bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inactivation of Bacteriophage Infecting Bacteroides Strain GB124 Using UV‐B Radiation
Authors: Diston David , Ebdon James E. , Taylor Huw D. 
Published: December 2013

AbstractUltraviolet‐B radiation (280–320 nm) has long been associated with the inactivation of microorganisms in the natural environment. Determination of the environmental inactivation kinetics of specific indicator organisms [used as tools in the field of microbial source tracking (MST)] is fundamental to their successful deployment, particularly in geographic regions subject to high levels of solar radiation. Phage infecting Bacteroides fragilis host strain GB124 (B124 phage) have been demonstrated to be highly specific indicators of human fecal contamination, but to date, little is known about their susceptibility to UV‐B radiation. Therefore, B124 phage (n = 7) isolated from municipal wastewater effluent, were irradiated in a controlled laboratory environment using UV‐B collimated beam experiments. All B124 phage suspensions possessed highly similar first order log‐linear inactivation profiles and the mean fluence required to inactivate phage by 4 − log10 was 320 mJ cm−2. These findings suggest that phage infecting GB124 are likely to be inactivated when exposed to the levels of UV‐B solar radiation experienced in a variety of environmental settings. As such, this may limit the utility of such methods for determining more remote inputs of fecal contamination in areas subject to high levels of solar radiation.
Electroretinography in the normal koala (Phascolarctos cinereus)
Authors: Liddle Vicki L. 
Published: December 2013

AbstractObjectiveTo perform electroretinography on normal anesthetized koalas (Phascolarctos cinereus).Animals studiedSix hospitalized koalas.ProcedureThe koalas were anesthetized using alfaxalone intramuscularly and isoflurane via face mask, then maintained on isoflurane after endotracheal intubation. After 20 min of dark adaptation, electroretinograms were obtained using a handheld electroretinography (ERG) machine using a single flash protocol at three light intensities: 10 mcd s/m2, 3000 mcd s/m2,and 10 000 mcd s/m2.ResultsAt 10 mcd s/m2,the mean b‐wave amplitude and implicit time were 49.5 μV (SD± 33.1 and 95%CI29.9–69.0) and 87.4 ms (SD± 6.5 and 95%CI83.6‐91.2). At 3000 mcd s/m2,the mean a‐wave amplitude and implicit time were 70.5 μV (SD± 30.7 and 95%CI52.3–88.7) and 20.6 ms (SD± 3.1 and 95%CI18.7–22.4), and the mean b‐wave amplitude and implicit time were 122.8 μV (SD± 49.3 and 95%CI93.7–151.9) and 63.1 ms (SD± 13.2 and 95%CI55.3–71.0). At 10 000 mcd sm2,the mean a‐wave amplitude and implicit time were 90.8 μV (SD± 37.2 and 95%CI68.8–112.8) and 16.1 ms (SD± 3.1 and 95%CI14.3–18.0), and the mean b‐wave amplitude and implicit time were 148.3 μV (SD± 54.9 and 95%CI115.9–180.8) and 67.4 ms (SD± 8.4 and 95%CI62.5–72.3).ConclusionElectroretinography in koalas is practical using a portableERGsystem and aDTLthread electrode and allows for rapid assessment of retinal function.
Contrasting host immuno‐inflammatory responses to bacterial challenge within venous and diabetic ulcers
Authors: McInnes Rachael L. , Cullen Breda M. , Hill Katja E. , Price Patricia E. , Harding Keith G. , Thomas David W. , Stephens Phil , Moseley Ryan 
Published: December 2013

AbstractWithin chronic wounds, the relationship between the clinical diagnosis of infection and bacterial/immuno‐inflammatory responses is imprecise. This study prospectively examined the interrelationship between clinical, microbiological, and proinflammatory biomarker levels between chronic venous leg ulcers (CVLUs) and diabetic foot ulcers (DFUs). Wound swabs and fluids were collected from CVLUs (n = 18) and DFUs (n = 15) and diagnosed clinically as noninfected or infected; and qualitative/quantitative microbiology was performed. CVLU and DFU fluids were also analyzed for cytokine, growth factor, receptor, proteinase/proteinase inhibitor; and oxidative stress biomarker (protein carbonyl, malondialdehyde, and antioxidant capacity) levels. While no correlations existed between clinical diagnosis, microbiology, or biomarker profiles, increasing bacterial bioburden (≥107 colony‐forming unit/mL) was associated with significant alterations in cytokine, growth factor, and receptor levels. These responses contrasted between ulcer type, with elevated and decreased cytokine, growth factor, and receptor levels in CVLUs and DFUs with increasing bioburden, respectively. Despite proteinase biomarkers exhibiting few differences between CVLUs and DFUs, significant elevations in antioxidant capacities correlated with increased bioburden in CVLU fluids, but not in DFUs. Furthermore, oxidative stress biomarker levels were significantly elevated in all DFU fluids compared with CVLUs. This study provides further insight into the contrasting disease‐specific host responses to bacterial challenge within infected CVLUs and DFUs.
The mechanisms and evidence of efficacy of electrical stimulation for healing of pressure ulcer: A systematic review
Authors: Kawasaki Lisa , Mushahwar Vivian K. , Ho Chester , Dukelow Sean P. , Chan Leo L. H. , Chan K. Ming 
Published: December 2013

