bluuebunny/crossref_metadata_2025_split huggingface dataset:
Roles and activities of chromatin remodeling ATPases in plants
Authors: Han Soon‐Ki , Wu Miin‐Feng , Cui Sujuan , Wagner Doris 
Published: May 2015

SummaryChromatin remodeling ATPases and their associated complexes can alter the accessibility of the genome in the context of chromatin by using energy derived from the hydrolysis of ATP to change the positioning, occupancy and composition of nucleosomes. In animals and plants, these remodelers have been implicated in diverse processes ranging from stem cell maintenance and differentiation to developmental phase transitions and stress responses. Detailed investigation of their roles in individual processes has suggested a higher level of selectivity of chromatin remodeling ATPase activity than previously anticipated, and diverse mechanisms have been uncovered that can contribute to the selectivity. This review summarizes recent advances in understanding the roles and activities of chromatin remodeling ATPases in plants.
Anti‐A and anti‐B titers in donor plasma, plasma pools, and immunoglobulin final products
Authors: McVey John , Baker Don , Parti Rajesh , Berg Roger , Gudino Maria , Teschner Wolfgang 
Published: May 2015

BACKGROUNDHigh‐dose intravenous immunoglobulin (IVIG) treatments are implicated in hemolytic events in some patients receiving treatment. The passive transfer of IgG anti‐A and anti‐B agglutinin is thought to play a role in the development of these events. The purpose of this study was to determine the prevalence of high‐titer IgG anti‐A and anti‐B in plasma donors and investigate if there is any advantage of excluding these donors from the donor pool to limit anti‐A and anti‐B content in IVIG product.STUDY DESIGN AND METHODSIgG anti‐A and anti‐B levels were assessed from group O donor plasma, manufacturing IgG plasma pools, and finished IVIG product (Gammagard Liquid). Antibody level in group O donors was also assessed by sex and age for their relative contribution of antibody to the plasma pool.RESULTSThe majority of group O donors (80%) had antibody titers of less than 1000. Of those with titers of at least 1000, theoretical estimates provide further evidence that the effects of high‐titer donors are minimal. Antibody levels in plasma pools both during the manufacturing process and from the final IVIG product also support that anti‐A and anti‐B levels are low. In general, there were more females than males with higher antibody titer levels, with significantly more females than males with anti‐A.CONCLUSIONExcluding donors with high anti‐A and anti‐B titers has minimal impact on the finished IVIG product titers due to ABO antibody neutralization and the dilution factor in the manufacturing pool.
Clinical effect of four different ointment bases on healthy cat eyes
Authors: Eördögh Réka , Schwendenwein Ilse , Tichy Alexander , Loncaric Igor , Nell Barbara 
Published: May 2015

AbstractObjectiveTo describe the effects of long‐term treatment with four different eye ointment bases (OBs) in cats.Animals studiedTen healthy cats.ProceduresThe study was performed in two periods. Four differentOBs were tested. Hundred grams ofOBcontained the following:OB‐A: 35.17 g liquid paraffin (lp), 64.83 g white petrolatum (wp);OB‐B: 10.03 g lp, 84.95 g wp 5.02 g lanolin;OB‐C: 18.34 g lp, 51.40 g wp, 25.00 mgKH2PO4, 57.00 mg K2HPO4, 18.90 g eucerinum anhydricum, 11.28 g water for injections; andOB‐D: 70 g unguentum lanalcoli, 20 g lp, 10 g aqua conservans. One eye was treated, and the other served as a negative control. Cats received theOBsTIDfor 28 days. The two study periods were separated by a 4‐month washout phase. Samples for conjunctival impression cytology, swabs for bacteriologic and mycologic examination, and cytobrush samples forFHV‐1 andChlamydophila felisPCRdetection were obtained. Both eyes were examined daily. Severity of ocular symptoms was scored using a modified Draize eye irritation test. A total of five eyes were treated withOB‐A, five withOB‐B, four withOB‐C, and five withOB‐D.ResultsTreated eyes had significantly higher clinical scores. Eyes receivingOB‐A had the highest overall clinical score. The results of bacteriologic and mycologic examination concur with the previously published data. All samples tested were negative forFHV‐1 andChlamydophila felis. There was no significant difference between treated and control eyes upon cytological examination.ConclusionThe application ofOBs resulted in clinical symptoms in treated eyes. The long‐term use of ointments is not well tolerated in cats and may lead to ocular irritation.
A single bout of whole‐leg, peristaltic pulse external pneumatic compression upregulates PGC‐1α mRNA and endothelial nitric oxide sythase protein in human skeletal muscle tissue
Authors: Kephart Wesley C. , Mobley C. Brooks , Fox Carlton D. , Pascoe David D. , Sefton JoEllen M. , Wilson Trent J. , Goodlett Michael D. , Kavazis Andreas N. , Roberts Michael D. , Martin Jeffrey S. 
Published: May 2015

New Findings
What is the central question of this study?
Does 60 min of peristaltic pulse external pneumatic compression (EPC) alter gene and protein expression patterns related to metabolism, vascular biology, redox balance and inflammation in vastus lateralis biopsy samples?

