bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for the rhythmic perceptual sampling of auditory scenes
Authors: Kayser Christoph 
Published: April 2019

AbstractConverging results suggest that perception is controlled by rhythmic processes in the brain. In the auditory domain, neuroimaging studies show that the perception of brief sounds is shaped by rhythmic activity prior to the stimulus and electrophysiological recordings have linked delta band (1-2 Hz) activity to the functioning of individual neurons. These results have promoted theories of rhythmic modes of listening and generally suggest that the perceptually relevant encoding of acoustic information is structured by rhythmic processes along auditory pathways. A prediction from this perspective – which so far has not been tested – is that such rhythmic processes also shape how acoustic information is combined over time to judge extended soundscapes. The present study was designed to directly test this prediction. Human participants judged the overall change in perceived frequency content in temporally extended (1.2 to 1.8 s) soundscapes, while the perceptual use of the available sensory evidence was quantified using psychophysical reverse correlation. Model-based analysis of individual participant’s perceptual weights revealed a rich temporal structure, including linear trends, a U-shaped profile tied to the overall stimulus duration, and importantly, rhythmic components at the time scale of 1 to 2Hz. The collective evidence found here across four versions of the experiment supports the notion that rhythmic processes operating on the delta band time scale structure how perception samples temporally extended acoustic scenes.
Versatile polyketide biosynthesis platform for production of aromatic compounds in yeast
Authors: Jakočiūnas Tadas , Klitgaard Andreas K. , Romero-Suarez David , Petzold Christopher J. , Gin Jennifer W. , Tong Yaojun , Frandsen Rasmus J.N. , Weber Tilmann , Lee Sang Yup , Jensen Michael K. , Keasling Jay D. 
Published: April 2019

AbstractTo accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms, development of new, versatile, bio-based production platforms is required. Here we present a novel yeast platform for biosynthesis of bacterial aromatic polyketides. The platform is based on a synthetic polyketide synthase system enabling a first demonstration of bacterial aromatic polyketide biosynthesis in a eukaryotic host.
First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)
Authors: Ananthasayanam Sudhakar , Kothandaraman Harish , Nayee Nilesh , Saha Sujit , Baghel Dushyant Singh , Gopalakrishnan Kishore , Peddamma Sathish , Singh Ram Bahadur , Schatz Michael 
Published: April 2019

AbstractThis study reports the first haplotype phased reference quality genome assembly of ‘Murrah’ an Indian breed of river buffalo. A mother-father-progeny trio was used for sequencing so that the individual haplotypes could be assembled in the progeny. Parental DNA samples were sequenced on the Illumina platform to generate a total of 274 Gb paired-end data. The progeny DNA sample was sequenced using PacBio long reads and 10x Genomics linked reads at 166x coverage along with 802Gb of optical mapping data. Trio binning based FALCON assembly of each haplotype was scaffolded with 10x Genomics reads and super-scaffolded with BioNano Maps to build reference quality assembly of sire and dam haplotypes of 2.63Gb and 2.64Gb with just 59 and 64 scaffolds and N50 of 81.98Mb and 83.23Mb, respectively. BUSCO single copy core gene set coverage was > 91.25%, and gVolante-CEGMA completeness was >96.14% for both haplotypes. Finally, RaGOO was used to order and build the chromosomal level assembly with 25 scaffolds and N50 of 117.48 Mb (sire haplotype) and 118.51 Mb (dam haplotype). The improved haplotype phased genome assembly of river buffalo may provide valuable resources to discover molecular mechanisms related to milk production and reproduction traits.
EEG resting-state large-scale brain network dynamics are related to depressive symptoms
Authors: Damborská Alena , Tomescu Miralena I. , Honzírková Eliška , Barteček Richard , Hořínková Jana , Fedorová Sylvie , Ondruš Šimon , Michel Christoph M. 
Published: April 2019

