bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Methanohalophilus mahii Strain DAL1 Reconstructed from a Hydraulic Fracturing-Produced Water Metagenome
Authors: Lipus Daniel , Vikram Amit , Ross Daniel E. , Bibby Kyle 
Published: September 2016

ABSTRACT

We report here the 1,882,100-bp draft genome sequence of
Methanohalophilus mahii
strain DAL1, recovered from Marcellus Shale hydraulic fracturing-produced water using metagenomic contig binning. Genome annotation revealed several key methanogenesis genes and provides valuable information on archaeal activity associated with hydraulic fracturing-produced water environments.
Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Pf1
Authors: Zhang Yulei , Nie Pin , Lin Li 
Published: September 2016

ABSTRACT

Flavobacterium columnare
is the etiologic agent of columnaris disease, a devastating fish disease prevailing in worldwide aquaculture industry. Here, we describe the complete genome of
F. columnare
strain Pf1, a highly virulent strain isolated from yellow catfish (
Pelteobagrus fulvidraco
) in China.
Draft Genome Sequence of the Psychrophilic Gliding Species Gelidibacter algens ACAM 536
Authors: Bowman John P. 
Published: September 2016

ABSTRACT

A draft genome sequence was obtained from the type strain of
Gelidibacter algens
(ACAM 536). This species was isolated from sea-ice diatom assemblages collected from Ellis Fjord, Eastern Antarctica. The genome of ACAM 536 is a single circular chromosome with an estimated size of 4.50 Mbp.
Draft Genome Sequence of Biocontrol Agent Bacillus cereus UW85
Authors: Lozano Gabriel L. , Holt Jonathan , Ravel Jacques , Rasko David A. , Thomas Michael G. , Handelsman Jo 
Published: September 2016

ABSTRACT

Bacillus cereus
UW85 was isolated from a root of a field-grown alfalfa plant from Arlington, WI, and identified for its ability to suppress damping off, a disease caused by
Phytophthora megasperma
f. sp.
medicaginis
on alfalfa. Here, we report the draft genome sequence of
B. cereus
UW85, obtained by a combination of Sanger and Illumina sequencing.
Complete Genome Sequence of Vibrio alginolyticus ZJ-T
Authors: Deng Yiqin , Chen Chang , Zhao Zhe , Huang Xiaochun , Yang Yiying , Ding Xiongqi 
Published: September 2016

ABSTRACT

Vibrio alginolyticus
is a ubiquitous Gram-negative bacterium which is normally distributed in the coastal and estuarine environments. It has been suggested to be an opportunistic pathogen to both marine animals and humans, Here, the completed genome sequence of
V. alginolyticus
ZJ-T was determined by Illumina high-throughput sequencing.
Making outcrops relevant for an unconventional source rock play: an example from the Eagle Ford Group of Texas
Authors: Donovan Arthur D. 
Published: September 2016

Abstract
The utility of outcrops to geoscientists working the subsurface is typically limited by provincial nomenclature, outcrop-based lithostratigraphic subdivisions, which commonly differ in name and numbers among researchers, and often a basic indifference to the subsurface stratigraphy. In the subsurface of South Texas, the Eagle Ford Group is commonly divided into an organic-rich Lower Eagle Formation and a carbonate-rich Upper Eagle Ford Formation. In contrast, coeval strata that crop out nearby in West Texas are traditionally referred to as the Boquillas Formation. Adding further complexity to the outcrop stratigraphy is that previous workers divided the Boquillas into two to five informal lithostratigraphic units whose names and boundaries differ among researchers. By convolving information from a handheld gamma ray spectrometer, outcrop geochemical data and sequence stratigraphy, the Lower and Upper Eagle formations, as defined in the subsurface of South Texas, can now be defined in the coeval Eagle Ford Group outcrops of West Texas. Integrating basic geochemical and petrophysical data to the updated stratigraphy on these outcrops was transformative. By doing this, these West Texas exposures became portals to examine, as well as explain and predict, the distribution and thickness variations of specific chronostratigraphic units that are critical to the economic success of exploiting the Eagle Group across the unconventional source rock play fairway in South Texas.
Molecular Differences between Screen-Detected and Interval Breast Cancers Are Largely Explained by PAM50 Subtypes
Authors: Li Jingmei , Ivansson Emma , Klevebring Daniel , Tobin Nicholas P. , Lindström Linda Sofie , Holm Johanna , Prochazka Gabriela , Cristando Camilla , Palmgren Juni , Törnberg Sven , Humphreys Keith , Hartman Johan , Frisell Jan , Rantalainen Mattias , Lindberg Johan , Hall Per , Bergh Jonas , Grönberg Henrik , Czene Kamila 
Published: September 2016

