bluuebunny/crossref_metadata_2025_split huggingface dataset:
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets
Authors: Wang Jianrong , Lunyak Victoria V. , Jordan I. King 
Published: January 2013

Abstract
Summary: Although some histone modification chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) signals show abrupt peaks across narrow and specific genomic locations, others have diffuse distributions along chromosomes, and their large contiguous enrichment landscapes are better modeled as broad peaks. Here, we present BroadPeak, an algorithm for the identification of such broad peaks from diffuse ChIP-seq datasets. We show that BroadPeak is a linear time algorithm that requires only two parameters, and we validate its performance on real and simulated histone modification ChIP-seq datasets. BroadPeak calls peaks that are highly coincident with both the underlying ChIP-seq tag count distributions and relevant biological features, such as the gene bodies of actively transcribed genes, and it shows superior overall recall and precision of known broad peaks from simulated datasets.
Availability: The source code and documentations are available at http://jordan.biology.gatech.edu/page/software/broadpeak/.
Contact: king.jordan@biology.gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
An ensemble analysis to predict future habitats of striped marlin (Kajikia audax) in the North Pacific Ocean
Authors: Su Nan-Jay , Sun Chi-Lu , Punt André E. , Yeh Su-Zan , DiNardo Gerard , Chang Yi-Jay 
Published: January 2013

Abstract
Su, N.-J., Sun, C.-L., Punt, A. E., Yeh, S.-Z., DiNardo, G., and Chang, Y.-J. 2013. An ensemble analysis to predict future habitats of striped marlin (Kajikia audax) in the North Pacific Ocean. – ICES Journal of Marine Science, 70: 1013–1022. Striped marlin is a highly migratory species distributed throughout the North Pacific Ocean, which shows considerable variation in spatial distribution as a consequence of habitat preference. This species may therefore shift its range in response to future changes in the marine environment driven by climate change. It is important to understand the factors determining the distribution of striped marlin and the influence of climate change on these factors, to develop effective fisheries management policies given the economic importance of the species and the impact of fishing. We examined the spatial patterns and habitat preferences of striped marlin using generalized additive models fitted to data from longline fisheries. Future distributions were predicted using an ensemble analysis, which represents the uncertainty due to several global climate models and greenhouse gas emission scenarios. The increase in water temperature driven by climate change is predicted to lead to a northward displacement of striped marlin in the North Pacific Ocean. Use of a simple predictor of water temperature to describe future distribution, as in several previous studies, may not be robust, which emphasizes that variables other than sea surface temperatures from bioclimatic models are needed to understand future changes in the distribution of large pelagic species.
Transgenic Enhancement of High‐Molecular‐Weight Glutenin Subunit 1Dy10 Concentration: Effects in Wheat Flour Blends and Sponge and Dough Baking
Authors: Graybosch Robert A. , Seabourn Bradford , Chen Yuanhong R. , Blechl Ann E. 
Published: January 2013

ABSTRACTDough strength is needed for efficient breadmaking quality. This property is strongly influenced in wheat (Triticum aestivum L.) by gluten seed storage proteins and, in particular, by high‐molecular‐weight (HMW) glutenin subunit composition. Experiments were designed to elevate expression of a key native HMW glutenin subunit (1Dy10) via genetic engineering and to determine whether resultant flours can be used in sponge and dough applications, the most common commercial bread‐baking procedure. Both unblended and blended samples from transgenic and nontransgenic sister lines were tested, with blended samples being formed by addition to a control sample. Dough properties, as determined by farinograph evaluation, were improved by the transgene‐encoded increases in 1Dy10 in both undiluted and blended flours. Mean farinograph stability of transgenic samples was twice that of the control, and blends with transgenic samples demonstrated increases in stabilities proportional to the amount of transgenic flour included. Mean farinograph quality numbers of transgenic samples, and of all blends containing transgenic flour, were significantly higher than both the control and all nontransgenic treatments. In the sponge and dough bake procedure, undiluted transgenic samples induced lower scores, relative to both control and undiluted nontransgenic samples, for water absorption, crumb body firmness, and loaf volume. In blends, however, the transgenic samples resulted in improvements in some sponge and dough loaf attributes, including loaf symmetry and crumb color score, without any concomitant loss of loaf volume in transgenic blends. These improved variables relate to finished product appearance and to consumer selection in markets. The use of transgenic flours with increased 1Dy10 glutenin content in commercial blends could provide advantages in sponge and dough bake applications.
Clinical impact of the publication of S3 guidelines for intensive care in cardiac surgery patients in Germany: results from a postal survey
Authors: KASTRUP M. , CARL M. , SPIES C. , SANDER M. , MARKEWITZ A. , SCHIRMER U. 
Published: January 2013

