bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-nucleotide and Copy-number variance related to severity of Hypospadias
Authors: Singh Neetu , Gupta Devendra Kumar , Sharma Shilpa , Sahu Dinesh Kumar , Mishra Archana , Yadav Devendra , Rawat Jiledar , Singh Arun K 
Published: March 2018

AbstractThe genetic association of Hypospadias-risk studies has been conducted in Caucasians, Chinese-Han populations and few in Indian populations. Although no comprehensive approach has been followed to assess genetic involvement in the severity of the disorder. The study evaluated to establish the correlation between genotyped SNPs/CNVs and Hypospadias-severity by an association in a total 30 SNPs in genes related to sex hormone-biosynthesis and metabolism; embryonic-development and Phospholipase-D-signalling pathways on 138 surgery-confirmed hypospadias-cases from North-India (84 Penile and 28 cases of Penoscrotal-Hypospadias compared against 31 cases of Glanular+Coronal), and analyzed and identified copy number variants (CNVs) in four Familial samples (18 members) and three paired-sporadic cases (6 samples) using array-based comparative-genomic-hybridization and validated in 32 Hypospadias samples by TaqMan assay. Based on Odds Ratio at 95% CI, Z Statistic and Significance Levels, STS gene-rs17268974 was associated with Penile-Hypospadias and 9-SNPs (seven-SNPs (rs5934740; rs5934842; rs5934913; rs6639811; rs3923341; rs17268974; rs5934937) of STS gene; rs7562326-SRD5A2 and rs1877031-STARD3 were associated with Penoscrotal-Hypospadias. On aggregate analysis with p <0.001, we identified homozygous-loss of Ch7:q34 (PRSS3P2, PRSS2). On validation in previously CNV-characterized and new (32-hypospadias-cases), we identified PRSS3P2-loss in most of the grade 3 and 4 hypospadias. Hence, Grade 1 and 2 (coronal and granular) show no-PRSS3P2-loss and no-association with SNPs in STS; SRD5A2; STARD3-gene but Grade 3 and 4 (Penile and Penoscrotal) show PRSS3P2-loss accompanied with the association of SNPs in STS; SRD5A2; STARD3. Hence, homozygous-loss of PRSS3P2 accompanied with the association of STS; SRD5A2; STARD3 may link to the severity of the disease.
Distinct housing conditions reveal a major impact of adaptive immunity on the course of obesity-induced type 2 diabetes
Authors: Sbierski-Kind Julia , Kath Jonas , Brachs Sebastian , Streitz Mathias , Herrath Matthias v. , Kühl Anja A. , Schmidt-Bleek Katharina , Mai Knut , Spranger Joachim , Volk Hans-Dieter 
Published: March 2018

AbstractObesity is associated with adipose tissue inflammation, insulin resistance and the development of type 2 diabetes. However, our knowledge is mostly based on conventional murine models and promising pre-clinical studies rarely translated into successful therapies.There is a growing awareness of the limitations of studies in laboratory mice, housed in abnormally hygienic specific pathogen-free (SPF) conditions, as relevant aspects of the human immune system remain unappreciated. Here, we assessed the impact of housing conditions on adaptive immunity and metabolic disease processes during high-fat diet. We therefore compared diet-induced obesity in SPF mice with those housed in non-SPF, so called “antigen exposed” (AE) conditions. Surprisingly, AE mice fed a high-fat diet maintained increased insulin levels to compensate for insulin resistance, which was reflected in islet hyperplasia and improved glucose tolerance compared to SPF mice. In contrast, we observed higher proportions of effector/memory T cell subsets in blood and liver of high-fat diet AE mice accompanied by the development of nonalcoholic steatohepatitis-like liver pathology. Thus, our data demonstrate the impact of housing conditions on metabolic alterations. Studies in AE mice, in which physiological microbial exposure was restored, could provide a tool for revealing therapeutic targets for immune-based interventions for type 2 diabetes patients.
GWAS identifies novel risk locus for erectile dysfunction and implicates hypothalamic neurobiology and diabetes in etiology
Authors: Bovijn Jonas , Jackson Leigh , Censin Jenny , Chen Chia-Yen , Laisk-Podar Triin , Laber Samantha , Ferreira Teresa , Glastonbury Craig , Smoller Jordan , Harrison Jamie W , Ruth Katherine S , Beaumont Robin N , Jones Samuel E , Tyrrell Jessica , Wood Andrew R , Weedon Michael N , Mägi Reedik , Neale Benjamin , Lindgren Cecilia M , Murray Anna , Holmes Michael V 
Published: March 2018

