niryuu/sni-each-converted huggingface dataset:
Humans are colonized after birth by microbial organisms that form a heterogeneous community, collectively termed microbiota. The genomic pool of this macro-community is named microbiome. The gut microbiota is essential for the complete development of the immune system, representing a binary network in which the microbiota interact with the host providing important immune and physiologic function and conversely the bacteria protect themselves from host immune defense. Alterations in the balance of the gut microbiome due to a combination of environmental and genetic factors can now be associated with detrimental or protective effects in experimental autoimmune diseases. These gut microbiome alterations can unbalance the gastrointestinal immune responses and influence distal effector sites leading to CNS disease including both demyelination and affective disorders. The current range of risk factors for MS includes genetic makeup and environmental elements. Of interest to this review is the consistency between this range of MS risk factors and the gut microbiome. We postulate that the gut microbiome serves as the niche where different MS risk factors merge, thereby influencing the disease process. (J. Ochoa-Repáraz). FEBS Letters 588 (2014) 4214-4222 j o u r n a l h o m e p a g e : w w w . F E B S L e t t e r s . o r g 2. Environmental, genetics and microbial risk factors associated with CNS demyelinating disease Environmental, genetic, immunological and infectious diseases have been associated with MS [2]. The genetic background is thought to be a critical epidemiologic risk factor. As reviewed by Compton and colleagues, the familial recurrence rate in MS is 20% [7] . Monozygotic twins, sharing the 100% of the genetic information, have an MS lifetime risk of approximately 25-30%, siblings with two affected parents approximately a 20%, whereas dizygotic twins have a 5% lifetime risk, frequencies that suggest that the genetic background could interact with other risk factors. Alterations in immuno-regulatory or structural genes might increase the susceptibility to MS. Differences in the human leukocyte antigen (HLA) system-genes in the chromosome 6 that serve as the major histocompatibility complex (MHC) in humans-haplotypes DRBl*1501 and DQ6 have been suggested as genetic risk factors [8] . Recent genome-wide association studies (GWAS) reveal an evident effect of these genetic risk factors, with particular importance of HLA class II region, but also class I [9,10]. Interestingly, the genetic factors associated with MS are involved in immunological processes [11] , providing strong theoretical support to the autoimmune nature of MS, and moreover, provides the potential framework that environmental factors may be intimately involved in the modulation and/or perhaps even the trigger for disease susceptibility.
Output: Gut microbiome and the risk factors in central nervous system autoimmunity
The changing spatiotemporal patterns of the individual susceptible-infected-symptomatic-treated-recovered epidemic process and the interactions of information/material flows between regions, along with the 2002-2003 Severe Acute Respiratory Syndrome (SARS) epidemiological investigation data in mainland China, including three typical locations of individuals (working unit/home address, onset location and reporting unit), are used to define the in-out flow of the SARS epidemic spread. Moreover, the input/output transmission networks of the SARS epidemic are built according to the definition of in-out flow. The spatiotemporal distribution of the SARS in-out flow, spatial distribution and temporal change of node characteristic parameters, and the structural characteristics of the SARS transmission networks are comprehensively and systematically explored. The results show that (1) Beijing and Guangdong had the highest risk of self-spread and output cases, and prevention/control measures directed toward self-spread cases in Beijing should have focused on the later period of the SARS epidemic; (2) the SARS transmission networks in mainland China had significant clustering characteristics, with two clustering areas of output cases centered in Beijing and Guangdong; (3) Guangdong was the original source of the SARS epidemic, and while the infected cases of most other provinces occurred mainly during the early period, there was no significant spread to the surrounding provinces; in contrast, although the input/output interactions between Beijing and the other provinces countrywide began during the mid-late epidemic period, SARS in Beijing showed a significant capacity for spatial spreading; (4) Guangdong had a significant range of spatial spreading throughout the entire epidemic period, while Beijing and its surrounding provinces formed a separate, significant range of high-risk spreading during the mid-late period; especially in late period, the influence range of Beijing's neighboring provinces, such as Hebei, was even slightly larger than that of Beijing; and (5) the input network had a low-intensity spread capacity and middle-level influence range, while the output network had an extensive high-intensity spread capacity and influence range that covered almost the entire country, and this spread and influence indicated that significant clustering characteristics increased gradually. This analysis of the epidemic in-out flow and its corresponding transmission network helps reveal the potential spatiotemporal characteristics and evolvement mechanism of the SARS epidemic and provides more effective theoretical support for prevention and control measures. SARS, epidemic spread, in-out flow, transmission network, characteristic parameter Citation: Hu B S, Gong J H, Sun J, et al. Exploring the epidemic transmission network of SARS in-out flow in mainland China.
