niryuu/sni-each-converted huggingface dataset:
Background H3N2 influenza viruses circulating in humans and European pigs originate from the pandemic A/Hong Kong/68 virus. Because of slower antigenic drift in swine, the antigenic divergence between swine and human viruses has been increasing. It remains unknown to what extent this results in a reduced cross-protection between recent human and swine H3N2 influenza viruses. Objectives We examined whether prior infection of pigs with an old [A/Victoria/3/75 (A/Vic/75)] or a more recent [A/Wisconsin/67/ 05 (A/Wis/05)] human H3N2 virus protected against a European swine H3N2 virus [sw/Gent/172/08 (sw/Gent/08)]. Genetic and antigenic relationships between sw/Gent/08 and a selection of human H3N2 viruses were also assessed. Results After challenge with sw/Gent/08, all challenge controls had high virus titers in the entire respiratory tract at 3 days postchallenge and nasal virus excretion for 5-6 days. Prior infection with sw/Gent/08 or A/Vic/75 offered complete virological protection against challenge. Pigs previously inoculated with A/Wis/05 showed similar virus titers in the respiratory tract as challenge controls, but the mean duration of nasal shedding was 1Á3 days shorter. Unlike sw/Gent/08-and A/Vic/75-inoculated pigs, A/Wis/05-inoculated pigs lacked cross-reactive neutralizing antibodies against sw/Gent/08 before challenge, but they showed a more rapid antibody response to sw/Gent/08 than challenge controls after challenge. Cross-protection and serological responses correlated with genetic and antigenic differences. Conclusions Infection immunity to a recent human H3N2 virus confers minimal cross-protection against a European swine H3N2 virus. We discuss our findings with regard to the recent zoonotic infections of humans in the United States with a swine-origin H3N2 variant virus. Please cite this paper as: Qiu et al. (2013) Prior infection of pigs with a recent human H3N2 influenza virus confers minimal cross-protection against a European swine H3N2 virus.
Output: Prior infection of pigs with a recent human H3N2 influenza virus confers minimal cross-protection against a European swine H3N2 virus
HF, B3LYP, and MP2 wave functions in combination with Pople 6-31, 6-311 augmented with polarization functions on all atoms and Dunning doubleand triple-zeta basis sets have been employed to investigate the structures and torsional potential function of the nitro group in 2-nitropyridine-N-oxide (2-NPO) and a variety of its fluorinated derivatives. The augmentation of the basis sets with diffuse functions showed a marked effect on the profile and barriers of the NO 2 torsional potential. Depending on the applied model chemistry, the heterocyclic ring in some 2-NPOs has proved to be non-planar. The non-planarity of the ring was characterized by Cremer-Pople puckering amplitude Q. The disruption of the ring planarity in some NPOs was accounted for the distinctive reactivity and impact sensitivity of these heterocycles. Consistently, the NBO and the AIM analyses furnished clear evidence for the accentuated weakness of the C-NO 2 bond and provided evidence for the electronic interplay between the NO 2 group, the fluorine substituent and the heterocyclic ring. Deletion of all off-diagonal Fock-matrix elements (NOSTAR) to separate hyperconjugative stabilizing interactions from steric interactions was used. The effect of nitration and fluorination on the aromaticity of the studied 2-NPOs was investigated by using the NICS descriptors NICS(1) and NICS(1) zz . These NICS indices have shown that the fluorination in para position to the nitro group exhibits the highest degree of aromaticity within the fluorinated 2-NPOs. Keywords 2-Nitropyridine-N-oxide Á Fluoro-2nitropyridine-N-oxide Á NO 2 torsional potential Á C-NO 2 bond Á Ring non-planarity Á NBO Á AIM Á NOSTAR deletion Á NICS(1) zz Electronic supplementary material The online version of this article (
Output: A theoretical investigation of the structure of 2-nitropyridine- N-oxide and the dependency of the NO 2 torsional motion on the applied wavefunction and basis set
Concepts are the most fundamental units of cognition in philosophy and how to learn concepts from various aspects in the real world is the main concern within the domain of conceptual knowledge presentation and processing. In order to improve efficiency and flexibility of concept learning, in this paper we discuss concept learning via granular computing from the point of view of cognitive computing. More precisely, cognitive mechanism of forming concepts is analyzed based on the principles from philosophy and cognitive psychology, including how to model concept-forming cognitive operators, define cognitive concepts and establish cognitive concept structure. Granular computing is then combined with the cognitive concept structure to improve efficiency of concept learning. Furthermore, we put forward a cognitive computing system which is the initial environment to learn composite concepts and can integrate past experiences into itself for enhancing flexibility of concept learning. Also, we investigate cognitive processes whose aims are to deal with the problem of learning one exact or two approximate cognitive concepts from a given object set, attribute set or pair of object and attribute sets.
Output: Concept learning via granular computing: A cognitive viewpoint
Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 10 2 copies for HCoV-OC43, and 3 × 10 1 copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 µL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples.