What is the main finding and its importance?
A single bout of EPC transiently upregulates PGC‐1α mRNA, while also upregulating endothelial nitric oxide synthase protein and nitric oxide metabolite concentrations in vastus lateralis biopsy samples.

We investigated whether a single 60 min bout of whole‐leg, lower pressure external pneumatic compression (EPC) altered select vascular, metabolic, antioxidant and inflammation‐related mRNAs. Ten participants (eight male, two female; aged 22.0 ± 0.4 years) reported to the laboratory 4 h postprandial, and vastus lateralis muscle biopsies were obtained before (PRE) and 1 and 4 h after EPC treatment. Messenger RNA expression was analysed using real‐time RT‐PCR, and significant mRNA findings were investigated further by Western blot analysis of respective protein concentrations. Peroxisome proliferator‐activated receptor γ coactivator‐1α (PGC‐1α) mRNA increased by 77% 1 h following EPC compared with PRE levels (P = 0.005), but no change in protein concentration 1 or 4 h post‐EPC was observed. Increases in endothelial nitric oxide sythase (eNOS) mRNA (+44%) and superoxide dismutase 2 (SOD2) mRNA (+57%) 1 h post‐EPC as well as an increase in interleukin‐10 mRNA (+132%) 4 h post‐EPC compared with PRE levels were observed, but only approached significance (P = 0.076, 0.077 and 0.074, respectively). Interestingly, eNOS protein (+40%, P = 0.025) and nitrate and nitrite (NOx) concentrations (+69%, P = 0.025) increased 1–4 h post‐EPC. Moreover, SOD2 protein tended to increase from PRE to 4 h post‐EPC (+43%, P = 0.074), although no changes in tissue 4‐hydroxnonenal levels was observed. An acute bout of EPC transiently upregulates PGC‐1α mRNA, while also upregulating eNOS protein and NOx concentrations in vastus lateralis biopsy samples. Future research should characterize the origin of these responses (e.g. vascular or muscle fibre cells) and how the acute effects of EPC application on gene and protein expression observed herein are associated with functional improvements (e.g. metabolism, vascular function) in acute and chronic models.
Draft Genome Sequence of Pantoea anthophila Strain 11-2 from Hypersaline Lake Laysan, Hawaii
Authors: Wan Xuehua , Hou Shaobin , Phan Nolwenn , Malone Moss Jennifer S. , Donachie Stuart P. , Alam Maqsudul 
Published: May 2015

ABSTRACT

Most
Pantoea
spp. have been isolated from plant sources or clinical samples. However, we cultivated
Pantoea anthophila
11-2 from hypersaline water from the lake on Laysan, Northwestern Hawaiian Islands. Draft genome sequencing of 11-2 provides a molecular basis for studies in evolution and pathogenicity in
Pantoea
spp.
Genome Sequences of 11 Shiga Toxin-Producing Escherichia coli Strains
Authors: Gabrielsen C. , Drabløs F. , Afset J. E. 
Published: May 2015

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) strains are a common cause of both sporadic infection and outbreaks of enteric disease in humans. Here, we present draft genome sequences of 11 STEC strains of different serotypes (O145, O121, O26, O177, and O-type unknown), that have been isolated from patients with enteric disease of various degrees of severity, in the years 2001 to 2014 at St. Olavs Hospital in Trondheim, Norway.
Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated from Uncontaminated Soil in Ecuador
Authors: Reznicek Ondrej , Luesken Francisca , Facey Sandra J. , Hauer Bernhard 
Published: May 2015

ABSTRACT

We report the draft genome sequence of 3.3 Mb and the sequence (19.2 kb) of a natural plasmid isolated from
Phenylobacterium immobile
strain E (DSM 1986), able to degrade xenobiotic compounds as the sole carbon source. The sequences reveal a large number of novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs).
Draft Genome Sequences of Four NDM-1-Producing Klebsiella pneumoniae Strains from a Health Care Facility in Northern California
Authors: Greninger Alexander L. , Chorny Ilya , Knowles Susan , Ng Valerie L. , Chaturvedi Vishnu 
Published: May 2015

