bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of physical interactions between genomic regions by enChIP-Seq
Authors: Fujita Toshitsugu , Yuno Miyuki , Suzuki Yutaka , Sugano Sumio , Fujii Hodaka 
Published: January 2016

AbstractPhysical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. However, the methods for confidently detecting physical interactions between genomic regions remain limited. Here, we demonstrate the feasibility of using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) in combination with next-generation sequencing (NGS) (enChIP-Seq) to detect such interactions. In enChIP-Seq, the target genomic region is captured by an engineered DNA-binding complex, such as a CRISPR system consisting of a catalytically inactive form of Cas9 (dCas9) and a single guide RNA (sgRNA). Subsequently, the genomic regions that physically interact with the target genomic region in the captured complex are sequenced by NGS. Using enChIP-Seq, we found that the 5’HS5 locus, which regulates expression of theβ-globingenes, interacts with multiple genomic regions upon erythroid differentiation in the human erythroleukemia cell line K562. Genes near the genomic regions inducibly associated with the 5’HS5 locus were transcriptionally up-regulated in the differentiated state, suggesting the existence of a coordinated transcription mechanism directly or indirectly mediated by physical interactions between these loci. Our data suggest that enChIP-Seq is a potentially useful tool for detecting physical interactions between genomic regions in a non-biased manner, which would facilitate elucidation of the molecular mechanisms underlying regulation of genome functions.
Inferring population size history from large samples of genome wide molecular data - an approximate Bayesian computation approach
Authors: Boitard Simon , Rodríguez Willy , Jay Flora , Mona Stefano , Austerlitz Frédéric 
Published: January 2016

AbstractInferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.
De novoGenome Assembly ofGeosmithia morbida, the Causal Agent of Thousand Cankers Disease
Authors: Aggarwal Taruna , Westbrook Anthony , Broders Kirk , Woeste Keith , MacManes Matthew D 
Published: January 2016

Background: Geosmithia morbida is a filamentous ascomycete that causes Thousand Cankers Disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle.Results: We present the first de novo draft genome of G. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins in G. morbida are homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted.Conclusions: Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops. G. morbida is one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome of G. morbida serves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within the Geosmithia genus.
Rare loss-of-function variants inKMT2Fare associated with schizophrenia and developmental disorders
Authors: Singh Tarjinder , Kurki Mitja I. , Curtis David , Purcell Shaun M. , Crooks Lucy , McRae Jeremy , Suvisaari Jaana , Chheda Himanshu , Blackwood Douglas , Breen Gerome , Pietiläinen Olli , Gerety Sebastian S. , Ayub Muhammad , Blyth Moira , Cole Trevor , Collier David , Coomber Eve L. , Craddock Nick , Daly Mark J. , Danesh John , DiForti Marta , Foster Alison , Freimer Nelson B. , Geschwind Daniel , Johnstone Mandy , Joss Shelagh , Kirov Georg , Körkkö Jarmo , Kuismin Outi , Holmans Peter , Hultman Christina M. , Iyegbe Conrad , Lönnqvist Jouko , Männikkö Minna , McCarroll Steve A. , McGuffin Peter , McIntosh Andrew M. , McQuillin Andrew , Moilanen Jukka S. , Moore Carmel , Murray Robin M. , Newbury-Ecob Ruth , Ouwehand Willem , Paunio Tiina , Prigmore Elena , Rees Elliott , Roberts David , Sambrook Jennifer , Sklar Pamela , St. Clair David , Veijola Juha , Walters James T. R. , Williams Hywel ,   Swedish Schizophrenia Study,   INTERVAL Study,   DDD Study,   UK10K Consortium, Sullivan Patrick F. , Hurles Matthew E. , O'Donovan Michael C. , Palotie Aarno , Owen Michael J. , Barrett Jeffrey C. 
Published: January 2016