Output: A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses
In the global eradication program for poliomyelitis, the laboratory diagnosis plays a critical role by isolating poliovirus (PV) from the stool samples of acute flaccid paralysis (AFP) cases. In this study, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) system for a rapid and highly sensitive detection of enterovirus including PV to identify stool samples positive for enterovirus including PV. A primer set was designed for RT-LAMP to detect enterovirus preferably those with PV-like 5'NTRs of the viral genome. The sensitivity of RT-LAMP system was evaluated with prototype strains of enterovirus. Detection of enterovirus from stool extracts was examined by using RT-LAMP system. We detected at least 400 copies of the viral genomes of PV(Sabin) strains within 90 min by RT-LAMP with the primer set. This RT-LAMP system showed a preference for Human enterovirus species C (HEV-C) strains including PV, but exhibited less sensitivity to the prototype strains of HEV-A and HEV-B (detection limits of 7,400 to 28,000 copies). Stool extracts, from which PV, HEV-C, or HEV-A was isolated in the cell culture system, were mostly positive by RT-LAMP method (positive rates of 15/16 (= 94%), 13/ 14 (= 93%), and 4/4 (= 100%), respectively). The positive rate of this RT-LAMP system for stool extracts from which HEV-B was isolated was lower than that of HEV-C (positive rate of 11/21 (= 52%)). In the stool samples, which were negative for enterovirus isolation by the cell culture system, we found that two samples were positive for RT-LAMP (positive rates of 2/38 (= 5.3%)). In these samples, enterovirus 96 was identified by sequence analysis utilizing a seminested PCR system. Conclusions: RT-LAMP system developed in this study showed a high sensitivity comparable to that of the cell culture system for the detection of PV, HEV-A, and HEV-C, but less sensitivity to HEV-B. This RT-LAMP system would be useful for the direct detection of enterovirus from the stool extracts.
Output: BMC Infectious Diseases Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) system for a highly sensitive detection of enterovirus in the stool samples of acute flaccid paralysis cases
Background: Human coronaviruses (HCoVs) are a well-known cause of respiratory infections but their role in gastrointestinal infections is unclear. The objective of our study was to assess the significance of HCoVs in the etiology of acute gastroenteritis (AGE) in children <6 years of age. Methods: Stool samples and nasopharyngeal (NP) swabs collected from 260 children hospitalized for AGE (160 also had respiratory symptoms) and 157 otherwise healthy control children admitted for elective surgery were tested for the presence of four HCoVs using real time RT-PCR. Registered at ClinicalTrials.gov (reg. NCT00987519). Results: HCoVs were more frequent in patients with AGE than in controls (23/260, 8.8% versus 4/151, 2.6%; odds ratio, OR 3.3; 95% confidence interval, CI 1.3-10.0; P = 0.01). Three of four HCoV-positive members in the control group, asymptomatic when sampled, recalled gastrointestinal or respiratory symptoms within the previous 14 days. In patients with AGE, HCoVs were present in NP samples more often than in stools (22/256, 8.6%, versus 6/ 260, 2.3%; P = 0.0004). In 5/6 children with HCoVs detected in stools, the viruses were also detected in NP swabs. Patients had a significantly higher probability of HCoV detection in stool (OR 4; 95% CI 1.4-15.3; P = 0.006) and also in stool and/or NP (OR 3.3, 95% CI 1.3-10.0; P = 0.01) than healthy controls. All four HCoVs species were detected in stool and NP samples. Conclusions: Although HCoVs were more frequently detected in patients with AGE than in the control group, high prevalence of HCoVs in NP swabs compounded by their low occurrence in stool samples and detection of other viruses in stool samples, indicate that HCoVs probably play only a minor role in causing gastrointestinal illness in children <6 years old.
Output: Detection of human coronaviruses in simultaneously collected stool samples and nasopharyngeal swabs from hospitalized children with acute gastroenteritis
The skin is the largest organ in the body and has haired and hairless portions (Figs. 17-1 and 17-2). It consists of epidermis, dermis, subcutis, and adnexa (hair follicles and sebaceous, sweat, and other glands). The histologic structure varies greatly by anatomic site and among different species of animals. The haired skin is thickest over the dorsal aspect of the body and on the lateral aspect of the limbs and is thinnest on the ventral aspect of the body and the medial aspect of the thighs. Haired skin has a thinner epidermis, whereas nonhaired skin of the nose and pawpads has a thicker epidermis (see Figs. 17-1 and 17-2) . The skin of large animals is generally thicker than the skin of small animals. The subcutis, consisting of lobules of adipose tissue and fascia, connects the more superficial layers (epidermis and dermis) with the underlying fascia and musculature.