Output: Article Geography Exploring the epidemic transmission network of SARS in-out flow in mainland China
Induction of effective cytotoxic T lymphocyte (CTL) and/or a specific antibody against conserved viral proteins may be essential to the development of a safe and effective severe acute respiratory syndrome coronavirus (SARS-Cov) vaccine. DNA vaccination represents a new strategy for induction of humoral and cellular immune response. To determine the ability of SARS-Cov nucleoprotein (N protein) to induce antiviral immunity, in this report, we established a stable C2C12 line expressing SARS-Cov N protein, which was used as a target for specific CTL assay. We also expressed recombinant N proteins in Escherichia coli and prepared N protein-specific polyclonal antibodies. C3H/He mice were immunized with N protein-expressible pcDN-fn vector by intramuscular injections. We found that the DNA vaccination induced both N protein-specific antibody and specific CTL activity to the target. When C3H/He mice were immunized by three separate injections, high antibody titre (1:3200-1:6400, average titre is 1:4580) and high CTL activity (67.4 ± 8.4% (E:T = 25:1), 69.6 ± 6.7% (E:T = 50:1) and 71.8 ± 6.2% (E:T = 100:1)) were observed. In the case of two vaccine injections, CTL activity was also high (56.6 ± 12.7% (E:T = 25:1), 57.4 ± 11.7% (E:T = 50:1) and 63.0 ± 6.3% (E:T = 100:1)). However, antibody titres were much lower (1:200-1:3200, average titre is 1:980). Our results suggest that SARS-Cov nucleocapsid gene might be a candidate gene for SARS DNA vaccination.
Output: Induction of SARS-nucleoprotein-specific immune response by use of DNA vaccine
Folding-defective proteins must be cleared efficiently from the endoplasmic reticulum (ER) to prevent perturbation of the folding environment and to maintain cellular proteostasis. Misfolded proteins engage dislocation machineries (dislocons) built around E3 ubiquitin ligases that promote their transport across the ER membrane, their polyubiquitylation, and their proteasomal degradation. Here, we report on the intrinsic instability of the HRD1 dislocon and the constitutive, rapid turnover of the scaffold protein HERP. We show that HRD1 dislocon integrity relies on the presence of HRD1 clients that interrupt, in a dose-dependent manner, the UBC6e/RNF5/p97/ proteasome-controlled relay that controls HERP turnover. We propose that ER-associated degradation (ERAD) deploys autoadaptive regulatory pathways, collectively defined as ERAD tuning, to rapidly adapt degradation activity to misfolded protein load and to preempt the unfolded protein response (UPR) activation.
Output: Article Autoadaptive ER-Associated Degradation Defines a Preemptive Unfolded Protein Response Pathway
A 71-year-old female patient with hepatitis C virus genotype 1 had previously discontinued interferon (IFN)-a plus ribavirin therapy, pegylated IFN-a (pegIFNa) monotherapy, and natural IFN-a monotherapy because of arrhythmia, interstitial pneumonia, and severe neurovegetative symptoms. She subsequently completed 72 weeks of natural IFN-b plus ribavirin therapy without remarkable adverse effects and achieved a sustained viral response, suggesting differences in the pharmacological properties and biological effects of IFN-a and IFN-b. Thus, natural IFN-b plus ribavirin therapy may be a treatment option for patients with poor tolerance to IFN-a or pegIFNa treatments.
Output: Successful natural interferon-b plus ribavirin therapy in a chronic hepatitis C patient after discontinuation of interferon-a treatment due to arrhythmia and interstitial pneumonia
Multifunctional nanoparticles are among the most exciting nanomaterials with promising applications in analytical chemistry. These applications include (bio)sensing, (bio)assays, catalysis and separations. Although most of these applications are based on the magnetic, optical and electrochemical properties of multifunctional nanoparticles, other aspects such as the synergistic effect of the functional groups and the amplification effect associated with the nanoscale dimension have also been observed. Considering not only the nature of the raw material but also the shape, there is a huge variety of nanoparticles. In this review only magnetic, quantum dots, gold nanoparticles, carbon and inorganic nanotubes as well as silica, titania and gadolinium oxide nanoparticles are addressed. This review presents a narrative summary on the use of multifuncional nanoparticles for analytical applications, along with a discussion on some critical challenges existing in the field and possible solutions that have been or are being developed to overcome these challenges.
