niryuu/sni-each-converted huggingface dataset:
The sudden outbreak of severe acute respiratory syndrome (SARS) in 2002 prompted the establishment of a global scientific network subsuming most of the traditional rivalries in the competitive field of virology. Within months of the SARS outbreak, collaborative work revealed the identity of the disastrous pathogen as SARS-associated coronavirus (SARS-CoV). However, although the rapid identification of the agent represented an important breakthrough, our understanding of the deadly virus remains limited. Detailed biological knowledge is crucial for the development of effective countermeasures, diagnostic tests, vaccines and antiviral drugs against the SARS-CoV. This article reviews the present state of molecular knowledge about SARS-CoV, from the aspects of comparative genomics, molecular biology of viral genes, evolution, and epidemiology, and describes the diagnostic tests and the anti-viral drugs derived so far based on the available molecular information.
Output: Molecular Advances in Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV)
A reverse transcriptase PCR (RT-PCR) targeting a 407 bp fragment of the nucleocapsid gene of bovine coronavirus (BCV) was developed for detection of BCV RNA in feces of experimentally inoculated cattle. The sensitivity and specificity of the RT-PCR were confirmed using tissue culture-adapted BCV strains and feces of 2 calves inoculated with BCV. Ten nonpregant, BCV seropositive, adult dairy cows were inoculated with winter dysentery (WD) (n = 8) or calf diarrhea (CD) (n = 2) strains of BCV intranasally and orally (n = 2) or through a surgically-placed duodenal catheter (n = 8) with and without dexamethasone treatment or feeding ice water. The 6 cows inoculated with BCV intranasally and through a duodenal catheter (2 of 2 cows given CD BCV and 4 of 6 cows given WD BCV) developed mild diarrhea, and BCV was detected in diarrheal feces by RT-PCR, ELISA or immune electron microscopy. These results suggest that CD and WD strains of BCV can cause diarrhea in adult cows in conjunction with host or environmental factors and that RT-PCR might be useful to diagnose BCV infections in calves and adult cows. * Bovine coronavirus (BCV) is an important pathogen of neonatal calf diarrhea (CD) [5] . The virus also has been isolated from adult cattle experiencing acute diarrhea during outbreaks of winter dysentery (WD) [19] . In a recent study individ- * Present address:
Output: Experimental inoculation of adult dairy cows with bovine coronavirus and detection of coronavirus in feces by RT-PCR Brief Report
IFITM3 is involved in cell adhesion, apoptosis, immune, and antivirus activity. Furthermore, IFITM3 gene has been considered as a preferential marker for inflammatory diseases, and positive correlation to pathological grades. Therefore, we assumed that IFITM3 was regulated by different signal pathways. To better understand IFITM3 function in inflammatory response, we cloned swine IFITM3 gene, and detected IFITM3 distribution in tissues, as well as characterized this gene. Results indicated that the length of swine IFITM3 gene was 438 bp, encoding 145 amino acids. IFITM3 gene expression abundance was higher in spleen and lungs. Moreover, we next constructed the eukaryotic expression vector PBIFM3 and transfected into PK15 cells, finally obtained swine IFITM3 gene stable expression cell line. Meanwhile, we explored the effects of LPS on swine IFITM3 expression. Results showed that LPS increased IFITM3 mRNA abundance and exhibited time-dependent effect for LPS treatment. To further demonstrate the mechanism that IFITM3 regulated type I IFNs production, we also detected the important molecules expression of TLR4 signaling pathway. In transfected and non-transfected IFITM3 PK15 cells, LPS exacerbated the relative expression of TLR4-NFκB signaling molecules. However, the IFITM3 overexpression suppressed the inflammatory development of PK15 cells. In conclusion, these data indicated that the overexpression of swine IFITM3 could decrease the inflammatory response through TLR4 signaling pathway, and participate in type I interferon production. These findings may lead to an improved understanding of the biological function of IFITM3 in inflammation. 152300410070, 15A230017) and Zhengzhou City Natural Science Fund (141PPTGG407). The funding sources had no involvement in study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.
Output: Characterization and anti-inflammation role of swine IFITM3
Many infectious/communicable diseases (IDs) are endemic in Nepal. Until a decade and half ago, IDs were the major cause of both morbidity and mortality accounting 70% for both. However, as a result of various preventive measures implemented by both the state and non-state actors, the overall IDs have shown a changing (declining) trend. The most impressive decline has been seen in the intestinal helminth infection. Though the overall burden of IDs is decreasing, several newer infectious diseases (emerging infections) namely, dengue fever, scrub typhus, influenza (H5N1 and H1N1), and others are posing a great public health problem. On the other hand, though sporadic, outbreaks of endemic diseases together with HIV-TB coinfection and infection with drug resistance microbes during recent years have constituted a serious public health as well as medical problem. On the contrary, with the decline of IDs, noninfectious diseases (noncommunicable disease, NCD) namely, diabetes, cancer (and cancer therapy), and others are on the rise particularly in urban areas. Hence, currently Nepal is trapped in "double burden" of diseases. Risk of opportunistic infection has increased in immunocompromised person with NCD. To address the present situation, the multi-sectoral plan and strategies developed must be implemented effectively.