AbstractSchizophrenia is a common, debilitating psychiatric disorder with a substantial genetic component. By analysing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls, and 1,077 parent-proband trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants inKMT2Fand risk for schizophrenia. In this dataset, we observed threede novoLoF mutations, seven LoF variants in cases, and none in controls (P = 3.3x10−9). To search for LoF variants inKMT2Fin individuals without a known neuropsychiatric diagnosis, we examined the exomes of 45,376 individuals in the ExAC database and found only two heterozygous LoF variants, showing thatKMT2Fis significantly depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carryingKMT2FLoF variants also had varying degrees of learning difficulties. We further identified fourKMT2FLoF carriers among 4,281 children with diverse, severe, undiagnosed developmental disorders, and two additional carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations show that LoF variants inKMT2Fcause a range of neurodevelopmental disorders, including schizophrenia. Combined with previous common variant evidence, we more generally implicate epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, as an important mechanism in the pathogenesis of schizophrenia.
Variation in the molecular clock of primates
Authors: Moorjani Priya , Amorim Carlos Eduardo G. , Arndt Peter F. , Przeworski Molly 
Published: January 2016

AbstractEvents in primate evolution are often dated by assuming a “molecular clock”, i.e., a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life-history traits, suggesting that it should also be found among primates. Motivated by these considerations, we analyze whole genomes from ten primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs) and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are ˜65% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are ˜2% higher in chimpanzees and ˜7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however: in particular, transitions at CpG sites exhibit a more clock-like behavior than do other types, presumably due to their non-replicative origin. Thus, not only the total rate, but also the mutational spectrum varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate that the average time to the most recent common ancestor of human and chimpanzee is 12.1 million years and their split time 7.9 million years.Significance statementMuch of our understanding of the chronology of human evolution relies on the “molecular clock”, i.e., a constant rate of substitutions per unit time. To evaluate the validity of this assumption, we analyze whole genome sequences from ten primate species. We find that there is substantial variation in the molecular clock between apes and monkeys, and rates even differ within hominoids. Importantly, not all mutation types behave similarly: notably, transitions at CpG sites exhibit a more clock-like behavior than other substitutions, presumably due to their non-replicative origin. Thus, the mutation spectra, and not just the overall substitution rates, are changing across primates. This finding further suggests that events in primate evolution are most reliably dated using CpG transitions.
Comparing the Citation Performance of PNAS Papers by Submission Track
Authors: Davis Philip M. 
Published: January 2016

AbstractPurpose:To determine whether papers contributed by National Academy of Sciences (NAS) members perform differently than direct submissions.Data/Methods:55,889 original papers published inPNASfrom 1997 through 2014. Regression analysis measuring total citations, controlling for editorial track (Contributed, Direct, Communicated), date of publication, and paper topic.Main findings:Contributed papers consistently underperformed against Direct submissions, receiving 9% fewer citations,ceteris paribus. The effect was greatest for Social Sciences papers (12% fewer citations). Nonetheless, the main effect has attenuated over the past decade, from 13.6% fewer citations in 2005 to just 2.2% fewer citations in 2014.Significance:Successive editorial policies placing limits, restrictions, and other qualifications on the publication privileges of NAS members may be responsible for the submission of better performing Contributed papers.
Advances in two photon scanning and scanless microscopy technologies for functional neural circuit imaging
Authors: Schultz Simon R. , Copeland Caroline S. , Foust Amanda J. , Quicke Peter , Schuck Renaud 
Published: January 2016

AbstractRecent years have seen substantial developments in technology for imaging neural circuits, raising the prospect of large scale imaging studies of neural populations involved in information processing, with the potential to lead to step changes in our understanding of brain function and dysfunction. In this article we will review some key recent advances: improved fluorophores for single cell resolution functional neuroimaging using a two photon microscope; improved approaches to the problem ofscanningactive circuits; and the prospect ofscanlessmicroscopes which overcome some of the bandwidth limitations of current imaging techniques. These advances in technology for experimental neuroscience have in themselves led to technical challenges, such as the need for the development of novel signal processing and data analysis tools in order to make the most of the new experimental tools. We review recent work in some active topics, such as region of interest segmentation algorithms capable of demixing overlapping signals, and new highly accurate algorithms for calcium transient detection. These advances motivate the development of new data analysis tools capable of dealing with spatial or spatiotem-poral patterns of neural activity, that scale well with pattern size.
Linking apple farmers to markets
Authors: Ma Wanglin , Abdulai Awudu 
Published: January 2016

Purpose
– The purpose of this paper is to investigate the determinants of marketing contract choices including written contracts, oral contracts and no contracts, as well as to examine the impact of marketing contracts on net returns from apple production in China.

