bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Coding Genome Sequence of Putative Novel Bluetongue Virus Serotype 27
Authors: Jenckel Maria , Bréard Emmanuel , Schulz Claudia , Sailleau Corinne , Viarouge Cyril , Hoffmann Bernd , Höper Dirk , Beer Martin , Zientara Stéphan 
Published: March 2015

ABSTRACT
We announce the complete coding genome sequence of a novel bluetongue virus (BTV) serotype (BTV-n = putative BTV-27) detected in goats in Corsica, France, in 2014. Sequence analysis confirmed the closest relationship between sequences of the novel BTV serotype and BTV-25 and BTV-26, recently discovered in Switzerland and Kuwait, respectively.
Complete Genome Sequence of a Metronidazole-Resistant Helicobacter pylori Strain
Authors: Binh Tran Thanh , Suzuki Rumiko , Kwon Dong Hyeon , Yamaoka Yoshio 
Published: March 2015

ABSTRACT

We report here the complete genome sequence of a metronidazole-resistant
Helicobacter pylori
strain (MET
r
). The MET
r
strain was obtained under exposure of
H. pylori
26695 on agar plates with low metronidazole concentrations. The genome data provide insight into the genomic changes of
H. pylori
under selection by metronidazole
in vitro
.
Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese
Authors: Storari Michelangelo , Wüthrich Daniel , Bruggmann Rémy , Berthoud Hélène , Arias-Roth Emmanuelle 
Published: March 2015

ABSTRACT

Clostridium tyrobutyricum
is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively.
High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater
Authors: Ramsay Bradley D. , Hwang Chiachi , Woo Hannah L. , Carroll Sue L. , Lucas Susan , Han James , Lapidus Alla L. , Cheng Jan-Fang , Goodwin Lynne A. , Pitluck Samuel , Peters Lin , Chertkov Olga , Held Brittany , Detter John C. , Han Cliff S. , Tapia Roxanne , Land Miriam L. , Hauser Loren J. , Kyrpides Nikos C. , Ivanova Natalia N. , Mikhailova Natalia , Pagani Ioanna , Woyke Tanja , Arkin Adam P. , Dehal Paramvir , Chivian Dylan , Criddle Craig S. , Wu Weimin , Chakraborty Romy , Hazen Terry C. , Fields Matthew W. 
Published: March 2015

ABSTRACT

Desulfovibrio carbinoliphilus
subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after
in situ
stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.
Genome Sequence of an Efficient Indole-Degrading Bacterium, Cupriavidus sp. Strain IDO, with Potential Polyhydroxyalkanoate Production Applications
Authors: Ma Qiao , Qu Yuanyuan , Zhang Zhaojing , Li Pengpeng , Tang Hongzhi 
Published: March 2015

ABSTRACT
Cupriavidus sp. strain IDO has been shown to efficiently transform indole, and the genus of Cupriavidus has been described as a promising cell factory for polyhydroxyalkanoate synthesis from low-cost wastes. Here, we report the draft genome sequence of strain IDO, which may provide useful genetic information on indole metabolism and polyhydroxyalkanoate production.
Evaluation of time to aneurysm treatment following subarachnoid hemorrhage: comparison of patients treated with clipping versus coiling
Authors: Attenello Frank J , Reid Patrick , Wen Timothy , Cen Steven , Kim-Tenser May , Sanossian Nerses , Russin Jonathan , Amar Arun , Giannotta Steven , Mack William J , Tenser Matthew 
Published: March 2015