Output: Multifunctional nanoparticles: Analytical prospects
Background: We and others have shown that dipeptidyl peptidase-IV (DPP4) expression is increased in obesity/ atherosclerosis and is positively correlated with atherosclerotic burden. However, the mechanism by which DPP4 expression is regulated in obesity remains unclear. In this study, we investigated the pathways regulating the expression of DPP4 on macrophages. Methods: Flowsight® Imaging Flow Cytometry was employed for the detection of DPP4 and immunophenotyping. DPP4 enzymatic activity was measured by a DPPIV-Glo™ Protease Assay kit. Findings: Human monocytes expressed a moderate level of membrane-bound DPP4. Obese patients with body mass index (BMI) ≥ 30 had a higher level of monocyte DPP4 expression, in parallel with higher levels of HOMA-IR, blood glucose, triglycerides, and non-HDL cholesterol, compared to those in the non-obese (BMI b 30) patients. Oxidized low-density lipoprotein (oxLDL), but not native LDL, up-regulated DPP4 expression on macrophages with a preferential increase in CD36 + cells. OxLDL mediated DPP4 up-regulation was considerably diminished by Toll-like receptor-4 (TLR4) knockdown and CD36 deficiency. TRIF deficiency, but not MyD88 deficiency, attenuated oxLDL-induced DPP4 increase. Interpretation: Our study suggests a key role for oxLDL and downstream CD36/TLR4/TRIF in regulating DPP4 expression. Increased DPP4 in response to oxidized lipids may represent an integrated mechanism linking postprandial glucose metabolism to lipoprotein abnormality-potentiated atherosclerosis.
Output: Oxidized LDL upregulates macrophage DPP4 expression via TLR4/TRIF/CD36 pathways-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/)
Overcrowding during the yearly Hajj mass gatherings is associated with increased risk of spreading infectious diseases, particularly respiratory diseases. Non-pharmaceutical interventions (e.g., hand hygiene, wearing face masks, social distancing) are known to reduce the spread of respiratory viruses from person to person and are therefore recommended to pilgrims by public health agencies. The implementation of effective public health policies and recommendations involves evaluating the adherence to and effectiveness of these measures in the specific context of the Hajj. This review summarizes the evidence related to the effectiveness of non-pharmaceutical interventions in preventing the spread of respiratory infectious diseases during the Hajj. Overall, although hand hygiene compliance is high among pilgrims, face mask use and social distancing remain difficult challenges. Data about the effectiveness of these measures at the Hajj are limited, and results are contradictory, highlighting the need for future large-scale studies. ª
Output: Non-pharmaceutical interventions for the prevention of respiratory tract infections during Hajj pilgrimage
This bibliography is compiled by biotechnologists from the journals listed at the end of this publication. It is based on literature entered into our database between 1 st August 1992 and 31st July 1993 (articles are generally added to the database about two and a half months after publication). In addition, the bibliography contains every paper annotated by reviewers; these references were obtained from a variety of bibliographic databases and published between the beginning of the review period and the time of going to press. The bibliography has been grouped into topics that relate to the reviews in this issue. 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: Bibliography of the current world literature
Delivery of native or chemically modified recombinant proteins into mammalian cells shows 31 promise for functional investigations and various technological applications, but concerns 32 that sub-cellular localization and functional integrity of delivered proteins may be affected 33 remain high. Here, we surveyed batch electroporation as a delivery tool for single 34 polypeptides and multi-subunit protein assemblies of kinetochores, a spatially confined and 35 well-studied subcellular structures. After electroporation in human cells, recombinant 36 fluorescent Ndc80 and Mis12 multi-subunit complexes displayed native localization, 37 physically interacted with endogenous binding partners, and functionally complemented 38 depleted endogenous counterparts to promote mitotic checkpoint signaling and 39 chromosome segregation. Farnesylation is required for kinetochore localization of the 40 Dynein adaptor Spindly. In cells with chronically inhibited farnesyl transferase activity, in 41 vitro farnesylation and electroporation reconstituted robust kinetochore localization of 42 Spindly. Thus, electroporation is uniquely versatile for delivering synthetic and, as required, 43 chemically modified functional mimics of endogenous proteins, and is therefore a promising 44 tool for chemical and synthetic biology.
Output: Electroporated recombinant proteins as tools for in vivo functional
Objectives Erysipelas is an animal disease caused by Grampositive bacteria Erysipelothrix rhusiopathiae. Among the domestic animals, domestic pig (Sus scrofa f. domestica) suffers most frequently from the disease in human environment. This is a typical animal-borne disease observed mainly in occupational groups employed in agriculture, farming (of animals and birds), fishing and manufacturing industry. Methods We are presenting the clinical course of infection (E. rhusiopathiae) and discuss clinical forms. E. rhusiopathiae in humans may have the following clinical course: mild form of skin infection diagnosed as local erythema (erysipeloid), disseminated form of skin infection and the most serious form of infection of systemic course (endocarditis and sepsis). Mild skin infection and local erythema are the most common forms. Very rare case of animal-borne infection course has been presented in which after initial phase the disease was generalised to the abscesses formation in paravertebral space, spondylitis and empyema formation in spinal canal. In the presented clinical case, the patient was suffering from diabetes. It was probably an additional risk factor of the disease generalisation. Patient underwent drainage of empyema in spinal canal, after which his neurological status gradually improved. Antibiotic therapy was implemented and continued for 8 weeks. Such course of erysipelas was not previously described in the literature. After therapy neurological status was improved. In follow MRI control exam empyema and spondylitis was successfully eliminated. Conclusions Various complications of the disease, such as endocarditis and heart valves disturbances, are well known and are the most severe complications of the generalised infection. Proper targeted and long-term antibiotic therapy is crucial.