Design/methodology/approach
– A two-stage selection correction approach (Bourguignon, Fournier, and Gurgand (BFG)) for the multinomial logit model is employed to estimate the impact of marketing contracts on net returns from apple production. On the basis of the BFG estimation, the authors also use an endogenous switching regression model and a propensity score matching technique to estimate the causal effects of marketing contract choices on net returns from apple production.

Findings
– The results reveal significant selectivity correction terms in the choices of both written contracts and no contracts and insignificant selectivity correction terms in the choice of oral contract, indicating that accounting for selection bias is a prerequisite for unbiased and consistent estimation. The findings also indicate written contracts increase apple farmers’ net returns, while oral contracts exert the opposite effect.

Originality/value
– To the best of the authors’ knowledge, this study is the first to examine the impact of marketing contract choices on net returns from apple production, accounting for selectivity effects.
An economic analysis on intergenerational lock-in effects of belief in rural China
Authors: Ruan Rongping , Xiuhua Wang , Zheng Fengtian 
Published: January 2016

Purpose– Rural China has been undergoing the “religion fever” since the Reform and Opening-up. By comparing the intergenerational lock-in effects of religious belief with that of non-religious belief, the purpose of this paper is to explain why more and more peasants convert to religion especially Christianity in China.Design/methodology/approach– Data used in this paper comes from a field survey conducted in villages, Funan county. The samples were obtained by the two-stage cluster probability proportional sampling method. Based on the collected survey data, econometric model on the intergenerational lock-in effects of belief was constructed and used for analysis.Findings– Compared with non-religious believers, religious believers can transmit their beliefs more successfully. In addition, the intergenerational lock-in effects of religious beliefs is weakened by oblique socialization in contemporary rural China.Originality/value– This is the first paper focussing on intergenerational transmission of belief in rural China; although many researchers did careful analyses on effects of parents’ belief or religiosity on children’s belief or religiosity in the West, few of them compared the success of intergenerational transmission between different beliefs. This paper fills this gap; as an interdisciplinary study, this paper tries to study religion in economics analysis approaches. This attempt extends research field in Economics and at the same time enriches analysis tools in Religion.
Can poor farmers afford higher micro-credit interest rates than the un-poor?
Authors: Tan Xiaoping , lin Wanlong 
Published: January 2016

Purpose
– The purpose of this paper is to test whether there is higher return rate of investment for poor farmers than for un-poor farmers and to discuss its implication for poverty reduction microcredit rate policy.

Design/methodology/approach
– By using the household-level data of six provinces of China, farmer household production function is used in this paper to estimate the investment return rate of farmer.

Findings
– The paper indicates that regardless which kind of grouping standard is adopted, the investment return rates of poor farmer households in general are far lower than the non-poor. In general, the richer a farmer household, the higher is the return rate of his household productive operations.

Practical implications
– The study of this paper reminds policy makers that poverty reduction microcredit rate should really take endurance capacity of poor farmers for credit rate into accounting because of the low return rate of their family investment. Exorbitant credit rate should be avoided to protect the credit right of poor farmers.

Originality/value
– There is seldom study on the comparison of return rates of family operation investment between poor and un-poor farmers; there is also unenough empirical study on the rationality of high interest rate on poor households from the return rate of investment point of view. The authors expect this paper will have some contribution on these two points.
A fresh look at calorie-income elasticities in China
Authors: Nie Peng , Sousa-Poza Alfonso 
Published: January 2016

Purpose
– The purpose of this paper is to use data from the 1991 to 2009 China Health and Nutrition Survey (CHNS) to analyze how income in China is related to calorie intake.

Design/methodology/approach
– The paper employs a variety of parametric, nonparametric, and semiparametric methods for cross-sectional and panel data, and estimates calorie-income elasticities for adults aged 18-60.