AbstractPurpose: Interval breast cancer is of clinical interest, as it exhibits an aggressive phenotype and evades detection by screening mammography. A comprehensive picture of somatic changes that drive tumors to become symptomatic in the screening interval can improve understanding of the biology underlying these aggressive tumors.Experimental Design: Initiated in April 2013, Clinical Sequencing of Cancer in Sweden (Clinseq) is a scientific and clinical platform for the genomic profiling of cancer. The breast cancer pilot study consisted of women diagnosed with breast cancer between 2001 and 2012 in the Stockholm/Gotland regions. A subset of 307 breast tumors was successfully sequenced, of which 113 were screen-detected and 60 were interval cancers. We applied targeted deep sequencing of cancer-related genes; low-pass, whole-genome sequencing; and RNA sequencing technology to characterize somatic differences in the genomic and transcriptomic architecture by interval cancer status. Mammographic density and PAM50 molecular subtypes were considered.Results: In the univariate analyses, TP53, PPP1R3A, and KMT2B were significantly more frequently mutated in interval cancers than in screen-detected cancers. Acquired somatic copy number aberrations with a frequency difference of at least 15% between the two groups included gains in 17q23-q25.3 and losses in 16q24.2. Gene expression analysis identified 447 significantly differentially expressed genes, of which 120 were replicated in an independent microarray dataset. After adjusting for PAM50, most differences were no longer significant.Conclusions: Molecular differences by interval cancer status were observed, but they were largely explained by PAM50 subtypes. This work offers new insights into the biological differences between the two tumor groups. Clin Cancer Res; 23(10); 2584–92. ©2016 AACR.
Cell Panel Profiling Reveals Conserved Therapeutic Clusters and Differentiates the Mechanism of Action of Different PI3K/mTOR, Aurora Kinase and EZH2 Inhibitors
Authors: Uitdehaag Joost C.M. , de Roos Jeroen A.D.M. , Prinsen Martine B.W. , Willemsen-Seegers Nicole , de Vetter Judith R.F. , Dylus Jelle , van Doornmalen Antoon M. , Kooijman Jeffrey , Sawa Masaaki , van Gerwen Suzanne J.C. , de Man Jos , Buijsman Rogier C. , Zaman Guido J.R. 
Published: September 2016

AbstractCancer cell line panels are important tools to characterize the in vitro activity of new investigational drugs. Here, we present the inhibition profiles of 122 anticancer agents in proliferation assays with 44 or 66 genetically characterized cancer cell lines from diverse tumor tissues (Oncolines). The library includes 29 cytotoxics, 68 kinase inhibitors, and 11 epigenetic modulators. For 38 compounds this is the first comparative profiling in a cell line panel. By strictly maintaining optimized assay protocols, biological variation was kept to a minimum. Replicate profiles of 16 agents over three years show a high average Pearson correlation of 0.8 using IC50 values and 0.9 using GI50 values. Good correlations were observed with other panels. Curve fitting appears a large source of variation. Hierarchical clustering revealed 44 basic clusters, of which 26 contain compounds with common mechanisms of action, of which 9 were not reported before, including TTK, BET and two clusters of EZH2 inhibitors. To investigate unexpected clusterings, sets of BTK, Aurora and PI3K inhibitors were profiled in biochemical enzyme activity assays and surface plasmon resonance binding assays. The BTK inhibitor ibrutinib clusters with EGFR inhibitors, because it cross-reacts with EGFR. Aurora kinase inhibitors separate into two clusters, related to Aurora A or pan-Aurora selectivity. Similarly, 12 inhibitors in the PI3K/AKT/mTOR pathway separated into different clusters, reflecting biochemical selectivity (pan-PI3K, PI3Kβγδ-isoform selective or mTOR-selective). Of these, only allosteric mTOR inhibitors preferentially targeted PTEN-mutated cell lines. This shows that cell line profiling is an excellent tool for the unbiased classification of antiproliferative compounds. Mol Cancer Ther; 15(12); 3097–109. ©2016 AACR.
Height and Body Size in Childhood, Adolescence, and Young Adulthood and Breast Cancer Risk According to Molecular Subtype in the Nurses' Health Studies
Authors: Warner Erica T. , Hu Rong , Collins Laura C. , Beck Andrew H. , Schnitt Stuart , Rosner Bernard , Eliassen A. Heather , Michels Karin B. , Willett Walter C. , Tamimi Rulla M. 
Published: September 2016

