bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of
Streptomyces ahygroscopicus
subsp.
wuyiensis
CK-15, Isolated from Soil in Fujian Province, China
Authors: Ge Beibei , Liu Yan , Liu Binghua , Zhang Kecheng 
Published: October 2015

ABSTRACT

We report the first high-quality draft genome sequence of an antibiotic (wuyiencin)-producing strain,
Streptomyces ahygroscopicus
subsp.
wuyiensis
CK-15, isolated from soil samples collected from Fujian Province, China. The 9.41-Mb genome comprises 8,311 protein-coding sequences, encodes 89 structural RNAs, and shows a G+C content of 72.25%.
Complete Genome Sequence of Bacillus megaterium Siphophage Silence
Authors: Solis Jonathan A. , Farmer Nicholas G. , Cahill Jesse L. , Rasche Eric S. , Kuty Everett Gabriel F. 
Published: October 2015

ABSTRACT

Silence is a newly isolated siphophage that infects
Bacillus megaterium
, a soil bacterium that is used readily in research and commercial applications. A study of
B. megaterium
phage Silence will enhance our knowledge of the diversity of
Bacillus
phages. Here, we describe the complete genome sequence and annotated features of Silence.
Complete Genome Sequence of
Coriobacteriaceae
Strain 68-1-3, a Novel Mucus-Degrading Isolate from the Swine Intestinal Tract
Authors: Looft T. , Bayles D. O. , Alt D. P. , Stanton T. B. 
Published: October 2015

ABSTRACT

A novel
Coriobacteriaceae
bacterium (strain 68-1-3) was isolated from the ileum of the swine intestinal tract using a selective mucus-based medium. Here we present the finished genome sequence for the swine commensal, totaling 1.97 Mb in size.
Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules
Authors: Crovadore Julien , Calmin Gautier , Cochard Bastien , Chablais Romain , Grizard Damien , Berthon Jean-Yves , Lefort François 
Published: October 2015

ABSTRACT

We report here the genome of
Pseudomonas putida
strain UASWS0946, a highly ammonia-tolerant nitrifying strain isolated from sewage sludge aerobic granules, which displays adequate genetic equipment for soil depollution, sludge treatment, and biological fertilization in agriculture.
Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates
Authors: Jeraldo Patricio , Cunningham Scott A. , Quest Daniel , Sikkink Robert A. , O’Brien Daniel , Eckloff Bruce W. , Patel Robin , Chia Nicholas 
Published: October 2015

ABSTRACT

We report on nine draft genomes of
Pseudomonas aeruginosa
isolates, assembled using a hybrid paired-end and Nextera mate-pair library approach. Eight are of clinical origin, and one is the ATCC 27853 strain. We also report their multilocus sequence types.
Draft Genome Sequence of
Ralstonia
sp. MD27, a Poly(3-Hydroxybutyrate)-Degrading Bacterium, Isolated from Compost
Authors: Zhu Morgan , McCully Lucy M. , Silby Mark W. , Charles-Ogan Tamunonengiyeofori I. , Huang Jean , Brigham Christopher J. 
Published: October 2015

ABSTRACT

Ralstonia
sp. strain MD27, a novel biopolymer-degrading betaproteobacterium, was isolated from compost samples. This organism has been shown to utilize the biopolymer poly(3-hydroxybutyrate) [P(3HB)] as a carbon source for growth. We report the draft genome sequence of MD27 with an estimated total sequence length of 5.9 Mb.
ControlIt! — A Software Framework for Whole-Body Operational Space Control
Authors: Fok Chien-Liang , Johnson Gwendolyn , Yamokoski John D. , Mok Aloysius , Sentis Luis 
Published: October 2015

