bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of Sedimenticola thiotaurini Strain SIP-G1, a Polyphosphate- and Polyhydroxyalkanoate-Accumulating Sulfur-Oxidizing Gammaproteobacterium Isolated from Salt Marsh Sediments
Authors: Flood Beverly E. , Jones Daniel S. , Bailey Jake V. 
Published: June 2015

ABSTRACT

We report the closed genome sequence of
Sedimenticola thiotaurini
strain SIP-G1 and an unnamed plasmid obtained through PacBio sequencing with 100% consensus concordance. The genome contained several distinctive features not found in other published
Sedimenticola
genomes, including a complete nitrogen fixation pathway, a complete ethanolamine degradation pathway, and an alkane-1-monooxygenase.
Genome Sequence of the Soil Bacterium
Janthinobacterium
sp. KBS0711
Authors: Shoemaker William R. , Muscarella Mario E. , Lennon Jay T. 
Published: June 2015

ABSTRACT

We present a draft genome of
Janthinobacterium
sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments.
The SQUIRE Guidelines: an evaluation from the field, 5 years post release
Authors: Davies Louise , Batalden Paul , Davidoff Frank , Stevens David , Ogrinc Greg 
Published: June 2015

BackgroundThe Standards for Quality Improvement Reporting Excellence (SQUIRE) Guidelines were published in 2008 to increase the completeness, precision and accuracy of published reports of systematic efforts to improve the quality, value and safety of healthcare. Since that time, the field has expanded. We asked people from the field to evaluate the Guidelines, a novel approach to a first step in revision.MethodsEvaluative design using focus groups and semi-structured interviews with 29 end users and an advisory group of 18 thinkers in the field. Sampling of end users was purposive to achieve variation in work setting, geographic location, area of expertise, manuscript writing experience, healthcare improvement and research experience.ResultsStudy participants reported that SQUIRE was useful in planning a healthcare improvement project, but not as helpful during writing because of redundancies, uncertainty about what was important to include and lack of clarity in items. The concept "planning the study of the intervention" (item 10) was hard for many participants to understand. Participants varied in their interpretation of the meaning of item 10b "the concept of the mechanism by which changes were expected to occur". Participants disagreed about whether iterations of an intervention should be reported. Level of experience in writing, knowledge of the science of improvement and the evolving meaning of some terms in the field are hypothesised as the reasons for these findings.ConclusionsThe original SQUIRE Guidelines help with planning healthcare improvement work, but are perceived as complicated and unclear during writing. Key goals of the revision will be to clarify items where conflict was identified and outline the key components necessary for complete reporting of improvement work.
Pipeline Embolization Device for treatment of high cervical and skull base carotid artery dissections: clinical case series
Authors: Brzezicki Grzegorz , Rivet Dennis J , Reavey-Cantwell John 
Published: June 2015

BackgroundMost cervical dissections are treated with anticoagulation or antiplatelet agents with very good results; however, some patients may benefit from endovascular intervention. High cervical and skull base dissections are often more challenging to treat because of the distal location and tortuous anatomy. The Pipeline Embolization Device (PED) may be a reasonable treatment option for this indication.ObjectivesTo report a case series of patients treated with the PED for high cervical and skull base dissections, focusing on their presentation, indications for treatment, dissection revascularization success, and pseudoaneurysm obliteration evaluated by imaging, and to review available pertinent literature.MethodsWe retrospectively reviewed all cases of high cervical and skull base dissections treated with a PED at our institution. Patient clinical characteristics, presentation, procedural and follow-up imaging, and clinical course were analyzed to evaluate for procedure complications, dissection revascularization success, pseudoaneurysm obliteration, and clinical outcome.ResultsThis is a retrospective case series including 11 patients with 13 carotid dissections treated in our center. There were nine traumatic and four spontaneous dissections. The most common presentation was cerebrovascular accident/transient ischemic attack (CVA/TIA; 5 patients) and headache/face pain (4 patients). Eleven dissections were associated with pseudoaneurysms. Three patients failed medical management with anticoagulation, although flow-limiting stenosis was the main indication for endovascular intervention. Up to three PEDs per vessel were deployed. Angioplasty was used in 10 cases. Complete revascularization (<10% residual stenosis) was achieved in 91% of vessels and 50% of pseudoaneurysms were completely or near completely obliterated immediately after PED(s) deployment. Proximal iatrogenic dissection was the only intraoperative complication. Follow-up imaging was available for nine treated vessels and demonstrated patent PEDs without significant in-stent stenosis up to 9 months after intervention. 75% of pseudoaneurysms were completely obliterated at follow-up. One PED partially collapsed but had no neurological consequences. There were no new CVA/TIAs.ConclusionsOur initial experience with treatment of high cervical and skull base dissections with the PED appears to show that this technique may be a safe and viable treatment option. However, long-term results are needed to fully evaluate the efficacy of such treatment.
CODE FAST: a quality improvement initiative to reduce door-to-needle times
Authors: Busby Leslie , Owada Kumiko , Dhungana Samish , Zimmermann Susan , Coppola Victoria , Ruban Rebecca , Horn Christopher , Rochestie Dustin , Khaldi Ahmad , Hormes Joseph T , Gupta Rishi 
Published: June 2015

