bluuebunny/crossref_metadata_2025 huggingface dataset:
Explicit strategies in force field adaptation
Authors: Schween Raphael , McDougle Samuel D. , Hegele Mathias , Taylor Jordan A.
Published: July 2019

In recent years, it has become increasingly clear that a number of learning processes are at play in visuomotor adaptation tasks. In addition to the presumed formation of an internal model of the perturbation, learners can also develop explicit knowledge allowing them to select better actions in responding to a given perturbation. Advances in visuomotor rotation experiments have underscored the important role that such “explicit learning” plays in shaping adaptation to kinematic perturbations. Yet, in adaptation to dynamic perturbations, its contribution has been largely overlooked, potentially because compensation of a viscous force field, for instance, is difficult to assess by commonly-used verbalization-based approaches. We therefore sought to assess the contribution of explicit learning in learners adapting to a dynamic perturbation by two novel modifications of a force field experiment. First, via an elimination approach, we asked learners to abandon any cognitive strategy before selected force channel trials to expose consciously accessible parts of overall learning. Learners indeed reduced compensatory force compared to standard Catch channels. Second, via a manual reporting approach, we instructed a group of learners to mimic their right hand’s adaptation by moving with their naïve left hand. While a control group displayed negligible left-hand force compensation, the Mimic group reported forces that approximated right-hand adaptation but appeared to under-report the velocity component of the force field in favor of a more position-based component. We take these results to clearly demonstrate the contribution of explicit learning to force adaptation, underscoring its relevance to motor learning in general.

New & Noteworthy

While the role of explicit learning has recently been appreciated in visuomotor adaptation tasks, their contribution to force field adaptation has not been as widely acknowledged. To address this issue, we employed two novel methods to assay explicit learning in force field adaptation tasks and found that learners can voluntarily control aspects of force production and manually report them with their untrained limb. This suggests that an explicit component contributes to force field adaptation and may provide alternative explanations to behavioral phenomena commonly thought to reveal a complex organization of internal models in the brain.
Development of a PC12 cell-based assay forin vitroscreening of catechol-O-methyltransferase inhibitors
Authors: Zhang Gongliang , Buchler Ingrid P. , DePasquale Michael , Wormald Michael , Liao Gangling , Wei Huijun , Barrow James C. , Carr Gregory V.
Published: July 2019

The male rat adrenal pheochromocytoma cell-originated PC12 cell line can synthesize and release catecholamine neurotransmitters, and it has been widely used as a model system in cell biology and toxicology research. Catechol-O-methyltransferase (COMT) is involved in the inactivation of the catecholamine neurotransmitters, and it is particularly important for theregulation of dopamine. In this study, we explored the feasibility of using PC12 cells as anin vitrodrug screening platform to compare the activity of multiple COMT inhibitors. Incubation of PC12 cells with tolcapone, a highly potent and selective COMT inhibitor, increased the concentrations of dopamine and its metabolite 3,4-dihydroxyphenylacetic acid (DOPAC) while reducing the metabolites 3-methoxytyramine (3-MT) and homovanillic acid (HVA) in the cell culture medium. LIBD-3, a novel, non-nitrocatechol COMT inhibitor produced similar effects compared to tolcapone. LIBD-4, a less potent inhibitor, exhibited the expected right-shift in functional inhibition in the assay. These results match the knownin vivoeffects of COMT inhibition in rodents. Together, these data support the continued use of PC12 cells as anin vitroscreen that bridges cell-free enzyme assays and more costlyin vivoassays.
Visualizing the periodic Ribo-seq reads with RiboPlotR
Authors: Wu Hsin-Yen Larry , Hsu Polly Yingshan
Published: July 2019

Background

Ribo-seq has revolutionized the study of mRNA translation in a genome-wide scale. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes decipher three nucleotides each time. While the 3-nt periodicity has been widely used to study novel translation events and identify small open reading frames on presumed non-coding RNAs, tools which allow the visualization of those events remain underdeveloped.

Findings

RiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads for all annotated transcript isoforms in a context of a given gene. In particular, RiboPlotR plots Ribo-seq reads mapped in three reading frames using three colors for one isoform model at a time. Moreover, RiboPlotR shows Ribo-seq reads on upstream ORFs, 5’ and 3’ untranslated regions and introns, which is critical for observing new translation events and potential regulatory mechanisms.