Findings
– The calorie-income elasticities are generally small, ranging from −0.031 to 0.022. In addition, the results show no clear nonlinearity, regardless of whether parametric, nonparametric, or semiparametric approaches are used.

Originality/value
– Using a wealth of estimation techniques, including parametric, nonparametric, and semiparametric approaches, this paper addresses some of the main methodological challenges encountered in estimating calorie-income elasticities. The magnitudes of calorie-income elasticities have policy implications especially with regards to the effectiveness of income-mediated policies aimed at combating food insecurity in China.
Maternity-care: measuring women’s perceptions
Authors: Clark Kim , Beatty Shelley , Reibel Tracy 
Published: January 2016

Purpose
– Achieving maternity-care outcomes that align with women’s needs, preferences and expectations is important but theoretically driven measures of women’s satisfaction with their entire maternity-care experience do not appear to exist. The purpose of this paper is to outline the development of an instrument to assess women’s perception of their entire maternity-care experience.

Design/methodology/approach
– A questionnaire was developed on the basis of previous research and informed by a framework of standard service quality categories covering the spectrum of typical consumer concerns. A pilot survey with a sample of 195 women who had recent experience of birth was undertaken to establish valid and reliable scales pertaining to different stages of maternity care. Exploratory factor analysis was used to interpret scales and convergent validity was assessed using a modified version of the Client Satisfaction Questionnaire.

Findings
– Nine theoretically informed, reliable and valid stand-alone scales measuring the achievement of different dimensions of women’s expectancies of public maternity care were developed. The study scales are intended for use in identifying some potential areas of focus for quality improvement in the delivery of maternity care.

Research limitations/implications
– Reliable and valid tools for monitoring the extent to which services respond to women’s expectations of their entire maternity care form part of the broader toolkit required to adequately manage health-care quality. This study offers guidance on the make-up of such tools.

Originality/value
– The scales produced from this research offer a means to assess maternity care across the full continuum of care and are brief and easy to use.
Environmental sustainability in European public healthcare
Authors: Chiarini Andrea , Vagnoni Emidia 
Published: January 2016

Purpose
– The purpose of this paper is to enlarge the debate concerning the influence of leadership on environmental sustainability implementation in European public healthcare organisations.

Design/methodology/approach
– This paper is a viewpoint. It is based on preliminary analysis of European standards dedicated to environmental sustainability and their spread across Europe in public healthcare organisations. Viewpoints concerning leadership are then discussed and asserted.

Findings
– This paper found a limited implementation of standards such as Green Public Procurement criteria, Eco-Management and Audit Scheme and ISO 14001 in public healthcare. Some clues indicate that the lack of implementation is related to leadership and management commitment.

Originality/value
– For the first time, this paper investigates relationships between leadership and environmental sustainability in European public healthcare opening further avenues of research on the subject.
Female aspirant human resources’ entrepreneurial orientation
Authors: Kundu Subhash C. , Rani Sunita 
Published: January 2016

Purpose– The main purpose of the study was to assess the entrepreneurial orientation based on personality and attitude of female aspirant human resources in India.Design/methodology/approach– For collecting primary data, the scale on entrepreneurial attitude orientation developed by Robinsonet al.(1991) was used. Statistical tools such as correlations, analysis of variance, means, grand means, standard deviations and percentages were used for the analysis of the primary data gathered from 500 female respondents.Findings– The results showed the highest score of the female respondents on the achievement motivation as compared to other three personality descriptors and lowest but positive score on the self-esteem dimension. Among attitude components, the cognition had emerged as highest. MBAs showed comparatively less entrepreneurial orientation than other categories of female aspirants. Results indicated that lower age, lower educational qualifications and high socioeconomic status supported the entrepreneurship.Research limitations/implications– The study was limited to only four personality traits and three attitude components. Another limitation of the study was that the data were collected from North India that could have been collected from the wider area.Practical implications– The study will be helpful to the female aspirant participants to decide whether to choose managerial or entrepreneurial careers. By taking cues from this study, educators can build curriculum and develop programs to encourage and empower future female entrepreneurs.Originality/value– Inclusion of Indian female aspirants of different backgrounds will definitely add value to the existing knowledge, management theory and practice.