Output: The Integument 1
Viral respiratory infections in CF patients are associated with an increase in morbidity at short and long term. Viral infections have a greater impact on CF patients compared to non-CF controls. They result in increased respiratory symptoms, deterioration of Shwachman and radiological scores, prolonged hospitalizations, a persistent decrease of pulmonary function, increased use of antibiotics and a higher frequency of exacerbations at follow-up. In addition, interaction between viruses and bacteria in CF is suggested. Some studies observe increased new bacterial colonization and raised antipseudomonal antibodies in episodes of viral respiratory infections. Experimental data suggest that increased virus replication, impaired specific anti-bacterial defense and increased adherence of bacteria play a role in the pathogenesis of viral respiratory infections in CF. Further knowledge about the role of viruses and interaction with bacteria in CF lung disease might result in new therapeutic strategies to improve prognosis of CF patients.
Output: Viral respiratory infections in cystic fibrosis
The study aims to examine the knowledge and the practice of the precautionary measures taken by older adults in Hong Kong against the outbreak of severe acute respiratory syndrome (SARS). Overall, more than half the participants responded correctly that droplet transmission is one of the main transmission routes of SARS. Those who received formal education demonstrated that they acquired greater knowledge of the sources and precautionary measures for SARS. The types of precautionary measures used and the factors affecting their behaviours were discussed. The results of the study could help the health-care professionals develop appropriate health promotion and disease prevention programmes for older adults. r
Output: The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong
Background: SARS-CoV-2 is the cause of the COVID-19 that has been declared a global pandemic by the WHO in 2020. The COVID-19 treatment guidelines vary in each country, and yet there is no approved therapeutic for COVID-19. were included. The search terms included combinations of: COVID, SARS-COV-2, glucocorticoids, convalescent plasma, antiviral, antibacterial. There were no restrictions on the type of study design eligible for inclusion. As of March 26, 2020, of the initial manuscripts identified (n=449) articles. Forty-one studies were included, of which clinical trials (n=3), (case reports n=7), case series (n=10), retrospective (n=11) and prospective (n=10) observational studies. Thirtysix studies were conducted in China (88%). The most common mentioned and reported medicine in this systematic review was corticosteroids (n=25), followed by Lopinavir (n=21) and oseltamivir (n=16).
Output: Therapeutic Management of COVID-19 Patients: A systematic review Corresponding Author
Although the initial outbreaks of the deadly coronavirus that causes severe acute respiratory syndrome (SARS-CoV) were controlled by public health measures, the development of vaccines and antiviral agents for SARS-CoV is essential for improving control and treatment of future outbreaks. One potential target for SARS-CoV antiviral drug development is the 3C-like protease (3CLpro). This enzyme is an attractive target since it is essential for viral replication, and since there are now a number of high resolution X-ray structures of SARS-CoV 3CLpro available making structure-based drug-design possible. As a result, SARS-CoV 3CLpro has become the focus of numerous drug discovery efforts worldwide, but as a consequence, a variety of different 3CLpro expression constructs and kinetic assays have been independently developed making evaluation and comparison between potential inhibitors problematic. Here, we review the literature focusing on different SARS-CoV 3CLpro expression constructs and assays used to measure enzymatic activity. Moreover, we provide experimental evidence showing that the activity of 3CLpro enzymatic is significantly reduced when non-native sequences or affinity-tags are added to the N-or C-termini of the enzyme, or when the enzyme used in assays is at concentrations below the equilibrium dissociation constant of the 3CLpro dimer. We demonstrate for the first time the utility of a highly sensitive and novel Alexa488-QSY7 FRET-based peptide substrate designed for routine analysis and high-throughput screening, and show that kinetic constants determined from FRET-based assays that are uncorrected for inner-filter effects can lead to artifacts. Finally, we evaluated the effects of common assay components including DTT, NaCl, EDTA and DMSO on enzymatic activity, and we recommend standardized assay conditions and constructs for routine SARS-CoV 3CLpro assays to facilitate direct comparisons between SARS-CoV 3CLpro inhibitors under development worldwide.
Output: Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for standardized assays for drug discovery
In this paper, we extend the model of Liu and Zhang (Math Comput Model 54:836-845, 2011) by incorporating three control terms and apply optimal control theory to the resulting model. Optimal control strategies are proposed to minimize both the disease burden and the intervention cost. We prove the existence and uniqueness of optimal control paths and obtain these optimal paths analytically using Pontryagin's Maximum Principle. We analyse our results numerically to compare various strategies of proposed controls. It is observed that implementation of three controls is most effective and less expensive among all the strategies. Thus, we conclude that in order to reduce tuberculosis threat all the three controls must be taken into consideration concurrently.
Output: Optimal control analysis of a tuberculosis model R , RR
Bacteriophage T7 infection has been studied in Escherichia coli strains showing both increased and decreased ribosome fidelity and in the presence of streptomycin, which stimulates translational misreading, in an effort to determine effects on the apparent programmed translational frameshift that occurs during synthesis of the gene 10 capsid protein. Quantitation of the protein bands from SDS-PAGE failed to detect any significant effects on the amounts of the shifted 10B protein relative to the in-flame 10A protein under all fidelity conditions tested. However, any changes in fidelity conditions led to inhibition of phage morphogenesis in single-step growth experiments, which could not be accounted for by reduced amounts of phage protein synthesis, nor, at least in the case of decreased accuracy, by reduced amounts of phage DNA synthesis. Reduction in phage DNA synthesis did appear to account for a substantial proportion of the reduction in phage yield seen under conditions of increased accuracy. Similar effects of varying ribosomal fidelity on growth were also seen with phage T3, and to a lesser extent with phage T4. The absence of change in the high-frequency T7 gene 10 frameshift differs from earlier reports that ribosomal fidelity affects tow-frequency frameshift errors.
