bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of the Thermophilic and Facultatively Chemolithoautotrophic Sulfate Reducer Archaeoglobus sulfaticallidus Strain PM70-1
T
Authors: Stokke Runar , Hocking William Peter , Steinsbu Bjørn Olav , Steen Ida Helene 
Published: July 2013

ABSTRACT

Dissimilatory sulfate-reducing archaea of the genus
Archaeoglobus
display divergent preferences in the use of energy sources and electron acceptors. Here we present the complete genome sequence of the thermophilic
Archaeoglobus sulfaticallidus
strain PM70-1
T
, which distinctly couples chemolithoautotrophic growth on H
2
/CO
2
to sulfate reduction in addition to heterotrophic growth.
Draft Genome Sequence of
Pandoraea
sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil
Authors: Pushiri Hafizah , Pearce Stephen L. , Oakeshott John G. , Russell Robyn J. , Pandey Gunjan 
Published: July 2013

ABSTRACT

Pandoraea
sp. strain SD6-2 is a δ-hexachlorocyclohexane-degrading bacterial strain isolated from lindane-contaminated soil in Queensland, Australia. The genome of SD6-2 was sequenced to investigate its ability to degrade δ-hexachlorocyclohexane. Here we report the annotated genome sequence of this strain.
Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete
Authors: Davis Jennifer R. , Goodwin Lynne , Teshima Hazuki , Detter Chris , Tapia Roxanne , Han Cliff , Huntemann Marcel , Wei Chia-Lin , Han James , Chen Amy , Kyrpides Nikos , Mavrommatis Kostas , Szeto Ernest , Markowitz Victor , Ivanova Natalia , Mikhailova Natalia , Ovchinnikova Galina , Pagani Ioanna , Pati Amrita , Woyke Tanja , Pitluck Sam , Peters Lin , Nolan Matt , Land Miriam , Sello Jason K. 
Published: July 2013

ABSTRACT

We announce the availability of the genome sequence of
Streptomyces viridosporus
strain T7A ATCC 39115, a plant biomass-degrading actinomycete. This bacterium is of special interest because of its capacity to degrade lignin, an underutilized component of plants in the context of bioenergy. It has a full complement of genes for plant biomass catabolism.
Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India
Authors: Malathi Jambulingam , Murugan Nandagopal , Umashankar Vetrivel , Bagyalakshmi Radhakrishnan , Madhavan Hajib Narahari Rao 
Published: July 2013

ABSTRACT

Multidrug-resistant
Pseudomonas aeruginosa
strains, which are notable nosocomial pathogens, have greatly increased the mortality rate of septicemic patients due to treatment failure. Here, we report the draft genome sequence of
P. aeruginosa
strain VRFPA02, a human bloodstream isolate that has phenotypically proven to be resistant to a broad spectrum of antibiotics.
Complete Genome Sequence of
Burkholderia
sp. Strain RPE64, Bacterial Symbiont of the Bean Bug
Riptortus pedestris
Authors: Shibata Tomoko F. , Maeda Taro , Nikoh Naruo , Yamaguchi Katsushi , Oshima Kenshiro , Hattori Masahira , Nishiyama Tomoaki , Hasebe Mitsuyasu , Fukatsu Takema , Kikuchi Yoshitomo , Shigenobu Shuji 
Published: July 2013

ABSTRACT

We isolated
Burkholderia
symbiont strain RPE64 from the bean bug
Riptortus pedestris
. Analysis of the complete 6.96-Mb genome, which consists of three chromosomes and two plasmids, will facilitate further understanding of insect–microbe symbiosis and the development of pest-control technologies.
Complete Genome Sequences of Helicobacter pylori Rifampin-Resistant Strains
Authors: Momynaliev Kuvat , Chelysheva Vera , Selezneva Oksana , Akopian Tatyana , Alexeev Dmitry , Govorun Vadim 
Published: July 2013

ABSTRACT

Here we present the complete genome sequences of two
Helicobacter pylori
rifampin-resistant (Rif
r
) strains (Rif1 and Rif2). Rif
r
strains were obtained by
in vitro
selection of
H. pylori
26695 on agar plates with 20 µg/ml rifampin. The genome data provide insights on the genomic diversity of
H. pylori
under selection by rifampin.
Draft Genome Sequence of Arthrobacter crystallopoietes Strain BAB-32, Revealing Genes for Bioremediation
Authors: Joshi M. N. , Pandit A. S. , Sharma A. , Pandya R. V. , Desai S. M. , Saxena A. K. , Bagatharia S. B. 
Published: July 2013

