bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Quality Draft Genome Sequence of “
Candidatus
Methanoperedens sp.” Strain BLZ2, a Nitrate-Reducing Anaerobic Methane-Oxidizing Archaeon Enriched in an Anoxic Bioreactor
Authors: Berger Stefanie , Frank Jeroen , Dalcin Martins Paula , Jetten Mike S. M. , Welte Cornelia U. 
Published: November 2017

ABSTRACT

The high-quality draft genome of “
Candidatus
Methanoperedens sp.” strain BLZ2, a nitrate-reducing archaeon anaerobically oxidizing methane, is presented. The genome was obtained from an enrichment culture and measures 3.74 Mb. It harbors two nitrate reductase gene clusters, an ammonium-forming nitrite reductase, and the complete reverse methanogenesis pathway. Methane that escapes to the atmosphere acts as a potent greenhouse gas. Global methane emissions are mitigated by methanotrophs, which oxidize methane to CO
2
. “
Candidatus
Methanoperedens spp.” are unique methanotrophic archaea that can perform nitrate-dependent anaerobic oxidation of methane. A high-quality draft genome sequence of only 85 contigs from this archaeon is presented here.
First Insight into the Genome Sequences of Two Linezolid-Resistant Nocardia farcinica Strains Isolated from Patients with Cystic Fibrosis
Authors: Valdezate Sylvia , Monzón Sara , Garrido Noelia , Zaballos Angel , Medina-Pascual María J. , Azcona-Gutiérrez José M. , Vilar Begoña , Cuesta Isabel 
Published: November 2017

ABSTRACT

The draft genome sequences of two
Nocardia farcinica
strains isolated from two patients with cystic fibrosis (CF), resistant to trimethoprim/sulfamethoxazole and linezolid, are reported here. The estimated genome sizes were 5.8 Mb with a 70.63% G+C content. Transposases from
Tn
916 were detected, but not 23S rRNA mutation (G2576T) related to linezolid resistance.
Genome Sequences of Four Subcluster L2
Mycobacterium
Phages, Finemlucis, Miley16, Wilder, and Zakai
Authors: Herren Christopher D. , Peister Alexandra , Breton Timothy S. , Hill Maggie S. , Anderson Marcy S. , Chang Adeline W. , Klein Sydney B. , Thornton Mackenzie M. , Vars Stacy J. , Wagner Kasey E. , Wiebe Paige L. , Williams Thomas G. , Yanez Coraima P. , Ackles Jasanta M. , Artis Darius , Brazier Ryan J. , Bryant Ronald J. , Callwood Kerel O. , Carter Isaiah H. , DeBose Cameron L. , Edwards Christian D. , Ezemba Isaiah C. , Joaquin Renshal R. , Meghoo-Peddie Zakai M. , Meghoo-Peddie Ziha G. , Moore Ryan W. , Smith Christopher E. , Turner Adam J. , Vorters Raymond L. , Wider Jeffrey J. , Krout Liesel L. , Comis Mia S. , Davick Madison J. , Michaud Eli E. , Shevenell Bailey E. , Stanley Sarah E. , Frank Chelsey I. , Montgomery Jacob R. , Blumer Lawrence S. , Doty Jean A. , Smith-Caldas Martha , Pope Welkin H. , Cresawn Steven G. , Russell Daniel A. , Garlena Rebecca A. , Jacobs-Sera Deborah , Hatfull Graham F. 
Published: November 2017

ABSTRACT

Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect
Mycobacterium smegmatis
mc
2
155 were isolated. The four phages are closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative protein-coding genes, including tyrosine integrases,
cro
, immunity repressors, and excise genes involved in the establishment of lysogeny.
Draft Genome Sequences of Eight Streptogramin-Resistant
Enterococcus
Species Isolated from Animal and Environmental Sources in the United States
Authors: Sharma Poonam , Gupta Sushim Kumar , Barrett John B. , Hiott Lari M. , House Sandra L. , Woodley Tiffanie A. , Frye Jonathan G. , Jackson Charlene R. 
Published: November 2017

ABSTRACT

Here, we present the draft genome sequences of eight streptogramin-resistant
Enterococcus
species isolated from animals and an environmental source in the United States from 2001 to 2004. Antimicrobial resistance genes were identified conferring resistance to the macrolide-lincosamide-streptogramins, aminoglycosides, tetracyclines, beta-lactams, and glycopeptides.
Complete Genome Sequences of BK Polyomavirus Strains from Two Patients with Urinary Tract Infection, Sequenced Using the Ion Torrent Platform
Authors: Rose Graham , Ranellou Kyriaki , Misra Raju , Crump Colin , Wooldridge David , Parmar Surendra , Maddren Christopher , Gharbia Saheer , Jalal Hamid 
Published: November 2017

