bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus Biotype 3
Authors: Danin-Poleg Yael , Elgavish Sharona , Raz Nili , Efimov Vera , Kashi Yechezkel 
Published: April 2013

ABSTRACT

We report the first genome sequence of the pathogenic
Vibrio vulnificus
biotype 3. This draft genome sequence of the environmental strain VVyb1(BT3), isolated in Israel, provides a representation of this newly emerged clonal group, which reveals higher similarity to the clinical strains of biotype 1 than to the environmental ones.
Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913
T
)
Authors: Golyshin Peter N. , Werner Johannes , Chernikova Tatyana N. , Tran Hai , Ferrer Manuel , Yakimov Michail M. , Teeling Hanno , Golyshina Olga V. ,   MAMBA Scientific Consortium
Published: April 2013

ABSTRACT

Thalassolituus oleivorans
is one of the most prevalent marine gammaproteobacteria in microbial communities, emerging after oil spills in coastal, estuarine, and surface seawaters. Here, we present the assembled genome of strain
T. oleivorans
MIL-1 (DSM 14913
T
), which is 3,920,328 bp with a G+C content of 46.6%.
Complete Genome Sequences of Classical Swine Fever Virus Strains Isolated from Wild Boars in South Korea
Authors: Jeoung Hye-Young , Lim Ji-Ae , Lim Seong-in , Kim Jae-Jo , Song Jae-Young , Hyun Bang-Hun , Kim Yong Kwan , An Dong-Jun 
Published: April 2013

ABSTRACT
Classical swine fever is a disease that is devastating the pig industry worldwide. Here, we report the complete genome sequences of two classical swine virus strains (YC11WB and PC11WB), isolated from Korean wild boars in 2011. Both strains belong to subgenotype 2.1b. The complete genome sequences of PC11WB and YC11WB are more similar to that of strain ZJ0801 (isolated in China) than to that of the SW03 strain isolated from domestic pigs in South Korea.
Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15
Authors: Kumar Shailesh , Kaur Navjot , Singh Nitin Kumar , Raghava Gajendra Pal Singh , Mayilraj Shanmugam 
Published: April 2013

ABSTRACT

We report the 7.3-Mbp genome sequence of
Streptomyces gancidicus
strain BKS 13-15, isolated from mangrove sediment samples collected from the Bhitar Kanika Mangrove Reserve Forest, Odissha, India. The draft genome of strain
Streptomyces gancidicus
strain BKS 13-15 consists of 7,300,479 bp with 72.6% G+C content, 6,631 protein-coding genes, and 71 RNAs.
Draft Genome Sequence of Ochrobactrum pseudogrignonense Strain CDB2, a Highly Efficient Arsenate-Resistant Soil Bacterium from Arsenic-Contaminated Cattle Dip Sites
Authors: Yang Yiren , Yu Xuefei , Zhang Ren 
Published: April 2013

ABSTRACT

We report the 4.97-Mb draft genome sequence of a highly efficient arsenate-resistant bacterium,
Ochrobactrum
sp. strain CDB2. It contains a novel arsenic resistance (
ars
) operon (
arsR
-
arsC1
-
ACR3
-
arsC2
-
arsH
-
mfs
) and two non-operon-associated
ars
genes,
arsC3
and
arsB
. The genome information will aid in the understanding of the arsenic resistance mechanism of this and other bacterial species.
Recovery from injury: the UK Burden of Injury Multicentre Longitudinal Study
Authors: Kendrick Denise , Vinogradova Yana , Coupland Carol , Mulvaney Caroline A , Christie Nicola , Lyons Ronan A , Towner Elizabeth L ,   on behalf of the UK Burden of Injuries Study Group
Published: April 2013

