bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal Small-Area Estimation and Design When Nonrespondents Are Subsampled for Follow-up
Authors: O'Malley A. James , Zaslavsky Alan M.
Published: January 2016

Many surveys use an inexpensive initial mode (e.g., mail questionnaires) and a more expensive follow-up mode (e.g., phone). The high unit costs of follow-up interviews may make it cost-effective to subsample the follow-up. We derive optimal follow-up subsampling rates for estimation with many domains. Optimal rates under design-based inference depart from the traditional formulae for Neyman allocation because the follow-up sample size at each plan is bounded by the size of the mail nonrespondent stratum, which may become a certainty stratum. When domain means for initial survey respondents are highly correlated with those for follow-up respondents, more precise estimates (at fixed overall cost) for potential follow-up respondents are obtained by jointly estimating initial and follow-up means using Bayesian bivariate small-area estimation (SAE) models. We compare the full Bayesian SAE procedure to both design-based estimation and univariate SAE. In our application to a large repeated health-care survey, the Medicare Consumer Assessments of Healthcare Providers and Systems survey, the performance of the Bayesian SAE procedure was uniformly superior to other approaches.
The JCMT Gould Belt Survey: Understanding the influence of outflows on Gould Belt clouds
Authors: Drabek-Maunder E. , Hatchell J. , Buckle J. V. , Di Francesco J. , Richer J.
Published: January 2016

Using James Clerk Maxwell Telescope (JCMT) Gould Belt Survey data from CO J = 3 → 2 isotopologues, we present a meta-analysis of the outflows and energetics of star-forming regions in several Gould Belt clouds. The majority of the regions are strongly gravitationally bound. There is evidence that molecular outflows transport large quantities of momentum and energy. Outflow energies are at least 20 per cent of the total turbulent kinetic energies in all of the regions studied and greater than the turbulent energy in half of the regions. However, we find no evidence that outflows increase levels of turbulence, and there is no correlation between the outflow and turbulent energies. Even though outflows in some regions contribute significantly to maintaining turbulence levels against dissipation, this relies on outflows efficiently coupling to bulk motions. Other mechanisms (e.g. supernovae) must be the main drivers of turbulence in most if not all of these regions.
Intraspecific genetic variation and species coexistence in plant communities
Authors: Ehlers Bodil K. , Damgaard Christian F. , Laroche Fabien
Published: January 2016

Many studies report that intraspecific genetic variation in plants can affect community composition and coexistence. However, less is known about which traits are responsible and the mechanisms by which variation in these traits affect the associated community. Focusing on plant–plant interactions, we review empirical studies exemplifying how intraspecific genetic variation in functional traits impacts plant coexistence. Intraspecific variation in chemical and architectural traits promotes species coexistence, by both increasing habitat heterogeneity and altering competitive hierarchies. Decomposing species interactions into interactions between genotypes shows that genotype × genotype interactions are often intransitive. The outcome of plant–plant interactions varies with local adaptation to the environment and with dominant neighbour genotypes, and some plants can recognize the genetic identity of neighbour plants if they have a common history of coexistence. Taken together, this reveals a very dynamic nature of coexistence. We outline how more traits mediating plant–plant interactions may be identified, and how future studies could use population genetic surveys of genotype distribution in nature and methods from trait-based ecology to better quantify the impact of intraspecific genetic variation on plant coexistence.
Self-enforcing regional vaccination agreements
Authors: Klepac Petra , Megiddo Itamar , Grenfell Bryan T. , Laxminarayan Ramanan
Published: January 2016

In a highly interconnected world, immunizing infections are a transboundary problem, and their control and elimination require international cooperation and coordination. In the absence of a global or regional body that can impose a universal vaccination strategy, each individual country sets its own strategy. Mobility of populations across borders can promote free-riding, because a country can benefit from the vaccination efforts of its neighbours, which can result in vaccination coverage lower than the global optimum. Here we explore whether voluntary coalitions that reward countries that join by cooperatively increasing vaccination coverage can solve this problem. We use dynamic epidemiological models embedded in a game-theoretic framework in order to identify conditions in which coalitions are self-enforcing and therefore stable, and thus successful at promoting a cooperative vaccination strategy. We find that countries can achieve significantly greater vaccination coverage at a lower cost by forming coalitions than when acting independently, provided a coalition has the tools to deter free-riding. Furthermore, when economically or epidemiologically asymmetric countries form coalitions, realized coverage is regionally more consistent than in the absence of coalitions.
Do online social media cut through the constraints that limit the size of offline social networks?
Authors: Dunbar R. I. M.
Published: January 2016