Conclusions

RiboPlotR is freely available (https://github.com/hsinyenwu/RiboPlotR) and allows the visualization of the translating features in Ribo-seq data.
Expression Profiling, Downstream Signaling and Subunit Interactions of GPA2/GPB5 in the Adult MosquitoAedes aegypti
Authors: Rocco David A. , Paluzzi Jean-Paul V.
Published: July 2019

GPA2/GPB5 and its receptor constitute a glycoprotein hormone-signalling system native to the genomes of most vertebrate and invertebrate organisms, including humans and mosquitoes. Unlike the well-studied gonadotropins and thyrotropin, the exact function of GPA2/GPB5 is unclear, and whether it elicits its functions as heterodimers, homodimers or as independent monomers remains unknown. Here, the glycoprotein hormone signalling system was investigated in adult mosquitoes, where GPA2 and GPB5 subunit transcripts co-localized to bilateral pairs of neuroendocrine cells within the first five abdominal ganglia of the central nervous system. Unlike human GPA2/GPB5 that demonstrated strong heterodimerization between subunits, the GPA2/GPB5 subunits inA. aegyptilacked evidence of heterodimerization when heterologously expressed. Interestingly, cross-linking analysis to determine subunit interactions revealedA. aegyptiandH. sapiensGPA2 and GPB5 subunits form homodimers, and treatments with independent subunits did not activateA. aegyptiLGR1 orH. sapiensTSH receptor, respectively. Since mosquito GPA2/GPB5 heterodimers were not evident by heterologous expression of independent subunits, a tethered construct was generated for expression of the subunits as a single polypeptide chain to improve heterodimer formation. Our findings revealedA. aegyptiLGR1 elicited constitutive activity that elevated levels of cAMP as determined by increased cAMP-dependent luminescence. However, upon treatment with recombinant tethered GPA2/GPB5 heterodimers, an inhibitory G protein (Gi) signalling cascade is initiated and forskolin-induced cAMP production is inhibited. These results provide evidence towards the functional deorphanization of LGR1 and, moreover, further support the notion that GPA2/GPB5 heterodimerization is a requirement for glycoprotein hormone receptor activation.
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Authors: Liang Qiaoxing , Bible Paul W. , Liu Yu , Zou Bin , Wei Lai
Published: July 2019

Taxonomic classification is a crucial step for metagenomics applications including disease diagnostics, microbiome analyses, and outbreak tracing. Yet it is unknown what deep learning architecture can capture microbial genome-wide features relevant to this task. We report DeepMicrobes (https://github.com/MicrobeLab/DeepMicrobes), a computational framework that can perform large-scale training on > 10,000 RefSeq complete microbial genomes and accurately predict the species-of-origin of whole metagenome shotgun sequencing reads. We show the advantage of DeepMicrobes over state-of-the-art tools in precisely identifying species from microbial community sequencing data. Therefore, DeepMicrobes expands the toolbox of taxonomic classification for metagenomics and enables the development of further deep learning-based bioinformatics algorithms for microbial genomic sequence analysis.
STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions
Authors: Lee Donghoon , Shi Manman , Moran Jennifer , Wall Martha , Zhang Jing , Liu Jason , Fitzgerald Dominic , Kyono Yasuhiro , Ma Lijia , White Kevin P , Gerstein Mark
Published: July 2019

Background

High-throughput reporter assays, such as self-transcribing active regulatory region sequencing (STARR-seq), allow for unbiased and quantitative assessment of enhancers at a genome-wide scale. Recent advances in STARR-seq technology have employed progressively more complex genomic libraries and increased sequencing depths, to assay larger sized regions, up to the entire human genome. These advances necessitate a reliable processing pipeline and peak-calling algorithm.

Results

Most STARR-seq studies have relied on chromatin immunoprecipitation sequencing (ChIP-seq) processing pipelines. However, there are key differences in STARR-seq versus ChIP-seq. First, STARR-seq uses transcribed RNA to measure the activity of an enhancer, making an accurate determination of the basal transcription rate important. Second, STARR-seq coverage is highly non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content and mappability. Lastly, here, we observed a clear correlation between RNA thermodynamic stability and STARR-seq readout, suggesting that STARR-seq may be sensitive to RNA secondary structure and stability. Considering these findings, we developed a negative-binomial regression framework for uniformly processing STARR-seq data, called STARRPeaker. In support of this, we generated whole-genome STARR-seq data from the HepG2 and K562 human cell lines and applied STARRPeaker to call enhancers.