ABSTRACT

Arthrobacter crystallopoietes
strain BAB-32, a Gram-positive obligate aerobic actinobacterium having potential application in bioremediation and bioreduction of a few metals, was isolated from rhizosphere soil of Gandhinagar, Gujarat, India. The draft genome (4.3 Mb) of the strain revealed a few vital gene clusters involved in the metabolism of aromatic compounds, zinc, and sulfur.
Prediction of sediment erosion after dam removal using a one-dimensional model
Authors: Greimann Blair 
Published: July 2013

Abstract
The accurate prediction of sediment erosion after dam removal is critical to quantifying the impact of dam removal on the reservoir and downstream environment. A variety of methods can be used to estimate this impact, and one of the most common is to use a one-dimensional mobile bed sediment transport model. I describe a one-dimensional sediment transport model (SRH-1D) and use it to simulate a laboratory experiment of incision through a reservoir delta deposit. The model allows the user to specify the erosion width through the deposit as a function of the flow rate. The model is shown to predict the vertical incision and downstream sediment load with reasonable accuracy if the erosion width is specified. Sensitivity tests to the transport equation parameters, erosion width, and angle of repose are conducted. The sediment loads exiting the dam are shown to be sensitive to the critical shear stress, but they are relatively insensitive to changes to the erosion width and angle of repose. One-dimensional models are shown to require the specification of the erosion width, but the results are not considered to be extremely sensitive to its value, so long as it is approximately equal to the observed river width under the same flow conditions. Further work on modeling of bank erosion is necessary to more accurately predict the long-term evolution of reservoir deposits.
Seeing you through London 2012: eye care at the Paralympics
Authors: Wilson Clare M , Thomson W David , D'Ath Penny J 
Published: July 2013

BackgroundThe provision of eye care services for competitors and support teams is integral to the modern Olympic Games. The eye clinic for the London 2012 Paralympic Games employed a multidisciplinary team of eye care professionals using state-of-the-art instrumentation to provide the highest level of eye care. The detailed organisation of the eye care clinic at London 2012 is described in a companion paper which summarises the eye care clinic during the London 2012 Olympic Games. These two reports will aid in planning eye care clinics at future Games.AimThis paper summarises the organisation of the eye clinic and provides outline audit data relating to eye conditions encountered during the Paralympic Games.ResultsA total of 870 patients representing 102 countries attended the eye clinic. 274 (31.5%) were competitors; the remainder were trainers and support staff. No serious ocular injuries resulted from competitor injury in the field of play during the Paralympic Games, although seven patients were referred urgently to hospital eye services for conditions including orbital cellulitis, retinal detachment, exudative macular degeneration, corneal ulcer, Stevens-Johnson syndrome and macular oedema. A total of 749 spectacles, 14 pairs of contact lenses and 7 low vision aids were dispensed.ConclusionsBy combining excellent facilities and equipment with a multidisciplinary team of eye care professionals, we feel we provided the highest level of eye care, providing a legacy for future Games.
Randomised controlled trial of weekly chloroquine to re-establish normal erythron iron flux and haemoglobin recovery in postmalarial anaemia
Authors: Cox Sharon E , Nweneka Chidi V , Doherty Conor P , Fulford Anthony J , Moore Sophie E , Prentice Andrew M 
Published: July 2013