ABSTRACT
BK polyomavirus is an important pathogen in kidney transplant patients. We report here two complete genome sequences, those of isolates CAMB-1035 and CAMB-1055, identified in two urine samples tested for urinary tract infection at a hospital in eastern England, United Kingdom. Variation and phylogenetic analyses indicate that both isolates belong to subtype Ib-1.
Draft Genome Sequence of
Myroides
sp. N17-2, a Multidrug-Resistant Bacterium Isolated from Radiation-Polluted Soils
Authors: Liu Tingting , Zhu Liying , Zhang Zhidong , Jiang Ling , Huang He 
Published: November 2017

ABSTRACT

We report here the 4.29-Mb draft genome sequence of
Myroides
sp. N17-2, a new bacterium isolated from radiation-polluted soils in Xinjiang, Uyghur Autonomous Region, China. The acquisition of its genome will provide valuable information to reveal the relationship between radiation and multidrug resistance.
Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides in Sinorhizobium meliloti
Authors: Barnett Melanie J. , Long Sharon R. 
Published: November 2017

ABSTRACT

Sinorhizobium meliloti
is a soil-dwelling alphaproteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important both for adapting to stresses in the soil and for the development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides I (EPS-I; succinoglycan) and II (EPS-II; galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots. Previous genetic screens discovered mutants with impaired EPS production, allowing the delineation of EPS biosynthetic pathways. Here we report on a genetic screen to isolate mutants with mucoid colonial morphologies that suggest EPS overproduction. Screening with Tn
5
-110, which allows the recovery of both null and upregulation mutants, yielded 47 mucoid mutants, most of which overproduce EPS-I; among the 30 unique genes and intergenic regions identified, 14 have not been associated with EPS production previously. We identified a new protein-coding gene,
emmD
, which may be involved in the regulation of EPS-I production as part of the EmmABC three-component regulatory circuit. We also identified a mutant defective in EPS-I production, motility, and symbiosis, where Tn
5
-110 was not responsible for the mutant phenotypes; these phenotypes result from a missense mutation in
rpoA
corresponding to the domain of the RNA polymerase alpha subunit known to interact with transcription regulators.

IMPORTANCE
The alphaproteobacterium
Sinorhizobium meliloti
converts dinitrogen to ammonium while inhabiting specialized plant organs termed root nodules. The transformation of
S. meliloti
from a free-living soil bacterium to a nitrogen-fixing plant symbiont is a complex developmental process requiring close interaction between the two partners. As the interface between the bacterium and its environment, the
S. meliloti
cell surface plays a critical role in adaptation to varied soil environments and in interaction with plant hosts. We isolated and characterized
S. meliloti
mutants with increased production of exopolysaccharides, key cell surface components. Our diverse set of mutants suggests roles for exopolysaccharide production in growth, metabolism, cell division, envelope homeostasis, biofilm formation, stress response, motility, and symbiosis.
Month of birth and risk of autism spectrum disorder: a retrospective cohort of male children born in Israel
Authors: Shalev Hila , Solt Ido , Chodick Gabriel 
Published: November 2017

BackgroundIncreased incidence and prevalence of autism spectrum disorder (ASD) over the last two decades have prompted considerable efforts to investigate its aetiological factors. We examined an association between month of birth and ASD incidence.MethodsIn a retrospective cohort of male children born from January 1999 to December 2008 in a large health organisation in Israel (Maccabi Healthcare Services), ASD was followed from birth through December 2015.ResultsOf 108 548 boys, 975 cases of ASD were identified. The highest rates (10.3 and 10.2 per 1000 male live births) were recorded for children born in May and August, respectively, and the lowest rates for February (7.6 per 1000 male live births). Among lower socioeconomic status households, boys born in August were more likely (OR=1.71; 95% CI 1.06 to 2.74) of being diagnosed with ASD than children born in January. Significantly higher rates were not observed for other months.ConclusionsIn line with several previous studies, we found a modestly higher likelihood of autism occurrence among male children of lower socioeconomic levels born in August.
Core Outcome Sets in Miscarriage Trials (COSMisT) study: a study protocol
Authors: Smith Paul , Cooper Natalie , Dhillon-Smith Rima , O’Toole Emily , Clark T Justin , Coomarasamy Arri 
Published: November 2017