Conclusions

We show STARRPeaker can unbiasedly detect active enhancers from both captured and whole-genome STARR-seq data. Specifically, we report ∼33,000 and ∼20,000 candidate enhancers from HepG2 and K562, respectively. Moreover, we show that STARRPeaker outperforms other peak callers in terms of identifying known enhancers with fewer false positives. Overall, we demonstrate an optimized processing framework for STARR-seq experiments can identify putative enhancers while addressing potential confounders.
A Comparison of Drug Delivery into Skin Using Topical Solutions, Needle Injections and Jet Injections
Authors: Cu Katharina , Bansal Ruchi , Mitragotri Samir , Rivas David Fernandez
Published: July 2019

Drug diffusion within the skin with a needle-free micro-jet injection (NFI) device was compared with two well-established delivery methods: topical application and solid needle injection. A permanent make-up (PMU) machine, normally used for dermal pigmentation, was utilized as a solid needle injection method. For NFIs a continuous wave (CW) laser diode was used to create a bubble inside a microfluidic device containing a light absorbing solution. Each method delivered two different solutions intoex-vivoporcine skin. The first solution consisted of a red dye (direct red 81) and rhodamine B in water. The second solution was direct red 81 and rhodamine B in water and glycerol. For PMU experiments, the skin samples were kept stationary and the diffusion depth, width and surface area were measured. The NFI has a higher vertical dispersion velocity of 3 × 105μm/s compared to topical (0.1 μm/s) and needle injection (53μm/s). The limitations and advantages of each method are discussed, and we conclude that the micro-jet injector represents a fast and minimally invasive injection method, while the solid needle injector causes notably tissue damage. In contrast, the topical method had the slowest diffusion rate but causes no visible damage to the skin.
Effects of prey turnover on poison frog toxins: a landscape ecology approach to assess how biotic interactions affect species phenotypes
Authors: Prates Ivan , Paz Andrea , Brown Jason L. , Carnaval Ana C.
Published: July 2019

Ecological studies of species pairs demonstrated that biotic interactions promote phenotypic change and eco-evolutionary feedbacks. However, we have a limited understanding of how phenotypes respond to interactions with multiple taxa. We investigate how interactions with a network of prey species contribute to spatially structured variation in the skin toxins of the Neotropical poison frog Oophaga pumilio. Specifically, we assess how beta-diversity of alkaloid-bearing arthropod prey assemblages (68 ant species) and evolutionary divergence among populations (from a neutral genetic marker) contribute to frog poison dissimilarity (toxin profiles composed of 230 different lipophilic alkaloids sampled from 934 frogs at 46 sites). We show that ant assemblage turnover predicts alkaloid turnover and unique toxin combinations across the range of O. pumilio. By contrast, evolutionary relatedness is barely correlated with toxin variation. We discuss how the analytical framework proposed here can be extended to other multi-trophic systems, coevolutionary mosaics, microbial assemblages, and ecosystem services.
Molecular insights from conformational ensembles via machine learning
Authors: Fleetwood O. , Kasimova M.A. , Westerlund A.M. , Delemotte L.
Published: July 2019

Biomolecular simulations are intrinsically high dimensional and generate noisy datasets of ever increasing size. Extracting important features in the data is crucial for understanding the biophysical properties of molecular processes, but remains a big challenge. Machine learning (ML) provides powerful dimensionality reduction tools. However, such methods are often criticized to resemble black boxes with limited human-interpretable insight.

We use methods from supervised and unsupervised ML to efficiently create interpretable maps of important features from molecular simulations. We benchmark the performance of several methods including neural networks, random forests and principal component analysis, using a toy model with properties reminiscent of macromolecular behavior. We then analyze three diverse biological processes: conformational changes within the soluble protein calmodulin, ligand binding to a G protein-coupled receptor and activation of an ion channel voltage-sensor domain, unravelling features critical for signal transduction, ligand binding and voltage sensing. This work demonstrates the usefulness of ML in understanding biomolecular states and demystifying complex simulations.

STATEMENT OF SIGNIFICANCE

Understanding how biomolecules function requires resolving the ensemble of structures they visit. Molecular dynamics simulations compute these ensembles and generate large amounts of data that can be noisy and need to be condensed for human interpretation. Machine learning methods are designed to process large amounts of data, but are often criticized for their black-box nature and have historically been modestly used in the analysis of biomolecular systems. We demonstrate how machine learning tools can provide an interpretable overview of important features in a simulation dataset. We develop a protocol to quickly perform data-driven analysis of molecular simulations. This protocol is applied to identify the molecular basis of ligand binding to a receptor and of voltage sensitivity of an ion channel.
Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma
Authors: Lee Bo-Young , Kim Min-Sub , Choi Beom-Soon , Nagano Atsushi J. , Ting Au Doris Wai , Sun Wu Rudolf Shiu , Takehana Yusuke , Lee Jae-Seong
Published: July 2019

