niryuu/sni-each-converted huggingface dataset:
Twenty-seven field samples that showed positive in PEDV detection were collected from different farms of Fujian province from 2010 to 2012. Their heterogeneity was investigated by analysis of the ORF3 gene because of its potential function as a representation of virulence. According to the results, six Fujian strains in Group 1 showed a different genotype with unique point mutations, which might be used in differentiation between PEDV groups and brought potential antigenic variation. P55 and five reference strains in Group 2 had a long length deletion, showing another genotype and might be involved in the variation of virulence. Phylogenetic analysis revealed that the collected Fujian strains were very distant from the vaccine development strain CV777, which might be the reason why the vaccine was inefficient to control the disease. The results can help to reconsider the strategy of PEDV vaccine management and prevent outbreaks of PEDV-induced diarrhea more efficiently.
Output: Sequence Heterogeneity of the ORF3 Gene of Porcine Epidemic Diarrhea Viruses Field Samples in Fujian
Enterovirus (EV) 71 infection is known to cause hand-foot-and-mouth disease (HFMD) and in severe cases, induces neurological disorders culminating in fatality. An outbreak of EV71 in South East Asia in 1997 affected over 120,000 people and caused neurological disorders in a few individuals. The control of EV71 infection through public health interventions remains minimal and treatments are only symptomatic. Recently, human scavenger receptor class B, member 2 (SCARB2) has been reported to be a cellular receptor of EV71. We expressed human SCARB2 gene in NIH3T3 cells (3T3-SCARB2) to study the mechanisms of EV71 entry and infection. We demonstrated that human SCARB2 serves as a cellular receptor for EV71 entry. Disruption of expression of SCARB2 using siRNAs can interfere EV71 infection and subsequent inhibit the expression of viral capsid proteins in RD and 3T3-SCARB2 but not Vero cells. SiRNAs specific to clathrin or dynamin or chemical inhibitor of clathrin-mediated endocytosis were all capable of interfering with the entry of EV71 into 3T3-SCARB2 cells. On the other hand, caveolin specific siRNA or inhibitors of caveolae-mediated endocytosis had no effect, confirming that only clathrin-mediated pathway was involved in EV71 infection. Endocytosis of EV71 was also found to be pHdependent requiring endosomal acidification and also required intact membrane cholesterol. In summary, the mechanism of EV71 entry through SCARB2 as the receptor for attachment, and its cellular entry is through a clathrin-mediated and pHdependent endocytic pathway. This study on the receptor and endocytic mechanisms of EV71 infection is useful for the development of effective medications and prophylactic treatment against the enterovirus.
Output: Human SCARB2-Mediated Entry and Endocytosis of EV71
Host protection against several intracellular pathogens requires the induction of CD8 + T cell responses. CD8 + T cells are potent effector cells that can produce high amounts of pro-inflammatory cytokines and kill infected target cells efficiently. However, a protective role for CD8 + T cells during Leishmania infections is still controversial and largely depends on the infection model. In this review, we discuss the role of CD8 + T cells during various types of Leishmania infections, following vaccination, and as potential immunotherapeutic targets.
Output: CD8 + T cells in Leishmania infections: friends or foes?
An actual indoor contact network can be affected by many factors such as the age, gender, occupation, personal habits, social status, geographical location, while many of these factors may correlate with each other. Hence, it is impossible to mathematically describe, accurately and completely, a real social contact network. To create a representative synthetic contact network and to simulate a possible infectious disease outbreak based on the network, we adopt a few simplifications. We separated population and indoor environments into representative groups and assumed that individuals in the same group share similar location visiting behaviors, and all of the indoor environments in the same group share similar characteristics such as the number of occupants, occupant density, and ventilation rate. Internal variations within each group can be simulated by assuming the possible distributions for different parameters. Visiting time The complex patterns of individuals arriving at and leaving a location are not considered. We simplified the scenario by dividing each indoor environment into different sub-visiting locations that represent different time durations for visiting each indoor environment. Thus, several locations may represent the same indoor environment at a different time. Therefore this approach differentiates individuals who visit the same indoor environment at different times. We also assumed that individuals who choose to visit a location (an indoor environment for a fixed duration) come at the same time and leave at the same time. Hence, the visiting time of all possible visitors to a given location is the same. We assumed that all of the individuals in a population group have the same location visiting schedule on weekdays. During a normal weekday, an individual may visit several locations in different location groups with a fixed order. To simulate the variations in an individual's daily choices, we assumed that for each step of an individual's schedule, he or she has a collection of favorite locations. Random contact is not considered in this model.