Introduction‘Core outcome sets’ are an agreed, standardised set of outcomes based on what key stakeholders (clinicians, patients, their partners, researchers, service developers, funding organisations and so on) consider the important outcomes in the management or prevention of a condition. This paper describes the rationale and design for the development of Core Outcome Sets for Miscarriage Trials.Methods and analysisSystematic reviews, interviews and focus groups with patients and their partners will be conducted to identify potential core outcomes that will be introduced into a modified Delphi survey. To ensure all key stakeholders are included, patients, partners, clinicians, charities and researchers will be invited to take part in the modified Delphi survey. There will be three rounds of scoring and rescoring during the Delphi survey to reach consensus regarding outcomes to be included in the core set, which will be subsequently refined through face-to-face consensus discussions.Ethics and disseminationThe use of core outcome sets allows results from different studies to be compared and combined, thereby reducing inconsistency and aiding interpretation of study findings. It also means research is more likely to report relevant outcomes and so can reduce reporting bias. Understanding which outcomes are important to patients has the potential to act as a driver to improve both the quality and cost-effectiveness of miscarriage services.
Mechanical thrombectomy performs similarly in real world practice: a 2016 nationwide study from the Czech Republic
Authors: Volny Ondrej , Krajina Antonin , Belaskova Silvie , Bar Michal , Cimflova Petra , Herzig Roman , Sanak Daniel , Tomek Ales , Köcher Martin , Rocek Miloslav , Padr Radek , Cihlar Filip , Nevsimalova Miroslava , Jurak Lubomir , Havlicek Roman , Kovar Martin , Sevcik Petr , Rohan Vladimir , Fiksa Jan , Menon Bijoy K , Mikulik Robert 
Published: November 2017

BackgroundRandomized clinical trials have proven mechanical thrombectomy (MT) to be a highly effective and safe treatment in acute stroke. The purpose of this study was to compare neurothrombectomy data from the Czech Republic (CR) with data from the HERMES meta-analysis.MethodsAvailable nationwide data for the CR from 2016 from the Safe Implementation of Treatments in Stroke–Thrombectomy (SITS-TBY) registry for patients with terminal internal carotid artery (ICA) and/or middle cerebral artery (MCA) occlusions were compared with data from HERMES. CR and HERMES patients were comparable in age, sex, and baseline National Institutes of Health Stroke Scale scores.ResultsFrom a total of 1053 MTs performed in the CR, 845 (80%) were reported in the SITS-TBY. From these, 604 (72%) were included in this study. Occlusion locations were as follows (CR vs HERMES): ICA 22% versus 21% (P=0.16), M1 MCA 62% versus 69% (P=0.004), and M2 MCA 16% versus 8% (P<0.0001). Intravenous thrombolysis was given to 76% versus 83% of patients, respectively (P=0.003). Median onset to reperfusion times were comparable: 232 versus 285 min, respectively (P=0.66). A modified Thrombolysis in Cerebral Infarction score of 2b/3 was achieved in 74% (433/584) versus 71% (390/549) of patients, respectively (OR 1.17, 95% CI 0.90–1.5, P=0.24). There was no statistically significant difference in the percentage of parenchymalhematoma type 2 (OR 1.12, 95% CI 0.66–1.90, P=0.68). A modified Rankin Scale score of 0–2 at 3 months was achieved in 48% (184/268) versus 46% (291/633) of patients, respectively (OR 0.92, 95% CI 0.71–1.18, P=0.48).ConclusionsData on efficacy, safety, and logistics of MT from the CR were similar to data from the HERMES collaboration.
Coherent structures induced by dielectric barrier discharge plasma actuator
Authors: Zhang Xin , Li Huaxing , Choi Kwing So , Song Longfei 
Published: November 2017

