bluuebunny/crossref_metadata_2025_split huggingface dataset:
Priors for genotyping polyploids
Authors: Gerard David , Ferrão Luís Felipe Ventorim 
Published: November 2019

AbstractMotivationEmpirical Bayes techniques to genotype polyploid organisms usually either (i) assume technical artifacts are known a priori or (ii) estimate technical artifacts simultaneously with the prior genotype distribution. Case (i) is unappealing as it places the onus on the researcher to estimate these artifacts, or to ensure that there are no systematic biases in the data. However, as we demonstrate with a few empirical examples, case (ii) makes choosing the class of prior genotype distributions extremely important. Choosing a class is either too flexible or too restrictive results in poor genotyping performance.ResultsWe propose two classes of prior genotype distributions that are of intermediate levels of flexibility: the class of proportional normal distributions and the class of unimodal distributions. We provide a complete characterization of and optimization details for the class of unimodal distributions. We demonstrate, using both simulated and real data that using these classes results in superior genotyping performance.Availability and implementationGenotyping methods that use these priors are implemented in the updog R package available on the Comprehensive R Archive Network: https://cran.r-project.org/package=updog. All code needed to reproduce the results of this article is available on GitHub: https://github.com/dcgerard/reproduce_prior_sims.Supplementary informationSupplementary data are available at Bioinformatics online.
Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences
Authors: Machado Talita Mota , Loiseau Oriane , Paris Margot , Weigand Anna , Versieux Leonardo M , Stehmann João Renato , Lexer Christian , Salamin Nicolas 
Published: November 2019

AbstractVriesea is the second largest genus in Tillandsioideae, the most diverse subfamily of Bromeliaceae. Although recent studies focusing on Tillandsioideae have improved the systematics of Vriesea, no consensus has been reached regarding the circumscription of the genus. Here, we present a phylogenetic analysis of core Tillandsioideae using the nuclear gene phyC and plastid data obtained from genome skimming. We investigate evolutionary relationships at the intergeneric level in Vrieseeae and at the intrageneric level in Vriesea s.s. We sampled a comprehensive dataset, including 11 genera of Tillandsioideae and nearly 50% of all known Vriesea spp. Using a genome skimming approach, we obtained a 78 483-bp plastome alignment containing 35 complete and 55 partial protein-coding genes. Phylogenetic trees were reconstructed using maximum-likelihood based on three datasets: (1) the 78 483 bp plastome alignment; (2) the nuclear gene phyC and (3) a concatenated alignment of 18 subselected plastid genes + phyC. Additionally, a Bayesian inference was performed on the second and third datasets. These analyses revealed that Vriesea s.s. forms a well-supported clade encompassing most of the species of the genus. However, our results also identified several remaining issues in the systematics of Vriesea, including a few species nested in Tillandsia and Stigmatodon. Finally, we recognize some putative groups within Vriesea s.s., which we discuss in the light of their morphological and ecological characteristics.
Bio-AnswerFinder: a system to find answers to questions from biomedical texts
Authors: Ozyurt Ibrahim Burak , Bandrowski Anita , Grethe Jeffrey S 
Published: November 2019