ObjectivesTo estimate the likelihood of recovery at 1, 4 and 12 months post injury and investigate predictors of recovery in injured people attending an emergency department (ED) or admitted to hospital in the UK.MethodsParticipants completed questionnaires at recruitment and 1, 4 and 12 months post injury or until recovered. Data were collected on injury details, sociodemographic characteristics, general health prior to injury and recovery. We compared three age groups: 5–17, 18–64 and 65 years and above. Modified Poisson regression estimated the relative risk of recovery. Multivariable models were built using backward stepwise regression. Sensitivity analyses assessed the effect of missing data.ResultsWe recruited 1517 participants, 55% (n=836) ED attenders and 44% (n=661) hospital admissions. By 1 month after injury, 28% (285/968) had fully recovered, 54% (440/820) at 4 months and 71% (523/738) at 12 months. Recovery was independently associated with gender, admission status, injury severity, body region injured and place of injury for 5–17 year olds and 18–64 year olds and with gender, admission status, injury severity and long-term illness for those aged 65+. Injury severity and hospital admission were associated with recovery across all age groups, but not at every time point in each age group. Other factors varied between age groups or time points. Results were generally robust to imputing missing data.ConclusionsA range of factors was found to predict recovery among injured people. These could be used to identify those at risk of delayed recovery and to inform the design of interventions to maximise recovery.
GEM APPLICATIONS OUTSIDE HIGH ENERGY PHYSICS
Authors: PINTO SERGE DUARTE 
Published: April 2013

From its invention in 1997, the Gas Electron Multiplier (GEM) has been applied in nuclear and high energy physics experiments. Over time however, other applications have also exploited the favorable properties of GEMs. The use of GEMs in these applications will be explained in principle and practice. This paper reviews applications in research, beam instrumentation and homeland security. The detectors described measure neutral radiations such as photons, x-rays, gamma rays and neutrons, as well as all kinds of charged radiation. This paper provides an overview of the still expanding range of possibilities of this versatile detector concept.
Cytotoxic Activity of Tivantinib (ARQ 197) Is Not Due Solely to c-MET Inhibition
Authors: Katayama Ryohei , Aoyama Aki , Yamori Takao , Qi Jie , Oh-hara Tomoko , Song Youngchul , Engelman Jeffrey A. , Fujita Naoya 
Published: April 2013

Abstract
The receptor tyrosine kinase c-MET is the high-affinity receptor for the hepatocyte growth factor (HGF). The HGF/c-MET axis is often dysregulated in tumors. c-MET activation can be caused by MET gene amplification, activating mutations, and auto- or paracrine mechanisms. Thus, c-MET inhibitors are under development as anticancer drugs. Tivantinib (ARQ 197) was reported as a small-molecule c-MET inhibitor and early clinical studies suggest antitumor activity. To assess whether the antitumor activity of tivantinib was due to inhibition of c-MET, we compared the activity of tivantinib with other c-MET inhibitors in both c-MET–addicted and nonaddicted cancer cells. As expected, other c-MET inhibitors, crizotinib and PHA-665752, suppressed the growth of c-MET-addicted cancers, but not the growth of cancers that are not addicted to c-MET. In contrast, tivantinib inhibited cell viability with similar potency in both c-MET-addicted and nonaddicted cells. These results suggest that tivantinib exhibits its antitumor activity in a manner independent of c-MET status. Tivantinib treatment induced a G2–M cell-cycle arrest in EBC1 cells similarly to vincristine treatment, whereas PHA-665752 or crizotinib treatment markedly induced G0–G1 cell-cycle arrest. To identify the additional molecular target of tivantinib, we conducted COMPARE analysis, an in silico screening of a database of drug sensitivities across 39 cancer cell lines (JFCR39), and identified microtubule as a target of tivantinib. Tivantinib-treated cells showed typical microtubule disruption similar to vincristine and inhibited microtubule assembly in vitro. These results suggest that tivantinib inhibits microtubule polymerization in addition to inhibiting c-MET. Cancer Res; 73(10); 3087–96. ©2013 AACR.
Dysregulated Expression of FOXM1 Isoforms Drives Progression of Pancreatic Cancer
Authors: Kong Xiangyu , Li Lei , Li Zhaoshen , Le Xiangdong , Huang Chen , Jia Zhiliang , Cui Jiujie , Huang Suyun , Wang Liwei , Xie Keping 
Published: April 2013