Output: Changing Trend of Infectious Diseases in Nepal
The paper reports on a research study undertaken on the differentiation of green building certification systems at an international, national and local level. Through a cross comparison, authors are able to explain the differences by the contextualism theory which could be traced back to the fundamental divergence on lifestyles, preferences, urban morphology besides climatic variations. The discussion is derived from a study of three green rating systems representing international, national and local systems with reference to intentions, mechanisms and benchmarks to facilitate objective assessments. For the case of Hong Kong, local challenges are identified and compared with counterparts at a national level. Two residential projects having certified by the 'modified, localized' national system is selected for a case study for synopsis with a view to explain the cause and effect of transferability versus non-transferability of assessment credits and protocols. Introducing and applying national and international systems to a local context can detect flaws in local design practices that may be ignored in the local rating system.
Output: Contextualizing green building rating systems: Case study of Hong Kong
RNA was isolated from fibroblast cultures infected with human cytomegalovirus (HCMV) strain AD169 during the late phase of viral replication. The RNA was selected by hybridization to a series of cosmid clones containing the entire viral genome in partially overlapping segments. Translation of this RNA in a reticulocyte cellfree system allowed the mapping of virus specific polypeptides. Nine polypeptides synthesized in vitro comigrated with major virion structural proteins. An in vitro-translated protein of 71 kDa was precipitated by a monoclonal antibody directed against the phosphorylated internal envelope protein of '71 kDa. The map coordinates of viral DNA coding for this phosphoprotein were localized by hybrid selection with subcloned DNA fragments, and the direction of transcription was determined by hybrid selection with single-stranded DNA cloned in bacteriophage vector M13mp9. An in witro translation with size-fractionated RNA, combined with immunoprecipitation and Northern blot analyses, indicated that an mRNA of 4 kb encodes the 71-kDa phosphoprotein. An mRNA of the same size, map coordinates, and orientation was translated into an abundant 65-kDa polypeptide which had the same size as the major structural phosphoprotein of HCMV.
Output: Physical Mapping of Human Cytomegalovirus Genes: identification of DNA Sequences Coding for a Virion Phosphoprotein of 71 kDa and a Viral 65kDa Polypeptide
Human metapneumovirus (hMPV) is a recently discovered virus that causes respiratory illness in children that can lead to hospitalization. Our study was undertaken to further understand hMPV-associated illness, compare clinical characteristics of hMPV and respiratory syncytial virus (RSV), and establish the utility of routine screening for hMPV. We retrospectively identified hMPV-associated illnesses described among children with respiratory symptoms admitted to a tertiary care center in southeast Michigan during the 2006-2007 respiratory viral season. A convenience sample of 256 nasopharyngeal specimens was subjected to nucleic acid extraction and amplification to identify those specimens positive for hMPV. A medical record review was undertaken to retrieve demographic and clinical data of patients with hMPV, comparing them to RSVpositive patients and patients evaluated for respiratory symptoms who were negative for hMPV and RSV. We found that hMPV was the second most commonly identified virus after RSV. hMPV-positive patients were older than RSV-positive patients. Among hMPV-positive patients, pneumonia was diagnosed in 37.5% and bronchiolitis in 31.2%, peribronchial cuffing was present on chest radiographs of 37.5%, antibiotic treatment was used in 81.2%, and admission to the ICU was seen in 37.5%. Finally, hMPV-positive patients were more likely to have fever than RSV-positive patients or patients negative for hMPV and RSV. We concluded that hMPV is a major pathogen associated with hospitalization of children and with the same severity of illness as RSV but in a slightly older population. Because of the apparent prevalence and severity of illness, routine screening should be implemented. This work is licensed under a Creative Commons Attribution 3.0 License (by-nc 3.0). ©Copyright N.
Output: Human metapneumovirus and respiratory syncytial virus: subtle differences but comparable severity
The sudden death of three calves, one diarrheic calf, and one aborted fetus from four farms in southern Brazil was investigated. Two Histophilus somni-associated syndromes were identified: systemic histophilosis (n=4) and abortion (n=1). The principal pathological findings included vasculitis, meningoencephalitis with thrombosis, necrotizing myocarditis, renal infarctions, hepatic abscesses, and bronchopneumonia. PCR assays were used to amplify specific amplicons of the ovine herpesvirus 2, bovine herpesvirus 1 and −5, Listeria monocytogenes, H. somni, and pestivirus; bovine group A rotavirus (BoRV-A) and bovine coronavirus (BCoV) were investigated in calves with diarrhea. H. somni DNA was amplified in tissues from all calves and the brain of the aborted fetus with pathological alterations consistent with histophilosis. All other PCR assays were negative; BoRV-A and BCoV were not identified. These findings confirm the participation of H. somni in the pathological alterations observed in this study and represent the first description of histophilosis in cattle from Brazil.