Abstract
Height and body size in childhood and young adulthood have been consistently associated with breast cancer risk; whether associations differ across molecular subtypes is unclear. In a pooled analysis of the Nurses' Health Studies, we prospectively examined the association of four exposures: height, body mass index (BMI) at the age of 18 years, childhood and adolescent somatotypes, with breast cancer risk according to molecular subtypes defined by immunohistochemical markers. We used multivariable-adjusted Cox proportional hazards regression to estimate HRs and 95% confidence intervals (CI). We identified 2,983 luminal A, 1,281 luminal B, 318 HER2-enriched, 408 basal-like, and 128 unclassified tumors. Height was positively associated with all subtypes (Pheterogeneity = 0.78). BMI at the age of 18 (Pheterogeneity = 0.001), childhood (Pheterogeneity = 0.51), and adolescent somatotype (Pheterogeneity = 0.046) were inversely associated, but with differences in magnitude of association. BMI at the age of 18 of ≥25 kg/m2 (compared with 20–21.9 kg/m2) was associated with a 52% decreased risk of HER2-enriched (HR, 0.48; 95% CI, 0.26–0.91; Ptrend &lt; 0.0001) and 39% reduced risk of basal-like tumors (HR, 0.61; 95% CI, 0.36–1.02; Ptrend = 0.008). Compared with the lowest category, women in the highest adolescent body size category were 71% less likely to develop HER2-enriched (HR, 0.29; 95% CI, 0.10–0.85; Ptrend = 0.0005) and 60% less likely to develop basal-like (HR, 0.40; 95% CI, 0.17–0.95; Ptrend = 0.0008). Height was positively associated with risk of all breast cancer molecular subtypes. BMI at 18 years and childhood and adolescent were inversely associated with risk of most breast cancer molecular subtypes with somewhat stronger associations with HER2-enriched and basal-like subtypes. Cancer Prev Res; 9(9); 732–8. ©2016 AACR.
Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy
Authors: Page David B. , Yuan Jianda , Redmond David , Wen Y Hanna , Durack Jeremy C. , Emerson Ryan , Solomon Stephen , Dong Zhiwan , Wong Phillip , Comstock Christopher , Diab Adi , Sung Janice , Maybody Majid , Morris Elizabeth , Brogi Edi , Morrow Monica , Sacchini Virgilio , Elemento Olivier , Robins Harlan , Patil Sujata , Allison James P. , Wolchok Jedd D. , Hudis Clifford , Norton Larry , McArthur Heather L. 
Published: September 2016

Abstract
In early-stage breast cancer, the degree of tumor-infiltrating lymphocytes (TIL) predicts response to chemotherapy and overall survival. Combination immunotherapy with immune checkpoint antibody plus tumor cryoablation can induce lymphocytic infiltrates and improve survival in mice. We used T-cell receptor (TCR) DNA sequencing to evaluate both the effect of cryoimmunotherapy in humans and the feasibility of TCR sequencing in early-stage breast cancer. In a pilot clinical trial, 18 women with early-stage breast cancer were treated preoperatively with cryoablation, single-dose anti–CTLA-4 (ipilimumab), or cryoablation + ipilimumab. TCRs within serially collected peripheral blood and tumor tissue were sequenced. In baseline tumor tissues, T-cell density as measured by TCR sequencing correlated with TIL scores obtained by hematoxylin and eosin (H&E) staining. However, tumors with little or no lymphocytes by H&E contained up to 3.6 × 106 TCR DNA sequences, highlighting the sensitivity of the ImmunoSEQ platform. In this dataset, ipilimumab increased intratumoral T-cell density over time, whereas cryoablation ± ipilimumab diversified and remodeled the intratumoral T-cell clonal repertoire. Compared with monotherapy, cryoablation plus ipilimumab was associated with numerically greater numbers of peripheral blood and intratumoral T-cell clones expanding robustly following therapy. In conclusion, TCR sequencing correlates with H&E lymphocyte scoring and provides additional information on clonal diversity. These findings support further study of the use of TCR sequencing as a biomarker for T-cell responses to therapy and for the study of cryoimmunotherapy in early-stage breast cancer. Cancer Immunol Res; 4(10); 835–44. ©2016 AACR.
Zeroing in on Tumor-Reactive TILs
Authors: Ohashi Pamela S. 
Published: September 2016

