bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disclosure of a mental health problem in the employment context: qualitative study of beliefs and experiences
Authors: Brohan E. , Evans-Lacko S. , Henderson C. , Murray J. , Slade M. , Thornicroft G. 
Published: August 2013

Aims.Decisions regarding disclosure of a mental health problem are complex and can involve reconciling conflicting needs and values. This article provides a qualitative account of the beliefs and experiences of mental health service users regarding disclosure in employment contexts.Methods.Total sample of 45 individuals were interviewed in two study phases. In phase one, semi-structured interviews were carried out with 15 mental health service users. The transcripts were analysed using interpretative phenomenological analysis (IPA). In phase two, identified themes were further explored through interviews with mental health service users (n = 30) in three employment contexts: in paid employment (n = 10); in study or voluntary work (n = 10); and currently unemployed (n = 10). These were analysed using directed content analysis.Results.Four super-ordinate themes were drawn from phase one analysis: (1) public understanding of mental health problems; (2) the employment context; (3) personal impact of labelling and (4) disclosure needs. These themes were reflective of the content of phase two interviews.Conclusions.Greater emphasis needs to be placed on considering the societal, employment and interpersonal influences which form the basis for disclosure beliefs and experiences.
Arbitrary Multicolor Photodetection by Hetero-integrated Semiconductor Nanostructures
Authors: Sang Liwen , Hu Junqing , Zou Rujia , Koide Yasuo , Liao Meiyong 
Published: August 2013

AbstractThe typical photodetectors can only detect one specific optical spectral band, such as InGaAs and graphene-PbS quantum dots for near-infrared (NIR) light detection, CdS and Si for visible light detection and ZnO and III-nitrides for UV light detection. So far, none of the developed photodetector can achieve the multicolor detection with arbitrary spectral selectivity, high sensitivity, high speed, high signal-to-noise ratio, high stability and simplicity (called 6S requirements). Here, we propose a universal strategy to develop multicolor photodetectors with arbitrary spectral selectivity by integrating various semiconductor nanostructures on a wide-bandgap semiconductor or an insulator substrate. Because the photoresponse of each spectral band is determined by each semiconductor nanostructure or the semiconductor substrate, multicolor detection satisfying 6S requirements can be readily satisfied by selecting the right semiconductors.
Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles
Authors: Takeoka Yukikazu , Yoshioka Shinya , Teshima Midori , Takano Atsushi , Harun-Ur-Rashid Mohammad , Seki Takahiro 
Published: August 2013

AbstractThis study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field.
Forebrain dopamine neurons project down to a brainstem region controlling locomotion
Authors: Ryczko Dimitri , Grätsch Swantje , Auclair François , Dubé Catherine , Bergeron Saskia , Alpert Michael H. , Cone Jackson J. , Roitman Mitchell F. , Alford Simon , Dubuc Réjean 
Published: August 2013

Significance
We found in lampreys that dopaminergic cells from the posterior tuberculum (homologue of the mammalian substantia nigra pars compacta and/or ventral tegmental area) not only send ascending projections to the striatum, but also have a direct descending projection to a brainstem region controlling locomotion—the mesencephalic locomotor region—where it releases dopamine (DA). DA increased locomotor output through a D1 receptor-dependent mechanism. The presence of this descending dopaminergic projection may have considerable implication for our understanding of the role of DA in motor control under physiological and pathological (i.e. Parkinson disease) conditions.
Unifying model for molecular determinants of the preselection Vβ repertoire
Authors: Gopalakrishnan Suhasni , Majumder Kinjal , Predeus Alexander , Huang Yue , Koues Olivia I. , Verma-Gaur Jiyoti , Loguercio Salvatore , Su Andrew I. , Feeney Ann J. , Artyomov Maxim N. , Oltz Eugene M. 
Published: August 2013

