bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of
Methylobacterium
sp. Strain ARG-1 Isolated from the White-Rot Fungus
Armillaria gallica
Authors: Collins Caitlin , Kowalski Caitlin , Zebrowski Jessica , Tulchinskaya Yevgeniya , Tai Albert K. , James-Pederson Magdalena , Hirst Rachel 
Published: June 2016

ABSTRACT

Methylobacterium
sp. strain ARG-1 was isolated from a cell culture of hyphal tips of the white-rot fungus
Armillaria gallica
. We describe here the sequencing, assembly, and annotation of its genome, confirming the presence of genes involved in methylotrophy. This is the first genome announcement of a strain of
Methylobacterium
associated with
A. gallica
.
Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies
Authors: Thibessard Annabelle , Leblond Pierre 
Published: June 2016

ABSTRACT

The sequence of
Streptomyces ambofaciens
DSM 40697 was completely determined. The genome consists of an 8.1-Mbp linear chromosome with terminal inverted repeats of 210 kb. Genomic islands were identified, one of which corresponds to a new putative integrative and conjugative element (ICE) called pSAM3.
Draft Genome Sequence of
Bacillus
sp. GZT, a 2,4,6-Tribromophenol-Degrading Strain Isolated from the River Sludge of an Electronic Waste-Dismantling Region
Authors: Liang Zhishu , Li Guiying , An Taicheng , Das Ranjit 
Published: June 2016

ABSTRACT

Here, we report the draft genome sequence of
Bacillus
sp. strain GZT, a 2,4,6-tribromophenol (TBP)-degrading bacterium previously isolated from an electronic waste-dismantling region. The draft genome sequence is 5.18 Mb and has a G+C content of 35.1%. This is the first genome report of a brominated flame retardant-degrading strain.
Complete Genome Sequence of the Endophytic Fungus
Diaporthe
(
Phomopsis
)
ampelina
Authors: Savitha J. , Bhargavi S. D. , Praveen V. K. 
Published: June 2016

ABSTRACT

Diaporthe ampelina
was isolated as an endophytic fungus from the root of
Commiphora wightii,
a medicinal plant collected from Dhanvantri Vana, Bangalore University, Bangalore, India
.
The whole genome is 59 Mb, contains a total of 905 scaffolds, and has a G+C content of 51.74%. The genome sequence of
D. ampelina
shows a complete absence of lovastatin (an anticholesterol drug) gene cluster.
Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates
Authors: Hayrapetyan Hasmik , Boekhorst Jos , de Jong Anne , Kuipers Oscar P. , Nierop Groot Masja N. , Abee Tjakko 
Published: June 2016

ABSTRACT

Bacillus cereus
is a foodborne pathogen causing emetic and diarrheal-type syndromes. Here, we report the whole-genome sequences of 11
B. cereus
food isolates.
Draft Genome Sequence of Bacillus cereus 905, a Plant Growth-Promoting Rhizobacterium of Wheat
Authors: Ding Haixia , Niu Ben , Fan Haiyan , Li Yan , Wang Qi 
Published: June 2016

ABSTRACT

Bacillus cereus
905 is a plant growth-promoting rhizobacterium, isolated from wheat rhizosphere. The draft genome sequence of this strain is 5.39 Mb and harbors 5,412 coding sequences.
Draft Genome Sequence of Arthrobacter enclensis NCIM 5488
T
for Secondary Metabolism
Authors: Neurgaonkar Priya S. , Dharne Mahesh S. , Dastager Syed G. 
Published: June 2016

ABSTRACT

Here, we report the draft genome sequence of
Arthrobacter enclensis
NCIM 5488
T
, an actinobacterium isolated from a marine sediment sample from Chorao Island, Goa, India. This draft genome sequence consists of 4,226,231 bp with a G+C content of 67.08%, 3,888 protein-coding genes, 50 tRNAs, and 10 rRNAs. Analysis of the genome using bioinformatics tools such as antiSMASH and NaPDoS showed the presence of many unique natural product biosynthetic gene clusters.
First Draft Genome Sequence of Staphylococcus condimenti F-2
T
Authors: Zheng Beiwen , Hu Xinjun , Jiang Xiawei , Li Ang , Yao Jian , Li Lanjuan 
Published: June 2016

