bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Neuro Bureau ADHD-200 Preprocessed Repository
Authors: Bellec Pierre , Chu Carlton , Chouinard-Decorte François , Benhajali Yassine , Margulies Daniel S. , Craddock R. Cameron 
Published: January 2016

AbstractIn 2011, the “ADHD-200 Global Competition” was held with the aim of identifying biomarkers of attention-deficit/hyperactivity disorder from resting-state functional magnetic resonance imaging (rs-fMRI) and structural MRI (s-MRI) data collected on 973 individuals. Statisticians and computer scientists were potentially the most qualified for the machine learning aspect of the competition, but generally lacked the specialized skills to implement the necessary steps of data preparation for rs-fMRI. Realizing this barrier to entry, the Neuro Bureau prospectively collaborated with all competitors by preprocessing the data and sharing these results at the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) (http://www.nitrc.org/frs/?group_id=383). This “ADHD-200 Preprocessed” release included multiple analytical pipelines to cater to different philosophies of data analysis. The processed derivatives included denoised and registered 4D fMRI volumes, regional time series extracted from brain parcellations, maps of 10 intrinsic connectivity networks, fractional amplitude of low frequency fluctuation, and regional homogeneity, along with grey matter density maps. The data was used by several teams who competed in the ADHD-200 Global Competition, including the winning entry by a group of biostaticians. To the best of our knowledge, the ADHD-200 Preprocessed release was the first large public resource of preprocessed resting-state fMRI and structural MRI data, and remains to this day the only resource featuring a battery of alternative processing paths.
AdmixSim: A Forward-Time Simulator for Various and Complex Scenarios of Population Admixture
Authors: Yang Xiong , Ni Xumin , Zhou Ying , Guo Wei , Yuan Kai , Xu Shuhua 
Published: January 2016

AbstractBackgroundPopulation admixture has been a common phenomenon in human, animals and plants, and plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is challenging and typically relies onin silicosimulation. We are aware of the lack of a computer tool for such a purpose, especially a simulator is not available for generating data under various and complex admixture scenarios.ResultsHere we developed a forward-time simulator (AdmixSim) under standard Wright Fisher model, which can simulate admixed populations with: 1) multiple ancestral populations; 2) multiple waves of admixture events; 3) fluctuating population size; and 4) fluctuating admixture proportions. Results of analysis of the simulated data by AdmixSim show that our simulator can fast and accurately generate data resemble real one. We included in AdmixSim all possible parameters that allow users to modify and simulate any kinds of admixture scenarios easily so that it is very flexible. AdmixSim records recombination break points and trace of each chromosomal segment from different ancestral populations, with which users can easily do further analysis and comparative studies with empirical data.ConclusionsAdmixSim is expected to facilitate the study of population admixture by providing a simulation framework with flexible implementation of various admixture models and parameters.
SPARC promotes cell invasion in vivo by decreasing type IV collagen levels in the basement membrane
Authors: Morrissey Meghan A. , Jayadev Ranjay , Miley Ginger R. , Blebea Catherine A. , Chi Qiuyi , Ihara Shinji , Sherwood David R. 
Published: January 2016

AbstractOverexpression of SPARC, a collagen-binding glycoprotein, is strongly associated with tumor invasion through extracellular matrix in many aggressive cancers. SPARC regulates numerous cellular processes including integrin-mediated cell adhesion, cell signaling pathways, and extracellular matrix assembly; however, the mechanism by which SPARC promotes cell invasionin vivoremains unclear. A main obstacle in understanding SPARC function has been the difficulty of visualizing and experimentally examining the dynamic interactions between invasive cells, extracellular matrix and SPARC in native tissue environments. Using the model of anchor cell invasion through the basement membrane (BM) extracellular matrix inCaenorhabditis elegans,we find that SPARC overexpression is highly pro-invasive and rescues BM transmigration in mutants with defects in diverse aspects of invasion, including cell polarity, invadopodia formation, and matrix metalloproteinase expression. By examining BM assembly, we find that overexpression of SPARC specifically decreases levels of BM type IV collagen, a crucial structural BM component. Reduction of type IV collagen mimicked SPARC overexpression and was sufficient to promote invasion. Tissue-specific overexpression and photobleaching experiments revealed that SPARC acts extracellularly to inhibit collagen incorporation into BM. By reducing endogenous SPARC, we also found that SPARC functions normally to traffic collagen from its site of synthesis to tissues that do not express collagen. We propose that a surplus of SPARC disrupts extracellular collagen trafficking and reduces BM collagen incorporation, thus weakening the BM barrier and dramatically enhancing its ability to be breached by invasive cells.
A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes
Authors: Mühlhausen Stefanie , Findeisen Peggy , Plessmann Uwe , Urlaub Henning , Kollmar Martin 
Published: January 2016

