bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydraulic constraints of reproduction do not explain sexual dimorphism in the genus Leucadendron (Proteaceae)
Authors: Roddy Adam B. , van Blerk Justin , Midgley Jeremy J. , West Adam G.
Published: October 2017

Because of the importance of reproduction in plant life history, the physiological costs of reproduction often influence vegetative structure and function. In dioecious species, these effects can be quite obvious, as different costs of male and female reproductive functions are entirely separated among different individuals in a population. In fire-prone ecosystems, in which recruitment is driven by fire frequency, many plants will maintain their seeds in the canopy, only to be released after a fire. The dioecious genus Leucadendron is a notable case of this, as females can maintain their seed cones for years, and, even more interestingly, species in the genus differ substantially in the degree to which males and females are sexually dimorphic. A recent study (Harris and Pannell 2010) argued that the hydraulic costs of maintaining seed cones for many years would effect the degree of sexual dimorphism among species. However, this assumed that shoot hydraulic architecture would be related to traits exhibiting sexual dimorphism. Here we explicitly test this hypothesis on two Leucadendron species. We found (1) that metrics of branch ramification used in the previous study to characterize dimorphism do not conform to known scaling relationships and (2) that sexual dimorphism in shoot architecture has no effect on hydraulic efficiency. Both of these results seriously question the pattern described by Harris and Pannell (2010) and suggest that the hydraulic costs of prolonged seed retention in Leucadendron do not significantly affect branch architecture.
Neurodevelopmental disease genes implicated byde novomutation and CNV morbidity
Authors: Coe Bradley P. , Stessman Holly A.F. , Sulovari Arvis , Geisheker Madeleine , Hormozdiari Fereydoun , Eichler Evan E.
Published: October 2017

We combinedde novomutation (DNM) data from 10,927 cases of developmental delay and autism to identify 301 candidate neurodevelopmental disease genes showing an excess of missense and/or likely gene-disruptive (LGD) mutations. 164 genes were predicted by two different DNM models, including 116 genes with an excess of LGD mutations. Among the 301 genes, 76% show DNM in both autism and intellectual disability/developmental delay cohorts where they occur in 10.3% and 28.4% of the cases, respectively. Intersecting these results with copy number variation (CNV) morbidity data identifies a significant enrichment for the intersection of our gene set and genomic disorder regions (36/301, LR+ 2.53, p=0.0005). This analysis confirms many recurrent LGD genes and CNV deletion syndromes (e.g.,KANSL1, PAFAH1B1, RA1,etc.), consistent with a model of haploinsufficiency. We also identify genes with an excess of missense DNMs overlapping deletion syndromes (e.g.,KIF1Aand the 2q37 deletion) as well as duplication syndromes, such as recurrentMAPK3missense mutations within the chromosome 16p11.2 duplication, recurrentCHD4missense DNMs in the 12p13 duplication region, and recurrentWDFY4missense DNMs in the 10q11.23 duplication region. Finally, we also identify pathogenic CNVs overlapping more than one recurrently mutated gene (e.g., Sotos and Kleefstra syndromes) raising the possibility that multiple gene-dosage imbalances may contribute to phenotypic complexity of these disorders. Network analyses of genes showing an excess of DNMs confirm previous well-known enrichments but also highlight new functional networks, including cell-specific enrichments in the D1+ and D2+ spiny neurons of the striatum for both recurrently mutated genes and genes where missense mutations cluster.
Bursts of amino acid replacements in protein evolution
Authors: Stolyarova Anastasia V. , Bazykin Georgii A. , Neretina Tatyana V. , Kondrashov Alexey S.
Published: October 2017

Evolution can occur both gradually and through alternating episodes of stasis and rapid changes. However, the prevalence and magnitude of fluctuations of the rate of evolution remains obscure. Detecting a rapid burst of changes requires a detailed record of past evolution, so that events that occurred within a short time interval can be identified. Here, we use the phylogenies of the Baikal Lake amphipods and of Catarrhini, which contain very short internal edges facilitating this task. We detect 6 radical bursts of evolution of individual proteins during such short time periods, each involving between 6 and 38 amino acid substitutions. These bursts were extremely unlikely to have occurred neutrally, and were apparently caused by positive selection. On average, in the course of a time interval required for one synonymous substitution per site, a protein undergoes a strong burst of rapid evolution with probability at least ~0.01.
Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed
Authors: Browett Sam , McHugo Gillian , Richardson Ian W. , Magee David A. , Park Stephen D. E. , Fahey Alan G. , Kearney John F. , Correia Carolina N. , Randhawa Imtiaz A. S. , MacHugh David E.
Published: October 2017

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP data (Illumina®BovineSNP50 array) to evaluate genomic diversity within the Kerry cattle population and between Kerry cattle and other European cattle breeds. Visualisation of patterns of genetic differentiation and gene flow among cattle breeds using phylogenetic trees with ancestry graphs highlighted, in particular, historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishingNeover time and that recent estimatedNevalues for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.