AbstractGWAS of erectile dysfunction (ED) in 6,175 cases among 223,805 European men identified one new locus at 6q16.3 (lead variant rs57989773, OR 1.20 per C-allele; p = 5.71×10−14), located between MCHR2 and SIM1. In-silico analysis suggests SIM1 to confer ED risk through hypothalamic dysregulation; Mendelian randomization indicates genetic risk of type 2 diabetes causes ED. Our findings provide novel insights into the biological underpinnings of ED.
Clustered, information-dense transcription factor binding sites identify genes with similar tissue-wide expression profiles
Authors: Lu Ruipeng , Rogan Peter K. 
Published: March 2018

ABSTRACTBackgroundThe distribution and composition ofcis-regulatory modules (e.g. transcription factor binding site (TFBS) clusters) in promoters substantially determine gene expression patterns and TF targets, whose expression levels are significantly regulated by TF binding. TF knockdown experiments have revealed correlations between TF binding profiles and gene expression levels. We present a general framework capable of predicting genes with similar tissue-wide expression patterns from activated or repressed TF targets using machine learning to combine TF binding and epigenetic features.MethodsGenes with correlated expression patterns across 53 tissues were identified according to their Bray-Curtis similarity. DNase I HyperSensitive region (DHS) -accessible promoter intervals of direct TF target genes were scanned with previously derived information theory-based position weight matrices (iPWMs) of 82 TFs. Features from information density-based TFBS clusters were used to predict target genes with machine learning classifiers. The accuracy, specificity and sensitivity of the classifiers were determined for different feature sets. Mutations in TFBSs were also introduced to examine their impact on cluster densities and the regulatory states of predicted target genes.ResultsWe initially chose the glucocorticoid receptor gene (NR3C1), whose regulation has been extensively studied, to test this approach.SLC25A32andTANKwere found to exhibit the most similar expression patterns to this gene across 53 tissues. Prediction of other genes with similar expression profiles was significantly improved by eliminating inaccessible promoter intervals based on DHSs. A Random Forest classifier exhibited the best performance in detecting such coordinately regulated genes (accuracy was 0.972 for training, 0.976 for testing). Target gene prediction was confirmed using CRISPR knockdown data of TFs, which was more accurate than siRNA inactivation. Mutation analyses of TFBSs also revealed that one or more information-dense TFBS clusters in promoters are required for accurate target gene prediction.ConclusionsMachine learning based on TFBS information density, organization, and chromatin accessibility accurately identifies gene targets with comparable tissue-wide expression patterns. Multiple, information-dense TFBS clusters in promoters appear to protect promoters from the effects of deleterious binding site mutations in a single TFBS that would effectively alter the expression state of these genes.
Personalized 3D mannequin reconstruction based on 3D scanning
Authors: Hu PengPeng , Li Duan , Wu Ge , Komura Taku , Zhang Dongliang , Zhong Yueqi 
Published: March 2018

Purpose
Currently, a common method of reconstructing mannequin is based on the body measurements or body features, which only preserve the body size lacking of the accurate body geometric shape information. However, the same human body measurement does not equal to the same body shape. This may result in an unfit garment for the target human body. The purpose of this paper is to propose a novel scanning-based pipeline to reconstruct the personalized mannequin, which preserves both body size and body shape information.