Output: Empyema in spinal canal in thoracic region, abscesses in paravertebral space, spondylitis: in clinical course of zoonosis Erysipelothrix rhusiopathiae
Background: The elevated risk of occupational infection such as tuberculosis among health workers in many countries raises the question of whether the quality of occupational health and safety (OHS) and infection prevention and control (IPC) can be improved by auditing. The objectives of this study were to measure (1) audited compliance of primary health-care facilities in South Africa with national standards for OHS and IPC, (2) change in compliance at reaudit three years after baseline, and (3) the inter-rater reliability of the audit. Methods: The study analyzed audits of 60 primary health-care facilities in the Western Cape Province of South Africa. Baseline external audits in the time period 2011e2012 were compared with follow-up internal audits in 2014e2015. Audits at 25 facilities that had both internal and external audits conducted in 2014/2015 were used to measure reliability. Results: At baseline, 25% of 60 facilities were "noncompliant" (audit score<50%), 48% "conditionally compliant" (score >50 < 80%), and only 27% "compliant" (score >80%). Overall, there was no significant improvement in compliance three years after baseline. Percentage agreement on specific items between internal and external audits ranged from 28% to 92% and kappa from -0.8 to 0.41 (poor to moderate). Conclusion: Low baseline compliance with OHSeIPC measures and lack of improvement over three years reflect the difficulties of quality improvement in these domains. Low inter-rater reliability of the audit instrument undermines the audit process. Evidence-based investment of effort is required if repeat auditing is to contribute to occupational risk reduction for health workers.
Output: Repeat Auditing of Primary Health-care Facilities Against Standards for Occupational Health and Infection Control: A Study of Compliance and Reliability-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Background: Clinical and laboratory data were collected and analysed from patients with Ebola virus disease (EVD) in Jui Government Hospital in Freetown, Sierra Leone, where patients with EVD were received and/or treated from October 1, 2014 to March 21, 2015 during the West Africa EVD outbreak. The study admitted 285 patients with confirmed EVD and followed them up till the endpoint (recovery or death). EVD was confirmed by quantitative RT-PCR assays detecting blood Ebola virus (EBOV). Results: Among the 285 lab-confirmed EVD cases in Jui Government Hospital, 146 recovered and 139 died, with an overall survival rate of 51.23 %. Patients under the age of 6 years had a lower survival rate (37.50 %). Most non-survivors (79.86 %) died within 7 days after admission and the mean hospitalization time for non-survivors was 5.56 ± 6.11 days. More than half survivors (63.69 %) turned blood EBOV negative within 3 weeks after admission and the mean hospitalization time for survivors was 20.38 ± 7.58 days. High blood viral load (≥10 6 copies/ml) was found to be predictive of the non-survival outcome as indicated by the Receiver Operating Characteristic (ROC) curve analysis. The probability of patients' survival was less than 15 % when blood viral load was greater than 10 6 copies/ml. Multivariate analyses showed that blood viral load (P = 0.005), confusion (P = 0.010), abdominal pain (P = 0.003), conjunctivitis (P = 0.035), and vomiting (P = 0.004) were factors independently associated with the outcomes of EVD patients. Conclusions: Most death occurred within 1 week after admission, and patients at the age of 6 or younger had a lower survival rate. Most surviving patients turned blood EBOV negative within 1-4 weeks after admission. Factors such as high blood viral load, confusion, abdominal pain, vomiting and conjunctivitis were associated with poor prognosis for EVD patients.
Output: Clinical presentations and outcomes of patients with Ebola virus disease in Freetown, Sierra Leone
Despite the formidable progress in Nuclear Magnetic Resonance (NMR) spectroscopy, quality assessment of NMR-derived structures remains as an important problem. Thus, validation of protein structures is essential for the spectroscopists, since it could enable them to detect structural flaws and potentially guide their efforts in further refinement. Moreover, availability of accurate and efficient validation tools would help molecular biologists and computational chemists to evaluate quality of available experimental structures and to select a protein model which is the most suitable for a given scientific problem. The 13 C α nuclei are ubiquitous in proteins, moreover, their shieldings are easily obtainable from NMR experiments and represent a rich source of encoded structural information that makes 13 C α chemical shifts an attractive candidate for use in computational methods aimed at determination and validation of protein structures. In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13 C α shielding for the amino acid residues in proteins is described. We also identify and examine the main factors affecting the 13 C α -shielding computation. Finally, we illustrate how the information encoded in the 13 C chemical shifts can be used for a number of applications, viz., from protein structure prediction of both α-helical and β-sheet conformations, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residuelevel, in NMR-determined protein models.