Output: Bacteriophage T7 morphogenesis and gene 10 frameshifting in Escherichia cob" showing different degrees of ribosomal fidelity
Evaluation Surveillance system Communicable diseases Epidemiology s u m m a r y Objectives: A sentinel surveillance system (SSS) was set up in Hong Kong to monitor hand, foot and mouth disease (HFMD) trends. This evaluation assessed the performance of the SSS from 2001 to 2009, and aimed to identify areas for improvement. Study design: A retrospective review using structured guidelines for evaluating public health surveillance systems published by the US Centers for Disease Control and Prevention. Methods: The effectiveness of the SSS was evaluated using routine service statistics, laboratory surveillance data, and results of an acceptability survey conducted among the sentinel doctors. This information was used to assess various attributes of the SSS including simplicity, flexibility, data quality, usefulness, sensitivity, specificity, positive predictive value (PPV), representativeness, timeliness and acceptability. Results: The SSS was simple and flexible with high-quality data. It correlated well with the laboratory surveillance data (P < 0.001) and facilitated early detection of community epidemics. It helped to identify seasonal trends and high-risk groups. Specificity was high (83.4e88.5%), while sensitivity and PPV were borderline satisfactory (38.4e56.8%). The sentinel clinics were representative of the population distribution. The SSS was acceptable to the sentinel doctors, but 17.9e28.2% of them had delays in reporting. The SSS is effective for monitoring HFMD trends in Hong Kong, and is useful for initiating preventive measures.
Output: Evaluation of sentinel surveillance system for monitoring hand, foot and mouth disease in Hong Kong
Here, we report the immunogenicity of a sublingually delivered, trivalent human papillomavirus (HPV) DNA vaccine encapsidated in a human endogenous retrovirus (HERV) envelopecoated, nonreplicable, baculovirus nanovector. The HERV envelope-coated, nonreplicable, baculovirus-based DNA vaccine, encoding HPV16L1, -18L1 and -58L1 (AcHERV-triHPV), was constructed and sublingually administered to mice without adjuvant. Following sublingual (SL) administration, AcHERV-triHPV was absorbed and distributed throughout the body. At 15 minutes and 1 day post-dose, the distribution of AcHERV-triHPV to the lung was higher than that to other tissues. At 30 days post-dose, the levels of AcHERV-triHPV had diminished throughout the body. Six weeks after the first of three doses, 1×10 8 copies of SL AcHERV-triHPV induced HPV type-specific serum IgG and neutralizing antibodies to a degree comparable to that of IM immunization with 1×10 9 copies. AcHERV-triHPV induced HPV type-specific vaginal IgA titers in a dose-dependent manner. SL immunization with 1×10 10 copies of AcHERV-triHPV induced Th1 and Th2 cellular responses comparable to IM immunization with 1×10 9 copies. Molecular imaging revealed that SL AcHERV-triHPV in mice provided complete protection against vaginal challenge with HPV16, HPV18, and HPV58 pseudoviruses. These results support the potential of SL immunization using multivalent DNA vaccine in baculovirus nanovector for induction of mucosal, systemic, and cellular immune responses.
Output: Sublingual Immunization of Trivalent Human Papillomavirus DNA Vaccine in Baculovirus Nanovector for Protection against Vaginal Challenge
Hepatitis C virus (HCV) is a small enveloped virus with a positive stranded RNA genome belonging to the Flaviviridae family. The virion has the unique ability of forming a complex with lipoproteins, which is known as the lipoviroparticle. Lipoprotein components as well as the envelope proteins, E1 and E2, play a key role in virus entry into the hepatocyte. HCV entry is a complex multistep process involving sequential interactions with several cell surface proteins. The virus relies on glycosaminoglycans and possibly the low-density lipoprotein receptors to attach to cells. Furthermore, four specific entry factors are involved in the following steps which lead to virus internalization and fusion in early endosomes. These molecules are the scavenger receptor SRB1, tetraspanin CD81 and two tight junction proteins, Claudin-1 and Occludin. Although they are essential to HCV entry, the precise role of these molecules is not completely understood. Finally, hepatocytes are highly polarized cells and which likely affects the entry process. Our current knowledge on HCV entry is summarized in this review. © Versita Sp. z o.o.