Whole Body Operational Space Control (WBOSC) enables floating-base highly redundant robots to achieve unified motion/force control of one or more operational space objectives while adhering to physical constraints. It is a pioneering algorithm in the field of human-centered Whole-Body Control (WBC). Although there are extensive studies on the algorithms and theory behind WBOSC, limited studies exist on the software architecture and APIs that enable WBOSC to perform and be integrated into a larger system. In this paper, we address this by presenting ControlIt!, a new open-source software framework for WBOSC. Unlike previous implementations, ControlIt! is multi-threaded to increase maximum servo frequencies using standard PC hardware. A new parameter binding mechanism enables tight integration between ControlIt! and external processes via an extensible set of transport protocols. To support a new robot, only two plugins and a URDF model is needed — the rest of ControlIt! remains unchanged. New WBC primitives can be added by writing Task or Constraint plugins. ControlIt!’s capabilities are demonstrated on Dreamer, a 16-DOF torque controlled humanoid upper body robot containing both series elastic and co-actuated joints, and using it to perform a product disassembly task. Using this testbed, we show that ControlIt! can achieve average servo latencies of about 0.5[Formula: see text]ms when configured with two Cartesian position tasks, two orientation tasks, and a lower priority posture task. This is 10 times faster than the 5[Formula: see text]ms that was achieved using UTA-WBC, the prototype implementation of WBOSC that is both application and platform-specific. Variations in the product’s position is handled by updating the goal of the Cartesian position task. ControlIt!’s source code is released under LGPL and we hope it will be adopted and maintained by the WBC community for the long term as a platform for WBC development and integration.
Clinical and Translational Assessment of VEGFR1 as a Mediator of the Premetastatic Niche in High-Risk Localized Prostate Cancer
Authors: Pal Sumanta Kumar , Vuong Winston , Zhang Wang , Deng Jiehui , Liu Xueli , Carmichael Courtney , Ruel Nora , Pinnamaneni Manasvi , Twardowski Przemyslaw , Lau Clayton , Yu Hua , Figlin Robert A. , Agarwal Neeraj , Jones Jeremy O. 
Published: October 2015

Abstract
Preclinical studies have suggested that VEGFR1-positive cells potentially foster the development of metastases by establishing a “premetastatic niche.” We sought to test this hypothesis in high-risk localized prostate cancer and assess potential niche modulation by the VEGFR1-targeting drug axitinib. Formalin-fixed, paraffin-embedded tissue derived from benign lymph nodes was collected and VEGFR1-positive cell clustering was assessed in benign lymph nodes via IHC. Recursive partitioning was used to define a threshold for VEGFR1 clustering that could segregate patients based on time to biochemical recurrence (TTBR). Multivariate analyses were used to determine whether VEGFR1 clustering, age, pathologic T-stage, Gleason score, or baseline PSA could independently predict TTBR. A randomized, phase II clinical trial comparing axitinib for 28 days followed by radical prostatectomy and pelvic lymph node dissection (RP/PLND) to RP/LND alone was then conducted, with the primary endpoint of demonstrating downregulation of VEGFR1-positve cell clustering in benign lymph nodes. Our retrospective analysis assessed a cohort of 46 patients. A threshold of 1.65 VEGFR1-positive cells per high power field was identified, below which TTBR was delayed. VEGFR1 clustering was an independent predictor of TTBR in a multivariate analysis. Only 11 out of the planned 44 patients were accrued to the phase II trial. While preoperative axitinib was safe and well tolerated, there was no sign of clinical activity or VEGFR1 downregulation. Our results validate previous findings that suggest VEGFR1-positive cells in benign lymph nodes can predict clinical outcome. Further work is needed to develop a viable clinical strategy for modulating VEGFR1 in these tissues. Mol Cancer Ther; 14(12); 2896–900. ©2015 AACR.
Myristoylated Alanine‐Rich Protein Kinase Substrate (MARCKS) Regulates Small GTPase Rac1 and Cdc42 Activity and Is a Critical Mediator of Vascular Smooth Muscle Cell Migration in Intimal Hyperplasia Formation
Authors: Yu Dan , Makkar George , Strickland Dudley K. , Blanpied Thomas A. , Stumpo Deborah J. , Blackshear Perry J. , Sarkar Rajabrata , Monahan Thomas S. 
Published: October 2015

Background

Transcription of the myristoylated alanine‐rich C kinase substrate (
MARCKS
) is upregulated in animal models of intimal hyperplasia.
MARCKS
knockdown inhibits vascular smooth muscle cell (
VSMC
) migration in vitro; however, the mechanism is as yet unknown. We sought to elucidate the mechanism of
MARCKS
‐mediated motility and determine whether
MARCKS
knockdown reduces intimal hyperplasia formation in vivo.

Methods and Results

MARCKS
knockdown blocked platelet‐derived growth factor (
PDGF)
‐induced translocation of cortactin to the cell cortex, impaired both lamellipodia and filopodia formation, and attenuated motility of human coronary artery smooth muscle cells (
CASMC
s). Activation of the small
GTP
ases, Rac1 and Cdc42, was prevented by
MARCKS
knockdown. Phosphorylation of
MARCKS
resulted in a transient shift of
MARCKS
from the plasma membrane to the cytosol.
MARCKS
knockdown significantly decreased membrane‐associated phosphatidylinositol 4,5‐bisphosphate (
PIP
2
) levels. Cotransfection with an intact, unphosphorylated
MARCKS
, which has a high binding affinity for
PIP
2
, restored membrane‐associated
PIP
2
levels and was indispensable for activation of Rac1 and Cdc42 and, ultimately,
VSMC
migration. Overexpression of
MARCKS
in differentiated
VSMC
s increased membrane
PIP
2
abundance, Rac1 and Cdc42 activity, and cell motility.
MARCKS
protein was upregulated early in the development of intimal hyperplasia in the murine carotid ligation model. Decreased
MARKCS
expression, but not total knockdown, attenuated intimal hyperplasia formation.