ABSTRACT

This report describes the draft genome sequence of
S. condimenti
strain F-2
T
(DSM 11674), a potential starter culture. The genome assembly comprised 2,616,174 bp with 34.6% GC content. To the best of our knowledge, this is the first documentation that reports the whole-genome sequence of
S. condimenti.
Treatment of Insulin Resistance by Acupuncture: A Review of Human and Animal Studies
Authors: Martinez Bridget , Peplow Philip V 
Published: June 2016

Background Numerous experimental studies have demonstrated that acupuncture can correct various metabolic disorders such as hyperglycaemia, overweight, hyperphagia, hyperlipidaemia, inflammation, altered activity of the sympathetic nervous system, and insulin signalling defects, all of which contribute to the development of insulin resistance. Objective To review human and animal studies investigating acupuncture as a treatment for insulin resistance, and to evaluate its potential to increase insulin sensitivity. Methods PubMed was searched for relevant articles published between January 2008 and October 2015. Search terms used were ‘acupuncture’, ‘insulin resistance’, ‘insulin sensitivity’, and ‘blood glucose’. Additional secondary sources of information included reference lists from retrieved papers and pertinent papers identified by hand searches of relevant journals not found in the database. Results In total, 31 articles were included in this review and comprised studies of the following insulin resistant conditions: obesity (n=9); diabetes mellitus (n=12); polycystic ovarian syndrome (n=7); skeletal muscle atrophy (n=1); ischaemic heart disease (n=1); and fatty liver disease (n=1). Of these articles, seven were human trials and 24 animal experiments. Collectively, the studies suggest that electroacupuncture (EA) at low intensity and low frequency can reduce insulin resistance and increase insulin sensitivity in a range of different insulin-resistant conditions. Conclusions EA, used alone or in combination with other therapies, such as Chinese herbs or diet-exercise interventions, has the potential to be an effective treatment for insulin resistance. Additional controlled clinical studies of acupuncture are needed in subjects with diabetes mellitus, ischaemic heart disease, muscle atrophy, and fatty liver disease.
Establishing the effectiveness, cost-effectiveness and student experience of a Simulation-based education Training program On the Prevention of Falls (STOP-Falls) among hospitalised inpatients: a protocol for a randomised controlled trial
Authors: Williams Cylie , Bowles Kelly-Ann , Kiegaldie Debra , Maloney Stephen , Nestel Debra , Kaplonyi Jessica , Haines Terry 
Published: June 2016

IntroductionSimulation-based education (SBE) is now commonly used across health professional disciplines to teach a range of skills. The evidence base supporting the effectiveness of this approach for improving patient health outcomes is relatively narrow, focused mainly on the development of procedural skills. However, there are other simulation approaches used to support non-procedure specific skills that are in need of further investigation. This cluster, cross-over randomised controlled trial with a concurrent economic evaluation (cost per fall prevented) trial will evaluate the effectiveness, cost-effectiveness and student experience of health professional students undertaking simulation training for the prevention of falls among hospitalised inpatients. This research will target the students within the established undergraduate student placements of Monash University medicine, nursing and allied health across Peninsula Health acute and subacute inpatient wards.Methods and analysisThe intervention will train the students in how to provide the Safe Recovery program, the only single intervention approach demonstrated to reduce falls in hospitals. This will involve redevelopment of the Safe Recovery program into a one-to-many participant SBE program, so that groups of students learn the communication skills and falls prevention knowledge necessary for delivery of the program. The primary outcome of this research will be patient falls across participating inpatient wards, with secondary outcomes including student satisfaction with the SBE and knowledge gain, ward-level practice change and cost of acute/rehabilitation care for each patient measured using clinical costing data.Ethics and disseminationThe Human Research Ethics Committees of Peninsula Health (LRR/15/PH/11) and Monash University (CF15/3523-2015001384) have approved this research. The participant information and consent forms provide information on privacy, storage of results and dissemination. Registration of this trial has been completed with the Australian and New Zealand Clinical Trials Registry: ACTRN12615000817549. This study protocol has been prepared according to the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist.Trial registration numberACTRN12615000817549; Pre-results.
Risk factors of direct heat-related hospital admissions during the 2009 heatwave in Adelaide, Australia: a matched case–control study
Authors: Zhang Ying , Nitschke Monika , Krackowizer Antoinette , Dear Keith , Pisaniello Dino , Weinstein Philip , Tucker Graeme , Shakib Sepehr , Bi Peng 
Published: June 2016