Abstract
The transcription factor Forkhead box M1 (FOXM1) plays important roles in oncogenesis. However, the expression statuses of FOXM1 isoforms and their impact on and molecular basis in oncogenesis are unknown. We sought to determine the identities of FOXM1 isoforms in and the impact of their expression on pancreatic cancer development and progression using human tissues, cell lines, and animal models. Overexpression of FOXM1 mRNA and protein was pronounced in human pancreatic tumors and cancer cell lines. We identified five FOXM1 isoforms present in pancreatic cancer: FOXM1a, FOXM1b, and FOXM1c along with two isoforms tentatively designated as FOXM1b1 and FOXM1b2 because they were closely related to FOXM1b. Interestingly, FOXM1c was predominantly expressed in pancreatic tumors and cancer cell lines, whereas FOXM1a expression was generally undetectable in them. Functional analysis revealed that FOXM1b, FOXM1b1, FOXM1b2, and FOXM1c, but not FOXM1a, promoted pancreatic tumor growth and metastasis. Consistently, FOXM1b, FOXM1b1, FOXM1b2, and FOXM1c activated transcription of their typical downstream genes. Also, Sp1 mechanistically activated the FOXM1 promoter, whereas Krüppel-like factor 4 (KLF4) repressed its activity. Finally, we identified an Sp1- and KLF4-binding site in the FOXM1 promoter and showed that both Sp1 and KLF4 protein bound directly to it. Deletion mutation of this binding site significantly attenuated the transcriptional regulation of the FOXM1 promoter positively by Sp1 and negatively by KLF4. We showed that overexpression of specific FOXM1 isoforms critically regulates pancreatic cancer development and progression by enhancing tumor cell invasion and metastasis. Our findings strongly suggest that targeting specific FOXM1 isoforms effectively attenuates pancreatic cancer development and progression. Cancer Res; 73(13); 3987–96. ©2013 AACR.
APOBEC3 Cytidine Deaminases in Double-Strand DNA Break Repair and Cancer Promotion
Authors: Nowarski Roni , Kotler Moshe 
Published: April 2013

Abstract
High frequency of cytidine to thymidine conversions was identified in the genome of several types of cancer cells. In breast cancer cells, these mutations are clustered in long DNA regions associated with single-strand DNA (ssDNA), double-strand DNA breaks (DSB), and genomic rearrangements. The observed mutational pattern resembles the deamination signature of cytidine to uridine carried out by members of the APOBEC3 family of cellular deaminases. Consistently, APOBEC3B (A3B) was recently identified as the mutational source in breast cancer cells. A3G is another member of the cytidine deaminases family predominantly expressed in lymphoma cells, where it is involved in mutational DSB repair following ionizing radiation treatments. This activity provides us with a new paradigm for cancer cell survival and tumor promotion and a mechanistic link between ssDNA, DSBs, and clustered mutations. Cancer Res; 73(12); 3494–8. ©2013 AACR.
REST Negatively and ISGF3 Positively Regulate the HumanSTAT1Gene in Melanoma
Authors: Amalraj James , Cutler Samuel J. , Ghazawi Ibtisam , Boyle Glen M. , Ralph Stephen J. 
Published: April 2013