Abstract
The ever accelerating pace of biomedical research results in corresponding acceleration in the volume of biomedical literature created. Since new research builds upon existing knowledge, the rate of increase in the available knowledge encoded in biomedical literature makes the easy access to that implicit knowledge more vital over time. Toward the goal of making implicit knowledge in the biomedical literature easily accessible to biomedical researchers, we introduce a question answering system called Bio-AnswerFinder. Bio-AnswerFinder uses a weighted-relaxed word mover's distance based similarity on word/phrase embeddings learned from PubMed abstracts to rank answers after question focus entity type filtering. Our approach retrieves relevant documents iteratively via enhanced keyword queries from a traditional search engine. To improve document retrieval performance, we introduced a supervised long short term memory neural network to select keywords from the question to facilitate iterative keyword search. Our unsupervised baseline system achieves a mean reciprocal rank score of 0.46 and Precision@1 of 0.32 on 936 questions from BioASQ. The answer sentences are further ranked by a fine-tuned bidirectional encoder representation from transformers (BERT) classifier trained using 100 answer candidate sentences per question for 492 BioASQ questions. To test ranking performance, we report a blind test on 100 questions that three independent annotators scored. These experts preferred BERT based reranking with 7% improvement on MRR and 13% improvement on Precision@1 scores on average.
Using Music to Develop a Multisensory Communicative Environment for People with Late-Stage Dementia
Authors: Clare Amy , Camic Paul M , Crutch Sebastian J , West Julian , Harding Emma , Brotherhood Emilie 
Published: November 2019

Abstract

Background and Objectives
Research has indicated the benefit of music interventions on biological, psychological, and cognitive aspects of dementias, yet there is limited research focusing on music’s role in communication. This study developed a conceptual understanding of how people with late-stage dementia may express themselves nonverbally and interact with others during a live music group over time.

Research Design and Methods
Eight people with advanced dementias in residential care (aged 82–97 years), four care staff, and three musicians participated in 8-hr-long weekly live Music for Life sessions and listened to 1-hr-long recorded music session. Visual grounded theory was used to analyze video data collected nonintrusively via the Fly 360-degree camera.

Results
The live music group facilitated a multisensory communicative environment allowing for verbal and nonverbal communicative actions, social interactional components and agency to develop over time. These aspects were influenced by three factors: time, one-to-one interaction within a group setting and the characteristics of the music.

Discussion and Implications
Nonverbal communication in later-stage dementia may be overlooked or underestimated by busy care staff and families. Using music as an interactive way to communicate can help develop mirroring and turn-taking which has been shown to improve quality of life for people with communication impairment, increase their nonverbal communication and allow for a connection to be built between people. Although further research is recommended, individuals responsible for residential care should feel confident that the development of ongoing music groups for this population is warranted as part of ongoing care.
The master transcription factor SOX2, mutated in anophthalmia/microphthalmia, is post-transcriptionally regulated by the conserved RNA-binding protein RBM24 in vertebrate eye development
Authors: Dash Soma , Brastrom Lindy K , Patel Shaili D , Scott C Anthony , Slusarski Diane C , Lachke Salil A 
Published: November 2019

AbstractMutations in the key transcription factor, SOX2, alone account for 20% of anophthalmia (no eye) and microphthalmia (small eye) birth defects in humans—yet its regulation is not well understood, especially on the post-transcription level. We report the unprecedented finding that the conserved RNA-binding motif protein, RBM24, positively controls Sox2 mRNA stability and is necessary for optimal SOX2 mRNA and protein levels in development, perturbation of which causes ocular defects, including microphthalmia and anophthalmia. RNA immunoprecipitation assay indicates that RBM24 protein interacts with Sox2 mRNA in mouse embryonic eye tissue. and electrophoretic mobility shift assay shows that RBM24 directly binds to the Sox2 mRNA 3’UTR, which is dependent on AU-rich elements (ARE) present in the Sox2 mRNA 3’UTR. Further, we demonstrate that Sox2 3’UTR AREs are necessary for RBM24-based elevation of Sox2 mRNA half-life. We find that this novel RBM24–Sox2 regulatory module is essential for early eye development in vertebrates. We show that Rbm24-targeted deletion using a constitutive CMV-driven Cre in mouse, and rbm24a-CRISPR/Cas9-targeted mutation or morpholino knockdown in zebrafish, results in Sox2 downregulation and causes the developmental defects anophthalmia or microphthalmia, similar to human SOX2-deficiency defects. We further show that Rbm24 deficiency leads to apoptotic defects in mouse ocular tissue and downregulation of eye development markers Lhx2, Pax6, Jag1, E-cadherin and gamma-crystallins. These data highlight the exquisite specificity that conserved RNA-binding proteins like RBM24 mediate in the post-transcriptional control of key transcription factors, namely, SOX2, associated with organogenesis and human developmental defects.
A tutorial on sample size calculation for multiple-period cluster randomized parallel, cross-over and stepped-wedge trials using the Shiny CRT Calculator
Authors: Hemming Karla , Kasza Jessica , Hooper Richard , Forbes Andrew , Taljaard Monica 
Published: November 2019