Medaka (Oryzias spp.) is an important fish species in ecotoxicology and considered as a model species due to its biological features including small body size and short generation time. Since Japanese medaka Oryzias latipes is a freshwater species with access to an excellent genome resources, the marine medaka Oryzias melastigma is also applicable for marine ecotoxicology. In genome era, a high-density genetic linkage map is a very useful resource in genomic research, providing a means for comparative genomic analysis and verification of de novo genome assembly. In this study, we developed a high-density genetic linkage map for O. melastigma using restriction-site associated DNA sequencing (RAD-seq). The genetic map consisted of 24 linkage groups with 2,481 RAD-tag markers. The total map length was 1,784 cM with an average marker space of 0.72 cM. The genetic map was integrated with the reference-assisted chromosome assembly (RACA) of O. melastigma, which anchored 90.7% of the assembled sequence onto the linkage map. The values of complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were similar to RACA assembly but N50 (23.74 Mb; total genome length 779.4 Mb; gap 5.29%) increased to 29.99 Mb (total genome length 778.7 Mb; gap 5.2%). Using MapQTL analysis with a single nucleotide polymorphism markers, we identified a major quantitative trait locus for sex traits on the Om10. The integration of the genetic map with the reference genome of marine medaka will serve as a good resource for studies in molecular toxicology, genomics, CRISPR/Cas9, and epigenetics.
Multivariate AND-gate substrate probes as enhanced contrast agents for fluorescence-guided surgery
Authors: Widen John C. , Tholen Martina , Yim Joshua J. , Antaris Alexander , Casey Kerriann M. , Rogalla Stephan , Klaassen Alwin , Sorger Jonathan , Bogyo Matthew
Published: July 2019

The greatest challenges for surgical management of cancer are precisely locating lesions and clearly defining the margins between tumors and normal tissues. This is confounded by the characteristics of the tissue where the tumor is located as well as its propensity to form irregular boundaries with healthy tissues. To address these issues, molecularly targeted optical contrast agents have been developed to define margins in real-time during surgery1,2. However, selectivity of a contrast agent is often limited by expression of a target enzyme or receptor in both tumor and healthy tissues. Here we introduce a concept of multivariate ‘AND-gate’ optical imaging probes that require sequential processing by multiple tumor-specific enzymes to produce a fluorescent signal. This results in dramatically improved specificity as well as overall enhanced sensitivity. This general approach has the potential to be broadly applied to selectively target complex patterns of enzyme activities in diverse disease tissues for detection, treatment and therapy response monitoring.
High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications
Authors: Stojković Vanja , Myasnikov Alexander G. , Young Iris D. , Frost Adam , Fraser James S. , Fujimori Danica Galonić
Published: July 2019

Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides’ positions, a task that has previously been accomplished by X-ray crystallography. Here we present a cryo-electron microscopy (cryo-EM) structure of Escherichia coli (E. coli) 50S subunit at an average resolution of 2.2Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for identification of post-transcriptional rRNA modifications using a cryo-EM map. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.
Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow
Authors: Crits-Christoph Alexander , Olm Matthew , Diamond Spencer , Bouma-Gregson Keith , Banfield Jillian
Published: July 2019

Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species and how population structures are affected by dispersal, recombination, and selection. Genomic inferences about population structure can be made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in the population. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in specialized metabolite biosynthesis and extracellular transport were characterized by elevated genetic diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high site-specific differentiation of alleles, fewer recombinant events, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape local soil bacterial genetic variation.
Conservation of gene architecture and domains amidst sequence divergence in thehsrωlncRNA gene across theDrosophilagenus: Anin silicoanalysis
Authors: Sahu Ranjan Kumar , Mutt Eshita , Lakhotia Subhash Chandra
Published: July 2019