Output: Supplementary Information for Building ventilation as an effective disease intervention strategy in a dense indoor contact network in an ideal city
Background Previous studies on the pneumonia outbreak caused by the 2019 novel coronavirus disease (COVID-19) were based on information from the general population. Evidence of intrauterine vertical transmission was assessed by testing for the presence of SARS-CoV-2 in amniotic fluid, cord blood, and neonatal throat swab samples. Breastmilk samples were also collected and tested from patients after the first lactation. , sore throat (in two), and malaise (in two), were also observed. Fetal distress was monitored in two cases. Five of nine patients had lymphopenia (<1·0 × 10⁹ cells per L). Three patients had increased aminotransferase concentrations. None of the patients developed severe COVID-19 pneumonia or died, as of Feb 4, 2020. Nine livebirths were recorded. No neonatal asphyxia was observed in newborn babies. All nine livebirths had a 1-min Apgar score of 8-9 and a 5-min Apgar score of 9-10. Amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples from six patients were tested for SARS-CoV-2, and all samples tested negative for the virus. Interpretation The clinical characteristics of COVID-19 pneumonia in pregnant women were similar to those reported for non-pregnant adult patients who developed COVID-19 pneumonia. Findings from this small group of cases suggest that there is currently no evidence for intrauterine infection caused by vertical transmission in women who develop COVID-19 pneumonia in late pregnancy.
Output: Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records
Background: Infection control practice compliance is commonly monitored by measuring hand hygiene compliance. The limitations of this approach were recognized in 1 acute health care organization that led to the development of an Infection Control Continuous Quality Improvement tool. Methods: The Pronovost cycle, Barriers and Mitigation tool, and Hexagon framework were used to review the existing monitoring system and develop a quality improvement data collection tool that considered the context of care delivery. Results: Barriers and opportunities for improvement including ambiguity, consistency and feasibility of expectations, the environment, knowledge, and education were combined in a monitoring tool that was piloted and modified in response to feedback. Local adaptations enabled staff to prioritize and monitor issues important in their own workplace. The tool replaced the previous system and was positively evaluated by auditors. Challenges included ensuring staff had time to train in use of the tool, time to collect the audit, and the reporting of low scores that conflicted with a target-based performance system. Conclusions: Hand hygiene compliance monitoring alone misses other important aspects of infection control compliance. A continuous quality improvement tool was developed reflecting specific organizational needs that could be transferred or adapted to other organizations.
Output: Moving beyond hand hygiene monitoring as a marker of infection prevention performance: Development of a tailored infection control continuous quality improvement tool
This study examined whether an infection with porcine reproductive and respiratory syndrome virus (PRRSV) potentiates respiratory signs upon exposure to bacterial lipopolysaccharides (LPS). Five-week-old conventional pigs were inoculated intratracheally with the Lelystad strain of PRRSV and received 5 days later one or two intratracheal LPS administrations. The necessary controls were included. After LPS administration, pigs were intensively monitored for clinical signs. Additionally, some pigs were euthanatized after a second LPS administration for bronchoalveolar cell analysis and virological examinations of the lungs. Broncho-alveolar lavage (BAL) cells were counted and differentiated. Lung suspensions and BAL fluids were titrated for PRRSV. Exposure of pigs to PRRSV only resulted in a fever for time periods ranging from 1 to 5 days and slight respiratory signs. Exposure of pigs to LPS only resulted in general signs, characterized by fever and depression, but respiratory signs were slight or absent. PRRSV-LPS exposed pigs, on the other hand, developed severe respiratory signs upon LPS exposure, characterized by tachypnoea, abdominal breathing and dyspnoea. Besides respiratory signs, these pigs also showed enhanced general signs, such as fever and depression. Lung neutrophil infiltration was similar in non-infected and PRRSV-infected pigs upon LPS exposure. PRRSV quantities were similar in lungs and BAL fluids of pigs infected with PRRSV only and PRRSV-LPS exposed pigs. These data show a clear synergism between PRRSV and LPS in the induction of respiratory signs in conventional pigs. The Veterinary Microbiology 88 (2002) 1-12 : S 0 3 7 8 -1 1 3 5 ( 0 2 ) 0 0 1 0 4 -9 synergism was observed in 87% of the pigs. So, it can be considered as reproducible and may be used to test the efficacy of preventive and therapeutic measures. #
Output: Porcine reproductive-respiratory syndrome virus infection predisposes pigs for respiratory signs upon exposure to bacterial lipopolysaccharide
Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health. 2 of 26 meningoencephalitis virus (ITV), a pathogen affecting poultry (turkeys) and close to West Nile virus (WNV) in several genomic regions [3, 11] . Although diverse studies have contributed greatly to our understanding of the transmission modes of BAGV [8, 12] and the pathogenesis of BAGV infection [13] , only one study has addressed BAGV genetic diversity, reporting a high homology >90% between Central African Republic, Indian and Spanish BAGV isolates [9] . In West Africa, there is a lack of data on BAGV genetic diversity. To fill this gap and gain better insights into BAGV molecular evolution, we characterized the full-genome of 11 BAGV isolates, sampled from 1988 to 2014 in Senegal and Côte d'Ivoire. Firstly, we assessed genetic distances, phylogenetically informative sites found in more than one sequence contributing to branch ordering, N-glycosylation patterns, recombination events, selective pressures on West African BAGV sequences and their evolutionary phylogenetic relationships with previously available BAGV genomes. Secondly, to assess evidence of future BAGV codon adaptation to human house-keeping genes, a bio-informatics approach was used for analysis of codon adaptation biases.
Output: Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus
Mixed viral and bacterial infections are widely described in community-acquired pneumonia; however, the clinical implications of co-infection on the associated immunopathology remain poorly studied. In this study, microRNA, mRNA and cytokine/chemokine secretion profiling were investigated for human monocyte-derived macrophages infected in-vitro with Influenza virus A/H1N1 and/or Streptococcus pneumoniae. We observed that the in-vitro co-infection synergistically increased interferon-γinduced protein-10 (CXCL10, IP-10) expression compared to the singly-infected cells conditions. We demonstrated that endogenous miRNA-200a-3p, whose expression was synergistically induced following co-infection, indirectly regulates CXCL10 expression by targeting suppressor of cytokine signaling-6 (SOCS-6), a well-known regulator of the JAK-STAT signaling pathway. Additionally, in a subsequent clinical pilot study, immunomodulators levels were evaluated in samples from 74 children (≤5 years-old) hospitalized with viral and/or bacterial community-acquired pneumonia. Clinically, among the 74 cases of pneumonia, patients with identified mixed-detection had significantly higher (3.6-fold) serum IP-10 levels than those with a single detection (P = 0.03), and were significantly associated with severe pneumonia (P < 0.01). This study demonstrates that viral and bacterial coinfection modulates the JAK-STAT signaling pathway and leads to exacerbated IP-10 expression, which could play a major role in the pathogenesis of pneumonia. Community-acquired pneumonia (CAP) is a common inflammatory illness of the lungs that remains the major cause of pediatric mortality in low-and middle-income countries 1 . Streptococcus pneumoniae (SP) is the main causative agent of pneumonia; however, concomitant viral infection occurs in up to 66% of cases of CAP 2,3 . Clinical data suggest mixed infections are related to a higher severity of inflammatory disease 4,5 -especially in secondary pneumococcal infection following influenza virus (IAV) infection 6-8 -and mixed infection represents a relevant risk factor for pediatric intensive care hospitalization 9 . However, the mechanisms underlying the pathogenesis of mixed viral and bacterial infection remain poorly understood. Assessment of induced blood immunomodulators during infection may assist clinical diagnosis and the management of severe CAP. Interferon (IFN)-γ -induced protein 10 (IP-10/CXCL10) appears to contribute to the
Output: Viral and bacterial co-infection in severe pneumonia triggers innate immune responses and specifically enhances IP-10: a translational study OPEN
A few decades have passed since intensive care unit (ICU) beds have been available for critically ill patients with cancer. Although the initial reports showed dismal prognosis, recent data suggest that an increased number of patients with solid and hematological malignancies benefit from intensive care support, with dramatically decreased mortality rates. Advances in the management of the underlying malignancies and support of organ dysfunctions have led to survival gains in patients with life-threatening complications from the malignancy itself, as well as infectious and toxic adverse effects related to the oncological treatments. In this review, we will appraise the prognostic factors and discuss the overall perspective related to the management of critically ill patients with cancer. The prognostic significance of certain factors has changed over time. For example, neutropenia or autologous bone marrow transplantation (BMT) have less adverse prognostic implications than two decades ago. Similarly, because hematologists and oncologists select patients for ICU admission based on the characteristics of the malignancy, the underlying malignancy rarely influences short-term survival after ICU admission. Since the recent data do not clearly support the benefit of ICU support to unselected critically ill allogeneic BMT recipients, more outcome research is needed in this subgroup. Because of the overall increased survival that has been reported in critically ill patients with cancer, we outline an easy-to-use and evidence-based ICU admission triage criteria that may help avoid depriving life support to patients with cancer who can benefit. Lastly, we propose a research agenda to address unanswered questions.