ObjectiveTo determine if low-dose weekly chloroquine (CQ) therapy improves recovery from malaria-associated anaemia.DesignProof of concept randomised clinical trial.SettingWest Kiang District, Lower River Region, The Gambia.ParticipantsChildren resident in participating communities, aged 12–72 months, with uncomplicated malaria identified using active case detection over two consecutive malaria transmission seasons.InterventionsIn 2007, eligible children were randomised to chloroquine-sulfadoxine/pyrimethamine (CQ-SP) or co-artemether (ACT) antimalarial therapy, and after parasite clearance on day 3 were subsequently re-randomised (double-blind) to weekly low-dose CQ (5 mg/kg) or placebo. In 2008, all eligible children were treated with ACT and subsequently randomised to CQ or placebo.Outcome measuresThe primary outcome was a change in haemoglobin from baseline (day 3 of antimalarial treatment) to day 90 in the CQ and placebo treatment arms. Secondary outcomes were changes in urinary neopterin as a marker of macrophage activation, markers of erythropoietic response and prevalence of submicroscopic parasitaemia. Change in haemoglobin in the placebo arm by initial antimalarial treatment was also assessed.ResultsIn 2007, 101 children with uncomplicated malaria were randomised to antimalarial treatment with CQ-SP or ACT and 65 were subsequently randomised to weekly CQ or placebo. In 2008, all children received ACT antimalarial treatment and 31 were subsequently randomised to receive weekly CQ or placebo. Follow-up to day 90 was 96%. There was no effect of weekly CQ vs placebo on change in haemoglobin at day 90 (CQ+10.04 g/L (95% CI 6.66 to 13.42) vs placebo +7.61 g/L (95% CI 2.88 to 12.35)). There was no effect on the secondary outcomes assessed, or effect of initial antimalarial therapy on haemoglobin recovery. Higher day 90 haemoglobin correlated independently with older age, not being stunted, higher haemoglobin at day 0 and adequate iron status at day 3.ConclusionsWeekly low-dose CQ after effective antimalarial treatment is not effective in improving recovery from postmalarial anaemia.Trial registrationThe clinical trial registration number isNCT00473837(ClinicalTrials.gov).
Psychosocial and educational outcomes of weight faltering in infancy in ALSPAC
Authors: Holme Amelia R , Blair Peter S , Emond Alan M 
Published: July 2013

ObjectivesTo investigate whether infants with weight faltering have impaired psychosocial and educational outcomes in later childhood.DesignFollow-up of infants with weight faltering in a large UK cohort study.SettingThe Avon Longitudinal Study of Parents and Children (ALSPAC).Participants11 534 term infants from ALSPAC with complete weight records. Weight gain (conditional on initial weight) was calculated for three periods: from birth to 8 weeks, 8 weeks to 9 months, and birth to 9 months. Cases of weight faltering were defined as those infants with a conditional weight gain below the 5th centile, and these were compared with the rest of the cohort as the control group.OutcomesBetween 6 and 11 years, social, emotional and behavioural development was measured by direct assessment of the children and parental and teacher report. Educational outcomes included Standardised Assessment Test results at 7 and 11 years and Special Educational Needs status at age 11.ResultsDifferences seen on univariate analysis in attention, non-verbal accuracy, educational attainment and special educational needs became non-significant after adjustment for confounding. Children with weight faltering in infancy did not differ from controls on any measures of self-esteem, peer relationships, experience of bullying, social cognition, antisocial activities, anxiety, depression or behavioural problems.ConclusionsWeight faltering in early infancy was associated with poorer educational outcomes in later childhood, but these associations were explained by confounding. The subsequent psychosocial development of infants with slow weight gain was not different from that of their peers.
Incorporating evidence review into quality improvement: meeting the needs of innovators
Authors: Danz Margie Sherwood , Hempel Susanne , Lim Yee-Wei , Shanman Roberta , Motala Aneesa , Stockdale Susan , Shekelle Paul , Rubenstein Lisa 
Published: July 2013