IntroductionThe development and implementation of practice guidelines might be an important tool to evaluate the different practices and to consider different local strategies.MethodsA postal questionnaire with 37 questions was sent to the leading physicians of 80 intensive care units in Germany, treating patients after cardiothoracic surgery. The survey covered the same core questions on current practice of hemodynamic monitoring, volume replacement, inotropic/vasopressor support, and transfusions before and after the publication of an S3 guideline.ResultsA total of 77.5 % of the completed questionnaires were returned. Monitoring changed to increased use of central venous oxygen saturation (ScvO2) in 55.1% (2005: 20.9%), end‐tidal CO2‐monitoring 36.2% (2005: 24.3%), and decreased use of the left atrial pressure with 12.3% (2005: 23.3%) and pulmonary artery catheter 47.5% (2005: 58.2%). For volume therapy, there is a decreased use of Hydroxyethyl starch (HES) with 38.7% (2005: 63.4%) and an increased use of crystalloids 41.9% (2005: 22.4%). For inotropes, there is a trend to a decreased use of dopamine with 9.7% (2005: 29.1%, P = 0.074). The clinical relevance of the guidelines was judged ‘high’ by 43.5% and ‘medium’ by 50% of the responding physicians; however, change of treatments was reported by one quarter of respondents.ConclusionDespite ongoing variability in the use of monitoring devices, volume replacement and vasopressor/inotrope use in cardiac surgery patients, there have been some changes in the therapy of these patients after publication of the guidelines. Because the guideline has been considered as clinically relevant, further interdisciplinary development and implementation support should be considered.
Fibrosis Progression in HCV Carriers with Mild Hepatitis Who Possess the High‐Repetition Variant of the DRD4 Gene, a Genetic Marker for Binge‐Drinking and Risk‐Seeking Behavior: A Longitudinal Study
Authors: Minisini Rosalba , Boccato Elisa , Favretto Serena , Alaimo Emanuele , Smirne Carlo , Burlone Michela E. , Bocchetta Simone , Vandelli Carmen , Colletta Cosimo , Colletta Alessandro , Pirisi Mario 
Published: January 2013

BackgroundAlcohol is a major determinant of the outcome of chronic hepatitis C virus (HCV) infection, but self‐reported drinking habits lack reliability. We hypothesized that carriage of high‐repetition variants (HRV) of the variable number of tandem repeats (VNTR) in exon III of the dopamine receptor D4 gene, linked to binge‐drinking and risk‐seeking behavior, might be a proxy measure of alcohol consumption, and aimed to verify whether it may affect histologic outcome.MethodsA cohort of HCV patients with normal or near‐normal aminotransferases (N = 128) underwent a liver biopsy as part of diagnostic work‐up. None admitted to exceed low‐risk alcohol consumption; most (90/128, 70%) described themselves as teetotalers. They received advice on abstaining from alcohol, but not antiviral treatment. After a median follow‐up period of 10 years, all underwent a second liver biopsy. HRV allele frequencies were compared with those of a group of healthy blood donors (N = 128) and related to liver histology.ResultsHRV allele frequencies were 0.19 in patients and 0.16 in controls (p = 0.182). In the subgroup of patients who admittedly had consumed alcohol, 20/38 (53%) carried HRV, in comparison with 27/90 patients (30%) who had denied to consume alcohol (p = 0.026 by Fisher's exact test). Carriage of HRV was associated with higher histologic grade (p = 0.002) and stage (p = 0.009) at the final biopsy. At multivariate analysis, among a set of variables also including viral genotype, viral load, body mass index, gender, and history of alcohol consumption, only age (OR = 1.06, 95% CI 1.02 to 1.11) and HRV (OR = 3.13, 95% CI 1.28 to 7.68) were independent predictors of significant fibrosis at the end of follow‐up.ConclusionsThe link between HRV carriage and histologic outcome in a subgroup of HCV patients at low risk of progression underlines the need for intense scrutiny of alcohol habits in hepatitis C.
GDNF is a novel ethanol‐responsive gene in the VTA: implications for the development and persistence of excessive drinking
Authors: Ahmadiantehrani Somayeh , Barak Segev , Ron Dorit 
Published: January 2013