Output: Histophilus somni-induced infections in cattle from southern Brazil
Tritrichomonas foetus is the causative agent of bovine trichomonosis, a sexually transmitted disease leading to infertility and abortion. A test based on loop mediated isothermal amplification (LAMP) targeting the 5.8S rDNA subunit was designed for the specific identification of T. foetus. The LAMP assay was validated using 28 T. foetus and 35 non-T. foetus trichomonads strains. It did not exhibit cross-reaction with closely related parasites commonly found in smegma cultures like Tetratrichomonas spp. and Pentatrichomonas hominis. Bovine smegma did not show interferences for the detection of the parasite and, the sensitivity of the method (4 × 10 3 CFU/mL, approximately 10 cells/reaction) was slightly higher than that found for PCR amplification with TFR3 and TFR4 primers. The LAMP approach has potential applications for diagnosis and control of T. foetus and, practical use for low skill operators in rural areas.
Output: Loop mediated isothermal amplification of 5.8S rDNA for specific detection of Tritrichomonas foetus
Graphical Abstract Highlights d Catalytic site mutations were introduced in vaccinia virus decapping enzymes, D9 and D10 d D9 and D10 catalytic mutant virus exhibits replication defects and attenuation in mice d Mutant virus increases dsRNA, activates RNase L, and induces PKR phosphorylation d Protein synthesis is inhibited and RNA degraded in absence of functional D9 and D10 SUMMARY Poxvirus replication involves synthesis of doublestranded RNA (dsRNA), which can trigger antiviral responses by inducing phosphorylation-mediated activation of protein kinase R (PKR) and stimulating 2 0 5 0 -oligoadenylate synthetase (OAS). PKR inactivates the translation initiation factor eIF2a via phosphorylation, while OAS induces the endonuclease RNase L to degrade RNA. We show that poxvirus decapping enzymes D9 and D10, which remove caps from mRNAs, inhibit these antiviral responses by preventing dsRNA accumulation. Catalytic site mutations of D9 and D10, but not of either enzyme alone, halt vaccinia virus late protein synthesis and inhibit virus replication. Infection with the D9-D10 mutant was accompanied by massive mRNA reduction, cleavage of ribosomal RNA, and phosphorylation of PKR and eIF2a that correlated with a 15-fold increase in dsRNA compared to wild-type virus. Additionally, mouse studies show extreme attenuation of the mutant virus. Thus, vaccinia virus decapping, in addition to targeting mRNAs for degradation, prevents dsRNA accumulation and anti-viral responses.
Output: Poxvirus Decapping Enzymes Enhance Virulence by Preventing the Accumulation of dsRNA and the Induction of Innate Antiviral Responses Article Poxvirus Decapping Enzymes Enhance Virulence by Preventing the Accumulation of dsRNA and the Induction of Innate Antiviral Responses
Purpose: To assess lung lesions in patients with pneumonia complicating novel influenza A (H1N1) by serial high-resolution computed tomography (HRCT) during the early, progressive and convalescent stages. Samples and methods: Serial HRCT scans in 39 patients with pneumonia complicating novel influenza A (H1N1) were reviewed for predominant patterns of lung abnormalities as well as distribution and extent of involvement. Longitudinal changes were assessed at different time points. Results: In the early stage, the most common HRCT finding was patchy ground-glass opacity (GGO) (n ¼ 4, 54.7%). In the progressive stage, bilaterally distributed GGO mixed with consolidation was the most commonly observed feature (n ¼ 28, 71.8%). The diffuse pattern deteriorated to a peak (n ¼ 17, 43.6%) at this stage. In the convalescent stage, the most common finding was fibrosis (n ¼ 25, 64.1%). Averagely, fibrosis was observed at d 18.5 ± 6.4 after the onset of symptoms. Three patterns of longitudinal changes of the lesions were observed, including: type 1, improvement after deterioration; type 2, concurrent improvement and deterioration followed by improvement; and type 3, gradual improvement. Type 1 was the more common pattern (n ¼ 27, 69.2%). Complete serial HRCT scans from initial and final scan were obtained in 24 patients, and the mean CT score peaked at d 8e14 of the illness. Conclusion: HRCT may play a role in detecting and characterizing pulmonary lesions for the cases of pneumonia complicating influenza A. In addition, it may contribute to monitoring longitudinal changes of pneumonia and assessing therapeutic response.
