bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Bufavirus-1 and Bufavirus-3 in Feces of Patients with Acute Diarrhea, China
Authors: Huang Dou-Dou , Wang Wei , Lu Qing-Bin , Zhao Jin , Guo Chen-Tao , Wang Hong-Yu , Zhang Xiao-Ai , Tong Yi-Gang , Liu Wei , Cao Wu-Chun 
Published: August 2015

AbstractBufavirus (BuV) is a newly discovered human parvovirus that has been detected in some countries. The current study was designed to understand the epidemic of BuV in China. Totally 1877 fecal specimens were collected from pediatric and adult patients with acute diarrhea in two large hospitals from 2010 to 2014. BuV was detected in 0.5% (9/1877) of the fecal samples by PCR and subsequent sequencing. The positive patients had a wide age range from 1 month through 60 years (median 24 years old) and 6 were male. A geographic specific pattern was obvious, with significantly higher frequency of BuV presented in Northern than in Southern China. Four BuV-1 and five BuV-3 were determined. Mixed-infections of BuV with sapovirus and novavirus were found in 2 cases, respectively. A temporal clustering was identified, with most positive detection focused in the cold weather. These findings have expanded the current knowledge on the geographic boundaries of BuV circulation.
Complexity of cardiac signals for predicting changes in alpha-waves after stress in patients undergoing cardiac catheterization
Authors: Chiu Hung-Chih , Lin Yen-Hung , Lo Men-Tzung , Tang Sung-Chun , Wang Tzung-Dau , Lu Hung-Chun , Ho Yi-Lwun , Ma Hsi-Pin , Peng Chung-Kang 
Published: August 2015

AbstractThe hierarchical interaction between electrical signals of the brain and heart is not fully understood. We hypothesized that the complexity of cardiac electrical activity can be used to predict changes in encephalic electricity after stress. Most methods for analyzing the interaction between the heart rate variability (HRV) and electroencephalography (EEG) require a computation-intensive mathematical model. To overcome these limitations and increase the predictive accuracy of human relaxing states, we developed a method to test our hypothesis. In addition to routine linear analysis, multiscale entropy and detrended fluctuation analysis of the HRV were used to quantify nonstationary and nonlinear dynamic changes in the heart rate time series. Short-time Fourier transform was applied to quantify the power of EEG. The clinical, HRV and EEG parameters of postcatheterization EEG alpha waves were analyzed using change-score analysis and generalized additive models. In conclusion, the complexity of cardiac electrical signals can be used to predict EEG changes after stress.
Elevated expression of mechanosensory polycystins in human carotid atherosclerotic plaques: association with p53 activation and disease severity
Authors: Varela Aimilia , Piperi Christina , Sigala Fragiska , Agrogiannis George , Davos Constantinos H. , Andri Maria-Anastasia , Manopoulos Christos , Tsangaris Sokrates , Basdra Efthimia K. , Papavassiliou Athanasios G. 
Published: August 2015

AbstractAtherosclerotic plaque formation is associated with irregular distribution of wall shear stress (WSS) that modulates endothelial function and integrity. Polycystins (PC)-1/-2 constitute a flow-sensing protein complex in endothelial cells, able to respond to WSS and induce cell-proliferation changes leading to atherosclerosis. An endothelial cell-culture system of measurable WSS was established to detect alterations in PCs expression under conditions of low- and high-oscillatory shear stress in vitro. PCs expression and p53 activation as a regulator of cell proliferation were further evaluated in vivo and in 69 advanced human carotid atherosclerotic plaques (AAPs). Increased PC-1/PC-2 expression was observed at 30–60 min of low shear stress (LSS) in endothelial cells. Elevated PC-1 expression at LSS was followed by p53 potentiation. PCs immunoreactivity localizes in areas with macrophage infiltration and neovascularization. PC-1 mRNA and protein levels were significantly higher than PC-2 in stable fibroatherotic (V) and unstable/complicated (VI) AAPs. Elevated PC-1 immunostaining was detected in AAPs from patients with diabetes mellitus, dyslipidemia, hypertension and carotid stenosis, at both arteries (50%) or in one artery (90%). PCs seem to participate in plaque formation and progression. Since PC-1 upregulation coincides with p38 and p53 activation, a potential interplay of these molecules in atherosclerosis induction is posed.
Effect of BIX-01294 on H3K9me2 levels and the imprinted geneSnrpnin mouse embryonic fibroblast cells
Authors: Chen Peng , Yao Jian-Feng , Huang Rong-Fu , Zheng Fang-Fang , Jiang Xiao-Hong , Chen Xuan , Chen Juan , Li Ming , Huang Hong-Feng , Jiang Yi-Ping , Huang Yan-Fang , Yang Xiao-Yu 
Published: August 2015

Histone H3 lysine 9 dimethylation (H3K9me2) hypermethylation is thought to be a major influential factor in cellular reprogramming, such as somatic cell nuclear transfer (SCNT) and induction of pluripotent stem cells (iPSCs). The diazepin-quinazolin-amine derivative (BIX-01294) specifically inhibits the activity of histone methyltransferase EHMT2 (euchromatic histone-lysine N-methyltransferase 2) and reduces H3K9me2 levels in cells. The imprinted gene small nuclear ribonucleoprotein N (Snrpn) is of particular interest because of its important biological functions. The objective of the present study was to investigate the effect of BIX-01294 on H3K9me2 levels and changes in Snrpn DNA methylation and histone H3K9me2 in mouse embryonic fibroblasts (MEFs). Results showed that 1.3 μM BIX-01294 markedly reduced global levels of H3K9me2 with almost no cellular toxicity. There was a significant decrease in H3K9me2 in promoter regions of the Snrpn gene after BIX-01294 treatment. A significant increase in methylation of the Snrpn differentially methylated region 1 (DMR1) and slightly decreased transcript levels of Snrpn were found in BIX-01294-treated MEFs. These results suggest that BIX-01294 may reduce global levels of H3K9me2 and affect epigenetic modifications of Snrpn in MEFs.
Cyclin-dependent kinase 5 activates guanine nucleotide exchange factor GIV/Girdin to orchestrate migration–proliferation dichotomy
Authors: Bhandari Deepali , Lopez-Sanchez Inmaculada , To Andrew , Lo I-Chung , Aznar Nicolas , Leyme Anthony , Gupta Vijay , Niesman Ingrid , Maddox Adam L. , Garcia-Marcos Mikel , Farquhar Marilyn G. , Ghosh Pradipta 
Published: August 2015

Significance
The guanine nucleotide exchange factor (GEF) GIV/Girdin has previously been shown to trigger noncanonical activation of trimeric G proteins in response to multiple chemical stimuli at the plasma membrane and at various locations within cells. In this work we identified a single phosphoevent and pinpointed cyclin-dependent kinase 5 (CDK5) as the responsible kinase that activates GIV's GEF function and initiates noncanonical G protein signaling via GIV. These studies provide evidence that CDK5 is essential for maximal activation of GIV-GEF in cells and insights into a hitherto unrecognized crosstalk between CDK5 and G proteins via GIV. Such crosstalk may shape migration–proliferation dichotomy during several physiological and pathological scenarios such as wound healing and cancer metastasis.
GenomeLaser: fast and accurate haplotyping from pedigree genotypes
Authors: Li Wenzhi , Fu Guoxing , Rao Weinian , Xu Wei , Ma Li , Guo Shiwen , Song Qing 
Published: August 2015

Abstract
Summary: We present a software tool called GenomeLaser that determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. This method features high accuracy, chromosome-range phasing distance, linear computing, flexible pedigree types and flexible genetic marker types.
Availability and implementation: http://www.4dgenome.com/software/genomelaser.html.
Contact: qsong@msm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
An integrated structure- and system-based framework to identify new targets of metabolites and known drugs
Authors: Naveed Hammad , Hameed Umar S. , Harrus Deborah , Bourguet William , Arold Stefan T. , Gao Xin 
Published: August 2015

Abstract
Motivation: The inherent promiscuity of small molecules towards protein targets impedes our understanding of healthy versus diseased metabolism. This promiscuity also poses a challenge for the pharmaceutical industry as identifying all protein targets is important to assess (side) effects and repositioning opportunities for a drug.
Results: Here, we present a novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called ‘drugs’). For a given drug, our method uses sequence order–independent structure alignment, hierarchical clustering and probabilistic sequence similarity to construct a probabilistic pocket ensemble (PPE) that captures promiscuous structural features of different binding sites on known targets. A drug’s PPE is combined with an approximation of its delivery profile to reduce false positives. In our cross-validation study, we use iDTP to predict the known targets of 11 drugs, with 63% sensitivity and 81% specificity. We then predicted novel targets for these drugs—two that are of high pharmacological interest, the peroxisome proliferator-activated receptor gamma and the oncogene B-cell lymphoma 2, were successfully validated through in vitro binding experiments. Our method is broadly applicable for the prediction of protein-small molecule interactions with several novel applications to biological research and drug development.
Availability and implementation: The program, datasets and results are freely available to academic users at http://sfb.kaust.edu.sa/Pages/Software.aspx.
Contact: xin.gao@kaust.edu.sa and stefan.arold@kaust.edu.sa
Supplementary information: Supplementary data are available at Bioinformatics online.
Experimental analysis of the use of fishery closures and cooperatives to reduce economic rent dissipation caused by assignment problems
Authors: Emery Timothy J. , Tisdell John , Green Bridget S. , Hartmann Klaas , Gardner Caleb , León Rafael 
Published: August 2015

AbstractAssignment problems in quota-managed fisheries are caused by spatial and temporal heterogeneity in the productivity of the stock. If the quota management system is not fully delineated (e.g. harvest rights assigned to particular areas) then fishers will compete with each other and overexploit parts of the fishery where or when the quota unit value is highest (i.e. fishing costs low and/or market price high), leading to economic rent dissipation. This study used experimental economics to assess the effectiveness of fishery temporal closures and income-sharing fishery cooperatives in resolving assignment problems across three different fisheries with varying levels of fisher heterogeneity (i.e. numbers of quota owners and lease quota fishers). While most fisheries were successful in reducing economic rent dissipation under the fishery closure management structure relative to their baseline(s), fisheries characterized by a greater number of lease quota fishers were less effective. This was due to the differential values that lease quota fishers place on the resource relative to quota owners, due to having insecurity of tenure and diminished wealth in having to bid for a quota package and pay for it using their revenue from fishing. Conversely, income-sharing fishery cooperatives were equally successful across all three fisheries in reducing assignment problems relative to their baseline(s). This was because income-sharing created an incentive to coordinate fishing effort, particularly among heterogeneous groups. While requiring further exposition in the field, these experimental results represent a first step in identifying management institutions that may assist fishers under quota management to resolve assignment problems in a dynamic environment.
Prospective evaluation of the Eppendorf–Cologne Scale
Authors: Hoffmann Michael , Lehmann Wolfgang , Schroeder Malte , Cramer Christopher , Grossterlinden Lars G. , Rueger Johannes M. , Lefering Rolf 
Published: August 2015

Objectives
Early diagnosis of traumatic brain injury and reliable prediction of outcome are essential for determining treatment strategies and allocating resources. This study re-evaluates the Eppendorf–Cologne Scale (ECS) and its predictive accuracy for outcome compared with the Glasgow Coma Scale (GCS).

Methods
A prospective cohort analysis of severely injured trauma patients registered in the Trauma Registry of the German Society for Trauma Surgery from 2012–2013 was carried out. Only directly admitted patients alive on admission with complete data on GCS, ECS and outcome in terms of survival to hospital discharge or death were included. The predictive accuracy in terms of the outcome of the ECS and the GCS was modelled using area under the receiver operating characteristic (AUROC) curve analysis.

Results
A total of 17 616 patients fulfilled the study inclusion criteria. The ECS outmatched the predictive accuracy of the GCS for outcome (AUROC, 0.853, 95% confidence interval, 0.831–0.854; and AUROC 0.836; 95% confidence interval, 0.825–0.848, respectively; P=0.062). An ECS score of 8 was associated with a 25-fold higher mortality compared with an ECS score of 0. Patients who had an ECS score of 8 had a 1.5-fold higher mortality compared with patients allocated a GCS score of 3.

Conclusion
The ECS shows a higher accuracy for prediction of outcome compared with the GCS and enables further differentiation within the critical GCS 3 collective.
Which adverse events should be reported in an emergency department? A Delphi study
Authors: Robinson Susan M. , Walker Ben F. , Brown Ruth M. 
Published: August 2015

Objective
The aim of this study was to determine if emergency medicine specific triggers for completing an incident form could be agreed and if a common definition for contributory factors could be achieved. Such definitions could be used to improve safety within the emergency department (ED) and share learning across the specialty.

Participants and methods
One hundred and fifteen ED safety leads in the UK and Ireland were invited to participate in a Delphi study. This process took 1 year to complete. In the first round, participants listed 20 events that should be reported as an adverse event and 20 contributory factors that could contribute to risk or harm. An 80% concordance level was sought for both aspects.

Results
Eighty-four per cent of safety leads participated in the first round, although this decreased over subsequent rounds to 43%. Four hundred and eighty-five triggers were initially suggested; eventually, 27 triggers that should always or usually be reported achieved 80% concordance. Sixty-eight contributory factors were initially identified with eventual agreement being reached on 27 remediable contributory factors.

Conclusion
The process demonstrated agreement amongst emergency physicians in the UK and Ireland on the type of events that should be formally reported. The lists emerging from this process should not be viewed as exhaustive; rather they should be used to encourage the reporting of incidents and designing safer systems and processes within the ED.
Use of checklists improves the quality and safety of prehospital emergency care
Authors: Kerner Thoralf , Schmidbauer Willi , Tietz Mares , Marung Hartwig , Genzwuerker Harald V. 
Published: August 2015

ObjectivesHigh-level emergency medical care requires transfer of evidence-based knowledge into practice. Our study is the first to investigate the feasibility of checklists in improving prehospital emergency care.Materials and methodsThree checklists based on standard operating procedures were introduced: General principles of prehospital care, acute coronary syndrome and acute asthma/acutely exacerbated chronic obstructive pulmonary disease. Subsequent to prehospital care and immediately before transport, information on medical history, diagnostic and therapeutic procedures was obtained. Data of 740 emergency missions were recorded prospectively before (control group) and after implementation of checklists and compared using theχ2-test (significance levelP<0.05).ResultsDocumentation on patients’ history (pre-existing diseases: 69.1 vs. 74.3%; medication: 55.8 vs. 68.0%; allergies: 6.2 vs. 27.7%) and diagnostic measures (oxygen saturation: 93.2 vs. 98.1%; auscultation: 11.1 vs. 19.9%) as well as basic treatment procedures (application of oxygen: 73.2 vs. 85.3%; intravenous access: 84.6 vs. 92.2%) increased significantly. Subanalysis of acute coronary syndrome cases showed a significant increase of 12-lead ECG use (74.3 vs. 92.4%), administration of oxygen (84.2 vs. 98.6%), ASA (71.7 vs. 81.9%), heparin (71.1 vs. 84.0%), β blockers (39.5 vs. 57.1%) and morphine (26.8 vs. 44.6%). In the chronic obstructive pulmonary disease subgroup, oxygen supply (78.8 vs. 98.5%) and application of inhalative and intravenous β2-mimetics (42.4 vs. 66.7% and 12.1 vs. 37.9%) increased significantly.ConclusionIntroduction of checklists for prehospital emergency care may help to improve adherence to treatment guidelines. Additional efforts (e.g. team trainings) have to be made to increase quality of care.
Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions
Authors: Ecovoiu Alexandru Al. , Ghionoiu Iulian Constantin , Ciuca Andrei Mihai , Ratiu Attila Cristian 
Published: August 2015

AbstractA critical topic of insertional mutagenesis experiments performed on model organisms is mapping the hits of artificial transposons (ATs) at nucleotide level accuracy. Obviously, mapping errors may occur when sequencing artifacts or mutations as SNPs and small indels are present very close to the junction between a genomic sequence and a transposon inverted repeat (TIR). Another particular item of insertional mutagenesis is mapping of the transposon self-insertions and, to our best knowledge, there is no publicly available mapping tool designed to analyze such molecular events. We developed Genome ARTIST, a pairwise gapped aligner tool which works out both issues by means of an original, robust mapping strategy. Genome ARTIST is not designed to use NGS data but to analyze ATs insertions obtained in small to medium-scale mutagenesis experiments. Genome ARTIST employs a heuristic approach to find DNA sequence similarities and harnesses a multi-step implementation of a Smith-Waterman adapted algorithm to compute the mapping alignments. The experience is enhanced by easily customizable parameters and a user-friendly interface that describes the genomic landscape surrounding the insertion. Genome ARTIST deals with many genomes of bacteria and eukaryotes available inEnsemblandGenBankrepositories. Our tool specifically harnesses/exploits the sequence annotation data provided byFlyBaseforDrosophila melanogaster(the fruit fly), which enables mapping of insertions relative to various genomic features such as natural transposons. Genome ARTIST was tested against other alignment tools using relevant query sequences derived from theD. melanogasterandMus musculus(mouse) genomes. Real and simulated query sequences were also comparatively inquired, revealing that Genome ARTIST is a very robust solution for mapping transposon insertions.Genome ARTIST is a stand-alone user-friendly application, designed for high-accuracy mapping of transposon insertions and self-insertions. The tool is also useful for routine aligning assessments like detection of SNPs or checking the specificity of primers and probes. Genome ARTIST is an open source software and is available for download atwww.genomeartist.roand atwww.bioinformatics.org.
Culture, corporate governance and analysts forecast in Malaysia
Authors: Abdul Wahab Effiezal Aswadi , Allah Pitchay Anwar , Ali Ruhani 
Published: August 2015

Purpose
– The purpose of this paper is to examine the relationship between Bumiputra (in reference to Malay indigenous race) directors, a proxy for culture and analysts forecast. In addition, the study investigates whether corporate governance affects that relationship.

Design/methodology/approach
– The sample of this study is based on 664 firm-year observations from 193 firms during the 1999-2009 periods. The authors employ a panel least square regression with both period and industry fixed effects. The authors retrieved of analyst data from the Institutional Broker Estimate System (I/B/E/S) database while the authors hand collected the corporate governance variables. The remaining data were collected from Compustat Global.

Findings
– The authors find a positive relationship between the proxy of culture, Bumiputra directors and analysts forecast error suggesting that cultural values influences the level of information in the Malaysian capital market.

Research limitations/implications
– The research is dependent on the data availability from I/B/E/S database.

Originality/value
– The authors extend the work of Haniffa and Cooke (2002) in investigating how cultural values influence the capital market. In addition, this is the first study that investigates culture values and the analysts forecast.
Contingency between S & OP design and planning environment
Authors: Ivert Linea Kjellsdotter , Dukovska-Popovska Iskra , Fredriksson Anna , Dreyer Heidi C. , Kaipia Riikka 
Published: August 2015

Purpose– The purpose of this paper is to understand how companies design sales and operations planning (S & OP) contingent on the planning environment (PE).Design/methodology/approach– On the basis of the literature, the paper creates an analytical framework identifying the main constructs related to the PE and S & OP design, which is the basis for gathering and analysing qualitative data from eight cases in the food industry. The findings highlight the relations between S & OP and the PE, and are used for generating three propositions.Findings– Responding to the complex and uncertain PE, the companies set up S & OP on a stock-keeping unit (SKU) level, with the possibility of re-planning and a flexible planning horizon, thus differing from what has generally been suggested in the literature. In addition, the companies are aligning the inputs, activities, and outcomes of the S & OP process to the PE. Particularly important environmental contingencies are uncertainty connected to demand and supply, frequent product launches, and production network complexity. Product-related variables have a lower impact on the S & OP design.Research limitations/implications– The present study is limited to one industry only and a comparison between industries with larger data sets would be valuable in future studies. The study selected cases based on their S & OP maturity; further studies need to explore the effect of the alignment of S & OP and the PE on the planning performance.Originality/value– In the literature, S & OP is presented as a generic process with a strict formal design that is equal for all companies. The study provides insights into how companies adjust S & OP according to the PE.