bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of Bacillus thuringiensis subsp.
thuringiensis
Strain IS5056, an Isolate Highly Toxic to
Trichoplusia ni
Authors: Murawska Emilia , Fiedoruk Krzysztof , Bideshi Dennis K. , Swiecicka Izabela 
Published: March 2013

ABSTRACT

The genome sequence of the entomopathogen
Bacillus thuringiensis
subsp.
thuringiensis
strain IS5056 was determined. The chromosome is composed of 5,491,935 bp. In addition, IS5056 harbors 14 plasmids ranging from 6,880 to 328,151 bp, four of which contain nine insecticidal protein genes,
cry1Aa3
,
cry1Ab21
,
cry1Ba1
,
cry1Ia14
,
cry2Aa9
,
cry2Ab1
,
vip1
,
vip2
, and
vip3Aa10
.
Genome Sequences of Avian Pathogenic Escherichia coli Strains Isolated from Brazilian Commercial Poultry
Authors: Rojas Thaís Cabrera Galvão , Maluta Renato Pariz , Parizzi Lucas Pedersen , Koenigkan Luciano Vieira , Yang Jian , Yu Jun , Pereira Gonçalo Amarante Guimarães , Dias da Silveira Wanderley 
Published: March 2013

ABSTRACT

Avian pathogenic
Escherichia coli
(APEC) infections are responsible for significant losses in the poultry industry worldwide. The disease might present as different local infections or as septicemia. Here, we present the draft genome sequences of three Brazilian APEC strains isolated from different kinds of infections. The availability of these APEC genome sequences is important for gaining a thorough understanding of the genomic features of
E. coli
, particularly those of this pathotype.
Draft Genome Sequence of Bacillus thuringiensis Strain DAR 81934, Which Exhibits Molluscicidal Activity
Authors: Wang Aisuo , Pattemore Julie , Ash Gavin , Williams Angela , Hane James 
Published: March 2013

ABSTRACT

Bacillus thuringiensis
has been widely used as a biopesticide for a long time. Its molluscicidal activity, however, is rarely realized. Here, we report the genome sequence of
B. thuringiensis
strain DAR 81934, a strain with molluscicidal activity against the pest snail
Cernuella virgata
.
Complete Genome Sequences of Two Novel
Puma concolor
Foamy Viruses from California
Authors: Kehl Timo , Bleiholder Anne , Roßmann Florian , Rupp Sebastian , Lei Janet , Lee Justin , Boyce Walter , Vickers Winston , Crooks Kevin , VandeWoude Sue , Löchelt Martin 
Published: March 2013

ABSTRACT

We report two complete foamy retrovirus (FV) genomes isolated from
Puma concolor
, a large cat native to the Americas. Due to high overall genetic relatedness to known feline foamy viruses (FFVs), we propose the name
Puma concolor
FFV (FFV
Pc
). The data confirm that felines are infected with distinct but closely related FVs.
Sustained Cardiovascular Actions of APJ Agonism During Renin–Angiotensin System Activation and in Patients With Heart Failure
Authors: Barnes Gareth D. , Alam Shirjel , Carter Gordon , Pedersen Christian M. , Lee Kristina M. , Hubbard Thomas J. , Veitch Scott , Jeong Herim , White Audrey , Cruden Nicholas L. , Huson Les , Japp Alan G. , Newby David E. 
Published: March 2013

Background—

To assess cardiovascular actions of APJ agonism during prolonged (Pyr
1
)apelin-13 infusion and renin–angiotensin system activation.

Methods and Results—

Forty-eight volunteers and 12 patients with chronic stable heart failure attended a series of randomized placebo–controlled studies. Forearm blood flow, cardiac index, left ventricular dimensions, and mean arterial pressure were measured using bilateral venous occlusion plethysmography, bioimpedance cardiography, transthoracic echocardiography, and sphygmomanometry, respectively, during brief local (0.3–3.0 nmol/min) and systemic (30–300 nmol/min) or prolonged systemic (30 nmol/min) (Pyr
1
)apelin-13 infusions in the presence or absence of renin–angiotensin system activation with sodium depletion or angiotensin II coinfusion. During sodium depletion and angiotensin II coinfusion, (Pyr
1
)apelin-13–induced vasodilatation was preserved (
P
<0.02 for both). Systemic intravenous (Pyr
1
)apelin-13 infusion increased cardiac index, whereas reducing mean arterial pressure and peripheral vascular resistance index (
P
<0.001 for all) irrespective of sodium depletion or angiotensin II (0.5 ng/kg per minute) coinfusion (
P
>0.05 for all). Prolonged 6-hour (Pyr
1
)apelin-13 infusion caused a sustained increase in cardiac index with increased left ventricular ejection fraction in patients with chronic heart failure (ANOVA;
P
<0.001 for all).