Conclusions

MARCKS
upregulation increases
VSMC
motility by activation of Rac1 and Cdc42. These effects are mediated by
MARCKS
sequestering
PIP
2
at the plasma membrane. This study delineates a novel mechanism for
MARCKS
‐mediated
VSMC
migration and supports the rational for
MARCKS
knockdown to prevent intimal hyperplasia.
Cholinergic Pathway Suppresses Pulmonary Innate Immunity Facilitating Pneumonia After Stroke
Authors: Engel Odilo , Akyüz Levent , da Costa Goncalves Andrey C. , Winek Katarzyna , Dames Claudia , Thielke Mareike , Herold Susanne , Böttcher Chotima , Priller Josef , Volk Hans Dieter , Dirnagl Ulrich , Meisel Christian , Meisel Andreas 
Published: October 2015

Background and Purpose—
Temporary immunosuppression has been identified as a major risk factor for the development of pneumonia after acute central nervous system injury. Although overactivation of the sympathetic nervous system was previously shown to mediate suppression of systemic cellular immune responses after stroke, the role of the parasympathetic cholinergic anti-inflammatory pathway in the antibacterial defense in lung remains largely elusive.

Methods—
The middle cerebral artery occlusion model in mice was used to examine the influence of the parasympathetic nervous system on poststroke immunosuppression. We used heart rate variability measurement by telemetry, vagotomy, α7 nicotinic acetylcholine receptor–deficient mice, and parasympathomimetics (nicotine, PNU282987) to measure and modulate parasympathetic activity.

Results—
Here, we demonstrate a rapidly increased parasympathetic activity in mice after experimental stroke. Inhibition of cholinergic signaling by either vagotomy or by using α7 nicotinic acetylcholine receptor–deficient mice reversed pulmonary immune hyporesponsiveness and prevented pneumonia after stroke. In vivo and ex vivo studies on the role of α7 nicotinic acetylcholine receptor on different lung cells using bone marrow chimeric mice and isolated primary cells indicated that not only macrophages but also alveolar epithelial cells are a major cellular target of cholinergic anti-inflammatory signaling in the lung.

Conclusions—
Thus, cholinergic pathways play a pivotal role in the development of pulmonary infections after acute central nervous system injury.
Intravenous Thrombolysis for Stroke Recurring Within 3 Months From the Previous Event
Authors: Karlinski Michal , Kobayashi Adam , Czlonkowska Anna , Mikulik Robert , Vaclavik Daniel , Brozman Miroslav , Gdovinova Zuzana , Švigelj Viktor , Csiba Laszlo , Fekete Klara , Kõrv Janika , Demarin Vida , Bašic-Kes Vanja , Vilionskis Aleksandras , Jatuzis Dalius , Krespi Yakup , Shamalov Nikolay , Andonova Silva , Ahmed Niaz , Wahlgren Nils ,   for the Safe Implementation of Treatments in Stroke–East Registry (SITS-EAST) Investigators
Published: October 2015

Background and Purpose—
According to the European license, alteplase can be given no sooner than 3 months after previous stroke. However, it is not known whether past history of stroke influences the effect of treatment. Our aim was to evaluate safety and functional outcome after intravenous thrombolysis administered in everyday practice to patients with previous stroke ≤3 months compared with those with first-ever stroke.

Methods—
We analyzed consecutive cases treated with alteplase between October 2003 and July 2014 contributed to the Safe Implementation of Thrombolysis for Stroke–Eastern Europe registry from 12 countries. Odds ratios were calculated using unadjusted and adjusted logistic regression.

Results—
Of 13 007 patients, 11 221 (86%) had no history of stroke and 249 (2%) experienced previous stroke ≤3 months before admission. Patients with previous stroke ≤3 months had a higher proportion of hypertension and hyperlipidemia. There were no significant differences in outcome, including symptomatic intracerebral hemorrhage according to European Cooperative Acute Stroke Study (unadjusted odds ratio 1.27, 95% confidence interval: 0.74–2.15), and being alive and independent at 3 months (odds ratio 0.81, 95% confidence interval: 0.61–1.09).

