bluuebunny/crossref_metadata_2025_split huggingface dataset:
PsyGeNET: a knowledge platform on psychiatric disorders and their genes
Authors: Gutiérrez-Sacristán Alba , Grosdidier Solène , Valverde Olga , Torrens Marta , Bravo Àlex , Piñero Janet , Sanz Ferran , Furlong Laura I. 
Published: May 2015

Abstract
Summary: PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of a database and a web interface supporting data search, visualization, filtering and sharing. PsyGeNET integrates information from DisGeNET and data extracted from the literature by text mining, which has been curated by domain experts. It currently contains 2642 associations between 1271 genes and 37 psychiatric disease concepts. In its first release, PsyGeNET is focused on three psychiatric disorders: major depression, alcohol and cocaine use disorders. PsyGeNET represents a comprehensive, open access resource for the analysis of the molecular mechanisms underpinning psychiatric disorders and their comorbidities.
Availability and implementation: The PysGeNET platform is freely available at http://www.psygenet.org/. The PsyGeNET database is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/).
Contact: lfurlong@imim.es
Supplementary information: Supplementary data are available at Bioinformatics online.
International collaboration and science in China: a Western perspective
Authors: Qiu Jane 
Published: May 2015

Abstract
As China is making great strides in economic development and innovative capacity, it has become an increasingly important player in major international scientific projects. But its role largely depends on the areas of research and can vary greatly—from being mainly a supplier of raw data to having genuine intellectual input. Last year, a panel of Chinese scientists had a heated debate over how China can get the most out of international collaboration, what government's role should be, and how Chinese scientists could go beyond the mainstream science (National Science Review 2014, 1: 318–21). In the second of a series of forums organized by NSR on the topic, its executive associate editor Mu-ming Poo discusses these issues with four leading scientists in Europe and the United States.

Jeremy Farrar
An expert on infectious diseases and Director of the Wellcome Trust in London, UK

Harrald Fuchs
Material scientist at the University Münster and Director of the Center for Nanotechnology (CeNTech), Germany

Jian Lin
Marine geophysicist at the Woods Hole Oceanographic Institution in Massachusetts, USA

Christopher White
Particle physicist and Vice Provost for academic affairs at the Illinois Institute of Technology, USA

Mu-ming Poo (Chair)
Neuroscientist and Director of the Institute of Neurosciences, Chinese Academy of Sciences, in Shanghai
Whole genome analysis of an extended pedigree with Prader–Willi Syndrome, hereditary hemochromatosis, and dysautonomia-like symptoms
Authors: Fang Han , Wu Yiyang , Yoon Margaret , Jiménez-Barrón Laura T. , O’Rawe Jason A. , Highnam Gareth , Mittelman David , Lyon Gholson J. 
Published: May 2015

ABSTRACTThis report includes the discovery and analysis of a pedigree with Prader–Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms. Nine members of the family participated in whole genome sequencing (WGS), which enabled a wide scope of variant calling from single-nucleotide polymorphisms to copy number variations. First, a 5.5 Mbde novodeletion is identified in the chromosome region 15q11.2 to 15q13.1 in the boy with PWS. Second, a female invididual with HH is homozygous for the p.C282Y variant inHFE, a mutation known to be associated with HH. Her brother is homozygous for the same variant, although he has yet to be clinically diagnosed with HH. Third, none of the people with dysautonomia-like symptoms carry any reported or novel rare variants inIKBKAPthat are implicated in familial dysautonomia (FD - HSAN III). Although two people with dysautonomia-like symptoms carry two heterozygous variants inNTRK1, a gene that has been shown to contribute to HSAN IV (congenital insensitivity to pain with anhidrosis, a disease that closely resembles FD), this variant is not present in the third proband. Fourth, WGS revealed pharmacogenetic variants influencing the metabolism of warfarin and simvastatin, which are being routinely prescribed to the proband. Finally, reports of the phenotypes were standardized with the Human Phenotype Ontology annotation, which may facilitate the search for other families with similar phenotypes. Due to the extreme heterogeneity and insufficient knowledge of human diseases, it is of crucial importance that both phenotypic data and genomic data are standardized and shared.
Genome Wide Variant Analysis of Simplex Autism Families with an Integrative Clinical-Bioinformatics Pipeline
Authors: Jiménez-Barrón Laura T. , O’Rawe Jason A. , Wu Yiyang , Yoon Margaret , Fang Han , Iossifov Ivan , Lyon Gholson J. 
Published: May 2015