AbstractBackgroundThe few previous studies on resting-state EEG microstates in depressive patients suggest altered temporal characteristics of microstates compared to those of healthy subjects. We tested whether resting-state microstate temporal characteristics could capture large-scale brain network dynamic activity relevant to depressive symptomatology.MethodsTo evaluate a possible relationship between the resting-state large-scale brain network dynamics and depressive symptoms, we performed EEG microstate analysis in patients with moderate to severe depression within bipolar affective disorder, depressive episode, and periodic depressive disorder, and in healthy controls.ResultsMicrostate analysis revealed six classes of microstates (A-F) in global clustering across all subjects. There were no between-group differences in the temporal characteristics of microstates. In the patient group, higher symptomatology on the Montgomery-Åsberg Depression Rating Scale, a questionnaire validated as measuring severity of depressive episodes in patients with mood disorders, correlated with higher occurrence of microstate A (Spearman’s rank correlation, r = 0.70, p < 0.01).ConclusionOur results suggest that the observed interindividual differences in resting-state EEG microstate parameters could reflect altered large-scale brain network dynamics relevant to depressive symptomatology during depressive episodes. These findings suggest the utility of the microstate analysis approach in an objective depression assessment.
Bifunctional Small Molecule Ligands of K-Ras Induce Its Association with Immunophilin Proteins
Authors: Zhang Ziyang , Shokat Kevan M. 
Published: April 2019

AbstractHere we report the design, synthesis and characterization of bifunctional chemical ligands that induce the association of Ras with ubiquitously expressed immunophilin proteins such as FKBP12 and cyclophilin A. We show this approach is applicable to two distinct Ras ligand scaffolds, and that both the identity of the immunophilin ligand and the linker chemistry affect compound efficacy in biochemical and cellular contexts. These ligands bind to Ras in an immunophilin-dependent fashion and mediate the formation of tripartite complexes of Ras, immunophilin and the ligand. The recruitment of cyclophilin A to GTP-bound Ras blocks its interaction with B-Raf in biochemical assays. Our study demonstrates the feasibility of ligand-induced association of Ras with intracellular proteins and suggests it as a promising therapeutic strategy for Rasdriven cancers.
Epigenetic bookmarking of H2S exposure in Caenorhabditis elegans
Authors: Fawcett Emily M. , Johnson Jenna K. , Braden Chris , Garcia Esteli M. , Miller Dana L. 
Published: April 2019

AbstractPhysiological memories of environmental stress can serve to predict future environmental changes, allowing the organism to initiate protective mechanisms and survive. Although physiological memories, or bookmarks, of environmental stress have been described in a wide range of organisms, from bacteria to plants to humans, the mechanism by which these memories persist in the absence of stress is still largely unknown. We have discovered that C. elegans transiently exposed to low doses of hydrogen sulfide (H2S) survive subsequent exposure to otherwise lethal H2S concentrations and induce H2S-responsive transcripts more robustly than naïve controls. H2S bookmarking can occur at any developmental stage and persists through cell divisions and development but is erased by fasting. We show that maintenance of the H2S bookmark requires the SET-2 histone methyltransferase and the CoREST-like demethylase complex. We propose a model in which exposure to low doses of H2S generates a long-lasting, epigenetic memory by modulating H3K4me2 modifications at specific promoters. Understanding the fundamental aspects of H2S bookmarking in this tractable system can provide mechanistic insight into how environmental exposures are translated into the epigenetic landscape in animals.
Finding high-quality metal ion-centric regions across the worldwide Protein Data Bank
Authors: Yao Sen , Moseley Hunter N.B. 
Published: April 2019