Abstract
Adoptive cell transfer of tumor-specific T cells provides an effective strategy for cancer immunotherapy. An article in this issue provides a novel approach to refine this technology by identifying tumor-reactive T cells based on frequency and PD-1 expression. Cancer Immunol Res; 4(9); 719. ©2016 AACR.
See article by Pasetto et al., p. 734.
Ideal Cardiovascular Health and Subclinical Markers of Carotid Structure and Function
Authors: Gaye Bamba , Mustafic Hazrije , Laurent Stéphane , Perier Marie-Cécile , Thomas Frédérique , Guibout Catherine , Tafflet Muriel , Pannier Bruno , Boutouyrie Pierre , Jouven Xavier , Empana Jean-Philippe 
Published: September 2016

Objective—
We hypothesized that subclinical markers of vascular structure and function, which are independent predictors of cardiovascular disease, would be less frequent in subjects with ideal than poor cardiovascular health (CVH) as defined by the American Heart Association (AHA).

Approach and Results—
Carotid parameters were measured using high-precision echotracking device in 9155 nonreferred participants attending a health checkup in a large health center in Paris (France) between 2008 and 2012. According to the AHA, participants with 0 to 2, 3 to 4, and 5 to 7 metrics (smoking, physical activity, body mass index, diet, blood glucose and total cholesterol, blood pressure) at the ideal level were categorized as having poor, intermediate, and ideal CVH. Carotid parameters were dichotomized according to their median value, and multivariable logistic regression analysis was performed. Mean age was 59.5 (SD 6.3) years; 39% were females, and ideal CVH was present in 10.11% of the study participants. After adjustment for age, sex, education, and living alone and compared with a poor CVH, an ideal CVH was associated with lower common carotid artery intima–media thickness (odds ratio=1.64; 95% confidence interval 1.40, 1.93), absence of carotid plaques (odds ratio=2.14; 95% confidence interval 1.60, 2.87), lower Young’s elastic modulus (odds ratio=2.43; 95% confidence interval 2.07, 2.84), and higher carotid distensibility coefficient (odds ratio=2.90; 95% confidence interval 2.47, 3.41).

Conclusions—
In community subjects aged 50 to 75 years, ideal CVH was associated with substantially less arterial stiffness and thickness. These associations might contribute to the lower risk of cardiovascular diseases in subjects with ideal CVH.
Neurologic Examination at 24 to 48 Hours Predicts Functional Outcomes in Basilar Artery Occlusion Stroke
Authors: Rangaraju Srikant , Jovin Tudor G. , Frankel Michael , Schonewille Wouter J. , Algra Ale , Kappelle L. Jaap , Nogueira Raul G. 
Published: September 2016

Background and Purpose—
Accurate long-term outcome prognostication in basilar artery occlusion strokes may guide clinical management in the subacute stage. We determine the prognostic value of the follow-up neurological examination using the National Institutes of Health stroke scale (NIHSS) and identify 24- to 48-hour NIHSS risk categories in basilar artery occlusion patients.

Methods—
Participants of an observational registry of radiologically confirmed acute basilar artery occlusion (BASICS [Basilar Artery International Cooperation Study]) with prospectively collected 24- to 48-hour NIHSS and 1-month modified Rankin scale scores were included. Uni- and multivariable modeling were performed to identify independent predictors of poor outcome. Predictive powers of baseline and 24- to 48-hour NIHSS for poor outcome (modified Rankin scale, 4–6) and 1-month mortality were determined by receiver operating characteristic analyses. Classification and regression tree analysis was performed to identify risk groups.

Results—
Three hundred seventy-six of 619 BASICS participants were included, of whom 65.4% had poor outcome. In multivariable analyses, 24- to 48-hour NIHSS (odds ratio=1.28 [1.21–1.35]), history of minor stroke (odds ratio=2.64 [1.04–6.74], time to treatment >6 hours (odds ratio=3.07 [1.35–6.99]), and age (odds ratio=1.02 [0.99–1.04]) were retained in the final model as predictors of poor outcome. Prognostic power of 24- to 48-hour NIHSS was higher than baseline NIHSS for 1-month poor outcome (area under the curve, 0.92 versus 0.75) and mortality (area under the curve, 0.85 versus 0.72). Classification and regression tree analysis identified five 24- to 48-hour NIHSS risk categories with poor outcome rates of 9.4% (NIHSS 0–4), 36% (NIHSS 5–11), 84.3% (NIHSS 12–22), 96.1% (NIHSS 23–27), and 100% (NIHSS≥28).

