bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering
Authors: Novitsky Vlad , Zahralban-Steele Melissa , McLane Mary Fran , Moyo Sikhulile , van Widenfelt Erik , Gaseitsiwe Simani , Makhema Joseph , Essex M. 
Published: June 2015

ABSTRACTThe goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838–3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV-infected subjects with suppressed viral loads (e.g., subjects on antiretroviral therapy [ART]). The two amplicons cover critical regions across the HIV-1 genome (includingpolandenv), allowing analysis of mutations associated with resistance to protease inhibitors, reverse transcriptase inhibitors (nucleoside reverse transcriptase inhibitors [NRTIs] and nonnucleoside reverse transcriptase inhibitors [NNRTIs]), integrase strand transfer inhibitors, and virus entry inhibitors. The two amplicons generated span 7,124 bp, providing substantial sequence length and numbers of informative sites for comprehensive phylogenic analysis and greater refinement of viral linkage analyses in HIV prevention studies. The long-range HIV genotyping from proviral DNA was successful in about 90% of 212 targeted blood specimens collected in a cohort where the majority of patients had suppressed viral loads, including 65% of patients with undetectable levels of HIV-1 RNA loads. The generated amplicons could be sequenced by different methods, such as population Sanger sequencing, single-genome sequencing, or next-generation ultradeep sequencing. The developed method is cost-effective—the cost of the long-range HIV genotyping is under $140 per subject (by Sanger sequencing)—and has the potential to enable the scale up of public health HIV prevention interventions.
A Novel Solid Medium for Culturing Mycobacterium tuberculosis Isolates from Clinical Specimens
Authors: Asmar S. , Chatellier S. , Mirande C. , van Belkum A. , Canard I. , Raoult D. , Drancourt M. 
Published: June 2015

ABSTRACT

The laboratory diagnosis of tuberculosis usually relies on culture-based isolation of the causative
Mycobacterium tuberculosis
bacteria. We developed and evaluated the performance of MOD9, a new blood-free derivative of the MOD4 solid medium on which we previously reported for the isolation and culture of mycobacteria. First, inoculation of Lowenstein-Jensen medium with 21
M. tuberculosis
isolates at 10
5
, 10
3
, and 10 CFU yielded colonies in 5.7 ± 1.5 days, 7.6 ± 0.8 days, and 10.8 ± 1.7 days versus 1.5 ± 0.4 days, 3.5 ± 0.6 days, and 4.9 ± 1 days in MOD9 (
P
< 0.05, Student's
t
test). Further, the time to detectable growth of
M. tuberculosis
was measured on MOD9 and Lowenstein-Jensen media after duplicate inoculation of 250 clinical specimens decontaminated with 0.7% chlorhexidine. The contamination rate was 1.6% (4/250) on MOD9 versus 4.4% (11/250) on Lowenstein-Jensen medium (
P
= 0.11, Fisher's exact test). Chlorhexidine-MOD9 yielded 38/250 (15.2%) isolates versus 32/250 (12.8%) isolates for the chlorhexidine-LJ (
P
= 0.5195, Fisher's exact test). All together, eight
M. tuberculosis
isolates were cultured solely from chlorhexidine-MOD9, and two
M. tuberculosis
isolates were cultured solely from chlorhexidine-LJ. The time to detection was 9.8 ± 3.9 (range, 5 to 18) days for chlorhexidine-MOD9 versus 17.4 ± 5.9 (range, 10 to 35) days for chlorhexidine-LJ (
P
< 0.05, Student's
t
test). These data indicate the superiority of the MOD9 medium over the standard LJ medium following chlorhexidine decontamination for the recovery of
M. tuberculosis
.
Thioredoxin 2 Is a Novel E2-Interacting Protein That Inhibits the Replication of Classical Swine Fever Virus
Authors: Li Su , Wang Jinghan , He Wen-Rui , Feng Shuo , Li Yongfeng , Wang Xiao , Liao Yajin , Qin Hua-Yang , Li Lian-Feng , Dong Hong , Sun Yuan , Luo Yuzi , Qiu Hua-Ji 
Published: June 2015