The developmentally active and cell-stress responsivehsrω locus inDrosophila melanogastercarries two exons, oneomegaintron, one short translatable open reading frame ORFω, long stretch of unique tandem repeats and an overlappingmir-4951near its 3’ end. It produces multiple lncRNAs using two transcription start and four termination sites. Earlier studies revealed functional conservation in severalDrosophilaspecies but with little sequence conservation, in three experimentally examined species, of ORFω, tandem repeat and other regions but ultra-conservation of 16nt at 5’ and 60nt at 3’ splice-junctions of theomegaintron. Present bioinformatic study, using the splice-junction landmarks inDrosophila melanogaster hsrω, identified orthologues in publicly available 34Drosophilaspecies genomes. Each orthologue carries the short ORFω, ultra-conserved splice junctions ofomegaintron, repeat region, conserved 3’-end locatedmir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in repeat sequences. Intriguingly, only the intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested inChironomusandCeratitisspecies. Amidst the high sequence divergence, the conserved organization of exons, ORFω andomegaintron in this gene’s proximal part and tandem repeats in distal part across theDrosophilagenus is remarkable and possibly reflects functional importance of higher order structure ofhsrω lncRNAs and the small Omega peptide.
Zika virus infection in Collaborative Cross mice
Authors: Mattocks Melissa D. , Plante Kenneth S. , Fritch Ethan J. , Baric Ralph S. , Ferris Martin T. , Heise Mark T. , Lazear Helen M.
Published: July 2019

The 2015-2016 emergence of Zika virus (ZIKV) in the Americas, and recognition that ZIKV infection during pregnancy can result in birth defects, revealed a need for small animal models to study ZIKV pathogenic mechanisms and evaluate candidate vaccines and antivirals. Mice would be an attractive system for such studies, but ZIKV replicates poorly in laboratory mice because it fails to antagonize murine STAT2 and STING. To address this, most ZIKV pathogenesis studies have used mice with impaired interferon signaling (e.g. Ifnar1−/− or treatment with IFNAR1-blocking antibodies). However, using mice with severe defects in innate antiviral signaling confounds studies of viral pathogenic mechanisms. Collaborative Cross (CC) mice have proven to be a valuable system for developing new mouse pathogenesis models for viral infections that are not well modeled in conventional laboratory mouse lines. To test whether CC mice could provide an immune-competent model for ZIKV pathogenesis, we infected CC lines with ZIKV and assessed weight loss, viremia, and production of neutralizing antibodies. We tested 21 CC lines (CC001, CC002, CC003, CC004, CC005, CC006, CC011, CC012, CC013, CC019, CC024, CC028, CC040, CC041, CC042, CC046, CC051, CC059, CC061, CC068, and CC072, 13 of which have non-functional alleles of the flavivirus restriction factor Oas1b) and 3 ZIKV strains (MR766, H/PF/2013, and a mouse-adapted variant of Dakar 41525). ZIKV infection did not induce weight loss compared to mock-infected controls and accordingly only low levels of viral RNA were detected in serum. Only a subset of mice developed neutralizing antibodies to ZIKV, likely due to overall low levels of infection and viremia. Our results are consistent with other studies demonstrating poor ZIKV infection in interferon-intact mice and suggest that the tested CC lines do not include polymorphic host genes that greatly increase susceptibility to ZIKV infection.
Local extinction of a montane, endemic grassland bird driven by landscape change across its global distribution
Authors: Lele Abhimanyu , Arasumani M. , Vishnudas C. K. , Jathanna Devcharan , Robin V. V.
Published: July 2019

Context

Tropical montane habitats support high biodiversity, and are hotspots of endemism, with grasslands being integral components of many such landscapes. The montane grasslands of the Western Ghats have seen extensive land-use change over anthropogenic timescales. The factors influencing the ability of grassland-dependent species to persist in habitats experiencing loss and fragmentation, particularly in montane grasslands, are poorly known.

Objectives

We studied the relationship between the Nilgiri pipit Anthus nilghiriensis, a threatened endemic bird that typifies these montane grasslands, and its habitat, across most of its global distribution. We examined what habitat features make remnants viable habitat, which is necessary for effective management.

Methods

We conducted 663 surveys in 170 sites and used both single-season occupancy modelling and N-mixture modelling to account for processes influencing detection, presence, and abundance.

Results

Elevation had a positive influence on species presence, patch size had a moderate positive influence and patch isolation a moderate negative influence. Species abundance was positively influenced by elevation and characteristics related to habitat structure, and negatively influenced by the presence of invasive woody vegetation.

Conclusions

The strong effect of elevation on the highly range-restricted Nilgiri pipit makes it vulnerable to, and an indicator of, climate change. This highly range-restricted species is locally extinct at several locations and persists at low densities in remnants of recent fragmentation, suggesting an extinction debt. Our findings indicate a need to control and reverse the spread of exotic woody invasives to preserve the grasslands themselves and the specialist species dependent upon them.
A comprehensive dataset of TLX1 positive ALL-SIL lymphoblasts and primary T-cell acute lymphoblastic leukemias
Authors: Verboom Karen , Van Loocke Wouter , Clappier Emmanuelle , Soulier Jean , Vandesompele Jo , Speleman Frank , Durinck Kaat
Published: July 2019