AbstractGlial cell line‐derived neurotrophic factor (GDNF) is a potent inhibitor of ethanol consumption and relapse, and GDNF heterozygous knockout mice display increased reward sensitivity to ethanol and consume more ethanol after a period of abstinence than their wild‐type littermates. Here, we tested whether ethanol alters GDNF expression in the ventral tegmental area (VTA; GDNF's site of action) and/or the nucleus accumbens (NAc; the main source of GDNF), and if so, determine the role of the endogenous growth factor in the regulation of ethanol consumption. Systemic administration of ethanol increased GDNF expression and protein levels in the VTA, but not the NAc. Additionally, GDNF levels were elevated after an ethanol‐drinking session in rats that consumed ethanol in the intermittent‐access two‐bottle choice procedure for 1 week, but not 7 weeks. Deprivation following 7 weeks of excessive ethanol intake reduced GDNF levels, while a short ethanol binge drinking period following deprivation upregulated GDNF expression. Importantly, knockdown of GDNF within the VTA using adenovirus expressing short hairpin RNA facilitated the escalation of ethanol drinking by ethanol‐naïve rats, but not by rats with a history of excessive ethanol consumption. These results suggest that during initial ethanol‐drinking experiences, GDNF in the VTA is increased and protects against the development of excessive ethanol intake. However, the growth factor's protective response to ethanol breaks down after protracted excessive ethanol intake and withdrawal, resulting in persistent, excessive ethanol consumption.
Efficacy of laser‐driven irrigation versus ultrasonic in removing an airlock from the apical third of a narrow root canal
Authors: Peeters Harry Huiz , Gutknecht Norbert 
Published: January 2013

AbstractThe purpose of the study was to test the hypothesis that air entrapment occurs in the apical third of a root canal during irrigation. A second objective was to test the null hypothesis that there is no difference between laser‐driven irrigation (an erbium, chromium:yttrium‐scandium‐gallium‐garnet laser) and passive ultrasonic irrigation in removing an airlock from the apical third. One hundred twenty extracted human teeth with single narrow root canals were randomised into two experimental groups (n = 40) and two control groups (n = 20). The specimens were shaped using hand instruments up to a size 30/0.02 file. The teeth were irrigated with a mixture of saline, radiopaque contrast and ink in solution. In the passive ultrasonic irrigation group, the irrigant was activated with an ultrasonic device for 60 s. In the laser group, the irrigant was activated with a laser for 60 s. It was concluded that if the insertion of irrigation needle is shorter than the working length, air entrapment may develop in the apical third, but the use of laser‐driven irrigation is completely effective in removing it.
Which farmers benefit the most from Bt corn adoption? Estimating heterogeneity effects in the Philippines
Authors: Mutuc Maria , Rejesus Roderick M. , Yorobe, Jr. Jose M. 
Published: January 2013

AbstractThe potential contributions of new biotechnologies to sustainable food and income security have been the subject of widespread discussions around the turn of the 21st century. But distributional issues of which segments of adopters of genetically modified (GM) crops benefit the most have not been given ample attention). Using propensity scores, we apply the (a) stratification‐multilevel method of estimating heterogeneous treatment effects; and the (b) matching‐smoothing method of estimating heterogeneous treatment effects proposed by Xie et al. We find that the incidence of higher yields, lower insecticide use, and reduced seed utilization in the Philippines diminishes progressively as a farmer's propensity to adopt Bt corn increases. Farmers with a low propensity to adopt Bt are those who farm smaller, nonirrigated farms located farther from seed suppliers and farmers without previous training on pest identification. In most cases, while these farmers are typically poorer farmers in smaller parcels, cannot afford irrigation and are situated in remote areas away from easily accessible seed suppliers, there is no evidence, however, that profits differ across farmers with varying propensities to adopt the Bt variety.
Adult height of subjects with nonclassical 21‐hydroxylase deficiency
Authors: Eyal Ori , Tenenbaum‐Rakover Yardena , Shalitin Shlomit , Israel Shoshana , Weintrob Naomi 
Published: January 2013