ABSTRACT

The E2 protein of classical swine fever virus (CSFV) is an envelope glycoprotein that is involved in virus attachment and entry. To date, the E2-interacting cellular proteins and their involvement in viral replication have been poorly documented. In this study, thioredoxin 2 (Trx2) was identified to be a novel E2-interacting partner using yeast two-hybrid screening from a porcine macrophage cDNA library. Trx2 is a mitochondrion-associated protein that participates in diverse cellular events. The Trx2-E2 interaction was further confirmed by glutathione
S
-transferase (GST) pulldown,
in situ
proximity ligation, and laser confocal assays. The thioredoxin domain of Trx2 and the asparagine at position 37 (N37) in the E2 protein were shown to be critical for the interaction. Silencing of the Trx2 expression in PK-15 cells by small interfering RNAs significantly promotes CSFV replication, and conversely, overexpression of Trx2 markedly inhibits viral replication of the wild-type (wt) CSFV and to a greater extent that of the CSFV N37D mutant, which is defective in binding Trx2. The wt CSFV but not the CSFV N37D mutant was shown to reduce the Trx2 protein expression in PK-15 cells. Furthermore, we demonstrated that Trx2 increases nuclear factor kappa B (NF-κB) promoter activity by promoting the nuclear translocation of the p65 subunit of NF-κB. Notably, activation of the NF-κB signaling pathway induced by tumor necrosis factor alpha (TNF-α) significantly inhibits CSFV replication in PK-15 cells, whereas blocking the NF-κB activation in Trx2-overexpressing cells no longer suppresses CSFV replication. Taken together, our findings reveal that Trx2 inhibits CSFV replication via the NF-κB signaling pathway.

IMPORTANCE
Thioredoxin 2 (Trx2) is a mitochondrion-associated protein that participates in diverse cellular events, such as antioxidative and antiapoptotic processes and the modulation of transcription factors. However, little is known about the involvement of Trx2 in viral replication. Here, we investigated, for the first time, the role of Trx2 in the replication of classical swine fever virus (CSFV), a devastating pestivirus of pigs. By knockdown and overexpression, we showed that Trx2 negatively regulates CSFV replication. Notably, we demonstrated that Trx2 inhibits CSFV replication by promoting the nuclear translocation of the p65 subunit of NF-κB, a key regulator of the host's innate immunity and inflammatory response. Our findings reveal a novel role of Trx2 in the host's antiviral response and provide new insights into the complex mechanisms by which CSFV interacts with the host cell.
mRNA Capping by Venezuelan Equine Encephalitis Virus nsP1: Functional Characterization and Implications for Antiviral Research
Authors: Li Changqing , Guillén Jaime , Rabah Nadia , Blanjoie Alexandre , Debart Françoise , Vasseur Jean-Jacques , Canard Bruno , Decroly Etienne , Coutard Bruno 
Published: June 2015

ABSTRACT

Alphaviruses are known to possess a unique viral mRNA capping mechanism involving the viral nonstructural protein nsP1. This enzyme harbors methyltransferase (MTase) and nsP1 guanylylation (GT) activities catalyzing the transfer of the methyl group from
S
-adenosylmethionine (AdoMet) to the N7 position of a GTP molecule followed by the formation of an m
7
GMP-nsP1 adduct. Subsequent transfer of m
7
GMP onto the 5′ end of the viral mRNA has not been demonstrated
in vitro
yet. Here we report the biochemical characterization of Venezuelan equine encephalitis virus (VEEV) nsP1. We have developed enzymatic assays uncoupling the different reactions steps catalyzed by nsP1. The MTase and GT reaction activities were followed using a nonhydrolyzable GTP (GIDP) substrate and an original Western blot assay using anti-m
3
G/m
7
G-cap monoclonal antibody, respectively. The GT reaction is stimulated by
S
-adenosyl-
l
-homocysteine (Ado-Hcy), the product of the preceding MTase reaction, and metallic ions. The covalent linking between nsP1 and m
7
GMP involves a phosphamide bond between the nucleotide and a histidine residue. Final guanylyltransfer onto RNA was observed for the first time with an alphavirus nsP1 using a 5′-diphosphate RNA oligonucleotide whose sequence corresponds to the 5′ end of the viral genome. Alanine scanning mutagenesis of residues H37, H45, D63, E118, Y285, D354, R365, N369, and N375 revealed their respective roles in MT and GT reactions. Finally, the inhibitory effects of sinefungin, aurintricarboxylic acid (ATA), and ribavirin triphosphate on MTase and capping reactions were investigated, providing possible avenues for antiviral research.