Output: Longitudinal changes of pneumonia complicating novel influenza A (H1N1) by high-resolution computed tomography-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Similarity in time series is an important feature of dynamical systems such as financial systems, with potential use for clustering of series in system. Here, we mainly introduce a novel method: the reconstructed phase space information clustering method to analyze the financial markets. The method is used to examine the similarity of different sequences by calculating the distances between them, which the main difference from previous method is the way to map the original time series to symbolic sequences. Here we make use of the state space reconstruction to construct the symbolic sequences and quantify the similarity of different stock markets and exchange rate markets considering the chaotic behavior between the complex time series. And we compare the results of similarity of artificial and real data using the modified method, information categorization method and system clustering method. We conclude that the reconstructed phase space information clustering method is effective to research the close relationship in time series and for short time series especially. Besides, we report the results of similarity of different exchange rate time series in different periods and find the effect of the exchange rate regime in 2008 on the time series. Also we acquire some characteristics of exchange rate time
Output: The similarity analysis of financial stocks based on information clustering
The mode of infection transmission has profound implications for effective containment by public health interventions. The mode of smallpox transmission was never conclusively established. Although, "respiratory droplet" transmission was generally regarded as the primary mode of transmission, the relative importance of large ballistic droplets and fine particle aerosols that remain suspended in air for more than a few seconds was never resolved. This review examines evidence from the history of variolation, data on mucosal infection collected in the last decades of smallpox transmission, aerosol measurements, animal models, reports of smallpox lung among healthcare workers, and the epidemiology of smallpox regarding the potential importance of fine particle aerosol mediated transmission. I introduce briefly the term anisotropic infection to describe the behavior of Variola major in which route of infection appears to have altered the severity of disease.
Output: What was the primary mode of smallpox transmission? Implications for biodefense
DAP-related apoptotic kinase-2 (DRAK2), a DAP kinase family member, is highly expressed in B and T lymphocytes in the human and the mouse. To determine whether DRAK2 plays a role in B cell activation and differentiation, we analyzed germinal centers (GCs) and the specific antibody response to NP in drak2 −/− mice immunized with the thymus-dependent (TD) conjugated hapten NP 16 -CGG. In drak2 −/− mice, spleen GCs were normal in size and morphology, but their number was reduced by as much as five-fold, as compared to their wild-type littermates. This was not due to a defect in B cell proliferation, as the BrdU uptake was comparable in DRAK2-deficient and wild-type B cells. Rather, the proportion of apoptotic GC B and T cells in drak2 −/− mice was significantly higher than that in wild-type control mice, as shown by 7-AAD and TUNEL staining. In drak2 −/− mice, the generation of high affinity IgG antibodies was impaired in spite of the seemingly normal somatic hypermutation (SHM) and class switch DNA recombination (CSR) machineries in drak2 −/− B cells. In NP 16 -CGG-immunized drak2 −/− mice, T cell-intrinsic Bcl-xL transgene expression increased the number of GCs and rescued the high affinity IgG response to NP. These findings suggest a novel role for DRAK2 in regulating the GC reaction and the response to TD antigens, perhaps through increased survival of T cells and enhanced B cell positive selection. They also suggest that DRAK2-deficiency is not involved in regulating intrinsic B cell apoptosis.
Output: A role for DRAK2 in the germinal center reaction and the antibody response
To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MR-PrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks.
Output: MRPrimerV: a database of PCR primers for RNA virus detection
Background The new influenza virus A ⁄ H1N1 (2009), identified in mid-2009, rapidly spread over the world. Estimating the transmissibility of this new virus was a public health priority. Methods We reviewed all studies presenting estimates of the serial interval or generation time and the reproduction number of the A ⁄ H1N1 (2009) virus infection. Results Thirteen studies documented the serial interval from household or close-contact studies, with overall mean 3 days (95% CI: 2AE4, 3AE6); taking into account tertiary transmission reduced this estimate to 2AE6 days. Model-based estimates were more variable, from 1AE9 to 6 days. Twenty-four studies reported reproduction numbers for community-based epidemics at the town or country level. The range was 1AE2-3AE1, with larger estimates reported at the beginning of the pandemic. Accounting for under-reporting in the early period of the pandemic and limiting variation because of the choice of the generation time interval, the reproduction number was between 1AE2 and 2AE3 with median 1AE5. The serial interval of A ⁄ H1N1 (2009) flu was typically short, with mean value similar to the seasonal flu. The estimates of the reproduction number were more variable. Compared with past influenza pandemics, the median reproduction number was similar (1968) or slightly smaller (1889, 1918, 1957).
Output: Transmission parameters of the A ⁄ H1N1 (2009) influenza virus pandemic: a review
A new disease, the severe acute respiratory distress syndrome (SARS), caused by the SARS coronavirus (SARS-CoV), emerged at the beginning of 2003 and rapidly spread throughout the world. Although the disease had disappeared in June 2003 its re-emergence cannot be excluded. The development of vaccines against SARS-CoV may take years. Therefore, the availability of effective antiviral drugs against SARS-CoV may be crucial for the control of future SARS outbreaks. In this review, experimental and clinical data about potential anti-SARS drugs is summarised and discussed. Animal model studies will be needed to help to determine which interventions warrant controlled clinical testing.
Output: Development of antiviral therapy for severe acute respiratory syndrome
BSC 40 cells do not permit the replication of superinfecting vaccinia virus. The extent of superinfecting virus propagation depends on the time of superinfection; there is 90% exclusion by 4 hr after the initial infection, and more than 99% by 6 hr. When superinfection is attempted at 6 hr after infection, the superinfecting virus is incapable of carrying out DNA replication or early gene transcription, demonstrating that an early event in the virus life cycle is inhibited. The rate of adsorption of the superinfecting virus is unaltered which shows that exclusion is affected at a point between adsorption and early gene transcription. In order to exclude superinfection, the primary infecting virus does not require replication of its DNA or expression of its late genes but it must express one or more early genes. Press, Inc.
