLP production by IECs is regulated in ulcerative colitis (UC), which appears to involve inflammatory Th2 responses. The aim of this study is to examine how TSLP production by IECs is regulated in ulcerative colitis. Results We show here that expression of TSLP was enhanced in mucosal lesions from UC patients in which inflammatory Th2 cytokine production was predominant. In addition, using a human colonic epithelial cell line, we demonstrated that a combination of tumor necrosis factoralpha (TNF-a) and interleukin-4 (IL-4) induced TSLP expression and that TSLP expression by TNF-a ? IL-4 was further enhanced by either Toll-like receptor 3 ligand or interferon (IFN)-c. Conclusions Taken together, as in human allergic diseases, an inflammatory Th2 condition in the mucosal lesions of UC patients may trigger increased TSLP expression by IECs, resulting in exacerbation of UC.
Output: Proinflammatory Th2 Cytokines Induce Production of Thymic Stromal Lymphopoietin in Human Colonic Epithelial Cells
We provide the first genetic sequence data for a Dipylidium species from a wild carnivore plus an analysis of the effects of ecological, demographic, physiological and behavioural factors on Dipylidium sp. infection prevalence in a social carnivore, the spotted hyaena (Crocuta crocuta), in the Serengeti National Park, Tanzania. Our sequence data from a mitochondrial gene fragment (1176 base pair long) had a similarity of between 99% and 89% to Dipylidium caninum. We determined infection prevalence in 146 faecal samples from 124 known animals in three social groups (termed clans) using molecular screening and Dipylidium proglottid presence. Our analysis revealed significantly higher infection prevalence in juveniles (55%) than adults (15.8%), indicating that predominantly juveniles maintained infection in clans. The likelihood of infection in juveniles significantly: (1) increased as the number of adults and older juveniles (>6 months) at communal dens increased, implying a positive relationship between this factor and the size of the intermediate host (probably a flea species) population at communal dens; (2) decreased as the number of younger juveniles (<6 months) increased, suggesting that the chance of susceptible juveniles ingesting infected fleas during self-grooming declined as the number of infected fleas per younger juvenile declined; and (3) decreased during periods of low prey abundance in clan territories when an increased reliance on long-distances foraging excursions reduces the number of clan members visiting communal dens, possibly resulting in a decline in flea populations at dens. Long-distance foraging also increases the intervals (in days) between nursing visits by lactating females to their offspring. Lengthy intervals between milk intake by infected juveniles may reduce adult Dipylidium fecundity and hence decrease infection prevalence in the den flea population. Our study provides useful insights into Dipylidium epidemiology in a social carnivore population subject to large fluctuations in prey abundance.
Output: Factors influencing Dipylidium sp. infection in a free-ranging social carnivore, the spotted hyaena (Crocuta crocuta)
The analysis presented in the paper, relies on an underlying epidemic model to obtain the infection probability r(f). This appendix presents two variants of the textbook SIR epidemic model, one with vital dynamics and one without. We derive a closed form solution for infection probability of an SIR model with vital dynamics which gives rise to the formulas used in the paper. Unfortunately, for an SIR model without vital dynamics, there is no closed-form solution. However, we show that, for diseases of interest and for realistic values of infection model parameters, the same formula can be used as an effective approximation for the true probability function. Using the notation in the paper, a vaccine's effectiveness is denoted by a parameter φ, where 0 < φ ≤ 1.