AbstractAutism spectrum disorders (ASD) are a group of developmental disabilities that affect social interaction, communication and are characterized by repetitive behaviors. There is now a large body of evidence that suggests a complex role of genetics in ASD, in which many different loci are involved. Although many current population scale genomic studies have been demonstrably fruitful, these studies generally focus on analyzing a limited part of the genome or use a limited set of bioinformatics tools. These limitations preclude the analysis of genome-wide perturbations that may contribute to the development and severity of ASD-related phenotypes. To overcome these limitations, we have developed and utilized an integrative clinical and bioinformatics pipeline for generating a more complete and reliable set of genomic variants for downstream analyses. Our study focuses on the analysis of three simplex autism families consisting of one affected child, unaffected parents, and one unaffected sibling. All members were clinically evaluated and widely phenotyped. Genotyping arrays and whole genome sequencing were performed on each member, and the resulting sequencing data were analyzed using a variety of available bioinformatics tools. We searched for rare variants of putative functional impact that were found to be segregating according to de-novo, autosomal recessive, x-linked, mitochondrial and compound heterozygote transmission models. The resulting candidate variants included three small heterozygous CNVs, a rare heterozygousde novononsense mutation inMYBBP1Alocated within exon 1, and a novelde novomissense variant inLAMB3. Our work demonstrates how more comprehensive analyses that include rich clinical data and whole genome sequencing data can generate reliable results for use in downstream investigations. We are moving to implement our framework for the analysis and study of larger cohorts of families, where statistical rigor can accompany genetic findings.
Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies
Authors: Palacios Julia A. , Wakeley John , Ramachandran Sohini 
Published: May 2015

AbstractSophisticated inferential tools coupled with the coalescent model have recently emerged for estimating past population sizes from genomic data. Accurate methods are available for data from a single locus or from independent loci. Recent methods that model recombination require small sample sizes, make constraining assumptions about population size changes, and do not report measures of uncertainty for estimates. Here, we develop a Gaussian process-based Bayesian nonparametric method coupled with a sequentially Markov coalescent model which allows accurate inference of population sizes over time from a set of genealogies. In contrast to current methods, our approach considers a broad class of recombination events, including those that do not change local genealogies. We show that our method outperforms recent likelihood-based methods that rely on discretization of the parameter space. We illustrate the application of our method to multiple demographic histories, including population bottlenecks and exponential growth. In simulation, our Bayesian approach produces point estimates four times more accurate than maximum likelihood estimation (based on the sum of absolute differences between the truth and the estimated values). Further, our method’s credible intervals for population size as a function of time cover 90 percent of true values across multiple demographic scenarios, enabling formal hypothesis testing about population size differences over time. Using genealogies estimated withARGweaver, we apply our method to European and Yoruban samples from the 1000 Genomes Project and confirm key known aspects of population size history over the past 150,000 years.
Down-Regulating the Expression of 53 Soybean Transcription Factor Genes Uncovers a Role for SPEECHLESS in Initiating Stomatal Cell Lineages during Embryo Development
Authors: Danzer John , Mellott Eric , Bui Anhthu Q. , Le Brandon H. , Martin Patrick , Hashimoto Meryl , Perez-Lesher Jeanett , Chen Min , Pelletier Julie M. , Somers David A. , Goldberg Robert B. , Harada John J. 
Published: May 2015