IntroductionPrior studies of aneurysmal subarachnoid hemorrhage (SAH) have shown that treatment at teaching institutions and decreased time to surgery are factors that correlate with improved patient outcome. We aimed to individually evaluate the effect of teaching institution treatment on rates of surgical clipping or endovascular coiling.MethodsPatients with SAH treated by either aneurysm clipping or coiling between 2002 and 2010 in the Nationwide Inpatient Sample were analyzed. Time to aneurysm treatment was dichotomized to >3 days or ≤3 days and evaluated by multivariable logistic regression modeling, controlling for patient and hospital covariates. Identified predictors for prolonged time to procedure were compared between the clipping and coiling populations.ResultsBetween 2002 and 2010 there were 90 684 SAH admissions with subsequent clipping and coiling procedures. Treatment at teaching hospitals was associated with faster time to clipping (OR 0.60, 95% CI 0.44 to 0.80, p=0.001) but not coiling procedures (p=0.66). Likewise, older age (≥80 years) was associated with delays to clipping (p<0.05) but not coiling procedures (p>0.05). Patients with delayed time to treatment were associated with increased rates of moderate to severe neurological disability.ConclusionsOlder patients with SAH and those treated at non-teaching hospitals were more likely to have delays to aneurysm clipping procedures. These associations were unique to open surgery as age and hospital teaching status did not affect time to coiling procedures.
Translational Implications of Tumor Heterogeneity
Authors: Jamal-Hanjani Mariam , Quezada Sergio A. , Larkin James , Swanton Charles 
Published: March 2015

Abstract
Advances in next-generation sequencing and bioinformatics have led to an unprecedented view of the cancer genome and its evolution. Genomic studies have demonstrated the complex and heterogeneous clonal landscape of tumors of different origins and the potential impact of intratumor heterogeneity on treatment response and resistance, cancer progression, and the risk of disease relapse. However, the significance of subclonal mutations, in particular mutations in driver genes, and their evolution through time and their dynamics in response to cancer therapies, is yet to be determined. The necessary tools are now available to prospectively determine whether clonal heterogeneity can be used as a biomarker of clinical outcome and to what extent subclonal somatic alterations might influence clinical outcome. Studies that use longitudinal tissue sampling, integrating both genomic and clinical data, have the potential to reveal the subclonal composition and track the evolution of tumors to address these questions and to begin to define the breadth of genetic diversity in different tumor types and its relevance to patient outcome. Such studies may provide further evidence for drug-resistance mechanisms informing combinatorial, adaptive, and tumor immune therapies placed within the context of tumor evolution. Clin Cancer Res; 21(6); 1258–66. ©2015 AACR.
Deletion of Myeloid GSK3α Attenuates Atherosclerosis and Promotes an M2 Macrophage Phenotype
Authors: McAlpine Cameron S. , Huang Aric , Emdin Abby , Banko Nicole S. , Beriault Daniel R. , Shi Yuanyuan , Werstuck Geoff H. 
Published: March 2015

Objective—

Glycogen synthase kinase (GSK)-3α/β has been implicated in the pathogenesis of diabetes mellitus, cancer, Alzheimer, and atherosclerosis. The tissue- and homolog-specific functions of GSK3α and β in atherosclerosis are unknown. This study examines the effect of hepatocyte or myeloid cell deletion of GSK3α or GSK3β on atherosclerosis in low-density lipoprotein receptor (LDLR)
−/−
mice.

Approach and Results—

We ablated GSK3α or GSK3β expression in hepatic or myeloid cells of LDLR
−/−
mice, and mice were fed a high-fat diet for 10 weeks. GSK3α or GSK3β deficiency in hepatic or myeloid cells did not affect metabolic parameters, including plasma lipid levels. Hepatic deletion of GSK3α or GSK3β did not affect the development of atherosclerosis or hepatic lipid content. Myeloid deletion of GSK3α, but not of GSK3β, reduced atherosclerotic lesion volume and lesion complexity. Mice lacking GSK3α in myeloid cells had a less inflammatory and more anti-inflammatory plasma cytokine profile. Macrophages within atherosclerotic lesions of myeloid GSK3α-deficient mice, but not of GSK3β-deficient mice, displayed reduced expression of markers associated with M1 macrophage polarization and enhanced expression of the M2 markers. Finally, bone marrow–derived macrophages were isolated and differentiated into classical M1 macrophages or alternative M2 macrophages in vitro. GSK3α deletion, but not GSK3β deletion, attenuated the expression of genes associated with M1 polarization while promoting the expression of genes associated with M2 polarization by modulating STAT3 and STAT6 activation.