AbstractIt has long been recognized that sample size calculations for cluster randomized trials require consideration of the correlation between multiple observations within the same cluster. When measurements are taken at anything other than a single point in time, these correlations depend not only on the cluster but also on the time separation between measurements and additionally, on whether different participants (cross-sectional designs) or the same participants (cohort designs) are repeatedly measured. This is particularly relevant in trials with multiple periods of measurement, such as the cluster cross-over and stepped-wedge designs, but also to some degree in parallel designs. Several papers describing sample size methodology for these designs have been published, but this methodology might not be accessible to all researchers. In this article we provide a tutorial on sample size calculation for cluster randomized designs with particular emphasis on designs with multiple periods of measurement and provide a web-based tool, the Shiny CRT Calculator, to allow researchers to easily conduct these sample size calculations. We consider both cross-sectional and cohort designs and allow for a variety of assumed within-cluster correlation structures. We consider cluster heterogeneity in treatment effects (for designs where treatment is crossed with cluster), as well as individually randomized group-treatment trials with differential clustering between arms, for example designs where clustering arises from interventions being delivered in groups. The calculator will compute power or precision, as a function of cluster size or number of clusters, for a wide variety of designs and correlation structures. We illustrate the methodology and the flexibility of the Shiny CRT Calculator using a range of examples.
Performance study of a dual-fluid photovoltaic thermal collector with reflection and refraction solar concentrators
Authors: Baljit S S S , Chan H Y , Zaidi S H , Sopian K 
Published: November 2019

Abstract
The temperature of a photovoltaic (PV) plate increases with increasing absorbed irradiation, leading to degradation of the electrical efficiency of the PV cells. The heat can be dissipated by air or water to prevent the deterioration of the cells. In this study, a concentrating photovoltaic thermal (PV-T) dual-fluid solar collector is proposed in which two types of concentrators are integrated. The collector’s performance was analysed with air and water as the working fluids. Analytical expressions were derived from the energy balance equations for each component of the collector. The mean temperature values of the PV plate, air inlet/outlet, water inlet/outlet, glaze and collector back wall were experimentally recorded under different fluid mass flow rates and solar irradiations. The readings were then used to compute the thermal and electrical efficiencies of the collector. The results obtained from the numerical and experimental analyses were compared and evaluated by employing the mean absolute percentage error method. The results show that incorporating two fluids increases the thermal and electrical efficiencies. The total thermal and electrical efficiencies achieved are 67.00% and 13.02%, respectively, at air and water mass flow rates of 0.0103 kg/s and 0.0164 kg/s, respectively, and a solar irradiation of 650 Wm−2. The outcomes of this research are expected to help advance the designs of dual-fluid PV-T solar collectors and offering a broader range of thermal applications.
Embodying the Pain and Cruelty of Others
Authors: Shapiro-Phim Toni 
Published: November 2019

Abstract
A ground-breaking performing arts-centered reparations project of the Extraordinary Chambers in the Courts of Cambodia – also known as the Khmer Rouge Tribunal – is entitled Phka Sla. The Phka Sla initiative was proposed by survivors of the practice of forced marriage under the Khmer Rouge. While organizations collaborating on Phka Sla are assessing the impact of its innovative dance drama, exhibition and other activities on audiences and survivors, this article offers initial observations regarding the impact of embodying survivor testimony on the artists themselves.
The Ethiopia healthcare quality initiative: design and initial lessons learned
Authors: Magge Hema , Kiflie Abiyou , Nimako Kojo , Brooks Kathryn , Sodzi-Tettey Sodzi , Mobisson-Etuk Nneka , Mulissa Zewdie , Bitewulign Befikadu , Abate Mehiret , Biadgo Abera , Alemu Haregweni , Seman Yakob , Kassa Munir , Barker Pierre , Burrsa Daniel Gebremichael 
Published: November 2019

Abstract

Objective
To describe the development, implementation and initial outcomes of a national quality improvement (QI) intervention in Ethiopia.