Output: Superinfection Exclusion of Vaccinia Virus in Virus-Infected Cell Cultures
Background: Canine parvovirus 2 (CPV 2) is a major infectious cause of mortality in puppies. The characteristic symptom of CPV 2 disease is intestinal hemorrhage with severe bloody diarrhea. Soon after CPV was first recognized in the late 1970s, the original virus, CPV 2, was replaced in the canine population by strains carrying minor antigenic variants (termed 2a, 2b, and 2c) of the VP2 gene that could be distinguished using monoclonal antibodies and molecular analyses. Here, we provide an updated molecular characterization of the CPV 2 circulating in Taiwan. Methods: In this study, 28 isolates of CPV 2 from 144 dogs with suspected CPV infection were obtained from northern, central, and southern Taiwan from 2008 to 2012 and screened by PCR. The 28 isolates were sequenced, and a phylogenetic analysis of the VP2 gene was performed. Results: Of the 28 Taiwanese CPV 2 isolates, 15 were identified as new CPV 2a, and 13 were identified as new CPV 2b. Compared to the reference CPV 2a, all 15 of the CPV 2a sequences collected in this study contain an Ile324 mutation caused by a TAT to ATT mutation at nucleotides 970-972 of the VP2 gene. Conclusion: Our VP2 sequence data revealed that both types are currently prevalent CPV 2 field strains circulating in Taiwan, and a unique Ile324 VP2 mutation was found in our Taiwanese CPV 2a isolates and recent Asian isolates. CPV 2c was not observed in this study.
Output: Genetic characterization of type 2a canine parvoviruses from Taiwan reveals the emergence of an Ile324 mutation in VP2
Pigs are believed to be one of the important sources of emerging human and swine influenza viruses (SwIV). Influenza virus conserved peptides have the potential to elicit crossprotective immune response, but without the help of potent adjuvant and delivery system they are poorly immunogenic. Biodegradable polylactic-co-glycolic acid (PLGA) nanoparticle (PLGA-NP) based vaccine delivery system enhances cross-presentation of antigens by the professional antigen presenting cells. In this study, Norovirus P particle containing SwIV M2e (extracellular domain of the matrix protein 2) chimera and highly conserved two each of H1N1 peptides of pandemic 2009 and classical human influenza viruses were entrapped in PLGA-NPs. Influenza antibody-free pigs were vaccinated with PLGA-NPs peptides cocktail vaccine twice with or without an adjuvant, Mycobacterium vaccae whole cell lysate, intranasally as mist. Vaccinated pigs were challenged with a virulent heterologous zoonotic SwIV H1N1, and one week later euthanized and the lung samples were analyzed for the specific immune response and viral load. Clinically, pigs vaccinated with PLGA-NP peptides vaccine had no fever and flu symptoms, and the replicating challenged SwIV was undetectable in the bronchoalveolar lavage fluid. Immunologically, PLGA-NP peptides vaccination (without adjuvant) significantly increased the frequency of antigen-specific IFNγ secreting CD4 and CD8 T cells response in the lung lymphocytes, despite not boosting the antibody response both at pre-and post-challenge. In summary, our data indicated that nanoparticlemediated delivery of conserved H1N1 influenza peptides induced the virus specific T cell response in the lungs and reduced the challenged heterologous virus load in the airways of pigs.
Output: Entrapment of H1N1 Influenza Virus Derived Conserved Peptides in PLGA Nanoparticles Enhances T Cell Response and Vaccine Efficacy in Pigs
Aims: To determine the seroprevalence of canine respiratory coronavirus (CRCoV) in New Zealand dogs, and to explore associations with age, sex, breed, month, and geographical region of sampling and reported presence of clinical signs suggestive of respiratory disease. Methods: A total of 1,015 canine serum samples were randomly selected from submissions to a diagnostic laboratory between March and December 2014, and were analysed for CRCoV antibodies using a competitive ELISA. Logistic regression analysis was used to determine associations between seroprevalence of CRCoV and breed category, age, sex, sampling month, region, and reported health status of dogs. Results: Overall, 538/1,015 (53.0%) samples were seropositive for CRCoV, with 492/921 (53.4%) positive dogs in the North Island and 46/94 (49%) in the South Island. Age of dog, sampling month, region, and presence of abnormal respiratory signs were included in the initial logistic regression model. Seroprevalence was higher in dogs aged ≥3 compared with ≤2 years (p < 0.01). The lowest seroprevalence was observed in July (30/105; 28.5%) and August (32/100; 32%), and the highest in June (74/100; 74%). Seroprevalence in dogs from Auckland was higher than in dogs from the Hawkes Bay, Manawatu, Marlborough, and Waikato regions (p < 0.05). Abnormal respiratory signs (coughing, nasal discharge, or sneezing) were reported for 28/1,015 (2.8%) dogs sampled. Seroprevalence for CRCoV tended to be higher among dogs with respiratory signs (67.9 (95% CI = 47.6-83.4)%) than dogs with no reported respiratory signs (52.6 (95% CI = 49.5-55.7)%). Conclusions: Serological evidence of infection with CRCoV was present in more than half of the dogs tested from throughout New Zealand. Differences in CRCoV seroprevalence between regions and lack of seasonal pattern indicate that factors other than external temperatures may be important in the epidemiology of CRCoV in New Zealand. Clinical relevance: Our data suggest that CRCoV should be included in investigations of cases of infectious canine tracheobronchitis, particularly if these occur among dogs vaccinated with current vaccines, which do not include CRCoV antigens.
