niryuu/sni-each-converted huggingface dataset:
Background: From October 2010 through February 2016, Arizona conducted surveillance for severe acute respiratory infections (SARI) among adults hospitalized in the Arizona-Mexico border region. There are few accurate mortality estimates in SARI patients, particularly in adults ≥ 65 years old. The purpose of this study was to generate mortality estimates among SARI patients that include deaths occurring shortly after hospital discharge and identify risk factors for mortality. Methods: Patients admitted to two sentinel hospitals between 2010 and 2014 who met the SARI case definition were enrolled. Demographic data were used to link SARI patients to Arizona death certificates. Mortality within 30 days after the date of admission was calculated and risk factors were identified using logistic regression models. Results: Among 258 SARI patients, 47% were females, 51% were white, non-Hispanic and 39% were Hispanic. The median age was 63 years (range, 19 to 97 years) and 80% had one or more pre-existing health condition; 9% died in hospital. Mortality increased to 12% (30/258, 30% increase) when electronic vital records and a 30-day posthospitalization time frame were used. Being age ≥ 65 years (OR = 4.0; 95% CI: 1.6-9.9) and having an intensive care unit admission (OR = 7.4; 95% CI: 3.0-17.9) were independently associated with mortality. Conclusion: The use of electronic vital records increased SARI-associated mortality estimates by 30%. These findings may help guide prevention and treatment measures, particularly in high-risk persons in this highly fluid border population.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding
Wedzicha JA: Respiratory syncytial virus, airway inflammation, and FEV1 decline in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2006, 173:871-876. This paper demonstrated that persistent respiratory syncytial virus infection could contribute to the progression of COPD severity. Models of infection and exacerbations in COPD Papi et al. 263 www.sciencedirect.com
Output: 1 - background, 2 - background, 3 - other, 4 - finding, 5 - other
0166-0934/$ -see front matter Published by Elsevier B.V.
Output: 1 - other
A 1520 bp region of Cochlosoma anatis mtDNA 16S gene was subjected to DNA sequencing and a 466 bp portion was compared with other protozoan 16S sequences to develop PCR primers specific for C. anatis. This PCR diagnostic method allowed identification of C. anatis from house flies, Musca domestica L., turkey gut, and fecal samples within 6 h after fieldcollected samples reached the laboratory. House flies detected carrying C. anatis using the diagnostic 374 bp amplicons represented the first record of this protozoan in house flies. #
Output: 1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding, 6 - other
The objectives of this study were to evaluate the effects of free-access acidified milk replacer feeding on the pre-and postweaning health of dairy and veal calves. Individually housed calves were systematically assigned at birth to 1 of 2 feeding programs: free-access feeding (ad libitum) of acidified milk replacer (ACD, n = 249) or traditional restricted feeding (3 L fed twice daily) of milk replacer (RES, n = 249). Calves were fed milk replacer containing 24% crude protein and 18% fat. Acidified milk replacer was prepared to a target pH between 4.0 and 4.5 using formic acid. Calves were weaned off milk replacer at approximately 6 wk of age. Weaning occurred over 5 d, and during this weaning period, ACD calves had access to milk replacer for 12 h/d and RES calves were offered only one feeding of milk replacer (3 L) daily. Calves were monitored daily for signs of disease. Fecal consistency scores were assigned each week from birth until weaning. A subset of calves was systematically selected for fecal sampling at 3 time points between 7 and 27 d of age. Fecal samples were analyzed for enterotoxigenic Escherichia coli F5, Cryptosporidium parvum, rotavirus, and coronavirus. Hip width, hip height, body length, heart girth, and body weight were measured at birth and weaning. Postweaning body weight measurements were collected from the heifers at approximately 8 mo of age. Postweaning body weight and carcass grading information was collected from the veal calves at slaughter once a live weight between 300 and 350 kg had been achieved. The odds of ACD calves being treated for a preweaning disease event tended to be lower than that of the RES calves (1.2 vs. 5.2%, respectively). Preweaning mortality, postweaning disease treatment, and postweaning mortality did not differ between feeding treatments. The ACD feeding treatment supported greater preweaning average daily gain (0.59 vs. 0.43 kg/d) and structural growth than RES feeding. Postweaning average daily gain and carcass characteristics were similar for ACD and RES calves. These results indicate that free-access acidified milk replacer feeding tended to support improved health, and greater body weight gain and structural growth during the preweaning period; these effects did not persist in the postweaning period. The growth advantage observed before weaning in the ACD calves likely disappeared due to the weaning methods used.