Design/methodology/approach
The authors first capture the body of a subject via 3D scanning, and a statistical body model is fit to the scanned data. This results in a skinned articulated model of the subject. The scanned body is then adjusted to be pose-symmetric via linear blending skinning. The mannequin part is then extracted. Finally, a slice-based method is proposed to generate a shape-symmetric 3D mannequin.

Findings
A personalized 3D mannequin can be reconstructed from the scanned body. Compared to conventional methods, the method can preserve both the size and shape of the original scanned body. The reconstructed mannequin can be imported directly into the apparel CAD software. The proposed method provides a step for digitizing the apparel manufacturing.

Originality/value
Compared to the conventional methods, the main advantage of the authors’ system is that the authors can preserve both size and geometry of the original scanned body. The main contributions of this paper are as follows: decompose the process of the mannequin reconstruction into pose symmetry and shape symmetry; propose a novel scanning-based pipeline to reconstruct a 3D personalized mannequin; and present a slice-based method for the symmetrization of the 3D mesh.
Moderating effects of age, income and internet usage on Online Brand Community (OBC)-induced purchase intention
Authors: Tiruwa Anurag , Yadav Rajan , Suri Pradeep Kumar 
Published: March 2018

PurposeThe purpose of this paper is to understand the customer attitude and perception towards the online brand communities (OBCs) and purchase intention (PI). The paper also analyses the moderating effects of age, income and internet usage on the relationship among the proposed variables.Design/methodology/approachThe study employed a multi-analytical approach through the use of structural equation modelling and neural networks to test the proposed framework. The information was obtained from 236 respondents using a web-based questionnaire survey. Further, moderation analysis, with age, annual family income and weekly internet usage as moderating variables, was conducted on the structural model.FindingsThe results of the analysis demonstrate that the multi-group moderating effect for different groups within age, income and internet usage have significant differences for the relationships between the independent variables content perception, perceived usefulness, critical mass, brand attachment and attitude towards brand and the dependent variable, PI.Originality/valueThe study is one of its kind to understand and analyse the role of moderating variables (age, income and internet usage) on OBC-induced PI.
Towards a resilient perspective in building conservation
Authors: Luciani Andrea , Del Curto Davide 
Published: March 2018

Purpose
The purpose of this paper is to describe the cross-fertilisation process between the concept of resilience and building conservation. The authors discuss how the conservation field can address new issues posed by climate change and whether the concept of resilience plays a role within the framework of sustainable building conservation.

Design/methodology/approach
Starting from the use of resilience as a “travelling concept”, different interpretations of the term emerging from different fields are compared and interrelated in order to understand how this concept can impact future research in building conservation.

Findings
In addition to summarising recent developments in conservation theory with a special focus on how sustainability has influenced the field, this work also suggests some lines of research where resilience could foster interdisciplinary approaches to building conservation and presents some controversial outcomes.

Originality/value
The paper raises a discussion on how the concept of resilience could renew the field of building conservation, helping contemporary society to address the challenges of climate change.
Sustainable public procurement: the Federal Public Institution’s shared system
Authors: Cader Da Silva Renato , Betiol Luciana , Villac Teresa , Nonato Raquel 
Published: March 2018

Purpose
The purpose of this paper is to report the experience of the Federal Public Institution with sustainable public procurement through the mechanism of shared acquisitions.

Design/methodology/approach
The analysis adopted a qualitative approach and an empirical investigation of MPF’s experience, based on a documentary research and participant observation.

Findings
The results allow the authors to demonstrate the economic, environmental and social advantages of the procurement made by MPF, thus granting to this new model of acquisition governance, the adherence to the organization’s institutional mission.

Research limitations/implications
This is a single case study.

Practical implications
It is a promising path that optimizes the institution’s use of its budgetary, human, logistical and information technology resources, focusing on the quality and sustainability of public biddings.