Output: A serological survey of canine respiratory coronavirus in New Zealand
This study investigated the role and mechanism of alprostadil in acute respiratory distress syndrome (ARDS) induced by oleic acid (OA) in rats. Sprague-Dawley rats were randomly divided into control, OA model, and OA + Alprostadil (2.5, 5, and 10 μg/kg, respectively) groups. The ARDS model was induced by femoral vein injection of OA, and alprostadil was administrated immediately. Lung injury was evaluated by lung wet-dry weight ratio (W/D) and histological analyses. Expressions of ACE, inflammatory mediators, apoptotic-related proteins, and proteins in the MAPKs and NF-kB signaling pathways were determined by Western blot or immunohistochemical staining. Compared with the control group, the OA model group had significantly increased W/D, lung injury score, and collagen deposition at 3 h after OA injection. However, alprostadil (10 μg/kg) treatment significantly reduced OA-induced elevation of these indicators. Additionally, OA-induced expression of TNF-a and IL-1b were suppressed by alprostadil. The OA-induced activation of nuclear factor (NF) kB p65 was also reduced by alprostadil. Furthermore, we found that Alprostadil had an inhibitory effect on the phosphorylation of JNK, ERK1/2, and p38 MAPKs. Alprostadil inhibited Bax but increased Bcl-2, indicating a suppressive role in apoptosis. Remarkably increased expression of ACE in the OA model group was observed, which was decreased by alprostadil. Alprostadil has a protective effect on ARDS induced by OA in rats, possibly through inhibiting apoptosis, suppressing the activation of MAPKs and NF-kB signaling pathways, and decreasing ACE protein expression. Therefore, the use of alprostadil in clinical ARDS treatment is promising.
Output: Protective Effect and Mechanism of Alprostadil in Acute Respiratory Distress Syndrome Induced by Oleic Acid in Rats
Hong Kong's new Police Commissioner Chris Tang announced in Beijing on December 7, 2019, that he would use "both hard and soft approaches" to end the anti-government protests. This article argues that such "approaches" amount to physical and non-physical repression-hard power, but employed by Hong Kong, rather than mainland, forces, combined with sharp power exercised by both Beijing and the local authorities. These measures are responses to the limits on what Beijing can do under the "one country, two systems" model. As Beijing cannot send the People's Liberation Army (PLA), it has subverted Hong Kong's once-respected civilian police force to act like the mainland's public security. And as Hong Kong's judiciary is relatively autonomous and many of the arrested would not be convicted or sentenced, the police have resorted to a decapacitation campaign to inflict direct violence on protesters. Moreover, as the city's freedom has allowed the public to support protesters in various ways,
Output: Beijing's Hard and Soft Repression in Hong Kong
Objective: Finding the longest common subsequence (LCS) among sequences is NP-hard. This is an important problem in bioinformatics for DNA sequence alignment and pattern discovery. In this research, we propose new CPU-based parallel implementations that can provide significant advantages in terms of execution times, monetary cost, and pervasiveness in finding LCS of DNA sequences in an environment where Graphics Processing Units are not available. For general purpose use, we also make the OpenMP-based tool publicly available to end users. In this study, we develop three novel parallel versions of the LCS algorithm on: (i) distributed memory machine using message passing interface (MPI); (ii) shared memory machine using OpenMP, and (iii) hybrid platform that utilizes both distributed and shared memory using MPI-OpenMP. The experimental results with both simulated and real DNA sequence data show that the shared memory OpenMP implementation provides at least two-times absolute speedup than the best sequential version of the algorithm and a relative speedup of almost 7. We provide a detailed comparison of the execution times among the implementations on different platforms with different versions of the algorithm. We also show that removing branch conditions negatively affects the performance of the CPU-based parallel algorithm on OpenMP platform.