Output: 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - method, 14 - method, 15 - method, 16 - method, 17 - method, 18 - method, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding, 25 - finding, 26 - finding
The aim in this study was to assess the effectiveness of a quaternary ammonium chloride (QAC) surfactant in reducing surface staphylococcal contamination in a routinely operating medical ward occupied by patients who had tested positive for methicillin-resistant Staphylococcus aureus (MRSA). The QAC being tested is an antibacterial film that is sprayed onto a surface and can remain active for up to 8 h. A field experimental study was designed with the QAC plus daily hypochlorite cleaning as the experimental group and hypochlorite cleaning alone as the control group. The method of swabbing on moistened surfaces was used for sampling. It was found that 83% and 77% of the bedside surfaces of MRSA-positive and MRSA-negative patients respectively were contaminated with staphylococci at 08:00 hours, and that the staphylococcal concentrations increased by 80% at 1200 h over a 4-hour period with routine ward and clinical activities. Irrespective of the MRSA status of the patients, high-touch surfaces around the bed-units within the studied medical ward were heavily contaminated (ranged 1 to 276 cfu/cm 2 amongst the sites with OPEN ACCESS Int. J. Environ. Res. Public Health 2015, 12 3027 positive culture) with staphylococcal bacteria including MRSA, despite the implementation of daily hypochlorite wiping. However, the contamination rate dropped significantly from 78% to 11% after the application of the QAC polymer. In the experimental group, the mean staphylococcal concentration of bedside surfaces was significantly (p < 0.0001) reduced from 4.4 ± 8.7 cfu/cm 2 at 08:00 hours to 0.07 ± 0.26 cfu/cm 2 at 12:00 hours by the QAC polymer. The results of this study support the view that, in addition to hypochlorite wiping, the tested QAC surfactant is a potential environmental decontamination strategy for preventing the transmission of clinically important pathogens in medical wards.
Output: 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - other, 10 - other, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding
The spike protein of Porcine epidemic diarrhea virus is the main surface glycoprotein involved in virus attachment and entry and therefore is the target of neutralizing antibodies. Here, the immunogenicity of a novel antigenic domain found on the carboxy-terminal of the spike protein characterized by the peptide motif GPRLQPY, was evaluated. A synthetic peptide whose linear sequence is identical to the 24 a.a. carboxy-terminal portion of the spike protein (S-CT24) elicited a strong antibody response in BALB/c mice that had specific reactivity against the S-CT24 and PEDV. These antibodies were shown to have a specific affinity to the GPRLQPY motif, as demonstrated by non-reactivity with a peptide that lacks this motif. In addition, antiS-CT24 antibodies exhibited neutralizing activities against KPEDV-9 in focus reduction neutralization tests suggesting that the GPRLQPY motif induces neutralizing antibodies against PEDV.
Output: 1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding
Host responses during lethal henipavirus infection in ferrets PLOS Neglected Tropical Diseases
Output: 1 - finding
The severe acute respiratory syndrome (SARS) has been one of the most epidemic diseases threatening human health all over the world. Based on clinical studies, SARS-CoV (the SARS-associated coronavirus), a novel coronavirus, is reported as the pathogen responsible for the disease. To date, no e¡ective and speci¢c therapeutic method can be used to treat patients su¡ering from SARS-CoV infection. RNA interference (RNAi) is a process by which the introduced small interfering RNA (siRNA) could cause the degradation of mRNA with identical sequence speci¢city. The RNAi methodology has been used as a tool to silence genes in cultured cells and in animals. Recently, this technique was employed in anti-virus infections in human immunode¢ciency virus and hepatitis C/B virus. In this study, RNAi technology has been applied to explore the possibility for prevention of SARS-CoV infection. We constructed speci¢c siRNAs targeting the S gene in SARS-CoV. We demonstrated that the siRNAs could e¡ectively and speci¢cally inhibit gene expression of Spike protein in SARS-CoV-infected cells. Our study provided evidence that RNAi could be a tool for inhibition of SARS-CoV. ß 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - finding, 11 - finding, 12 - other
The full genome sequence of a Middle East respiratory syndrome coronavirus (MERS-CoV) was identified from cultured and isolated in Vero cells. The viral genome sequence has high similarity to 53 human MERS-CoVs, ranging from 99.5% to 99.8% at the nucleotide level.