Output: Electronic Companion to: Operational Issues and Network Effects in Vaccine Markets A.1 An SIR Model with Vital Dynamics (Endemic Model)
A temperature-sensitive mutant of vesicular stomatitis virus was inoculated intranasally into inlant Sprague Dawley rats aged 9 to 17 days. Rats receiving the virus at 9 days ol'age had an extensive spread of int'ection throughout the brain and the animals died after a few days. Rats inoculated at day I I postnatally survived and the infection was limited to the olfactory pathways, hypothalamus, diagonal bands and the anterior raphe nuclei. Stereological measurements showed that the volume of infected neurons constituted 67+ 10% of the total neuronal volume in the dorsal raphe nucleus. Doublelabelling experiments revealed that both 5-hydroxytryptamine-and substance P-immunoreactive neurons contained the virus antigen. The motor stimulant effect of amphetamine was studied at 3 months post infection. The increase in amphetamine-induced frequency and duration of rearing was significantly attenuated in infected rats and the amphetamine-induced locomotion was slightl~ reduced. KI Y W(IRI)N: Virus infection 5-Hydroxytryptaminc Immunohistochemislrv
Output: Immunohistochemical and Behaviour Pharmacological Analysis of Rats Inoculated Intranasally with Vesicular Stomatitis Virus
Background: Cell-based influenza vaccines can solve the problem of the frequent occurrence of egg adaptation-associated antigenic changes observed in egg-based vaccines. Seed viruses for cell-based vaccines can be prepared from clinical specimens by cell culture; however, clinical samples risk harboring respiratory viruses other than influenza virus. Therefore, it is necessary to investigate the patterns of co-infection in clinical samples and explore whether cell culture technology can selectively propa-
Output: Comparison of suspension MDCK cells, adherent MDCK cells, and LLC-MK2 cells for selective isolation of influenza viruses to be used as vaccine seeds Present addresses
Objectives: The outbreak of Middle Eastern respiratory syndrome coronavirus (MERS-CoV) was one of the major events in South Korea in 2015. In particular, this study pays attention to formulating a mathematical model for MERS transmission dynamics and estimating transmission rates. Methods: Incidence data of MERS-CoV from the government authority was analyzed for the first aim and a mathematical model was built and analyzed for the second aim of the study. A mathematical model for MERS-CoV transmission dynamics is used to estimate the transmission rates in two periods due to the implementation of intensive interventions. Results: Using the estimates of the transmission rates, the basic reproduction number was estimated in two periods. Due to the superspreader, the basic reproduction number was very large in the first period; however, the basic reproduction number of the second period has reduced significantly after intensive interventions. Conclusion: It turned out to be the intensive isolation and quarantine interventions that were the most critical factors that prevented the spread of the MERS outbreak. The results are expected to be useful to devise more efficient intervention strategies in the future.
Output: The Characteristics of Middle Eastern Respiratory Syndrome Coronavirus Transmission Dynamics in South Korea
Background: Human adenoviruses are common causes of community-acquired respiratory tract and enteric infections. Severe disseminated infections with high mortality rates may be seen in immunocompromised individuals. An accurate and cost-effective quantitative assay is essential not only for laboratory diagnosis of adenoviral infections, but also for monitoring of response to antiviral treatment. The diagnostic performance of an in-house quantitative polymerase chain reaction assay was compared to a commercial system. Methods: The analytical sensitivity, specificity, linearity, precision and accuracy of an in-house adenovirus quantitative polymerase chain reaction assay were evaluated against the RealStar® Adenovirus PCR Kit (Altona Diagnostics GmbH, Hamburg, Germany), using 122 clinical specimens and 18 proficiency testing samples. Results: Linear regression analysis of the quantitative results by the in-house assay showed the dynamic range from 2.60 to 9 log 10 (plasma) and 2.94 to 9 log 10 (viral transport medium) copies/mL, with the coefficient of determination (R 2 ) of 0.996 and 0.998, respectively. A dilution series demonstrated the limits of detection and lower limits of quantification for plasma were 2.06 log 10 and 2.60 log 10 copies/mL and those for viral transport medium were 2.31 log 10 and 2.94 log 10 copies/mL respectively. The precision of the in-house assay was highly reproducible among runs with coefficients of variance ranging from 0.07 to 3.21% for plasma and 0.17% to 2.11% for viral transport medium. A comparison of 52 matched samples showed an excellent correlation between the quantitative viral loads measured by the in-house assay and the RealStar® Adenovirus PCR Kit (R 2 = 0.984), with an average bias of − 0.16 log 10 copies/mL. Conclusions: The in-house adenovirus assay is a sensitive and reliable assay with lower cost for the detection and quantification of adenoviral DNA when compared to the RealStar® Adenovirus PCR Kit.
