bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research Ethics II: Mentoring, Collaboration, Peer Review, and Data Management and Ownership
Authors: Horner Jennifer , Minifie Fred D. 
Published: November 2010

PurposeIn this series of articles—Research Ethics I,Research Ethics II,andResearch EthicsIII—the authors provide a comprehensive review of the 9 core domains for the responsible conduct of research (RCR) as articulated by the Office of Research Integrity. InResearch Ethics II,the authors review the RCR domains of mentoring, collaboration, peer review, and data management and ownership.MethodThey relied on authoritative documents, both historical and contemporary, insightful commentary, and empirical research in order to identify current issues and controversies of potential interest to both faculty and students.ConclusionsThe authors close by urging readers to stay abreast of the manifold ethics issues facing today’s community of scientists, policymakers, and research institutions, and to adhere to best practices as they evolve.
iMAT: an integrative metabolic analysis tool
Authors: Zur Hadas , Ruppin Eytan , Shlomi Tomer 
Published: November 2010

Abstract
Summary: iMAT is an Integrative Metabolic Analysis Tool, enabling the integration of transcriptomic and proteomic data with genome-scale metabolic network models to predict enzymes' metabolic flux, based on the method previously described by Shlomi et al. The prediction of metabolic fluxes based on high-throughput molecular data sources could help to advance our understanding of cellular metabolism, since current experimental approaches are limited to measuring fluxes through merely a few dozen enzymes.
Availability and Implementation: http://imat.cs.tau.ac.il/
Contact: zurhadas@post.tau.ac.il; ruppin@post.tau.ac.il; tomersh@cs.technion.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments
Authors: van Heeringen Simon J. , Veenstra Gert Jan C. 
Published: November 2010

Abstract
Summary: Accurate prediction of transcription factor binding motifs that are enriched in a collection of sequences remains a computational challenge. Here we report on GimmeMotifs, a pipeline that incorporates an ensemble of computational tools to predict motifs de novo from ChIP-sequencing (ChIP-seq) data. Similar redundant motifs are compared using the weighted information content (WIC) similarity score and clustered using an iterative procedure. A comprehensive output report is generated with several different evaluation metrics to compare and evaluate the results. Benchmarks show that the method performs well on human and mouse ChIP-seq datasets. GimmeMotifs consists of a suite of command-line scripts that can be easily implemented in a ChIP-seq analysis pipeline.
Availability: GimmeMotifs is implemented in Python and runs on Linux. The source code is freely available for download at http://www.ncmls.eu/bioinfo/gimmemotifs/.
Contact: s.vanheeringen@ncmls.ru.nl
Supplementary Information: Supplementary data are available at Bioinformatics online.
Aquaculture site selection for Japanese kelp (Laminaria japonica) in southern Hokkaido, Japan, using satellite remote sensing and GIS-based models
Authors: Radiarta I Nyoman , Saitoh Sei-Ichi , Yasui Hajime 
Published: November 2010

Abstract
Radiarta, I N., Saitoh, S-I., and Yasui, H. 2011. Aquaculture site selection for Japanese kelp (Laminaria japonica) in southern Hokkaido, Japan, using satellite remote sensing and GIS-based models. – ICES Journal of Marine Science, 68: 773–780. Japanese kelp (Laminaria japonica) is an important species cultured and harvested in Japan. The most suitable areas for hanging culture in southern Hokkaido were determined using geographic information system (GIS) models and a multicriteria evaluation approach. Analyses of physical parameters (sea surface temperature and suspended solid from SeaWiFS and MODIS) and available bathymetric data indicated that some 74% (1139 km2) of the total potential area with bottom depths <60 m had the two highest suitability scores. A local sensitivity analysis indicated that suspended solids were more important than temperature in affecting model output. This study demonstrates that GIS databases of different formats and sources can be used effectively to construct spatial models for kelp aquaculture.
Functional Assignments for the Carboxyl-Terminal Domains of the Ferrochelatase from Synechocystis PCC 6803: The CAB Domain Plays a Regulatory Role, and Region II Is Essential for Catalysis
Authors: Sobotka Roman , Tichy Martin , Wilde Annegret , Hunter C. Neil 
Published: November 2010