Output: An OpenMP-based tool for finding longest common subsequence in bioinformatics
A temporal series of demyelinating lesions in experimental canine distemper virus (CDV) infection was examined with immunohistological techniques demonstrating myelin basic protein (MBP), myelinassociated glycoprotein (MAG), and glial fibrillary acidic protein (GFAP) on serial sections. The earliest lesions were characterized by decreased MBP and MAG and increased GFAP. During the further progression of the disease, MBP and MAG losses continued to match each other. There was no indication of MAG loss preceding the disappearance of MBP. In the more advanced lesions there was a marked decrease of GFAP positive cells. Since these findings differed considerably from similar immunohistochemical studies in progressive multifocal leukoencephalopathy (PML) where demyelination results from oligodendroglial infection, it was concluded that the oligodendroglial cell body is not the primary target of CDV. The marked astrogtial changes were also considered to contribute to demyelination in CDV infection but the mechanism by which this happens remains unknown.
Output: Acta Neuropathol (Berl) Acta Neuropathologica Glial Proteins in Canine Distemper Virus-induced Demyelination A Sequential Immunocytochemical Study*
, are considered to be responsible for tumor growth and chemoresistance. Different hypotheses have been proposed to explain the origin of CICs, including mutations in adult stem/ progenitor cells or the acquisition of stem-like characteristics in differentiated cells; however, studies have yielded conflicting identification for CICs and have little information for the origin to generate CICs. Part of the difficulty in identifying CICs may stem from the fact that the CICs studied have been largely derived from cancer cell lines or well-developed tumors. In previous studies, we have reported the enrichment of mouse pulmonary stem/progenitor cells (mPSCs) by using serumfree primary selection culture followed by FACS isolation using the coxsackievirus/ adenovirus receptor (CAR) as the positive selection marker. Here, we demonstrated that overexpression of the pluripotent transcription factor Oct-4 is sufficient to induce CAR + /mPSCs transformation, which we name CAR + /mPSCs Oct-4_hi . These transformed cells possess cancer initiating and chemoresistance potential, as well as exhibiting remarkable expression of certain proangiogenic factors, including angiopoietins (ANGs) and VEGF, and enhanced angiogenic potential. Moreover, CAR + /mPSCs Oct-4_hi actively participated in tumor blood vessel formation and triggered a novel angiogenic mechanism, the angiopoietins/Tie2 signaling pathway. These study provide critical evidence supporting the possible origin to generate CICs, and help elucidate the pathways responsible for CICs-mediated blood vessel formation.
Output: Acquisition of tumorigenic potential and enhancement of angiogenesis in pulmonary stem/progenitor cells through Oct-4 hyperexpression
To reduce the use of antibiotics in animal agriculture, a number of effective or commercially viable alternatives have been implemented by food animal producers or are under development. Perhaps the most well-established strategies are flock and herd management practices to mitigate disease introduction and spread, and, subsequently, reduce the need for antibiotic use. While vaccines in food animal production have been used to prevent both bacterial and viral diseases, but historically, most vaccines have targeted viral diseases. Though vaccines against viral diseases can help reduce the need for antibiotic use by controlling the spread of secondary bacterial infections, more recent vaccines under development specifically target bacteria. New developments in selecting and potentially tailoring bacteriophages provide a promising avenue for controlling pathogenic bacteria without the need for traditional small-molecule antibiotics. In this article we discuss these established and emerging strategies, which are anticipated to reduce the reliance on antibiotics in food animal production and should reduce the prevalence and transmission to humans of antimicrobial resistant bacteria from these systems.
Output: ANNALS OF THE NEW YORK ACADEMY OF SCIENCES From farm management to bacteriophage therapy: strategies to reduce antibiotic use in animal agriculture
Respiratory viruses (RV) are a leading cause of infection-related morbidity and mortality for patients undergoing treatment for cancer. This analysis compared duration of RV shedding as detected by culture and PCR among patients in a high-risk oncology setting (adult patients with haematological malignancy and/or stem cell transplant and all paediatric oncology patients) and determined risk factors for extended shedding. RV infections due to influenza virus, parainfluenza virus (PIV), human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) from two study periods(PCR-based testing)-were reviewed retrospectively. Data were collected from patients in whom re-testing for viral clearance was carried out within 5-30 days after the most recent test. During the study period 456 patients were diagnosed with RV infection, 265 by PCR and 191 by culture. The median range for duration of shedding (days) by culture and PCR, respectively, were as follows-influenza virus: 13 days (5-38 days) versus 14 days (5-58 days), p 0.5; RSV: 11 days (5-35 days) versus 16 days (5-50 days), p 0.001; PIV: 9 days (5-41 days) versus 17 days (5-45 days), p 0.0001; HMPV 10.5 days (5-29 days) versus 14 days (5-42 days), p 0.2. In multivariable analysis, age and underlying disease or transplant were not independently associated with extended shedding regardless of testing method. In high-risk oncology settings for respiratory illness due to RSV and PIV, the virus is detectable by PCR for a longer period of time than by culture and extended shedding is observed. Clinical Microbiology and Infection