Output: 1 - finding, 2 - finding, 3 - finding
PLOS Neglected Tropical Diseases, caused by the filarial parasitic nematode Onchocerca volvulus, remains a significant source of morbidity throughout sub-Saharan Africa and is a primary cause of infectious blindness. Research on this disease has been hindered by an absence of suitable small animal hosts. Here we describe the development of humanized mouse models that are susceptible to O. volvulus infection supporting both growth and maturation of the parasite. These novel mouse models have enabled the identification of a number of new O. volvulus biomarkers with potential to play a role in the development of specific and sensitive diagnostic tests for presence of viable parasites. Development of Onchocerca volvulus in NSG mice PLOS Neglected Tropical Diseases
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding
Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.
Output: 1 - background, 2 - background, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
The current re-emergence of human monkeypox (HMPX) is a global concern for endemic and non-endemic countries, but healthcare workers in some regions, like Asia, have less experience with identifying and treating HMPX cases. This study aimed to assess the confidence and its predictors in HMPX case management among general practitioners (GPs), the frontline doctors in Indonesia, and to explore their perspectives on HMPX. Between May and July 2019, GPs in Indonesia completed an online-based survey. The questionnaire collected information on GPs' confidence, perspective, sociodemographic, workplace and professional characteristics, exposure to HMPX information and knowledge on HMPX. A logistic regression analysis was employed to explore the explanatory variables influencing the confidence and the perspective. We included 395 GPs in our analysis (77.4% out of 510 responses received) of which 10.1% and 34.9% were classified having good confidence using an 80% and 70% cut-off for confidence score, respectively. In the adjusted analysis, receiving information about HMPX during medical training was the only variable significantly associated with good confidence (adjusted odds ratio 2.74, 95% confidence interval 1.57 to 4.78 and p < 0.001). Approximately 73.6% and 77.
Output: 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - purpose, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding
Rhinovirus was the most prevalent virus and the only virus with a significantly different infection rate in CRS patients and controls in both samples (odds ratio, 3.2 in lavage and 3.4 in scraping samples). This study detected a higher prevalence of respiratory viruses in CRS patients than controls, suggesting that there may be significant associations between inflammation of CRS and respiratory viruses, particularly rhinovirus. Further studies should investigate the exact role of highly prevalent respiratory viruses in CRS patients during symptomatic aggravation and ongoing mucosal inflammation.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding
A 31 year old male with a history of diabetes mellitus type 1 and recent skin infection of the neck (for which he underwent incision and drainage and levofloxacin treatment) presented to the emergency department with a three day history of fever, cough productive of bloody sputum, and shortness of breath. He had recently returned from a trip to Asia. He was tachycardic but normotensive and had an oxygen saturation of 93 % on 3 L nasal cannula. WBC count was 21.8 K/UL with 90 % neutrophils, BUN and creatinine were 8 mg/dL and 1.0 mg/dL, respectively, and glucose >350 mg/dL. Suspicion of cavitary pneumonia on chest radiograph was confirmed by computed tomography (Fig. 20.1 ).
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - finding
Objective: In cases of community acquired pneumonia (CAP), it has been known that blood cultures have low yields and rarely affect clinical outcomes. Despite many studies predicting the likelihood of bacteremia in CAP patients, those results have been rarely implemented in clinical practice, and use of blood culture in CAP is still increasing. This study evaluated impact of implementing a previously derived and validated bacteremia prediction rule. Methods: In this registry-based before and after study, we used piecewise regression analysis to compare the blood culture rate before and after implementation of the prediction rule. We also compared 30-day mortality, emergency department (ED) length of stay, time-interval to initial antibiotics after ED arrival, and any changes to the antibiotics regimen as results of the blood cultures. In subgroup analysis, we compared two groups (with or without the use of the prediction rule) after implementation period, using propensity score matching. Results: Following the implementation, the blood culture rate declined from 85.5% to 78.1% (P = 0.003) without significant changes in 30-day mortality and antibiotics regimen. The interval to initial antibiotics (231 min vs. 221 min, P = 0.362) and length of stay (1019 min vs. 954 min, P = 0.354) were not significantly changed. In subgroup analysis, the group that use the prediction rule showed 25 min faster antibiotics initiation (P = 0.002) and 48 min shorter length of stay (P = 0.007) than the group that did not use the rule. Conclusion: Implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30-day mortality and antibiotics regimen.