SignificanceThe assembly of immunoglobulin and T-cell receptor genes by V(D)J (variable, diversity, joining) recombination must strike a balance between maximum diversification of antigen receptors and favoring gene segments with specialized functions. We quantified the use of V gene segments in the primary T-cell receptor β repertoire, defining the relative contribution of 13 parameters in shaping their recombination efficiencies. Computational analysis of these data provides a unifying model, revealing a minimal set of five parameters that predict Vβ use. This model building approach will help predict how natural alterations of large V clusters impact immune receptor repertoires.
Comparative studies of Munc18c and Munc18-1 reveal conserved and divergent mechanisms of Sec1/Munc18 proteins
Authors: Yu Haijia , Rathore Shailendra S. , Lopez Jamie A. , Davis Eric M. , James David E. , Martin Jennifer L. , Shen Jingshi 
Published: August 2013

SignificanceSec1/Munc18 (SM) proteins are essential for every vesicle fusion pathway, but their molecular mechanisms remain poorly understood. Our comparative studies of two functionally distinct SM proteins, Munc18c and Munc18-1, suggest that one conserved function of SM proteins is to recognize their cognatetrans-SNARE complexes and accelerate fusion kinetics. The “closed” syntaxin binding mode of Munc18-1, however, is not conserved in Munc18c. Unexpectedly, we discovered that the architecture of the SNARE/SM complex differs across fusion pathways. Together, these findings reveal conserved as well as divergent functions of SM proteins in vesicle fusion.
Field and Laboratory Evaluation of Dam Escapement of Muskellunge
Authors: Wolter Max H. , DeBoom Corey S. , Wahl David H. 
Published: August 2013

Abstract
Muskellunge Esox masquinongy occur in many Midwestern reservoirs where dam escapement is often reported. Because densities of Muskellunge in many reservoirs are low, escapement is a concern. Little is known regarding the factors that influence rates of Muskellunge dam escapement or the proportion of reservoir populations that escape annually. We used controlled laboratory experiments to examine how juvenile Muskellunge interact with flow over a barrier at varying levels of turbidity, flow rate, habitat availability, and periods in the diel cycle. In the field we inserted PIT tags into juvenile and adult Muskellunge, monitored their escapement over a dam with an antenna array, and then compared escapement among demographic groups and described escapement in relation to precipitation events, water temperature, and water clarity. Both laboratory and field studies found Muskellunge were more likely to escape during the day than at night. We estimated that 25% of a reservoir Muskellunge population escaped within the 1-year period of this study, with escapement occurring during late spring but not during fall. Adults were more likely to escape than juveniles, and both sexes escaped at equal rates. Methods developed here can be used to provide useful information to managers and develop mitigation practices to limit escapement in situations where it is not desirable.
Received March 19, 2013; accepted June 3, 2013
Sexual Dimorphism in Alligator Gar
Authors: McDonald D. L. , Anderson J. D. , Hurley C. , Bumguardner B. W. , Robertson C. R. 
Published: August 2013

Abstract
The Alligator Gar Atractosteus spatula is currently imperiled due to habitat alterations and overharvest within much of this species’ range. Recent interest in improving management for this species within the USA and Mexico has spurred new creel restrictions, spawning area closures, and stocking programs, along with increased research on life history and population dynamics. These management and research measures can be improved by a noninvasive method for determining sex. Previous methods have required sacrificing the fish (for internal anatomy confirmation) or using costly and time-consuming assays from a specialized laboratory. Evidence from other gar species suggests that sex determination is possible by examining sexually dimorphic external characters. We evaluated the utility of 13 morphological measurements for determining the sex of Alligator Gars of known gender (n = 117; SL range, 591–1,255 mm). Discriminate analysis identified two influential variables (snout length and caudal peduncle height) as sexually dimorphic. Univariate analyses identified three variables as sexually dimorphic (head length, snout length, and anal fin base length). Sexually dimorphic variables were used with SL to develop a method using serial body ratios (SL/snout length) followed by (snout length/anal fin base length) to identify sex in Alligator Gar to 93% accuracy in males and 72% accuracy in females.
Received April 1, 2013; accepted June 3, 2013
Effects of Salmon Gonadotropin-Releasing Hormone Analog (GnRHa) on Reproductive Success and Egg Size in Rainbow Trout and Brook Trout
Authors: Svinger Viktor W , Policar Tomáš , Kallert Dennis M , Kouřil Jan 
Published: August 2013