AbstractAimTo determine whether nonclassical 21‐hydroxylase deficiency (NC21OHD) compromises adult height (AH), and to establish the clinical parameters affecting AH in subjects with NC21OHD.MethodsThis is a multicenter, retrospective review of medical records for clinical and biochemical parameters. The corrected height (CH) standard deviation score (SDS), defined as AH SDS minus mean parental height (MPH) SDS, was calculated for each patient, where MPH SDS is the average of the father's height SDS and the mother's height SDS.ResultsThe study group consisted of 122 NC21OHD subjects whose median age at diagnosis was 8.7 years (range, 0.1–36). Seventy‐two patients had two mild mutations, 22 had one mild and one severe mutation, 10 were heterozygous for one mild mutation, and 18 did not undergo molecular analysis. The CH SDS of the 66 patients who initiated hydrocortisone treatment during childhood was significantly lower than those who presented after achieving AH (p = 0.03). However, there was a negative correlation between age at diagnosis and AH SDS in the former group (R = −0.7, p = 0.03). Being heterozygous for one mild and one severe mutation (R = −0.7, p < 0.02) and age at diagnosis (R = −0.7, p = 0.03) were negatively associated with CH SDS. The CH SDS was significantly lower in those who had bone age advancement at diagnosis compared to those who did not (p = 0.04).ConclusionThe main determinants of AH in patients with NC21OHD are apparently age at diagnosis and initiation of therapy, and genotype. Early diagnosis and initiation of glucocorticoids therapy may improve height outcome in those presenting during childhood.
Retracted: Isolation, characterization, and effect of administration in vivo, a novel probiotic strain from pig feces
Authors: Ihara Yasuhiro , Hyodo Hideki , Sukegawa Shin , Murakami Hiroshi , Morimatsu Fumiki 
Published: January 2013

AbstractFrom porcine rectal swabs or feces, we isolated lactic acid bacteria and used porcine Peyer's patch cells to select them for inducibility of IgA production as an indicator of probiotic effects. The strain selected as a new probiotic was named ‘Enterococcus faecium NHRD IHARA‘. To verify the probiotic effects of this strain in vivo, 536 piglets at age 25 days were assigned to either the trial group, which administrated the strain, or the control group. An increase in IgA in the feces was observed at age 45 days (P < 0.05 compared with the control group); a significant increase in serum IgA was also observed at the end of the study (P < 0.01) in the trial group. In addition, significant differences between the groups in terms of body weight (P < 0.05) and average daily gain (P < 0.01) were observed. The rate of detection of swine‐pathogenic Escherichia coli gene in the feces tended to be lower in the trial group than in the controls. The novel probiotic strain; E. faecium NHRD IHARA may have beneficial effects on swine growth by inducing IgA production and reducing rates of colonization by pathogens in the body.
Effect of co‐culture with intact embryos on development of bovine separated blastomeres
Authors: Nagai Makoto , Hori Noboru , Miyamoto Michiko , Sakaguchi Masanobu , Hayakawa Yuji , Kawai Megumi , Kita Mitsuo , Furuya Tetsuya , Imai Kei 
Published: January 2013

AbstractTo improve embryo development in bovine separated blastomeres, we evaluated applicability of co‐culture with intact embryos. The morphological quality of blastocysts derived from separated blastomeres and rate of blastocyst formation were only slightly increased when the cells were co‐cultured with intact embryos, which did not provide significant differences when statistically analyzed. However, the cell count of inner cell mass (ICM), trophectoderm (TE) and total number of cells in Day 8 blastocysts were significantly higher when the cells were co‐cultured with the intact embryos than those with the cells cultured individually (P < 0.05). Transfer of four monozygotic pairs of blastocysts derived from the cells co‐cultured with intact embryos led to three pregnancies even when the blastomeres were produced by in vitro maturation and in vitro fertilization of oocytes collected by ovum pick‐up from elite cows. These results suggest that co‐culturing with intact embryos may enhance development of bovine separated blastomere.
Glycogen synthase kinase‐3 (GSK‐3) regulatesTGF‐β1‐induced differentiation of pulmonary fibroblasts
Authors: Baarsma Hoeke A , Engelbertink Lilian HJM , van Hees Lonneke J , Menzen Mark H , Meurs Herman , Timens Wim , Postma Dirkje S , Kerstjens Huib AM , Gosens Reinoud 
Published: January 2013