Output: Comparison of respiratory virus shedding by conventional and molecular testing methods in patients with haematological malignancy
Rationale: Emphysema and osteoporosis are epidemiologically associated diseases of cigarette smokers. The causal mechanism(s) linking these illnesses is unknown. We hypothesized autoimmune responses may be involved in both disorders. Objectives: To discover an antigen-specific autoimmune response associated with both emphysema and osteoporosis among smokers. Methods: Replicate nonbiased discovery assays indicated that autoimmunity to glucose regulated protein 78 (GRP78), an endoplasmic reticulum chaperone and cell surface signaling receptor, is present in many smokers. Subject assessments included spirometry, chest CT scans, dual x-ray absorptiometry, and immunoblots for anti-GRP78 IgG. Anti-GRP78 autoantibodies were isolated from patient plasma by affinity chromatography, leukocyte functions assessed by flow cytometry, and soluble metabolites and mediators measured by immunoassays. Measurements and Main Results: Circulating anti-GRP78 IgG autoantibodies were detected in plasma specimens from 86 (32%) of the 265 smoking subjects. Anti-GRP78 autoantibodies were singularly prevalent among subjects with radiographic emphysema (OR 3.1, 95%CI 1.7-5.7, p = 0.003). Anti-GRP78 autoantibodies were also associated with osteoporosis (OR 4.7, 95%CI 1.7-13.3, p = 0.002), and increased circulating bone metabolites (p = 0.006). Among emphysematous subjects, GRP78 protein was an autoantigen of CD4 T-cells, stimulating lymphocyte proliferation (p = 0.0002) and IFN-gamma production (p = 0.03). Patient-derived anti-GRP78 autoantibodies had avidities for osteoclasts and macrophages, and increased macrophage NFkB phosphorylation (p = 0.005) and productions of IL-8, CCL-2, and MMP9 (p = 0.005, 0.007, 0.03, respectively). Conclusions: Humoral and cellular GRP78 autoimmune responses in smokers have numerous biologically-relevant proinflammatory and other deleterious actions, and are associated with emphysema and osteoporosis. These findings may have relevance for the pathogenesis of smoking-associated diseases, and development of biomarker immunoassays and/or novel treatments for these disorders.
Output: Autoreactivity to Glucose Regulated Protein 78 Links Emphysema and Osteoporosis in Smokers
Editor: M. Leeflang Multiplex PCR Point-of-care test Respiratory virus infection a b s t r a c t Objectives: To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)dBioFire FilmArray RP (FilmArray), Nanosphere Verigene RVþ test (Verigene RVþ) and Hologic Gen-Probe Prodesse assaysdon the detection of viral respiratory infections. Methods: A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RVþ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay. Results: Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RVþ and ProFluþ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848e0.949), 0.949 (95% confidence interval, 0.882e0.979) and 0.954 (95% confidence interval, 0.871e0.985), respectively. The three mPCRs were comparable in terms of detection of FluA. Conclusions: Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RVþ and ProFluþ) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments. H.-S. Huang, Clin Microbiol Infect 2018;24:1055
Output: Systematic review Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis
A simple, cell-based, membrane fusion assay system that uses split green fluorescent proteins (spGFPs) as an indicator was developed. The attachment of the pleckstrin homology (PH) domain to the N-termini of each spGFP not only localized the reporter signal to the plasma membrane but also helped the stable expression of the smaller spGFP of seventeen amino acid residues. It was shown that this system allowed real-time monitoring of membrane fusion by HIV-1 envelope protein (Env) without the addition of external substrates. This method can be adapted to the analyses of other viral membrane fusion.
Output: Monitoring of HIV-1 envelope-mediated membrane fusion using modified split green fluorescent proteins
The genome of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) contains four structural genes that are homologous to genes found in other coronaviruses, and also contains six subgroup-specific open reading frames (ORFs). Expression of one of these subgroupspecific genes, ORF7a, resulted in apoptosis via a caspase-dependent pathway. Here, we observed that transient expression of ORF7a protein fused with myc or GFP tags at its N or C terminus inhibited cell growth and prevented BrdU incorporation in different cultural cells, suggesting that ORF7a expression may regulate cell cycle progression. Analysis by flow cytometry demonstrated that ORF7a expression was associated with blockage of cell cycle progression at G0/G1 phase in HEK 293 cells after 24 to 60 h post-transfection. Similar results were observed in COS-7 and Vero cells. Mutation analysis of ORF7a revealed that the domain spanning aa 44 -82 of 7a protein was essential for its cytoplasmic localization and for induction of the cell cycle arrest. After analyzing the cellular proteins involving in regulation of cell cycle progression, we demonstrated that ORF7a expression was correlated with a significant reduction of cyclin D3 level of mRNA transcription and expression, and phosphorylation of retinoblastoma (Rb) protein at ser795 and ser809/811, not with the expression of cyclin D1, D2, cdk4 and cdk6 in HEK 293 cells. These results suggest that the insufficient expression of cyclin D3 may cause a decreased activity of cyclin D/cdk4/6, resulting in the inhibition of Rb phosphorylation. Accumulation of hypo-or non-phosphorylated pRb thus prevents cell cycle progression at G0/G1 phase. D
Output: SARS coronavirus 7a protein blocks cell cycle progression at G0/G1 phase via the cyclin D3/pRb pathway