BackgroundAchieving quality improvement (QI) aims often requires local innovation. Without objective evidence review, innovators may miss previously tested approaches, rely on biased information, or use personal preferences in designing and implementing local QI programmes.AimTo develop a practical, responsive approach to evidence review for QI innovations aimed at both achieving the goals of the Patient Centered Medical Home (PCMH) and developing an evidence-based QI culture.DesignDescriptive organisational case report.MethodsAs part of a QI initiative to develop and spread innovations for achieving the Veterans Affairs (VA) PCMH (termed Patient Aligned Care Team, or PACT), we involved a professional evidence review team (consisting of review experts, an experienced librarian, and administrative support) in responding to the evidence needs of front-line primary care innovators. The review team developed a systematic approach to responsive innovation evidence review (RIER) that focused on innovator needs in terms of time frame, type of evidence and method of communicating results. To assess uptake and usefulness of the RIERs, and to learn how the content and process could be improved, we surveyed innovation leaders.ResultsIn the first 16 months of the QI initiative, we produced 13 RIERs on a variety of topics. These were presented as 6–15-page summaries and as slides at a QI collaborative. The RIERs focused on innovator needs (eg, topic overviews, how innovations are carried out, or contextual factors relevant to implementation). All 17 innovators who responded to the survey had read at least one RIER; 50% rated the reviews as very useful and 31%, as probably useful.ConclusionsThese responsive evidence reviews appear to be a promising approach to integrating evidence review into QI processes.
An intervention to improve transitions from NICU to ambulatory care: quasi-experimental study
Authors: Moyer Virginia A , Papile Lu-Ann , Eichenwald Eric , Giardino Angelo P , Khan Myrna M , Singh Hardeep 
Published: July 2013

BackgroundInfants born prematurely or with complex medical problems are surviving to discharge in growing numbers and often require significant monitoring and coordination of care in the ambulatory setting. Using Healthcare Failure Modes and Effects Analysis (HFMEA), we identified a large number of potentially serious error points in this transition of care.PurposeTo test whether a multifaceted intervention that included a health coach to assist families and an enhanced personal health record to improve the quality of information available to parents and community professionals would decrease adverse events and improve family assessment of the transition.MethodsUsing a concurrent cohort design, infants in one geographic area (pod) of the intensive care nursery received the intervention; infants in two other pods received routine discharge care. Primary outcomes included deaths, sick visits, unplanned readmissions and missed appointments within 1 month of discharge. The family assessed the transition using a modified version of the Care Transitions Measure.Results125 intervention infants (54% boys) and 104 control infants (48% boys) were enrolled over 18 months. The groups were similar in maternal education, insurance status, language spoken and number of adults in the home, birth weight and length of stay. At least one adverse outcome occurred in 63 (50.4%) intervention infants and 56 (53.8%) control infants (p=0.55). At 24–48 h post discharge, caregivers in the intervention group had significantly higher scores on the adapted care transitions measure (3.51 vs 3.27, p<0.0001); however, at 30 days, the difference was no longer significant (3.45 vs 3.40, p=0.27).ConclusionsA multicomponent discharge intervention designed to address specific problems identified using HFMEA did not reduce certain adverse outcomes in the post-discharge period.Trial RegistrationNCT01088945.
Cooperation and Antagonism among Cancer Genes: The Renal Cancer Paradigm
Authors: Peña-Llopis Samuel , Christie Alana , Xie Xian-Jin , Brugarolas James 
Published: July 2013

Abstract
It is poorly understood how driver mutations in cancer genes work together to promote tumor development. Renal cell carcinoma (RCC) offers a unique opportunity to study complex relationships among cancer genes. The four most commonly mutated genes in RCC of clear-cell type (the most common type) are two-hit tumor suppressor genes, and they cluster in a 43-Mb region on chromosome 3p that is deleted in approximately 90% of tumors: VHL (mutated in ∼80%), PBRM1 (∼50%), BAP1 (∼15%), and SETD2 (∼15%). Meta-analyses that we conducted show that mutations in PBRM1 and SETD2 co-occur in tumors at a frequency higher than expected by chance alone, indicating that these mutations may cooperate in tumorigenesis. In contrast, consistent with our previous results, mutations in PBRM1 and BAP1 tend to be mutually exclusive. Mutation exclusivity analyses (often confounded by lack of statistical power) raise the possibility of functional redundancy. However, mutation exclusivity may indicate negative genetic interactions, as proposed herein for PBRM1 and BAP1, and mutations in these genes define RCC with different pathologic features, gene expression profiles, and outcomes. Negative genetic interactions among cancer genes point toward broader context dependencies of cancer gene action beyond tissue dependencies. An enhanced understanding of cancer gene dependencies may help to unravel vulnerabilities that can be exploited therapeutically. Cancer Res; 73(14); 4173–9. ©2013 AACR.
Lessons from Functional Analysis of Genome-Wide Association Studies
Authors: Sur Inderpreet , Tuupanen Sari , Whitington Thomas , Aaltonen Lauri A. , Taipale Jussi 
Published: July 2013