The social brain hypothesis has suggested that natural social network sizes may have a characteristic size in humans. This is determined in part by cognitive constraints and in part by the time costs of servicing relationships. Online social networking offers the potential to break through the glass ceiling imposed by at least the second of these, potentially enabling us to maintain much larger social networks. This is tested using two separate UK surveys, each randomly stratified by age, gender and regional population size. The data show that the size and range of online egocentric social networks, indexed as the number of Facebook friends, is similar to that of offline face-to-face networks. For one sample, respondents also specified the number of individuals in the inner layers of their network (formally identified as support clique and sympathy group), and these were also similar in size to those observed in offline networks. This suggests that, as originally proposed by the social brain hypothesis, there is a cognitive constraint on the size of social networks that even the communication advantages of online media are unable to overcome. In practical terms, it may reflect the fact that real (as opposed to casual) relationships require at least occasional face-to-face interaction to maintain them.
Teaching in hunter–gatherer infancy
Authors: Hewlett Barry S. , Roulette Casey J.
Published: January 2016

A debate exists as to whether teaching is part of human nature and central to understanding culture or whether it is a recent invention of Western, Educated, Industrial, Rich, Democratic cultures. Some social–cultural anthropologists and cultural psychologists indicate teaching is rare in small-scale cultures while cognitive psychologists and evolutionary biologists indicate it is universal and key to understanding human culture. This study addresses the following questions: Does teaching of infants exist in hunter–gatherers? If teaching occurs in infancy, what skills or knowledge is transmitted by this process, how often does it occur and who is teaching? The study focuses on late infancy because cognitive psychologists indicate that one form of teaching, called natural pedagogy, emerges at this age. Videotapes of Aka hunter–gatherer infants were used to evaluate whether or not teaching exists among Aka hunter–gatherers of central Africa. The study finds evidence of multiple forms of teaching, including natural pedagogy, that are used to enhance learning of a variety of skills and knowledge.
Sharpening coarse-to-fine stereo vision by perceptual learning: asymmetric transfer across the spatial frequency spectrum
Authors: Li Roger W. , Tran Truyet T. , Craven Ashley P. , Leung Tsz-Wing , Chat Sandy W. , Levi Dennis M.
Published: January 2016

Neurons in the early visual cortex are finely tuned to different low-level visual features, forming a multi-channel system analysing the visual image formed on the retina in a parallel manner. However, little is known about the potential ‘cross-talk’ among these channels. Here, we systematically investigated whether stereoacuity, over a large range of target spatial frequencies, can be enhanced by perceptual learning. Using narrow-band visual stimuli, we found that practice with coarse (low spatial frequency) targets substantially improves performance, and that the improvement spreads from coarse to fine (high spatial frequency) three-dimensional perception, generalizing broadly across untrained spatial frequencies and orientations. Notably, we observed an asymmetric transfer of learning across the spatial frequency spectrum. The bandwidth of transfer was broader when training was at a high spatial frequency than at a low spatial frequency. Stereoacuity training is most beneficial when trained with fine targets. This broad transfer of stereoacuity learning contrasts with the highly specific learning reported for other basic visual functions. We also revealed strategies to boost learning outcomes ‘beyond-the-plateau’. Our investigations contribute to understanding the functional properties of the network subserving stereovision. The ability to generalize may provide a key principle for restoring impaired binocular vision in clinical situations.
A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding
Authors: Vartia Salla , Villanueva-Cañas José L. , Finarelli John , Farrell Edward D. , Collins Patrick C. , Hughes Graham M. , Carlsson Jeanette E. L. , Gauthier David T. , McGinnity Philip , Cross Thomas F. , FitzGerald Richard D. , Mirimin Luca , Crispie Fiona , Cotter Paul D. , Carlsson Jens
Published: January 2016