Most currently available transcriptome data of T-cell acute lymphoblastic leukemia (T-ALL) are based on polyA[+] RNA sequencing methods thus lacking non-polyadenylated transcripts. Here, we present the data of polyA[+] and total RNA sequencing in the context of in vitro TLX1 knockdown in ALL-SIL cells and a primary T-ALL cohort. We extended this dataset with ATAC sequencing and H3K4me1 and H3K4me3 ChIP sequencing data to map putative gene regulatory regions. In this data descriptor, we present a detailed report of how the data were generated and which bioinformatics analyses were performed. Through several technical validations, we showed that our sequencing data are of high quality and that our in vitro TLX1 knockdown was successful. We also validated the quality of the ATAC and ChIP sequencing data and showed that ATAC and H3K4me3 ChIP peaks are enriched at transcription start sites. We believe that this comprehensive set of sequencing data can be reused by others to further unravel the complex biology of T-ALL in general and TLX1 in particular.
The effect of competency-based education in obstetric emergencies on midwifery students in clinical skill lab, based on Kirkpatrick evaluation model: A randomized controlled trial
Authors: Hakimi Masumah , Kheirkhah Masoomeh , Abolghasemi Jamileh , Hakimi Razia , farshad Fatemeh
Published: July 2019

Background

Obstetric emergency is one of the most important causes of maternal and neonatal mortality, and competency-based education is one of the efficient approaches to cover this. Objective structured clinical examination is one of the valid methods in measuring students’ competency and performance. Kirkpatrick evaluation model is a great method to assess a training impact.

Objectives

This study was designed to determine the effect of competency-based education on midwifery students based on Kirkpatrick evaluation model.

Design

Randomized controlled trial

Setting

Nursing and Midwifery School in Islamic Republic of Iran (Iran University of Medical Sciences)

Participants

eighty students in third to fifth term of associate and bachelor’s degree in midwifery (intervention group=40, control group=40)

Methods

Using stratified random sampling, research team trained learners of intervention group in 4 sessions, 5 hours/day in a month in emergency obstetric cares. Both groups had been receiving the routine schedule of the faculty. Knowledge, skills, and self-confidence were assessed three times, before, immediately and 6 weeks after training by researcher made questionnaire, Objective Structured Clinical Examination (OSCE) and self-reported questionnaire respectively. Data were analyzed with descriptive, inferential statistics.

Results

The level of knowledge, skills, and self-confidence increased significantly in the intervention group, in immediate and 6 weeks after intervention (P<0.001). In intervention group, Mean ± S.D of all variables were 5.05±2.074, 143.30±12.146 and 11.65±2.045, which increased to 10.17±1.318, 527.70±19.995 and 18.97±1.980 and remained at the same levels 6 weeks later, 9.37±2.215, 521.80±19.784 and 19.00±2.631; in the control group, this trend was not significant (P=0.380, P=0.455 and P=0.191).

Conclusion

Competency-based education can be used in midwifery education and in-service training. We need to use new educational approaches such as competency-based to have a valuable impact on knowledge skills and self-confidence. This may affect health indexes indirectly.
Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes
Authors: Sharma Vasudha , Majumdar Sharmistha
Published: July 2019

Background

ChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task.

Results

This study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by each peak-caller is compared followed by a comparison of the annotated motifs present in the reported peaks. The significance of peaks is assessed based on the presence of a motif in top peaks. Indirect binding tools have been compared on the basis of their ability to identify annotated motifs and predict mode of protein-DNA interaction.

Conclusion

By studying the output of the peak-callers investigated in this study, it is concluded that the tools that use self-learning algorithms, i.e. the tools that estimate all the essential parameters from the aligned reads, perform better than the algorithms which require formation of peak-pairs. The latest tools that account for indirect binding of TFs appear to be an upgrade over the available tools, as they are able to reveal valuable information about the mode of binding in addition to direct binding. Furthermore, the quality of ChIP-exo reads have important consequences on the output of data analysis.
Modelling variation in bushmeat harvesting among seven African ecosystems using the Madingley Model: yield, survival and ecosystem impacts
Authors: Barychka Tatsiana , Mace Georgina M. , Purves Drew W.
Published: July 2019

