bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?
Authors: Latorre-Margalef Neus , Avril Alexis , Tolf Conny , Olsen Björn , Waldenström Jonas 
Published: December 2015

ABSTRACT

Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (

C
t

) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given

C
t

value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data.
Diguanylate Cyclases AdrA and STM1987 Regulate Salmonella enterica Exopolysaccharide Production during Plant Colonization in an Environment-Dependent Manner
Authors: Cowles Kimberly N. , Willis David K. , Engel Tyler N. , Jones Jeffrey B. , Barak Jeri D. 
Published: December 2015

ABSTRACT

Increasing evidence indicates that despite exposure to harsh environmental stresses,
Salmonella enterica
successfully persists on plants, utilizing fresh produce as a vector to animal hosts. Among the important
S. enterica
plant colonization factors are those involved in biofilm formation.
S. enterica
biofilm formation is controlled by the signaling molecule cyclic di-GMP and represents a sessile lifestyle on surfaces that protects the bacterium from environmental factors. Thus, the transition from a motile, planktonic lifestyle to a sessile lifestyle may represent a vital step in bacterial success. This study examined the mechanisms of
S. enterica
plant colonization, including the role of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), the enzymes involved in cyclic di-GMP metabolism. We found that two biofilm components, cellulose and curli, are differentially required at distinct stages in root colonization and that the DGC STM1987 regulates cellulose production in this environment independent of AdrA, the DGC that controls the majority of
in vitro
cellulose production. In addition, we identified a new function for AdrA in the transcriptional regulation of colanic acid and demonstrated that
adrA
and colanic acid biosynthesis are associated with
S. enterica
desiccation tolerance on the leaf surface. Finally, two PDEs with known roles in motility, STM1344 and STM1697, had competitive defects in the phyllosphere, suggesting that regulation of motility is crucial for
S. enterica
survival in this niche. Our results indicate that specific conditions influence the contribution of individual DGCs and PDEs to bacterial success, perhaps reflective of differential responses to environmental stimuli.
Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches
Authors: Mikaelyan Aram , Thompson Claire L. , Hofer Markus J. , Brune Andreas 
Published: December 2015

ABSTRACT

The gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroach
Shelfordella lateralis
as a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such as
Dysgonomonas
and
Parabacteroides
spp., were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.
The effect of metformin on cardiovascular risk profile in patients without diabetes presenting with acute myocardial infarction: data from the Glycometabolic Intervention as adjunct to Primary Coronary Intervention in ST Elevation Myocardial Infarction (GIPS-III) trial
Authors: Lexis Chris P H , van der Horst-Schrivers Anouk N A , Lipsic Erik , Valente Mattia A E , Muller Kobold Anneke C , de Boer Rudolf A , van Veldhuisen Dirk J , van der Harst Pim , van der Horst Iwan C C 
Published: December 2015