Conclusions—
APJ agonism has sustained cardiovascular effects that are preserved in the presence of renin–angiotensin system activation or heart failure. APJ agonism may hold major promise to complement current optimal medical therapy in patients with chronic heart failure.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifiers: NCT00901719, NCT00901888, NCT01049646, NCT01179061.
Compliance With the Stroke Education Performance Measure in the Michigan Paul Coverdell National Acute Stroke Registry
Authors: Nickles Adrienne , Fiedler Jay , Roberts Stacey , Lyon-Callo Sarah , Hurst Rochelle , Reeves Mathew 
Published: March 2013

Background and Purpose—
Stroke education, 1 of 8 endorsed stroke performance measures, consists of 5 specific subcomponents: risk factors, stroke warning signs, emergency medical service activation, physician follow-up, and discharge medications. We identified predictors of stroke education performance measure compliance in the Michigan Paul Coverdell National Acute Stroke Registry.

Methods—
Data were collected on 9609 acute stroke admissions to 20 registry hospitals during 2008 and 2009. Predictors of measure compliance (delivery of all 5 subcomponents) were determined using multivariable logistic regression.

Results—
Overall compliance with the stroke education measure was 61.8% (hospital-level compliance ranged between 16% and 93%). Compliance with individual subcomponents were risk factors (65.5%), stroke warning signs (68.9%), emergency medical service activation (66.8%), physician follow-up (92.9%), and discharge medications (91.5%). Age, gender, stroke subtype, prestroke ambulation, discharge destination, and hospital size were all significant independent predictors of compliance. Stroke education was delivered less often to patients who were ≥70 years of age, nonambulatory prestroke, not discharged to home, had transient ischemic attack, or hemorrhagic stroke.

Conclusions—
Only 60% of patients received stroke education consistent with the endorsed performance measures. Strategies to increase stroke education, including the impact of incorporating stroke-specific education measures into hospital care protocols, should be explored.
Towards a competence-based evaluation framework: The personal growth of volunteers in a child injury prevention program
Authors: Chan Charles CH , Chan Kevin , Tsui Ming-Sum , Kwok Astor 
Published: March 2013

Summary In this study, the researchers created a development-oriented evaluation framework, which provides constructive feedback on the personal growth of volunteers. To assess the process by which a volunteer becomes a competent practitioner, a competence taxonomy with five levels of attainment was adopted. Findings The competence of volunteers could be measured by the volunteers' attainments in three areas: degree of commitment, acquisition of knowledge, and utilization of skills. A competence-based evaluation framework of volunteer progress ensures that volunteers receive structured and constructive feedback. Applications The proposed development-oriented evaluation tool will help keep track of volunteers' progress and encourage the development of personalized strategies according to each volunteer's needs. It will also be informative to the quality improvement of volunteer services.
Host-derived CD8+ dendritic cells are required for induction of optimal graft-versus-tumor responses after experimental allogeneic bone marrow transplantation
Authors: Toubai Tomomi , Sun Yaping , Luker Gary , Liu Jun , Luker Kathryn E. , Tawara Isao , Evers Rebecca , Liu Chen , Mathewson Nathan , Malter Chelsea , Nieves Evelyn , Choi Sung , Murphy Kenneth M. , Reddy Pavan 
Published: March 2013

Key PointsTargeting APCs to enhance GVT. CD8+ DCs are important for optimizing antitumor responses after allogeneic bone marrow transplantation.
Ex vivomicro-computed tomography analysis of bleomycin-induced lung fibrosis for preclinical drug evaluation
Authors: Scotton Chris J. , Hayes Brian , Alexander Robert , Datta Arnab , Forty Ellen J. , Mercer Paul F. , Blanchard Andy , Chambers Rachel C. 
Published: March 2013