Social implications
The process of collective construction, improvement of knowledge management, standardization, procedural and scale economies, and the use of sustainability criteria are the main reasons for the implementation of the sustainable shared acquisitions system in the institution.

Originality/value
This is a development process of a new paradigm of procurement at MPF.
Contemporary climate‐driven range shifts: Putting evolution back on the table
Authors: Diamond Sarah E. 
Published: March 2018

AbstractAs the climate continues to change, species are moving to track their climatic niches. Although we are gaining a clearer picture of where and how quickly species ranges are moving, a mechanistic understanding of these changes is still nascent.Evolutionary changes in ranges and range‐limiting traits over contemporary time‐scales have received relatively little attention, possibly due to the mismatch in scale between rapid contemporary range shifts and the historical evolution of species ranges over millions of years. But recent experimental work has shown that range‐limiting traits can evolve rapidly over decadal time‐scales, effectively putting evolution back on the table towards the goal of a mechanistic understanding of contemporary range shifts.Here, I review the role of evolution in shaping range shift responses to recent climate change from the perspective of the past (shared evolutionary history, or phylogenetic signal in range shifts and range‐limiting traits), present (variation in range‐limiting traits) and future (incorporating evolution of range‐limiting traits into range forecasts from species distribution models).In each of these areas, I found a critical role for evolution in understanding historical constraints and future changes in species ranges over contemporary time‐scales: shared evolutionary history may constrain range shift responses for some taxa; compensatory mechanisms of phenotypic plasticity and adaptive evolution can modulate the range shift response; and incorporating evolution into species distribution models can qualitatively alter forecasts of future range shifts.Yet, more can be done in this context, and so I conclude by outlining near‐ and long‐term goals for improving our understanding of the role of evolution in shaping species ranges in a rapidly changing world.Aplain language summaryis available for this article.
Environmental filtering and competitive exclusion drive biodiversity‐invasibility relationships in shallow lake plant communities
Authors: Muthukrishnan Ranjan , Hansel‐Welch Nicole , Larkin Daniel J. 
Published: March 2018

Abstract

Understanding the processes that influence the diversity of ecological communities and their susceptibility to invasion by exotic species remains a challenge in ecology. In many systems, a positive relationship between the richness of native species and exotic species has been observed at larger spatial (e.g., regional) scales, while a negative pattern has been observed at local (e.g., plot) scales. These patterns are widely attributed to (1) biotic interactions, particularly biotic resistance, limiting invasions in high‐diversity locations, producing negative local‐scale relationships, and (2) native and exotic richness covarying at larger spatial scales as a function of environmental conditions and heterogeneity, producing positive large‐scale relationships. However, alternative processes can produce similar patterns and need to be critically evaluated to make sound inferences about underlying mechanisms.

We aggregated a large dataset of aquatic vegetation surveys from 1,102 Minnesota shallow lakes collected over 13 years to quantify spatial and temporal patterns of community composition. Using those data and additional information on environmental conditions we evaluated evidence for four distinct mechanisms that could drive patterns of native and exotic species richness: biotic resistance, competitive exclusion, environmental filtering and environmental heterogeneity.

We found the classic pattern of a negative native‐exotic richness relationship at local scales and a positive relationship at lake scales. However, we found no evidence for local‐scale biotic resistance; instead, competitive exclusion by invasive species appeared to reduce native species richness after locations became invaded. Evaluating the influence of environmental filtering and heterogeneity, we found that native and exotic species occupied somewhat different niches. Invaders were less sensitive to environmental gradients and more tolerant of a wider range of conditions. This segregation of habitat preferences alone could produce a negative local native‐exotic richness relationship and a positive regional pattern without the involvement of biotic interactions.