Note 1:This is an Associate Editor (D.E.M) Inaugural Article submission toFrontiers in Genetics: Livestock Genomics

Note 2:British English language style preferred for publication of this article.
Quantifying the effects of single mutations on viral escape from broad and narrow antibodies to an H1 influenza hemagglutinin
Authors: Doud Michael B. , Lee Juhye M. , Bloom Jesse D.
Published: October 2017

Influenza virus can completely escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if it was under strong pressure to do so. Here we map all single amino-acid mutations that increase resistance to broad antibodies targeting an H1 hemagglutinin. Crucially, our approach not only identifies antigenic mutations but also quantifies their effect sizes. All antibodies select mutations, but the effect sizes vary widely. The virus can escape a broad antibody that targets residues in hemagglutinin’s receptor-binding site the same way it escapes narrow strain-specific antibodies: via single mutations with huge effects. In contrast, broad antibodies targeting hemagglutinin’s stalk only select mutations with small effects. Therefore, among the antibodies we have examined, breadth is an imperfect indicator of the potential for viral escape via single mutations. Broadly neutralizing antibodies targeting the H1 hemagglutinin stalk are quantifiably harder to escape than the other antibodies tested here.
Bayesian Confidence Intervals for Multiplexed Proteomics Integrate lon-Statistics with Peptide Quantification Concordance
Authors: Peshkin Leonid , Gupta Meera , Ryazanova Lillia , Wühr Martin
Published: October 2017

Multiplexed proteomics has emerged as a powerful tool to measure relative protein expression levels across multiple conditions. The relative protein abundances are inferred by comparing the signal generated by isobaric tags, which encode the samples’ origins. Intuitively, the trust associated with a protein measurement depends on the similarity of ratios from the protein’s peptides and the signal level of these measurements. However, typically only the most likely results are reported without providing confidence for these measurements. Here we present a mathematically rigorous approach that integrates peptide MS-signal and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence (BACIQ). The main advantages of BACIQ are: 1) it removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; 2) confidence can be assigned without replicates; 3) for repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; 4) for repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. To demonstrate the power of BACIQ we reanalyzed previously published data on subcellular protein movement upon treatment with an Exportin 1 inhibiting drug. We detect ~2x more highly significant movers, down to subcellular localization changes of ~1%. Thus, our method drastically increases the value obtainable from quantitative proteomics experiments helping researchers to interpret their data and prioritize resources. To make our approach easily accessible we distribute it via a Python/Stan package.
Subsets of NLR genes drive adaptation of tomato to pathogens during colonisation of new habitats
Authors: Stam Remco , Silva-Arias Gustavo A. , Tellier Aurelien
Published: October 2017

Nucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonisation of novel habitats in a model tomato species,Solanum chilense.

We used R-gene enrichment sequencing (RENSeq) to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonisation by resequencing whole genomes from threeS. chilenseplants from three key populations, and performing Approximate Bayesian Computation using data from the 14 populations.

Using these parameters we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution, and identified small subsets of outlier NLRs exhibiting signatures of selection across populations.

NLRs under selection between habitats are more often helper genes, while those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R gene adaptation during colonisation of different habitats.
Machine-assisted cultivation and analysis of biofilms
Authors: Hansen Silla H. , Kabbeck Tobias , Radtke Carsten P. , Krause Susanne , Krolitzki Eva , Peschke Theo , Gasmi Jannis , Rabe Kersten S. , Wagner Michael , Horn Harald , Hubbuch Jürgen , Gescher Johannes , Niemeyer Christof M.
Published: October 2017

Biofilms are the natural form of life of the majority of microorganisms. These multispecies consortia are intensively studied not only for their effects on health and environment but also because they have an enormous potential as tools for biotechnological processes. Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy, chromatography and optical coherence tomography. The system is operable under oxic and anoxic conditions, allowing for different gases as feeding sources and offers high spatiotemporal resolution in the analysis of metabolites and biofilm composition. We demonstrate the platform’s performance by monitoring the self-organized separation of mixed cultures along autonomously created gradients, the productivity of biofilms along the microfluidic channel and the enrichment of microbial nanoorganisms.
A Double Error Dynamic Asymptote Model of Associative Learning
Authors: Kokkola Niklas H. , Mondragón Esther , Alonso Eduardo
Published: October 2017