ObjectiveThe extreme heatwave of 2009 in South Australia dramatically increased morbidity, with a 14-fold increase in direct heat-related hospitalisation in metropolitan Adelaide. Our study aimed to identify risk factors for the excess morbidity.DesignA matched case–control study of risk factors was conducted.SettingPatients and matched community controls were interviewed to gather data on demographics, living environment, social support, health status and behaviour changes during the heatwave.ParticipantsCases were all hospital admissions with heat-related diagnoses during the 5-day heatwave in 2009. Controls were randomly selected from communities.Outcome measuresDescriptive analyses, simple and multiple conditional logistic regressions were performed. Adjusted ORs (AORs) were estimated.ResultsIn total, 143 hospital patients and 143 matched community controls were interviewed, with a mean age of 73 years (SD 21), 96% European ethnicity, 63% retired, 36% with high school or higher education, and 8% institutional living. The regression model indicated that compared with the controls, cases were more likely to have heart disease (AOR=13.56, 95% CI 1.27 to 144.86) and dementia (AOR=26.43, 95% CI 1.99 to 350.73). The protective factors included higher education level (AOR=0.48, 95% CI 0.23 to 0.99), having air-conditioner in the bedroom (AOR=0.12, 95% CI 0.02 to 0.74), having an emergency button (AOR=0.09, 95% CI 0.01 to 0.96), using refreshment (AOR=0.10, 95% CI 0.01 to 0.84), and having more social activities (AOR=0.11, 95% CI 0.02 to 0.57).ConclusionsPre-existing heart disease and dementia significantly increase the risk of direct heat-related hospitalisations during heatwaves. The presence of an air-conditioner in the bedroom, more social activities, a higher education level, use of emergency buttons and refreshments reduce the risk during heatwaves.
Retrospective angiographic study to determine the effect of atherosclerotic stenoses of upstream arteries on the degree of atherosclerosis in distal vascular territories
Authors: Rehwald Rafael , Petersen Johannes , Gratl Alexandra , Zoller Heinz , Mader Andreas , Loizides Alexander , Grams Astrid E , Klocker Josef , Glodny Bernhard 
Published: June 2016

ObjectiveExperimental coarctation of the aorta prevents the development of downstream atherosclerosis. The aim of this study was to find out whether or not atherosclerotic stenoses protect distal vascular territories from developing atherosclerosis in humans.Design and settingA total of 2125 vascular segments from angiographies of 101 patients were evaluated by calculating the maximum degree of stenosis (NASCET criteria), the degree of calcification, the degree of collaterals and the Friesinger score.ResultsStenosis ≥30–49% was found in 685 vascular segments (32.2%), ≥50–69% in 490 (23.1%), ≥70–89% in 373 (17.6%) and ≥90% in 265 (12.5%). If a stenosis of at least ≥70–89% was present in the common iliac, the external iliac or the common femoral artery, the degrees of stenosis distal to it were lower than those on the contralateral side (19.8±22.3% (CI 11.7 to 28.0) vs 25.2±20.7% (CI 21.2 to 29.1); Friesinger scores 1.1±1.2 (CI 0.6 to 1.5) vs 1.4±1.1 (CI 1.2 to 1.6); degrees of calcification 0.8±1.0 (CI 0.4 to 1.1) vs 1.2±1.1 (CI 1.2 to 1.6); p<0.05 each). This effect depended on the degree of proximal stenosis, but not on collaterals, and was most pronounced distal to stenoses of the common iliac, the superficial femoral and the popliteal artery. In regression models, stenoses of the pelvic arteries were shown to be an independent protective factor for the distal vascular territories.ConclusionsAtherosclerotic stenoses seem to protect distal vascular territories from developing atherosclerosis. The underlying pathophysiological mechanism of this phenomenon remains to be determined. It could be based on pulse pressure reduction.
Protocol of a randomised phase III clinical trial of sequential capecitabine or 5-fluorouracil plus bevacizumab (Cape/5-FU-Bmab) to capecitabine or 5-fluorouracil plus oxaliplatin plus bevacizumab (CapeOX/mFOLFOX6-Bmab) versus combination CapeOX/mFOLFOX6-Bmab in advanced colorectal cancer: the C-cubed (C3) study
Authors: Nagasaka Takeshi , Mishima Hideyuki , Sawaki Akira , Shimokawa Mototsugu , Inukai Michio , Shinozaki Katsunori , Tanioka Hiroaki , Nasu Junichiro , Nishina Tomohiro , Hazama Shoichi , Okajima Masazumi , Yamaguchi Yoshiyuki 
Published: June 2016