Research into the pathogenesis underlying the development of idiopathic pulmonary fibrosis is hampered by a repertoire of animal models that fail to recapitulate all the features of the human disease. Better use and understanding of what the animal models represent may improve clinical predictability. We interrogatedex vivomicro-computed tomography (CT) as a novel end-point measure in the mouse model of bleomycin-induced lung fibrosis (BILF), and to evaluate a therapeutic dosing regimen for preclinical drug evaluation.A detailed characterisation of BILF was performed using standard end-point measures (lung hydroxyproline and histology). High resolution micro-CT (∼13.7 μm voxel size) was evaluated for quantifying the extent and severity of lung fibrosis.The period from 14 to 28 days following bleomycin instillation represents progression of established fibrosis. A therapeutic dosing regimen during this period was validated using a transforming growth factor-β receptor-1 kinase inhibitor, and micro-CT provided a highly sensitive and quantitative measure of fibrosis. Moreover, fibrotic lesions did not completely resolve, but instead persisted for ≥6 months following a single insult with bleomycin.Ex vivomicro-CT analysis of BILF allows robust evaluation of therapeutic dosing once fibrosis is already well established, requiring fewer mice than conventional biochemical end-points.
Implications of adopting the Global Lungs Initiative 2012 all-age reference equations for spirometry
Authors: Quanjer Philip H. , Brazzale Danny J. , Boros Piotr W. , Pretto Jeffrey J. 
Published: March 2013

The aim of this study was to determine the diagnostic and interpretative consequences of adopting the Global Lungs Initiative (GLI) 2012 spirometric prediction equations.We assessed spirometric records from 17 572 subjects (49.5% females), aged 18–85 years, from hospitals in Australia and Poland.We calculated predicted forced expiratory volume in 1 s (FEV1), forced expiratory volume (FVC), FEV1/FVC and lower limits of normal (LLN) using European Community for Steel and Coal (ECSC), National Health and Nutrition Examination Survey (NHANES) III and GLI 2012 equations. Obstruction was defined as FEV1/FVC<LLN and a restrictive pattern as FEV1/FVC>LLN and FVC<LLN. Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 2 and higher was defined as FEV1/FVC <0.70 and FEV1<80% pred.GLI 2012 equations produce similar predicted values for FEV1and FVC compared with NHANES, but produce larger values than ECSC. Differences in the LLN lead to an important increase in the prevalence rate of a low FVC compared to ECSC, and a significant decrease compared to NHANES prediction equations. Adopting GLI 2012 equations has small effects on the prevalence rate of airway obstruction. GOLD stages 2–4 lead to >20% underdiagnosis of airway obstruction up to the age of 55 years and to 16–23% overdiagnosis in older subjects. GLI 2012 equations increase the prevalence of a “restrictive spirometric pattern” compared to ECSC but decrease it compared to NHANES.
Comparative genome analysis of Streptococcus infantarius subsp. infantariusCJ18, an African fermented camel milk isolate with adaptations to dairy environment
Authors: Jans Christoph , Follador Rainer , Hochstrasser Mira , Lacroix Christophe , Meile Leo , Stevens Marc J A 
Published: March 2013

Abstract

Background

Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of Sii strain CJ18 was compared with that of other Streptococcus species to identify dairy adaptations including genome decay such as in Streptococcus thermophilus, traits for its competitiveness in spontaneous milk fermentation and to assess potential health risks for consumers.

Results
The genome of Sii CJ18 harbors several unique regions in comparison to Sii ATCC BAA-102T, among others an enlarged exo- and capsular polysaccharide operon; Streptococcus thermophilus-associated genes; a region containing metabolic and hypothetical genes mostly unique to CJ18 and the dairy isolate Streptococcus gallolyticus subsp. macedonicus; and a second oligopeptide transport operon. Dairy adaptations in CJ18 are reflected by a high percentage of pseudogenes (4.9%) representing genome decay which includes the inactivation of the lactose phosphotransferase system (lacIIABC) by multiple transposases integration. The presence of lacS and lacZ genes is the major dairy adaptation affecting lactose metabolism pathways also due to the disruption of lacIIABC.
We constructed mutant strains of lacS, lacZ and lacIIABC and analyzed the resulting strains of CJ18 to confirm the redirection of lactose metabolism via LacS and LacZ.
Natural competence genes are conserved in both Sii strains, but CJ18 contains a lower number of CRISPR spacers which indicates a reduced defense capability against alien DNA. No classical streptococcal virulence factors were detected in both Sii strains apart from those involved in adhesion which should be considered niche factors. Sii-specific virulence factors are not described. Several Sii-specific regions encoding uncharacterized proteins provide new leads for virulence analyses and investigation of the unclear association of dairy and clinical Sii with human diseases.