AbstractAs the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. In this study, we systematically analyzed 3.5 Å regions around all metal ions across all PDB entries with supporting electron density maps available from the PDB in Europe. All resulting metal ion-centric regions were evaluated with respect to four quality-control criteria involving electron density resolution, atom occupancy, symmetry atom exclusion, and regional electron density discrepancy. The resulting list of metal binding sites passing all four criteria possess high regional structural quality and should be beneficial to a wide variety of downstream analyses. This study demonstrates an approach for the pan-PDB evaluation of metal binding site structural quality with respect to underlying x-ray crystallographic experimental data represented in available electron density maps of proteins. For non-crystallographers in particular, we hope to change the focus and discussion of structural quality from a global evaluation to a regional evaluation, since all structural entries in the wwPDB appear to have both regions of high and low structural quality.
Effect of Septoria brown spot on soybean yield in Illinois
Authors: Lin Heng-An , Villamil María B. , Mideros Santiago X. 
Published: April 2019

AbstractBrown spot caused by Septoria glycines is a prevalent foliar disease in all soybean production areas. Application of foliar fungicides after bloom reduces the disease severity, yet yield responses are not consistent among locations and years. Our research goal was to determine the effect of different levels of Septoria brown spot on yield. Different levels of disease severity were effectively obtained in the field by weekly application of chlorothalonil for three, six, and nine times after disease inoculation at V3/V4 stage. Fungicide treatments had a significant effect on vertical progress and chlorotic area with no statistically significant effect on yield. Soybean yield was negatively correlated with vertical progress of the disease (r = −0.36). The vertical progress was the best linear predictor of yield. Based on this model, when the vertical progress of brown spot at R6 increased by 10%, the yield decreased by 142.13 kg/ha (3.4%). A variance component analyses of our data showed that location was the most critical factor, illustrating the significant effect of local environmental conditions on the disease. Power analyses indicated that at least eight locations are needed to detect an effect of 269 kg/ha. Our results provide useful information to improve the experimental design for future experiments addressing the yield constrain by late season diseases of soybean.
Dropout from maternity continuum of care and associated factors among women in Debre Markos town, Northwest Ethiopia
Authors: Amare Nakachew Sewnet , Araya Bilen Mekonnen , Asaye Mengstu Melkamu 
Published: April 2019

AbstractIntroductionMaternity continuum of care is the continuity of maternity health care services that a woman uses antenatal care, skill birth attendant, and postnatal care. This Continuum of care in maternal health has become one of the government concern and program for planning and evaluating strategies within currently existing maternal health system of Ethiopia. It is an important intervention in reducing maternal and neonatal morbidity and mortality. However, there is no clear information on the proportion of dropout from maternity continuum of care in Ethiopia.ObjectiveThe aim of this study was to assess proportion and associated factors of dropout from maternity continuum of care among mothers who gave birth in the last 12 months in Debre Markos town, Northwest Ethiopia, 2018.MethodsA community-based cross-sectional study with cluster sampling technique was conducted among 605 mothers who gave birth in the last 12 months in Debre Markos town. The data were collected from August 1-30/ 2018 by face to face interview through pretested and semi-structured questionnaire. Binary logistic regressions (Bivariable and Multivariable) logistic regression model were done. In multivariable analysis variables with P-value < 0.05 in 95% confidence interval for Adjusted odds ratio (AOR) was used to determine factors associated with dropout from maternity continuum of care.ResultsThe proportion of drop out from maternity continuum of care was found to be 32.2 %(95%CI: 28.4-36.2). Have not exposure to media (AOR= 2.62, CI: 1.465-4.675), women who heard about PNC (AOR= 0.07, 95%CI: 0.035-0.154), unplanned pregnancy (AOR= 3.40, CI: 1.114-10.389), and having<4 ANC follow up (AOR = 3.03, CI: 1.963-4.685) were statistically significant variable with the dropout from maternity continuum of care.Conclusion and recommendationsIn this study, the proportion of dropout from maternity continuum of care is found to be high. The greatest gap and predictors for dropout was observed at postnatal care level, to reduce this drop out interventions on specified associated factors need to be implemented.
Learning supervised embeddings for large scale sequence comparisons
Authors: Kimothi Dhananjay , Biyani Pravesh , Hogan James M , Soni Akshay , Kelly Wayne 
Published: April 2019