BackgroundRapid delivery of IV tissue plasminogen activator (tPA) in qualifying patients leads to better clinical outcomes. The American Heart Association has reduced target door-to-needle (DTN) times from 60 to 45 min in the hopes of continued process improvements across institutions.ObjectiveTo start a quality improvement project called CODE FAST in order to reduce DTN times at our institution.Materials and methodsWe retrospectively reviewed data from our internally maintained database of patients treated with intravenous tPA before and after implementation of the CODE FAST protocol. We assessed demographic information, time of day and times of arrival to first image and delivery of tPA in patients from February 2014 to February 2015. Outcomes were assessed based on discharge to home. Univariate analysis was performed to assess for improvement in DTN times before and after implementation of the protocol.ResultsA total of 93 patients (41 pre-CODE FAST and 52 post-CODE FAST) received IV tPA during the study period. Patients were equally matched between the two groups except that in the pre-CODE FAST era patients receiving tPA were younger and more likely to be men. There was a substantial reduction in door-to-imaging time from a median of 16 to 8 min (p<0.0001) and DTN time with a reduction in the median from 62 to 25 min (p<0.0001). In logistic regression modeling, there was a trend towards more discharges to home in patients treated during the CODE FAST era.ConclusionsWe present a quality improvement project that has been overwhelmingly successful in reducing DTN time to <30 min. The template we present may be helpful to other institutions looking to reduce their DTN times and may also reduce costs as we note a trend towards more discharges to home.
Hydroxamic Acid and Benzoic Acid–Based STAT3 Inhibitors Suppress Human Glioma and Breast Cancer Phenotypes In Vitro and In Vivo
Authors: Yue Peibin , Lopez-Tapia Francisco , Paladino David , Li Yifei , Chen Chih-Hong , Namanja Andrew T. , Hilliard Tyvette , Chen Yuan , Tius Marcus A. , Turkson James 
Published: June 2015

Abstract
STAT3 offers an attractive target for cancer therapy, but small-molecule inhibitors with appealing pharmacologic properties have been elusive. Here, we report hydroxamic acid–based and benzoic acid–based inhibitors (SH5-07 and SH4-54, respectively) with robust bioactivity. Both inhibitors blocked STAT3 DNA-binding activity in vitro and in human glioma, breast, and prostate cancer cells and in v-Src–transformed murine fibroblasts. STAT3-dependent gene transcription was blocked along with Bcl-2, Bcl-xL, Mcl-1, cyclin D1, c-Myc, and survivin expression. Nuclear magnetic resonance analysis of STAT3-inhibitor complexes defined interactions with the SH2 and DNA-binding domains of STAT3. Ectopic expression of the SH2 domain in cells was sufficient to counter the STAT3-inhibitory effects of SH4-54. Neither compound appreciably affected STAT1 or STAT5 DNA-binding activities, STAT3-independent gene transcription, or activation of a panel of oncogenic kinases in malignant cells. Each compound decreased the proliferation and viability of glioma, breast, and prostate cancer cells and v-Src–transformed murine fibroblasts harboring constitutively active STAT3. Further, in mouse xenograft models of glioma and breast cancer, administration of SH5-07 or SH4-54 effectively inhibited tumor growth. Our results offer preclinical proof of concept for SH5-07 and SH4-54 as candidates for further development as cancer therapeutics. Cancer Res; 76(3); 652–63. ©2015 AACR.
The Role of Human Papillomavirus Genotyping in Cervical Cancer Screening: A Large-Scale Evaluation of the cobas HPV Test
Authors: Schiffman Mark , Boyle Sean , Raine-Bennett Tina , Katki Hormuzd A. , Gage Julia C. , Wentzensen Nicolas , Kornegay Janet R. , Apple Raymond , Aldrich Carrie , Erlich Henry A. , Tam Thanh , Befano Brian , Burk Robert D. , Castle Philip E. 
Published: June 2015