Output: 3 C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information
Relevant pandemic-spread scenario simulations provide guiding principles for containment and mitigation policy developments. Here we devise a simple model to predict the effectiveness of different mitigation strategies. The model consists of a set of simple differential equations considering the population size, reported and unreported infections, reported and unreported recoveries and the number of Covid-19-inflicted deaths. For simplification, we assume that Covid-19 survivors are immune (e.g. mutations are not considered) and that the virus can only be passed on by persons with undetected infections. While the latter assumption is a simplification (it is neglected that e.g. hospital staff may be infected by detected patients with symptoms), it was introduced here to keep the model as simple as possible. Moreover, the current version of the model does not account for age-dependent differences in the death rates, but considers higher mortality rates due to temporary shortage of intensive care units. Some of the model parameters have been fitted to the reported cases outside of China 1 from January 22 to March 12 of the 2020 Covid-19 pandemic. The other parameters were chosen in a plausible range to the best of our knowledge. We compared infection rates, the total number of people getting infected and the number of deaths in six different scenarios. Social distancing or increased testing can contain or drastically reduce the infections and the predicted number of deaths when compared to a situation without mitigation. We find that mass-testing alone and subsequent isolation of detected cases can be an effective mitigation strategy, alone and in combination with social distancing. However, unless one assumes that the virus can be globally defeated by reducing the number of infected persons to zero, testing must be upheld, albeit at reduced intensity, to prevent subsequent waves of infection. The model suggests that testing strategies can be equally effective as social distancing, though at much lower economical costs. We discuss how our mathematical model may help to devise an optimal mix of mitigation strategies against the Covid-19 pandemic. The website corona-lab.ch provides an interactive simulation tool based on the presented model. The Covid-19 pandemic is a serious threat that can be mitigated by different strategies. Social isolation is currently practiced in most countries in Europe, at least until alternative mitigation strategies can be implemented or therapies and vaccines become available. We have formulated a simple mathematical model to estimate how well social isolation or improved identification of Covid-19 infected people can slow down virus spread and reduce the death toll.
Output: Dynamic Modeling to Identify Mitigation Strategies for Covid-19 Pandemic
Zika virus (ZIKV) belongs to the Flavivirus genus of the Flaviviridae family. It is an arbovirus that can cause congenital abnormalities and is sexually transmissible. A series of outbreaks accompanied by unexpected severe clinical complications have captured medical attention to further characterize the clinical features of congenital ZIKV syndrome and its underlying pathophysiological mechanisms. Endoplasmic reticulum (ER) and ER-related proteins are essential in ZIKV genome replication. This review highlights the subcellular localization of ZIKV to the ER and ZIKV modulation on the architecture of the ER. This review also discusses ZIKV interaction with ER proteins such as signal peptidase complex subunit 1 (SPCS1), ER membrane complex (EMC) subunits, and ER translocon for viral replication. Furthermore, the review covers several important resulting effects of ZIKV infection to the ER and cellular processes including ER stress, reticulophagy, and paraptosis-like death. Pharmacological targeting of ZIKVaffected ER-resident proteins and ER-associated components demonstrate promising signs of combating ZIKV infection and rescuing host organisms from severe neurologic sequelae.
Output: Endoplasmic reticulum: a focal point of Zika virus infection
The speed with which disease outbreaks are recognized is critical for establishing effective control efforts. We evaluate global improvements in the timeliness of outbreak discovery and communication during 2010-2014 as a follow-up to a 2010 report. For all outbreaks reported by the World Health Organization's Disease Outbreak News, we estimate the number of days from first symptoms until outbreak discovery and until first public communication. We report median discovery and communication delays overall, by region, and by Human Development Index (HDI) quartile. We use Cox proportional hazards regression to assess changes in these 2 outcomes over time, along with Loess curves for visualization. Improvement since 1996 was greatest in the Eastern Mediterranean and Western Pacific regions and in countries in the middle HDI quartiles. However, little progress has occurred since 2010. Further improvements in surveillance will likely require additional international collaboration with a focus on regions of low or unstable HDI.