AbstractSTAT1 plays a pivotal role in signal transduction and transcriptional activation in response to type I and II IFNs. Regulation of STAT1 expression has significant consequences in human cancer cells, where STAT1 deficiencies have been associated with cellular resistance to type I IFN. Distinct promoter, enhancer, and repressor regions have previously been described in the regulatory part of the human STAT1 gene extending as far as the second intron. A putative IFN-stimulated response element sequence in the STAT1 promoter is inducible by type I IFN and binds the IFN-α/β–induced complex, ISGF3. Together with the previously characterized IRF-E/GAS/IRF-E (IGI) motif, these positive regulatory elements provide a means for intracellular amplification of STAT1 expression, which is necessary for increasing cell responsiveness to the IFNs. In contrast, the transcriptional repressor REST binds to an RE-1 element in the STAT1 repressor region and in doing so represses transcription from the STAT1 gene regulatory region in melanoma cells lines. Repression significantly decreased in a REST-null cell line. Altering REST function from a transcriptional repressor into an activator as REST-VP16 increased expression from RE-1–targeted reporters. RNA expression of 65 melanoma cell lines by microarray and selected lines with known IFN responsiveness showed significant inverse correlations between STAT1/REST that were related to cellular responses to IFN. Thus REST, through the intronic RE-1 element, provides a means for downregulating STAT1 expression, affecting melanoma responsiveness to IFN. Intracellular levels of REST may be a useful marker to test for IFN resistance and as a novel therapeutic target in IFN-resistant melanomas. Mol Cancer Ther; 12(7); 1288–98. ©2013 AACR.
Prediction of Recurrence and Survival in Hepatocellular Carcinoma Based on Two Cox Models Mainly Determined by FoxP3+ Regulatory T Cells
Authors: Lin Sheng-Zhang , Chen Kang-Jie , Xu Zhi-Yuan , Chen Hui , Zhou Lin , Xie Hai-Yang , Zheng Shu-Sen 
Published: April 2013

Abstract
Hepatocellular carcinoma (HCC) is an aggressive disease with poor prognosis and limited methods to predict patient survival. Immune cells infiltrating tumors is known to impact clinical outcome. Here, we investigated the prognostic significance of immune infiltration within the tumor microenvironment in 245 specimens from two independent cohorts by immunohistochemical analyses. A Cox regression model was constructed using a training cohort and validated in an independent cohort. The diagnostic accuracy was evaluated by receiver operating characteristic curve. The activation, function, and chemotaxis of intratumoral regulatory T cells (Treg) were analyzed using flow cytometry, quantitative PCR, and chemotaxis assay. We identified that the proportion of FoxP3+ cells within tumors is negatively associated with patient prognosis, whereas the proportion of interleukin (IL)-17+ cell and the number of trypase+ cells are positive predictor. The two Cox models, composed of independent predictors in multivariate analysis, provided a high diagnostic accuracy of prognosis for patients with HCC. The proportion of FoxP3+ cells showed the most significant predictive power, with the highest Cox score in the two models. Furthermore, we found Tregs from tumor with high FoxP3+ proportion were more active and powerful than the counterparts from tumor with low FoxP3+ proportion. In conclusion, two Cox models are established that have considerable clinical value in predicting tumor recurrence and survival of patients with HCC, respectively. In the both models, the proportion of Tregs among CD4+ T cells plays a central role. Cancer Prev Res; 6(6); 594–602. ©2013 AACR.
Genetic Risk Prediction and a 2-Stage Risk Screening Strategy for Coronary Heart Disease
Authors: Tikkanen Emmi , Havulinna Aki S. , Palotie Aarno , Salomaa Veikko , Ripatti Samuli 
Published: April 2013

Objective—
Genome-wide association studies have identified several genetic variants associated with coronary heart disease (CHD). The aim of this study was to evaluate the genetic risk discrimination and reclassification and apply the results for a 2-stage population risk screening strategy for CHD.