AbstractThe objective of this article is to provide a systematic review of the efficacy of electrical stimulation in healing pressure ulcer and to review its mechanism of action. The Cochrane Library, PubMed, CINAHL, Medline, EMBASE, and NHS EED were searched for relevant interventional studies including randomized controlled trials (RCTs) and observational studies. A best‐evidence synthesis was performed to summarize the results of the included studies. A total of seven RCTs and two observational studies met the inclusion criteria. Moderate level of evidence of efficacy with low risk of bias was shown in all seven RCTs. Although some studies have used continuous direct current, most other investigators opted to use high‐voltage pulsed current to minimize the risk of skin burn and to achieve greater current penetration. Overall, the incidence of adverse effects was very low. Two studies that assessed the economic impacts of electrical stimulation revealed substantial health care cost savings. The mechanisms through which electrical stimulation exerts a positive effect on pressure ulcer healing are reasonably well established. Clinical trials have revealed a moderate level of evidence to support its use as an ancillary treatment modality for healing pressure ulcer. Recommendations regarding the optimal electrical stimulation parameters and dosage of use are provided. Further studies to investigate potential barriers that may impede widespread use in different clinical settings are needed.
Erythropoietin, a novel repurposed drug: An innovative treatment for wound healing in patients with diabetes mellitus
Authors: Hamed Saher , Bennett Charles L. , Demiot Claire , Ullmann Yehuda , Teot Luc , Desmoulière Alexis 
Published: December 2013

AbstractDeveloping a new drug is expensive: the cost of going from bench to bedside is about $US1 billion. Therefore, the repurposing of an approved drug is potentially rewarding because it expands the drug's existing therapeutic profile and preempts additional development costs. As the safety profile of a repurposed drug is already well known, any new investigations could then focus on its efficacy and other therapeutic benefits. Recombinant erythropoietin (EPO) is a potential candidate for repurposing because the results of numerous studies have shown that systemic and topical EPO is therapeutically beneficial when it is administered to healthy and diabetic animals with acute and chronic skin wounds and burns. Moreover, the molecular mechanisms of EPO's actions have been elucidated: EPO acts on those nonhematopoietic cells which are involved in the innate immune response where it promotes cellular proliferation and differentiation, exerts its cytoprotective actions, and inhibits apoptosis. In this review, the mechanism of EPO's action in skin wound healing is reviewed, and its potential for treating acute and chronic skin wounds and stimulating tissue regeneration in diabetic patients is discussed.
Complete Genome of Bacillus megaterium Siphophage Slash
Authors: DeCrescenzo Andrew J. , Ritter Matthew A. , Chamakura Karthik R. , Kuty Everett Gabriel F. 
Published: December 2013

ABSTRACT

The complete annotated genome sequence of
Bacillus megaterium
bacteriophage Slash is described here. Several key features related to morphogenesis, replication/recombination, DNA metabolism, and lysis are described. Slash also encodes a homolog of SleB, a germination-specific cell wall amidase.
Draft Genome Sequence of Salmonella enterica subsp.
enterica
Serotype Saintpaul Strain S-70, Isolated from an Aquatic Environment
Authors: Estrada-Acosta Mitzi , Medrano-Félix Andrés , Jiménez Maribel , Gómez-Gil Bruno , León-Félix Josefina , Amarillas Luis , Chaidez Cristóbal 
Published: December 2013