The structures of a flow field induced by a plasma actuator were investigated experimentally in quiescent air using high-speed Particle Image Velocimetry (PIV) technology. The motivation behind was to figure out the flow control mechanism of the plasma technique. A symmetrical Dielectric Barrier Discharge (DBD) plasma actuator was mounted on the suction side of the SC (2)-0714 supercritical airfoil. The results demonstrated that the plasma jet had some coherent structures in the separated shear layer and these structures were linked to a dominant frequency of [Formula: see text] = 39 Hz when the peak-to-peak voltage of plasma actuator was 9.8 kV. The high speed PIV measurement of the induced airflow suggested that the plasma actuator could excite the flow instabilities which lead to production of the roll-up vortex. Analysis of transient results indicated that the roll-up vortices had the process of formation, movement, merging and breakdown. This could promote the entrainment effect of plasma actuator between the outside airflow and boundary layer flow, which is very important for flow control applications.
CAR T-Cell Therapies in Glioblastoma: A First Look
Authors: Migliorini Denis , Dietrich Pierre-Yves , Stupp Roger , Linette Gerald P. , Posey Avery D. , June Carl H. 
Published: November 2017

Abstract
Glioblastoma is an aggressive malignancy with a poor prognosis. The current standard of care for newly diagnosed glioblastoma patients includes surgery to the extent, temozolomide combined with radiotherapy, and alternating electric fields therapy. After recurrence, there is no standard therapy and survival is less than 9 months. Recurrent glioblastoma offers a unique opportunity to investigate new treatment approaches in a malignancy known for remarkable genetic heterogeneity, an immunosuppressive microenvironment, and a partially permissive anatomic blood–brain barrier. Results from three first-in-man chimeric antigen receptor (CAR) T-cell trials targeting IL13Rα2, Her2/CMV, and EGFRvIII have recently been reported. Each one of these trials addresses important questions, such as T-cell trafficking to CNS, engraftment and persistence, tumor microenvironment remodeling, and monitoring of glioma response to CAR T cells. Objective radiologic responses have been reported. Here, we discuss and summarize the results of these trials and suggest opportunities for the field. Clin Cancer Res; 24(3); 535–40. ©2017 AACR.
Three-Vessel Assessment of Coronary Microvascular Dysfunction in Patients With Clinical Suspicion of Ischemia
Authors: Kobayashi Yuhei , Lee Joo Myung , Fearon William F. , Lee Jang Hoon , Nishi Takeshi , Choi Dong-Hyun , Zimmermann Frederik M. , Jung Ji-Hyun , Lee Hyun-Jung , Doh Joon-Hyung , Nam Chang-Wook , Shin Eun-Seok , Koo Bon-Kwon 
Published: November 2017

Background—
Difficulty directly visualizing the coronary microvasculature as opposed to the epicardial coronary artery makes its assessment challenging. The goal of this study is to measure the index of microcirculatory resistance (IMR) in all 3 major coronary vessels to identify the clinical and angiographic predictors of an abnormal IMR.

Methods and Results—

Ninety-three patients who underwent coronary physiological assessment in all 3 major coronary vessels were prospectively enrolled (59.8±9.4 years with 77.4% men). IMR was corrected using Yong’s formula and coronary microvascular dysfunction (CMD) was defined using vessel-specific cutoffs. A global IMR was calculated as the sum of the IMR in all 3 major epicardial vessels. Angiographic epicardial disease severity was assessed with vessel-specific and overall SYNTAX score. Median IMR and fractional flow reserve was 17.2 (Q1–Q3: 13.3–22.9) and 0.92 (0.85–0.97). The majority of patients (59.1%) had no CMD, 23.7% had 1-vessel CMD, 14.0% had 2-vessel CMD, and 3.2% had 3-vessel CMD. CMD was observed at a similar rate in the territories supplied by all 3 major coronary vessels (left anterior descending coronary artery 28.0%, left circumflex artery 19.4%, and right coronary artery 23.7%;
P
=0.39). Fractional flow reserve had a weak, positive correlation with IMR (ρ=0.16;
P
<0.01). The SYNTAX score had no significant correlation with IMR, both at a patient level (ρ=−0.002;
P
=0.99) and a vessel-specific level (ρ=−0.06;
P
=0.36). By multivariable ordinal logistic regression analysis, no variable was left as an independent predictor of an abnormal IMR.

Conclusions—
Clinical factors and epicardial coronary disease severity are not predictors of the extent of CMD.

Clinical Trial Registration—

URL:
https://www.clinicaltrials.gov
. Unique identifier: NCT01621438.
Long-Term Outcomes in Patients With Type 2 Myocardial Infarction and Myocardial Injury
Authors: Chapman Andrew R. , Shah Anoop S.V. , Lee Kuan Ken , Anand Atul , Francis Oliver , Adamson Philip , McAllister David A. , Strachan Fiona E. , Newby David E. , Mills Nicholas L. 
Published: November 2017

Background:
Type 2 myocardial infarction and myocardial injury are common in clinical practice, but long-term consequences are uncertain. We aimed to define long-term outcomes and explore risk stratification in patients with type 2 myocardial infarction and myocardial injury.