Abstract
Ferrochelatase (FeCH) catalyzes the insertion of Fe2+ into protoporphyrin, forming protoheme. In photosynthetic organisms, FeCH and magnesium chelatase lie at a biosynthetic branch point where partitioning down the heme and chlorophyll (Chl) pathways occurs. Unlike their mammalian, yeast, and other bacterial counterparts, cyanobacterial and algal FeCHs as well as FeCH2 isoform from plants possess a carboxyl-terminal Chl a/b-binding (CAB) domain with a conserved Chl-binding motif. The CAB domain is connected to the FeCH catalytic core by a proline-rich linker sequence (region II). In order to dissect the regulatory, catalytic, and structural roles of the region II and CAB domains, we analyzed a FeCH ƊH347 mutant that retains region II but lacks the CAB domain and compared it with the ƊH324-FeCH mutant that lacks both these domains. We found that the CAB domain is not required for catalytic activity but is essential for dimerization of FeCH; its absence causes aberrant accumulation of Chl-protein complexes under high light accompanied by high levels of the Chl precursor chlorophyllide. Thus, the CAB domain appears to serve mainly a regulatory function, possibly in balancing Chl biosynthesis with the synthesis of cognate apoproteins. Region II is essential for the catalytic function of the plastid-type FeCH enzyme, although the low residual activity of the ƊH324-FeCH is more than sufficient to furnish the cellular demand for heme. We propose that the apparent surplus of FeCH activity in the wild type is critical for cell viability under high light due to a regulatory role of FeCH in the distribution of Chl into apoproteins.
The effects of a large reduction in alcohol prices on hospitalizations related to alcohol: a population‐based natural experiment
Authors: Herttua Kimmo , Mäkelä Pia , Martikainen Pekka 
Published: November 2010

ABSTRACTAims  Finland experienced a large reduction in alcohol prices in 2004 due to in the lowering of alcohol taxes by about one‐third and the abolition of duty‐free allowances for travellers from the European Union. We examined the effects of these changes on alcohol‐related hospitalizations.Design and participants  Time—series intervention analyses of monthly aggregations of hospitalization for acute and chronic causes among men and women aged 15–39, 40–49, 50–69 and more than 69 years.Setting  Finland, 1996–2006.Findings  After the price reduction the chronic hospitalization rate for men increased among those below age 70 years. It was largest among those aged 50–69 years: 22%, which implies an increase of 18.0 monthly hospitalizations per 100 000 person‐years, and there was an 11% and 16% (11.5 and 4.8 monthly hospitalizations) increase among those aged 40–49 and 15–39, respectively. Among the women the rate increased by 23% (4.0 monthly hospitalizations) in the 50–69‐year‐olds, and decreased in the under‐40s. The increase in all the population groups was due mainly to an increase in mental and behavioural disorders due to alcohol. Acute hospitalizations increased by 17% and 20% (6.2 and 7.0 per month) among men aged 40–49 and 50–69 years, respectively, and by 38% among women aged 50–69 years (2.3 per month).Conclusions  The results, obtained in a natural experimental setting when trends and seasonal variation had been taken into account, suggest that the reduction in alcohol prices led to increases in alcohol‐related hospitalization in certain population groups, mainly among 50–69‐year‐olds, in Finland.
Daily administration of the TP receptor antagonist terutroban improved endothelial function in high‐cardiovascular‐risk patients with atherosclerosis
Authors: Lesault Pierre‐François , Boyer Laurent , Pelle Gabriel , Covali‐Noroc Ala , Rideau Dominique , Akakpo Servais , Teiger Emmanuel , Dubois‐Randé Jean‐Luc , Adnot Serge 
Published: November 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Terutroban is a selective TP receptor antagonist, i.e. a specific antagonist of the thromboxane A2 and prostaglandin endoperoxide receptors, shown to improve endothelial function after a single administration in patients with coronary artery disease. WHAT THIS STUDY ADDS • This randomized, double‐blind, placebo‐controlled trial demonstrates that repeated‐dose terutroban for 15 days improves endothelial function and inhibits thromboxane A2‐induced platelet aggregation in high‐cardiovascular‐risk patients taking 300 mg of aspirin per day. Terutroban may prove useful for preventing cardiovascular events in such patients.AIMS The specific TP receptor antagonist terutroban improves endothelial function after a single dose in patients with coronary artery disease. Our aim was to evaluate the effects and dose dependency of repeated‐dose terutroban on endothelial function and platelet aggregation in high‐cardiovascular‐risk patients with carotid atherosclerosis.METHODS We randomly allocated 48 patients taking 300 mg aspirin per day to placebo or to one of three terutroban dosages (2.5, 5 or 10 mg) for 15 days in a double‐blind study. Flow‐mediated vasodilatation was evaluated before and 2 h after the first oral dose on day 0 and 2 h after the last oral dose on day 14.RESULTS On day 0 and day 14, all three terutroban dosages improved flow‐mediated vasodilatation and abolished platelet aggregation induced by the TP receptor agonist U46619, without changing the aggregation response to ADP or collagen.CONCLUSION Terutroban, by chronically improving endothelium‐dependent vasodilatation and inhibiting platelet aggregation, may prove useful for preventing cardiovascular events in high‐risk patients.
A systematic review of therapeutic interventions for poststroke depression and the role of nurses
Authors: De Man‐van Ginkel Janneke M , Gooskens Floor , Schuurmans Marieke J , Lindeman Eline , Hafsteinsdottir Thóra B ,   on Behalf of the Rehabilitation Guideline Stroke Working Group
Published: November 2010