ABSTRACT

Salmonella
is a pathogen of worldwide importance, causing disease in a vast range of hosts, including humans. We report the genome sequence of
Salmonella enterica
subsp.
enterica
serotype Saintpaul strain S-70, isolated from an aquatic environment.
Draft Genome Sequence of Salmonella enterica subsp.
enterica
Serotype Oranienburg Strain S-76, Isolated from an Aquatic Environment
Authors: Medrano-Félix Andrés , Estrada-Acosta Mitzi , Jiménez Maribel , Gómez-Gil Bruno , León-Félix Josefina , Amarillas Luis , Chaidez Cristóbal 
Published: December 2013

ABSTRACT

Salmonella
is a widespread microorganism and a common causative agent of food-borne illnesses.
Salmonella enterica
subsp.
enterica
serotype Oranienburg is highly prevalent in surface water from tropical ecosystems and is not commonly related to illnesses. Here, we report the first genome sequence of
Salmonella
Oranienburg strain S-76, isolated from an aquatic environment.
Genome Sequence of an Enterobacter helveticus Strain, 1159/04 (LMG 23733), Isolated from Fruit Powder
Authors: Grim Christopher J. , Gopinath Gopal R. , Mammel Mark K. , Sathyamoorthy Venugopal , Trach Larisa H. , Chase Hannah R. , Tall Ben D. , Fanning Séamus , Stephan Roger 
Published: December 2013

ABSTRACT

We report the draft genome sequence of
Enterobacter helveticus
strain LMG 23733, isolated from fruit powder. The draft genome assembly for
E. helveticus
strain LMG 23733 has a size of 4,635,476 bp and a G+C content of 55.9%.
Draft Genome Sequence of Fusobacterium nucleatum subsp.
nucleatum
ChDC F316, Isolated from a Human Peri-implantitis Lesion in the Republic of Korea
Authors: Park Soon-Nang , Cho Eugene , Kim Hwa-Sook , Kim Dae-Soo , Jung Jaeeun , Baek Jeong-Hun , Kyong Lim Yun , Jo Eojin , Chang Young-Hyo , Hwan Shin Jeong , Choi Sang-Haeng , Kang Jihee , Choi YongUn , Park Hong-Seog , Kim Hongik , Kook Joong-Ki 
Published: December 2013

ABSTRACT

Fusobacterium nucleatum
is a Gram-negative anaerobe and is one of the causative agents of periodontal diseases, including peri-implantitis.
Fusobacterium nucleatum
subsp.
nucleatum
ChDC F316 (KCOM 1322) was isolated from a human peri-implantitis lesion. Here, we report the draft genome sequence of this strain.
Genome Sequence of Cupriavidus metallidurans Strain H1130, Isolated from an Invasive Human Infection
Authors: Monsieurs Pieter , Provoost Ann , Mijnendonckx Kristel , Leys Natalie , Gaudreau Christiane , Van Houdt Rob 
Published: December 2013

ABSTRACT

Cupriavidus metallidurans
H1130 was repeatedly isolated from different blood culture sets taken from a patient suffering from significant nosocomial septicemia. Here, we announce the H1130 genome sequence for use in comparative analyses and for exploring the adaptation and pathogenic potential of this bacterium.
Serum Hepcidin Is Associated With Presence of Plaque in Postmenopausal Women of a General Population
Authors: Galesloot Tessel E. , Holewijn Suzanne , Kiemeney Lambertus A.L.M. , de Graaf Jacqueline , Vermeulen Sita H. , Swinkels Dorine W. 
Published: December 2013

Objective—
Iron and the iron regulatory hormone hepcidin, major determinant of body iron distribution, are hypothesized to play a role in cardiovascular disease. Here, we assess the associations of hepcidin as well as ferritin, iron, total iron-binding capacity, and transferrin saturation (ie, iron parameters) with noninvasive measurements of atherosclerosis in men and women of a population-based cohort.

Approach and Results—
We included 766 participants of the Nijmegen Biomedical Study aged 46 to 67 years for whom serum measurements of hepcidin, iron parameters, and noninvasive measurements of atherosclerosis were available. Noninvasive measurements of atherosclerosis were presence of plaque, ankle-brachial index, and intima-media thickness. We performed multivariable logistic and linear regression analyses using quartiles of hepcidin and iron parameters. Analyses were stratified by sex and adjusted for several demographic, clinical, and biochemical determinants, including traditional risk factors of cardiovascular disease based on the Framingham risk score. Hepcidin and the hepcidin/ferritin ratio, reflecting hepcidin expression relative to iron stores, were significantly associated with the presence of plaque in women (adjusted odds ratios for quartile 4 versus quartile 1 [95% confidence intervals] of 3.07 [1.36–6.90] and 2.31 [1.03–5.18], respectively). The hepcidin/ferritin ratio was significantly and negatively associated with ankle-brachial index at rest in men and women (adjusted β for quartile 4 versus quartile 1 [95% confidence intervals] of −0.03 [−0.07 to 0.00] and −0.04 [−0.06 to −0.01], respectively).