Conclusions—
Twenty-four- to 48-hour NIHSS accurately predicts 1-month poor outcome and mortality and represents a clinically valuable prognostic tool for the care of basilar artery occlusion patients.
Convectively Coupled Kelvin Waves and Tropical Cyclogenesis in a Semi-Lagrangian Framework
Authors: Schreck Carl J. 
Published: September 2016

AbstractThis study examines how convectively coupled Kelvin waves interact with the semi-Lagrangian circulation of easterly waves to modulate tropical cyclogenesis. Recent studies have shown that fewer tropical cyclones form in the three days before passage of the Kelvin wave’s peak convection and more develop in the three days thereafter. Separately, other studies have identified the recirculation of moisture and vorticity within easterly waves using a semi-Lagrangian frame of reference. That framework is achieved by subtracting the easterly wave phase speed from the earth-relative winds. This study combines these recent findings by testing whether the equatorial westerlies from Kelvin waves can help close the semi-Lagrangian circulation.Past studies have shown that Kelvin waves tilt westward with height in the troposphere such that equatorial westerlies build upward from the surface in the days following the convective peak. This study shows that the easterly wave’s semi-Lagrangian closed circulation grows upward as it intersects the Kelvin wave’s westward tilt. The Kelvin wave’s westerly anomalies reach 500 hPa about three days after the convection has passed, which establishes the deep, vertically aligned easterly wave vortex necessary for tropical cyclogenesis. This study focuses on the eastern Pacific, but similar results are found for the North Atlantic. In other basins, the Kelvin wave accentuates the westerlies from the Madden–Julian oscillation and/or the monsoon trough. Given that Kelvin waves often last weeks and circumnavigate the globe, these results may advance long-range tropical cyclogenesis forecasting.
Subseasonal Prediction of Significant Wave Heights over the Western Pacific and Indian Ocean Region
Authors: Shukla Ravi P. , Kinter James L. 
Published: September 2016

Abstract
The bias and skill of multi-week predictions of significant wave height (SWH) in the western Pacific and Indian Ocean (WP–IO) region are investigated. The WaveWatch III (WW3) model is forced with daily 10-m winds from the National Centers for Environmental Prediction (NCEP) Climate Forecast System, version 2 (CFSv2), retrospective forecasts (CFSR). Reforecasts using January and May initial conditions for the period 1999–2009 are considered. The main features of the climatological mean 10-m winds in weeks 1–4 are well captured by CFSv2, although the magnitude of the bias increases with lead time over much of the region in both the January and May cases. The CFSv2–WW3 system similarly captures the magnitude and spatial structure of SWH in weeks 1–4 well in both cases; however, the magnitude of the positive biases increases with lead time over the Southern Ocean (SO), the South China Sea, and the northwestern Pacific region in the January cases, and over SO in the May cases. The magnitude of the SWH variability grows weaker with lead time over SO, which may be related to the weaker interannual variability of 10-m winds in weeks 1–4 over S0 in CFSR. During the first two forecast weeks, the temporal anomaly correlation skill of SWH is significantly higher than it is during weeks 3 and 4 in the WP–IO region. Based on a categorical forecast verification, the CFSv2–WW3 can predict rare events at these lead times.
Clinical roles in clinical biochemistry: a national survey of practice in the UK
Authors: Choudhury Sirazum M , Williams Emma L , Barnes Sophie C , Alaghband-Zadeh Jamshid , Tan Tricia M , Cegla Jaimini 
Published: September 2016

Background Using an online survey, we collected data to present a picture of how clinical authorization is performed in the UK. Methods A 21-question survey was uploaded to www.surveymonkey.com , and responses were invited via the mail base of the Association for Clinical Biochemistry and Laboratory Medicine. The questionnaire examined the intensity and function of the duty biochemist role and how different types of authorization are used to handle and release results. Results Of 70 responses received, 60 were suitable for analysis. Responses were received from every region of the UK. A typical duty biochemist shift started on average at 8:50, and finished at 17:25. The mean duration was 8 h 58 min. Clinical scientists are the most abundantly represented group on duty biochemist rotas. Higher banded clinical scientists and chemical pathologists covered out-of-hours shifts. Results were handled differently depending on the level of abnormality and the requesting area. Normal results tended to be released either directly from the analyser or after technical then autoauthorization (90%). A greater preference for clinical authorization was seen for abnormal and critical results originating from outpatients (49% and 69%, respectively) or general practice (51% and 71%) than for inpatients (33% and 53%) or A&E (25% and 37%). Conclusions The handling and authorization of biochemistry results varies greatly between laboratories. The role is clearly heterogeneous in the UK. Guidance from the Association for Clinical Biochemistry and Royal College of Pathologists may help to clarify the essential roles of the duty biochemist.