bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impaired reproduction in Japanese Black cattle under cold environmental conditions
Authors: Nabenishi H , Yamazaki A 
Published: February 2017

ContentsEnvironmental factors such as the temperature–humidity index (THI) are known to affect reproductive parameters in cattle. Therefore, here, we examined whether there was any correlation between the THI and the reproductive performance of Japanese Black cattle by analysing the first‐service conception rates of 178,492 artificially inseminated cows across 9,833 herds in south‐western Japan over a 3‐year period. The daily mean (±SD) THI over the study period was 63.6 ± 11.3 (range: 41.4–81.5). The calving to first artificial insemination (AI) interval was significantly negatively correlated with THI in the month of AI (r = −.75, p < .001), whereas conception rate to first AI (CRFA) showed a cyclical change that did not correspond with that of THI, resulting in a time lag between CRFA and THI in the month of AI. Furthermore, there was a stronger correlation between CRFA and THI between 3 and 2 months before AI (r = .76 vs. .83, p < .001) than in the month of AI (r = .34, p = .04). Therefore, this extensive field study showed that a decrease in THI was associated with declined reproductive performance in Japanese Black cattle and that the impact of the cold environment on the conception rate is attributable to a carryover effect from the cold season before AI rather than conditions at the time of AI.
Improved detection of Zika virus RNA in human and animal specimens by a novel, highly sensitive and specific real‐time RT‐PCR assay targeting the 5′‐untranslated region of Zika virus
Authors: Chan Jasper Fuk‐Woo , Yip Cyril Chik‐Yan , Tee Kah‐Meng , Zhu Zheng , Tsang Jessica Oi‐Ling , Chik Kenn Ka‐Heng , Tsang Terance Gi‐Wai , Chan Chris Chung‐Sing , Poon Vincent Kwok‐Man , Sridhar Siddharth , Yin Feifei , Hung Ivan Fan‐Ngai , Chau Sandy Ka‐Yee , Zhang Anna Jinxia , Chan Kwok‐Hung , Yuen Kwok‐Yung 
Published: February 2017

AbstractObjective and MethodWe developed and evaluated five novel real‐time RT‐PCR assays targeting conserved regions in the 5′‐untranslated region (5′‐UTR), envelope (E'), non‐structural protein 2A (NS2A), NS5 and 3′‐UTR of the ZIKV genome.ResultsThe ZIKV‐5′‐UTR assay exhibited the lowest in vitro limit of detection (5–10 RNA copies/reaction and 3.0 × 10−1 plaque‐forming units/ml). Compared to the modified version of a widely adopted RT‐PCR assay targeting the ZIKV‐E gene, the ZIKV‐5′‐UTR assay showed better sensitivity in human clinical specimens, and representative mouse specimens, including many organs which are known to be involved in human ZIKV infection but difficult to obtain in clinical settings. The ZIKV‐5′‐UTR assay detected ZIKV RNA in 84/84 (100.0%) ZIKV‐E'‐positive and an additional 30/296 (10.1%, P < 0.01) ZIKV‐E'‐negative mouse specimens. The higher sensitivity of the ZIKV‐5′‐UTR assay was most significant in kidney and testis/epididymis specimens (P < 0.01). No in vitro or in vivo cross‐reactivity was found between the ZIKV‐5′‐UTR assay and dengue virus, yellow fever virus, Japanese encephalitis virus, West Nile virus, hepatitis C virus and Chikungunya virus.ConclusionsThe highly sensitive and specific ZIKV‐5′‐UTR assay may help to improve the laboratory diagnosis of ZIKV infection.
Identification of Arabidopsis genic and non‐genic promoters by paired‐end sequencing of TSS tags
Authors: Tokizawa Mutsutomo , Kusunoki Kazutaka , Koyama Hiroyuki , Kurotani Atsushi , Sakurai Tetsuya , Suzuki Yutaka , Sakamoto Tomoaki , Kurata Tetsuya , Yamamoto Yoshiharu Y. 
Published: February 2017

SummaryInformation about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired‐ and single‐end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein‐coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA‐type promoters, but not for Coreless‐type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene.
Monetary policy spillovers and currency crisis in comparative perspective: East Asia before the 1997 crisis and Eastern Europe after tapering
Authors: Kim Jong‐Hee 
Published: February 2017