IMPORTANCE
Emergence or reemergence of alphaviruses represents a serious health concern, and the elucidation of their replication mechanisms is a prerequisite for the development of specific inhibitors targeting viral enzymes. In particular, alphaviruses are able, through an original reaction sequence, to add to their mRNA a cap required for their protection against cellular nucleases and initiation of viral proteins translation. In this study, the capping of a 5′ diphosphate synthetic RNA mimicking the 5′ end of an alphavirus mRNA was observed
in vitro
for the first time. The different steps for this capping are performed by the nonstructural protein 1 (nsP1). Reference compounds known to target the viral capping inhibited nsP1 enzymatic functions, highlighting the value of this enzyme in antiviral development.
Robust Protection against Highly Virulent Foot-and-Mouth Disease Virus in Swine by Combination Treatment with Recombinant Adenoviruses Expressing Porcine Alpha and Gamma Interferons and Multiple Small Interfering RNAs
Authors: Kim Su-Mi , Park Jong-Hyeon , Lee Kwang-Nyeong , Kim Se-Kyung , You Su-Hwa , Kim Taeseong , Tark Dongseob , Lee Hyang-Sim , Seo Min-Goo , Kim Byounghan 
Published: June 2015

ABSTRACT
Because the currently available vaccines against foot-and-mouth disease (FMD) provide no protection until 4 to 7 days postvaccination, the only alternative method to halt the spread of the FMD virus (FMDV) during outbreaks is the application of antiviral agents. Combination treatment strategies have been used to enhance the efficacy of antiviral agents, and such strategies may be advantageous in overcoming viral mechanisms of resistance to antiviral treatments. We have developed recombinant adenoviruses (Ads) for the simultaneous expression of porcine alpha and gamma interferons (Ad-porcine IFN-αγ) as well as 3 small interfering RNAs (Ad-3siRNA) targeting FMDV mRNAs encoding nonstructural proteins. The antiviral effects of Ad-porcine IFN-αγ and Ad-3siRNA expression were tested in combination in porcine cells, suckling mice, and swine. We observed enhanced antiviral effects in porcine cells and mice as well as robust protection against the highly pathogenic strain O/Andong/SKR/2010 and increased expression of cytokines in swine following combination treatment. In addition, we showed that combination treatment was effective against all serotypes of FMDV. Therefore, we suggest that the combined treatment with Ad-porcine IFN-αγ and Ad-3siRNA may offer fast-acting antiviral protection and be used with a vaccine during the period that the vaccine does not provide protection against FMD.

IMPORTANCE
The use of current foot-and-mouth disease (FMD) vaccines to induce rapid protection provides limited effectiveness because the protection does not become effective until a minimum of 4 days after vaccination. Therefore, during outbreaks antiviral agents remain the only available treatment to confer rapid protection and reduce the spread of foot-and-mouth disease virus (FMDV) in livestock until vaccine-induced protective immunity can become effective. Interferons (IFNs) and small interfering RNAs (siRNAs) have been reported to be effective antiviral agents against FMDV, although the virus has associated mechanisms of resistance to type I interferons and siRNAs. We have developed recombinant adenoviruses for the simultaneous expression of porcine alpha and gamma interferons (Ad-porcine IFN-αγ) as well as 3 small interfering RNAs (Ad-3siRNA) to enhance the inhibitory effects of these antiviral agents observed in previous studies. Here, we show enhanced antiviral effects against FMDV by combination treatment with Ad-porcine IFN-αγ and Ad-3siRNA to overcome the mechanisms of resistance of FMDV in swine.
Mapping of a Region of the PA-X Protein of Influenza A Virus That Is Important for Its Shutoff Activity
Authors: Oishi Kohei , Yamayoshi Seiya , Kawaoka Yoshihiro 
Published: June 2015

ABSTRACT
Influenza A virus PA-X comprises an N-terminal PA endonuclease domain and a C-terminal PA-X-specific domain. PA-X reduces host and viral mRNA accumulation via its endonuclease function. Here, we found that the N-terminal 15 amino acids, particularly six basic amino acids, in the C-terminal PA-X-specific region are important for PA-X shutoff activity. These six basic amino acids enabled a PA deletion mutant to suppress protein expression at a level comparable to that of wild-type PA-X.
Gestational age and adolescent mental health: evidence from Hong Kong's ‘Children of 1997’ birth cohort
Authors: Wang Hui , Leung Gabriel M , Lam HS , Schooling C Mary 
Published: June 2015