Output: 1 - purpose, 2 - purpose, 3 - purpose, 4 - purpose, 5 - purpose, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - method, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding
Objective: Tumor-treating fields are currently used to successfully treat various cancers; however, the specific pathways associated with its efficacy remain unknown in the immune responses. Here, we evaluated tumor-treating fields-mediated initiation of the macrophage-specific immune response. Materials and Methods: We subjected RAW 264.7 mouse macrophages to clinically relevant levels of tumor-treating fields (0.9 V/cm, 150 kHz) and evaluated alterations in cytokine expression and release, as well as cell viability. Additionally, we investigated the status of immunomodulatory pathways to determine their roles in tumor-treating fields-mediated immune activation. Results and Discussion: Our results indicated that tumor-treating fields treatment at 0.9 V/cm decreased cell viability and increased cytokine messenger RNA/protein levels, as well as levels of nitric oxide and reactive oxygen species, relative to controls. The levels of tumor necrosis factor a, interleukin 1b, and interleukin 6 were markedly increased in tumor-treating fields-treated RAW 264.7 cells cocultured with 4T1 murine mammary carcinoma cells compared with those in 4T1 or RAW 264.7 cells with or without tumor-treating fields treatment. Moreover, the viability of 4T1 cells treated with the conditioned medium of tumor-treating fields-stimulated RAW 264.7 cells decreased, indicating that macrophage activation by tumor-treating fields effectively killed the tumor cells. Moreover, tumor-treating fields treatment activated the nuclear factor kB and mitogen-activated protein kinase pathways involved in immunomodulatory signaling. Conclusion: These results provide critical insights into the mechanisms through which tumor-treating fields affect macrophagespecific immune responses and the efficacy of this method for cancer treatment.
Output: 1 - background, 2 - background, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding
She was treated successfully with a corticosteroid and anti-mycobacterial therapy. Our observations suggest that pulmonary M. abscessus infection should be added to the list of infectious conditions associated with OP.
Output: 1 - finding, 2 - finding
Multiple sclerosis (MS) is the prototypic inflammatory disease of the central nervous system (CNS) characterized by multifocal areas of demyelination, axonal damage, activation of glial cells, and immune cell infiltration. Despite intensive years of research, the etiology of this neurological disorder remains elusive. Nevertheless, the abundance of immune cells such as T lymphocytes and their products in CNS lesions of MS patients supports the notion that MS is an immune-mediated disorder. An important body of evidence gathered from MS animal models such as experimental autoimmune encephalomyelitis (EAE), points to the central contribution of CD4 T lymphocytes in disease pathogenesis. Both Th1 (producing interferon-γ) and Th17 (producing interleukin 17) CD4 T lymphocytes targeting CNS self-antigens have been implicated in MS and EAE pathobiology. Moreover, several publications suggest that CD8 T lymphocytes also participate in the development of MS lesions. The migration of activated T lymphocytes from the periphery into the CNS has been identified as a crucial step in the formation of MS lesions. Several factors promote such T cell extravasation including: molecules (e.g., cell adhesion molecules) implicated in the T cell-blood brain barrier interaction, and chemokines produced by neural cells. Finally, once in the CNS, T lymphocytes need to be reactivated by local antigen presenting cells prior to enter the parenchyma where they can initiate damage. Further investigations will be necessary to elucidate the impact of environmental factors (e.g., gut microbiota) and CNS intrinsic properties (e.g., microglial activation) on this inflammatory neurological disease.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - background, 12 - background, 13 - background, 14 - background, 15 - finding
HealthMap is a useful free and open resource employing text-processing algorithms to identify important disease outbreak information through a user-friendly interface. Ⅲ J Am Med Inform Assoc. 2008;15:150 -157.
Output: 1 - background, 2 - other
0 1992 Academic PVE.S. Inc.