Output: Intensive care of the cancer patient: recent achievements and remaining challenges
Viruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect virulencerelated genes in novel agents, as we show here for the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020.
Output: Interpretable detection of novel human viruses from genome sequencing data
Most models of the COVID-19 pandemic in the United States do not consider geographic variation, and their relevance to public policies is not straightforward. We developed a mathematical model that characterizes infections by state and incorporates inflows and outflows of interstate travelers. Modeling reveals that curbing interstate travel when the disease is already widespread will make little difference. Meanwhile, increased testing capacity (facilitating early identification of infected people and quick isolation) and strict social-distancing and self-quarantine rules are effective in abating the outbreak. The modeling has also produced state-specific information. For example, for New York and Michigan, isolation of persons exposed to the virus needs to be imposed within 2 days to prevent a broad outbreak, whereas for other states this period can be 3.6 days. This model could be used to determine resources needed before safely lifting state policies on social distancing.
Output: Mitigating COVID-19 outbreak via high testing capacity and strong transmission-intervention in the United States
Background: Bovine respiratory disease (BRD) is 1 of the 2 most important causes of morbidity and mortality in dairy calves. Surprisingly, field data are scant concerning the prevalence of respiratory pathogens involved in BRD in preweaned dairy calves, especially in small herds. Objectives: To identify the main respiratory pathogens isolated from calves in Qu ebec dairy herds with a high incidence of BRD, and to determine if there is an association between the presence of these pathogens and clinical signs of pneumonia, lung consolidation, or average daily gain. Animals: Cross-sectional study using a convenience sample of 95 preweaned dairy calves from 11 dairy herds. Methods: At enrollment, calves were weighed, clinically examined, swabbed (nasal and nasopharyngeal), and lung ultrasonography was performed. One month later, all calves were reweighed. Results: Twenty-two calves had clinical BRD and 49 had ultrasonographic evidence of lung consolidation. Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni were isolated in 54, 17, and 12 calves, respectively. Mycoplasma bovis was identified by PCR testing or culture in 19 calves, and 78 calves were found to be positive for Mycoplasma spp. Bovine coronavirus was detected in 38 calves and bovine respiratory syncytial virus in 1. Only the presence of M. bovis was associated with higher odds of clinical signs, lung consolidation, and lower average daily gain. 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: Respiratory Pathogens in Qu ebec Dairy Calves and Their Relationship with Clinical Status, Lung Consolidation, and Average Daily Gain
Gold nanoparticles (GNPs) have been widely utilized to develop various biosensors for molecular diagnosis, as they can be easily functionalized and exhibit unique optical properties explained by plasmonic effects. These unique optical properties of GNPs allow the expression of an intense color under light that can be tuned by altering their size, shape, composition, and coupling with other plasmonic nanoparticles. Additionally, they can also enhance other optical signals, such as fluorescence and Raman scattering, making them suitable for biosensor development. In this review, we provide a detailed discussion of the currently developed biosensors based on the aforementioned unique optical features of GNPs. Mainly, we focus on four different plasmonic biosensing methods, including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), fluorescence enhancement, and quenching caused by plasmon and colorimetry changes based on the coupling of GNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of novel GNP-based biosensors in the future.
Output: Molecular Sciences Application of Gold Nanoparticle to Plasmonic Biosensors
This paper discusses the history of emerging infectious diseases, risk communication and perception, and the Supercourse lectures as means to strengthen the concepts and definition of risk management and global governance of zoonosis. The paper begins by outlining some of the key themes and issues in infectious diseases, highlighting the way which historical analysis challenges ideas of the 'newness' of some of these developments. It then discusses the role of risk communication to public accountability. The bulk of the paper presents an overview of developments of the Internet-based learning system through the Supercourse lectures that may prove to be a strong arm for the promotion of the latest medical information particularly to developing countries.