Abstract
Background: The cobas HPV Test (“cobas”; Roche Molecular Systems) detects HPV16 and HPV18 individually, and a pool of 12 other high-risk (HR) HPV types. The test is approved for (i) atypical squamous cells of undetermined significance (ASC-US) triage to determine need for colposcopy, (ii) combined screening with cytology (“cotesting”), and (iii) primary HPV screening.
Methods: To assess the possible value of HPV16/18 typing, &gt;17,000 specimens from a longitudinal cohort study of initially HPV-positive women (HC2, Qiagen) were retested with cobas. To study accuracy, cobas genotyping results were compared with those of an established method, the Linear Array HPV Genotyping Test (LA, Roche Molecular Systems). Clinical value of the typing strategy was evaluated by linking the cobas results (supplemented by other available typing results) to 3-year cumulative risks of CIN3+.
Results: Grouped hierarchically (HPV16, else HPV18, else other HR types, else negative), the κ statistic for agreement between cobas and LA was 0.86 [95% confidence interval (CI), 0.86–0.87]. In all three scenarios, HPV16-positive women were at much higher 3-year risk of CIN3+ than HPV16-negative women: women ages 21 and older with ASC-US (14.5%; 95% CI, 13.5%–15.5% vs. 3.5%; 95% CI, 3.3–3.6); women ages 30 years and older that were HPV-positive cytology-negative (10.3%; 95% CI, 9.6–11.1 vs. 2.3%; 95% CI, 2.2–2.4); and all women 25 years and older that were HPV-positive (18.5%; 95% CI, 17.8–19.2 vs. 4.3%; 95% CI, 4.2–4.4).
Conclusion: The cobas and LA results show excellent agreement. The data support HPV16 typing.
Impact: HPV16 typing is useful in the management of HPV-positive/cytology-negative women in cotesting, of all HPV-positive women in primary HPV testing, and perhaps in the management of HPV-positive women with ASC-US. Cancer Epidemiol Biomarkers Prev; 24(9); 1304–10. ©2015 AACR.
See related commentary by Del Mistro, p. 1302
A miRNA-Based Signature Detected in Primary Melanoma Tissue Predicts Development of Brain Metastasis
Authors: Hanniford Doug , Zhong Judy , Koetz Lisa , Gaziel-Sovran Avital , Lackaye Daniel J. , Shang Shulian , Pavlick Anna , Shapiro Richard , Berman Russell , Darvishian Farbod , Shao Yongzhao , Osman Iman , Hernando Eva 
Published: June 2015

AbstractPurpose: Brain metastasis is the major cause of mortality among patients with melanoma. A molecular prognostic test that can reliably stratify patients at initial melanoma diagnosis by risk of developing brain metastasis may inform the clinical management of these patients.Experimental Design: We performed a retrospective, cohort-based study analyzing genome-wide and targeted microRNA expression profiling of primary melanoma tumors of three patient cohorts (n = 92, 119, and 45) with extensive clinical follow-up. We used Cox regression analysis to establish a microRNA-based signature that improves the ability of the current clinicopathologic staging system to predict the development of brain metastasis.Results: Our analyses identified a 4-microRNA (miR-150-5p, miR-15b-5p, miR-16-5p, and miR-374b-3p) prognostic signature that, in combination with stage, distinguished primary melanomas that metastasized to the brain from nonrecurrent and non–brain metastatic primary tumors (training cohort: C-index = 81.4%, validation cohort: C-index = 67.4%, independent cohort: C-index = 76.9%). Corresponding Kaplan–Meier curves of high- versus low-risk patients displayed a clear separation in brain metastasis-free and overall survival (training: P &lt; 0.001; P &lt; 0.001, validation: P = 0.033; P = 0.007, independent: P = 0.021; P = 0.022, respectively). Finally, of the microRNA in the prognostic model, we found that the expression of a key lymphocyte miRNA, miR-150-5p, which is less abundant in primary melanomas metastatic to brain, correlated with presence of CD45+ tumor-infiltrating lymphocytes.Conclusions: A prognostic assay based on the described miRNA expression signature combined with the currently used staging criteria may improve accuracy of primary melanoma patient prognoses and aid clinical management of patients, including selection for adjuvant treatment or clinical trials of adjuvant therapies. Clin Cancer Res; 21(21); 4903–12. ©2015 AACR.
Nucleoside Diphosphate Kinase B–Activated Intermediate Conductance Potassium Channels Are Critical for Neointima Formation in Mouse Carotid Arteries
Authors: Zhou Xiao-Bo , Feng Yu-Xi , Sun Qiang , Lukowski Robert , Qiu Yi , Spiger Katharina , Li Zhai , Ruth Peter , Korth Michael , Skolnik Edward Y. , Borggrefe Martin , Dobrev Dobromir , Wieland Thomas 
Published: June 2015