Aims and objectives.  This systematic review explores the nursing role in the management of poststroke depression and identifies effective non‐pharmacological interventions that nurses can use in the daily care of patients with stroke.Background.  Depression is a common complication poststroke and affects one‐third of patients with stroke. It has a negative impact on functional recovery and social activities and is associated with increased morbidity and mortality. Detection and diagnosis of poststroke depression is inconsistent, and many depressed patients are under‐treated. Although nurses recognise that observation and assessment are parts of their role in rehabilitation care, little is known about their role in assessing depression or the interventions they can use.Design.  A systematic review was conducted using the Cochrane method.Methods.  Literature for the period 1993–2008 was searched in the electronic databases of CINAHL, Medline (PubMed), Nursing Journals (PubMed) and PsycINFO using the following keywords: cerebrovascular accident, stroke, depression, poststroke depression, treatment, therapy, treatment outcome, management.Results.  Fifteen articles and one systematic review were identified. There was strong evidence that information provision reduces the severity of depression. Other interventions with positive effects on the occurrence or severity of poststroke depression were as follows: life review therapy, motivational interviewing, a specific nursing support programme and physical exercise.Conclusion.  Depression after stroke is an important problem with adverse effects on the patient’s ability to participate in rehabilitation and on rehabilitation outcome. The interventions described can be implemented in nursing care of patients with poststroke depression. The variety of such interventions and the diversity of their nature and design are consistent with the practice of rehabilitation nursing.Relevance to clinical practice.  The findings of this review enable nurses to intervene effectively to reduce the occurrence and severity of depression in patients with stroke.
Allogeneic mesenchymal stem cells prevent allergic airway inflammation by inducing murine regulatory T cells
Authors: Kavanagh H. , Mahon B. P. 
Published: November 2010