AbstractThe genetic code is the universal cellular translation table to convert nucleotide into amino acid sequences. Changes to sense codons are expected to be highly detrimental. However, reassignments of single or multiple codons in mitochondria and nuclear genomes demonstrated that the code can evolve. Still, alterations of nuclear genetic codes are extremely rare leaving hypotheses to explain these variations, such as the ‘codon capture’, the ‘genome streamlining’ and the ‘ambiguous intermediate’ theory, in strong debate. Here, we report on a novel sense codon reassignment inPachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons we show that inPachysolenCUG codons are translated as alanine and not as the universal leucine. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by atRNA loss driven codon reassignmentmechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is outside the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.
Psychological interventions for adults with ASD: clinical approaches
Authors: Spain Debbie , O'Neill Lucy , Harwood Laura , Chaplin Eddie 
Published: January 2016

Purpose
– Empirical research indicates that adults who have autism spectrum disorders (ASD) can derive clinically and statistically meaningful benefits from individual and group-based psychological interventions, specifically those which employ skills-based, behavioural, and cognitive techniques. Given the inherent socio-communication, executive functioning, and theory of mind impairments that individuals with ASD can experience, it is deemed necessary to modify the design and delivery of interventions so as to enhance engagement and outcomes. The paper aims to discuss these issues.

Design/methodology/approach
– This general review provides a summary of the extant literature and clinical guidelines for the provision of psychological interventions for adults with ASD.

Findings
– Adaptations to the structure, process, content, and outcome measurement are outlined. It is likely that optimal treatment gains for adults with ASD are contingent on a prolonged assessment phase, pre-therapy interventions including psycho-education and skills-based interventions, thoughtful regard to the formulation of presenting difficulties, and consideration of, and methods to overcome, the difficulties that may arise when seeking to implement change, identify goals, and manage endings.

Originality/value
– This is one of the first reviews to condense the clinical implications for providing psychological interventions for adults with ASD.
Barriers to healthcare for people on the autism spectrum
Authors: Dern Sebastian , Sappok Tanja 
Published: January 2016

Purpose– Adults on the autism spectrum experience difficulties in receiving health care, and health care providers face difficulties in offering health care to adults on the autism spectrum. The purpose of this paper is first, to assess the various difficulties and second, to provide strategies to overcome them.Design/methodology/approach– In this qualitative research project, current barriers and facilitators to health care services were sampled from a collaboration of autistic self-advocates and autism professionals in Berlin, Germany. The findings were complemented by a review of practical guidelines and research about the service accessibility of patients on the autism spectrum.Findings– A comprehensive list of barriers to health care was compiled and structured according to various aspects, such as “making appointments”, “waiting area”, “communication”, and “examination”. Strategies considering the perceptual and communicative peculiarities of autism were found to improve access to health care for autistic adults.Practical implications– Providing access to the health care system may improve the diagnosis and treatment of mental and somatic illnesses, and thereby, the health status and quality of life for people on the autism spectrum. This recognition of the needs of adults on the autism spectrum may serve as a model for other areas in society, such as education and employment.Originality/value– Data acquisition in this project is of special value because it resulted from collaboration between an autistic self-advocacy organization and professionals working in the field of intellectual developmental disabilities considering the experiences of autistic adults in the entire range of intellectual functioning.
Conceptualization of science using collaboration and competences
Authors: Karlovcec Mario , Mladenic Dunja , Grobelnik Marko , Jermol Mitja 
Published: January 2016

Purpose
The purpose of this paper is to propose an approach for conceptualizing science based on collaboration and competences of researchers.

Design/methodology/approach
The research is conducted by exploratory analysis of collaboration and competences using case studies from humanistic, engineering, natural sciences and a general topic.

Findings
The findings show that by applying the proposed approach on bibliographic data that readily exist for many national sciences as well as for international scientific communities, one can obtain useful new insights into the research. The approach is demonstrated with the following exploratory findings: identification of important connections and individual researchers that connect the community of anthropologists; collaboration of technical scientists in the community of anthropologists caused by an interdisciplinary research project; connectivity, interdisciplinary and structure of artificial intelligence, nanotechnology and a community based on a general topic; and identifying research interest shift described with concretization and topic-shift.