AbstractThis paper estimates the possibility of currency crisis in Eastern Europe that can be triggered by monetary policy change in the key currency countries, such as tapering measure. We examine the crisis possibility in the five Eastern European nations—the Czech Republic, Poland, Hungary, Bulgaria and Romania—by performing a comparative analysis with East Asian countries before the 1997 currency crisis. For the analysis, we estimate how much the exchange rate deviates from the estimated equilibrium exchange rate, as well as the synchronicity of currency value towards some of the key currencies by creating market pressure index. The results can be explained in two ways. First, the market pressure in the Eastern Europe after 2012 is smaller than they were in East Asia before 1997. The crisis possibility especially intensifies when more the exchange rate deviates from the equilibrium value. Second, the monetary policy change in the key currency countries does not greatly affect the crisis possibility in Eastern Europe when their local currencies have the strong synchronisation with euro. Therefore, Eastern European countries show strong synchronicity towards the euro, so the crisis possibility may be alleviated if the Eurozone continues its expansionary monetary policy.
Effects of Gelling Agent and Extracellular Signaling Molecules on the Culturability of Marine Bacteria
Authors: Rygaard Anita Mac , Thøgersen Mariane Schmidt , Nielsen Kristian Fog , Gram Lone , Bentzon-Tilia Mikkel 
Published: February 2017

ABSTRACT
Only 1% of marine bacteria are currently culturable using standard laboratory procedures, and this is a major obstacle for our understanding of the biology of marine microorganisms and for the discovery of novel microbial natural products. Therefore, the purpose of this study was to investigate if improved cultivation conditions, including the use of an alternative gelling agent and supplementation with signaling molecules, improve the culturability of bacteria from seawater. Replacing agar with gellan gum improved viable counts 3- to 40-fold, depending on medium composition and incubation conditions, with a maximum of 6.6% culturability relative to direct cell counts. Through V4 amplicon sequencing we found that culturable diversity was also affected by a change in gelling agent, facilitating the growth of orders not culturable on agar-based substrates. Community analyses showed that communities grown on gellan gum substrates were significantly different from communities grown on agar and that they covered a larger fraction of the seawater community. Other factors, such as incubation temperature and time, had less obvious effects on viable counts and culturable diversity. Supplementation with acylated homoserine lactones (AHLs) did not have a positive effect on total viable counts or a strong effect on culturable diversity. However, low concentrations of AHLs increased the relative abundance of sphingobacteria. Hence, with alternative growth substrates, it is possible to significantly increase the number and diversity of cultured marine bacteria.

IMPORTANCE
Serious challenges to human health, such as the occurrence and spread of antibiotic resistance and an aging human population in need of bioactive pharmaceuticals, have revitalized the search for natural microbial products. The marine environment, representing the largest ecosystem in the biosphere, harbors an immense and virtually untapped microbial diversity producing unique bioactive compounds. However, we are currently able to cultivate only a minute fraction of this diversity. The lack of cultivated microbes is hampering not only bioprospecting efforts but also our general understanding of marine microbes. In this study, we present a means to increase the number and diversity of cultured bacteria from seawater, showing that relatively simple changes to medium components may facilitate the isolation and growth of hitherto unknown bacterial orders.
Gut Microbiota Colonization and Transmission in the Burying Beetle Nicrophorus vespilloides throughout Development
Authors: Wang Yin , Rozen Daniel E. 
Published: February 2017

ABSTRACT

Carrion beetles in the genus
Nicrophorus
rear their offspring on decomposing carcasses where larvae are exposed to a diverse community of decomposer bacteria. Parents coat the carcass with antimicrobial secretions prior to egg hatch (defined as prehatch care) and also feed regurgitated food, and potentially bacteria, to larvae throughout development (defined as full care). Here, we partition the roles of prehatch and posthatch parental care in the transmission and persistence of culturable symbiotic bacteria to larvae. Using three treatment groups (full care, prehatch care only, and no care), we found that larvae receiving full care are predominantly colonized by bacteria resident in the maternal gut while larvae receiving no care are colonized with bacteria from the carcass. More importantly, larvae receiving only prehatch care were also predominantly colonized by maternal bacteria; this result indicates that parental treatment of the carcass, including application of bacteria to the carcass surface, is sufficient to ensure symbiont transfer even in the absence of direct larval feeding. Later in development, we found striking evidence that pupae undergo an aposymbiotic stage, after which they are recolonized at eclosion with bacteria similar to those found on the molted larval cuticle and on the wall of the pupal chamber. Our results clarify the importance of prehatch parental care for symbiont transmission in
Nicrophorus vespilloides
and suggest that these bacteria successfully outcompete decomposer bacteria during larval and pupal gut colonization.