Output: Global Capacity for Emerging Infectious Disease Detection, 1996-2014 ONLINE REPORT EID journal EID journal Follow the EID journal on Twitter and get the most current information from Emerging Infectious Diseases. @CDC_EIDjournal
Background: The goal of this study was to evaluate whether a live attenuated poliovirus vaccine (OPV) has clinically relevant interfering effect with non-polio infections causing otitis media in young children. Methods: Open trial in which the intervention group (64 children) received OPV at the age of 2, 3, 6 and 12 months. The control group (250 children) received IPV (inactivated polio vaccine) at the age of 6 and 12 months. Clinical symptoms were recorded by a questionnaire at the age of 3, 6, 12, 18 and 24 months. Results: Otitis media episodes were less frequent in the OPV than in the control group. A significant difference was seen at the age of 6-18 months (IRR = 0.76 [95% CI 0.59-0.94], P = 0.011) and was particularly clear among children, who attended daycare (IRR 0.37 [95% CI 0.19-0.71], P = 0.003). Conclusions: OPV provides some protection against otitis media. This effect may be mediated by viral interference with non-polio viruses.
Output: Viral interference induced by live attenuated virus vaccine (OPV) can prevent otitis media
Only a month after the outbreak of pneumonia caused by 2019-nCoV, more than forty-thousand people were infected. This put enormous pressure on the Chinese government, medical healthcare provider, and the general public, but also made the international community deeply nervous. On the 25th day after the outbreak, the Chinese government implemented strict traffic restrictions on the area where the 2019-nCoV had originateddHubei province, whose capital city is Wuhan. Ten days later, the rate of increase of cases in Hubei showed a significant difference (p ¼ 0.0001) compared with the total rate of increase in other provinces of China. These preliminary data suggest the effectiveness of a traffic restriction policy for this pandemic thus far. At the same time, solid financial support and improved research ability, along with network communication technology, also greatly facilitated the application of epidemic prevention measures. These measures were motivated by the need to provide effective treatment of patients, and involved consultation with three major groups in policy formulationdpublic health experts, the government, and the general public. It was also aided by media and information technology, as well as international cooperation. This experience will provide China and other countries with valuable lessons for quickly coordinating and coping with future public health emergencies.
Output: Lessons learned from the 2019-nCoV epidemic on prevention of future infectious diseases
Introduction: Acute viral bronchiolitis (AB) is one of the most common respiratory diseases in infants. However, diagnostic criteria for AB are heterogeneous and not very well known. Objective: To identify the diagnostic criteria for AB used by experts and clinical paediatricians in Spain. Methods: Delphi study with Spanish AB experts, looking for the points of agreement about AB diagnosis. A subsequent cross-sectional study was conducted by means of an online questionnaire addressed to all Spanish paediatricians, reached through electronic mail messages sent by nine paediatric scientific societies. Descriptive and factorial analyses were carried out, looking for any association of diagnostic criteria with demographic or geographic variables, or with paediatric subspecialty. Results: Agreement was reached by 40 experts in many issues (first episode of respiratory distress and high respiratory frequency, diagnosis in any season of the year, and usefulness of virus identification in making diagnosis), but opposite views were maintained on key characteristics
Output: Criteria heterogeneity in the diagnosis of acute bronchiolitis in Spain ଝ,ଝଝ Group of Experts for the Diagnosis of Bronchiolitis ♦
Pulmonary complications are common and often lethal in hematopoietic SCT recipients. The objective of this prospective interventional study was to evaluate the etiology, diagnostic procedures, risk factors and outcome of pulmonary complications in a cohort of hematopoietic SCT recipients followed up for 1 year. For patients suffering from a pulmonary complication, a diagnostic algorithm that included non-invasive and bronchoscopic procedures was performed. We identified 73 pulmonary complications in 169 patients: 50 (68%) were pneumonias; 21 (29%) were non-infectious complications and 2 (3%) were undiagnosed. Viruses (particularly Rhinovirus) and bacteria (particularly P. aeruginosa) (28 and 26%, respectively) were the most common causes of pneumonia. A specific diagnosis was obtained in 83% of the cases. A non-invasive test gave a specific diagnosis in 59% of the episodes. The diagnostic yield of bronchoscopy was 67 and 78% in pulmonary infections. Early bronchoscopy (⩽5 days) had higher diagnostic yield than late bronchoscopy (78 vs 23%; P = 0.02) for pulmonary infections. Overall mortality was 22 and 32% of all fatalities were due to pulmonary complications. Pulmonary complications are common and constitute an independent risk factor for mortality, stressing the importance of an appropriate clinical management.
Output: Pulmonary complications in hematopoietic SCT: a prospective study
Critical care has evolved from treatment of poliomyelitis victims with respiratory failure in an intensive care unit to treatment of severely ill patients irrespective of location or specifi c technology. Population-based studies in the developed world suggest that the burden of critical illness is higher than generally appreciated and will increase as the population ages. Critical care capacity has long been needed in the developing world, and eff orts to improve the care of the critically ill in these settings are starting to occur. Expansion of critical care to handle the consequences of an ageing population, natural disasters, confl ict, inadequate primary care, and higher-risk medical therapies will be challenged by high costs at a time of economic constraint. To meet this challenge, investigators in this discipline will need to measure the global burden of critical illness and available critical-care resources, and develop both preventive and therapeutic interventions that are generalisable across countries.