IntroductionResults from several randomised trials suggest that the sequential use of cytotoxic agents in patients with metastatic colorectal cancer (mCRC) has the potential to improve overall survival compared with combination chemotherapy. This study is designed to investigate whether sequential treatment with bevacizumab-based first-line treatment with oxaliplatin is superior to combination treatment of mCRC.Methods and analysisThe C-cubed (C3) study is a two-arm, multicentre, open-label, randomised phase III trial in Japan comparing the efficacy and safety of sequential capecitabine or 5-fluorouracil plus bevacizumab (Cape/5-FU-Bmab) with escalation to capecitabine or 5-fluorouracil plus oxaliplatin plus bevacizumab (CapeOX/mFOLFOX6-Bmab) versus combination CapeOX/mFOLFOX6-Bmab as the first-line treatment of mCRC. In the sequential arm (Arm A: oxaliplatin ‘wait-and-go’), treatment escalation from Cape/5-FU-Bmab to CapeOX/mFOLFOX6-Bmab is recommended in the case of progressive disease. In the combination arm (Arm B: oxaliplatin ‘stop-and-go’), de-escalation from CapeOX/mFOLFOX6-Bmab to Cape/5-FU-Bmab is possible after 12 weeks of treatment. Re-escalation to CapeOX/mFOLFOX6-Bmab after progressive disease is considered only for patients who received de-escalation of oxaliplatin after 12 weeks of treatment not caused by oxaliplatin-associated toxicity. A target sample size of 304 evaluable patients is considered sufficient to validate an expected HR for time to failure of strategy of the sequential approach ‘wait-and-go’ compared to the combination approach ‘stop-and go’ with 80% power and 2-sided 5% α in case of a true HR<0.69.Ethics and disseminationThis study is conducted according to the standards of Good Clinical Practice and in compliance with the Declaration of Helsinki 2013 and local regulations, and has been submitted and approved by the Ethical Committee of the Non-Profit Organization MINS Institutional Review Board. The protocol and the trial results, even inconclusive, will be presented at international oncology congresses and published in peer-reviewed journals.Trial registration numberUMIN000015405, Pre-results.
Ricci inheritance collineations in Bianchi type II spacetime
Authors: Hussain Tahir , Akhtar Sumaira Saleem , Bokhari Ashfaque H. , Khan Suhail 
Published: June 2016

In this paper, we present a complete classification of Bianchi type II spacetime according to Ricci inheritance collineations (RICs). The RICs are classified considering cases when the Ricci tensor is both degenerate as well as non-degenerate. In case of non-degenerate Ricci tensor, it is found that Bianchi type II spacetime admits 4-, 5-, 6- or 7-dimensional Lie algebra of RICs. In the case when the Ricci tensor is degenerate, majority cases give rise to infinitely many RICs, while remaining cases admit finite RICs given by 4, 5 or 6.
Assessing tsunami hazard using heterogeneous slip models in the Mentawai Islands, Indonesia
Authors: Griffin Jonathan D. , Pranantyo Ignatius R. , Kongko Widjo , Haunan Afif , Robiana Rahayu , Miller Victoria , Davies Gareth , Horspool Nick , Maemunah Imun , Widjaja Wisnu B. , Natawidjaja Danny H. , Latief Hamzah 
Published: June 2016

Abstract
Tsunami hazard maps are generated for the coastline of the Mentawai Islands, West Sumatra, Indonesia, to support evacuation and disaster response planning. A random heterogeneous slip generator is used to forward model a suite of earthquake rupture scenarios on the Mentawai Segment of the Sunda Subduction Zone. Up to 1000 rupture models that fit constraints provided by coral and geodetic records of coseismic vertical deformation from major earthquakes in 1797, 1833 and 2007 are used to model inundation and to define a maximum inundation zone that envelopes all of these scenarios. Comparison with single-scenario hazard assessments developed by experts and agreed through scientific consensus shows that there is value in modelling a suite of scenarios in order to obtain a more robust and conservative estimate of potential inundated areas. Although both the model presented here and the single-scenario models are based on assumptions about the characteristics of future events using knowledge of past events, by sampling a range of plausible outcomes we gain a more robust estimate of which areas may be inundated during a tsunami within the bounds of the assumptions applied.
Treatment Preferences for Active Surveillance versus Active Treatment among Men with Low-Risk Prostate Cancer
Authors: Taylor Kathryn L. , Hoffman Richard M. , Davis Kimberly M. , Luta George , Leimpeter Amethyst , Lobo Tania , Kelly Scott P. , Shan Jun , Aaronson David , Tomko Catherine A. , Starosta Amy J. , Hagerman Charlotte J. , Van Den Eeden Stephen K. 
Published: June 2016