In this paper a formal model of associative learning is presented which incorporates representational and computational mechanisms that, as a coherent corpus, empower it to make accurate predictions of a wide variety of phenomena that so far have eluded a unified account in learning theory. In particular, the Double Error Dynamic Asymptote (DDA) model introduces: 1) a fully-connected network architecture in which stimuli are represented as temporally clustered elements that associate to each other, so that elements of one cluster engender activity on other clusters, which naturally implements neutral stimuli associations and mediated learning; 2) a predictor error term within the traditional error correction rule (the double error), which reduces the rate of learning for expected predictors; 3) a revaluation associability rate that operates on the assumption that the outcome predictiveness is tracked over time so that prolonged uncertainty is learned, reducing the levels of attention to initially surprising outcomes; and critically 4) a biologically plausible variable asymptote, which encapsulates the principle of Hebbian learning, leading to stronger associations for similar levels of cluster activity. The outputs of a set of simulations of the DDA model are presented along with empirical results from the literature. Finally, the predictive scope of the model is discussed.
MetaCompass: Reference-guided Assembly of Metagenomes
Authors: Cepeda Victoria , Liu Bo , Almeida Mathieu , Hill Christopher M. , Koren Sergey , Treangen Todd J. , Pop Mihai
Published: November 2017

Metagenomic studies have primarily relied on de novo approaches for reconstructing genes and genomes from microbial mixtures. While database driven approaches have been employed in certain analyses, they have not been used in the assembly of metagenomes. Here we describe the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods. When combined with de novo assembly approaches, we show that MetaCompass can generate more complete assemblies than can be obtained by de novo assembly alone, and improve on assemblies from the Human Microbiome Project (over 2,000 samples).
OMGene: Mutual improvement of gene models through optimisation of evolutionary conservation
Authors: Dunne Michael P. , Kelly Steven
Published: November 2017

Background

The accurate determination of the genomic coordinates for a given gene – itsgene model –is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, often disagree on the model for a given predicted gene, with some or all of the variant gene models failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq and mass spectrometry. However, these resources are not always available, and rarely give a comprehensive portrait of an organism’s transcriptome due to temporal and tissue-specific expression profiles.

Results

Orthology between genes provides evolutionary evidence to guide the construction of gene models. OMGene (Optimise My Gene) aims to optimise gene models in the absence of experimental data by optimising the derived amino acid alignments for gene models within orthogroups. Using RNA-seq data sets from plants and fungi, considering intron/exon junction representation and exon coverage, and assessing the intra-orthogroup consistency of subcellular localisation predictions, we demonstrate the utility of OMGene for improving gene models in annotated genomes.

Conclusions

We show that significant improvements in the accuracy of gene model annotations can be made in both established andde novoannotated genomes by leveraging information from multiple species.
Equality between the sexes in plants for costs of reproduction; evidence from the dioecious Cape genusLeucadendron(Proteaceae)
Authors: Midgley Jeremy J. , West Adam G. , Cramer Michael D.
Published: November 2017

It has been argued that sexual allocation is greater for female function than male function in plants in general and specifically for the large dioecious Cape genusLeucadendron. Here, we use new interpretations of published information to support the hypothesis of equality between sexes in this genus. The explanations are based on the fire ecology of the Cape that results in reproductive synchrony, reproductive doubling and competitive symmetry. Firstly, strict post-fire seedling establishment of the reseeder life-history in the Cape results in single-aged populations. Consequently, the reproductive and vegetative schedules of males must synchronously track that of females. This implies equal allocation to sex. Secondly, after fires, dioecious females have double the seedling to adult ratio of co-occurring hermaphrodites. This indicates that being liberated from male function allows females access to resources that double their fitness compared to hermaphrodites. Therefore, male and female costs of reproduction are equal in hermaphrodites. Thirdly, competitive symmetry must occur because males and female plants will frequently encounter each other as close near neighbours. Competitive asymmetry would both reduce mating opportunities and skew local sex ratios. The evidence to date is for 1:1 sex ratios in small plots and this indicates competitive symmetry and a lack of dimorphic niches. Finally, vegetatively dimorphic species must also allocate equally to sex, or else sexual asynchrony, lack of reproductive doubling or competitive asymmetry will occur.
Subsoil arbuscular mycorrhizal fungal communities in arable soil differ from those in topsoil
Authors: Sosa-Hernández Moisés A. , Roy Julien , Hempel Stefan , Kautz Timo , Köpke Ulrich , Uksa Marie , Schloter Michael , Caruso Tancredi , Rillig Matthias C.
Published: November 2017