Objective—

Vascular smooth muscle cells (VSMC) proliferation is a hallmark of atherosclerosis and vascular restenosis. The intermediate conductance Ca
2+
-activated K
+
(SK4) channel is required for pathological VSMC proliferation. In T lymphocytes, nucleoside diphosphate kinase B (NDPKB) has been implicated in SK4 channel activation. We thus investigated the role of NDPKB in the regulation of SK4 currents (I
SK4
) in proliferating VSMC and neointima formation.

Approach and Results—

Function and expression of SK4 channels in VSMC from injured mouse carotid arteries were assessed by patch-clamping and real-time polymerase chain reaction. I
SK4
was detectable in VSMC from injured but not from uninjured arteries correlating with the occurrence of the proliferative phenotype. Direct application of NDPKB to the membrane of inside-out patches increased I
SK4
, whereas NDPKB did not alter currents in VSMC obtained from injured vessels of SK4-deficient mice. The NDPKB-induced increase in I
SK4
was prevented by protein histidine phosphatase 1, but not an inactive protein histidine phosphatase 1 mutant indicating that I
SK4
is regulated via histidine phosphorylation in proliferating VSMC; moreover, genetic NDPKB ablation reduced I
SK4
by 50% suggesting a constitutive activation of I
SK4
in proliferating VSMC. In line, neointima formation after wire injury of the carotid artery was substantially reduced in mice deficient in SK4 channels or NDPKB.

Conclusions—
NDPKB to SK4 signaling is required for neointima formation. Constitutive activation of SK4 by NDPKB in proliferating VSMC suggests that targeting this interaction via, for example, activation of protein histidine phosphatase 1 may provide clinically meaningful effects in vasculoproliferative diseases such as atherosclerosis and post angioplasty restenosis.
High-Density Lipoproteins Reduce Endothelial-to-Mesenchymal Transition
Authors: Spillmann Frank , Miteva Kapka , Pieske Burkert , Tschöpe Carsten , Van Linthout Sophie 
Published: June 2015

Objective—
Endothelial-to-mesenchymal transition is an inflammation-induced process by which endothelial cells can transdifferentiate into fibroblasts. Based on the endothelial-protective and antifibrotic effects of high-density lipoproteins (HDL), we aimed to investigate whether HDL can reduce endothelial-to-mesenchymal transition.

Approach and Results—
Therefore, human aortic endothelial cells were stimulated with the profibrotic factor transforming growth factor (TGF)-β1 in the presence or absence of HDL. Their impact on the transition of endothelial cells to mesenchymal-like cells was analyzed. Phase contrast microscopy demonstrated that HDL abrogated the TGF-β1–induced spindle-shape morphology in human aortic endothelial cells. Furthermore, HDL decreased the TGF-β1–mediated induction of α-smooth muscle actin expression and concomitant loss in endothelial cadherin expression, as shown by immunofluorescence staining and flow cytometry. In addition, HDL decreased the TGF-β1–induced collagen deposition in human aortic endothelial cells involving the scavenger receptor class B, type 1 and downstream phosphatidyl inositol-3-kinase following the findings that the HDL-mediated reduction was abrogated by scavenger receptor class B, type 1 siRNA knockdown and phosphatidyl inositol-3-kinase inhibition, respectively. The HDL-mediated reduction in endothelial-to-mesenchymal transition was associated with an induction of the inhibitory Smad, Smad 7.

Conclusions—
We provide the first in vitro evidence that the endothelial-protective and antifibrotic effects of HDL include the reduction in endothelial-to-mesenchymal transition.
Meta‐Analysis of Intracranial Hemorrhage in Acute Coronary Syndromes: Incidence, Predictors, and Clinical Outcomes
Authors: Mahaffey Kenneth W. , Hager Rebecca , Wojdyla Daniel , White Harvey D. , Armstrong Paul W. , Alexander John H. , Tricoci Pierluigi , Lopes Renato D. , Ohman E. Magnus , Roe Matthew T. , Harrington Robert A. , Wallentin Lars 
Published: June 2015

Background

Little is known about the incidence, predictors, or outcomes of intracranial hemorrhage (
ICH
) in patients with non–
ST
‐segment elevation acute coronary syndromes (
NSTE ACS
). We aimed to determine the incidence and timing of
ICH
, characterize the location of
ICH
, and identify independent baseline predictors of
ICH
in
NSTE ACS
patients.