This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.
Attack risk for butterflies changes with eyespot number and size
Authors: Ho Sebastian , Schachat Sandra R. , Piel William H. , Monteiro Antónia
Published: January 2016

Butterfly eyespots are known to function in predator deflection and predator intimidation, but it is still unclear what factors cause eyespots to serve one function over the other. Both functions have been demonstrated in different species that varied in eyespot size, eyespot number and wing size, leaving the contribution of each of these factors to butterfly survival unclear. Here, we study how each of these factors contributes to eyespot function by using paper butterfly models, where each factor is varied in turn, and exposing these models to predation in the field. We find that the presence of multiple, small eyespots results in high predation, whereas single large eyespots (larger than 6 mm in diameter) results in low predation. These data indicate that single large eyespots intimidate predators, whereas multiple small eyespots produce a conspicuous, but non-intimidating signal to predators. We propose that eyespots may gain an intimidation function by increasing in size. Our measurements of eyespot size in 255 nymphalid butterfly species show that large eyespots are relatively rare and occur predominantly on ventral wing surfaces. By mapping eyespot size on the phylogeny of the family Nymphalidae, we show that these large eyespots, with a potential intimidation function, are dispersed throughout multiple nymphalid lineages, indicating that phylogeny is not a strong predictor of eyespot size.
Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales
Authors: da Silva Sara Graça , Tehrani Jamshid J.
Published: January 2016

Ancient population expansions and dispersals often leave enduring signatures in the cultural traditions of their descendants, as well as in their genes and languages. The international folktale record has long been regarded as a rich context in which to explore these legacies. To date, investigations in this area have been complicated by a lack of historical data and the impact of more recent waves of diffusion. In this study, we introduce new methods for tackling these problems by applying comparative phylogenetic methods and autologistic modelling to analyse the relationships between folktales, population histories and geographical distances in Indo-European-speaking societies. We find strong correlations between the distributions of a number of folktales and phylogenetic, but not spatial, associations among populations that are consistent with vertical processes of cultural inheritance. Moreover, we show that these oral traditions probably originated long before the emergence of the literary record, and find evidence that one tale (‘The Smith and the Devil’) can be traced back to the Bronze Age. On a broader level, the kinds of stories told in ancestral societies can provide important insights into their culture, furnishing new perspectives on linguistic, genetic and archaeological reconstructions of human prehistory.
When are inter-individual brain-behavior correlations informative?
Authors: Lebreton Maël , Palminteri Stefano
Published: January 2016

Characterizing inter-individual differences induced by clinical and social factors constitutes one of the most promising applications of neuroimaging. Paving the way for such applications, neuroimaging studies often report between-group differences in “activations” or correlations between such “activations” and individual traits. Here we raise cautionary warnings about some of those inter-individual analytic strategies. These warnings become critical when measures of “activations” are unstandardized coefficients of regressions between BOLD signal and individual behavior.

First, using simple algebraic derivations, we show how inter-individual differences results can spuriously arise from neglecting the statistical relationships which link the ranges of individual BOLD activation and of recorded behavior. We also demonstrate how apparently contradictory results and interpretations may simply arise from the interaction of this scaling issue and the pre-processing of the behavioral variables. Second, using computational simulations, we illustrate how this issue percolates the booming field of model-based fMRI. Finally, we outline a set of recommendations, which might prove useful for researcher and reviewers confronted with questions involving inter-individual differences in neuroimaging.

Author Summary

Characterizing inter-individual differences induced by clinical and societal factors constitutes one of the most promising applications of neuroimaging. Paving the way for such applications, an increasing fraction of neuroimaging studies reports between-group differences in “activations” or correlations between “activations” and individual traits. In this manuscript, we focus on the typical analytical strategies employed in studies investigating how differences in behavior between individuals or groups of individuals are translated to differences of activations in specific brain regions. We notably question whether they are suitable to support inferences and claims about the neural underpinnings of differential cognition. Our core results demonstrate that typical inter-individual results can spuriously arise by overlooking plausible statistical relationships that link the ranges of individual BOLD activation with the ranges of produced behavior. We argue that these results challenge current classical interpretations of inter-individual results. Highlighting the methodological and theoretical gaps regarding the analysis and interpretation of inter-individual differences is fundamental to fulfilling the promises of neuroimaging.
How clonal are bacteria over time?
Authors: Shapiro B. Jesse
Published: January 2016

abstract

Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality – defined here as the balance between vertical and horizontal inheritance – is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial population’s past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively – but not completely – stable over evolutionary time.
The 2-approximation algorithm of sorting by prefix transposition revisited
Authors: Islam Md. Shafiqul , Rahman Md. Khaledur , Rahman M. Sohel
Published: January 2016