Output: 1 - other, 2 - other
Results: We found that while the early events in HCV infection (i.e. entry plus replication initiation) are cumulatively equivalent or only marginally reduced in PLC and Hep3B cells, later steps of the viral life cycle such as steady-state replication, de novo virus production and/or spread are impaired to different degrees in PLC and Hep3B cultures compared to Huh7 cell cultures. Interestingly, we also observed that interferon stimulated gene (i.e. ISG56) expression was significantly and differentially up-regulated in PLC and Hep3B cells following viral infection. Conclusions: We conclude that the restrictions observed later during HCV infection in these cell lines could in part be attributed to HCV-induced innate signaling. Nevertheless, the identification of two new cell lines capable of supporting authentic HCVcc infection, even at reduced levels, expands the current repertoire of cell lines amendable for the study of HCV in vitro and should aid in further elucidating HCV biology and the cellular determinants that modulate HCV infection.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding
: Viral diseases are one of the leading causes of morbidity and mortality in the world. Virus-specific vaccines and antiviral drugs are the most powerful tools to combat viral diseases. However, broad-spectrum antiviral agents (BSAAs, i.e. compounds targeting viruses belonging to two or more viral families) could provide additional protection of general population from emerging and reemerging viral diseases reinforcing the arsenal of available antiviral options. Here, we reviewed discovery and development of BSAAs and summarized the information on 119 safe-in-man agents in freely accessible database. Future and ongoing pre-clinical and clinical studies will increase the number of BSAAs, expand spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections as well as co-infections.
Output: 1 - background, 2 - background, 3 - background, 4 - method, 5 - finding, 6 - finding, 7 - finding
Background: During the early phases of the 2009 pandemic, subjects with influenza-like illness only had laboratory testing specific for the new A(H1N1)pdm09 virus. Findings: Between 25 th May and 7 th June 2009, during the pandemic CONTAIN phase, A(H1N1)pdm09 virus was detected using nucleic acid tests in only 56 of 1466 (3.8%) samples meeting the clinical case definition required for A(H1N1)pdm09 testing. Two hundred and fifty-five randomly selected A(H1N1)pdm09 virus-negative samples were tested for other respiratory viruses using a real-time multiplex PCR assay. Of the 255 samples tested, 113 (44.3%) had other respiratory viruses detected: rhinoviruses 63.7%, seasonal influenza A 17.6%, respiratory syncytial virus 7.9%, human metapneumovirus 5.3%, parainfluenzaviruses 4.4%, influenza B virus 4.4%, and enteroviruses 0.8%. Viral co-infections were present in 4.3% of samples. Conclusions: In the very early stages of a new pandemic, limiting testing to only the novel virus will miss other clinically important co-circulating respiratory pathogens.
Output: 1 - background, 2 - background, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding
We evaluated if interventions aimed at air travellers can delay establishment of a SARS-CoV-2 outbreak in a previously unaffected country. Methods: For countries with no sustained SARS-CoV-2 transmission and with no shared border with affected regions we simulated arriving infected air travellers. We assessed the effectiveness of syndromic screening at departure and/or arrival & traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduce the average number of secondary cases. We report the minimal expected delay achievable in 50% (75% & 97.5%) of simulations. In the simulations we account for uncertainty in the number of secondary cases in the absence of air traveller targeted interventions and the arrival times of infected cases and also present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. Results: Under baseline assumptions exit and entry screening combined with traveller sensitisation can delay a local SARS-CoV-2 outbreak by at least 83 (75% of simulations: at least 36, 97.5% 8) days while there is no more than 1 infected traveller per week. The benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by at least 76 (75%: 33, 97.5%: 7) days. With increasing rates of infected travellers, less effective sensitisation or without screening these delays shrink rapidly to a week or less. Conclusion: Syndromic screening and traveller sensitisation in combination could delay outbreaks in yet unaffected countries and support local containment efforts, but only if infected traveller numbers are very low.
Output: 1 - background, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
Conclusions and Clinical Importance: Results suggested that nasopharyngeal carriage of M. bovis was detrimental to health and growth of dairy calves in small herds with a high incidence of BRD.
Output: 1 - finding
The porcine respiratory and reproductive syndrome virus (PRRSV) nucleocapsid (N) protein is a multiphosphorylated protein.It has been proved that the phosphorylation of N protein could regulate the growth ability of PRRSV in Marc-145 cells. However, further investigation is needed to determine whether phosphorylation of the N protein could affect PRRSV virulence in piglets. In this study, we confirmed that the mutations could impair PRRSV replication ability in porcine primary macrophages (PAMs) as they did in Marc-145 cells. The animal experiments suggested that the pathogenicity of the mutated virus (A105-120) was significantly reduced compared with parent strain (XH-GD). Our results suggested that the phosphorylation of the N protein contributes to virus replication and virulence. This study is the first to identify a specific modification involved in PRRSV pathogenicity. Mutation of PTMs sites is also a novel way to attenuate PRRSV virulence. The mutations could be a marker in a vaccine. In conclusion, our study will improve our understanding of the molecular mechanisms of PRRSV pathogenicity.