Output: Special Issue Advocacy, Promotion and e-Learning: Supercourse for Zoonosis
Attenuated Salmonella have been used as vectors to deliver foreign antigens as live vaccines. We have previously developed an efficient surface-display system by genetically engineering 987P fimbriae to present transmissible gastroenteritis virus (TGEV) C and A epitopes for the induction of anti-TGEV antibodies with a Salmonella vaccine vector. Here, this system was compared with an autotransporter protein surface display system. The TGEV C and A epitopes were fused to the passenger domain of the MisL autotransporter of Salmonella. Expression of both the MisL-and 987P subunit FasA-fusions to the TGEV epitopes were under the control of in vivo-induced promoters. Expression of the TGEV epitopes from the Salmonella typhimurium CS4552 (crp cya asd pgtE) vaccine strain was greater when the epitopes were fused to MisL than when they were fused to the 987P FasA subunit. However, when BALB/c mice were orally immunized with the Salmonella vector expressing the TGEV epitopes from either one of the fusion constructs or both together, the highest level of anti-TGEV antibody was obtained with the 987P-TGEV immunogen-displaying vector. This result suggested that better immune responses towards specific epitopes could be obtained by using a polymeric display system such as fimbriae.
Output: Comparison of a fimbrial versus an autotransporter display system for viral epitopes on an attenuated Salmonella vaccine vector
This paper combines two advances to detect MERS-CoV, the causative agent of Middle East Respiratory Syndrome, that have emerged over the past few years from the new field of "synthetic biology". Both are based on an older concept, where molecular beacons are used as the downstream detection of viral RNA in biological mixtures followed by reverse transcription PCR amplification. The first advance exploits the artificially expanded genetic information systems (AEGIS). AEGIS adds nucleotides to the four found in standard DNA and RNA (xNA); AEGIS nucleotides pair orthogonally to the A:T and G:C pairs. Placing AEGIS components in the stems of molecular beacons is shown to lower noise by preventing unwanted stem invasion by adventitious natural xNA. This should improve the signal-to-noise ratio of molecular beacons operating in complex biological mixtures. The second advance introduces a nicking enzyme that allows a single target molecule to activate more than one beacon, allowing "signal amplification". Combining these technologies in primers with components of a self-avoiding molecular recognition system (SAMRS), we detect 50 copies of MERS-CoV RNA in a multiplexed respiratory virus panel by generating fluorescence signal visible to human eye and/or camera.
Output: Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus
Background: COVID-19 is an emerging disease caused by the SARS-CoV-2 virus; no specific medication has been identified to date. We aimed to investigate the administered medications and intervention times for patients who completely recovered from COVID-19. Methods: This single-center, retrospective, and observational study included 55 patients with COVID-19 who were transferred to Shenyang Sixth People's Hospital between January 20 and March 15, 2020. Demographic information, symptoms, laboratory indicators, treatment processes, and clinical outcomes were collected. Administered drugs and intervention times were compared in 47 and eight patients with mild and severe symptoms, respectively. Findings: All 55 patients recovered. Fifty-three patients (96·36%) received antiviral therapy, including 45 in the mild group (median treatment: 14 days; 17 received umifenovir) and all eight severe-group patients (median treatment: 17·5 days; four received lopinavir/ritonavir). Twenty-nine patients (52·72%) were administered antibiotics, including 21 in the mild group (median treatment: 13·5 days; 15 received moxifloxacin) and all eight in the severe group (median treatment: 9 days; two received linezolid). Moreover, seven patients (12·72%) were treated with glucocorticoids and nine (16·36%) with immunomodulators.