A transposition is an operation that exchanges two adjacent blocks in a permutation. A prefix transposition always moves a prefix of the permutation to another location. In this article, we use a data structure, called the permutation tree, to improve the running time of the best known approximation algorithm (with approximation ratio 2) for sorting a permutation by prefix transpositions. By using the permutation tree, we improve the running time of the 2-approximation algorithm toO(nlogn).
Ageing, TOR and amino acid restriction: a cross-tissue transcriptional network connects GATA factors toDrosophilalongevity
Authors: Dobson Adam J , He Xiaoli , Blanc Eric , Bolukbasi Ekin , Feseha Yodit , Yang Mingyao , Piper Matthew DW
Published: January 2016

Animal lifespan can be extended by dietary restriction (DR), but at a cost to fitness. This phenomenon depends on essential amino acids (EAAs) and TOR signalling, but roles of specific tissues and downstream transcriptional regulators are poorly characterised. Manipulating relevant transcription factors (TFs) specifically in lifespan-limiting tissues may ameliorate ageing without costs of DR. Here we identify TFs which regulate the DR phenotype inDrosophila, analysing organs as an interacting system and reducing its transcriptional complexity by two orders of magnitude. Evolutionarily conserved GATA TFs are predicted to regulate the overlapping effects of DR and TOR on organs, and genetic analyses confirmed that these TFs interact with diet to determine lifespan. Importantly,Srpknockdown insulated fly lifespan from the pernicious effects of EAAs, but tissue-specific knockdown reduced the corrolary costs. These results provide the first indication that benefits of EAAs for early-life fitness can be decoupled from longevity by tissue-specific transcriptional reprogramming.
A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population
Authors: Hehir-Kwa Jayne Y. , Marschall Tobias , Kloosterman Wigard P. , Francioli Laurent C. , Baaijens Jasmijn A. , Dijkstra Louis J. , Abdellaoui Abdel , Koval Vyacheslav , Thung Djie Tjwan , Wardenaar René , Renkens Ivo , Coe Bradley P. , Deelen Patrick , de Ligt Joep , Lameijer Eric-Wubbo , van Dijk Freerk , Hormozdiari Fereydoun ,   The Genome of the Netherlands Consortium, Uitterlinden André G. , Eichler Evan E. , de Bakker Paul , Swertz Morris A. , Wijmenga Cisca , van Ommen Gert-Jan B. , Eline Slagboom P. , Boomsma Dorret I. , Schöenhuth Alexander , ye Kai , Guryev Victor
Published: January 2016

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation.

Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals. Our findings are essential for genome-wide association studies.
Changes in bioactive components ofAristolochia tagala. Cham, a rare species of medicinal importance during itsin vitrodevelopment through direct regeneration
Authors: Remya M , Narmatha Bai V , Murugesan S , Mutharaian VN
Published: January 2016

Tissue culture propagation system was developed forAristolochia tagala, a threatened medicinal plant, using apical bud explants. The most effective medium was found to be MS medium supplemented with BAP (3 μM), KIN (0.5 μM) and activated charcoal (0.1%). The addition of activated charcoal helped in circumventing the problem of polyphenol exudation from the explants which hampered the regeneration of adventitious shoots. A maximum of 12.6 shoots were obtained on average from the apical bud explants after 25 days of inoculation. Well developed shoots were rooted on MS medium supplemented with indole acetic acid (1.5 μM), Kinetin (1.5 μM) and 6-benzylaminopurine (0.5 μM). Regenerated shoots from the apical buds were successfully rooted and acclimated to greenhouse conditions. Qualitative and quantitative analysis of bioactive compounds was done at various stages of development, so as establish the effect of culture conditions on the production of bioactive components. Comparisons were made between three types of plant material from the same clone: leaves from field-grown plant, leaves fromin vitroapical bud cultures and leaf derived callus. It was observed that the leaf derived callus showed the presence of components which were not there in thein vivoleaves, suggesting the influence ofin vitrodevelopmental conditions.