Conclusions—
Our findings suggest that deletion of myeloid GSK3α attenuates the progression of atherosclerosis by promoting an M2 macrophage phenotype.
Preexisting Serum Autoantibodies Against the NMDAR Subunit NR1 Modulate Evolution of Lesion Size in Acute Ischemic Stroke
Authors: Zerche Maria , Weissenborn Karin , Ott Christoph , Dere Ekrem , Asif Abdul R. , Worthmann Hans , Hassouna Imam , Rentzsch Kristin , Tryc Anita B. , Dahm Liane , Steiner Johann , Binder Lutz , Wiltfang Jens , Sirén Anna-Leena , Stöcker Winfried , Ehrenreich Hannelore 
Published: March 2015

Background and Purpose—

Recently, we reported high seroprevalence (age-dependent up to >19%) of
N
-methyl-
d
-aspartate-receptor subunit NR1 (NMDAR1) autoantibodies in both healthy and neuropsychiatrically ill subjects (N=4236). Neuropsychiatric syndrome relevance was restricted to individuals with compromised blood–brain barrier, for example, apolipoprotein E4 (APOE4) carrier status, both clinically and experimentally. We now hypothesized that these autoantibodies may upon stroke be protective in individuals with hitherto intact blood–brain barrier, but harmful for subjects with chronically compromised blood–brain barrier.

Methods—
Of 464 patients admitted with acute ischemic stroke in the middle cerebral artery territory, blood for NMDAR1 autoantibody measurements and APOE4 carrier status as indicator of a preexisting leaky blood–brain barrier was collected within 3 to 5 hours after stroke. Evolution of lesion size (delta day 7–1) in diffusion-weighted magnetic resonance imaging was primary outcome parameter. In subgroups, NMDAR1 autoantibody measurements were repeated on days 2 and 7.

Results—
Of all 464 patients, 21.6% were NMDAR1 autoantibody–positive (immunoglobulin M, A, or G) and 21% were APOE4 carriers. Patients with magnetic resonance imaging data available on days 1 and 7 (N=384) were divided into 4 groups according to NMDAR1 autoantibody and APOE4 status. Groups were comparable in all stroke-relevant presenting characteristics. The autoantibody+/APOE4− group had a smaller mean delta lesion size compared with the autoantibody−/APOE4- group, suggesting a protective effect of circulating NMDAR1 autoantibodies. In contrast, the autoantibody+/APOE4+ group had the largest mean delta lesion area. NMDAR1 autoantibody serum titers dropped on day 2 and remounted by day 7.

Conclusions—
Dependent on blood–brain barrier integrity before an acute ischemic brain injury, preexisting NMDAR1 autoantibodies seem to be beneficial or detrimental.
Objective Diagnostics and the Madden–Julian Oscillation. Part I: Methodology
Authors: Wolding Brandon O. , Maloney Eric D. 
Published: March 2015

AbstractDiagnostics obtained as an extension of empirical orthogonal function (EOF) analysis are shown to address many disadvantages of using EOF-based indices to assess the state of the Madden–Julian oscillation (MJO). The real-time multivariate MJO (RMM) index and the filtered MJO OLR (FMO) index are used to demonstrate these diagnostics. General characteristics of the indices, such as the geographical regions that most heavily influence each index, are assessed using the diagnostics. The diagnostics also identify how a given field, at various geographical locations, influences the index value at a given time. Termination (as defined by the RMM index) of the October 2011 MJO event that occurred during the Cooperative Indian Ocean Experiment on Intraseasonal Variability in the Year 2011 (CINDY) Dynamics of the MJO (DYNAMO) field campaign is shown to have resulted from changes in zonal wind anomalies at 200 hPa over the eastern Pacific Ocean, despite the onset of enhanced convection in the Indian Ocean and the persistence of favorable lower- and upper-level zonal wind anomalies near this region. The diagnostics objectively identify, for each specific geographical location, the index phase where the largest MJO-related anomalies in a given field are likely to be observed. This allows for the geographical variability of anomalous conditions associated with the MJO to be easily assessed throughout its life cycle. In Part II of this study, unique physical insight into the moist static energy and moisture budgets of the MJO is obtained from the application of diagnostics introduced here.
A Content Analysis of Infant and Toddler Food Advertisements in Taiwanese Popular Pregnancy and Early Parenting Magazines
Authors: Chen Yi-Chun , Chang Jung-Su , Gong Yu-Tang 
Published: March 2015