BackgroundChronic lung diseases such as asthma,COPDand pulmonary fibrosis are characterized by abnormal extracellular matrix (ECM) turnover.TGF‐β is a key mediator stimulatingECMproduction by recruiting and activating lung fibroblasts and initiating their differentiation process into more active myofibroblasts. Glycogen synthase kinase‐3 (GSK‐3) regulates various intracellular signalling pathways; its role inTGF‐β1‐induced myofibroblast differentiation is currently largely unknown.PurposeTo determine the contribution ofGSK‐3 signalling inTGF‐β1‐induced myofibroblast differentiation.Experimental ApproachWe usedMRC5 human lung fibroblasts and primary pulmonary fibroblasts of individuals with and withoutCOPD. Protein and mRNAexpression were determined by immunoblotting andRT‐PCRanalysis respectively.ResultsStimulation ofMRC5 and primary human lung fibroblasts withTGF‐β1resulted in time‐ and dose‐dependent increases of α‐sm‐actin and fibronectin expression, indicative of myofibroblast differentiation. Pharmacological inhibition ofGSK‐3 bySB216763 dose‐dependently attenuatedTGF‐β1‐induced expression of these myofibroblasts markers. Moreover, silencing ofGSK‐3 by siRNAor pharmacological inhibition byCT/CHIR99021 fully inhibited theTGF‐β1‐induced expression of α‐sm‐actin and fibronectin. The effect ofGSK‐3 inhibition on α‐sm‐actin expression was similar in fibroblasts from individuals with and withoutCOPD. Neither smad,NF‐κBnorERK1/2 were involved in the inhibitory actions ofGSK‐3 inhibition bySB126763 on myofibroblast differentiation. Rather,SB216763 increased the phosphorylation ofCREB, which in its phosphorylated form acts as a functional antagonist ofTGF‐β/smad signalling.Conclusion and ImplicationWe demonstrate thatGSK‐3 signalling regulatesTGF‐β1‐induced myofibroblast differentiation by regulatingCREBphosphorylation.GSK‐3 may constitute a useful target for treatment of chronic lung diseases.
Circulating endothelial cells and tumor blood volume as predictors in lung cancer
Authors: Wang Jing , Xiao Jianyu , Wei Xiyin , Wang Liuchun , Lin Li , Liu Zhujun , Wang Xinyue , Sun Baocun , Li Kai 
Published: January 2013

The current criteria for evaluating antiangiogenic efficacy is insufficient as tumor shrinkage occurs after blood perfusion decreases. Tumor blood volume (BV) in computed tomography perfusion imaging and circulating endothelial cells (CEC) might predict the status of angiogenesis. The present study aimed to validate their representation as feasible predictors in non‐small‐cell lung carcinoma (NSCLC). A total of 74 patients was categorized randomly into two arms undergoing regimens of vinorelbine and cisplatin (Navelbine and platinum [NP]) with rh‐endostatin or single NP. The response rate, perfusion imaging indexes and activated CEC (aCEC) during treatment were recorded. Progression‐free survival (PFS) was determined through follow up. Correlations among the above indicators, response and PFS were analyzed: aCEC increased significantly in cases of progressive disease after single NP chemotherapy (P = 0.024). Tumor BV decreased significantly in cases with a clinical benefit in the combined arm (P = 0.026), whereas inverse correlations existed between ∆aCEC (post‐therapeutic value minus the pre‐therapeutic value) and PFS (P = 0.005) and between ∆BV and PFS (P = 0.044); a positive correlation existed between ∆aCEC and ∆BV. Therefore, both aCEC and tumor BV can serve as predictors, and detection of both indicators can help evaluate the chemo‐antiangiogenic efficacy in NSCLC more accurately.
Epithelial expression of interleukin-37b in inflammatory bowel disease
Authors: Imaeda H , Takahashi K , Fujimoto T , Kasumi E , Ban H , Bamba S , Sonoda H , Shimizu T , Fujiyama Y , Andoh A 
Published: January 2013

Summary
Interleukin (IL)-37 is a member of the IL-1 cytokine family. We investigated IL-37b expression in the inflamed mucosa of inflammatory bowel disease (IBD) patients. Furthermore, we analysed IL-37b expression in human colonic epithelial cells. The human colonic epithelial cell line T84 and human colonic subepithelial myofibroblasts (SEMFs) were used. IL-37b expression in the IBD mucosa was evaluated by immunohistochemistry. IL-37b mRNA and protein expression were determined by real time-polymerase chain reaction (PCR) and Western blotting, respectively. IL-37b was not detected in the normal colonic mucosa. In the inflamed mucosa of IBD patients, epithelial IL-37b expression was increased markedly. In ulcerative colitis (UC) and Crohn's disease (CD) patients, IL-37b expression was enhanced in the affected mucosa. In the intestinal epithelial cell line T84, the expression of IL-37b mRNA and protein was enhanced by tumour necrosis factor (TNF)-α. This IL-37b induction by TNF-α was mediated by nuclear factor (NF)-κB and activator protein (AP)-1 activation. Furthermore, IL-37b inhibited TNF-α-induced interferon-γ-inducible protein (IP)-10 expression significantly in human colonic SEMFs. Epithelial IL-37b expression was increased in IBD patients, especially UC patients. IL-37b may be involved in the pathophysiology of IBD as an anti-inflammatory cytokine and an inhibitor of both innate and acquired immune responses.