Abstract
Most cancer-associated single-nucleotide polymorphisms (SNP) identified using genome-wide association studies are located outside of protein-coding regions, and their significance and mode of action have been a source of continuing debate. One proposed mechanism of action of the SNPs is that they would affect the activity of enhancer elements regulating critical target genes. In this review, we summarize recent results that substantiate this model. These studies have identified a cancer-specific enhancer element at the 8q24 gene desert that controls the expression of the MYC oncogene. We further discuss implications of the observed difference between normal growth control and cancer for drug development, and the inherent features of genome-wide association studies that may specifically lead to identification of disease-specific regulatory elements. Cancer Res; 73(14); 4180–4. ©2013 AACR.
C1GALT1 Enhances Proliferation of Hepatocellular Carcinoma Cells via Modulating MET Glycosylation and Dimerization
Authors: Wu Yao-Ming , Liu Chiung-Hui , Huang Miao-Juei , Lai Hong-Shiee , Lee Po-Huang , Hu Rey-Heng , Huang Min-Chuan 
Published: July 2013

Abstract
Altered glycosylation is a hallmark of cancer. The core 1 β1,3-galactosyltransferase (C1GALT1) controls the formation of mucin-type O-glycans, far overlooked and underestimated in cancer. Here, we report that C1GALT1 mRNA and protein are frequently overexpressed in hepatocellular carcinoma tumors compared with nontumor liver tissues, where it correlates with advanced tumor stage, metastasis, and poor survival. Enforced expression of C1GALT1 was sufficient to enhance cell proliferation, whereas RNA interference–mediated silencing of C1GALT1 was sufficient to suppress cell proliferation in vitro and in vivo. Notably, C1GALT1 attenuation also suppressed hepatocyte growth factor (HGF)–mediated phosphorylation of the MET kinase in hepatocellular carcinoma cells, whereas enforced expression of C1GALT1 enhanced MET phosphorylation. MET blockade with PHA665752 inhibited C1GALT1-enhanced cell viability. In support of these results, we found that the expression level of phospho-MET and C1GALT1 were associated in primary hepatocellular carcinoma tissues. Mechanistic investigations showed that MET was decorated with O-glycans, as revealed by binding to Vicia villosa agglutinin and peanut agglutinin. Moreover, C1GALT1 modified the O-glycosylation of MET, enhancing its HGF-induced dimerization and activation. Together, our results indicate that C1GALT1 overexpression in hepatocellular carcinoma activates HGF signaling via modulation of MET O-glycosylation and dimerization, providing new insights into how O-glycosylation drives hepatocellular carcinoma pathogenesis. Cancer Res; 73(17); 5580–90. ©2013 AACR.
Distinct FAK Activities Determine Progenitor and Mammary Stem Cell Characteristics
Authors: Luo Ming , Zhao Xiaofeng , Chen Song , Liu Suling , Wicha Max S. , Guan Jun-Lin 
Published: July 2013

Abstract
Mammary stem cells (MaSC) and progenitor cells are important for mammary gland development and maintenance and may give rise to mammary cancer stem cells (MaCSC). Yet, there remains limited understanding of how these cells contribute to tumorigenesis. Here, we show that conditional deletion of focal adhesion kinase (FAK) in embryonic mammary epithelial cells (MaEC) decreases luminal progenitors and basal MaSCs, reducing their colony-forming and regenerative potentials in a cell-autonomous manner. Loss of FAK kinase activity in MaECs specifically impaired luminal progenitor proliferation and alveologenesis, whereas a kinase-independent activity of FAK supported ductal invasion and basal MaSC activity. Deficiency in luminal progenitors suppressed tumorigenesis and MaCSC formation in a mouse model of breast cancer. In contrast with the general inhibitory effect of FAK attenuation, inhibitors of FAK kinase preferentially inhibited proliferation and tumorsphere formation of luminal progenitor-like, but not MaSC-like, human breast cancer cells. Our findings establish distinct kinase-dependent and -independent activities of FAK that differentially regulate luminal progenitors and basal MaSCs. We suggest that targeting these distinct functions may tailor therapeutic strategies to address breast cancer heterogeneity more effectively. Cancer Res; 73(17); 5591–602. ©2013 AACR.