Background: Mothers who are exposed to formula advertisements (ads) are less likely to initiate breastfeeding and more likely to breastfeed for a shorter duration than other mothers. Objective: The purpose of this study was to examine infant and toddler food ads in pregnancy and early parenting magazines. Methods: A content analysis of infant and toddler food ads printed in 12 issues of 4 magazines published in 2011 was performed. Coding categories of ads included product category, advertisement category, marketing information, and advertising appeal. The target age and health-related message of each product were coded. Results: The researchers identified 756 infant and toddler food ads in the magazines. Compared with complementary food ads, formula product ads used more marketing strategies such as antenatal classes and baby contests to influence consumers and promote products. Nutritional quality and child health benefits were the two most frequently used advertising appeals. In addition, this study identified 794 formula products and 400 complementary food products; 42.8% of the complementary food products were intended for 4-month-old infants. Furthermore, 91.9% of the ads for formula products and 81% of the ads for complementary food products contained claims concerning health function or nutrient content. Conclusions: Taiwanese pregnancy and early parenting magazines contain numerous infant and toddler food ads. These ads generally use health-related claims regarding specific nutrient content and health functions to promote infant and toddler foods. Health professionals should provide more information to parents on the differences between breast milk and formula milk, and they should be aware of the potential effect of infant and toddler food ads on parents’ infant feeding decisions.
The privatisation of Australian electricity: Claims, myths and facts
Authors: Chester Lynne 
Published: March 2015

AbstractAustralia has one of the most ‘liberalised’ electricity sectors in the world. The sale of government-owned electricity companies has contributed to that liberalisation and a quarter of the proceeds of one of the world’s largest privatisation programmes. In 2014, the state governments of New South Wales and Queensland announced further electricity privatisations if re-elected. Advocates claim private ownership will mean more productive investment, lower costs leading to more efficient operations, lower prices for all consumers and better market functioning without government interference. Opponents contend that the true value of government businesses is not being realised at sale, retention can achieve returns greater than those from a sale, and that follow sale, prices will rise and jobs will be lost. This article demonstrates that the claims of either lower or higher prices, of job losses and of more efficient operations are tantamount to being myths of privatisation not borne out by reality.
Obesity Is Associated With Increased Complications After Operative Management of End-Stage Ankle Arthritis
Authors: Werner Brian C. , Burrus M. Tyrrell , Looney Austin M. , Park Joseph S. , Perumal Venkat , Cooper M. Truitt 
Published: March 2015