Output: Hepatitis C virus entry into the hepatocyte
Recent outbreak of coronavirus disease 2019 in China has lead a global pandemic around the world. For controlling COVID-19 outbreaks, most countries take two typical intervention strategies: suppression approach like immediately lock-downing cities at epicentre of and mitigation; or mitigation approach that slows down but not stopping epidemic of COVID-19 for reducing peak healthcare demand. Both strategies have their apparent merits and limitations; it becomes extremely hard to conduct one intervention strategy as the most feasible way to certain country. Targeting at this problem, this paper conducts a feasibility study by defining a mathematical model named SEMCR that access the effectiveness of mitigation, suppression and hybrid interventions for controlling COVID-19 outbreaks in London and Wuhan. The model first extends traditional SEIR (Susceptible-Exposed-Infectious-Recovered) model by considering one key fact: there is a direct link between Exposed and Recovered population. Then, it defines threshold and parameters to classify two stages of COVID control: active contain by isolation of cases and contacts, passive contain by suppression or mitigation. The model was fitted and evaluated with public dataset containing daily number of confirmed active cases including Wuhan, London, Hubei province and the UK during January, 2020 and March 2020. The simulated results show that 1) Suppression taken in Wuhan significantly reduces total exposed and infectious populations, but it has to be consistently maintained at least a period of 90 days (by the middle of April 2020) where its success relies on sufficient support from other parts of China. 2) In London, it is possible to take a hybrid intervention of suppression and mitigation for every 2 or 3 weeks over a longer period. While the total infectious populations will be doubled, the economic performance of London will be less affected due to limited mobility constraints. 3) Both in Wuhan and London cases,
Output: Feasibility Study of Mitigation and Suppression Intervention Strategies for Controlling COVID-19 Outbreaks in London and Wuhan
Diagnosis of MERS-Cov still a major concern in most of daignostic laboratories. To date the Real-time Polymerase Chain reaction (RT-PCR) is the mainstay for diagnosis of MERS-CoV. RT-PCR has limitations, including a long turnaround time and lack of common measurements and correlations with Viral Load (VL). It is recommended to screen for MERS-CoV using RT-PCR of the upstream of envelope gene (upE) followed by confirmation of the presence of one of the following genes; open reading frame 1A, 1B genes or nucleocapsid (N) gene. Scientists are looking to implement viral sequencing on all negative samples by RT-PCR and they beleive that can be exposed to another level of testing using sequencing of the RNA-dependent RNA polymerase (RdRp) gene or N gene and in this case a positive result is diagnostic. It is also very important to maintain a contineous and random sequencing for MERS-Cov samples to be able to pick early viral mutations. Serological assays still not widely or routinely performed, and a lot of studies looking to implement such method in routine patient's testings.
Output: MERS-CoV diagnosis: An update
In the last half century, significant attention has been given to animal diseases; however, our understanding of disease processes and how to manage them at the livestock-wildlife interface remains limited. In this study, we conduct a systematic review of the scientific literature to evaluate the status of diseases at the livestock-wildlife interface in the United States. Specifically, the goals of the literature review were three fold: first to evaluate domestic animal diseases currently found in the United States where wildlife may play a role; second to identify critical issues faced in managing these diseases at the livestock-wildlife interface; and third to identify potential technical and policy strategies for addressing these issues. We found that of the 86 avian, ruminant, swine, poultry, and lagomorph diseases that are reportable to the World Organization for Animal Health (OIE), 53 are present in the United States; 42 (79%) of these have a putative wildlife component associated with the transmission, maintenance, or life cycle of the pathogen; and 21 (40%) are known to be zoonotic. At least six of these reportable diseases-bovine tuberculosis, paratuberculosis, brucellosis, avian influenza, rabies, and cattle fever tick (vector control)-have a wildlife reservoir that is a recognized impediment to eradication in domestic populations. The complex nature of these systems highlights the need to understand the role of wildlife in the epidemiology, transmission, and maintenance of infectious diseases of livestock. Successful management or eradication of these diseases will require the development of cross-discipline and institutional collaborations. Despite social and policy challenges, there remain opportunities to develop new collaborations and new technologies to mitigate the risks posed at the livestock-wildlife interface. Published by Elsevier B.V.
Output: Diseases at the livestock-wildlife interface: Status, challenges, and opportunities in the United States
Nervilia fordii (Hance) Schltr. has been widely used as a medicinal and edible herb in Southwest China and Southeast Asia. In this study, NFP-1, a new water-soluble polysaccharidewith a purity of 97.8%, was purified from water extract of Nervilia fordii by DEAE-cellulose and Sephadex G-100 chromatography. NFP-1 has a relative molecular weight of 950 kDa determined by high performance gel-permeation chromatography (HPGPC). Its monosaccharide compositions were analyzed by high performance liquid chromatography (HPLC) after pre-column derivatizing its hydrolysate with 1-phenyl-3-methyl-5-pyrazolone (PMP). NFP-1 mainly consists of galactose, arabinose, rhamnose, and galacturonic acid. Based on FT-IR, methylation and GC-MS analysis, and NMR, the structure unit of NFP-1 was established as →4)-α-Rhap-(2→ 4)-α-GalpA-(1→2)-α-Rhap-(1→2)-α-Rhap-(4→1)-β-Galp-T containing two branch chains of →2,4)-α-Rhap-(1→5)-α-Araf-(1→3)-α-Araf-(1→, and →2,4)-α-Rhap-(1→4)-β-Galp-(1→. The immunomodulatory assays revealed the dual-functionalities of NFP-1. NFP-1 could significantly induce the secretion of nitric oxide (NO), and promote the secretions of TNF-α, IL-6, and IL-1β in RAW264.7 macrophages. NFP-1 could also significantly inhibit the production of NO, depress the secretions of TNF-α, IL-6 and IL-1β in RAW264.7 macrophages activated by lipopolysaccharide (LPS), and promote the production of IL-10 meanwhile. Our study suggested that Nervilia fordii could be an ideal medicinal or functional food due to its dual immunomodulatory activities.