Conclusions
The genome of the African dairy isolate Sii CJ18 clearly differs from the human isolate ATCC BAA-102T. CJ18 possesses a high natural competence predisposition likely explaining the enlarged genome. Metabolic adaptations to the dairy environment are evident and especially lactose uptake corresponds to S. thermophilus. Genome decay is not as advanced as in S. thermophilus (10-19%) possibly due to a shorter history in dairy fermentations.
Characterisation of CD154+ T cells following ex vivo birch allergen stimulation defines a close relationship between T cell subsets in healthy volunteers
Authors: Smith Karen A , Gray Nicola J , Cheek Elizabeth , Saleh Femi , Lavender Jo , Frew Anthony J , Kern Florian , Tarzi Michael D 
Published: March 2013

Abstract

Background
Allergic sensitisation has been ascribed to a dysregulated relationship between allergen-specific Th1, Th2 and regulatory T cells. We hypothesised that the relationship between these T cell subsets could be better defined using a short-term allergen stimulation system followed by direct analysis of CD154-positive T cells. Using peripheral blood samples from birch pollinosis patients and healthy non-atopic controls, we sought to explore the frequencies and phenotype of birch-stimulated CD154-positive T helper cells following ex vivo birch allergen stimulation.

Results
Activated CD154-positive Th1, Th2 and Tr1-like cells, that co-expressed IFNγ, IL-4 and IL-10 respectively, were identified in both birch-allergic and non-allergic participants. We observed a close correlation between Th1, Th2 and Tr1-like cell frequency in non-allergic volunteers, such that the three parameters increased together to maintain a low Th2: Th1 ratio. The relationship between Th1, Th2 and Tr1-like responses was dysregulated in birch-allergic patients, with abrogation of the IL-10 response and a higher Th2: Th1 ratio. A close correlation was observed between Th2 cell frequency and the absolute concentration of birch-specific IgE within the birch-allergic group, and we confirmed previous reports of a more differentiated T cell phenotype in allergic subjects.

Conclusions
The findings demonstrate an important balance between IFNγ, IL-4 and IL-10 T cell responses to birch allergen in health, where Th2 responses to allergens were frequently observed, but apparently balanced by Th1 and regulatory responses. The detection of CD154 positive T cells after short-term antigen stimulation may be a useful method for the detection of T cell responses to allergens when cost, speed and convenience are priorities.
Alcohol dehydrogenase, iron containing, 1promoter hypermethylation associated with colorectal cancer differentiation
Authors: Tae Chung Hyun , Ryu Kyung Ju , Kim Seok-Hyung , Kim Hee Cheol , Chun Ho-Kyung , Min Byung-Hoon , Chang Dong Kyung , Rhee Poong-Lyul , Kim Jae J , Rhee Jong Chul , Kim Young-Ho 
Published: March 2013

Abstract

Background
The aberrant methylation of CpG islands in the promoter is associated with colorectal cancer (CRC) carcinogenesis. In our previous study, the promoter of alcohol dehydrogenase, iron containing, 1 (ADHFE1) was most highly methylated in CRC compared to normal colorectal mucosa. In this study, we examined the expression and function of the ADHFE1 in CRC.

Methods
We examined the promoter methylation and mRNA expression of ADHFE1 with 5-aza-2′-deoxycytidine (5-Aza-2-dC) in 12 CRC cell lines, 124 paired CRC and adjacent normal mucosa, and 59 advanced adenomas. To confirm methylation of ADHFE1, we performed bisulfite genomic sequencing in 3 CRC cell lines, 6 paired CRC and adjacent normal mucosa. ADHFE1 protein expression was studied using western blot and immunohistochemistry, respectively in the 36 and 243 paired CRC and adjacent normal tissue. We transfected the DLD-1 with pcDNA3.1 vector containing ADHFE1 and examined the expression of differentiation marker, such as ALP, CEA and Cdx2. We examined the ADHFE1 expression at distinct developmental stages in mouse embryos.

Results
The ADHFE1 promoter was hypermethylated in all CRC cell lines, 81.8% in CRCs, and 84.7% in advanced adenomas, with reciprocal change by 5-Aza-2-dC. The expression of ADHFE1 mRNA was down-regulated in all CRC cell lines and 96.3% in CRC tissues. The expression of ADHFE1 protein was down-regulated in 91.7% of CRC tissues. In the immunohistochemistry, normal epithelial cells at the crypt top showed very strong ADHFE1 expression, whereas they were much weaker at the crypt base. In CRC, the good differentiation was significantly associated with high ADHFE1 expression. The activity of differentiation marker, such as ALP and CEA, was higher in pcDNA3.1-ADHFE1 transfected CRC cells with consistent correlation with ADHFE1 protein than control. In mouse embryos, ADHFE1 in the large intestine was the first detected at E15.5. At E18.5, ADHFE1 was predominantly expressed in the top of the mature crypt epithelium.