ObjectiveIn patients with diabetes mellitus, metformin treatment is associated with reduced mortality and attenuation of cardiovascular risk. As a subanalysis of the Glycometabolic Intervention as adjunct to Primary Coronary Intervention in ST Elevation Myocardial Infarction (GIPS-III) study, we evaluated whether metformin treatment in patients with ST-segment elevation myocardial infarction (STEMI) without diabetes improves the cardiovascular risk profile.MethodsA total of 379 patients, without known diabetes, presenting with STEMI were randomly allocated to receive metformin 500 mg twice daily or placebo for 4 months.ResultsAfter 4 months, the cardiovascular risk profile of patients receiving metformin (n=172) was improved compared with placebo (n=174); glycated hemoglobin (5.83% (95% CI 5.79% to 5.87%) vs 5.89% (95% CI 5.85% to 5.92%); 40.2 mmol/mol (95% CI 39.8 to 40.6) vs 40.9 mmol/mol (40.4 to 41.2), p=0.049); total cholesterol (3.85 mmol/L (95% CI 3.73 to 3.97) vs 4.02 mmol/L (95% CI 3.90 to 4.14), p=0.045); low-density lipoprotein cholesterol (2.10 mmol/L (95% CI 1.99 to 2.20) vs 2.3 mmol/L (95% CI 2.20 to 2.40), p=0.007); body weight (83.8 kg (95% CI 83.0 to 84.7) vs 85.2 kg (95% CI 84.4 to 86.1), p=0.024); body mass index (26.8 kg/m2(95% CI 26.5 to 27.0) vs 27.2 kg/m2(95% CI 27.0 to 27.5), p=0.014). Levels of fasting glucose, postchallenge glucose, insulin, high-density lipoprotein cholesterol, and blood pressure were similar in both groups.ConclusionsAmong patients with STEMI without diabetes, treatment with metformin for 4 months resulted in a modest improvement of the cardiovascular risk profile compared with placebo.Trial register numberNCT01217307.
Moxibustion as an adjuvant for benign prostatic hyperplasia with lower urinary tract symptoms: a protocol for a parallel-group, randomised, controlled pilot trial
Authors: Lee Hye-Yoon , Nam Jong-Kil , Lee Sang-Don , Lee Dong-Hoon , Han Ji-Yeon , Yun Young-Ju , Lee Ji-Hye , Park Hye-lim , Park Seong-Ha , Kwon Jung-Nam 
Published: December 2015

IntroductionThis study aims to explore the feasibility of using moxibustion as a supplementary intervention and to assess the sample size for verifying the effectiveness and safety of integrative treatment involving moxibustion compared with conventional treatment for patients with benign prostatic hyperplasia accompanying moderate to severe lower urinary tract symptoms.Methods and analysisA total of 60 patients diagnosed with benign prostatic hyperplasia by a urologist based on prostate size, prostate-specific antigen and clinical symptoms will participate of their own free will; urologists will monitor the patients and evaluate their symptoms. The patients will be randomised to either a conventional group or an integrative group with a 1:1 allocation according to computer-generated random numbers concealed in opaque, sealed, sequentially numbered envelopes. Watchful waiting or oral medication including α blocker, 5α-reductase inhibitors or antimuscarinic drugs will be offered as conventional treatment. Integrative treatment will include moxibustion therapy in addition to the conventional treatment. The moxibustion therapy will be conducted twice a week for 4 weeks on the bilateral acupoints SP6, LR3 and CV4 by a qualified Korean medical doctor. The primary outcome will be the International Prostate Symptom Score (IPSS) after eight sessions. The secondary outcomes will be the post-void residual urine volume, the maximum urinary flow rate, IPSS, the results of a Short-Form 36-Question Health Survey after 12 weeks, and the patients’ global impression of changes at each visit.Ethics and disseminationWritten informed consent will be obtained from all participants. This study was approved by the institutional review boards of both Pusan National University Yangsan Hospital and Pusan National University Korean Medicine Hospital. The trial results will be disseminated through open-access journals and conferences.Trial registration numberNCT02051036.
Association of GDF1 rs4808863 with fetal congenital heart defects: a case–control study
Authors: Zhang Juan , Wu Qingqing , Wang Li , Li Xiaofei , Ma Yuqing , Yao Ling 
Published: December 2015