Conclusions—
Patients currently treated with alteplase, despite a history of previous stroke ≤3 months, do not seem to achieve worse outcome than those with first-ever stroke. Although careful patient selection was probably of major importance, our findings provide reassurance that this group of patients may safely benefit from thrombolysis and should not be arbitrarily excluded as a whole. Further studies are needed to identify the shortest safe time lapse from the previous event to treatment with alteplase.
Risk Factors Associated With the Presence of Unruptured Intracranial Aneurysms
Authors: Kang Hyun Goo , Kim Bum Joon , Lee Jisung , Kim Mi-Jung , Kang Dong-Wha , Kim Jong S. , Kwon Sun U. 
Published: October 2015

Background and Purpose—
With the increased investigation of cerebral arteries using magnetic resonance angiography in the general population, the detection of unruptured intracranial aneurysms (UIAs) has increased. Understanding the distribution and factors associated with UIAs might be helpful for understanding the pathomechanism.

Methods—
Subjects who underwent magnetic resonance angiography with a health examination at the Health Screening and Promotion Center were enrolled. The incidence and risk factors of UIAs (age, sex, hypertension, diabetes mellitus, smoking, alcohol, and coronary artery disease) were investigated by comparing patients with and without UIAs. These risk factors were also investigated by the UIA location, distal internal carotid artery, anterior cerebral artery and middle cerebral artery (MCA), MCA bifurcation, anterior and posterior communicating artery, and posterior circulation.

Results—

Among 187 166 subjects who received health examination, 18 954 underwent magnetic resonance angiography. Of them, 367 (1.93%) had UIAs. Age (odds ratio [OR], 1.02;
P
=0.003), women (OR, 2.00;
P
<0.001), hypertension (OR, 2.21;
P
<0.001), smoking (OR, 1.66;
P
=0.001), and coronary artery disease (OR, 0.23;
P
<0.001) were independently associated with the presence of UIAs. Hypertension was associated with most UIAs, except for those located at sidewalls (anterior cerebral artery and MCA). MCA aneurysms were associated with old age and smoking. Distal internal carotid artery, posterior communicating artery, and MCA-bifurcation aneurysms were associated with female sex. Anterior communicating artery aneurysms were associated with smoking and alcohol. Posterior circulation UIAs were only associated with hypertension. Coronary artery disease was negatively associated with anterior circulation aneurysms.

Conclusions—
The risk factors for UIAs differ by their location, compared with the control. Interestingly, the presence of coronary artery disease was protective against the presence of UIAs.
Characteristics and Synoptic Environment of Drylines Occurring over the Higher Terrain of Southeastern Wyoming
Authors: Bergmaier Philip T. , Geerts Bart 
Published: October 2015

Abstract
Commonly observed over the broadly sloped terrain of the southern Great Plains (SGP), drylines are frequent loci of warm season deep convection and have been the focus of numerous observational, theoretical, and climatological studies over last half century. In this study, a 3-yr (2010–12) analysis of the characteristics and synoptic environment of drylines occurring elsewhere, over the high terrain in southeastern Wyoming just east of the Rocky Mountains, is presented. Observed on ~11% of the days between May and August of the years examined, southeastern Wyoming drylines were often associated with large moisture gradients [~5–10 g kg−1 (100 km)−1], large horizontal virtual potential temperature differences (~2–5 K), and convergent zonal wind flow at the surface. The synoptic conditions leading to their formation and their relationship to thunderstorm activity are also explored in an effort to aid local forecasters in anticipating the development and convective impact of drylines across the region. Similarities exist between these drylines and those found over the SGP, especially with regard to their strength and close relationship to deep convection. However, the frequency at which they occur, some characteristics of their diurnal motion, and the synoptic conditions driving their formation differ noticeably.
Social Predictors of Active Life Engagement
Authors: Sabbath Erika L. , Matz-Costa Christina , Rowe John W. , Leclerc Annette , Zins Marie , Goldberg Marcel , Berkman Lisa F. 
Published: October 2015

Background: Active life engagement is important for successful aging of societies and individuals. We tested predictors of engagement in French adults aged 60–74 (the GAZEL cohort). Methods: Participants ( n = 10,764) reported the previous day’s activities in a time-use survey. We modeled concurrent social, demographic, and health predictors of participation incidence and intensity in paid work, volunteering, caregiving, community involvement, and informal social interaction. Results: Men were more active in volunteering/community activities and women in caregiving and informal social interaction. Participation varied inversely with socioeconomic status (SES). Paid work participation declined linearly with age and health status, but this relationship did not hold for other activities. Conclusions: Men and those of higher SES were more likely to participate in certain activities than were women and those of low lifetime SES, potentially limiting the latter groups’ future health and well-being benefits from such activities. Findings suggest groups that could benefit from interventions to increase engagement.
Increased Expression of FGF19 Contributes to Tumor Progression and Cell Motility of Human Thyroid Cancer
Authors: Zhang Xiliang , Wang Zhonghua , Tian Lei , Xie Jiangping , Zou Guijun , Jiang Futing 
Published: October 2015