Design
Retrospective descriptive study of initial prototype phase implementation outcomes.

Setting
All public facilities in one selected prototype district in each of four agrarian regions.

Participants
Facility QI teams composed of managers, healthcare workers and health extension workers.

Interventions
The Ethiopian Federal Ministry of Health (FMoH) and the Institute for Healthcare Improvement co-designed a three-pronged approach to accelerate health system improvement nationally, which included developing a national healthcare quality strategy (NHQS); building QI capability at all health system levels and introducing scalable district MNH QI collaboratives across four regions, involving healthcare providers and managers.

Outcome measures
Implementation outcomes including fidelity, acceptability, adoption and program effectiveness.

Results
The NHQS was launched in 2016 and governance structures were established at the federal, regional and sub-regional levels to oversee implementation. A total of 212 federal, regional and woreda managers have been trained in context-specific QI methods, and a national FMoH-owned in-service curriculum has been developed. Four prototype improvement collaboratives have been completed with high fidelity and acceptability. About 102 MNH change ideas were tested and a change package was developed with 83 successfully tested ideas.

Conclusion
The initial successes observed are attributable to the FMoH’s commitment in implementing the initiative, the active engagement of all stakeholders and the district-wide approach utilized. Challenges included weak data systems and security concerns. The second phase—in 26 district-level collaboratives—is now underway.
An HMM-based synthetic view generator to improve the efficiency of ensemble systems
Authors: Borrajo L , Vieira A Seara , Iglesias E L 
Published: November 2019

AbstractOne of the most active areas of research in semi-supervised learning has been to study methods for constructing good ensembles of classifiers. Ensemble systems are techniques that create multiple models and then combine them to produce improved results. These systems usually produce more accurate solutions than a single model would. Specially, multi-view ensemble systems improve the accuracy of text classification because they optimize the functions to exploit different views of the same input data. However, despite being more promising than the single-view approaches, document datasets often have no natural multiple views available. This study proposes an algorithm to generate a synthetic view from a standard text dataset. The model generates a new view from the standard bag-of-words approach using an algorithm based on hidden Markov models (HMMs). To show the effectiveness of the proposed HMM-based synthetic view generation method, it has been integrated in a co-training ensemble system and tested with four text corpora: Reuters, 20 Newsgroup, TREC Genomics and OHSUMED. The results obtained are promising, showing a significant increase in the efficiency of the ensemble system compared to a single-view approach.
Solid-state formation of CO and H2CO via the CHOCHO + H reaction
Authors: Leroux Killian , Guillemin Jean-Claude , Krim Lahouari 
Published: November 2019

ABSTRACT
Glycolaldehyde (CHOCH2OH) and ethylene glycol (HOCH2CH2OH) are among many complex organic molecules detected in the interstellar medium (ISM). Astrophysical models proposed very often that the formation of these compounds would be directly linked to the hydrogenation of glyoxal (CHOCHO), a potential precursor which is not yet detected in the ISM. We have performed, in this work, surface and bulk hydrogenations of solid CHOCHO under ISM conditions in order to confirm or invalidate the astrophysical modelling of glyoxal transformation. Our results show that the hydrogenation of glyoxal does not lead to the formation of detectable amounts of heavier organic molecules such as glycolaldehyde and ethylene glycol but rather to lighter CO-bearing species such as CO, H2CO, and CO–H2CO, a reaction intermediate resulting from an H-addition–elimination process on CHOCHO and where CO is linked to H2CO. The solid phase formation of such a reaction intermediate has been confirmed through the neon matrix isolation of CO–H2CO species. Additionally, the CHOCHO + H solid-state reaction might also lead to the production of CH3OH formed under our experimental conditions as a secondary product resulting from the hydrogenation of formaldehyde.
Visual Opsin Diversity in Sharks and Rays
Authors: Hart Nathan S , Lamb Trevor D , Patel Hardip R , Chuah Aaron , Natoli Riccardo C , Hudson Nicholas J , Cutmore Scott C , Davies Wayne I L , Collin Shaun P , Hunt David M 
Published: November 2019