Methods:
We identified consecutive patients (n=2122) with elevated cardiac troponin I concentrations (≥0.05 µg/L) at a tertiary cardiac center. All diagnoses were adjudicated as per the universal definition of myocardial infarction. The primary outcome was all-cause death. Secondary outcomes included major adverse cardiovascular events (eg, nonfatal myocardial infarction or cardiovascular death) and noncardiovascular death. To explore competing risks, cause-specific hazard ratios were obtained using Cox regression models.

Results:
The adjudicated index diagnosis was type 1 or 2 myocardial infarction or myocardial injury in 1171 (55.2%), 429 (20.2%), and 522 (24.6%) patients, respectively. At 5 years, all-cause death rates were higher in those with type 2 myocardial infarction (62.5%) or myocardial injury (72.4%) compared with type 1 myocardial infarction (36.7%). The majority of excess deaths in those with type 2 myocardial infarction or myocardial injury were because of noncardiovascular causes (hazard ratio, 2.32; 95% confidence interval, 1.92–2.81 versus type 1 myocardial infarction). Despite this finding, the observed crude major adverse cardiovascular event rates were similar between groups (30.6% versus 32.6%), with differences apparent after adjustment for covariates (hazard ratio, 0.82; 95% confidence interval, 0.69–0.96). Coronary heart disease was an independent predictor of major adverse cardiovascular events in those with type 2 myocardial infarction or myocardial injury (hazard ratio, 1.71; 95% confidence interval, 1.31–2.24).

Conclusions:
Despite an excess in noncardiovascular death, patients with type 2 myocardial infarction or myocardial injury have a similar crude rate of major adverse cardiovascular events as those with type 1 myocardial infarction. Identifying underlying coronary heart disease in this vulnerable population may help target therapies that could modify future risk.
Why Truth Matters for the Study of Religion: A Defense of a Truth-Conditional Semantics
Authors: Gardiner Mark Q. 
Published: November 2017

AbstractTruth-conditional semantics holds that the meaning of a linguistic expression is a function of the conditions under which it would be true. This seems to require limiting meaningfulness to linguistic phenomena for which the question of truth or falsity is relevant. Criticisms have been raised that there are vast swatches of meaningful language that are simply not truth-related, with religion representing a particularly rich and prevalent source. I argue that if the concept of truth as used in a truth-conditional semantics is understood in ways other than correspondence to fact, there are suitable reformulations of a truth-conditional semantics that may be appropriate for understanding religion. I further argue that these reformulations offer considerable methodological advantages to the scholar of religion.
Rivalry between Presbyters and Deacons in the Roman Church
Authors: Hunter David G. 
Published: November 2017

Abstract
In this article I offer three brief notes on Ambrosiaster’s Q. 101, De iactantia Romanorum leuitarum. First, I discuss its relation to Letter 146 of Jerome, which also deals with the rivalry between presbyters and deacons and which bears a close resemblance to Q. 101; second, I examine the peculiar features of the church hierarchy at Rome that led the anonymous deacon to claim a superior status to presbyters; and, third, I explore some indications in Q. 101 and in Jerome, Letter 146, which point to the activity of deacons in elite households at Rome.
Research for Regions: Strengthening Marine Technology Transfer for Pacific Island Countries and Biodiversity beyond National Jurisdiction
Authors: Harden-Davies Harriet R. 
Published: November 2017

Abstract
Pacific Island Countries have limited capacity to engage in scientific research involving marine genetic resources in areas beyond national jurisdiction (abnj). Marine scientific research and capacity development are central to the regime for technology transfer established by the 1982 United Nations Convention on the Law of the Sea (losc), but gaps and ambiguities weaken this framework. In this article, options to strengthen scientific capacity in Pacific Island Countries, through the development of a new international legally binding instrument for the conservation and sustainable use of biodiversity in abnj under the losc, are examined. The international framework for technology transfer could be strengthened by fostering an integrated approach to the advancement, sharing and application of scientific knowledge. Coordination and collaboration at global and regional levels will be required to increase marine science cooperation, improve access to data and information, deliver training, and overcome barriers to develop institutional and individual scientific capacity.