Conclusions
It showed that the hypermethylation of ADHFE1 promoter in CRC is concordance with down-regulation of ADHFE1 mRNA and ADHFE1 protein. ADHFE1 has an important role of differentiation in CRC, as well as normal colorectal mucosa and embryonic developmental processes.
Patterns of childhood adverse events are associated with clinical characteristics of bipolar disorder
Authors: Larsson Sara , Aas Monica , Klungsøyr Ole , Agartz Ingrid , Mork Erlend , Steen Nils Eiel , Barrett Elizabeth A , Lagerberg Trine V , Røssberg Jan Ivar , Melle Ingrid , Andreassen Ole A , Lorentzen Steinar 
Published: March 2013

Abstract

Background
Previous studies in bipolar disorder investigating childhood trauma and clinical presentations of the illness have mainly focused on physical and sexual abuse. Our aim was to explore further the relationship between childhood trauma and disease characteristics in bipolar disorder to determine which clinical characteristics were most strongly associated with childhood trauma total score, as well as subtypes of adverse childhood events, including physical, sexual, emotional abuse and neglect.

Methods
141 Patients with bipolar disorder were consecutively recruited, and disease history and clinical characteristics were assessed. History of childhood abuse was obtained using the Childhood Trauma Questionnaire (CTQ). Statistical methods used were factor analysis, Poisson and linear regression, and generalized additive modeling (GAM).

Results
The factor analysis of CTQ identified three factors: emotional abuse/neglect, sexual abuse and physical abuse. There were significant associations between CTQ total score and earlier onset of illness, reduced level of psychosocial functioning (GAF; Global Assessment of Functioning) and decreased number of hospitalization, which mainly were due to the factor emotional abuse/neglect. Physical abuse was significantly associated with lower GAF scores, and increased number of mood episodes, as well as self-harm. Sexual abuse was significantly associated with increased number of mood episodes. For mood episodes and self-harm the associations were characterized by great variance and fluctuations.

Conclusions
Our results suggest that childhood trauma is associated with a more severe course of bipolar illness. Further, childhood abuse (physical and sexual), as well as emotional abuse and neglect were significantly associated with accelerating staging process of bipolar disorder. By using specific trauma factors (physical abuse, sexual abuse and emotional abuse/neglect) the associations become both more precise, and diverse.
Does medial support decrease major complications of unstable proximal humerus fractures treated with locking plate?
Authors: Jung Woo-Bin , Moon Eun-Sun , Kim Sung-Kyu , Kovacevic David , Kim Myung-Sun 
Published: March 2013

AbstractBackgroundThe purpose of this study was to evaluate the role of medial support and clinical factors responsible on outcomes and major complications associated with treatment of unstable proximal humerus fractures using a locking plate and suture augmentation.MethodsSixty-three cases in 62 patients (42 female, 20 male) were evaluated between September 2004 and October 2008. Cases were divided into either a medial support group (36 cases) or non-medial support group (27 cases). Clinical and radiographic evaluations included Neer’s evaluation criteria, the neck-shaft angle using the Paavolainen method, and complications. We analyzed the correlation between bone- and fracture- related complications and three independent clinical variables, such as the presence of medial support, fracture type, and osteoporosis by way of multivariate logistic regression.ResultsThere were statistically significant differences in the overall incidence of complications based on the presence of medial support (p = 0.014) and preoperative fracture type (p = 0.018), but no differences based on the presence of osteoporosis (p = 0.157). According to multivariate logistic regression analysis, the restoration of medial support was the most reliable factor to prevent bone- and fracture- related complications. In addition, when we compared the incidence of bone- and fracture-related complications in the presence or absence of medial support among 30 patients with osteoporosis, the group with restoration of medial support had only one complication of humeral head osteonecrosis despite the presence of osteoporosis (5.9% vs. 46.2%, p = 0.025). According to Neer’s criteria, excellent or satisfactory clinical results accounted for seventy-three percent of the total cases (46 of 63 cases). Seventy-eight percent (49 of 55 cases) showed good radiographic results by the Paavolainen method. There were 14 complications in 13 of 63 cases (20.6%).ConclusionsIn the treatment of unstable proximal humerus fractures with locking plate technology and suture augmentation, we suggest that obtaining medial support is an important factor in preventing major bone- and fracture-related postoperative complications such as reduction loss or nonunion.