Output: Article Medical treatment of 55 patients with COVID-19 from seven cities in northeast China who fully recovered: a single-center, retrospective, observational study
Background: The Ebola epidemic in West Africa caused global fear and stirred up worldwide preparedness activities in countries sharing borders with those affected, and in geographically far-away countries such as Iceland. Objective: To describe and analyse Ebola preparedness activities within the Icelandic healthcare system, and to explore the perspectives and experiences of managers and frontline health workers. Methods: A qualitative case study, based on semi-structured interviews with 21 staff members in the national Ebola Treatment Team, Emergency Room at Landspitali University Hospital, and managers of the response team. Results: Contextual factors such as culture and demography influenced preparedness, and contributed to the positive state of mind of participants, and ingenuity in using available resources for preparedness. While participants believed they were ready to take on the task of Ebola, they also had doubts about the chances of Ebola ever reaching Iceland. Yet, factors such as fear of Ebola and the perceived stigma associated with caring for a potentially infected Ebola patient, influenced the preparation process and resulted in plans for specific precautions by staff to secure the safety of their families. There were also concerns about the teamwork and lack of commitment by some during training. Being a 'tiny' nation was seen as both an asset and a weakness in the preparation process. Honest information sharing and scenario-based training contributed to increased confidence amongst participants in the response plans. Conclusions: Communication and training were important for preparedness of health staff in Iceland, in order to receive, admit, and treat a patient suspected of having Ebola, while doubts prevailed on staff capacity to properly do so. For optimal preparedness, likely scenarios for future global security health threats need to be repeatedly enacted, and areas plagued by poverty and fragile healthcare systems require global support. ARTICLE HISTORY
Output: 'Tiny Iceland' preparing for Ebola in a globalized world
A simple apparatus was designed to effectively isolate magnetotactic bacteria from soils or sediments based on their magnetotaxis. Through a series of processes including sample incubation, MTB harvesting, isolation， purification and identification, several strains of bacteria were isolated from the samples successfully. By Transmission Electron Microscopy (TEM) and Energy-Dispersive X-ray Analysis (EDXA), these bacteria were certificated to be magnetotactic bacteria. The phylogenetic relationship between the isolated magnetic strains and some known magnetotactic bacteria was inferred by the construction of phylogenetic tree based on 16SrDNA sequences. This apparatus has been proven to have the advantages of being inexpensive, simple to assemble, easy to perform and highly efficient to isolate novel magnetotactic bacteria. The research indicated that the combined approach of harvesting MTB by home-made apparatus and the method of plate colony isolation could purify and isolate magnetotactic bacteria effectively.
Output: Design and application of the method for isolating magnetotactic bacteria
Background: Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. Results: We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. Conclusion: This is the first genomic characterization of HMPV genomes from African patients.
Output: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia
It is not clear whether turning on the gaspers in the cabins of commercial airliners actually improves the air quality. To answer this question, this study first developed a hybrid turbulence model which was suitable for predicting the air distribution in an aircraft cabin with gaspers turned on. Next, the investigation validated the model using two sets of experimental data from a cabin mockup and an actual airplane. This study then used the validated model to systematically investigate the impact of gaspers on cabin air quality in a seven-row section of the fully-occupied, economy-class cabin of Boeing 767 and 737 airplanes. The CFD calculations formed a database consisting of 9660 data points that provide information about SARS infection risk. It was found that the distribution of opened gaspers can influence the infection risk for passengers. Even though the gasper supplies clean air, it is possible for it to have a negative impact on the passengers' health. Statistically speaking, the overall effect of turning on the gaspers on the mean infection risk for the general population was neutral.
Output: Investigating the impact of gaspers on cabin air quality in commercial airliners with a hybrid turbulence model
This study aimed to examine the relationship between macroeconomic and nonmacroeconomic variables and hotel stock returns using hotel companies listed on the Taiwan Stock Exchange. The regression analysis indicated that among the macroeconomic variables (i.e., money supply, the growth rate of industrial production, expected inflation, the change of unemployment rate, and the yield spread), only money supply and the unemployment rate significantly explained the movement of hotel stock returns. On the other hand, all nonmacroeconomic forces selected (i.e., presidential elections, the 921 earthquake, the 2003 Iraqi war, the outbreak of SARS, sports mega-events, the Asian financial crisis, and the 911 terrorist attacks) had significant influences on the hotel stock returns. The empirical results of this study may be used as valuable information for local and global stock investors who seek an investment opportunity in the hospitality industry. r
Output: The impact of macroeconomic and non-macroeconomic forces on hotel stock returns
Background: Nonadditivity in fitness effects from two or more mutations, termed epistasis, can result in compensation of deleterious mutations or negation of beneficial mutations. Recent evidence shows the importance of epistasis in individual evolutionary pathways. However, an unresolved question in molecular evolution is how often and how significantly fitness effects change in alternative genetic backgrounds. Results: To answer this question, we quantified the effects of all single mutations and double mutations between all positions in the IgG-binding domain of protein G (GB1). By observing the first two steps of all possible evolutionary pathways using this fitness profile, we were able to characterize the extent and magnitude of pairwise epistasis throughout an entire protein molecule. Furthermore, we developed a novel approach to quantitatively determine the effects of single mutations on structural stability (DDG U ). This enabled determination of the importance of stability effects in functional epistasis. Conclusions: Our results illustrate common biophysical mechanisms for occurrences of positive and negative epistasis. Our results show pervasive positive epistasis within a conformationally dynamic network of residues. The stability analysis shows that significant negative epistasis, which is more common than positive epistasis, mostly occurs between combinations of destabilizing mutations. Furthermore, we show that although significant positive epistasis is rare, many deleterious mutations are beneficial in at least one alternative mutational background. The distribution of conditionally beneficial mutations throughout the domain demonstrates that the functional portion of sequence space can be significantly expanded by epistasis.