Abstract
Rainbow Trout Oncorhynchus mykiss were treated with a 100- or 25-μg/kg dose of salmon gonadotropin-releasing hormone analog (sGnRHa) that was emulsified in Freund's incomplete adjuvant (FIA). Controls were treated with a mixture of FIA and physiological saline. Latency (number of days from the first injection to the date of detected ovulation) was significantly shortened in treated groups compared with the control group. Egg weight, eyeing rate, and hatching rate were significantly reduced in treated groups; mortality after the eyed stage was significantly higher in treated groups. The relationship between latency and the eyeing rate or hatching rate was positive, but the relationship between latency and mortality after the eyed stage was negative. Brook Trout Salvelinus fontinalis were treated with a single injection of sGnRHa–FIA at 12.5 μg/kg, double acute injections of sGnRHa at 12.5 μg/kg administered 3 d apart, or a single acute injection of sGnRHa at 50 μg/kg. Controls were injected with FIA and physiological saline. Latency was significantly shortened in treated groups except the group that received the single acute injection of 50 μg/kg. Egg weight and alevin weight were significantly lower in treated groups. Egg mortality after the eyed stage was significantly higher in the double-injected group than in the 12.5-μg/kg sGnRHa–FIA group and the control group. Latency had a negative relationship with the eyeing rate and hatching rate. This result for Brook Trout is opposite that observed for Rainbow Trout. Latency and mortality after the eyed stage were not correlated. It is evident that the experimental designs currently used in salmonid research should be updated to determine reliable means of avoiding egg mortality, particularly in Rainbow Trout, after GnRHa treatment.
Would you be a geriatrician? Student career preferences and attitudes to a career in geriatric medicine
Authors: Ní Chróinín Danielle , Cronin Edel , Cullen Walter , O'Shea Diarmuid , Steele Michael , Bury Gerard , Kyne Lorraine 
Published: August 2013

AbstractBackground: career intentions of medical students may impact on education and workforce planning. We sought to determine (i) career choices of senior medical students; (ii) interest in geriatric medicine; (iii) factors influencing such choices; and (iv) the impact of a 6-week Medicine in the Community module.Methods: cross-sectional survey of all senior UCD medical students, before and after completion of a ‘Medicine in the Community’ module, 2009–11.Results: eighty-two per cent (274/336) completed the survey at module's end. Two-thirds (174) had chosen a future speciality, most frequently general practice (32.1%) and internal medicine (17%). Half (49.8%) believed career selection is made during medical school. Thirty-one per cent would consider a career in geriatric medicine; reasons cited were interesting field (34.5%), clinical variety (25%) and perception as emotionally rewarding (20.2%). Commonest deterrents were perceived slowness-of-pace and not wanting to work with older patients. Female students (adjusted OR: 1.89, P = 0.05) and those prioritising travel opportunities (adjusted OR: 2.77, P = 0.01) were more likely to consider geriatric medicine. Half (51.5%) reported that the community medicine module increased their interest in geriatric medicine; 91.3% that it would positively influence how they treated older patients. Students reporting a positive influence of the module were more likely to consider a career in geriatric medicine (OR: 1.62, P = 0.02).Conclusion: two-thirds of students had already chosen a future speciality. One-third would consider geriatric medicine. This may have important implications for workforce planning and development of geriatric medicine. Undergraduate exposure to the discipline may increase interest in geriatric medicine as a career, and positively influence management of older patients.
Impact of Cost Shocks on Consumer Prices in Vertically‐Related Markets: The Case of The French Soft Drink Market
Authors: Bonnet Céline , Réquillart Vincent 
Published: August 2013