Similarity-based search of sequence collections is a core task in bioinformatics, one dominated for most of the genomic era by exact and heuristic alignment-based algorithms. However, even efficient heuristics such as BLAST may not scale to the data sets now emerging, motivating a range of alignment-free alternatives exploiting the underlying lexical structure of each sequence.In this paper, we introduce SuperVec, a novel supervised approach to learning sequence embeddings. Our method extends earlier Representation Learning (RL) based methods to include jointly contextual and class-related information for each sequence during training. This ensures that related sequence fragments have proximal representations in the target space, better reflecting the structure of the domain.Such representations may be used for downstream machine learning tasks or employed directly. Here, we apply SuperVec embeddings to a sequence retrieval task, where the goal is to retrieve sequences with the same family label as a given query. The SuperVec approach is extended further through H-SuperVec, a tree-based hierarchical method which learns embeddings across a range of feature spaces based on the class labels and their exclusive and exhaustive subsets.Experiments show that supervised learning of embeddings based on sequence labels using SuperVec and H-SuperVec provides a substantial improvement in retrieval performance over existing (unsupervised) RL-based approaches. Further, the new methods are an order of magnitude faster than BLAST for the database retrieval task, supporting hybrid approaches in which SuperVec rapidly filters the collection so that only potentially relevant records remain, allowing slower, more accurate methods to be executed quickly over a far smaller dataset. Thus, we may achieve faster query processing and higher precision than before.Finally, for some problems, direct use of embeddings is already sufficient to yield high levels of precision and recall. Extending this work to encompass weaker homology is the subject of ongoing research.
Mapping of multiple complementary sex determination loci in a parasitoid wasp
Authors: Matthey-Doret Cyril , van der Kooi Casper J. , Jeffries Daniel L. , Bast Jens , Dennis Alice B. , Vorburger Christoph , Schwander Tanja 
Published: April 2019

AbstractSex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, a large insect order comprising ants, bees and wasps, is known as complementary sex determination (CSD). In species with CSD, heterozygosity at one or several loci induces female development. Here, we identify the genomic regions putatively underlying multi-locus CSD in the parasitoid wasp Lysiphlebus fabarum using restriction-site associated DNA sequencing. By analysing segregation patterns at polymorphic sites among 331 diploid males and females, we identify four CSD candidate regions, all on different chromosomes. None of the candidate regions feature evidence for homology with the csd gene from the honeybee, the only species in which CSD has been characterized, suggesting that CSD in L. fabarum is regulated via a novel molecular mechanism. Moreover, no homology is shared between the candidate loci, in contrast to the idea that multi-locus CSD should emerge from duplications of an ancestral single-locus system. Taken together, our results suggest that the molecular mechanisms underlying CSD in Hymenoptera are not conserved between species, raising the question as to whether CSD may have evolved multiple times independently in the group.Author summaryThe genetic or environmental signals that govern whether an organism develops into a male or female differ across species, and understanding their evolution is a key aspect of biology. In this paper, we focus on complementary sex determination (CSD), a genetic sex determination system found in many species of bees, ants and wasps where heterozygosity at one or multiple genetic regions determines the sex of the individual. We identify multiple genetic regions in the parasitoid wasp species Lysiphlebus fabarum that are likely underlying CSD. We show that these candidate CSD regions share no similarity with each other and that they differ from the CSD region known in the honey bee, the only species with a well-characterized CSD system. Our results suggest a different molecular mechanism underlying CSD in the wasp and that multiple CSD regions do not necessarily arise from duplications as generally thought.
Accounting for modern slavery: an analysis of Australian listed company disclosures
Authors: Christ Katherine Leanne , Rao Kathyayini Kathy , Burritt Roger Leonard 
Published: April 2019

Purpose
Given the impending introduction of legislation requiring large Australian listed companies to make supply chain disclosures about modern slavery, the paper aims to reveal current voluntary practice. The purpose of this paper is to provide a benchmark for assessing the current engagement of large companies with modern slavery in Australia.