Output: Structural characterization and immunomodulating activities of a novel polysaccharide from Nervilia fordii
Patients with highly infectious diseases require safe, secure, high-quality medical care with high-level infection control, which may be most eff ectively delivered by specially trained staff in the setting of a high-level isolation unit (HLIU). The European Network of Infectious Diseases is a European Commission co-funded network of experts in the management of highly infectious diseases from national (or regional) centres designated for the care of this patient population. Participants took a consensus-based approach to develop a framework for the design and operation of HLIUs in Europe, covering clinical care provision, diagnostic services, transport, health and safety, and essential design and construction features, to support planning by health authorities for the safe and eff ective management of highly infectious diseases and preparedness for infectious disease emergencies in Europe.
Output: Framework for the design and operation of high-level isolation units: consensus of the European Network of Infectious Diseases
The fusion subunit of the SARS-CoV S glycoprotein contains two regions of hydrophobic heptad-repeat amino acid sequences that have been shown in biophysical studies to form a six-helix bundle structure typical of the fusion-active core found in Class I viral fusion proteins. Here, we have applied serine-scanning mutagenesis to the C-terminal-most heptad-repeat region in the SARS-CoV S glycoprotein to investigate the functional role of this region in membrane fusion. We show that hydrophobic sidechains at a and d positions only within the short helical segment of the C-terminal heptad-repeat region (I1161, I1165, L1168, A1172, and L1175) are critical for cell -cell fusion. Serine mutations at outlying heptad-repeat residues that form an extended chain in the core structure (V1158, L1179, and L1182) do not affect fusogenicity. Our study provides genetic evidence for the important role of a-helical packing in promoting S glycoprotein-mediated membrane fusion. D
Output: Serine-scanning mutagenesis studies of the C-terminal heptad repeats in the SARS coronavirus S glycoprotein highlight the important role of the short helical region
Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. In the present study, we employed multiple codon usage analysis indices to determine genotype specific codon usage patterns of Zika virus (ZIKV) strains from the current outbreak and those reported previously. Several genotype specific and common codon usage traits were noted in ZIKV coding sequences, indicative of independent evolutionary origins from a common ancestor. The overall influence of natural selection was found to be more profound than that of mutation pressure and acting on specific set of viral genes belonging to ZIKV strains of Asian genotype from the recent outbreak. Furthermore, an interplay of codon adaptation and deoptimization have been observed in ZIKV genomes. The collective findings of codon analysis in association with the geographical data of Aedes populations in the Americas suggests that ZIKV have evolved a dynamic set of codon usage patterns in order to maintain a successful replication and transmission chain within multiple hosts and vectors.
Output: Zika virus outbreak in the Americas: Is Aedes albopictus an overlooked culprit?
Adenovirus is one of the most common causes of viral acute respiratory infections. To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. Through the surveillance project, 4617 cases of respiratory infections were identified during 2011-2013. Throat swabs (pharynx and tonsil secretions) were collected from all the patients, and 15 different respiratory viruses were screened by multiplex one-step PCR method. 45 were identified as adenovirus-positive from sporadic and outbreak cases of respiratory infection by a multiplex one-step RT-PCR method, and a total of 21 adenovirus isolates were obtained. Five HAdV types among three species, including HAdV-3 (species HAdV-B), HAdV-4 (species HAdV-E), HAdV-7 (species HAdV-B), HAdV-55 (species HAdV-B), and an undefined HAdV type (species HAdV-C) were identified. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. This study confirmed that at least 5 HAdV types including HAdV-3, HAdV-4, HAdV-7, HAdV-55 and an undefined HAdV type were co-circulating and were the causative agents of respiratory tract infections in recent years in Beijing. HAdV-3, HAdV-4, HAdV-7, and HAdV-55 showed the apparent stability of the genomes, while intraspecies recombination was identified in strain BJ04 and BJ09. The recombinants carrying penton base gene of HAdV-1 as well as hexon and fiber genes of HAdV-2 might be a novel type of HAdV worthy of further study. Adenoviruses in Beijing during 2011 PLOS ONE |
Output: Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013
Little is known about the long-term consequence of severe acute respiratory syndrome (SARS). We carried out an assessment on SARS patients after their recovery from their acute illness. Method: Postal survey comprising Health-Related Quality of Life (HRQoL) questionnaires and anxiety and depression measures was sent to them at 3 months' postdischarge. Results: There was a significant impairment in both the HRQoL and mental functioning. Forty-one percent had scores indicative of a posttraumatic stress disorder (PTSD); about 30% had likely anxiety and depression. Conclusion: SARS has significant impact on HRQoL and psychological status at 3 months. D
Output: Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge B