Output: Comparative evaluation of a laboratory- developed real-time PCR assay and RealStar® Adenovirus PCR Kit for quantitative detection of human adenovirus
Context: Over the past decade, a number of high-impact natural hazard events, together with the increased recognition of pandemic risks, have intensified interest in health systems' ability to prepare for, and cope with, "surges" (sudden large-scale escalations) in treatment needs. In this article, we identify key concepts and components associated with this emerging research theme. We consider the requirements for a standardized conceptual framework for future research capable of informing policy to reduce the morbidity and mortality impacts of such incidents. Here our objective is to appraise the consistency and utility of existing conceptualizations of health systems' surge capacity and their components, with a view to standardizing concepts and measurements to enable future research to generate a cumulative knowledge base for policy and practice. A systematic review of the literature on concepts of health systems' surge capacity, with a narrative summary of key concepts relevant to public health. The academic literature on surge capacity demonstrates considerable variation in its conceptualization, terms, definitions, and applications. This, together with an absence of detailed and comparable data, has hampered efforts to develop standardized conceptual models, measurements, and metrics. Some degree of consensus is evident for the components of surge capacity, but more work is needed to integrate them. The overwhelming concentration in the United States complicates the generalizability of existing approaches and findings. The concept of surge capacity is a useful addition to the study of health systems' disaster and/or pandemic planning, mitigation, and response,
Output: Health Systems' "Surge Capacity": State of the Art and Priorities for Future Research
The global boom in premature mortality and morbidity from noncommunicable diseases (NCDs) shares many similarities with pandemics of infectious diseases, yet public health professionals have resisted the adoption of this label. It is increasingly apparent that NCDs are actually communicable conditions, and although the vectors of disease are nontraditional, the pandemic label is apt. Arguing for a change in terminology extends beyond pedantry as the move carries serious implications for the public health community and the general public. Additional resources are unlocked once a disease reaches pandemic proportions and, as a long-neglected and underfunded group of conditions, NCDs desperately require a renewed sense of focus and political attention. This paper provides objections, definitions, and advantages to approaching the leading cause of global death through an alternative lens. A novel framework for managing NCDs is presented with reference to the traditional influenza pandemic response.
Output: Are we facing a noncommunicable disease pandemic?
The protective roles of endosomal toll-like receptors (TLRs) and cytosolic nucleic acid sensors are well elucidated, but the pathogenic host factors during viral infections remain unclear. Spleen tyrosine kinase (Syk)-coupled C-type lectins (CLECs) CLEC2 and CLEC5A are highly expressed on platelets and myeloid cells, respectively. CLEC2 has been shown to recognize snake venom aggretin and the endogenous ligand podoplanin and acts as a critical regulator in the development and immunothrombosis. Although CLEC2 has been reported to interact with type I immunodeficiency virus (HIV-1), its role in viral infections is still unclear. CLEC5A binds to fucose and mannose moieties of dengue virus membrane glycans, as well as to N-acetylglucosamine (GlcNAc)/N-acetylmuramic acid (MurNAc) disaccharides that form the backbone of L. monocytogenes peptidoglycans. Recently, we demonstrated that both CLEC2 and CLEC5A are critical in microbe-induced "neutrophil extracellular trap" (NET) formation and proinflammatory cytokine production. Moreover, activation of CLEC2 by dengue virus (DV) and H5N1 influenza virus (IAV) induces the release of extracellular vesicles (EVs), which further enhance NETosis and proinflammatory cytokine production via CLEC5A and Toll-like receptor 2 (TLR2). These findings not only illustrate the immunomodulatory effects of EVs during platelet-leukocyte interactions, but also demonstrate the critical roles of CLEC2 and CLEC5A in acute viral infections.
Output: CLEC2 and CLEC5A: Pathogenic Host Factors in Acute Viral Infections
As the world faces its first influenza pandemic in 40 years, it has been argued that we have never been better prepared. Concern about emerging infectious diseases has fuelled significant public health and political developments, such as the coming into force of the International Health Regulations (IHR). Since the turn of the century, the World Health Organization (WHO) has documented a historically unprecedented number of emerging infectious disease outbreaks, and lessons drawn from their management have confirmed the critical importance of effective communications, specifically through formal channels such as WHO and in the public domain. In concert with novel emerging infectious diseases, the communication landscape itself has also changed radically. We now live in an era of real-time electronic communications; consequently, approaches to surveillance are being transformed. Data sources, information messengers, mechanisms of data and information transfer and audiences are all changing. Instant and global transmission of information has become a powerful ally, along with peer pressure, for WHO in ensuring that member states comply with new obligations to swiftly declare outbreaks considered to be of public health importance. There is now significant global attention and accompanying investment which should, the authors suggest, be used as an opportunity to improve strategic and operational communication capacity to respond not only to pandemic influenza but also to other public health threats. There are many concepts of communication in relation to risk associated with outbreaks. As these are relatively new concepts, this article will consider approaches relating to highlighting public health threats and supporting operational management, addressing these as the communication of risk and subsequent risk management. Strategic considerations are critical to both, although information, messengers, communication tools and audiences may differ. The communication of risk refers to the process by which information regarding outbreaks is identified and shared with the purpose of increasing awareness amongst key stakeholders of the threat. Key stakeholders for public health threats include WHO, national governments and the public. Risk management, by contrast, refers to the management processes associated with response to the outbreak, for which communication is crucial at each stage. Three examples are used to explore the challenges and demands of communicating effectively and coherently given this changing landscape. This brief paper will attempt to show the progress made, draw lessons to be learned and outline the ways forward.