Arbuscular mycorrhizal fungi are recognized as important drivers of plant health and productivity in agriculture but very often existing knowledge is limited to the topsoil. With growing interest in the role of subsoil in sustainable agriculture, we used high-throughput Illumina sequencing on a set of samples encompassing drilosphere, rhizosphere and bulk soil, in both top- and subsoil. Our results show subsoil AMF communities harbor unique Operational Taxonomic Units (OTUs) and that both soil depths differ in community structure both at the OTU and family level. Our results emphasize the distinctness of subsoil AMF communities and the potential role of subsoil as a biodiversity reservoir.
The molecular basis for Pompe disease revealed by the structure of human acid α-glucosidase
Authors: Deming Derrick , Lee Karen , McSherry Tracey , Wei Ronnie R. , Edmunds Tim , Garman Scott C.
Published: November 2017

Pompe disease results from a defect in human acid α-glucosidase (GAA), a lysosomal enzyme that cleaves terminal α1-4 and α1-6 glucose from glycogen. In Pompe disease (also known as Glycogen Storage Disorder type II), the accumulation of undegraded glycogen in lysosomes leads to cellular dysfunction, primarily in muscle and heart tissues. Pompe disease is an active candidate of clinical research, with pharmacological chaperone therapy tested and enzyme replacement therapy approved. Despite production of large amounts of recombinant GAA annually, the structure of GAA has not been reported until now. Here, we describe the first structure of GAA, at 1.7Å resolution. Three structures of GAA complexes reveal the molecular basis for the hundreds of mutations that lead to Pompe disease and for pharmacological chaperoning in the protein. The GAA structure reveals a surprising second sugar-binding site 34Å from the active site, suggesting a possible mechanism for processing of large glycogen substrates. Overall, the structure will assist in the design of next-generation treatments for Pompe disease.
Head-Direction drift in rat pups is consistent with an angular path-integration process
Authors: Tocker Gilad , Borodach Eli , Bjerknes Tale L. , Moser May-Britt , Moser Edvard I. , Derdikman Dori
Published: November 2017

The sense of direction is a vital computation, whose neural basis is considered to be carried out by head-direction cells. One way to estimate head-direction is by integrating head angular-velocity over time. However, this process results in error accumulation resembling a random walk, proportional to , which constitutes a mark for a path integration process. In the present study we analyzed previously recorded data to quantify the drift in head-direction cells of rat pups before and after eye-opening. We found that in rat pups before eye-opening the drift propagated as a random walk, while in rats after eye-opening the drift was lower. This suggests that a path-integration process underlies the estimation of head-direction, such that before eye-opening the head-direction system runs in an open-loop manner and accumulates error. After eye-opening, visual-input, such as arena shape, helps to correct errors and thus compute the sense of direction accurately.
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
Authors: Cameron Daniel L. , Schröder Jan , Penington Jocelyn Sietsma , Do Hongdo , Molania Ramyar , Dobrovic Alexander , Speed Terence P. , Papenfuss Anthony T.
Published: November 2017

The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.
Molecular characterization of metastatic pancreatic neuroendocrine tumors (PNETs) using whole-genome and transcriptome sequencing
Authors: Wong Hui-li , Yang Kevin C. , Shen Yaoqing , Zhao Eric Y. , Loree Jonathan M. , Kennecke Hagen F. , Kalloger Steve E. , Karasinska Joanna M. , Lim Howard J. , Mungall Andrew J. , Feng Xiaolan , Davies Janine M. , Schrader Kasmintan , Zhou Chen , Karsan Aly , Jones Steven J.M. , Laskin Janessa , Marra Marco A. , Schaeffer David F. , Gorski Sharon M. , Renouf Daniel J.
Published: November 2017

Pancreatic neuroendocrine tumors (PNETs) are a genomically and clinically heterogeneous group of pancreatic neoplasms often diagnosed with distant metastases. Recurrent somatic mutations, chromosomal aberrations, and gene expression signatures in PNETs have been described, but the clinical significance of these molecular changes is still poorly understood, and the clinical outcomes of PNET patients remain highly variable. To help identify the molecular factors that contribute to PNET progression and metastasis, and as part of an ongoing clinical trial at the BC Cancer Agency (clinicaltrials.gov ID: NCT02155621), the genomic and transcriptomic profiles of liver metastases from five patients (four PNETs and one neuroendocrine carcinoma) were analyzed. In four of the five cases, we identified biallelic loss of MEN1 and DAXX as well as recurrent regions with loss of heterozygosity. Several novel findings were observed, including focal amplification of MYCN concomitant with loss of APC and TP53 in one sample with wild-type MEN1 and DAXX. Transcriptome analyses revealed up-regulation of MYCN target genes in this sample, confirming a MYCN-driven gene expression signature. We also identified a germline NTHL1 fusion event in one sample that resulted in a striking C>T mutation signature profile not previously reported in PNETs. These varying molecular alterations suggest different cellular pathways may contribute to PNET progression, consistent with the heterogeneous clinical nature of this disease. Furthermore, genomic profiles appeared to correlate well with treatment response, lending support to the role of prospective genotyping efforts to guide therapy in PNETs.
Distribution features and intellectual structures of digital humanities
Authors: Wang Qing
Published: November 2017