Approach and Results—

We genotyped 28 genetic variants in 24 124 participants in 4 Finnish population-based, prospective cohorts (recruitment years 1992–2002). We constructed a multilocus genetic risk score and evaluated its association with incident cardiovascular disease events. During the median follow-up time of 12 years (interquartile range 8.75–15.25 years), we observed 1093 CHD, 1552 cardiovascular disease, and 731 acute coronary syndrome events. Adding genetic information to conventional risk factors and family history improved risk discrimination of CHD (C-index 0.856 versus 0.851;
P
=0.0002) and other end points (cardiovascular disease: C-index 0.840 versus 0.837,
P
=0.0004; acute coronary syndrome: C-index 0.859 versus 0.855,
P
=0.001). In a standard population of 100 000 individuals, additional genetic screening of subjects at intermediate risk for CHD would reclassify 2144 subjects (12%) into high-risk category. Statin allocation for these subjects is estimated to prevent 135 CHD cases over 14 years. Similar results were obtained by external validation, where the effects were estimated from a training data set and applied for a test data set.

Conclusions—
Genetic risk score improves risk prediction of CHD and helps to identify individuals at high risk for the first CHD event. Genetic screening for individuals at intermediate cardiovascular risk could help to prevent future cases through better targeting of statins.
Population-Based Study of Incidence and Outcome of Acute Aortic Dissection and Premorbid Risk Factor Control
Authors: Howard Dominic P.J. , Banerjee Amitava , Fairhead Jack F. , Perkins Jeremy , Silver Louise E. , Rothwell Peter M. 
Published: April 2013

Background—
Acute aortic dissection is a preventable life-threatening condition. However, there have been no prospective population-based studies of incidence or outcome to inform an understanding of risk factors, strategies for prevention, or projections for future clinical service provision.

Methods and Results—

We prospectively determined incidence and outcomes of all acute aortic dissections in a population of 92 728 in Oxfordshire, United Kingdom, from 2002 to 2012. Among 155 patients with 174 acute aortic events, 54 patients had 59 thoracoabdominal aortic dissections (52 incident events: 6/100 000, 95% confidence interval, 4–7; 37 Stanford type A, 15 Stanford type B; 31 men, mean age=72.0 years). Among patients with type A incident events, 18 (48.6%) died before hospital assessment (61.1% women). The 30-day fatality rate was 47.4% for patients with type A dissections who survived to hospital admission and 13.3% for patients with type B dissections, although subsequent 5-year survival rates were high (85.7% for type A; 83.3% for type B). Even though 67.3% of patients were on antihypertensive drugs, 46.0% of all patients had at least 1 systolic BP ≥180 mm Hg in their primary care records over the preceding 5 years, and the proportion of blood pressures in the hypertensive range (>140/90 mm Hg) averaged 56.0%. Premorbid blood pressure was higher in patients with type A dissections that were immediately fatal than in those who survived to admission (mean/standard deviation pre-event systolic blood pressure=151.2/19.3 versus 137.9/17.9;
P
<0.001).

Conclusions—
Uncontrolled hypertension remains the most significant treatable risk factor for acute aortic dissection. Prospective population-based ascertainment showed that hospital-based registries will underestimate not only incidence and case fatality, but also the association with premorbid hypertension.
Coronary Artery Disease and Risk of Major Vascular Events After Cerebral Infarction
Authors: Amarenco Pierre , Lavallée Philippa C. , Labreuche Julien , Ducrocq Gregory , Juliard Jean-Michel , Feldman Laurent , Cabrejo Lucie , Meseguer Elena , Guidoux Céline , Adraï Valérie , Ratani Samina , Kusmierek Jérôme , Lapergue Bertrand , Klein Isabelle F. , Gongora-Rivera Fernando , Jaramillo Arturo , Abboud Halim , Olivot Jean-Marc , Mazighi Mikael , Touboul Pierre-Jean , Steg Philippe Gabriel 
Published: April 2013

Background and Purpose—
The impact of asymptomatic coronary artery disease on the risk of major vascular events in patients with cerebral infarction is unknown.