ABSTRACT

We report the draft genome sequences of
Klebsiella pneumoniae
strains from four patients at a northern California health care facility. All strains contained the New Delhi metallo-β-lactamase (NDM1) carbapenemase with extended antibiotic resistance, including resistance to expanded-spectrum cephalosporins, imipenem, ertapenem, and meropenem. NDM gene alignments revealed that the resistance was plasmid encoded.
Draft Whole-Genome Sequence of Lactobacillus fermentum LfQi6, Derived from the Human Microbiome
Authors: Subhadra Bobban , Krier Jill , Hofstee Karina , Monsul Nicholas , Berkes Eva 
Published: May 2015

ABSTRACT

We report a 2.21-Mbp draft whole-genome sequence of
Lactobacillus fermentum
Qi6 (LfQi6). This strain demonstrates activity against pathogenic biofilms, enhances the skin barrier, and upregulates innate immune defenses. The genome sequence information of this strain will help to identify molecules that hold promise for the discovery of novel therapeutics for dermatological disorders.
Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium
Authors: Yaakop Amira Suriaty , Chan Chia Sing , Kahar Ummirul Mukminin , Ee Robson , Chan Kok-Gan , Goh Kian Mau 
Published: May 2015

ABSTRACT

Erythrobacter vulgaris
strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium.
Complete Genome Assemblies for Two Single-Chromosome Vibrio cholerae Isolates, Strains 1154-74 (Serogroup O49) and 10432-62 (Serogroup O27)
Authors: Johnson S. L. , Khiani A. , Bishop-Lilly K. A. , Chapman C. , Patel M. , Verratti K. , Teshima H. , Munk A. C. , Bruce D. C. , Han C. S. , Xie G. , Davenport K. W. , Chain P. , Sozhamannan S. 
Published: May 2015

ABSTRACT

Here, we report the completed genome sequences for two non-O1/non-O139
Vibrio cholerae
isolates. Each isolate has only a single chromosome, as opposed to the normal paradigm of two chromosomes found in all other
V. cholerae
isolates.
Draft Genome Sequence of Oleiagrimonas soli 3.5X
T
, a Type Species in a Newly Identified Genus, Isolated from an Oil Field in China
Authors: Huang Yong , Fang Tingting , Wang Hui , Zhou Haiyan 
Published: May 2015

ABSTRACT

Oleiagrimonas gudaosoli
3.5X
T
was isolated from an oil field and identified as a new member of a novel genus. The draft genome sequence of this strain, which comprises 3,379,958 bp encoding 3,010 open reading frames (ORFs), can provide insight into the life style of this newly identified genus in petroleum-contaminated soil.
Draft Genome Sequence of
Anaeromyxobacter
sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil
Authors: Tonomura Mimori , Ehara Ayaka , Suzuki Haruo , Amachi Seigo 
Published: May 2015

ABSTRACT

Here, we report a draft genome sequence of
Anaeromyxobacter
sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (
ars
operons), while no respiratory arsenate reductase gene (
arr
) was identified.
Draft Genome Sequence of Pseudomonas abietaniphila KF701 (NBRC110664), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil
Authors: Fujihara Hidehiko , Yamazoe Atsushi , Hosoyama Akira , Suenaga Hikaru , Kimura Nobutada , Hirose Jun , Watanabe Takahito , Futagami Taiki , Goto Masatoshi , Furukawa Kensuke 
Published: May 2015

ABSTRACT

Pseudomonas abietaniphila
KF701 utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report the 6,886,250-bp draft genome sequence of KF701, which contains 6,315 coding sequences and 59.4 mol% G+C content. The strain possesses genes for biphenyl catabolism and other genes that mediate the degradation of benzoate, salicylate, and phenol.
Draft Genome Sequence of Lactobacillus rhamnosus CLS17
Authors: Kozhakhmetov Samat S. , Kushugulova Almagul R. , Saduakhasova Saule A. , Shakhabayeva Gulnara S. , Khassenbekova Zhanagul R. , Molkenov Askhat B. , Kairov Ulykbek E. , Issayeva Raushan B. , Nurgozhin Talgat S. , Zhumadilov Zhaxybay S. 
Published: May 2015