Purpose

The purpose of this paper is to conduct a retrospective bibliometric analysis of documents about digital humanities, an emerging but interdisciplinary movement. It examines the distribution of research outputs and languages, identifies the active journals and institutions, dissects the network of categories and cited references, and interprets the hot research topics.

Design/methodology/approach

The source data are derived from the Web of Science (WoS) core collection. To reveal the holistic landscape of this field, VOSviewer and CiteSpace as popular visualization tools are employed to process the bibliographic data including author, category, reference, and keyword. Furthermore, the parameter design of the visualization tools follows the general procedures and methods for bibliometric analysis.

Findings

There is an obviously rapid growth in digital humanities research. English is still the leading academic language in this field. The most influential authors all come from or have scientific relationships with Europe and North America, and two leading countries of which are the UK and USA. Digital humanities is the result of a dynamic dialogue between humanistic exploration and digital means. This research field is closely associated with history, literary and cultural heritage, and information and library science.

Research limitations/implications

This analysis relies on the metadata information extracted from the WoS database; however, some valuable literatures in the field of digital humanities may not be retrieved from the database owing to the inherent challenge of topic search. This study is also restricted by the scope of publications, the limitation regarding the source of data is that WoS database may have underrepresented publications in this domain.

Originality/value

The output of this paper could be a valuable reference for researchers and practitioners interesting in the knowledge domain of digital humanities. Moreover, the conclusions of this retrospective analysis can be deemed as the comparable foundation for future study.
Prevalence and predictors of occupational stress among quarry workers in rural Rajasthan, India
Authors: Ahmad Absar
Published: November 2017

Purpose

Despite increasing recognition of the importance of mental health at the workplace, there is very little evidence and limited research information on the issue of the poor mental health of the workers, especially miners. The purpose of this paper is to assess the relationship between stress faced by quarry workers in consonance with their socio-demographic characteristics and their working conditions.

Design/methodology/approach

This study was a cross-sectional study of quarry workers with comparison groups in the Karauli district of Rajasthan, a state located in north-western India. The study was conducted during the period May-September 2014, as part of a doctoral program. The study sample comprised a total of 218 quarry workers along with a comparison group of 203 non-miners. The level of occupational stress was assessed by using a General Health Questionnaire consisting of 12 questions.

Findings

This study found that the comparison group was at a low risk of psychological stress as compared to the mine workers. The independent risk factors for occupational stress among workers were illiteracy, gender (female), married, divorced/separated, and suffering from some occupational health problem.

Social implications

This study concluded that mine workers are at a high level of stress, which underscores the need for urgent interventions from the government to address the issue. This is especially important as mine workers make significant contributions to the national income.

Originality/value

This paper fulfills an identified need to study the mental health status of quarry workers, thereby helping fill a persistent gap in Indian research on this issue.
Modes of soft skills learning: a case of university information professionals’ in Pakistan
Authors: Ahmad Sajjad , Ameen Kanwal , Ullah Midrar
Published: November 2017

Purpose

The purpose of this paper is to investigate the university information professionals (UIPs) preferred modes of soft skills learning and differences in their opinions based on gender, designations and experience.

Design/methodology/approach

Quantitative research design using a questionnaire was used for data collection. Data were analyzed through SPSSS version 20.0, using descriptive and inferential statistics. The population of the study included all the UIPs working in the central libraries of the general public sector 33 universities in Pakistan, with nearly a population of 560.

Findings

The major findings showed that “mentoring sessions by experts” was the most preferred mode of soft skills learning followed by “learning from colleagues”. It showed that UIPs preferred to learn soft skills from experts and colleagues. Independent-samples t-test results found that “mentoring session by experts” was more preferred by females than males. A one-way ANOVA results found significant differences of opinion regarding the “mentoring session by experts” method between librarians and assistant librarians (p = 0.044). Results were statistically significant also between more experienced and less experienced regarding “real project/assignment-based method” and “mentoring session by experts”. In addition, for “formal online courses” and “self-training through reading books”, results were statistically significant between experienced groups of 1-5 years and 11-15 years. Overall results indicated that from UIPs’ perspective, soft skills should be taught to them using face-to-face methods.