Purpose: Interest in a variety of neoplastic, functional, neurological, and age-related laryngeal disorders has contributed to the development of laryngology as an established subspecialty. Funding support plays a critical role in facilitating scholarship within the field. Our objectives were to evaluate who is receiving funding from the NIH for topics relevant to voice disorders, and further describe temporal trends in grants awarded. Methods: The NIH RePORTER database was searched for grants relevant to voice disorders. Data were further organized by PI specialty, academic department, and funding totals. Furthermore, PI scholarly impact, as measured by the h-index, was calculated. Results: A total of 830 funded fiscal years (for 232 unique projects) totaling $203 million have supported projects examining voice disorders. A plurality of projects (32.8%) was awarded to PIs in otolaryngology departments, followed by 17.2% to speech pathology/communication sciences departments. Although year-to-year variation was noted, otolaryngology departments received approximately 15% of funding annually. Funded otolaryngologists had similar scholarly impact values to individuals in other specialties. Conclusions: The study of voice disorders involves an interdisciplinary approach, as PIs in numerous specialties receive NIH funding support. As they receive a considerable proportion of this funding and had similar h-indices compared to other specialties involved, otolaryngologists
Output: Voicing an impact: who does the National Institutes of Health support for voice disorder research? ☆
Backgound: High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution, thus enabling the close examination of viral mutational dynamics both within-and between-hosts. The challenge however, is to accurately model the errors in the sequencing data and differentiate real viral mutations, particularly those that exist at low frequencies, from sequencing errors. Results: We demonstrate that overlapping read pairs (ORP) --generated by combining short fragment sequencing libraries and longer sequencing reads --significantly reduce sequencing error rates and improve rare variant detection accuracy. Using this sequencing protocol and an error model optimized for variant detection, we are able to capture a large number of genetic mutations present within a viral population at ultra-low frequency levels (<0.05%). Conclusions: Our rare variant detection strategies have important implications beyond viral evolution and can be applied to any basic and clinical research area that requires the identification of rare mutations.
Output: Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs
private residential drinking water wells, one dewatering well at a lignite mine, eight surface water sites, and lignite from an active coal mine were sampled in five Parishes of northwestern Louisiana, USA. Using a geographic information system (GIS), wells were selected that were likely to draw water that had been in contact with lignite; control wells were located in areas devoid of lignite deposits. Well water samples were analyzed for pH, conductivity, organic compounds, and nutrient and anion concentrations. All samples were further tested for presence of fungi (cultures maintained for up to 28 days and colonies counted and identified microscopically) and for metal and trace element concentration by inductively-coupled plasma mass spectrometry and atomic emission spectrometry. Surface water samples were tested for dissolved oxygen and presence of pathogenic leptospiral bacteria. The Spearman correlation method was used to assess the association between the endpoints for these field/laboratory analyses and incidence of cancer of the renal pelvis (RPC) based on data obtained from the Louisiana Tumor Registry for the five Parishes included in the study. Significant associations were revealed between the cancer rate and the presence in drinking water of organic compounds, the fungi Zygomycetes, the nutrients PO 4 and NH 3 , and 13 chemical elements. Presence of human pathogenic leptospires was detected in four out of eight (50%) of the surface water sites sampled. The present study of a stable rural Ó Springer Science+Business Media B.V. 2006 population examined possible linkages between aquifers containing chemically reactive lignite deposits, hydrologic conditions favorable to the leaching and transport of toxic organic compounds from the lignite into the groundwater, possible microbial contamination, and RPC risk.
Output: Possible linkages between lignite aquifers, pathogenic microbes, and renal pelvic cancer in northwestern Louisiana, USA
Background: Interaction between immune system and Chandipura virus (CHPV) during different stages of its life cycle remain poorly understood. The exact route of virus entry into the blood and CNS invasion has not been clearly defined. The present study was undertaken to assess the population in PBMC that supports the growth of virus and to detect active virus replication in PBMC as well as its subsets. Methods: PBMC subsets viz.: CD3 + , CD14 + , CD19 + , CD56 + cells were separated and infected with CHPV. The infected cells were then assessed for transcription (N gene primer) and replication (NP gene primer) of CHPV by PCR. The supernatant collected from infected cells were titrated in Baby Hamster Kidney (BHK) cells to assess virus release. The cytokine and chemokine expression was quantified by flow cytometry. Results: Amplification of N and NP gene was detected in CD14 + (monocyte) and CD19 + (B cell), significant increase in virus titre was also observed in these subsets. It was observed that, although the levels of IL-6 and IL-10 were elevated in CD14 + cells as compared to CD19 + cells, the differences were not significant. However the levels of TNFα and IL-8 were significantly elevated in CD14 + cells than in CD19 + cells. The levels of chemokine (CXCL9, CCL5, CCL2, CXCL10) were significantly elevated in CHPV infected PBMC as compared to uninfected cells. CCL2 and CXCL9 were significantly increased in CHPV infected CD14 + cells as compared to CD19 + cells. Conclusion: CD14 + and CD19 + cells support active replication of CHPV. High viral load was detected in CD14 + cells infected with CHPV hence it might be the primary target cells for active replication of CHPV. An elevated levels of cytokines and chemokines observed in CD14 + cells may help in predicting the pathogenecity of CHPV and possible entry into the central nervous system.