To cite this article: Kavanagh H, Mahon BP. Allogeneic mesenchymal stem cells prevent allergic airway inflammation by inducing murine regulatory T cells. Allergy 2011; 66: 523–531.AbstractBackground:  Adult bone marrow‐derived mesenchymal stem cells (MSC) possess potent immune modulatory effects which support their possible use as a therapy for immune‐mediated disease. MSC induce regulatory T cells (Treg) in vitro although the in vivo relevance of this is not clear.Objective:  This study addressed the hypothesis that adult bone marrow derived‐MSC would prevent the pathology associated with allergen‐driven airway inflammation, and sought to define the effector mechanism.Methods:  The influence of allogeneic MSC was examined in a model system where Treg induction is essential to prevent pathology. This was tested using a combination of a model of ovalbumin‐driven inflammation with allogeneic MSC cell therapy.Results:  Systemic administration of allogeneic MSC protected the airways from allergen‐induced pathology, reducing airway inflammation and allergen‐specific IgE. MSC were not globally suppressive but induced CD4+FoxP3+ T cells and modulated cell‐mediated responses at a local and systemic level, decreasing IL‐4 but increasing IL‐10 in bronchial fluid and from allergen re‐stimulated splenocytes. Moderate dose cyclophosphamide protocols were used to differentially ablate Treg responses; under these conditions the major beneficial effect of MSC therapy was lost, suggesting induction of Treg as the key mechanism of action by MSC in this model. In spite of the elimination of Treg, a significant reduction in airway eosinophilia persisted in those treated with MSC.Conclusion:  These data demonstrate that MSC induce Tregin vivo and reduce allergen‐driven pathology. Multiple Treg dependent and independent mechanisms of therapeutic action are employed by MSC.
Structural and functional analyses of a saturated acyl ACP thioesterase, type B from immature seed tissue of Jatropha curcas
Authors: Srikanta Dani K. G. , Hatti K. S. , Ravikumar P. , Kush A. 
Published: November 2010

AbstractThe distinguishing structural and functional domains of plant acyl‐acyl carrier protein (ACP) thioesterases and their complex interaction with the ACP‐linked fatty acid substrate complex have remained elusive. E. coli based heterologous expression and characterisation of many plant thioesterases reported so far have not been extended and linked to in silico modelling studies to explain the diversity in plant thioesterase substrate specificities. In this study, a thioesterase cDNA isolated from immature seed tissues of Jatropha curcas was found to be type B and specific to stearoyl acyl ACP when expressed in E. coli K27fadD88, a lipid utilisation mutant. Homology modelling and molecular docking of a selected region of the isolated JcFatB protein predicted that it had high affinity towards both stearate (18:0) and palmitate (16:0). Structural analysis of the sequence confirmed the presence of a transit peptide that is processed in multiple steps. The enzyme is localised in the chloroplasts and has an N‐terminal inner chloroplast transmembrane domain characteristic of type B plant thioesterases. Docking of ligands with JcFatB and its comparison with a modelled Jatropha thioesterase type A provided further evidence for native substrate preferences of Jatropha thioesterases. This study provides essential clues to develop future methods for large‐scale bacterial production of free fatty acids and for design of strategies to modulate the seed oil composition in this important non‐edible, seed oil plant.
Obesity, metabolic syndrome, adipocytes and vascular function: A holistic viewpoint
Authors: Achike Francis I , To Nim‐Hin Peter , Wang Huidi , Kwan Chiu‐Yin 
Published: November 2010

Summary1. Obesity is a metabolic disease of pandemic proportions largely arising from positive energy balance, a consequence of sedentary lifestyle, conditioned by environmental and genetic factors. Several central and peripheral neurohumoral factors (the major ones being the anorectic adipokines leptin and adiponecin and the orexigenic gut hormone ghrelin) acting on the anorectic (pro‐opiomelanocortin and cocaine‐ and amphetamine‐regulated transcript) and orexigenic (neuropeptide Y and agouti gene‐related protein) neurons regulate energy balance. These neurons, mainly in the arcuate nucleus of the hypothalamus, project to parts of the brain modulating functions such as wakefulness, autonomic function and learning. A tilt in the anorectic–orexigenic balance, perhaps determined genetically, leads to obesity.2. Excess fat deposition requires space, created by adipocyte (hypertrophy and hyperplasia) and extracellular matrix (ECM) remodelling. This process is regulated by several factors, including several adipocyte‐derived Matrix metalloproteinases and the adipokine cathepsin, which degrades fibronectin, a key ECM protein. Excess fat, also deposited in visceral organs, generates chronic low‐grade inflammation that eventually triggers insulin resistance and the associated comorbidities of metabolic syndrome (hypertension, atherosclerosis, dyslipidaemia and diabetes mellitus).3. The perivascular adipose tissue (PVAT) has conventionally been considered non‐physiological structural tissue, but has recently been shown to serve a paracrine function, including the release of adipose‐derived relaxant and contractile factors, akin to the role of the vascular endothelium. Thus, PVAT regulates vascular function in vivo and in vitro, contributing to the cardiovascular pathophysiology of the metabolic syndrome. Defining the mechanism of PVAT regulation of vascular reactivity requires more and better controlled investigations than currently seen in the literature.
Clinical significance of the highly sensitive fucosylated fraction of α‐fetoprotein in patients with chronic liver disease
Authors: Hanaoka Takuya , Sato Shuichi , Tobita Hiroshi , Miyake Tatsuya , Ishihara Shunji , Akagi Shuji , Amano Yuji , Kinoshita Yoshikazu 
Published: November 2010