Output: Risk communication and management in public health crises
Background: Acquisition of resistance to "anoikis" facilitates the survival of cells under independent matrix-deficient conditions, such as cells in tumor progression and the production of suspension culture cells for biomedical engineering. There is evidence suggesting that CD147, an adhesion molecule associated with survival of cells in tumor metastasis and cell-cell contacts, plays an important role in resistance to anoikis. However, information regarding the functions of CD147 in mediating cell-cell contacts and anoikis-resistance remains limited and even self-contradictory. Results: An anoikis-resistant clone (HEK293ar), derived from anoikis-sensitive parental Human Embryonic Kidney 293 cells, survived anoikis by the formation of cell-cell contacts. The expression of HAb18G/CD147 (a member of the CD147 family) was upregulated and the protein was located at cell-cell junctions. Upregulation of HAb18G/CD147 in suspended HEK293ar cells suppressed anoikis by mediating the formation of cell-cell adhesions. Anoikis resistance in HEK293ar cells also required E-cadherin-mediated cell-cell contacts. Knock-down of HAb18G/CD147 and E-cadherin inhibited cell-cell contacts formation and increased anoikis sensitivity respectively. When HAb18G/CD147 was downregulated, E-cadherin expression in HEK293ar cells was significantly suppressed; however, knockdown of Ecadherin by E-cadherin siRNA or blocking of E-cadherin binding activity with a specific antibody and EDTA had no significant effect on HAb18G/CD147 expression. Finally, pretreatment with LY294002, a phosphoinositide 3-kinase (PI3K/AKT) inhibitor, disrupted cell-cell contacts and decreased cell number, but this was not the case in cells treated with the extracellular signal-regulated kinase (ERK) inhibitor PD98059. Our results provide new evidence that HAb18G/CD147-mediated cell-cell contact confers anoikis resistance in an E-cadherin-dependent manner; and cell-cell contact mediated resistance to anoikis implicates PI3K pathway in a highly relevant cell model (HEK293ar). Understanding of the role of HAb18G/CD147 cell-cell contacts in anoikis resistance may help in understanding the survival of cells in anchorage-independent growth, such as cells in tumor metastasis and suspension culture produced for biomedical engineering. Our results also contribute to a better understanding of the biology of HEK293 cell spheroids, a major workhorse for producing human therapeutic agents and viral vaccines.
Output: HAb18G/CD147 cell-cell contacts confer resistance of a HEK293 subpopulation to anoikis in an E-cadherin-dependent manner
Traditional Chinese herbal medicine (TCHM) is widely used in the prevention and treatment of viral infectious diseases. However, the operative mechanisms of TCHM remain largely obscure, mainly because of its complicated nature and the fragmented nature of research. In recent years, systematic methodologies have been developed to discover the active compounds in TCHM and to elucidate its underlying mechanisms. In this review, we summarize recent progress in TCHM-based antiviral research in China and other Asian countries. In particular, this review focuses on progress in targeting key steps in the viral replication cycle and key cellular components of the host defense system. Recent developments in centralized and standardized TCHM screening and databases are also summarized.
Output: Traditional Chinese herbal medicine as a source of molecules with antiviral activity
Profiles of antibodies to the nucleocapsid protein of the severe acute respiratory syndrome (SARS)-associated coronavirus in 445 probable SARS patients and 3,749 healthy people or non-SARS patients were analyzed by antigen-capturing enzyme-linked immunosorbent assay. Antinucleocapsid antibodies were elucidated in 17.5% of the probable SARS patients 1 to 7 days after the onset of symptoms and in 80% of the patients 8 to 14 days after the onset. About 90% of the probable SARS patients were positive 15 or more days after illness. Antibody titers increased up to 70 days, and high antibody titers were maintained at least for another 3 months. Of the healthy people and non-SARS patients, only seven (0.187%) were weakly positive. FIG. 1. Development of anti-N protein antibody titers over time in 445 patients who probably had SARS. 228 NOTES CLIN. DIAGN. LAB. IMMUNOL.