ABSTRACT

We announce the draft genome sequence of the type strain
Lactobacillus rhamnosus
CLS17 (2,889,314 nt, with a GC content of 46.8%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of dairy products; the genome consists of 71 large contigs (>100 bp in size). It contains 2,643 protein-coding sequences, single predicted copies of the 5S, 16S, and 23S rRNA genes, and 51 predicted tRNAs.
Complete Genome Sequence of Scardovia inopinata JCM 12537
T
, Isolated from Human Dental Caries
Authors: Oshima Kenshiro , Hayashi Jun-ichiro , Toh Hidehiro , Nakano Akiyo , Omori Emi , Hattori Yasue , Morita Hidetoshi , Honda Kenya , Hattori Masahira 
Published: May 2015

ABSTRACT

Scardovia inopinata
JCM 12537
T
was isolated from human dental caries. Here, we report the complete genome sequence of this organism. This paper is the first report to demonstrate the fully sequenced and completely annotated genome of an
S. inopinata
strain.
Sphingomonas taxi
, Isolated from
Cucurbita pepo
, Proves to Be a DDE-Degrading and Plant Growth-Promoting Strain
Authors: Eevers Nele , Van Hamme Jonathan D. , Bottos Eric M. , Weyens Nele , Vangronsveld Jaco 
Published: May 2015

ABSTRACT

The draft genome of
Sphingomonas taxi
, a strain of the
Sphingomonadaceae
isolated from
Cucurbita pepo
root tissue, is presented. This Gram-negative bacterium shows 2,2-bis(
p
-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading potential and plant growth-promoting capacities. An analysis of its 3.9-Mb draft genome will enhance the understanding of DDE-degradation pathways and phytoremediation applications for DDE-contaminated soils.
Drug use in French children: a population-based study
Authors: Bénard-Laribière Anne , Jové Jérémy , Lassalle Régis , Robinson Philip , Droz-Perroteau Cécile , Noize Pernelle 
Published: May 2015

Background and objectiveTo provide an overview of drug use in outpatient children in France, a population-based study using a national reimbursement claims database representative of 90% of the French population was conducted.DesignCross-sectional study performed between January and December 2011 using the EGB database (Echantillon Généraliste de Bénéficiaires), a 1/97th sample of the national healthcare insurance system beneficiaries. Drug use in children <18 years old was estimated through reimbursements for prescribed drugs excluding vaccines. Prevalences of use were calculated for different levels of the Anatomical Therapeutic Chemical classification by considering as users children who had at least one reimbursement during the study period.ResultsIn 2011, 133 800 children were included in the study. The overall prevalence of drug use was 84% and the median number of different drugs per child was 5. Drug use was greatest in children aged <2 years. The most widely used drugs were paracetamol, systemic anti-infectives, nasal corticosteroids and decongestants, and anti-histamines. 21% children <2 years received domperidone.ConclusionsThere is widespread use of medicines that are unlikely to be effective and may have significant toxicity in French children. Irrational use of medicines appears to be greatest in children aged 5 years and under.
Time-varying impact of comorbidities on mortality after liver transplantation: a national cohort study using linked clinical and administrative data
Authors: Tovikkai Chutwichai , Charman Susan C , Praseedom Raaj K , Gimson Alexander E , van der Meulen Jan 
Published: May 2015

ObjectiveWe assessed the impact of comorbidity on mortality in three periods after liver transplantation (first 90 days, 90 days–5 years and 5–10 years).DesignProspective cohort study using records from the UK Liver Transplant Audit (UKLTA) linked to Hospital Episode Statistics (HES), an administrative database of hospital admissions in the English National Health Service (NHS). Comorbidities relevant for liver transplantation were identified from the 10th revision of the International Classification of Diseases (ICD-10) codes in HES records of admissions in the year preceding their operation. Multivariable Cox regression was used to estimate HRs for three different time periods after liver transplantation.SettingAll liver transplant centres in the NHS hospitals in England.ParticipantsAdults who received a first elective liver transplant between April 1997 and March 2010 in the linked UKLTA-HES database.OutcomesPatient mortality in three different time periods after transplantation.ResultsAmong 3837 recipients, 45.1% had comorbidities. Recipients with cardiovascular disease had statistically significantly higher mortality in all three periods after transplantation (first 90 days: HR=2.0; 95% CI 1.4 to 2.9, 90 days–5 years: 1.6; 1.2 to 2.2, beyond 5 years: 2.8; 1.7 to 4.4). Prior congestive cardiac failure (3.2; 2.1 to 4.9) significantly increased mortality only in the first 90 days. History of non-hepatic malignancy appeared to increase risk over all periods, but significantly only in the first 90 days (1.9; 1.0 to 3.6). A diagnosis of connective tissue disease, dementia, diabetes, chronic pulmonary and renal disease did not have a significant impact on mortality in any period.ConclusionsThe impact of comorbidities present at the time of transplantation changes with time after transplantation. Renal disease, pulmonary disease and diabetes had no impact on mortality in contrast to previous reports.
Hyaluronan for knee osteoarthritis: an updated meta-analysis of trials with low risk of bias
Authors: Richette Pascal , Chevalier Xavier , Ea Hang Korng , Eymard Florent , Henrotin Yves , Ornetti Paul , Sellam Jérémie , Cucherat Michel , Marty Marc 
Published: May 2015