IMPORTANCE
Here, we examine the origin and persistence of the culturable gut microbiota of larvae in the burying beetle
Nicrophorus vespilloides
. This insect is particularly interesting for this study because larvae are reared on decomposing vertebrate carcasses, where they are exposed to high densities of carrion-decomposing microbes. Larvae also receive extensive parental care in the form of carcass preservation and direct larval feeding. We find that parents transmit their gut bacteria to larvae both directly, through regurgitation, and indirectly via their effects on the carcass. In addition, we find that larvae become aposymbiotic during pupation but are recolonized apparently from bacteria shed onto the insect cuticle before adult eclosion. Our results highlight the diverse interactions between insect behavior and development on microbiota composition. They further suggest that competitive interactions mediate the bacterial composition of
Nicrophorus
larvae together with or apart from the influence of beetle immunity, suggesting that the bacterial communities of these insects may be highly coevolved with those of their host species.
Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils
Authors: Masse Jacynthe , Prescott Cindy E. , Renaut Sébastien , Terrat Yves , Grayston Sue J. 
Published: February 2017

ABSTRACT
The Athabasca oil sand deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess whether the soil prokaryotic alpha diversity (α-diversity) and β-diversity in oil sand soils reconstructed 20 to 30 years previously and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal forest soils subject to wildfire disturbance. Prokaryotic α-diversity and β-diversity were assessed using massively parallel sequencing of 16S rRNA genes. The β-diversity, but not the α-diversity, differed between reconstructed and natural soils. Bacteria associated with an oligotrophic lifestyle were more abundant in natural forest soils, whereas bacteria associated with a copiotrophic lifestyle were more abundant in reconstructed soils. Ammonia-oxidizing archaea were most abundant in reconstructed soils planted with grasses. Plant species were the main factor influencing α-diversity in natural and in reconstructed soils. Nitrogen deposition, pH, and plant species were the main factors influencing the β-diversity of the prokaryotic communities in natural and reconstructed soils. The results highlight the importance of nitrogen deposition and aboveground-belowground relationships in shaping soil microbial communities in natural and reconstructed soils.

IMPORTANCE
Covering over 800 km
2
, land disturbed by the exploitation of the oil sands in Canada has to be restored. Here, we take advantage of the proximity between these reconstructed ecosystems and the boreal forest surrounding the oil sand mining area to study soil microbial community structure and processes in both natural and nonnatural environments. By identifying key characteristics shaping the structure of soil microbial communities, this study improved our understanding of how vegetation, soil characteristics and microbial communities interact and drive soil functions.
Randomised, double-blind, parallel group, placebo-controlled study to evaluate the analgesic efficacy and safety of VVZ-149 injections for postoperative pain following laparoscopic colorectal surgery
Authors: Nedeljkovic Srdjan S , Correll Darin J , Bao Xiaodong , Zamor Natacha , Zeballos Jose L , Zhang Yi , Young Mark J , Ledley Johanna , Sorace Jessica , Eng Kristen , Hamsher Carlyle P , Maniam Rajivan , Chin Jonathan W , Tsui Becky , Cho Sunyoung , Lee Doo H 
Published: February 2017

IntroductionIn spite of advances in understanding and technology, postoperative pain remains poorly treated for a significant number of patients. In colorectal surgery, the need for developing novel analgesics is especially important. Patients after bowel surgery are assessed for rapid return of bowel function and opioids worsen ileus, nausea and constipation. We describe a prospective, double-blind, parallel group, placebo-controlled randomised controlled trial testing the hypothesis that a novel analgesic drug, VVZ -149, is safe and effective in improving pain compared with providing opioid analgesia alone among adults undergoing laparoscopic colorectal surgery.Methods and analysisBased on sample size calculations for primary outcome, we plan to enrol 120 participants. Adult patients without significant medical comorbidities or ongoing opioid use and who are undergoing laparoscopic colorectal surgery will be enrolled. Participants are randomly assigned to receive either VVZ-149 with intravenous (IV) hydromorphone patient-controlled analgesia (PCA) or the control intervention (IV PCA alone) in the postoperative period. The primary outcome is the Sum of Pain Intensity Difference over 8 hours (SPID-8 postdose). Participants receive VVZ-149 for 8 hours postoperatively to the primary study end point, after which they continue to be assessed for up to 24 hours. We measure opioid consumption, record pain intensity and pain relief, and evaluate the number of rescue doses and requests for opioid. To assess safety, we record sedation, nausea and vomiting, respiratory depression, laboratory tests and ECG readings after study drug administration. We evaluate for possible confounders of analgesic response, such as anxiety, depression and catastrophising behaviours. The study will also collect blood sample data and evaluate for pharmacokinetic and pharmacodynamic relationships.Ethics and disseminationEthical approval of the study protocol has been obtained from Institutional Review Boards at the participating institutions. Trial results will be disseminated through scientific conference presentations and by publication in scientific journals.Trial registration numberNCT02489526; pre-results.
Retrospective examination of lipid-lowering treatment patterns in a real-world high-risk cohort in the UK in 2014: comparison with the National Institute for Health and Care Excellence (NICE) 2014 lipid modification guidelines
Authors: Steen Dylan L , Khan Irfan , Ansell David , Sanchez Robert J , Ray Kausik K 
Published: February 2017