Output: Monocytes and B cells support active replication of Chandipura virus
We measured the effect of pharmacological doses of glucocorticoid on piglet jejunal structure and function during acute viral diarrhea. Weaned piglets, infected experimentally with transmissible gastroenteritis virus, a coronavirus that induces a diarrheal illness similar to human rotavirus infection, received methylprednisolone (30 mg/kg) or saline intramuscularly at 48 and 72 h after infection; noninfected littermate controls were similarly injected with methylprednisolone. Animals were killed at 96 h, at the height of diarrhea, and jejunal epithelium was studied in vitro. Transmissible gastroenteritis, as expected, induced structural, enzyme, and Na transport abnormalities. Methylprednisolone did not affect small intestinal structure or function of noninfected control piglets. In transmissible gastroenteritis-infected piglets, jejunal villi were longer and glucose-facilitated Na absorption was greater after methylprednisolone than after saline treatment. Increased glucose stimulation of Na flux in vitro in the methylprednisolone-treated infected group was not attributable to enhanced Na+-K+-ATPase activity and occurred d e s~i t e ~ersistence of the virus within mucosal cells.
Output: Effect of Glucocorticoid on Piglet Jejunal Mucosa during Acute Viral Enteritis1
Pathogenesis of sepsis includes complex interaction between pathogen activities and host response, manifesting highly variable signs and symptoms, possibly delaying diagnosis and timely life-saving interventions. This study applies traditional Chinese medicine (TCM) Zheng diagnosis in patients with severe sepsis and septic shock to evaluate its adaptability and use as an early predictor of sepsis mortality. Three-year prospective observational study enrolled 126 septic patients. TCM Zheng diagnosis, Acute Physiology and Chronic Health Evaluation (APACHE) II score, and blood samples for host response cytokines measurement (tumor necrosis factor-, Interleukin-6, Interleukin-8, Interleukin-10, Interleukin-18) were collected within 24 hours after admission to Intensive Care Unit. Main outcome was 28-day mortality; multivariate logistic regression analysis served to determine predictive variables of the sepsis mortality. APACHE II score, frequency of Nutrient-phase heat, and Qi-Xu and Yang-Xu Zhengs were significantly higher in nonsurvivors. The multivariate logistic regression analysis identified Yang-Xu Zheng as the outcome predictor. APACHE II score and levels of five host response cytokines between patients with and without Yang-Xu Zheng revealed significant differences. Furthermore, cool extremities and weak pulse, both diagnostic signs of Yang-Xu Zheng, were also proven independent predictors of sepsis mortality. TCM diagnosis "Yang-Xu Zheng" may provide a new mortality predictor for septic patients.
Output: Significant Prognostic Predictor for Patients with Severe Sepsis and Septic Shock
In this study, we compare the development of infection and/or disease in Beagle dogs intradermally infected with Leishmania chagasi, in the presence or absence of Lutzomyia longipalpis saliva, with those of intravenously infected animals. Spleen samples of all the animals inoculated with parasites had positive polymerase chain reaction tests for Leishmania DNA. Positive spleen cultures for Leishmania were detected earlier (P ≤ 0.018) and were more frequent (five out of the five animals) in intravenously infected animals than in the intradermally infected animals, in presence (two out of the six animals) or absence (three out of the five animals) of salivary gland lysate of L. longipalpis. Significant increase in serum antibodies against Leishmania was observed only in the intravenously infected group (P = 0.004). In addition, dogs with infection confirmed by isolation of amastigotes or detection of parasite DNA were, nevertheless, negative for anti-Leishmania antibodies up to 5 months or more after infection. Only animals of the intravenously infected group developed progressive decreases in hematocrit (Pearson r = −0.8076, P = 0.0026) and hemoglobin (Pearson r = −0.8403, P = 0.0012) during the infection period. No significant difference in the course of infection was observed between groups of intradermally infected animals. M. Paranhos-Silva et al. / Veterinary Parasitology 114 (2003) 97-111 inoculation of dogs with Leishmania produces an asymptomatic form of infection. It also fails to show an advantage in using L. longipalpis saliva as an infection-enhancing agent in experimental canine leishmaniasis.
Output: A follow-up of Beagle dogs intradermally infected with Leishmania chagasi in the presence or absence of sand fly saliva