AbstractWe develop a structural econometric model of the vertical contracts between soft drink manufacturers and retailers to assess the impact of taxes or changes in production costs on consumer prices. Using individual data on food purchases from a representative survey of 19,000 French households in 2005, we estimate consumer demand using a random utility approach. Among a set of possible vertical relationships, we select the model that best fits the data. We evaluate the pass‐through rate of changes in input costs (sugar) or of taxes and show that the industry over‐shifts cost changes or excise taxes to the consumers. This result challenges the belief that firms do not pass on the full extent of cost changes or excise taxes to consumers.
Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities
Authors: Taghavi Zeinab , Movahedi Narjes S. , Drǎghici Sorin , Chitsaz Hamidreza 
Published: August 2013

Abstract
Motivation: Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of which elude cultivation. The most accurate method to date is exhaustive single-cell sequencing using multiple displacement amplification, which is simply intractable for a large number of cells. However, there is hope for breaking this barrier, as the number of different cell types with distinct genome sequences is usually much smaller than the number of cells.
Results: Here, we present a novel divide and conquer method to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells. The method is implemented in a tool called Squeezambler. We evaluated Squeezambler on simulated data. The proposed divide and conquer method successfully reduces the cost of sequencing in comparison with the naïve exhaustive approach.
Availability: Squeezambler and datasets are available at http://compbio.cs.wayne.edu/software/squeezambler/.
Contact: ztaghavi@wayne.edu
CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays
Authors: Masuzzo Paola , Hulstaert Niels , Huyck Lynn , Ampe Christophe , Van Troys Marleen , Martens Lennart 
Published: August 2013

Abstract
Summary: Automated image processing has allowed cell migration research to evolve to a high-throughput research field. As a consequence, there is now an unmet need for data management in this domain. The absence of a generic management system for the quantitative data generated in cell migration assays results in each dataset being treated in isolation, making data comparison across experiments difficult. Moreover, by integrating quality control and analysis capabilities into such a data management system, the common practice of having to manually transfer data across different downstream analysis tools will be markedly sped up and made more robust. In addition, access to a data management solution creates gateways for data standardization, meta-analysis and structured public data dissemination.
We here present CellMissy, a cross-platform data management system for cell migration data with a focus on wound healing data. CellMissy simplifies and automates data management, storage and analysis from the initial experimental set-up to data exploration.
Availability and implementation: CellMissy is a cross-platform open-source software developed in Java. Source code and cross-platform binaries are freely available under the Apache2 open source license at http://cellmissy.googlecode.com.
Contact: lennart.martens@ugent.be
Supplementary Information: Supplementary data are available at Bioinformatics online.
Scaffold network generator: a tool for mining molecular structures
Authors: Matlock Matt K. , Zaretzki Jed M. , Swamidass S. Joshua 
Published: August 2013

Abstract
Summary: Scaffold network generator (SNG) is an open-source command-line utility that computes the hierarchical network of scaffolds that define a large set of input molecules. Scaffold networks are useful for visualizing, analysing and understanding the chemical data that is increasingly available through large public repositories like PubChem. For example, some groups have used scaffold networks to identify missed-actives in high-throughput screens of small molecules with bioassays. Substantially improving on existing software, SNG is robust enough to work on millions of molecules at a time with a simple command-line interface.
Availability and implementation: SNG is accessible at http://swami.wustl.edu/sng
Contact: swamidass@wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A distance-based test of association between paired heterogeneous genomic data
Authors: Minas Christopher , Curry Edward , Montana Giovanni 
Published: August 2013