Output: 1 - background, 2 - background, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding
The results of this study support previous findings that points towards genus Enterococcus and species E. coli to be involved in the pathogenesis of NNPD. Moreover, the results indicate that NNPD is associated with a disturbed bacterial composition and larger variation between the diarrhoeic piglets.
Output: 1 - finding, 2 - finding
Citation Avirutnan P, et al. 2011. Complement-mediated neutralization of dengue virus requires mannose-binding lectin. mBio 2(6):e00276-11.
Output: 1 - other, 2 - finding, 3 - other
In this study, infrared thermography (IRT) was assessed as a means of detecting foot-and-mouth disease virus (FMDV)-infected cattle before and after the development of clinical signs. Preliminary IRT imaging demonstrated that foot temperatures increased in FMDVinfected animals. The maximum foot temperatures of healthy (n = 53), directly inoculated (DI) (n = 12), contact (CT) (n = 6), and vaccine trial (VT) (n = 21) cattle were measured over the course of FMD infection. A cut-off value was established at 34.4°C (sensitivity = 61.1%, specificity = 87.7%) with the aim of detecting FMDV-infected animals both before and after clinical signs were observed. Seven of 12 (58%) DI and 3/6 (50%) CT animals showed maximum foot temperatures exceeding the 34.4°C cut-off before the development of foot vesicles. In contrast, only 5/21 (24%) VT animals displayed pre-clinical foot temperatures above this cut-off possibly indicating partial vaccine protection of this group. These results show IRT as a promising screening technology to quickly identify potentially infected animals for confirmatory diagnostic testing during FMD outbreaks. Further evaluation of this technology is needed to determine the value of IRT in detecting animals with mild clinical signs or sub-clinical infections. Published by Elsevier Ltd.
Output: 1 - purpose, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - other
In the present work, a single-step purification of recombinant nucleocapsid protein (NP) of the Newcastle disease virus (NDV) directly from unclarified feedstock using an expanded bed adsorption chromatography (EBAC) was developed. Streamline 25 column (ID = 25 mm) was used as a contactor and Streamline chelating adsorbent immobilized with Ni 2+ ion was used as affinity adsorbent. The dynamic binding capacity of Ni 2+ -loaded Streamline chelating adsorbent for the NP protein in unclarified feedstock was found to be 2.94 mg ml À1 adsorbent at a superficial velocity of 200 cm h À1 . The direct purification of NP protein from unclarified feedstock using expanded bed adsorption has resulted in a 31% adsorption and 9.6% recovery of NP protein. The purity of the NP protein recovered was about 70% and the volume of processing fluid was reduced by a factor of 10. The results of the present study show that the IMA-EBAC developed could be used to combine the clarification, concentration and initial purification steps into a single-step operation.
Output: 1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding
The prevalence of antibodies to bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) infections was studied in 20 conventional and 20 organic dairy herds. The organic farms had produced 'certified' milk for at least 2 years. On two occasions, with a 1-year interval, 699 serum samples from 624 peri-parturient cows were tested by ELISA for antibodies to BCV and BRSV. Accompanying data relating to the sampled animals were collected in order to identify potential factors associated with increased antibody prevalence. The antibody prevalence was high at both sampling times with approximately 85% and 80% of animals positive for antibodies to BCV and to BRSV, respectively. Conventional herds had a significantly higher mean antibody prevalence to BCV and BRSV than the organically managed herds (P < 0.01). Animal age was significantly associated with increased antibody prevalence (P < 0.001). The findings of this study suggest that organic farm management may be effective in reducing the seroprevalence of these viruses relative to conventional farming methods.
Output: 1 - background, 2 - background, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding
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: 1 - background, 2 - purpose, 3 - background, 4 - background, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding
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: 1 - background, 2 - background, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - other, 9 - finding, 10 - other, 11 - other, 12 - other, 13 - other
Trial registration: ClinicalTrials.gov NCT02644135 (retrospectively registered).