Methods and Results

We pooled patient‐level data from 4 contemporary antithrombotic therapy trials. Multivariable modeling identified independent predictors of
ICH
.
ICH
s were adjudicated by a clinical events committee. Of 37 815 patients, 135 (0.4%) had an
ICH
. The median (25th, 75th percentiles) follow‐up was 332 (184, 434) days but differed across trials. Locations of
ICH
were intracerebral (50%), subdural (31%), subarachnoid (18.5%), and intraventricular (11%). Independent predictors of
ICH
were older age (
HR
per 10 years, 1.61; 95%
CI
, 1.35 to 1.91); prior stroke/transient ischemic attack;
HR
, 1.95; 95%
CI
, 1.14 to 3.35), higher systolic blood pressure;
HR
per 10 mm Hg increase, 1.09; 95%
CI
, 1.01 to 1.18), and larger number of antithrombotic agents (
HR
per each additional agent, 2.06; 95%
CI
, 1.49 to 2.84). Of all
ICH
s, 45 (33%) were fatal.

Conclusions

In patients with
NSTE ACS
enrolled in recent clinical trials of antithrombotic therapies,
ICH
was uncommon. Patients with older age, prior transient ischemic attack/stroke, higher systolic blood pressure, or larger number of antithrombotic agents were at increased risk. One‐third of patients with
ICH
died. These data may be useful to trialists and data and safety monitoring committees for trial conduct and monitoring.

Clinical Trial Registration

URL:
https://www.clinicaltrials.gov/
. Unique identifiers: TRACER: NCT00527943, PLATO: NCT00391872, APPRAISE‐2: NCT00831441, TRILOGY ACS: NCT00699998.
Meta-Analysis of Genome-Wide Association Studies Identifies Genetic Risk Factors for Stroke in African Americans
Authors: Carty Cara L. , Keene Keith L. , Cheng Yu-Ching , Meschia James F. , Chen Wei-Min , Nalls Mike , Bis Joshua C. , Kittner Steven J. , Rich Stephen S. , Tajuddin Salman , Zonderman Alan B. , Evans Michele K. , Langefeld Carl D. , Gottesman Rebecca , Mosley Thomas H. , Shahar Eyal , Woo Daniel , Yaffe Kristine , Liu Yongmei , Sale Michèle M. , Dichgans Martin , Malik Rainer , Longstreth W.T. , Mitchell Braxton D. , Psaty Bruce M. , Kooperberg Charles , Reiner Alexander , Worrall Bradford B. , Fornage Myriam 
Published: June 2015

Background and Purpose—
The majority of genome-wide association studies (GWAS) of stroke have focused on European-ancestry populations; however, none has been conducted in African Americans, despite the disproportionately high burden of stroke in this population. The Consortium of Minority Population Genome-Wide Association Studies of Stroke (COMPASS) was established to identify stroke susceptibility loci in minority populations.

Methods—

Using METAL, we conducted meta-analyses of GWAS in 14 746 African Americans (1365 ischemic and 1592 total stroke cases) from COMPASS, and tested genetic variants with
P
<10
−6
for validation in METASTROKE, a consortium of ischemic stroke genetic studies in European-ancestry populations. We also evaluated stroke loci previously identified in European-ancestry populations.

Results—

The 15q21.3 locus linked with lipid levels and hypertension was associated with total stroke (rs4471613;
P
=3.9×10
−8
) in African Americans. Nominal associations (
P
<10
−6
) for total or ischemic stroke were observed for 18 variants in or near genes implicated in cell cycle/mRNA presplicing (
PTPRG
,
CDC5L
), platelet function (
HPS4
), blood–brain barrier permeability (
CLDN17
), immune response (
ELTD1, WDFY4
, and
IL1F10-IL1RN
), and histone modification (
HDAC9
). Two of these loci achieved nominal significance in METASTROKE: 5q35.2 (
P
=0.03), and 1p31.1 (
P
=0.018). Four of 7 previously reported ischemic stroke loci (
PITX2, HDAC9, CDKN2A/CDKN2B
, and
ZFHX3
) were nominally associated (
P
<0.05) with stroke in COMPASS.

Conclusions—
We identified a novel genetic variant associated with total stroke in African Americans and found that ischemic stroke loci identified in European-ancestry populations may also be relevant for African Americans. Our findings support investigation of diverse populations to identify and characterize genetic risk factors, and the importance of shared genetic risk across populations.