Methods—
Four hundred five patients with acute cerebral infarction underwent carotid, femoral artery, thoracic, and abdominal aorta ultrasound examination. Of 342 patients with no known coronary heart disease, 315 underwent coronary angiography. We evaluated the 2-year risk of major vascular events (myocardial infarction, resuscitation after cardiac arrest, hospitalization for unstable angina or heart failure, stroke, or major peripheral arterial disease events) in patients with known coronary heart disease (n=63), and in the no known coronary heart disease group (n=315) as a function of coronary angiographic status (n=315).

Results—

At 2 years, the estimated risk of major vascular events was 11.0% (95% confidence interval, 8.2–14.7). According to baseline coronary angiography, estimated risk was 3.4% in patients with no coronary artery disease (n=120), 8.0% with asymptomatic coronary artery stenosis <50% (n=113), 16.2% with asymptomatic coronary artery stenosis ≥50% (n=81), and 24.1% with known coronary heart disease (
P
<0.0001). Using no coronary artery disease as the reference, the age- and sex-adjusted hazard ratio (95% confidence interval) of vascular events was 2.10 (0.63–6.96) for asymptomatic coronary stenosis <50%, 4.36 (1.35–14.12) for asymptomatic coronary stenosis ≥50%, and 6.86 (2.15–21.31) for known coronary artery disease.

Conclusions—
In patients with nonfatal cerebral infarction, presence and extent of asymptomatic stenoses on coronary angiography are strong predictors of major vascular events within 2 years.
CLOTBUST-Hands Free
Authors: Barlinn Kristian , Barreto Andrew D. , Sisson April , Liebeskind David S. , Schafer Mark E. , Alleman John , Zhao Limin , Shen Loren , Cava Luis F. , Rahbar Mohammad H. , Grotta James C. , Alexandrov Andrei V. 
Published: April 2013

Background and Purpose—
We aimed to evaluate safety and tolerability of a novel operator-independent ultrasound device among stroke-free volunteers.

Methods—
A headframe containing 18 ultrasound transducers (each operating at 2 MHz, pulsed-wave) was used to expose both temporal windows and the suboccipital window. The transmission characteristics were set to emulate the acoustic characteristics of the exposure levels in the Combined Lysis of Thrombus in Brain Ischemia using Transcranial Ultrasound and Systemic tPA (CLOTBUST) trial and to never exceed Food and Drug Administration mandated diagnostic ultrasound exposure limits. Volunteers underwent 2 hours of insonation with transducer activation one at a time. Safety was captured using serial neurological examinations and pre- and postinsonation MRI for detection of the blood brain barrier permeability.

Results—
A total of 15 volunteers (40% men; 49±16 years; 27% black; all pre-exposure National Institutes of Health Stroke Scale scores 0) were enrolled. Five volunteers received pulsed-wave ultrasound via the best pair temporal transducers, 5 via sequential activation of the suboccipital transducers, and 5 via sequential activation of all bilateral temporal and suboccipital transducers. All subjects were safely insonated with no adverse effects as indicated by the neurological examinations during, immediately after the exposure, and at 24 hours, and no abnormality of the blood brain barrier was found on any of the MRIs.

Conclusions—
Our novel device was well tolerated by stroke-free volunteers and did not cause any neurological dysfunction nor did it affect blood brain barrier integrity. The safety and efficacy of the device are now being tested in stroke patients receiving intravenous tissue-type plasminogen activator in phase II–III clinical trials.
Womanist Ways and Pentecostalism: The Work of Recovery and Critique
Authors: Pierce Yolanda 
Published: April 2013

Abstract
This essay questions the notion that a womanist identity and Pentecostal faith are mutually exclusive. Using major tenets of womanist theology, I argue for an honest recovery of all the personal and political influences on classical Pentecostalism as a way to move forward to a more egalitarian faith. Seeking to redress the lack of scholarship about women of color in early Pentecostalism, the essay raises questions that, I hope, will spur more research and interest in a womanist Pentecostal theology.