Output: Article A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
Backgrounds: In December 2019, a novel coronavirus (COVID-19) pneumonia hit Wuhan, Hubei Province, China and spread to the rest of China and overseas. The emergence of this virus coincided with the Spring Festival Travel Rush in China. It is possible to estimate total number of cases of COVID-19 in Wuhan, by 23 January 2020, given the cases reported in other cities and population flow data between cities. Methods: We built a model to estimate the total number of cases in Wuhan by 23 January 2020, based on the number of cases detected outside Wuhan city in China, with the assumption that if the same screening effort used in other cities applied in Wuhan. We employed population flow data from different sources between Wuhan and other cities/regions by 23 January 2020. The number of total cases was determined by the maximum log likelihood estimation. Findings: From overall cities/regions data, we predicted 1326 (95% CI: 1177, 1484), 1151 (95% CI: 1018, 1292) and 5277 (95% CI: 4732, 5859) as total cases in Wuhan by 23 January 2020, based on different source of data from Changjiang Daily newspaper, Tencent, and Baidu. From separate cities/regions data, we estimated 1059 (95% CI: 918, 1209), 5214 (95% CI: 4659, 5808) as total cases in Wuhan in Wuhan by 23 January 2020, based on different sources of population flow data from Tencent and Baidu. Conclusion: Sources of population follow data and methods impact the estimates of local cases in Wuhan before city lock down.
Output: Estimation of local novel coronavirus (COVID-19) cases in Wuhan, China from off-site reported cases and population flow data from different sources
The Iberian lynx is the most endangered felid species in the world, confined nowadays to two isolated metapopulations in the southwest of Spain, where less than 200 individuals survive. Little is known about the diseases that affect these animals in the wild or in captivity. Kidney samples from necropsies of 27 Iberian lynxes, wild and captive, were examined by histopathology, immunohistochemistry (IgG, IgM, IgA, laminin, type IV collagen, and fibronectin), electron microscopy (n = 8) and immunogold labelling for IgM, IgG and IgA in one case, in order to characterize the glomerulopathy prevalent in this species. Urinalyses from records were available for 9 of the necropsied animals and blood and urine samples from 23 free ranging and captive Iberian lynxes were prospectively obtained in order to evaluate the renal function of the living population. A focal, diffuse membranous glomerulonephritis (MGN) that progressed with age was diagnosed in all but one of the animals in different stages not associated to concurrently known infectious diseases. Positive immunoexpression of IgM and IgG was observed in the glomerular capillary basement membranes and intramembranous electron-dense deposits, compatible with immune complexes (ICs) were seen with electron microscopy. The immunogold labelling was also positive for IgM and IgG in the electron-dense areas. The serum biochemistry and urinalyses also revealed signs of mild chronic kidney disease in 16 of the 23 animals evaluated. In conclusion, the membranous glomerulopathy affecting the Iberian lynx is a progressive disease of immune origin. We postulate a possible genetic predisposition towards the disease, enhanced by inbreeding and a possible connection to an immune-mediated systemic disease. #
Output: Membranous glomerulonephritis in the Iberian lynx (Lynx pardinus)
A brief description of the importance of communicable diseases in history and the development of mathematical modelling of disease transmission is given. This includes reasons for mathematical modelling, the history of mathematical modelling from the foundations laid in the late nineteenth century to the present, some of the accomplishments of mathematical modelling, and some challenges for the future. Our purpose is to demonstrate the importance of mathematical modelling for the understanding and management of infectious disease transmission.