AbstractThe diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal’s behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.
Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5′ and 3′ flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion
Authors: Csumita Mária , Csermely Attila , Horvath Attila , Nagy Gergely , Monori Fanny , Göczi Loránd , Orbea Hans-Acha , Reith Walter , Széles Lajos 
Published: November 2019

Abstract
IRF3, IRF5 and IRF9 are transcription factors, which play distinct roles in the regulation of antiviral and inflammatory responses. The determinants that mediate IRF-specific enhancer selection are not fully understood. To uncover regions occupied predominantly by IRF3, IRF5 or IRF9, we performed ChIP-seq experiments in activated murine dendritic cells. The identified regions were analysed with respect to the enrichment of DNA motifs, the interferon-stimulated response element (ISRE) and ISRE half-site variants, and chromatin accessibility. Using a machine learning method, we investigated the predictability of IRF-dominance. We found that IRF5-dominant regions differed fundamentally from the IRF3- and IRF9-dominant regions: ISREs were rare, while the NFKB motif and special ISRE half-sites, such as 5′-GAGA-3′ and 5′-GACA-3′, were enriched. IRF3- and IRF9-dominant regions were characterized by the enriched ISRE motif and lower frequency of accessible chromatin. Enrichment analysis and the machine learning method uncovered the features that favour IRF3 or IRF9 dominancy (e.g. a tripartite form of ISRE and motifs for NF-κB for IRF3, and the GAS motif and certain ISRE variants for IRF9). This study contributes to our understanding of how IRF members, which bind overlapping sets of DNA sequences, can initiate signal-dependent responses without activating superfluous or harmful programmes.
An R-loop-initiated CSB–RAD52–POLD3 pathway suppresses ROS-induced telomeric DNA breaks
Authors: Tan Jun , Duan Meihan , Yadav Tribhuwan , Phoon Laiyee , Wang Xiangyu , Zhang Jia-Min , Zou Lee , Lan Li 
Published: November 2019

Abstract
Reactive oxygen species (ROS) inflict multiple types of lesions in DNA, threatening genomic integrity. How cells respond to ROS-induced DNA damage at telomeres is still largely unknown. Here, we show that ROS-induced DNA damage at telomeres triggers R-loop accumulation in a TERRA- and TRF2-dependent manner. Both ROS-induced single- and double-strand DNA breaks (SSBs and DSBs) contribute to R-loop induction, promoting the localization of CSB and RAD52 to damaged telomeres. RAD52 is recruited to telomeric R-loops through its interactions with both CSB and DNA:RNA hybrids. Both CSB and RAD52 are required for the efficient repair of ROS-induced telomeric DSBs. The function of RAD52 in telomere repair is dependent on its ability to bind and recruit POLD3, a protein critical for break-induced DNA replication (BIR). Thus, ROS-induced telomeric R-loops promote repair of telomeric DSBs through CSB–RAD52–POLD3-mediated BIR, a previously unknown pathway protecting telomeres from ROS. ROS-induced telomeric SSBs may not only give rise to DSBs indirectly, but also promote DSB repair by inducing R-loops, revealing an unexpected interplay between distinct ROS-induced DNA lesions.