Abstract
We used an RNA interference screen to assay the function of 53 transcription factor messenger RNAs (mRNAs) that accumulate specifically within soybean (Glycine max) seed regions, subregions, and tissues during development. We show that basic helix-loop-helix (bHLH) transcription factor genes represented by Glyma04g41710 and its paralogs are required for the formation of stoma in leaves and stomatal precursor complexes in mature embryo cotyledons. Phylogenetic analysis indicates that these bHLH transcription factor genes are orthologous to Arabidopsis (Arabidopsis thaliana) SPEECHLESS (SPCH) that initiate asymmetric cell divisions in the leaf protoderm layer and establish stomatal cell lineages. Soybean SPCH (GmSPCH) mRNAs accumulate primarily in embryo, seedling, and leaf epidermal layers. Expression of Glyma04g41710 under the control of the SPCH promoter rescues the Arabidopsis spch mutant, indicating that Glyma04g41710 is a functional ortholog of SPCH. Developing soybean embryos do not form mature stoma, and stomatal differentiation is arrested at the guard mother cell stage. We analyzed the accumulation of GmSPCH mRNAs during soybean seed development and mRNAs orthologous to MUTE, FAMA, and INDUCER OF C-REPEAT/DEHYDRATION RESPONSIVE ELEMENT-BINDING FACTOR EXPRESSION1/SCREAM2 that are required for stoma formation in Arabidopsis. The mRNA accumulation patterns provide a potential explanation for guard mother cell dormancy in soybean embryos. Our results suggest that variation in the timing of bHLH transcription factor gene expression can explain the diversity of stomatal forms observed during plant development.
Inference of the Arabidopsis Lateral Root Gene Regulatory Network Suggests a Bifurcation Mechanism That Defines Primordia Flanking and Central Zones
Authors: Lavenus Julien , Goh Tatsuaki , Guyomarc’h Soazig , Hill Kristine , Lucas Mikael , Voß Ute , Kenobi Kim , Wilson Michael H. , Farcot Etienne , Hagen Gretchen , Guilfoyle Thomas J. , Fukaki Hidehiro , Laplaze Laurent , Bennett Malcolm J. 
Published: May 2015

Abstract
A large number of genes involved in lateral root (LR) organogenesis have been identified over the last decade using forward and reverse genetic approaches in Arabidopsis thaliana. Nevertheless, how these genes interact to form a LR regulatory network largely remains to be elucidated. In this study, we developed a time-delay correlation algorithm (TDCor) to infer the gene regulatory network (GRN) controlling LR primordium initiation and patterning in Arabidopsis from a time-series transcriptomic data set. The predicted network topology links the very early-activated genes involved in LR initiation to later expressed cell identity markers through a multistep genetic cascade exhibiting both positive and negative feedback loops. The predictions were tested for the key transcriptional regulator AUXIN RESPONSE FACTOR7 node, and over 70% of its targets were validated experimentally. Intriguingly, the predicted GRN revealed a mutual inhibition between the ARF7 and ARF5 modules that would control an early bifurcation between two cell fates. Analyses of the expression pattern of ARF7 and ARF5 targets suggest that this patterning mechanism controls flanking and central zone specification in Arabidopsis LR primordia.
HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis
Authors: Qiu Yongjian , Li Meina , Pasoreck Elise K. , Long Lingyun , Shi Yiting , Galvão Rafaelo M. , Chou Conrad L. , Wang He , Sun Amanda Y. , Zhang Yiyin C. , Jiang Anna , Chen Meng 
Published: May 2015