Output: Critical Care 1 Critical care and the global burden of critical illness in adults
In this paper, a modified susceptible infected susceptible (SIS) epidemic model is proposed on community structure networks considering birth and death of node. For the existence of node's death would change the topology of global network, the characteristic of network with death rate is discussed. Then we study the epidemiology behavior based on the mean-field theory and derive the relationships between epidemic threshold and other parameters, such as modularity coefficient, birth rate and death rates (caused by disease or other reasons). In addition, the stability of endemic equilibrium is analyzed. Theoretical analysis and simulations show that the epidemic threshold increases with the increase of two kinds of death rates, while it decreases with the increase of the modularity coefficient and network size.
Output: The Journal of China Universities of Posts and Telecommunications Modeling and analysis of epidemic spreading on community network with node's birth and death
The genomic region that codes for New SARS-Like Coronavirus 3C-like Protease was chemical synthesized following the sequence of Human betacoronavirus 2c EMC/2012 (HCoV-EMC). BamHI and XhoI restriction sites were attached to the 5' and 3' ends separately by PCR, and the PCR product was inserted into the pET-28b-SUMO vector. The recombinant plasmids were transformed into Escherichia coli strain BL21 (DE3) (TransGen Biotech). kanamycin-resistant colonies were grown in Luria-Bertani medium at 37 °C until the OD 600 reached 0.8. Isopropyl β-D-1-thiogalactopyranoside was added to a final concentration of 0.1 mM, and the cultures were grown for an additional 20 h at 16 °C. Cells were harvested by centrifugation, resuspended, and homogenized in lysis buffer containing 20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 4 mM MgCl 2
Output: Supplementary Experiment Procedures Protein production and crystallization
Background: Outbreaks of avian influenza (AI) caused by infection with low pathogenic H9N2 viruses have occurred in poultry, resulting in serious economic losses in Asia and the Middle East. It has been difficult to eradicate the H9N2 virus because of its low pathogenicity, frequently causing in apparent infection. It is important for the control of AI to assess whether the H9N2 virus acquires pathogenicity as H5 and H7 viruses. In the present study, we investigated whether a non-pathogenic H9N2 virus, A/chicken/Yokohama/aq-55/2001 (Y55) (H9N2), acquires pathogenicity in chickens when a pair of di-basic amino acid residues is introduced at the cleavage site of its HA molecule.
Output: H9N2 influenza virus acquires intravenous pathogenicity on the introduction of a pair of di-basic amino acid residues at the cleavage site of the hemagglutinin and consecutive passages in chickens
This study is the first attempt to investigate the drivers of Chinese industrial SO 2 and NO x emissions from both periodic and structural perspectives through a decomposition analysis using the logarithmic mean Divisia index (LMDI). The two pollutants' emissions were decomposed into output effects, structural effects, clean production effects, and pollution abatement effects. The results showed that China's industrial SO 2 discharge increased by 1.14 Mt during 2003-2014, and the contributions from the four effects were 23.17, − 1.88, − 3.80, and − 16.36 Mt, respectively. Likewise, NO x discharge changed by − 3.44 Mt over 2011-2014, and the corresponding contributions from the four effects were 2.97, − 0.62, − 1.84, and − 3.95 Mt. Thus, the output effect was mainly responsible for the growth of the two discharges. The average annual contribution rates of SO 2 and NO x from output were 14.33 and 5.97%, respectively, but pollution abatement technology presented the most obvious mitigating effects (− 10.11 and − 7.92%), followed by the mitigating effects of clean production technology (− 2.35 and − 3.7%), and the mitigation from the structural effect was the weakest (− 1.16 and − 1.25%, respectively), which meant pollutant reduction policies related to industrial structure adjustment should be a long-term measure for the two discharges. In addition, the sub-sectors of I20 (manufacture of raw chemical materials and chemical products), I24 (manufacture of non-metallic mineral products), and I26 (smelting and pressing of non-ferrous metals) were the major contributors to both discharges. Thus, these sub-sectors should be given priority consideration when designing mitigation-related measures. Last, some particular policy implications were recommended for reducing the two discharges, including that the government should seek a technological discharge reduction route.
Output: Multi-perspective comparisons and mitigation implications of SO 2 and NO x discharges from the industrial sector of China: a decomposition analysis
Background: Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected. Methodology/Principle Findings: Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe. The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission.