Output: BMC Public Health Mathematical epidemiology is not an oxymoron
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: The phosphorylation of the N protein could affect PRRSV virulence in vivo
Unlike local transmission of pandemic influenza A (H1N1-2009), which was frequently driven by school children, most cases identified in long-distance intranational and international travelers have been adults. The present study examines the relationship between the probability of temporary extinction and the age-dependent next-generation matrix, focusing on the impact of assortativity. Preferred mixing captures as a good approximation the assortativity of a heterogeneously mixing population. We show that the contribution of a nonmaintenance host (i.e., a host type which cannot sustain transmission on its own) to the risk of a major epidemic is greatly diminished as mixing patterns become more assortative, and in such a scenario, a higher proportion of non-maintenance hosts among index cases elevates the probability of extinction. Despite the presence of various other epidemiological factors that undoubtedly influenced the delay between first importations and the subsequent epidemic, these results suggest that the dominance of adults among imported cases represents one of the possible factors explaining the delays in geographic spread observed during the recent pandemic.
Output: Assortativity and the Probability of Epidemic Extinction: A Case Study of Pandemic Influenza A (H1N1-2009)
Human coronavirus NL63 (HCoV-NL63) is a global respiratory tract pathogen; however, the epidemiology of this virus in subtropical area is not well known. To evaluate the epidemics and disease spectrum of HCoV-NL63 infection in children in Taiwan, we prospectively screened children admitted to the hospital with respiratory tract infection from May 2004 to April 2005. Every enrolled child had a nasopharyngeal aspirate (NPA) sample taken. Quantitative RT-PCR was used to detect 1b gene of HCoV-NL63. A total of 539 NPAs were collected. Seven (1.3%) were positive for HCoV-NL63. All cases were boys younger than 3 years of age and most cases occurred in autumn. Co-infection with other pathogens was observed in three cases. The most common symptoms/signs of HCoV-NL63 infection were cough, fever, and inspiratory stridor. HCoV-NL63 was the most common pathogen (14.7%) in children with croup and was the cause of three cases of croup in October. The odds ratio of croup in children infected with HCoV-NL63 was 43.4 (95% CI 8.1∼233.1). In conclusion, HCoV-NL63 is an important respiratory tract pathogen as the main cause in children admitted to the hospital in Taiwan. Keywords Coronavirus infections . Respiratory tract infections . Croup . Taiwan seasons in temperate countries, and peaks in summer in Hong Kong [3] . This study is aimed to understand the seasonal distribution and clinical manifestations of HCoV-NL63 infection in children in Taiwan.
Output: Clinical manifestations of human coronavirus NL63 infection in children in Taiwan
Oral administration of specific antibodies is an attractive approach to establish protective immunity against gastrointestinal pathogens in humans and animals. The increasing number of antibiotic-resistant bacteria emphasize the need to find alternatives to antibiotics. Immunotherapy can also be used against pathogens that are difficult to treat with traditional antibiotics. Laying hens are very good producers of specific antibodies. After immunization, the specific antibodies are transported to the egg yolk from which the antibodies then can be purified. A laying hen produces more than 20 g of yolk antibodies (IgY) per year. These antibodies also have biochemical properties that make them attractive for peroral immunotherapy: They neither activate mammalian complement nor interact with mammalian Fc receptors that could mediate inflammatory response in the gastrointestinal tract. Eggs are also normal dietary components and thus there is practically no risk of toxic side effects of IgY. Yolk antibodies have been shown in several studies to prevent bacterial and viral infections.
Output: Peroral Immonutheraphy with Yolk Antibodies Peroral Immunotheraphy with Yolk Antibodies for the Prevention and Treatment of Enteric Infections
Since the first imported case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection was reported on May 20, 2015 in Korea, there have been 186 laboratoryconfirmed cases of MERS-CoV infection with 36 fatalities. Ninety-seven percent (181/186) of the cases had exposure to the health care facilities. We are reporting a superspreading event that transmitted MERS-CoV to 81 persons at a hospital emergency room (ER) during the Korean outbreak in 2015. The index case was a 35-yr-old man who had vigorous coughing while staying at the ER for 58 hr. As in severe acute respiratory syndrome outbreaks, superspreading events can cause a large outbreak of MERS in healthcare facilities with severe consequences. All healthcare facilities should establish and implement infection prevention and control measure as well as triage policies and procedures for early detection and isolation of suspected MERS-CoV cases.
Output: Middle East Respiratory Syndrome Coronavirus Superspreading Event Involving 81 Persons, Korea 2015