Practical implications
As demonstrated with the practical implementation (http://scienceatlas.ijs.si/), users can obtain information of the most relevant competences of a researcher and his most important collaborators. It is possible to obtaining researchers, community structure and competences of an arbitrary research topic.

Social implications
The map for collaboration and competences of a complete science can be a crucial tool for policy-making. Social scientists can use the results of the proposed approach to better understand and direct the development of science.

Originality/value
Originality and value of the paper is in combining text (competences) and network (research collaboration and co-authoring) approaches for exploring science. Additional values give the results of analysis that demonstrate the approach.
Effect of gender on collaborative associations of researchers in Malaysia
Authors: Kumar Sameer 
Published: January 2016

Purpose
This study aims to find the level of gender-based assortativity in the association of researchers and investigate if gender has influence over social capital of researchers and their research performance in the context of a multi-ethnic nation, such as Malaysia.

Design/methodology/approach
Social network analysis is used as a primary research method to analyse the associations between the authors. Mann-Whitney test is used for testing the significant differences in research performance and social capital based on gender.

Findings
The assortative mixing patterns of 187 researchers revealed positive assortativity, meaning that more authors preferred to co-author with authors of their gender. No influence of gender was seen on the social capital of authors. However, gender did significantly influence the research productivity of authors.

Originality/value
This is one of the first studies that attempts to find the influence of gender on collaborative associations of researchers in Malaysia.
Towards a global hub
Authors: Oseni Umar A. , Ahmad Abu Umar Faruq 
Published: January 2016

Purpose
– The paper aims to examine significant developments in the institutional framework for dispute resolution in the Islamic finance industry in Malaysia. Malaysia, as part of its efforts to consolidate its enviable Islamic finance industry, has strengthened its institutional framework for dispute resolution.

Design/methodology/approach
– Data for this study were collected from both primary and secondary legal sources. Through a conceptual legal analysis, the institutional frameworks of dispute resolution in the Malaysia’s Islamic finance industry are studied.

Findings
– The study finds that Malaysia is far ahead of other jurisdictions by a significant margin in spearheading reforms in the emerging global Islamic finance industry. The dispute resolution framework has been largely affected by the recent reforms.

Research limitations/implications
– Other jurisdictions may borrow a leaf from Malaysia’s initiative in providing a robust legal framework for dispute management in the Islamic finance industry.

Practical implications
– Apart from adopting Malaysia’s framework and possibly adapting it to suit their specific local variations, other jurisdictions may also encourage Islamic financial institutions to incorporate effective dispute resolution processes in Islamic finance contracts.

Originality value
– This study critically discussed most recent developments in the institutional framework on dispute resolution in the Islamic finance industry in Malaysia.
Muslim women contribution to economic activities: a viewpoint
Authors: Ridley Yvonne 
Published: January 2016

Purpose
– The purpose of this paper is to highlight the role of Muslim women in economic activities.

Design/methodology/approach
– The paper is a historical account on the important role played by Muslim women in business and governance during the Islamic formative years.

Findings
– While women in the West still struggle with the rights to equal position and pay till today, Islamic teaching provides Muslim women with the rights to earn and spend as they wished as well as selected to lead economic activities based on their personal merit and wisdom.

Practical implications
– The paper highlights that Islamic Sharia does not discriminate Muslim women economically nor socially as often portrayed in the Western media. Islam outlines the specific rights and obligations of men and women to ensure development of a healthy society.

Social implications
– Society should appreciate that Islamic Sharia work out favourably for women. They are trusted to lead based on their own merit and wisdom and not for their beauty.

Originality/value
– This is a keynote speech delivered at the Islamic Perspective of Accounting, Finance, Economics and Management (IPAFEM) 2015 conference: 7th-9th April, Adam Smith Business School, The University of Glasgow – on the economic role played by early Muslim women.
Creating a healthy company by occupational health promotion as a part of social responsibility
Authors: Šarotar Žižek Simona , Mulej Matjaž 
Published: January 2016

Purpose
– The purpose of this paper is to provide a new non-technological innovation concerning management processes in organization, focussing on occupational health promotion as a part of social responsibility (SR). Employer’s occupational health promotion includes systemic and systematic activities for good employees’ social, physical and mental health; synergy is suggested.

Design/methodology/approach
– A qualitative analysis using SR, dialectical systems theory and human resource management is applied.

Findings
– A healthy company can be built by occupational health promotion, which must take place socially responsibly and requisitely holistically.

Research limitations/implications
– Qualitative analysis is applied in desk and field research on Slovenia.