Abstract
Background: Due to the concerns about the overtreatment of low-risk prostate cancer, active surveillance (AS) is now a recommended alternative to the active treatments (AT) of surgery and radiotherapy. However, AS is not widely utilized, partially due to psychological and decision-making factors associated with treatment preferences.
Methods: In a longitudinal cohort study, we conducted pretreatment telephone interviews (N = 1,140, 69.3% participation) with newly diagnosed, low-risk prostate cancer patients (PSA ≤ 10, Gleason ≤ 6) from Kaiser Permanente Northern California. We assessed psychological and decision-making variables, and treatment preference [AS, AT, and No Preference (NP)].
Results: Men were 61.5 (SD, 7.3) years old, 24 days (median) after diagnosis, and 81.1% white. Treatment preferences were: 39.3% AS, 30.9% AT, and 29.7% NP. Multinomial logistic regression revealed that men preferring AS (vs. AT) were older (OR, 1.64; CI, 1.07–2.51), more educated (OR, 2.05; CI, 1.12–3.74), had greater prostate cancer knowledge (OR, 1.77; CI, 1.43–2.18) and greater awareness of having low-risk cancer (OR, 3.97; CI, 1.96–8.06), but also were less certain about their treatment preference (OR, 0.57; CI, 0.41–0.8), had greater prostate cancer anxiety (OR, 1.22; CI, 1.003–1.48), and preferred a shared treatment decision (OR, 2.34; CI, 1.37–3.99). Similarly, men preferring NP (vs. AT) were less certain about treatment preference, preferred a shared decision, and had greater knowledge.
Conclusions: Although a substantial proportion of men preferred AS, this was associated with anxiety and uncertainty, suggesting that this may be a difficult choice.
Impact: Increasing the appropriate use of AS for low-risk prostate cancer will require additional reassurance and information, and reaching men almost immediately after diagnosis while the decision-making is ongoing. Cancer Epidemiol Biomarkers Prev; 25(8); 1240–50. ©2016 AACR.
ERK1 as a Therapeutic Target for Dendritic Cell Vaccination against High-Grade Gliomas
Authors: Ku Min-Chi , Edes Inan , Bendix Ivo , Pohlmann Andreas , Waiczies Helmar , Prozorovski Tim , Günther Martin , Martin Conrad , Pagès Gilles , Wolf Susanne A. , Kettenmann Helmut , Uckert Wolfgang , Niendorf Thoralf , Waiczies Sonia 
Published: June 2016

Abstract
Glioma regression requires the recruitment of potent antitumor immune cells into the tumor microenvironment. Dendritic cells (DC) play a role in immune responses to these tumors. The fact that DC vaccines do not effectively combat high-grade gliomas, however, suggests that DCs need to be genetically modified specifically to promote their migration to tumor relevant sites. Previously, we identified extracellular signal–regulated kinase (ERK1) as a regulator of DC immunogenicity and brain autoimmunity. In the current study, we made use of modern magnetic resonance methods to study the role of ERK1 in regulating DC migration and tumor progression in a model of high-grade glioma. We found that ERK1-deficient mice are more resistant to the development of gliomas, and tumor growth in these mice is accompanied by a higher infiltration of leukocytes. ERK1-deficient DCs exhibit an increase in migration that is associated with sustained Cdc42 activation and increased expression of actin-associated cytoskeleton-organizing proteins. We also demonstrated that ERK1 deletion potentiates DC vaccination and provides a survival advantage in high-grade gliomas. Considering the therapeutic significance of these results, we propose ERK1-deleted DC vaccines as an additional means of eradicating resilient tumor cells and preventing tumor recurrence. Mol Cancer Ther; 15(8); 1975–87. ©2016 AACR.
Something Old, Something New, Something Borrowed, Something Fused: Novel EGFR Rearrangements in Lung Adenocarcinomas
Authors: Paik Paul K. 
Published: June 2016

Abstract
Summary: Mutations in EGFR stand as the archetype for somatic alterations that lead to oncogene addiction and that predict for response to targeted therapies. In this issue of Cancer Discovery, Konduri and colleagues report on a pair of novel oncogenic and actionable EGFR fusion events in a series of patients with lung adenocarcinomas, casting new light on this model gene. Cancer Discov; 6(6); 574–5. ©2016 AACR.
See related article by Konduri et al., p. 601.