Tagala

Summary Statement

This is the first report on direct regeneration ofAristolochia tagala, (a threatened yet important medicinal plant) using apical bud explants derived from mature plants. Also, for the very first time we report the results of analysis of secondary metabolites during its various stages ofin vitrodevelopment.

Abbreviations

AC - activated charcoal; BAP – 6-benzylaminopurine; 2,4-D - 2,4- dichloro phenoxyacetic acid, IAA - indole acetic acid, IBA - indolebutyric acid, KIN- kinetin, MS- Murashige and Skoog (1962); NAA- α-naphthaleneacetic acid.
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

In 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.
RFPRED: A RANDOM FOREST APPROACH FOR PREDICTION OF MISSENSE VARIANTS IN HUMAN EXOME
Authors: JABOT-HANIN Fabienne , Varet Hugo , Tores Frederic , Alcais Alexandre , Jais Jean-Philippe
Published: January 2016

Exome sequencing is becoming a standard tool for gene mapping of genetic diseases. Given the vast amount of data generated by Next Generation Sequencing techniques, identification of disease causal variants is like finding a needle in a haystack. The impact assessment and the prioritization of potential pathogenic variants are expected to reduce work in biological validation, which is long and costly. One of the possible approaches to determine the most probable deleterious variants in individual exomes is to use protein function alteration prediction. We propose in this paper to use a machine learning approach, the random forest to build a new meta-score based on five previously described scores (SIFT, Polyphen2, LRT, PhyloP and MutationTaster) and compiled in the dbNSFP database. The functional meta-score was trained on a dataset of 61500 non-synonymous Single Nucleotide Polymorphisms (SNPs). The random forest method (rfPred) appears to be globally better than each of the classifiers separately or in combination in a logistic regression model, and better than a newly described score (CADD) on independent validation sets. RfPred scores have been pre-calculated for all the possible non-synonymous SNPs of human exome and are freely accessible at the web-server http://www.sbim.fr/rfPred/
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

Background

Population 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.

Results

Here 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.

Conclusions

AdmixSim 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

Overexpression 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

The 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.
Optimization of visual training for full recovery from severe amblyopia in adults
Authors: Eaton Nicolette C. , Sheehan Hanna Marie , Quinlan Elizabeth M.
Published: January 2016

The severe amblyopia induced by chronic monocular deprivation is highly resistant to reversal in adulthood. Here we use a rodent model to show that recovery from deprivation amblyopia can be achieved in adults by a two-step sequence, involving enhancement of synaptic plasticity in the visual cortex by dark exposure followed immediately by visual training. The perceptual learning induced by visual training contributes to the recovery of vision and can be optimized to drive full recovery of visual acuity in severely amblyopic adults.
Morphology control of BiFeO3aggregatesviahydrothermal synthesis
Authors: Suzuki Kazumasa , Tokudome Yasuaki , Tsuda Hiroshi , Takahashi Masahide
Published: January 2016

The assembly of crystalline building units with specific shape-derived properties into aggregates is often required to broaden their practical applications because the properties of the building units can be fully integrated and used in the aggregates owing to their orientation. Herein, morphology-controlled BiFeO3aggregates composed of oriented crystalline building units were fabricatedviaa hydrothermal process without any additives, and the effects of the supersaturation conditions on the aggregation state were investigated. The supersaturation condition, controlled by varying the KOH concentration, was found to affect the shape of the crystalline building units. For lower supersaturation conditions, the morphology of the aggregates was found to be closely related to the shape of the fundamental building units, and the results indicated that oriented attachment occurred between specific crystal faces of the building units. Under a high supersaturation condition, the morphology of the aggregate did not reflect the shape of the building units and a monodispersed spherical aggregate was obtained. Further, the internal microstructures of the aggregates changed from homogeneous and dense to sparse core and dense shell structures with an increasing supersaturation condition. The formation mechanism of these morphology-controlled aggregates is discussed using microstructure analyses. The present approach to control the morphology of aggregates using the shape of the building units and aggregation kinetics could also be applicable for other microcrystalline aggregated systems in addition to BiFeO3.
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.