In principle, both the maximum sustainable yields of bushmeat, and the ecosystem impacts of extracting those yields, are likely to vary among ecosystems due to differences in the structure and function of ecosystems, but the data necessary to estimate this variation is lacking. Here, we compare seven different ecosystems on a North-South latitudinal gradient in Central Africa in terms of their trophic structure and capacity to support yields from bushmeat harvesting, using the Madingley General Ecosystem Model. The only factor that varies across simulations of these ecosystems is the climate which drives differences in vegetation structure and function, leading in turn to differences in the structure of the ecological community that emerge from the model. In a series of experiments (n=30), we simulate constant proportional harvesting of small and medium-sized warm-bloodied heterotrophs (1-23kg) over 30 years, recording expected bushmeat yields, and impacts on ecosystem structure, including trophic structure. Predictions for animal densities and trophic structures in the pristine (no harvesting) case varied among the ecosystems, with implications for bushmeat harvesting. For example, wooded savannah ecosystems stood out as having the greatest pristine densities in the target groups (11000-12000 animals per kilometre squared), greatest yields (100% higher than the tropical forest and 1000% higher than the desert ecosystem), and were the most resilient to harvesting. By contrast, small and medium-sized endothermic heterotrophs contributed only a small proportion of heterotrophs in the desert ecosystem, and thus the potential for bushmeat harvesting here was low. In all ecosystems, harvesting at the rate that maximised yield (55-65% population per year, except for the southern desert ecosystem) had strong impacts, causing drastic reductions in target functional groups, coupled with increases in smaller- and larger-bodied animals. Forest and desert ecosystems were particularly sensitive. Overall, the results suggest that, even for similar functional groups, bushmeat harvesting policies will need to vary substantially among ecosystems – and show that general ecosystem models could be a useful tool in helping to guide these policies.
Promoter-specific dynamics of TATA-binding protein association with the human genome
Authors: Hasegawa Yuko , Lieb Jason D. , Struhl Kevin
Published: July 2019

Transcription factor binding to target sites in vivo is a dynamic process that involves cycles of association and dissociation, with individual proteins differing in their binding dynamics. The dynamics at individual sites on a genomic scale has been investigated in yeast cells, but comparable experiments have not been done in multicellular eukaryotes. Here, we describe a tamoxifen-inducible, time-course ChIP-seq approach to measure transcription factor binding dynamics at target sites throughout the human genome. As observed in yeast cells, the TATA-binding protein (TBP) typically displays rapid turnover at RNA polymerase (Pol) II-transcribed promoters, slow turnover at Pol III promoters, and very slow turnover at the Pol I promoter. Interestingly, turnover rates vary widely among Pol II promoters in a manner that does not correlate with the level of TBP occupancy. Human Pol II promoters with slow TBP dissociation preferentially contain a TATA consensus motif, support high transcriptional activity of downstream genes, and are linked with specific activators and chromatin remodelers. These properties of human promoters with slow TBP turnover differ from those of yeast promoters with slow turnover. These observations suggest that TBP binding dynamics differentially affect promoter function and gene expression, possibly at the level of transcriptional reinitiation/bursting.
BIM-linked data integration for asset management
Authors: Farghaly Karim , Abanda F.H. , Vidalakis Christos , Wood Graham
Published: July 2019

Purpose

The purpose of this paper is to investigate the transfer of information from the building information modelling (BIM) models to either conventional or advanced asset management platforms using Linked Data. To achieve this aim, a process for generating Linked Data in the asset management context and its integration with BIM data is presented.

Design/methodology/approach

The research design employs a participatory action research (PAR) approach. The PAR approach utilized two qualitative data collection methods, namely; focus group and interviews to identify and evaluate the required standards for the mapping of different domains. Also prototyping which is an approach of Software Development Methodology is utilized to develop the ontologies and Linked Data.

Findings

The proposed process offers a comprehensive description of the required standards and classifications in construction domain, related vocabularies and object-oriented links to ensure the effective data integration between different domains. Also the proposed process demonstrates the different stages, tools, best practices and guidelines to develop Linked Data, armed with a comprehensive use case Linked Data generation about building assets that consume energy.

Originality/value

The Linked Data generation and publications in the domain of AECO is still in its infancy and it also needs methodological guidelines to support its evolution towards maturity in its processes and applications. This research concentrates on the Linked Data applications with BIM to link across domains where few studies have been conducted.
Effect of leadership and communication practices on the safety climate and behaviour of construction workgroups
Authors: Lingard Helen , Zhang Rita Peihua , Oswald David
Published: July 2019

Purpose

The leadership style and communication practices of supervisors in the Australian construction industry were measured. The purpose of this paper is to investigate the effect of leadership style and communication practices of Australian construction supervisors on workgroup health and safety (H&S) climate and behaviour.