Design/methodology/approach
Institutional theory provides the foundation for assessing current voluntary practice in relation to modern slavery disclosures by large Australian listed companies. Content analysis is used to identify quantity and quality of modern slavery disclosures of the top 100 companies listed on the Australian Stock Exchange. The contents of annual and standalone reports available on websites, as well as other online disclosures, are examined using terms associated with modern slavery identified from the literature.

Findings
Evidence gathered about modern slavery disclosures by ASX 100 companies shows information in annual and standalone reports reveal far less than other disclosures on company websites. Overall, the volume and quality of disclosures are low and, where made, narrative. A wide range of themes on modern slavery are disclosed with bribery and corruption and human rights issues dominant. Although currently in line with institutional theory, as there appear to be mimetic processes encouraging disclosure, results support the idea that legislation is needed to encourage further engagement.

Research limitations/implications
The paper provides a baseline of understanding about the volume and quality of modern slavery disclosures as a foundation for future research into the practices of Australian companies prior to the signalled introduction of legislation mandating reporting. It also identifies potential lines of research. The sample only examines large Australian listed companies which restricts generalisation from the results.

Originality/value
This is the first academic research paper to examine quantity and quality of modern slavery disclosures of large Australian companies. Results add support for the introduction of legislation by government.
Incivility, satisfaction and turnover intention of tourist hotel chefs
Authors: Chen Hsi-Tien , Wang Chih-Hung 
Published: April 2019

PurposeThis study examines the relationships among workplace incivility, job satisfaction and turnover intention for tourist hotel chefs. Furthermore, emotional intelligence is taken as the moderating variable on the relationships between workplace incivility and job satisfaction and workplace incivility and turnover intention.Design/methodology/approachTourist hotel chefs were invited to participate in this study using purposive sampling, and a structured questionnaire was administered to carry out the investigation on tourist hotel chefs.FindingsThe results show that workplace incivility has negative effects on job satisfaction and casts positive effects on turnover intention through job satisfaction. Emotional intelligence has a significant moderating effect on the relationship between workplace incivility and job satisfaction.Originality/valueThis study firstly demonstrated the relationships among workplace incivility, job satisfaction and turnover intention for tourist hotel chefs. Furthermore, the moderating effect of emotional intelligence on the relationship between workplace incivility and job satisfaction was also validated.
Indonesian clinical psychologists’ perceptions of complementary and alternative medicine research and knowledge: a content analysis study
Authors: Liem Andrian 
Published: April 2019

PurposeAs part of a nationwide research about knowledge, attitude, experiences and educational needs towards complementary and alternative medicine (CAM) among Indonesian clinical psychologists (CPs), the purpose of this paper is to explore CPs’ perceptions of CAM research and their interest in learning CAM.Design/methodology/approachA link to an online survey was e-mailed to all 1,045 CPs across Indonesia. At the end of the survey, two open-ended questions were asked: “What do you think about CAM research in Indonesia?” and “Why are you interested in learning about CAM?”, which were responded to by 127 participants (87 per cent of females;Mage=36.67, SD=9.02). Participants’ responses were analysed using inductive qualitative content analysis.FindingsIt was found that two global themes for CPs’ perceptions of CAM were to improve participants’ professionalism and as part of continuing education and development for mental health professionals. The favourable responses in this study may reflect participants’ willingness to be involved in collaborative CAM research and education. Moreover, CAM was perceived as part of Indonesian culture and participants viewed CAM research and knowledge as a chance to promote Indonesian local wisdom to complement conventional psychotherapy.Research limitations/implicationsThese findings might call for stakeholders to integrate CAM knowledge into psychology education, facilitate CAM research in psychology settings and encourage collaborative CAM research. However, self-selection bias may limit the findings of this study.Originality/valueThis study explored perceptions of CAM research and interest in learning CAM that have rarely been investigated among mental health professionals and particularly, until now, have not been investigated in Indonesia.