AbstractBackground and Aim:  The purpose of the present study was to investigate the clinical significance of the highly sensitive fucosylated fraction of α‐fetoprotein (hs‐AFP‐L3) in patients with chronic liver disease (CLD) and low serum α‐fetoprotein (AFP) concentration.Methods:  A total of 241 patients being treated at our institute with CLD and low serum AFP concentration (3–10 ng/mL) were investigated retrospectively. We measured total AFP and the percentage of AFP‐L3 using a µTAS Wako i30 device. The possible presence of hepatocellular carcinoma (HCC) was thoroughly investigated by various examinations carried out from 1 month before to 1 month after measurements. In addition, hs‐AFP‐L3 elevated and non‐elevated groups, divided by the cut‐off value based on a receiver–operator characteristic (ROC) curve, were followed for possible future development of HCC.Results:  hs‐AFP‐L3 was above the detectable range in 60 patients (24.9%). Among those AFP‐L3 positive cases, 20 (33.3%) were found to be HCC prevalent, whereas HCC was found in just 16 patients (8.8%) with undetectable hs‐AFP‐L3 levels. We determined the cut‐off value of hs‐AFP‐L3%, which shows the proportion of AFP L3 in total AFP, to be 5.75%. During the follow‐up period, HCC was newly detected in six patients (22.2%) in the hs‐AFP‐L3% elevated group and in 10 (5.6%) in the non‐elevated group. Analysis using the Kaplan–Meier method showed the HCC‐free rate of the hs‐AFP‐L3% elevated group was significantly lower than that of the non‐elevated group (P = 0.0038). Independent predicting variants were female sex (P = 0.0024) and hs‐AFP‐L3% elevation (P = 0.0036).Conclusion:  Our results suggest hs‐AFP‐L3 level is a useful tumor marker for HCC in patients with CLD and low serum AFP concentration.
Epidemiology of lower gastrointestinal bleeding in China: Single‐center series and systematic analysis of Chinese literature with 53 951 patients
Authors: Bai Yu , Peng Jun , Gao Jun , Zou Duo‐Wu , Li Zhao‐Shen 
Published: November 2010

AbstractObjectives:  The epidemiology of lower gastrointestinal bleeding (LGIB) in Western populations has been reported; however, there are scant Asian reports. The aim of the present study was to determine the etiology of LGIB in a Chinese population by reporting a retrospective case series and a systematic analysis of Chinese literature.Methods:  A large colonoscopy database in a tertiary endoscopic center was searched to identify all patients with the indication of LGIB. The data, including patients' sex, age, endoscopic and pathological findings, were collected and analyzed. A comprehensive database search of the Chinese literature was carried out to obtain all relevant studies.Results:  In our series, a total of 720 patients with LGIB were included. There were 425 males and 295 females with a median age of 50 years, the most common etiologies of LGIB were inflammatory bowel disease (IBD; 30.2%), polyps (23.4%) and cancer (10.7%). In 30.2% of all the patients, no obvious causes were identified. A systematic analysis of Chinese literature found an additional 160 studies providing relevant data in 53 951 patients. Overall, colorectal cancer (24.4%), colorectal polyps (24.1%), colitis (16.8%), anorectal disease (9.8%) and IBD (9.5%) were the most common etiologies of LGIB. The main etiologies were different between adults, the elderly and children.Conclusion:  The study shows colorectal cancer, colorectal polyps, colitis, anorectal disease and IBD were the most common etiologies of LGIB in the Chinese adult and elderly population, whereas colorectal polyps, chronic colitis and intussusception were the main causes of LGIB in Chinese children. Whereas diverticulum, the most common cause of LGIB in Western populations, is uncommon in China.