Synthesis. Our findings conflict with established expectations, which come from research predominantly conducted in terrestrial ecosystems. This illustrates the importance of explicitly evaluating underlying mechanisms in diversity‐invasibility research and for comparisons across different types of ecosystems. Identification of different drivers of diversity also has direct implications for decisions about management of freshwater plant communities.
Competition reverses the response of shrub seedling mortality and growth along a soil moisture gradient
Authors: Esch Ellen H. , Ashbacher Angelita C. , Kopp Christopher W. , Cleland Elsa E. 
Published: March 2018

Abstract

Predicting species responses to climate change involves understanding both the direct effects of environmental change, as well as indirect effects mediated by altered interspecific interactions. Indirect effects may be particularly important for understanding native species responses in systems invaded by highly competitive exotic species. For instance, Mediterranean climate regions are predicted to experience more frequent drought, and are increasingly invaded by exotic annual plants. For native shrubs in these regions, seedling establishment is episodic, and associated with high rainfall years. However, exotic annual plants also often increase in abundance with high rainfall, suggesting competition from exotic annual species could alter the relationship between rainfall and shrub seedling establishment. Theories such as the stress gradient hypothesis predict competition intensity should increase with resource supply, but there have been few evaluations of competitive interactions across experimental gradients of soil moisture availability.

Here we examined how competition from an exotic annual influenced native shrub establishment, across an experimental soil moisture gradient. Seedlings of two native shrub species (Encelia californica and Eriogonum fasciculatum) were grown with and without an exotic grass competitor (Avena fatua) across eight water availability levels, and monitored for growth and survival. These species are common and abundant in the Mediterranean climate region of coastal Southern California, where climate change projections include long‐term drought for the coming decades.

Without competition, shrub seedlings achieved higher growth and survival at high water availability levels. However, when grown in competition with the exotic grass, shrub seedlings had higher growth and/or survival under relatively dry conditions, suggesting competition can modify and even reverse species responses to changing rainfall patterns, compared to predictions made in the absence of competitors. The exotic grass strongly reduced soil nitrate and water availability when it was planted with the native shrub seedlings, and the exotic grass responded with positive but saturating growth with increasing levels of water addition.

Synthesis. This experiment demonstrates that competition from invasive species can alter native species responses to climate change; consistent with ecological theories predicting a positive association between the supply of limiting resources and the intensity of competition.
What ‘form’ does informal assessment take? A scoping review of the informal assessment literature for aphasia
Authors: Thomson Jennifer , Gee Melanie , Sage Karen , Walker Traci 
Published: March 2018

AbstractBackgroundAphasia assessment is traditionally divided into formal and informal approaches. Informal assessment is useful in developing a rich understanding of the person with aphasia's performance, e.g., describing performance in the context of real‐world activities, and exploring the impact of environmental and/or partner supports upon communication. However, defining ‘informal assessment’ is problematic and can result in clinical issues including idiosyncratic practices regarding why, when and how to apply informal assessment.AimsTo examine the extent to which the informal assessment literature can guide speech and language therapists (SLTs) in their clinical application of informal assessment for post‐stroke aphasia.Methods & ProceduresA scoping review methodology was used. A systematic search of electronic databases (Scopus, Embase, PyscInfo, CINAHL, Ovid Medline and AMED) gave informal assessment references between 2000 and 2017 to which title/abstract and full‐text screening against inclusion criteria were applied. Data were extracted from 28 resulting documents using an extraction template with fields based on the review's purpose.Main ContributionThis review examines the informal assessment guidance regarding: rationale; areas of interest for informal assessment; available methods; procedural guidance; documentation; and analytical frameworks. The rationale for using informal assessment included several aspects such as gaining a ‘representative’ sample of the individual's language. Ten communication areas of interest were found with 13 different assessment methods. The procedural guidance for these methods varied considerably, with the exception of conversation and semi‐structured interviewing. Overall, documentation guidance was limited but numerous analytical frameworks were found.ConclusionsSeveral informal assessment methods are available to SLTs. However, information is mixed regarding when they might be used or how they might be applied in terms of their administration, documentation and analysis.