BackgroundCongenital heart defects (CHDs) are the most common fetal defects and the most important cause of child mortality and morbidity.ObjectiveTo investigate the association between growth/differentiation factor 1 (GDF1) polymorphisms and fetal CHDs, by evaluating the association of GDF1 rs4808863 with fetal CHDs.DesignA case–control study.SettingBeijing, China.ParticipantsWe selected 124 fetuses with a CHD and a normal karyotype and normal array-based comparative genomic hybridisation analysis and compared them with 124 normal fetuses matched for gestational age and sex. Fetuses with a CHD, from 20 to 32 weeks of gestation were included. Fetuses with any chromosomal abnormalities, and fetuses from multiple pregnancies and those carried by pregnant women with chronic diseases, were excluded from this research. DNA extraction and genotyping were carried out for all cases to investigate the genotype distributions of GDF1 rs4808863.ResultsA significant difference was noted for the CT phenotype of GDF1 rs4808863 between the controls and the fetuses with CHDs using homozygote and heterozygote comparisons. The minor allele (T allele) of GDF1 rs4808863 was associated with an increased risk of CHD (p<0.05). A statistically significant difference between controls and fetuses with CHDs was noted in a comparison with the mutation genotype CT+TT and wild-type genotype CC (p<0.05) using dominant modal analysis. After stratification analysis, the CT phenotype, the minor allele (T allele) and the mutation genotype CT+TT of the rs4808863 polymorphism were associated with atrioventricular septal defect (AVSD), left ventricular outflow tract obstruction (LVOTO) and left–right laterality defects (p<0.05).ConclusionsOur results suggest that the GDF1 rs4808863 polymorphism contributes to an increased risk of fetal CHDs, especially the subtypes of AVSD, LVOTO and left–right laterality defects.
To what extent are surgery and invasive procedures effective beyond a placebo response? A systematic review with meta-analysis of randomised, sham controlled trials
Authors: Jonas Wayne B , Crawford Cindy , Colloca Luana , Kaptchuk Ted J , Moseley Bruce , Miller Franklin G , Kriston Levente , Linde Klaus , Meissner Karin 
Published: December 2015

ObjectivesTo assess the quantity and quality of randomised, sham-controlled studies of surgery and invasive procedures and estimate the treatment-specific and non-specific effects of those procedures.DesignSystematic review and meta-analysis.Data sourcesWe searched PubMed, EMBASE, CINAHL, CENTRAL (Cochrane Library), PILOTS, PsycInfo, DoD Biomedical Research, clinicaltrials.gov, NLM catalog and NIH Grantee Publications Database from their inception through January 2015.Study selectionWe included randomised controlled trials of surgery and invasive procedures that penetrated the skin or an orifice and had a parallel sham procedure for comparison.Data extraction and analysisThree authors independently extracted data and assessed risk of bias. Studies reporting continuous outcomes were pooled and the standardised mean difference (SMD) with 95% CIs was calculated using a random effects model for difference between true and sham groups.Results55 studies (3574 patients) were identified meeting inclusion criteria; 39 provided sufficient data for inclusion in the main analysis (2902 patients). The overall SMD of the continuous primary outcome between treatment/sham-control groups was 0.34 (95% CI 0.20 to 0.49; p<0.00001; I2=67%). The SMD for surgery versus sham surgery was non-significant for pain-related conditions (n=15, SMD=0.13, p=0.08), marginally significant for studies on weight loss (n=10, SMD=0.52, p=0.05) and significant for gastroesophageal reflux disorder (GERD) studies (n=5, SMD=0.65, p<0.001) and for other conditions (n=8, SMD=0.44, p=0.004). Mean improvement in sham groups relative to active treatment was larger in pain-related conditions (78%) and obesity (71%) than in GERD (57%) and other conditions (57%), and was smaller in classical-surgery trials (21%) than in endoscopic trials (73%) and those using percutaneous procedures (64%).ConclusionsThe non-specific effects of surgery and other invasive procedures are generally large. Particularly in the field of pain-related conditions, more evidence from randomised placebo-controlled trials is needed to avoid continuation of ineffective treatments.
Predictors of lower extremity injuries in team sports (PROFITS-study): a study protocol
Authors: Pasanen Kati , Rossi Marko T , Parkkari Jari , Heinonen Ari , Steffen Kathrin , Myklebust Grethe , Krosshaug Tron , Vasankari Tommi , Kannus Pekka , Avela Janne , Kulmala Juha-Pekka , Perttunen Jarmo , Kujala Urho M , Bahr Roald 
Published: December 2015