Conclusions—
Our results suggest that the body iron distribution as determined by hepcidin affects the development of atherosclerosis in women.
Apolipoprotein A-I Protection Against Atherosclerosis Is Dependent on Genetic Background
Authors: Sontag Timothy J. , Krishack Paulette A. , Lukens John R. , Bhanvadia Clarissa V. , Getz Godfrey S. , Reardon Catherine A. 
Published: December 2013

Objective—
Inbred mouse strains have different susceptibilities to experimental atherosclerosis. The C57BL/6 strain is among the most sensitive and has, therefore, been the most widely used in atherosclerosis studies, whereas many strains are resistant. The FVB/N strain is highly resistant to atherosclerosis on the apolipoprotein E (apoE)– and low-density lipoprotein (LDL) receptor–deficient backgrounds. High-density lipoprotein and its major apoprotein, apoA-I, have been shown to be protective against atherogenesis on the C57BL/6 background. We here examine the influence of genetic background on the atheroprotective nature of apoA-I.

Approach and Results—
ApoE-deficient/apoA-I-deficient mice were generated in the C57BL/6 and FVB/N strains from apoE-deficient mice. After 6 to 10 weeks on a Western-type diet, plasma lipids and atherosclerotic lesion size were assessed. Macrophage recruitment, cholesterol regulation, and blood monocyte levels were examined as potential mechanisms driving lesion size differences. FVB/N knockout mice had higher plasma very-LDL/LDL cholesterol than their C57BL/6 counterparts. ApoA-I deficiency decreased very-LDL/LDL cholesterol in C57BL/6 mice but not in FVB/N mice. FVB/N single and double knockout mice had less lesion than C57BL/6 6 to 10 weeks on diet. ApoA-I deficiency augmented lesion development only in C57BL/6 mice. Macrophage recruitment to thioglycollate-treated peritoneum and diet-induced blood monocyte levels reflected the pattern of lesion development among the 4 genotypes. ApoA-I deficiency increased macrophage cholesterol content only in C57BL/6. FVB/N plasma was a better acceptor for macrophage cholesterol efflux than C57BL/6.

Conclusions—
ApoA-I is atheroprotective only in certain genetic contexts. In the C57BL/6 context, but not FVB/N, apoA-I decreases inflammatory macrophage recruitment and monocytosis, contributors to lesion formation.
Benefit of Pacemaker Therapy in Patients With Presumed Neurally Mediated Syncope and Documented Asystole Is Greater When Tilt Test Is Negative
Authors: Brignole Michele , Donateo Paolo , Tomaino Marco , Massa Riccardo , Iori Matteo , Beiras Xulio , Moya Angel , Kus Teresa , Deharo Jean Claude , Giuli Silvia , Gentili Alessandra , Sutton Richard 
Published: December 2013

Background—
In the Third International Study on Syncope of Uncertain Etiology (ISSUE-3), cardiac pacing was effective in reducing recurrence of syncope in patients with presumed neurally mediated syncope (NMS) and documented asystole but syncope still recurred in 25% of them at 2 years. We have investigated the role of tilt testing (TT) in predicting recurrences.

Methods and Results—

In 136 patients enrolled in the ISSUE-3, TT was positive in 76 and negative in 60. An asystolic response predicted a similar asystolic form during implantable loop recorder monitoring, with a positive predictive value of 86%. The corresponding values were 48% in patients with non–asystolic TT and 58% in patients with negative TT (
P
=0.001 versus asystolic TT). Fifty-two patients (26 TT+ and 26 TT–) with asystolic neurally mediated syncope received a pacemaker. Syncope recurred in 8 TT+ and in 1 TT– patients. At 21 months, the estimated product-limit syncope recurrence rates were 55% and 5%, respectively (
P
=0.004). The TT+ recurrence rate was similar to that seen in 45 untreated patients (control group), which was 64% (
P
=0.75). The recurrence rate was similar between 14 patients with asystolic and 12 with non–asystolic responses during TT (
P
=0.53).