Output: Profile of Antibodies to the Nucleocapsid Protein of the Severe Acute Respiratory Syndrome (SARS)-Associated Coronavirus in Probable SARS Patients
Objective-To develop a method to perform multiple tests on single nasopharyngeal (NP) swab. Study design-We collected a NP swab on children aged 2-12 years with acute sinusitis and processed it for bacterial culture, viruses, cytokine expression, and 16S ribosomal RNA gene sequencing analysis. During the course of the study, we expand the scope of evaluation to include RNA sequencing, which we accomplished by cutting the tip of the swab. Results-Of the 174 children enrolled, 126 (72.4%) had a positive bacterial culture and 121(69.5%) tested positive for a virus. Cytokine measurement, as judged by the adequate levels of a housekeeping enzyme (GAPDH), appeared successful. From the samples used for 16S ribosomal sequencing we recovered, on average, 16,000 sequences per sample, accounting for a total of 2,646 operational taxonomic units across all samples sequenced. Samples used for RNA sequencing had a mean RNA Integrity number of 6.0. Cutting the tip of the swab did not affect the recovery yield for viruses or bacteria, nor did it affect species richness in microbiome analysis. Conclusion-We describe a minimally invasive sample collection protocol that allows for multiple diagnostic and research investigations in young children. Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:
Output: A method of processing nasopharyngeal swabs to enable multiple testing HHS Public Access
Madin Darby canine kidney (MDCK) cells were adapted to serum-free RPMI 1640 medium and used for cultivation of canine viruses. RPMI 1640 medium was supplemented with a soybean peptone, l-glutamine and antibiotics, so that the protein concentration was less than 5 g/ml (RPMI/SP medium). The resulting adapted MDCK-SP cells showed steady growth after the twenty-eighth passage in RPMI/SP medium (MDCK-SP cell culture). Canine distemper virus, canine parvovirus, canine adenoviruses and canine parainfluenza virus, which are the principal components of canine combined virus vaccines, grew in the MDCK-SP cell culture as efficiently as the parental MDCK cells cultured in the conventional Eagle's MEM containing fetal bovine serum. Consequently, the use of MDCK-SP cell culture can make current canine vaccine products much safer, of higher quality and at lower cost.
Output: Growth characteristics of canine pathogenic viruses in MDCK cells cultured in RPMI 1640 medium without animal protein
Enveloped viruses need to fuse with a host cell membrane in order to deliver their genome into the host cell. While some viruses fuse with the plasma membrane, many viruses are endocytosed prior to fusion. Specific cues in the endosomal microenvironment induce conformational changes in the viral fusion proteins leading to viral and host membrane fusion. In the present study we investigated the entry of coronaviruses (CoVs). Using siRNA gene silencing, we found that proteins known to be important for late endosomal maturation and endosome-lysosome fusion profoundly promote infection of cells with mouse hepatitis coronavirus (MHV). Using recombinant MHVs expressing reporter genes as well as a novel, replication-independent fusion assay we confirmed the importance of clathrin-mediated endocytosis and demonstrated that trafficking of MHV to lysosomes is required for fusion and productive entry to occur. Nevertheless, MHV was shown to be less sensitive to perturbation of endosomal pH than vesicular stomatitis virus and influenza A virus, which fuse in early and late endosomes, respectively. Our results indicate that entry of MHV depends on proteolytic processing of its fusion protein S by lysosomal proteases. Fusion of MHV was severely inhibited by a pan-lysosomal protease inhibitor, while trafficking of MHV to lysosomes and processing by lysosomal proteases was no longer required when a furin cleavage site was introduced in the S protein immediately upstream of the fusion peptide. Also entry of feline CoV was shown to depend on trafficking to lysosomes and processing by lysosomal proteases. In contrast, MERS-CoV, which contains a minimal furin cleavage site just upstream of the fusion peptide, was negatively affected by inhibition of furin, but not of lysosomal proteases. We conclude that a proteolytic cleavage site in the CoV S protein directly upstream of the fusion peptide is an essential determinant of the intracellular site of fusion. Citation: Burkard C, Verheije MH, Wicht O, van Kasteren SI, van Kuppeveld FJ, et al. (2014) Coronavirus Cell Entry Occurs through the Endo-/Lysosomal Pathway in a Proteolysis-Dependent Manner. PLoS Pathog 10(11): e1004502.