Originality/value

This is the first study in Pakistan that dealt with the preferred modes of soft skills learning of UIPs by using a large group (N = 372) of respondents.
Nutritional functional trait diversity of crops in south‐eastern Senegal
Authors: Wood Stephen A.
Published: November 2017

Ecological trait diversity metrics have been used to highlight the impacts of agriculture. Such metrics can also be used to include human nutrition—an important dimension of human well‐being—into assessments of agroecosystem function and services. Although crop yield is a common agroecosystem metric, it does not capture the multiple ways in which agriculture impacts people and the environment.

Given that nutrient composition of crops is a set of functional traits, I apply a suite of functional diversity metrics—functional divergence, richness, evenness and dispersion—to crop production data from south‐eastern Senegal. I also propose a new nutritional diversity metric—potential nutrient adequacy—to assess nutritional outcomes of different agricultural systems.

I demonstrate high variability in nutritional diversity and potential adequacy among households and administrative departments in south‐eastern Senegal. I show that most households produce nutritionally similar crops, rather than crops with high nutritional diversity. As a result, most households currently do not produce enough nutrients to meet minimal nutritional requirements.

Using a scenario approach, I show that intensifying yields of staple crops and diversifying production to include non‐staples can increase nutritional production and the potential to meet nutritional needs. I further show that a combination of intensification and diversification is needed to meet the need for a diverse group of nutrients.

Policy implications. I develop a new metric that indicates the potential for a food system to meet the nutritional requirements of a population. This tool will allow practitioners to assess the nutritional adequacy of a food system and to design food systems that optimize nutritional outcomes. Application of this metric to different production scenarios showed that combining yield intensification with crop diversification is important to meeting full nutritional targets for smallholder agriculture. There is a broader need for incorporating other social and socio‐ecological traits into trait‐based assessments of agroecosystems.
Expanding opportunities to learn to support inclusive education through drama‐enhanced literacy practices
Authors: Kilinc Sultan , Farrand Kathleen , Chapman Kathryn , Kelley Michael , Millinger Jenny , Adams Korbi
Published: November 2017

This study examines how the Early Years Educators at Play (EYEPlay) professional development (PD) programme supported inclusive learning settings for all children, including English language learners and students with disabilities. The EYEPlay PD model is a year‐long programme that integrates drama strategies into literacy practices within real‐classroom contexts. Inclusive education refers to ensuring equal opportunities to access and participation in learning activities for all students. Cultural‐historical activity theory was used to understand and unpack the drama practices. Twelve semi‐structured focus group interviews were conducted with 19 preschool teachers. The data were analysed via constant‐comparative and interpretive methods. The study findings showed that EYEPlay PD practices enhanced inclusive learning settings for diverse groups of students by increasing access and expanding opportunities to learn, and supporting a positive learning environment.
Review article: Sepsis in the emergency department – Part 1: Definitions and outcomes
Authors: Macdonald Stephen PJ , Williams Julian M , Shetty Amith , Bellomo Rinaldo , Finfer Simon , Shapiro Nathan , Keijzers Gerben
Published: November 2017

Sepsis has recently been redefined as acute organ dysfunction due to infection. The ED plays a critical role in identifying patients with sepsis. This is challenging due to the heterogeneity of the syndrome, and the lack of an objective standard diagnostic test. While overall mortality rates from sepsis appear to be falling, there is an increasing burden of morbidity among survivors. This largely reflects the growing proportion of older patients with comorbid illnesses among those treated for sepsis.
Consequences of proceeding with surgery after resuscitation from intra‐operative anaphylaxis
Authors: Sadleir P. H. M. , Clarke R. C. , Bozic B. , Platt P. R.
Published: November 2017

Intra‐operative acute hypersensitivity reactions require a decision to be made regarding whether to proceed with or abandon the planned surgical procedure once the patient has stabilised. Using retrospective case controls, we examined all cases (223) of proven acute hypersensitivity reactions from 2005 to 2014 in Western Australia, in which the syndrome was recognised by the treating clinician before or during surgery, to determine whether recovery outcomes were adversely affected by proceeding with the planned procedure. Surgery proceeded in 104 patients (47%) and was abandoned in 119 (53%). The severity of acute hypersensitivity reactions was Société Française d'Anesthésie et de Réanimation grade 1 or 2 in 56 patients (25%), grade 3 in 128 (56%) and grade 4 in 39 (17%). Abandoning surgery was more common in patients with increasing severity of hypersensitivity. The rate of major hypersensitivity‐related complications for all patients was zero for grade 1 and 2 reactions, 4.7% for grade 3 and 12.8% for grade 4. There were no deaths. Patients in whom surgery was completed were not observed to have a higher frequency of major hypersensitivity‐related complications when compared with cases of similar severity in whom surgery was abandoned. For patients admitted to the intensive care unit, proceeding with surgery was not associated with an increased duration of mechanical ventilation of the lungs. Our results suggest that, once initial resuscitation has been achieved and if resuscitative efforts can be re‐instituted if required, continuing with planned surgery in grade 1, 2 and 3 immediate hypersensitivity was not associated with poorer outcomes. After grade 3 reactions, there was a significant incidence of complications attributable to acute hypersensitivity regardless of whether surgery proceeded or was abandoned. Surgery was frequently abandoned in grade 4 immediate hypersensitivity and was associated with a high rate of complications.
Morningness–eveningness is not associated with academic performance in the afternoon school shift: Preliminary findings
Authors: Arrona‐Palacios Arturo , Díaz‐Morales Juan F.
Published: November 2017