Abstract
Phytochromes (phys) are red and far-red photoreceptors that control plant development and growth by promoting the proteolysis of a family of antagonistically acting basic helix-loop-helix transcription factors, the PHYTOCHROME-INTERACTING FACTORs (PIFs). We have previously shown that the degradation of PIF1 and PIF3 requires HEMERA (HMR). However, the biochemical function of HMR and the mechanism by which it mediates PIF degradation remain unclear. Here, we provide genetic evidence that HMR acts upstream of PIFs in regulating hypocotyl growth. Surprisingly, genome-wide analysis of HMR- and PIF-dependent genes reveals that HMR is also required for the transactivation of a subset of PIF direct-target genes. We show that HMR interacts with all PIFs. The HMR-PIF interaction is mediated mainly by HMR's N-terminal half and PIFs’ conserved active-phytochrome B binding motif. In addition, HMR possesses an acidic nine-amino-acid transcriptional activation domain (9aaTAD) and a loss-of-function mutation in this 9aaTAD impairs the expression of PIF target genes and the destruction of PIF1 and PIF3. Together, these in vivo results support a regulatory mechanism for PIFs in which HMR is a transcriptional coactivator binding directly to PIFs and the 9aaTAD of HMR couples the degradation of PIF1 and PIF3 with the transactivation of PIF target genes.
Economic welfare as ethical concept and economic policy
Authors: Merrill David 
Published: May 2015

Purpose– Paper argues that the proper approach to the topic of economic welfare should include an appreciation that markets are not characterized by an endogenous tendency towards equilibrium. The economists, Schumpeter, Keynes and Minsky are right in this regard as opposed to Adam Smith and contemporary economic orthodoxy. However, today’s liberal political theories largely assumes the tendency towards equilibrium and so are inadequate to deal with economic issues such as economic welfare which arise in conditions of non-equilibrium. The purpose of this paper is to propose Winfield’s reconstruction of Hegel’s social philosophy as more fitted to deal with market realities.Design/methodology/approach– Paper starts with a debate within economics and uses it as a basis to evaluate different schools of normative philosophy. Paper concludes by showing how the preferred philosophy is capable to rule between different economic policies responding to economic disequilibrium.Findings– Hegelian philosophy has capacity to adjudicate between economic policies to resolve market failure that contemporary liberal theory lacks.Practical implications– Paper provides the ethical justification for economic policies that have heretofore only been recommend by economists.Originality/value– Paper points to the largely overlooked fact that most contemporary political theory assumes market equilibrium. Paper argues that Hegelian philosophy provides the ethical justification for certain post-Keynesian economic policies, a position no one else is making.
Practice-integrated care teams – learning for a better future
Authors: Beacon Angela 
Published: May 2015

Purpose
– The purpose of this paper is to present a case study of one element of the integrated work which has taken place in Central Manchester, the development of multi-disciplinary Practice-Integrated Care Teams (PICT). The paper will show how working together has become a practical reality for members of these teams, and is forming the building blocks for further integration across neighbourhoods.

Design/methodology/approach
– This paper draws on the author’s experience of working in the PICT project from 2012 to 2014. The report will draw on the evaluation work which took place during the project, and will include reflections from others involved in the project and members of the teams.

Findings
– The integrated care teams which have been developed in Central Manchester have started to make significant changes to the ways that professionals work together, to the experience that patients have and to the costs of urgent care provision. Whilst there is still a long way to go, there has been significant learning from the PICT. This includes improved patient outcomes and experience. There has been an overall reduction in secondary care activity for patients the teams have been working with, with the largest reduction being in emergency admissions. Alongside this, patient feedback has reinforced the value of this personalised approach and increased overall satisfaction with the care and advice received from health and social care professionals and an improved professional experience. Evaluation has demonstrated that amongst professionals involved in the team there is a strong commitment to the principles of integrated care and that the confidence, skills and capacity of the teams have strengthened since this way of working has been introduced. As monitoring of financial impact continues to develop, cost savings from secondary care, particularly around emergency unplanned care, are encouraging.