IntroductionSeveral intrinsic risk factors for lower extremity injuries have been proposed, including lack of proper knee and body control during landings and cutting manoeuvres, low muscular strength, reduced balance and increased ligament laxity, but there are still many unanswered questions. The overall aim of this research project is to investigate anatomical, biomechanical, neuromuscular, genetic and demographic risk factors for traumatic non-contact lower extremity injuries in young team sport athletes. Furthermore, the research project aims to develop clinically oriented screening tools for predicting future injury risk.MethodsYoung female and male players (n=508) from nine basketball teams, nine floorball teams, three ice hockey teams, and one volleyball team accepted the invitation to participate in this four-and-half-year prospective follow-up study. The players entered the study either in 2011, 2012 or 2013, and gave blood samples, performed physical tests and completed the baseline questionnaires. Following the start of screening tests, the players will be followed for sports injuries through December 2015. The primary outcome is a traumatic non-contact lower extremity injury. The secondary outcomes are other sports-related injuries. Injury risk is examined on the basis of anatomical, biomechanical, neuromuscular, genetic and other baseline factors. Univariate and multivariate regression models will be used to investigate association between investigated parameters and injury risk.
Development of a cross-cultural deprivation index in five European countries
Authors: Guillaume Elodie , Pornet Carole , Dejardin Olivier , Launay Ludivine , Lillini Roberto , Vercelli Marina , Marí-Dell'Olmo Marc , Fernández Fontelo Amanda , Borrell Carme , Ribeiro Ana Isabel , Pina Maria Fatima de , Mayer Alexandra , Delpierre Cyrille , Rachet Bernard , Launoy Guy 
Published: December 2015

BackgroundDespite a concerted policy effort in Europe, social inequalities in health are a persistent problem. Developing a standardised measure of socioeconomic level across Europe will improve the understanding of the underlying mechanisms and causes of inequalities. This will facilitate developing, implementing and assessing new and more effective policies, and will improve the comparability and reproducibility of health inequality studies among countries. This paper presents the extension of the European Deprivation Index (EDI), a standardised measure first developed in France, to four other European countries—Italy, Portugal, Spain and England, using available 2001 and 1999 national census data.Methods and resultsThe method previously tested and validated to construct the French EDI was used: first, an individual indicator for relative deprivation was constructed, defined by the minimal number of unmet fundamental needs associated with both objective (income) poverty and subjective poverty. Second, variables available at both individual (European survey) and aggregate (census) levels were identified. Third, an ecological deprivation index was constructed by selecting the set of weighted variables from the second step that best correlated with the individual deprivation indicator.ConclusionsFor each country, the EDI is a weighted combination of aggregated variables from the national census that are most highly correlated with a country-specific individual deprivation indicator. This tool will improve both the historical and international comparability of studies, our understanding of the mechanisms underlying social inequalities in health and implementation of intervention to tackle social inequalities in health.
Effect of immunosuppressive therapy on interferon γ release assay for latent tuberculosis screening in patients with autoimmune diseases: a systematic review and meta-analysis
Authors: Wong Sunny H , Gao Qinyan , Tsoi Kelvin K F , Wu William K K , Tam Lai-shan , Lee Nelson , Chan Francis K L , Wu Justin C Y , Sung Joseph J Y , Ng Siew C 
Published: December 2015