BackgroundThe effectiveness of intra-articular hyaluronic acid (IAHA) injection for knee osteoarthritis (KOA) is debated.ObjectivesTo evaluate the effect of IAHA for patients with KOA by analysing data from trials of IAHA versus placebo with low risk of bias, to provide the highest level of evidence.MethodsA systematic review and meta-analysis was conducted. Randomised controlled trials (RCTs) with a low risk of bias (adequate randomisation and concealment and double-blind design) that investigated IAHA versus placebo (saline solution) injection were eligible. The primary efficacy measure was pain intensity and secondary outcome function at 3 months. The treatment effect was summarised with the standardised mean difference (SMD) calculated from differences in means of pain and function measures between treatment and control groups at 3 months. Trials were pooled by a random-effects model with DerSimonian and Laird weights. Statistical heterogeneity was explored by a visual exploration of forest plots and the I2statistic.ResultsA total of eight RCTs (2 199 randomised patients) met our inclusion criteria. IAHA significantly reduced the pain intensity (SMD=−0.21, 95% CI (95% CI) −0.32 to −0.10) and improved function (SMD=−0.12, 95% CI −0.22 to −0.02). Trials showed no heterogeneity.ConclusionsThis meta-analysis of high-quality trials of IAHA versus placebo shows that IAHA provides a moderate but real benefit for patients with KOA.
Enhanced volcanic hot-spot detection using MODIS IR data: results from the MIROVA system
Authors: Coppola D. , Laiolo M. , Cigolini C. , Donne D. Delle , Ripepe M. 
Published: May 2015

Abstract
We describe a new volcanic hotspot detection system, named Middle InfraRed Observation of Volcanic Activity (MIROVA), based on the analysis of infrared data acquired by the Moderate Resolution Imaging Spectroradiometer sensor (MODIS). MIROVA uses the middle infrared radiation (MIR), measured by MODIS, in order to detect and measure the heat radiation deriving from volcanic activity. The algorithm combines spectral and spatial principles, allowing the detection of heat sources from 1 megawatt (MW) to more than 10 gigawatt (GW). This provides a unique opportunity to: (i) recognize small-scale variations in thermal output that may precede the onset of effusive activity; (ii) track the advance of large lava flows; (iii) estimate lava discharge rates; (iv) identify distinct effusive trends; and, lastly, (v) follow the cooling process of voluminous lava bodies for several months. Here we show the results obtained from data sets spanning 14 years recorded at the Stromboli and Mt Etna volcanoes, Italy, and we investigate the above aspects at these two persistently active volcanoes. Finally, we describe how the algorithm has been implemented within an operational near-real-time processing chain that enables the MIROVA system to provide data and infrared maps within 1–4 h of the satellite overpass.
On the use of type predicates in object-oriented software
Authors: Callaú Oscar , Robbes Romain , Tanter Éric , Röthlisberger David , Bergel Alexandre 
Published: May 2015

Object-orientation relies on polymorphism to express behavioral variants. As opposed to traditional procedural design, explicit type-based conditionals should be avoided. This message is conveyed in introductory material on object orientation, as well as in object-oriented reengineering patterns. Is this principle followed in practice? In other words, are type predicates actually used in object-oriented software, and if so, to which extent?
Answering these questions will assist practitioners and researchers with providing information about the state of the practice, and informing the active research program of retrofitting type systems, clarifying whether complex flow-sensitive typing approaches are necessary. Other areas, such as refactoring and teaching object orientation, can also benefit from empirical evidence on the matter.
We report on a study of the use of type predicates in a large base of over 4 million lines of Smalltalk code. Our study shows that type predicates are in fact widely used to do explicit type dispatch, suggesting that flow-sensitive typing approaches are necessary for a type system retrofitted for a dynamic object-oriented language.