BackgroundIn 2014, guidelines from the National Institute for Health and Care Excellence (NICE) provided updated recommendations on lipid-modifying therapy (LMT). We assessed clinical practice contemporaneous to release of these guidelines in a UK general practice setting for secondary and high-risk primary-prevention populations, and extrapolated the findings to UK nation level.MethodsPatients from The Health Improvement Network database with the following criteria were included: lipid profile in 2014 (index date); ≥20 years of age; ≥2 years representation in database prior to index; ≥1 statin indication either for atherosclerotic cardiovascular disease (ASCVD) or the non-ASCVD conditions high-risk diabetes mellitus and/or chronic kidney disease.ResultsOverall, 183 565 patients met the inclusion criteria (n=91 479 for ASCVD, 92 086 for non-ASCVD). In those with ASCVD, 79% received statin treatment and 31% received high-intensity statin. In the non-ASCVD group, 62% were on a statin and 57% received medium-intensity or high-intensity statin. In the ASCVD and non-ASCVD cohorts, 6% and 15%, respectively, were already treated according to dosing recommendations as per updated NICE guidelines. Extrapolation to the 2014 UK population indicated that, of the 3.3 million individuals with ASCVD, 2.4 million would require statin uptitration and 680 000 would require statin initiation (31% de novo initiation, 60% reinitiation, 9% addition to non-statin LMT) to achieve full concordance with updated guidelines. Of the 3.5 million high-risk non-ASCVD individuals, 1.6 million would require statin uptitration and 1.4 million would require statin initiation (59% de novo initiation, 36% reinitiation, 5% addition to non-statin LMT).ConclusionsA large proportion of UK individuals with ASCVD and high-risk non-ASCVD received statin treatment (79% and 62%, respectively) during the year of NICE 2014 guidelines release. Up to 94% of patients with ASCVD and 85% of high-risk non-ASCVD individuals, representing ∼3 million individuals in each group, would require statin uptitration or initiation to achieve full concordance with updated guidelines.
Informing efficient randomised controlled trials: exploration of challenges in developing progression criteria for internal pilot studies
Authors: Avery Kerry N L , Williamson Paula R , Gamble Carrol , O'Connell Francischetto Elaine , Metcalfe Chris , Davidson Peter , Williams Hywel , Blazeby Jane M 
Published: February 2017

ObjectivesDesigning studies with an internal pilot phase may optimise the use of pilot work to inform more efficient randomised controlled trials (RCTs). Careful selection of preagreed decision or ‘progression’ criteria at the juncture between the internal pilot and main trial phases provides a valuable opportunity to evaluate the likely success of the main trial and optimise its design or, if necessary, to make the decision not to proceed with the main trial. Guidance on the appropriate selection and application of progression criteria is, however, lacking. This paper outlines the key issues to consider in the optimal development and review of operational progression criteria for RCTs with an internal pilot phase.DesignA structured literature review and exploration of stakeholders' opinions at a Medical Research Council (MRC) Hubs for Trials Methodology Research workshop. Key stakeholders included triallists, methodologists, statisticians and funders.ResultsThere is considerable variation in the use of progression criteria for RCTs with an internal pilot phase, although 3 common issues predominate: trial recruitment, protocol adherence and outcome data. Detailed and systematic reporting around the decision-making process for stopping, amending or proceeding to a main trial is uncommon, which may hamper understanding in the research community about the appropriate and optimal use of RCTs with an internal pilot phase. 10 top tips for the development, use and reporting of progression criteria for internal pilot studies are presented.ConclusionsSystematic and transparent reporting of the design, results and evaluation of internal pilot trials in the literature should be encouraged in order to facilitate understanding in the research community and to inform future trials.