Practical implications
– The novel socially responsible, requisitely holistic approach to managing employee’s health, exposing personal and corporate SR prevents oversights and resulting failures.

Originality/value
– Available literature offers no similar concept.
An improved artificial fish swarm algorithm optimized by particle swarm optimization algorithm with extended memory
Authors: Duan Qichang , Mao Mingxuan , Duan Pan , Hu Bei 
Published: January 2016

Purpose
– The purpose of this paper is to solve the problem that the standard particle swarm optimization (PSO) algorithm has a low success rate when applied to the optimization of multi-dimensional and multi-extreme value functions, the authors would introduce the extended memory factor to the PSO algorithm. Furthermore, the paper aims to improve the convergence rate and precision of basic artificial fish swarm algorithm (FSA), a novel FSA optimized by PSO algorithm with extended memory (PSOEM-FSA) is proposed.

Design/methodology/approach
– In PSOEM-FSA, the extended memory for PSO is introduced to store each particle’ historical information comprising of recent places, personal best positions and global best positions, and a parameter called extended memory effective factor is employed to describe the importance of extended memory. Then, stability region of its deterministic version in a dynamic environment is analyzed by means of the classic discrete control theory. Furthermore, the extended memory factor is applied to five kinds of behavior pattern for FSA, including swarming, following, remembering, communicating and searching.

Findings
– The paper proposes a new intelligent algorithm. On the one hand, this algorithm makes the fish swimming have the characteristics of the speed of inertia; on the other hand, it expands behavior patterns for the fish to choose in the search process and achieves higher accuracy and convergence rate than PSO-FSA, owning to extended memory beneficial to direction and purpose during search. Simulation results verify that these improvements can reduce the blindness of fish search process, improve optimization performance of the algorithm.

Research limitations/implications
– Because of the chosen research approach, the research results may lack persuasion. In the future study, the authors will conduct more experiments to understand the behavior of PSOEM-FSA. In addition, there are mainly two aspects that the performance of this algorithm could be further improved.

Practical implications
– The proposed algorithm can be used to many practical engineering problems such as tracking problems.

Social implications
– The authors hope that the PSOEM-FSA can increase a branch of FSA algorithm, and enrich the content of the intelligent algorithms to some extent.

Originality/value
– The novel optimized FSA algorithm proposed in this paper improves the convergence speed and searching precision of the ordinary FSA to some degree.
Issues involved in methodological analyses of research interviews
Authors: Roulston Kathryn 
Published: January 2016

Purpose– The purpose of this paper is to argue that qualitative researchers have much to learn from conducting methodological analyses of their own talk in relation to research participants in interviews. Yet there are specific difficulties in representing findings from methodological analyses of research interviews.Design/methodology/approach– Although qualitative researchers have for some time followed recommendations to analyze both “how” interview data are generated in addition to “what” is discussed, little has been written about the challenges of representing these sorts of analyses. The paper uses a case to first examine difficulties in the representation of an analysis of interview data that draws on discursive psychology. After discussing the case, the paper further explores the challenges of conducting and presenting these sorts of methodological analyses of interview data to research participants and readers in ways that clearly convey what might be learned by examining how interviews are accomplished.Findings– The paper outlines considerations for researchers in doing methodological analyses of interview data, including challenges, reconciling interpretations of “what” and “how” topics are discussed in research studies, and possible areas of focus.Research limitations/implications– This paper examines what researchers might learn from examinations of their own interview practice and does not focus on representations of topical analyses.Practical implications– The paper argues that when interviewers subject their own talk to analysis, they learn about themselves, their craft, and the ways in which knowledge about social worlds are collaboratively produced in research encounters with participants.Originality/value– By developing expertise in how to analyze their interview interaction methodologically, qualitative researchers can attend to significant features of their interview practice and in so doing, develop a reflexive research practice.
Fieldwork in philosophy, emancipation and researcher dis-position
Authors: Heimans Stephen 
Published: January 2016

Purpose– The purpose of this paper is to offer an exemplar of post-qualitative “fieldwork in philosophy” research. The paper proposes features of such philosophical fieldwork and adumbrates examples of concepts that have emerged in the process of undertaking the research.Design/methodology/approach– The paper is conceptual, drawing on an abductive approach. Post-qualitative understandings that question the validity of methodology and theory as separable entities are operationalised.Findings– The paper provides insights into how post-qualitative research might be undertaken and what might emerge in the process.Originality/value– This paper fulfils a need for an example of research that is post-qualitative. Additionally, the possibilities for doing “fieldwork in philosophy” are extended, as is the work of Jacque Rancière with respect to emancipation.