Originality/value
– This paper draws on the recent experience of designing and delivering integrated care across a range of multi-agency, multi-professional partners. The model which has been developed centres around the role of general practice, and has enabled primary care to take a key role in the development of an out-of-hospital integrated care system. This has enabled community professionals such as nurses and social workers to build a much stronger relationship with general practice and enable system linkages which will be essential to the delivery of joined-up health and social care in the future. The project has been accompanied by thorough and ongoing evaluation to support the validity of the learnings which have been reported.
New conversations between old players? The relationship between general practice and social care
Authors: Glasby Jon , Miller Robin 
Published: May 2015

Purpose
– With the advent of Clinical Commissioning Groups, the English health system has abolished more managerially led Primary Care Trusts and given greater responsibilities to groups of local general practitioners (GPs). As with all major changes, this brings both opportunities and risks, and the authors know relatively little about what impact this might have on relationships between the NHS and local government. Against this background, the purpose of this paper is to report key findings from a scoping review commissioned by the National Institute of Health Research School for Social Care Research in order to summarise learning from recent literature.

Design/methodology/approach
– The paper is based on a review of the literature on older people’s services and the relationship between general practice and adult social care, published in the UK from 2000 onwards.

Findings
– Despite the longstanding nature of the issues at stake, the review identified only nine relevant studies. These were of mixed quality, and tended to focus on lessons learned from the late 1990s/early 2000s rather than more recent reforms. Overall, these studies suggest similar barriers to those identified in previous policy contexts, and there is a strong sense of relationships starting from a low base (hence the title of our title of “new conversations between old players”).

Research limitations/implications
– This review is based on literature on older people’s services published since 2000 – so only provides a snapshot of the issues at stake. However, it confirms the relatively limited nature of the evidence base and the need for new research to help shape future policy and practice.

Originality/value
– Despite the central contribution of GPs, the authors still know relatively little about the relationship between general practice and adult social care. Reviewing previous literature (however, limited) is crucial to current attempts to develop more effective joint working at local level.
Nutrient limitation of woody debris decomposition in a tropical forest: contrasting effects of N and P addition
Authors: Chen Yao , Sayer Emma J. , Li Zhian , Mo Qifeng , Li Yingwen , Ding Yongzhen , Wang Jun , Lu Xiankai , Tang Jianwu , Wang Faming 
Published: May 2015

Summary

Tropical forests represent a major terrestrial store of carbon (C), a large proportion of which is contained in the soil and decaying organic matter. Woody debris plays a key role in forest C dynamics because it contains a sizeable proportion of total forest C. Understanding the factors controlling the decomposition of organic matter in general, and woody debris in particular, is hence critical to assessing changes in tropical C storage.

We conducted a factorial fertilization experiment in a tropical forest in South China to investigate the influence of nitrogen (N) and phosphorus (P) availability on woody debris decomposition using branch segments (5 cm diameter) of four species (Acacia auriculaeformis, Aphanamixis polystachya, Schefflera octophylla, and Carallia brachiata) in plots fertilized with +N, +P, or +NP, and controls.

Fertilization with +P and +NP increased decomposition rates by 5–53%, and the magnitude was species specific. Contrary to expectations, we observed no negative effect of +N addition on decay rates or mass loss of woody debris in any of the four study species. Decomposition rates of woody debris were higher in species with lower C : P ratios regardless of treatment.

We observed significant accumulation of P in the woody debris of all species in plots fertilized with +P and +NP during the early stages of decomposition. N release from woody debris of Acacia (N‐fixing) was greater in the +P plots towards the end of the study, whereas fertilization with +N had no impact on the patterns of nutrient release during decomposition.

Synthesis: Our results indicate that decomposition of woody debris is primarily constrained by P availability in this tropical forest. However, contrary to expectations, +N addition did not exacerbate P limitation. It is conceivable that decay rates of woody debris in tropical forests can be predicted by C : P or lignin : P ratios, but additional work with more tree species is needed to determine whether the patterns we observed are more generally applicable.