Background

The effect of morningness–eveningness, sleep habits, and intelligence on academic performance has been studied in a fixed morning school shift. However, no studies have analysed these variables in an afternoon school shift and tested whether morningness–eveningness is related to academic performance beyond sleep habits and intelligence effects.

Aims

The psychometric properties of the Morningness–Eveningness Scale for Children (MESC) were analysed. Additionally, academic performance, sex, intelligence, sleep habits, and morningness–eveningness relationship in a morning and afternoon school shift were compared.

Sample

The sample consisted of 400 students at a secondary public school in Reynosa, Tamaulipas, in north‐eastern Mexico (195 boys and 205 girls; mean ± SD: 13.85 ± 0.70 years old) attending a double‐shift school system: 200 from the morning shift (99 boys and 101 girls) and 200 from the afternoon shift (96 boys and 104 girls).

Methods

The students completed the MESC as a measure of morningness–eveningness, a sleep habits survey, a test of academic performance, and the inductive reasoning subtest (R) of the Primary Mental Abilities battery.

Results

Adolescents in the two school shifts did not differ in academic performance and intelligence. In the afternoon shift, adolescents slept longer, reported less sleep deficit and social jet lag, and were more oriented to eveningness than adolescents in the morning shift. Sex (girls), sleep length, inductive reasoning, and morningness were associated with academic performance in the morning shift but only sex and intelligence in the afternoon shift.

Conclusions

The role of morningness–eveningness in academic performance in the afternoon shift is examined.
Development of motor imagery ability in children with developmental coordination disorder – A goal‐directed pointing task
Authors: Adams Imke L. J. , Lust Jessica M. , Steenbergen Bert
Published: November 2017

Children with developmental coordination disorder (DCD) have difficulties with the predictive control of movements. This was shown in studies that target motor imagery and motor planning, and appears to become particularly evident with increases in task complexity. In this study, we used a complex mental chronometry paradigm to examine the development of motor imagery ability in children with DCD, using a longitudinal design. Thirty children were included in the DCD group (aged 6–11 years) and age‐ and gender‐matched to 30 controls. The DCD group had a Movement Assessment Battery for Children‐2 score ≤16th percentile and the control group ≥25th percentile. Results of this study showed that children with DCD indeed had a significantly lower correlation between executed and imagined movements. Importantly, the increase in the correlation and linear fit during subsequent measurements was comparable for the DCD and control group. Together, these findings suggest a delayed developmental onset of motor imagery ability in DCD, but a similar rate of development over time compared to the control group. Based on these results, it seems likely that explicit motor imagery instructions can be used to improve predictive control in children with DCD.
Sometimes It's Good to be Short: The Serotonin Transporter Gene, Positive Parenting, and Adolescent Depression
Authors: Little Keriann , Olsson Craig A. , Whittle Sarah , Macdonald Jacqui A. , Sheeber Lisa B. , Youssef George J. , Simmons Julian G. , Sanson Ann V. , Foley Debra L. , Allen Nicholas B.
Published: November 2017

In threatening environments, the short (S) allele of 5‐HTTLPR is proposed to augment risk for depression. However, it is unknown whether 5‐HTTLPR variation increases risk for depression in environments of deprivation, lacking positive or nurturant features. Two independent longitudinal studies (n = 681 and 176, respectively) examined whether 5‐HTTLPR moderated associations between low levels of positive parenting at 11–13 years and subsequent depression at 17–19 years. In both studies only LL homozygous adolescents were at greater risk for depression with decreasing levels of positive parenting. Thus, while the S allele has previously been identified as a susceptible genotype, these findings suggest that the L allele may also confer sensitivity to depression in the face of specific environmental challenges.
Social Beliefs and Visual Attention: How the Social Relevance of a Cue Influences Spatial Orienting
Authors: Gobel Matthias S. , Tufft Miles R. A. , Richardson Daniel C.
Published: November 2017