BackgroundPreterm, and more recently early term, birth has been identified as a risk factor for poor health. Whether the sequelae of late preterm or early term birth extends to poor mental health and well-being in adolescence is unclear and has not been systematically assessed.MethodLinear regression was used to assess the adjusted associations of gestational age (very/moderate preterm (<34 weeks, n=85), late preterm (34–36 weeks, n=305), early term (37–38 weeks, n=2228), full term (39–40 weeks, n=4018), late term (41 weeks, n=809), post-term (≥42 weeks, n=213)) with self-reported self-esteem at ∼11 years (n=6935), parent-reported Rutter score assessing the common emotional and behavioural problems at ∼7 years (n=6292) and ∼11 years (n=5596) and self-reported depressive symptoms at ∼13 years (n=5795) in a population-representative Hong Kong Chinese birth cohort ‘Children of 1997’ where gestational age has little social patterning.ResultsVery/moderate preterm birth was associated with higher Rutter subscore for hyperactivity (ß coefficients 0.5, 95% CI 0.01 to 1.00) at ∼7 years but not at ∼11 years, adjusted for sex, age, socio-economic position, parents’ age at birth, birth order and secondhand smoke exposure. Similarly adjusted, late preterm, early term, late term and post-term birth were not associated with self-esteem or depressive symptoms.ConclusionsIn a population-representative birth cohort from a non-Western-developed setting, gestational age had few associations with mental health and well-being in adolescence, whereas very preterm birth was specifically associated with hyperactivity in childhood. Inconsistencies with studies from Western settings suggest setting specific unmeasured confounding may underlie any observed associations.
Is traditional Chinese medicine recommended in Western medicine clinical practice guidelines in China? A systematic analysis
Authors: Ren Jun , Li Xun , Sun Jin , Han Mei , Yang Guo-Yan , Li Wen-Yuan , Robinson Nicola , Lewith George , Liu Jian-Ping 
Published: June 2015

BackgroundEvidence-based medicine promotes and relies on the use of evidence in developing clinical practice guidelines (CPGs). The Chinese healthcare system includes both traditional Chinese medicine (TCM) and Western medicine, which are expected to be equally reflected in Chinese CPGs.ObjectiveTo evaluate the inclusion of TCM-related information in Western medicine CPGs developed in China and the adoption of high level evidence.MethodsAll CPGs were identified from the China Guideline Clearinghouse (CGC), which is the main Chinese organisation maintaining the guidelines issued by the Ministry of Health of China, the Chinese Medical Association and the Chinese Medical Doctors’ Association.TCM-related contents were extracted from all the CPGs identified. Extracted information comprised the institution issuing the guideline, date of issue, disease, recommendations relating to TCM, evidence level of the recommended content and references supporting the recommendations.ResultsA total of 604 CPGs were identified, only a small number of which (74/604; 12%) recommended TCM therapy and only five guidelines (7%) had applied evidence grading. The 74 CPGs involved 13 disease systems according to the International Classification of Diseases 10th edition. TCM was mainly recommended in the treatment part of the guidelines (73/74, 99%), and more than half of the recommendations (43/74, 58%) were related to Chinese herbal medicine (single herbs or herbal treatment based on syndrome differentiation).ConclusionsFew Chinese Western medicine CPGs recommend TCM therapies and very few provide evidence grading for the TCM recommendation. We suggest that future guideline development should be based on systematic searches for evidence to support CPG recommendations and involve a multidisciplinary approach including TCM expertise.
Do patterns of mental healthcare predict treatment failure in young people with schizophrenia? Evidence from an Italian population-based cohort study
Authors: Corrao Giovanni , Soranna Davide , Merlino Luca , Monzani Emiliano , Viganò Caterina , Lora Antonio 
Published: June 2015