Output: Distinguishing Molecular Features and Clinical Characteristics of a Putative New Rhinovirus Species, Human Rhinovirus C (HRV C)
Feline infectious peritonitis (FIP) is a feline coronavirus-induced fatal disease in domestic and wild cats. Several studies have investigated potential treatments for FIP. However, there have been no reports on agents that have exhibited a therapeutic effect. Recently, chloroquine has been reported to antiviral effect. We investigated whether chloroquine can be used to treat FIP in vitro and in vivo. It was demonstrated that chloroquine has inhibitory effect against the replication of FIPV and anti-inflammatory effect in vitro. In vivo study using cats with experimentally induced FIP, the clinical score of chloroquine-treatment groups were better than in chloroquine-untreated group. However, alanine aminotransferase levels increased in the chloroquine-treated groups. It will be necessary to further investigate the possibility of FIP treatment with a combination of chloroquine and other agents.
Output: Effect of chloroquine on feline infectious peritonitis virus infection in vitro and in vivo
The influences of indoor environment quality on occupant health have long been one of the main focuses in built environment and public health research. However, evidence to this effect has been inconsistent. Furthermore, previous urban studies have indicated the interaction between urban morphology and indoor environment. This study thus goes beyond indoor environment to investigate: i) the effects of neighborhood environment on occupant health; and ii) the mediating roles of indoor environment on the neighborhood environment and occupant health relationships. To achieve this aim, buildings located in different neighborhood environment in Hong Kong are selected. Data are collected by post-occupancy evaluation (occupant health), indoor environment assessment (thermal comfort, indoor air quality, ventilation, visual comfort, and acoustic comfort) and neighborhood environment assessment (neighborhood building density, building height, cleanliness and greenspace) through questionnaire survey. Through correlation analysis, regression modelling and Sobel test, it is found that: i) occupant health is significantly affected by neighborhood building height, building density and cleanliness; ii) the relationships between neighborhood environment and occupant health are significantly mediated by indoor environment, in terms of visual and acoustic comfort; and iii) neighborhood greenspace affects occupant health indirectly through influencing indoor air quality. To cross validate the results of the survey study, which is conducted using subjective data, objective measurements and analyses are further conducted. The objective study, echoing the survey study results, indicates that buildings with lower neighborhood building density and height, and cleaner neighborhood environment have better visual (higher illuminance level) and acoustic (lower noise level) performances.
Output: Effects of neighborhood building density, height, greenspace, and cleanliness on indoor environment and health of building occupants
Background: The burden of Hepatitis C virus (HCV) has become more and more considerable in China. A macroscopic spatial analysis of HCV infection that can provide scientific information for further intervention and disease control is lacking. Methods: All geo-referenced HCV cases that had been recorded by the China Information System for Disease Control and Prevention (CISDCP) during 2005-2011 were included in the study. In order to learn about the changes of demographic characteristics and geographic distribution, trend test and spatial analysis were conducted to reflect the changing pattern of HCV infection. Results: Over 770,000 identified HCV infection cases had specific geographic information during the study period (2005)(2006)(2007)(2008)(2009)(2010)(2011). Ratios of gender (Male/Female, Z-value = 218.53, P,0.001), age group (#30 years old/$31 years old, Z-value = 2 51.03, P,0.001) and diagnosis type (Clinical diagnosis/Laboratory diagnosis, Z-value = 2130.47, P,0.001) declined. HCV infection was not distributed randomly. Provinces Henan, Guangdong, Guangxi, Xinjiang, and Jilin reported more than 40,000 HCV infections during 2005 to 2011, accounting for 43.91% of all cases. The strength of cluster of disease was increasing in China during the study period. Overall, 11 provinces had once been detected as hotspots during 7 years, most of which were located in the central or border parts of China. Tibet, Qinghai, Jiangxi were the regions that had coldspots. The number of clustering of HCV infection among older adults increased in recent years. Specific interventions and prevention programs targeting at main HCV epidemic areas are urgently in need in mainland China.
Output: Spatial Analysis on Hepatitis C Virus Infection in Mainland China: From 2005 to 2011
Annotation The process of adding descriptive information to a data set and the individual data elements that comprise that data set. May include both computational analyses and manual curation. Curation The process of manually adding descriptive information or explanatory material to a data set usually based on a review of the existing literature. Database A collection of information, usually stored electronically on a computer. Database, hierarchical (XML) Extensible markup language. A formally defined hierarchical organization of data. A database software package designed to operate on a particular computer platform and operating system. Database schema A map of the database structure, including all of the fields, tables, and relationships that comprise the framework for storage of information within that database. Database, relational A database structure that provides the ability to define formal relationships between all data elements stored within the database. Ontology A controlled vocabulary used to formally describe (for our purposes) a biological process or entity. SQL Structured Query Language. A computer language used to query relational databases for information.
Output: Virus Databases