Background: Total ankle arthroplasty (TAA) and ankle arthrodesis (AA) are two operative options for the management of end-stage ankle arthritis that has failed conservative interventions. Obesity is associated with a greater incidence of musculoskeletal disease, particularly osteoarthritis of the weight-bearing joints, including the ankle. The objective of the present study was to use a national database to examine the association between obesity and postoperative complications after TAA and AA. Methods: The PearlDiver database was queried for patients undergoing AA and TAA using International Classification of Diseases, 9th Revision (ICD-9) procedure codes. Patients were divided into obese (body mass index ≥30 kg/m2) and nonobese (body mass index <30 kg/m2) cohorts using ICD-9 codes for body mass index and obesity. Complications within 90 days postoperatively were assessed using ICD-9 and Current Procedural Terminology (CPT) codes. Results: 23,029 patients were identified from 2005 to 2011, including 5361 with TAA and 17,668 with AA. Obese TAA patients had a significantly increased risk of 90-day major, minor, local, systemic, venous thromboembolic, infectious, and medical complications compared with nonobese patients. The incidence of revision TAA was also significantly higher in obese patients compared with nonobese patients. Findings were similar for AA, as all types of complications were significantly higher in obese patients compared with nonobese patients. Conclusion: Obesity was associated with significantly increased rates of all complications after both TAA and AA. The cause of this association was likely multifactorial, including increased rates of medical comorbidities, intraoperative factors, and larger soft tissue envelopes. Level of Evidence: Level III, comparative series.
Identification of a dibenzocyclooctadiene lignan as a HIV-1 non-nucleoside reverse transcriptase inhibitor
Authors: Han Ying-Shan , Xiao Wei-Lie , Xu Hongtao , Kramer Victor G , Quan Yudong , Mesplède Thibault , Oliveira Maureen , Colby-Germinario Susan P , Sun Han-Dong , Wainberg Mark A 
Published: March 2015

Background Due to resistance to all classes of anti-HIV drugs and drug toxicity, there is a need for the discovery and development of new anti-HIV drugs. Methods HIV-1 inhibitors were identified and biologically characterized for mechanism of action. Results We identified a dibenzocyclooctadiene lignan, termed HDS2 that possessed anti-HIV activity against a wide variety of viral strains with EC50 values in the 1–3 µM range. HDS2 was shown to act as an NNRTI by qPCR and in vitro enzyme assays. Conclusions This compound provides a new scaffold for further optimization of activity through structure-guided design.
Effect of oral melatonin and wearing earplugs and eye masks on nocturnal sleep in healthy subjects in a simulated intensive care unit environment: which might be a more promising strategy for ICU sleep deprivation?
Authors: Huang Hua-Wei , Zheng Bo-Lu , Jiang Li , Lin Zong-Tong , Zhang Guo-Bin , Shen Ling , Xi Xiu-Ming 
Published: March 2015

Abstract
Introduction
Sleep deprivation is common in critically ill patients in the intensive care unit (ICU). Noise and light in the ICU and the reduction in plasma melatonin play the essential roles. The aim of this study was to determine the effect of simulated ICU noise and light on nocturnal sleep quality, and compare the effectiveness of melatonin and earplugs and eye masks on sleep quality in these conditions in healthy subjects.

Methods
This study was conducted in two parts. In part one, 40 healthy subjects slept under baseline night and simulated ICU noise and light (NL) by a cross-over design. In part two, 40 subjects were randomly assigned to four groups: NL, NL plus placebo (NLP), NL plus use of earplugs and eye masks (NLEE) and NL plus melatonin (NLM). 1 mg of oral melatonin or placebo was administered at 21:00 on four consecutive days in NLM and NLP. Earplugs and eye masks were made available in NLEE. The objective sleep quality was measured by polysomnography. Serum was analyzed for melatonin levels. Subjects rated their perceived sleep quality and anxiety levels.

Results
Subjects had shorter total sleep time (TST) and rapid eye movement (REM) sleep, longer sleep onset latency, more light sleep and awakening, poorer subjective sleep quality, higher anxiety level and lower serum melatonin level in NL night (P <0.05). NLEE had less awakenings and shorter sleep onset latency (P <0.05). NLM had longer TST and REM and shorter sleep onset latency (P <0.05). Compared with NLEE, NLM had fewer awakenings (P = 0.004). Both NLM and NLEE improved perceived sleep quality and anxiety level (P = 0.000), and NLM showed better than NLEE in perceived sleep quality (P = 0.01). Compared to baseline night, the serum melatonin levels were lower in NL night at every time point, and the average maximal serum melatonin concentration in NLM group was significantly greater than other groups (P <0.001).

Conclusions
Compared with earplugs and eye masks, melatonin improves sleep quality and serum melatonin levels better in healthy subjects exposed to simulated ICU noise and light.

Trial registration
Chinese Clinical Trial Registry ChiCTR-IPR-14005458. Registered 10 November 2014.