Abstract
Motivation: Due to rapid technological advances, a wide range of different measurements can be obtained from a given biological sample including single nucleotide polymorphisms, copy number variation, gene expression levels, DNA methylation and proteomic profiles. Each of these distinct measurements provides the means to characterize a certain aspect of biological diversity, and a fundamental problem of broad interest concerns the discovery of shared patterns of variation across different data types. Such data types are heterogeneous in the sense that they represent measurements taken at different scales or represented by different data structures.
Results: We propose a distance-based statistical test, the generalized RV (GRV) test, to assess whether there is a common and non-random pattern of variability between paired biological measurements obtained from the same random sample. The measurements enter the test through the use of two distance measures, which can be chosen to capture a particular aspect of the data. An approximate null distribution is proposed to compute P-values in closed-form and without the need to perform costly Monte Carlo permutation procedures. Compared with the classical Mantel test for association between distance matrices, the GRV test has been found to be more powerful in a number of simulation settings. We also demonstrate how the GRV test can be used to detect biological pathways in which genetic variability is associated to variation in gene expression levels in an ovarian cancer sample, and present results obtained from two independent cohorts.
Availability: R code to compute the GRV test is freely available from http://www2.imperial.ac.uk/∼gmontana
Contact: g.montana@imperial.ac.uk
Supplementary data: Supplementary data are available at Bioinformatics online.
The BioPAX Validator
Authors: Rodchenkov Igor , Demir Emek , Sander Chris , Bader Gary D. 
Published: August 2013

Abstract
Summary: BioPAX is a community-developed standard language for biological pathway data. A key functionality required for efficient BioPAX data exchange is validation—detecting errors and inconsistencies in BioPAX documents. The BioPAX Validator is a command-line tool, Java library and online web service for BioPAX that performs &gt;100 classes of consistency checks.
Availability and implementation: The validator recognizes common syntactic errors and semantic inconsistencies and reports them in a customizable human readable format. It can also automatically fix some errors and normalize BioPAX data. Since its release, the validator has become a critical tool for the pathway informatics community, detecting thousands of errors and helping substantially increase the conformity and uniformity of BioPAX-formatted data. The BioPAX Validator is open source and released under LGPL v3 license. All sources, binaries and documentation can be found at sf.net/p/biopax, and the latest stable version of the web application is available at biopax.org/validator.
Contact: igor.rodchenkov@utoronto.ca or gary.bader@utoronto.ca
Identification of a Probable Pore-Forming Domain in the Multimeric Vacuolar Anion Channel AtALMT9
Authors: Zhang Jingbo , Baetz Ulrike , Krügel Undine , Martinoia Enrico , De Angeli Alexis 
Published: August 2013

Abstract
Aluminum-activated malate transporters (ALMTs) form an important family of anion channels involved in fundamental physiological processes in plants. Because of their importance, the role of ALMTs in plant physiology is studied extensively. In contrast, the structural basis of their functional properties is largely unknown. This lack of information limits the understanding of the functional and physiological differences between ALMTs and their impact on anion transport in plants. This study aimed at investigating the structural organization of the transmembrane domain of the Arabidopsis (Arabidopsis thaliana) vacuolar channel AtALMT9. For that purpose, we performed a large-scale mutagenesis analysis and found two residues that form a salt bridge between the first and second putative transmembrane α-helices (TMα1 and TMα2). Furthermore, using a combination of pharmacological and mutagenesis approaches, we identified citrate as an “open channel blocker” of AtALMT9 and used this tool to examine the inhibition sensitivity of different point mutants of highly conserved amino acid residues. By this means, we found a stretch within the cytosolic moiety of the TMα5 that is a probable pore-forming domain. Moreover, using a citrate-insensitive AtALMT9 mutant and biochemical approaches, we could demonstrate that AtALMT9 forms a multimeric complex that is supposedly composed of four subunits. In summary, our data provide, to our knowledge, the first evidence about the structural organization of an ion channel of the ALMT family. We suggest that AtALMT9 is a tetramer and that the TMα5 domains of the subunits contribute to form the pore of this anion channel.