Design/methodology/approach

A questionnaire was administered to members of 20 workgroups engaged in rail construction work on the Level Crossing Removal Project and the Melbourne Metro Tunnel Project in Victoria, Australia. The survey measured components of supervisors’ transformational and transactional leadership, communication practices, the group H&S climate and workers’ self-reported H&S compliance and participation.

Findings

Supervisors’ transformational and transactional leadership, as well as communication practices, were all positively and significantly correlated with group H&S climate and workers’ self-reported H&S behaviours. The transformational leadership component of providing an appropriate model was the strongest predictor of H&S participation, while H&S compliance was predicted by the transactional leadership component of providing contingent reward, as well as supervisors’ communication practices. H&S climate fully mediated the relationship between supervisory leadership and workers’ self-reported H&S behaviour.

Originality/value

The research demonstrates that both transformational and transactional supervisory leadership are important in the construction context. Effective communication between supervisors and workers is also important for H&S. The findings suggest that supervisory leadership development programmes may be an effective way to improve H&S performance in predominantly subcontracted construction workgroups.
Weak economic institutions in Africa: a destiny or design?
Authors: Alhassan Abdulkareem , Kilishi Abdulhakeem Abdullahi
Published: July 2019

Purpose

The primacy of institutions for economic progress has been established in the literature. Yet, less research attention is paid to the existence and persistence of weak economic institutions in Africa. Thus, the purpose of this paper is to empirically explore the determinants of the quality of economic institutions in Africa.

Design/methodology/approach

Hausman–Taylor instrumental variable estimator of panel regression was employed for a sample of 43 Sub-Sahara African countries over the period 1995–2017.

Findings

The study finds that the existence and persistence of weak economic institutions in Africa is more of design than destiny. That is, weak economic institutions are created and sustained more by bad political institutions rather than cultural diversity and geographical factors. Therefore, strong political institutions need to be entrenched to reverse the equilibrium of weak economic institutions and dismal economic performance in the continent.

Practical implications

The study provides deep understanding of the determinants of economic institutions. This is imperative for policy makers, development agencies and stakeholders in designing viable economic policies and programs for the continent.

Originality/value

The novelty of the study is rooted in the examination of the factors responsible for the development and persistence of weak economic institutions in Africa. The idea is original because previous studies focus on political institutions and neglected economic institutions.
Towards a better understanding of organizational buying behavior across cultures: empirical evidence from the Arabian Gulf
Authors: Bachkirov Alexandre Anatolievich
Published: July 2019

Purpose

The purpose of this study is to examine, through the lens of the buying center concept, a theorized link between organizational buying behavior (OBB) and a national culture of collectivism, large power distance, particularism and a wasta practice.

Design/methodology/approach

A qualitative methodology was used to gain better understanding of OBB in an under-researched business environment of the Arabian Gulf. The data come from 41 organizational practitioners who reported on the industrial buying processes in their organizations with reference to the buying center framework.

Findings

The study developed a model of the buying center for the emerging markets governed by socio-political institutions.

Research limitations/implications

The data were obtained only from one culturally specific world region.

Practical implications

To attain efficacious results in culturally distant business environments, industrial marketers should complement home country experience with a thorough understanding of how national cultures affect the dynamics of OBB.

Originality/value

The study updates the conceptualization of the buying center’s organizational actors (OAs) for business contexts beyond traditional, mature markets. It reveals the typology of decisional influencers, introduces and defines the role of advisers and clarifies the role of the gatekeeping bureaucracy and differing perceptions thereof by OAs.
Consumer centric antecedents to personal financial planning
Authors: Guzman Francisco , Paswan Audhesh , Tripathy Niranjan
Published: July 2019

Purpose

Personal finance influences everything we buy and is a key driver of all economies. It has attracted significant research attention, mostly grounded in rational economics. However, it has not received adequate research attention in the consumer behavior literature. This study aims to address this gap by looking at some of the consumer-centric antecedents of short- and long-term personal financial planning, i.e. self-other orientation, cognitive style and time orientation.

Design/methodology/approach

A self-administered survey was used to collect data from full time employees. Hypotheses were tested using multiple regression analyses.

Findings

Both short- and long-term financial planning are positively associated with non-impulsive and analytical decision-making styles; whereas self and other orientation are only associated with short-term financial planning. Intuitive decision-making is not associated to either short- or long-term financial planning.

Research limitations/implications

While analytical and long-term orientation are still important for personal finance, in the short run, consumers are also driven by self and other orientation.

Practical implications

The results are relevant for both products and services that have long-term and short-term financial implications for consumers.

Originality/value

This study explores financial planning decision-making from a consumer behavior perspective, and addresses a gap in consumer behavior literature.