Output: 1 - other
To reduce computation time, scalar transport for airborne virus spread was simulated based on a database for the CFD computed airflow in the investigated area using representative wind conditions. The simulation results, and the weather data were then used to make a database for a web-based forecasting system that could be accessible to users. ScienceDirect jo urnal homepage: www .e lsev ie r.com/ locate/issn/153 75110 b i o s y s t e m s e n g i n e e r i n g 1 2 9 ( 2 0 1 5 ) 1 6 9 e1 8 4
Output: 1 - finding, 2 - finding, 3 - finding, 4 - other
Conclusions. Streptococcus pneumoniae, RSV, and rhinovirus may be the major microorganisms associated with pneumonia infections in children <5 years of age from developing and emerging countries. Increasing S. pneumoniae vaccination coverage may substantially reduce the burden of pneumonia among children in developing countries.
Output: 1 - finding, 2 - finding, 3 - finding
Detection and characterisation of the canine parvovirus (CPV-2) strains that are currently circulating are essential for the understanding of viral evolution and the development of measures to control its spread. In the present study, stool samples from 144 dogs were analysed by polymerase chain reaction (PCR) for CPV-2, and 29.2% (42/144) of them were positive. From the 42 positive strains, 71.4% (30) of the dogs had signs of haemorrhagic gastroenteritis. The sequencing of the 583 bp fragment of the VP2 gene from the positive strains identified 78.6% (33/42) of them as type 2c, 19% (8/42) as type 2b and 2.4% (1/42) as type 2a. A phylogenetic analysis of the variants circulating in the canine population of Brazil showed that they are very similar to those found in other countries and type 2c has become the predominant type circulating in Brazil.
Output: 1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding
The number in square brackets following a selected paper, e.g. [7], refers to its number in the annotated references of the corresponding review.
Output: 1 - method, 2 - method
Even after one hundred years, the Golgi apparatus remains a major challenge in the field of Cell Biology. This is particularly true in terms of transport and of protein sorting. For example, the question how cargo proteins are transported through this organelle is still a matter of debate. Emphasis has been put on the role of anterograde and retrograde transport vesicles. These have been proposed to carry cargo from cisterna to cisterna and to recycle components needed for further rounds of transport. Alternatively, anterograde movement of cargo takes place in cisternal membranes rather than transport vesicles. These membranes assemble and mature in a cis to trans direction. In this case, retrograde transport vesicles need to recycle all components of the Golgi apparatus and this demands a highly dynamic and efficient sorting machinery. Here we will discuss possible mechanisms for protein sorting in the context of cisternal maturation and propose that a common mechanism is sufficient to explain both transport of cargo and sorting of resident proteins. ß 1998 Elsevier Science B.V. All rights reserved.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - purpose, 11 - other
Porcine aminopeptidase N (pAPN) is a cellular membrane protein and a functional receptor for porcine coronaviruses. Here, we describe the heterologous expression of pAPN without signal peptide in BL21(DE3)pLysS host cells. The Escherichia coli (E. coli) harboring the recombinant construct was efficiently induced to express the pAPN protein at a high level. The most optimal expression profile for pAPN expression was investigated. By inoculating a rabbit with the purified pAPN, a high tittered specific antibody was achieved. Biologically, the antibody reacted with either pAPN-expressing E. coli or native pAPN on the surface of swine testis cells. The pAPN and its specific antibody blocked transmissible gastroenteritis coronavirus infection in vitro. Furthermore, the localization of pAPN on the small intestine of swine was analyzed by immunohistochemistry.
Output: 1 - background, 2 - purpose, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding
We have investigated the role of two polymorphic sites (R190W and N192K) on the binding and activation of the formyl peptide receptor (FPR) by viral and formyl peptides. WEDWVGWI, a peptide with antiviral activity derived from the membrane proximal region of feline immunodeficiency virus, binds with high affinity to FPR. The three tryptophans in the peptide are all essential for FPR binding, just as they were essential for antiviral activity (Giannecchini, S. et al., J. Virol. 77 (2003) 3724). Formyl-NleWEDWVGWI behaved as a weak partial agonist with FPR W190/N192 but a stronger partial agonist with FPR R190/K192 and FPR R190/N192. Formyl-NleNleWEDWVGWI behaved as a full agonist toward all three FPRs but exhibited a much higher EC 50 with W190/N192 FPR (300±45 nM) than for R190/K192 FPR (40±3 nM) or R190/N192 (60 ±8 nM). Formyl-MYKWPWYVWL preferentially activated R190/K192 and R190/N192 FPRs by >5 fold compared to W190/N192 FPR. Formyl-MFEDAVAWF, a peptide derived from a protein in Mycobacterium avium subsp. paratuberculosis and formyl-MFTFEPFPTN, a peptide derived from the N-terminus of chemotaxis inhibitory protein of Staphylococcus aureus with an added N-terminal methionine exhibited the greatest selectivity for R190/K192 and R190/N192 FPRs with ~10 fold lower EC 50S than that observed with FPR W190/N192. Thus, individuals with the W190 polymorphism may display a reduced ability to detect certain formyl peptides.