ObjectiveLittle is known about the practice of predicting community-based care effectiveness of patients affected by schizophrenic disorders. We assessed predictors of treatment failure in a large sample of young people affected by schizophrenia.MethodsA cohort of 556 patients aged 18–35 years who were originally diagnosed with schizophrenia during 2005–2009 in a Mental Health Service (MHS) of the Italian Lombardy Region was identified. Intensity of mental healthcare received during the first year after index visit (exposure) was measured by patients’ regularity in MHS attendance and the length of time covered with antipsychotic drug therapy. Patients were followed from index visit until 2012 for identifying hospital admission for mental disorder (outcome). A proportional hazards model was fitted to estimate the HR and 95% CIs for the exposure-outcome association, after adjusting for several covariates. A set of sensitivity analyses were performed in order to account for sources of systematic uncertainty.ResultsDuring follow-up, 144 cohort members experienced the outcome. Compared with patients on low coverage with antipsychotic drugs (≤4 months), those on intermediate (5–8 months) and high (≥9 months) coverage, had HRs (95% CI) of 0.94 (0.64 to 1.40) and 0.69 (0.48 to 0.98), respectively. There was no evidence that regular attendance at the MHS affected the outcome.ConclusionsPatients in the early phase of schizophrenia and their families should be cautioned about the possible consequences of poor antipsychotic adherence. Physicians and decision makers should increase their contribution towards improving mental healthcare.
The ETTAA study protocol: a UK-wide observational study of ‘Effective Treatments for Thoracic Aortic Aneurysm’
Authors: Sastry Priya , Hughes Victoria , Hayes Paul , Vallabhaneni Srinivasa , Sharples Linda , Thompson Matt , Catarino Pedro , Moorjani Narain , Vale Luke , Gray Joanne , Cook Andrew , Elefteriades John A , Large Stephen R 
Published: June 2015

IntroductionChronic thoracic aortic aneurysm (CTAA) affecting the arch or descending aorta is an indolent but life-threatening condition with a rising prevalence as the UK population ages. Treatment may be in the form of open surgical repair (OSR) surgery, endovascular stent grafting (ESG) or best medical therapy (BMT). Currently, there is no consensus on the best management strategy, and no UK-specific economic studies that assess outcomes beyond the chosen procedure, but this is required in the context of greater demand for treatment and limited National Health Service (NHS) resources.Methods and analysisThis is a prospective, multicentre observational study with statistical and economic modelling of patients with CTAA affecting the arch or descending aorta. We aim to gain an understanding of how treatments are currently chosen, and to determine the clinical effectiveness and cost-effectiveness of the three available treatment strategies (BMT, ESG and OSR). This will be achieved by: (1) following consecutive patients who are referred to the teams collaborating in this proposal and collecting data regarding quality of life (QoL), medical events and hospital stays over a maximum of 5 years; (2) statistical analysis of the comparative effectiveness of the three treatments; and (3) economic modelling of the comparative cost-effectiveness of the three treatments. Primary study outcomes are: aneurysm growth, QoL, freedom from reintervention, freedom from death or permanent neurological injury, incremental cost per quality-adjusted life year gained.Ethics and disseminationThe study will generate an evidence base to guide patients and clinicians to determine the indications and timing of treatment, as well as informing healthcare decision-makers about which treatments the NHS should provide. The study has achieved ethical approval and will be disseminated primarily in the form of a Health Technology Assessment monograph at its completion.Trial registration numberISRCTN04044627.
A systematic review of measurement tools of health and well-being for evaluating community-based interventions
Authors: Dronavalli Mithilesh , Thompson Sandra C 
Published: June 2015

BackgroundThose interested in evaluating the effectiveness of community interventions on health and well-being need information about what tools are available and best suited to measure improvements that could be attributed to the intervention.This study evaluated published measurement tools of health and well-being that have the potential to be used before and after an intervention.MethodsA literature search of health and sociological databases was undertaken for articles that utilised measurement tools in community settings to measure overall health, well-being or quality of life. Articles were considered potentially relevant because they included use of measurement tools related to general health or well-being. These tools were evaluated by further searching of the literature to assess each tool's properties including: reliability; validity; responsiveness; length; use in cross-cultural settings; global health or well-being assessment; use of subjective measures; clarity and cost. A composite score was made based on the average rating of all fields.ResultsOf 958 abstracts that were screened, 123 articles were extracted for review. From those articles, 27 measurement tools were selected and assessed. Based on the composite score assessing across all domains, five tools were rated as excellent.ConclusionsWhile tools may need to be selected for particular aims and interventions, a range of potential well-described tools already exist and should be considered for use in preference to ad hoc or bespoke tools. Any of the five tools rated as excellent are recommended to assess the impact of a community intervention.