Output: Coronavirus Cell Entry Occurs through the Endo-/ Lysosomal Pathway in a Proteolysis-Dependent Manner
Background. Human coronavirus HKU1 (HCoV-HKU1), a new group 2 coronavirus, was first characterized in 2005 from 2 adults with pneumonia in Hong Kong, China. To the best of our knowledge, there is no other report to date about the detection of this new virus. We report a molecular method allowing for the detection of HCoV-HKU1 and also report the clinical presentation of 6 infected patients. Methods. We screened 141 specimens (135 nasal samples and 6 stool samples) received in February and March 2005 in our laboratory and obtained from 135 hospitalized patients (61.5% of whom were !5 years old and 34.1% of whom were 120 years old) for HCoV-HKU1. Results. HCoV-HKU1 was detected in 6 (4.4%) of the 135 nasal specimens and in 2 (33.3%) of the 6 stool samples; the positive samples were obtained from 6 patients (5 children and 1 adult). The clinical presentation of these 6 patients was as follows: 3 were admitted to the hospital for acute enteric disease resulting in severe dehydration associated with upper respiratory symptoms; 1 had fever, otitis, and febrile seizure; 1 had a sample obtained to investigate failure to thrive; and 1 had a sample obtained for exploration of X-linked agammaglobulinemia and hyperleucocytosis. Conclusion. HCoV-HKU1 can be detected in respiratory and stool samples from children and adults in a part of the world other than Hong Kong. Our results suggest that HCoV-HKU1 could be associated with respiratory and enteric diseases, and its detection can be related to a persistent asymptomatic infection in patients with poor underlying conditions.
Output: Detection of the New Human Coronavirus HKU1: A Report of 6 Cases
Bovine NK-lysins, which are functionally and structurally similar to human granulysin and porcine NK-lysin, are predominantly found in the granules of cytotoxic T-lymphocytes and NKcells. Although antimicrobial activity of bovine NK-lysin has been assessed for several bacterial pathogens, not all the important bacterial pathogens that are involved in the bovine respiratory disease complex have been studied. Therefore the objective of the present study was to evaluate the antimicrobial activity of bovine NK-lysin-derived peptides on bovine respiratory pathogen Histophilus somni. Four, 30-mer peptides corresponding to the functional region of NK-lysin helices 2 and 3 were synthesized and assessed for antibacterial activity on four bovine pneumonic H. somni isolates. Although there were some differences in the efficiency of bactericidal activity among the NK-lysin peptides at lower concentrations (2-5 μM), all four peptides effectively killed most H. somni isolates at higher concentrations (10-30 μM) as determined by a bacterial killing assay. Confocal microscopic and flow cytometric analysis of Live/Dead Baclight stained H. somni (which were preincubated with NK-lysin peptides) were consistent with the killing assay findings and suggest NK-lysin peptides are bactericidal for H. somni. Among the four peptides, NK2A-derived peptide consistently showed the highest antimicrobial activity against all four H. somni isolates. Electron microscopic examination of H. somni following incubation with NK-lysin revealed extensive cell membrane damage, protrusions of outer membranes, and cytoplasmic content leakage. Taken together, the findings from this study clearly demonstrate the antimicrobial activity of all four bovine NK-lysinderived peptides against bovine H. somni isolates.
Output: Antimicrobial activity of bovine NK-lysin- derived peptides on bovine respiratory pathogen Histophilus somni
This study investigates the impacts of high-speed rail (HSR) on domestic air transportation in China using a new comprehensive modeling framework utilizing both demand and supply perspectives. For the first time the assessment was conducted using an improved panel regression model by taking into account of the detailed opening schedules of various HSR services during the period 2001-2014. The research findings reveal that the deployed HSR services have a significant substitutional effect on domestic air transportation in China, but the effect varies across different HSR routes, travel distance and city type. Specifically, the research found a decrease in domestic passengers of 28.2%, in flights of 24.6% and in seat capacity of 27.9% after the introduction of HSR services. The impacts are found much stronger among those air routes that connect major hub within a distance range of 500 to 800 km. The uneven nature of the impact can be seen in the different experiences of selected cities. For example, air travel declined approximately 45% after commencement of the Wuhan-Guangzhou HSR, whereas it fell by 34% after the opening of the Beijing-Shanghai HSR. http://dx.
Output: Impacts of high-speed rail on domestic air transportation in China