ObjectiveInterferon γ release assay (IGRA) is commonly used to diagnose latent TB infection (LTBI). Immunosuppressive therapy may affect its performance but data are conflicting. We aimed to determine the effect of immunosuppressive therapy on the performance of IGRA in patients with autoimmune diseases.MethodsWe searched PubMed, MEDLINE, EMBASE and the Cochrane Library up to December 2014. We included studies that reported the IGRA results in patients with autoimmune disease with or without immunosuppressive therapy. The pooled effect of immunosuppressive therapy on IGRA was estimated using a Peto fixed-effects model.ResultsWe included 17 studies with 3197 participants in the meta-analysis. Among the subjects, 71.5% were taking immunosuppressive therapy and 56.7% had received Bacillus Calmette–Guérin vaccination. Compared with patients not on immunosuppressants, patients receiving immunosuppressive therapy were less likely to have a positive IGRA result (OR 0.66, 95% CI 0.53 to 0.83, I2=23%), especially patients receiving anti-tumour necrosis factor (anti-TNF) treatment (OR 0.50, 95% CI 0.29 to 0.88). The use of immunosuppressive therapy was also associated with a lower rate of positive tuberculin skin test result (OR 0.51, 95% CI 0.42 to 0.61).ConclusionsOur meta-analysis showed that IGRA results are negatively affected by immunosuppressive therapy. IGRA alone may not be sufficiently sensitive to diagnose LTBI in patients on immunosuppressive therapy. Patients should preferably be screened for LTBI before initiation of immunosuppressive therapy, especially before anti-TNF therapy.
Late Quaternary glaciations in the eastern Mediterranean
Authors: Sarıkaya Mehmet Akif , Çiner Attila 
Published: December 2015

Abstract
Fourteen mountains in the eastern Mediterranean, between southern Turkey and Lebanon, are high enough to support Quaternary valley glaciers or ice caps. The timing of the glaciations has been established mainly by cosmogenic dating. We re-evaluated the dated sites and recalculated some of the published cosmogenic ages using up-to-date production rates. The oldest geochronological records reported from the region belong to glaciations before the globally defined Last Glacial Maximum (LGM). These glaciers probably developed during the beginning of the last glaciation (Marine Isotope Stage (MIS) 4; around 71 ka) and stopped advancing at the end of MIS 3 (at 29–35 ka). Later, glaciers expanded and reached their most extensive positions during MIS 2 (after 29 ka). This locally occurred between 21.5 and 18.5 ka, which was synchronous with the global LGM. After the LGM, glaciers started to retreat to less extensive positions and deposited their moraines ∼16 ka during the late-glacial. Younger Dryas (∼12 ka) advances have also been reported from a few mountains. Rare early Holocene glaciations were dated to 8.5 ka in the interior regions. Late Holocene (1–4 ka) and Little Ice Age advances have also been observed on mountains higher than 3500 m.
Deciphering multiple controls on reservoir quality and inhibition of quartz cement in a complex reservoir: Ordovician glacial sandstones, Illizi Basin, Algeria
Authors: Wells Martin , Hirst Philip , Bouch Jon , Whear Emma , Clark Nigel 
Published: December 2015

Abstract

Late Ordovician (
c.
445 Ma) glacial sandstones form important gas reservoirs in the Illizi Basin, SW Algeria. These reservoirs have a high degree of depositional and diagenetic complexity, such that understanding and predicting reservoir quality (RQ) presents a major challenge to their economic development. Porosity is typically 1–10%, but reaches up to 15% and permeability is typically <10
−15
m
2
(<1 mD), but locally reaches >10
−13
m
2
(>100 mD). The key questions addressed herein concern the development and distribution of this RQ variability, specifically why has good RQ been locally preserved?

Primary depositional fabric exerts a strong control on RQ. Muddy sandstones are either highly compacted or pervasively cemented by quartz and microporous illite, and have very poor RQ. Only fine- to medium-grained, moderately well sorted, clean sandstones can contain good RQ, but texturally and mineralogically similar sandstones span a wide range of porosity and permeability. This range is primarily driven by the degree of quartz cementation, with incomplete cementation resulting in the best RQ. Quartz overgrowths in incompletely cemented clean sandstones are patchy and non-luminescent in scanning electron microscopy with cathodoluminescence (SEM-CL), possibly indicating slow growth rates. There is tentative evidence to link incomplete quartz cementation with oil charging of the reservoir. An alternative or additional explanation of RQ preservation may be related to limited silica supply in the centres of the thickest, stacked, clean sandstones, where the better RQ tends to reside.
The results of this study imply that sustained high-energy depositional processes, coupled with an early oil charge, are prerequisites for retaining the best RQ. This has important implications for the exploration and development of Late Ordovician glacial sandstones in the Illizi Basin, and potentially similar plays elsewhere.