Output: 1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
A multiplex quantitative real-time polymerase chain reaction (mqPCR) assay was developed and validated for the detection and differentiation of porcine circovirus type 3 (PCV3) and type 2 (PCV2) strains. The assay coverage was 97.9% (184/188) for PCV3 and 99.1% (1889/1907) for PCV2 sequences that were available from the current GenBank database. The PCR amplification efficiencies were 98-99% for plasmids, and 92-96% for diagnostic samples, with correlation coefficients all greater than 0.99. The limit of detection (LOD) determined as plasmid copies per reaction was 17 for PCV3 and 14 for PCV2. The assay specifically detected the targeted viruses without cross reacting to each other or to other common porcine viruses. Among 336 swine clinical samples collected in 2018, 101 (30.1%) were PCV3 positive, 56 (16.7%) were PCV2 positive and 18 (5.4%) were co-positives. Sixty selected PCV3 positives were confirmed by Sanger sequencing, and 53 of the 56 PCV2 positive samples were tested positive by another validated PCR assay.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
Results: During OV, the number of patients simultaneously treated at the NIMCU increased from 18 to 22, resulting in a reduced bed-to-bed space. Nurse: patient ratio was 4:22 during OV compared to 3:18 during PRAE-OV. Cumulative incidence of MDRGN was 4.7% in OV and 2.4% POST-OV compared to 4.8% to PRAE-OV, respectively, without any significant variations. During OV and POST-OV, septic episodes due to MDRGN were not observed. In one case, potential nosocomial transmission of Enterobacter cloacae resistant to Piperacillin and 3rd/4th generation cephalosporins was observed. Conclusions: Prevention of nosocomial spread of MDRGN in an overcrowded NIMCU is based on staff's diligent training and adequate staffing. Concise microbiological surveillance should be guaranteed to escort through overcrowding periods. In our setting, impact of bed-to-bed distance on MDRGN transmission seemed to be less strong.
Output: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding
Pet owners frequently administer antimicrobials to their pets and therefore have an important role to play in promoting antimicrobial stewardship in veterinary medicine. However, best methods of educating pet owners about antimicrobial stewardship have yet to be defined. While visual materials such as brochures and posters are often used in health promotion campaigns, their effectiveness in veterinary medicine is unknown. The objective of this study was to determine whether pet owners noticed and retained the message of a poster with an antimicrobial stewardship message placed in veterinary clinic exam rooms. A total of 111 pet owners from five veterinary clinics (three general practices, two low-cost clinics) in the greater Philadelphia area participated in the study. Participants completed a survey asking whether they noticed the poster and if they could paraphrase its message. In a follow-up survey, an antibiotic knowledge score was calculated from answers to questions assessing their knowledge of the poster message. Baseline knowledge was assessed by asking participants to define antibiotic resistance. At the end of the study, veterinarians at participating clinics were interviewed about their experiences with the poster. Only 51 (46.4%) participants noticed the poster, and only 11 (9.9%) could partially or completely reproduce its message. No demographic or clinic-level factors were significantly associated with noticing the poster or recalling its message. Antibiotic knowledge scores were highly correlated (ρ = 0.87, p < 0.001) with baseline knowledge and not affected by viewing the poster (p = 0.955). Veterinarians expressed skepticism that the poster was effective in conveying a message of judicious antibiotic use to clients and noted no difference in the frequency with which they discussed antibiotic resistance or felt pressured to prescribe antibiotics by their clients. Posters alone will likely have limited impact in conveying a message of judicious antibiotic use to pet owners. However, they might be useful as part of an active, multi-modal education strategy, especially if complemented by veterinarian actions.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding