bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of FOB testing in eastern‐Australian general practice patients: what has a national bowel cancer screening program delivered?
Authors: Paul Christine L. , Carey Mariko L. , Russell Grant , D'Este Cate , Sanson‐Fisher Rob W. , Zwar Nicholas 
Published: March 2015

Issues addressedThe National Bowel Cancer Screening Program (NBCSP) was introduced in Australia in 2006, offering free immunochemical Faecal Occult Blood Test (FOBT) to persons aged 50, 55 or 65. The study aimed to examine the prevalence of selfreported screening for colorectal cancer (CRC) using the FOBT and factors associated with not having an FOBT.MethodsA cross‐sectional study of Australian general practice patients aged 50 and over with no personal history of CRC completed a health risk survey while waiting for scheduled appointments between November 2010 and November 2011.ResultsA total of 5671 patients from 12 practices were approached to participate. Of the 4707 eligible patients (adults attending for care who understood English and were capable of providing informed consent), 4062 (86%) consented to participate, with 2269 eligible to complete the FOBT items. Approximately half (52%) of participants reported ever having an FOBT. More than one‐third (39.7%) of the sample reported having an FOBT in the prior three years. Those who recalled receiving a mailed kit as part of the NBCSP were five times more likely to report being screened. Those less likely to report screening were aged 50–59 years, were female and had been diagnosed with a form of cancer other than CRC.ConclusionsThere is justification for the extension of the NBCSP to ensure a majority of the age‐appropriate population is screened for CRC.
A mechanism for nano-titanium dioxide-induced cytotoxicity in HaCaT cells under UVA irradiation
Authors: Xue Chengbin , Luo Wen , Yang Xiang liang 
Published: March 2015

Abstract
Nano-TiO2 has been reported to be an efficient photocatalyst, which is able to produce reactive oxygen species (ROS) under UVA irradiation. In this study, we investigated the effects of nano-TiO2 on the cytotoxicity, induction of apoptosis, and the putative pathways of its actions in HaCaT cells. We show that nano-TiO2 is a potent inducer of apoptosis and that it transduces the apoptotic signal via ROS generation, thereby inducing mitochondrial permeability transition (MPT) and activating Caspase-3 from HaCaT cells. ROS production, mitochondrial alteration, and subsequent apoptotic cell death in nano-TiO2-treated cells were blocked by the MPT pore-blocker cyclosporin A. Taken together, our data indicate that nano-TiO2 induces the ROS-mediated MPT and resultant Caspase-3 activation.
Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (Equisetum arvense)
Authors: Inamine Saki , Onaga Shoko , Ohnuma Takayuki , Fukamizo Tamo , Taira Toki 
Published: March 2015

Abstract
Chitinase-A (EaChiA), molecular mass 36 kDa, was purified from the vegetative stems of a horsetail (Equisetum arvense) using a series of column chromatography. The N-terminal amino acid sequence of EaChiA was similar to the lysin motif (LysM). A cDNA encoding EaChiA was cloned by rapid amplification of cDNA ends and polymerase chain reaction. It consisted of 1320 nucleotides and encoded an open reading frame of 361 amino acid residues. The deduced amino acid sequence indicated that EaChiA is composed of a N-terminal LysM domain and a C-terminal plant class IIIb chitinase catalytic domain, belonging to the glycoside hydrolase family 18, linked by proline-rich regions. EaChiA has strong chitin-binding activity, however, no antifungal activity. This is the first report of a chitinase from Equisetopsida, a class of fern plants, and the second report of a LysM-containing chitinase from a plant.
Research on food and nutrition characteristics of conjugated fatty acids
Authors: Tsuduki Tsuyoshi 
Published: March 2015

Abstract
In this study, the physiological effects of fatty acids with conjugated double bonds were widely examined in vitro and in vivo. Initially, a method for determination of conjugated fatty acids in food and biological samples was established. I then clarified that the oxidative stability of conjugated fatty acids was improved by the form of triacylglycerol and addition of an antioxidant, and the influence of this effect on the metabolism and pharmacokinetics of conjugated fatty acids was clarified in vivo. In addition, antitumor, anti-angiogenesis, and antiobesity effects of conjugated fatty acids were found for the first time, thus demonstrating the usefulness of conjugated fatty acids. This communication mainly outlines the data obtained for conjugated linolenic acid. In addition, this review summarizes my research on conjugated fatty acid.
bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby
Authors: Etherington Graham J. , Ramirez-Gonzalez Ricardo H. , MacLean Dan 
Published: March 2015

Abstract
Motivation: bio-samtools is a Ruby language interface to SAMtools, the highly popular library that provides utilities for manipulating high-throughput sequence alignments in the Sequence Alignment/Map format. Advances in Ruby, now allow us to improve the analysis capabilities and increase bio-samtools utility, allowing users to accomplish a large amount of analysis using a very small amount of code. bio-samtools can also be easily developed to include additional SAMtools methods and hence stay current with the latest SAMtools releases.
Results: We have added new Ruby classes for the MPileup and Variant Call Format (VCF) data formats emitted by SAMtools and introduced more analysis methods for variant analysis, including alternative allele calculation and allele frequency calling for SNPs. Our new implementation of bio-samtools also ensures that all the functionality of the SAMtools library is now supported and that bio-samtools can be easily extended to include future changes in SAMtools. bio-samtools 2 also provides methods that allow the user to directly produce visualization of alignment data.
Availability and implementation: bio-samtools is available as a BioGem from http://www.biogems.info or as source code from https://github.com/helios/bioruby-samtools under the MIT License.
Contact: dan.maclean@tsl.ac.uk
Global optimization-based inference of chemogenomic features from drug–target interactions
Authors: Zu Songpeng , Chen Ting , Li Shao 
Published: March 2015

AbstractMotivation: Gaining insight into chemogenomic drug–target interactions, such as those involving the substructures of synthetic drugs and protein domains, is important in fragment-based drug discovery and drug repositioning. Previous studies evaluated the interactions locally, thereby ignoring the competitive effects of different substructures or domains, but this could lead to high false-positive estimation, calling for a computational method that presents more predictive power.Results: A statistical model, termed Global optimization-based InFerence of chemogenomic features from drug–Target interactions, or GIFT, is proposed herein to evaluate substructure-domain interactions globally such that all substructure-domain contributions to drug–target interaction are analyzed simultaneously. Combinations of different chemical substructures were included since they may function as one unit. When compared to previous methods, GIFT showed better interpretive performance, and performance for the recovery of drug–target interactions was good. Among 53 known drug–domain interactions, 81% were accurately predicted by GIFT. Eighteen of the top 100 predicted combined substructure-domain interactions had corresponding drug–target structures in the Protein Data Bank database, and 15 out of the 18 had been proved. GIFT was then implemented to predict substructure-domain interactions based on drug repositioning. For example, the anticancer activities of tazarotene, adapalene, acitretin and raloxifene were identified. In summary, GIFT is a global chemogenomic inference approach and offers fresh insight into drug–target interactions.Availability and implementation: The source codes can be found at http://bioinfo.au.tsinghua.edu.cn/software/GIFT.Contact: shaoli@mail.tsinghua.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA
Authors: Kelly Brendan J. , Gross Robert , Bittinger Kyle , Sherrill-Mix Scott , Lewis James D. , Collman Ronald G. , Bushman Frederic D. , Li Hongzhe 
Published: March 2015

Abstract
Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA.
Results: We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study.
Availability and implementation: http://github.com/brendankelly/micropower.
Contact: brendank@mail.med.upenn.edu or hongzhe@upenn.edu
ExaML version 3: a tool for phylogenomic analyses on supercomputers
Authors: Kozlov Alexey M. , Aberer Andre J. , Stamatakis Alexandros 
Published: March 2015

Abstract
Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.
Results: We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.
Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/ExaML.
Contact: Alexandros.Stamatakis@h-its.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Disturbance of poised chromatin coincides with increased expression of developmental genes in cancer
Authors: Bernhart Stephan H , Kretzmer Helene , Jühling Frank , Stadler Peter F , Hoffmann Steve 
Published: March 2015

ABSTRACTPoised (bivalent or paused) chromatin comprises activating and repressing histone modifications at the same location (Voigt et al., 2013). This combination of epigenetic marks keeps genes expressed at low levels but poised for rapid activation (Margaritis and Holstege, 2008; Mikkelsen et al., 2007). Typically, DNA at poised promoters carries low levels of methylation in normal cells (Meissner et al., 2008; Roadmap Epigenomics Consortium et al., 2015), but frequently shows elevated methylation levels in cancer samples (Hinoue et al., 2012; Gal-Yam et al., 2008; Ohm et al., 2007; Rodriguez et al., 2008; Easwaran et al., 2012). Although higher levels of methylation are normally associated with transcriptional silencing, recently counter-intuitive positive correlations between methylation and expression levels have been reported for two cancer types (Hahn et al., 2014; Kretzmer et al.,). Here, we analyze one of the largest combined expression and methylation data-sets to date, comprising over 5,000 samples and demonstrate that the hypermethylation of poised chromatin in conjunction with up-regulation of the corresponding genes is a general phenomenon in cancer. This up-regulation affects developmental genes and transcription factors, including many genes implicated in cancer. From analysis of 7,000 methylation data sets, we built a universal classifier that can identify cancer samples solely from the hypermethylation status of originally poised chromatin. We reason that the alteration of the epigenetic status of poised chromatin is intimately linked to tumorigenesis.
Network analysis of genome-wide selective constraint reveals a gene network active in early fetal brain intolerant of mutation
Authors: Choi Jinmyung , Shooshtari Parisa , Samocha Kaitlin E , Daly Mark J , Cotsapas Chris 
Published: March 2015

AbstractUsing robust, integrated analysis of multiple genomic datasets, we show that genes depleted for non-synonymousde novomutations form a subnetwork of 72 members under strong selective constraint. We further show this subnetwork is preferentially expressed in the early development of the human hippocampus and is enriched for genes mutated in neurological, but not other, Mendelian disorders. We thus conclude that carefully orchestrated developmental processes are under strong constraint in early brain development, and perturbations caused by mutation have adverse outcomes subject to strong purifying selection. Our findings demonstrate that selective forces can act on groups of genes involved in the same process, supporting the notion that adaptation can act coordinately on multiple genes. Our approach provides a statistically robust, interpretable way to identify the tissues and developmental times where groups of disease genes are active. Our findings highlight the importance of considering the interactions between genes when analyzing genome-wide sequence data.
Sustainability index of micro finance institutions (MFIs) and contributory factors
Authors: Bhanot Disha , Bapat Varadraj 
Published: March 2015

Purpose
– The purpose of this paper is to conceptualize the sustainability of micro finance institutions (MFIs) in a holistic manner. The idea is to create an index of sustainability for MFIs which includes financial and outreach aspects of sustainability. Further, it also discerns the factors which contribute to high (low) sustainability scores of MFIs.

Design/methodology/approach
– Data on Indian MFIs was collected from Microfinance Information Exchange database. Using the technique of order preference by similarity to ideal solution (TOPSIS), an Index of sustainability is built by aggregating multiple indicators (operational self-sufficiency ratio, the average loan balance per borrower and the number of active borrowers) to arrive at composite sustainability score of MFIs. Contributory factors of sustainability were identified using a multiple regression model.

Findings
– The sustainability score for MFIs ranges from a maximum score of 0.80 to a minimum of 0.26. Gross loan portfolio, No. of borrower per staff member, portfolio at risk>30 days and return on assets, are significant contributors to sustainability scores of Indian MFIs.

Practical implications
– The index of sustainability is a useful tool to rank the MFIs on a multi-dimensional construct of sustainability. The study also helps to unravel factors that significantly contribute to sustainability of Indian MFIs.

Originality/value
– This study is novel in its attempt to measure sustainability in a holistic fashion by focussing not just on the financial performance of the MFI but also on outreach dimensions. It is also unique in its approach to adopt a multi criteria decision-making technique of TOPSIS to measure sustainability of Indian MFIs.
Gender and other repayment determinants of microfinancing in Indonesia and Sri Lanka
Authors: Nanayakkara Gemunu , Stewart Jenny 
Published: March 2015

Purpose– The repayment performance of microfinancing loans funded by donors amounting to hundreds of millions of dollars is an important issue, because it indicates the effectiveness of utilising these funds to alleviate poverty. The purpose of this paper is to develop models to predict the repayment success of microfinancing loans.Design/methodology/approach– Analysing data relating to 1,109 random loan records from Indonesia and Sri Lanka, the study develops models to predict the repayment probability of microfinancing loans using logistic regression.Findings– There are significant differences between the two countries. In Sri Lanka, the time to approve and disburse the loan, loan cycle, gender and age of the borrower, whether a group or individual borrower, the purpose for which the loan is used and visiting frequency by the loan officers were found to be significant when predicting the repayment. Only three factors were significant in Indonesia: time to approve and disburse the loan, interest repayment frequency and gender. Both models have over 70 per cent prediction accuracy.Originality/value– The models developed can be used in the loan appraisal stage to improve the repayment performance of microfinancing institutions saving hundreds of millions of dollars in bad debt write offs.
Financial service outreach correlates
Authors: Nkundabanyanga Stephen Korutaro , Opiso Julius , Balunywa Waswa , Nkote Isaac Nabeeta 
Published: March 2015

Purpose– The purpose of this paper is to establish the relationship between managerial competence, managerial risk-taking behaviour and financial service outreach of microfinance institutions (MFIs).Design/methodology/approach– In this cross-sectional and correlational study, the authors surveyed 52 branches of MFIs from a population of 60 branches of 20 MFIs in eastern Uganda. Two respondents, a branch manager and a senior loan officer, were the units of enquiry for each branch. The authors put forward and tested four hypotheses relating to the significance of the relationship between perceived managerial competence, risk-taking behaviour and financial service outreach using SPSS version 20. The authors established the hypothesized relationships using Pearson correlation coefficients and obtain a mediating effect of risk-taking behaviour using partial corrections and regression analysis.Findings– The results suggest positive and significant relationships between perceived managerial competence, risk-taking behaviour and financial service outreach. However, while the direct relationship between managerial competence and financial service outreach without the mediation effect of risk-taking behaviour of managers was found to be significant, its magnitude reduces when mediation of risk-taking behaviour is allowed. Thus the entire effect does not only go through managerial competence but majorly also, through risk-taking behaviour of managers.Research limitations/implications– This study did not control for environmental factors such as laws and regulations. As such the model may have been under fitted. Nevertheless, the study has introduced a clearer understanding that outreach performance in MFIs rests with competent managers in strategic positions operating in synergy with their risk-taking behaviour. The study informs policy makers that outreach performance of the MFIs depends on the quality of the competence managers have in addition to their risk-taking propensities.Practical implications– Efforts by the stakeholders to improve financial service outreach must be matched with appropriate competences and risk-taking behaviour of managers.Originality/value– The results contribute to extant literature by investigating two explanatory variables for financial service outreach and provide initial evidence of the mediating effect of intrinsic high risk-taking behaviour of managers. Results add to the conceptual improvement in risk-taking behaviour and lend considerable support for the behavioural perspective in the study of financial service outreach of MFIs.
Natural experiments and debt-driven financial crises: mortgage finance booms in the 1920s and 2000s
Authors: Leathers Charles G. , Raines J. Patrick , Richardson-Bono Heather R. 
Published: March 2015

Purpose
– The role of debt in episodes of financial stability is a topic of increasing important as the global economy struggles to recover from the worst crisis since the Great Depression of the 1930s. The purpose of this paper is to examine the mortgage finance booms of the 1920s and 2000s as natural experiments, new insights into debt-driven financial crises are gained.

Design/methodology/approach
– The general methodology is interpreting anomalous historical events as natural experiments. The specific methodology is the approach to natural experiments provided by Joseph A. Schumpeter and Milton Friedman. The hypothesis tested is that laxity in lending standards was the prime contributor to the mortgage debt booms. In each case, we explain why factors other than laxity in lending standards would be secondary factors, with the pre-boom and post-boom lending standards providing the control groups of natural experiments. The two episodes of mortgage debt booms occurring under very different general economic and financial conditions provide an especially strong test of the hypothesized functional relationship.

Findings
– The results of the two natural experiments support the hypothesis that lax lending standards were the prime contributors to the two episodes of debt-driven financial crisis.

Originality/value
– From a social economics perspective, the insights gained are important because a major social goal has been to encourage greater opportunities for home ownership. The results of these natural experiments provide guidance for policymakers in the search for a viable balance between achieving that social goal and maintaining financial stability.
The long run impact of immigration on labor market in an advanced economy
Authors: Islam Faridul , Khan Saleheen 
Published: March 2015

Purpose– The purpose of this paper is to examine the dynamic relationship among immigration rate, GDP per capita, and and real wage rates in the USA.Design/methodology/approach– The paper implements the Johansen-Juselius (1990, 1992) cointegration technique to test for a long-run relationship; and for short-run dynamics the authors apply Granger causality tests under the vector error-correction model.Findings– The results show that the long-run causality runs from GDP per capita to immigration, not vice versa. Growing economy attracts immigrants. The authors also find that immigration flow depresses average weekly earnings of the natives in the long-run.Originality/value– The authors are not aware of any study on the USA addressing the impact of immigrants on labor market using a tripartite approach by explicitly incorporating economic growth. It is therefore important to pursue a theoretically justified empirical model in search of a relation to resolve on apparent immigration debate.