ObjectiveNumerous reports indicate a role for aberrant expression of fibroblast growth factor 19 (FGF19) in tumor development and progression, and several drugs have been developed to target it. The aim of this study was to investigate the clinical significance of FGF19 and examine whether it plays any roles in progression of thyroid cancer.Study DesignTranslation research.SettingNavy General Hospital of Chinese PLA, China.Subjects and MethodsExpression patterns of FGF19 protein in 100 paired formalin‐fixed and paraffin‐embedded cancerous and adjacent noncancerous tissues from patients with thyroid cancer were detected by immunohistochemistry. Then, in vitro migration and invasion assays of siRNA‐targeted FGF19‐transfected cells were performed.ResultsPositive immunostaining of FGF19 protein expression was localized in cytoplasm with or without membrane of malignant cells and was observed in 82 (82.0%) of 100 patients with thyroid cancer. Statistically, the expression level of FGF19 protein in thyroid cancer tissues was significantly higher than that in normal tissues. In addition, FGF19 overexpression was significantly associated with the advanced tumor node metastasis staging (P =. 008), the presence of extrathyroidal invasion (P =. 01), lymph nodes metastasis (P =. 01), and distant metastasis (P =. 02). Furthermore, knockdown of FGF19 by transfection of siRNA‐FGF19 could efficiently suppress the migration and invasion abilities of thyroid cancer cells in vitro.ConclusionOur data revealed that the increased expression of FGF19 might be involved in the malignant behaviors of thyroid cancer, highlighting its potential as a molecular marker for early diagnosis and as a possible target for therapeutic intervention of this disease.
Association of socioeconomic status with diagnosis, treatment and control of hypertension in diabetic hypertensive individuals in Bangladesh: a population-based cross-sectional study
Authors: Rahman Mosiur , H Syed Emdadul , Islam Md. Jahirul , Mostofa Md. Golam , Saadat Khandakar ASM 
Published: October 2015

Objectives This study aimed to examine if socioeconomic status could affect the likelihood of diagnosis, treatment and control of hypertension in diabetic hypertensive individuals. Design Cross-sectional nationally representative study. Settings Bangladesh. Participants This paper used data from the 2011 Bangladesh Demographic Health Survey. The analyses were based on the responses of 339 diabetes hypertensive individuals. Main outcome measures Diagnosis, treatment and control of hypertension. Results The age-adjusted prevalence of hypertension in diabetes individuals was 38.4% in the study population. Among diabetic hypertensive subjects only 65.7% had been diagnosed, 58.4% were receiving treatment and 42% controlled their hypertension. Individuals from high socioeconomic status (AOR 2.60; 95% CI 1.16–5.83) had an increased likelihood of reporting diagnosis of hypertension. Individuals from medium (AOR 2.22; 95% CI 1.11–4.46) and high socioeconomic status (AOR 3.47; 95% CI 1.59–7.58) had increased chance of receiving treatment. In addition, individuals belonging to high socioeconomic status (AOR 2.53; 95% CI 1.14–5.63) were more likely to report of controlling hypertension. Conclusions This study indicated that hypertension is more prevalent among diabetic patients. Furthermore, diabetic hypertensive patients from the low socioeconomic status group are also less likely to be diagnosed and also less likely to receive treatment for hypertension. In addition, diabetic hypertensive patients from the low socioeconomic status were less likely to control hypertension compared with an individual belonging to the high socioeconomic status group. This reduced likelihood of receiving proper treatment will lead to a rapid increase in the prevalence of macrovascular and microvascular diseases among diabetic hypertensive patients.
C-reactive protein enhances murine antibody–mediated transfusion-related acute lung injury
Authors: Kapur Rick , Kim Michael , Shanmugabhavananthan Shanjeevan , Liu Jonathan , Li Yuan , Semple John W. 
Published: October 2015

Key Points
CRP enhances antibody-mediated lung damage when infused into TRALI-resistant mice. CRP and TRALI-inducing antibodies generate a synergistic increase in MIP-2 production and pulmonary neutrophil accumulation in vivo.