We are highly tuned to each other's visual attention. Perceiving the eye or hand movements of another person can influence the timing of a saccade or the reach of our own. However, the explanation for such spatial orienting in interpersonal contexts remains disputed. Is it due to the social appearance of the cue—a hand or an eye—or due to its social relevance—a cue that is connected to another person with attentional and intentional states? We developed an interpersonal version of the Posner spatial cueing paradigm. Participants saw a cue and detected a target at the same or a different location, while interacting with an unseen partner. Participants were led to believe that the cue was either connected to the gaze location of their partner or was generated randomly by a computer (Experiment 1), and that their partner had higher or lower social rank while engaged in the same or a different task (Experiment 2). We found that spatial cue‐target compatibility effects were greater when the cue related to a partner's gaze. This effect was amplified by the partner's social rank, but only when participants believed their partner was engaged in the same task. Taken together, this is strong evidence in support of the idea that spatial orienting is interpersonally attuned to the social relevance of the cue—whether the cue is connected to another person, who this person is, and what this person is doing—and does not exclusively rely on the social appearance of the cue. Visual attention is not only guided by the physical salience of one's environment but also by the mental representation of its social relevance.
Incidence of gastric adenocarcinoma among lesions diagnosed as low‐grade adenoma/dysplasia on endoscopic biopsy: A multicenter, prospective, observational study
Authors: Maekawa Akira , Kato Motohiko , Nakamura Takeshi , Komori Masato , Yamada Takuya , Yamamoto Katsumi , Ogiyama Hideharu , Nakahara Masanori , Kawai Naoki , Yabuta Takamasa , Mukai Akira , Hayashi Yoshito , Nishida Tsutomu , Iijima Hideki , Tsujii Masahiko , Morii Eiichi , Takehara Tetsuo
Published: November 2017

Background and Aim

Differentiation between gastric adenocarcinoma and low‐grade adenoma/dysplasia (LGA) on endoscopic forceps biopsy is difficult. We aim to clarify the incidence of carcinoma in specimens, obtained by endoscopic resection (ER), from cases that had been diagnosed as LGA (Vienna category 3) on endoscopic biopsy.

Methods

In this multicenter, prospective, observational study, patients with gastric adenoma (Vienna category 3 or 4.1) diagnosed on endoscopic forceps biopsy were enrolled. All the specimens were subjected to histopathological central review. Primary endpoint was the incidence of carcinoma (Vienna category 4.2 or over) among the biopsy‐proven gastric LGA. Secondary endpoints were the histological findings of resected specimens, clinicopathological features of carcinoma, and short‐term outcomes of all ER cases.

Results

Ninety‐five patients with 104 lesions diagnosed as gastric adenoma were enrolled. After central review of the biopsy specimens, 47 lesions were diagnosed as LGA and seven lesions (15%) as adenocarcinoma (95% confidence interval, 7.6–28%). Carcinoma was detected in lesions that had a minimum size of 6 mm; the incidence of carcinoma was higher in the larger lesions. There was a histological discrepancy between biopsy and ER material in more than 60% of the cases.

Conclusions

A substantial proportion of biopsy‐proven gastric LGA specimens were diagnosed as adenocarcinoma after ER. This indicated histological discrepancy between biopsy‐proven gastric LGA and histology of the resected material.
Do Board Gender Diversity and Director Typology Impact CSR Reporting?
Authors: Cabeza‐García Laura , Fernández‐Gago Roberto , Nieto Mariano
Published: November 2017

By studying female directors and their typology, this paper contributes to the empirical evidence relating to board gender diversity and the disclosure of corporate social responsibility (CSR) information. An ordered random effect probit model was applied to a panel of Spanish non‐financial and non‐insurance listed firms over the 2009–2013 period. The analyses revealed that a higher percentage of women in boardrooms and in groups of outside and independent directors imply better CSR disclosure. These results hold for corporations with a critical mass of three women on the board and among outside directors.
Meta‐heuristic multi‐ and many‐objective optimization techniques for solution of machine learning problems
Authors: Rodrigues Douglas , Papa João P. , Adeli Hojjat
Published: November 2017

Recently, multi‐ and many‐objective meta‐heuristic algorithms have received considerable attention due to their capability to solve optimization problems that require more than one fitness function. This paper presents a comprehensive study of these techniques applied in the context of machine learning problems. Three different topics are reviewed in this work: (a) feature extraction and selection, (b) hyper‐parameter optimization and model selection in the context of supervised learning, and (c) clustering or unsupervised learning. The survey also highlights future research towards related areas.