Conclusions—
Cardiac pacing was effective in neurally mediated syncope patients with documented asystolic episodes in whom TT was negative; conversely, there was insufficient evidence of efficacy from this data set in patients with a positive TT even when spontaneous asystole was documented. Present observations are unexpected and need to be confirmed by other studies.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT01463358.
Contrasting Relationship between Tropical Western North Pacific Convection and Rainfall over East Asia during Indian Ocean Warm and Cold Summers
Authors: Song Jie , Li Chongyin 
Published: December 2013

Abstract
Using daily data, this study compares the subseasonal seesaw relationship between anomalous tropical western North Pacific (WNP) convection and anomalous rainfall over subtropical East Asia during boreal summers (June–August) in which the Indian Ocean (IO) sea surface temperature is either warmer or colder than normal. It is found that the precipitation anomalies over central-eastern China (25°–35°N, 110°–120°E) associated with the anomalous tropical WNP convection activities during the IO cold summers are weaker and less evident compared to that in the IO warm summers, indicating the seesaw relationship in the IO cold summers becomes obscure. This contrasting seesaw relationship between the IO warm and cold summers is attributed to different patterns of anomalous moisture transportation and vertical motion over central-eastern China. The anomalous circulations associated with the anomalous tropical WNP convection [the Pacific–Japan (PJ) pattern] during the IO warm and cold summers show that, relative to the IO warm summers, the Japan action center of the PJ pattern has an evident northwestward displacement in the IO cold summers. It is argued that this northwestward displacement of the Japan action center plays a key role in the formation of the distinct seesaw relationship through modifying the anomalous moisture transportation and vertical motion.
Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data
Authors: González-Agüero Mauricio , García-Rojas Miguel , Di Genova Alex , Correa José , Maass Alejandro , Orellana Ariel , Hinrichsen Patricio 
Published: December 2013

Abstract

Background
Data normalization is a key step in gene expression analysis by qPCR. Endogenous control genes are used to estimate variations and experimental errors occurring during sample preparation and expression measurements. However, the transcription level of the most commonly used reference genes can vary considerably in samples obtained from different individuals, tissues, developmental stages and under variable physiological conditions, resulting in a misinterpretation of the performance of the target gene(s). This issue has been scarcely approached in woody species such as grapevine.

Results
A statistical criterion was applied to select a sub-set of 19 candidate reference genes from a total of 242 non-differentially expressed (NDE) genes derived from a RNA-Seq experiment comprising ca. 500 million reads obtained from 14 table-grape genotypes sampled at four phenological stages. From the 19 candidate reference genes, VvAIG1 (AvrRpt2-induced gene) and VvTCPB (T-complex 1 beta-like protein) were found to be the most stable ones after comparing the complete set of genotypes and phenological stages studied. This result was further validated by qPCR and geNorm analyses.

Conclusions
Based on the evidence presented in this work, we propose to use the grapevine genes VvAIG1 or VvTCPB or both as a reference tool to normalize RNA expression in qPCR assays or other quantitative method intended to measure gene expression in berries and other tissues of this fruit crop, sampled at different developmental stages and physiological conditions.
A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus
Authors: Tan Joon Liang , Khang Tsung Fei , Ngeow Yun Fong , Choo Siew Woh 
Published: December 2013

Abstract

Background

Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12 M. abscessus strains and used phylogenomic analysis to perform subspecies classification.

Results
A data mining approach was used to rank and select informative genes based on the relative entropy metric for the construction of a phylogenetic tree. The resulting tree topology was similar to that generated using the concatenation of five classical housekeeping genes: rpoB, hsp65, secA, recA and sodA. Additional support for the reliability of the subspecies classification came from the analysis of erm41 and ITS gene sequences, single nucleotide polymorphisms (SNPs)-based classification and strain clustering demonstrated by a variable number tandem repeat (VNTR) assay and a multilocus sequence analysis (MLSA). We subsequently found that the concatenation of a minimal set of three median-ranked genes: DNA polymerase III subunit alpha (polC), 4-hydroxy-2-ketovalerate aldolase (Hoa) and cell division protein FtsZ (ftsZ), is sufficient to recover the same tree topology. PCR assays designed specifically for these genes showed that all three genes could be amplified in the reference strain of M. abscessus ATCC 19977T.

Conclusion
This study provides proof of concept that whole-genome sequence-based data mining approach can provide confirmatory evidence of the phylogenetic informativeness of existing markers, as well as lead to the discovery of a more economical and informative set of markers that produces similar subspecies classification in M. abscessus. The systematic procedure used in this study to choose the informative minimal set of gene markers can potentially be applied to species or subspecies classification of other bacteria.