bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tackling the research capacity challenge in Africa: An overview of African-led approaches to strengthen research capacity
Authors: Ngongalah Lem , Rawlings Ngwa Niba , Wepngong Emerson , Musisi James , Ngwayu Claude , Mumah Sharon 
Published: January 2019

AbstractBackgroundImproved capacity for research is a valuable and sustainable means of advancing health and development in Africa. Local leadership in research capacity strengthening is important for developing contextually appropriate programs that increase locally-driven research, and improve Africa’s ability to adapt and use scientific knowledge. This study provides an overview of African organisations that aim to strengthen research capacity in Africa, and the major initiatives or approaches being used for this purpose.MethodsA desk review of grey and published literature on research capacity strengthening in Africa was conducted, in addition to panel discussions on the determinants of research capacity in Africa. Data was analysed through thematic analysis and a framework developed by the Collaboration for Research Excellence in Africa (CORE Africa).Results11 organisations were identified, spread across South, Central, East and West Africa. The main approaches to improving research capacity were: providing opportunities for academic research and research training. Initiatives to provide research equipment, funding and facilitate research use for policy-making were limited; while strategies to increase research awareness, promote collaboration, and provide guidance and incentives for research were lacking. Most organisations had programs for researchers and academics, with none targeting funders or the general public.ConclusionLocal leadership is essential for improving research capacity in Africa. In addition to providing adequate support to academics and researchers, initiatives that help revitalize the education system in Africa, promote collaboration and engage funders and the general public will be helpful for strengthening research capacity in Africa.
Do Synthesis Centers Synthesize? A semantic analysis of diversity and performance
Authors: Hackett Edward J. , Leahey Erin , Parker John N. , Rafols Ismael , Hampton Stephanie , Corte Ugo , Drake John M. , Penders Bart , Sheble Laura , Vermeulen Niki , Vision Todd 
Published: January 2019

AbstractSynthesis centers are a recently-developed form of scientific organization that catalyzes and supports a form of interdisciplinary research that integrates diverse theories, methods and data across spatial or temporal scales, scientific phenomena, and forms of expertise to increase the generality, parsimony, applicability, or empirical soundness of scientific explanations. Research has shown the synthesis working group to be a distinctive form of scientific collaboration that reliably produces consequential, high-impact publications, but no one has asked: do synthesis working groups produce publications that are substantially more diverse than those produced outside of synthesis centers, and if so, how and with what effects? We have investigated these questions through a novel textual analysis. We found that if diversity is measured solely by mean difference in the Rao-Stirling (aggregate) measure of diversity, then the answer is no. But synthesis center papers have significantly greater variety and balance, but significantly lower disparity, than papers in the reference corpus. Synthesis center influence is mediated by the greater size of synthesis center collaborations (numbers of authors, distinct institutions, and references) but even when taking size into account, there is a persistent direct effect: synthesis center papers have significantly greater variety and balance, but less disparity, than papers in the reference corpus. We conclude by inviting further exploration of what this novel textual analysis approach might reveal about interdisciplinary research and by offering some practical implications of our results.
Skeletal descriptions of shape provide unique perceptual information for object recognition
Authors: Ayzenberg Vladislav , Lourenco Stella F. 
Published: January 2019

AbstractWith seemingly little effort, humans can both identify an object across large changes in orientation and extend category membership to novel exemplars. Although researchers argue that object shape is crucial in these cases, there are open questions as to how shape is represented for object recognition. Here we tested whether the human visual system incorporates a three-dimensional skeletal descriptor of shape to determine an object’s identity. Skeletal models not only provide a compact description of an object’s global shape structure, but also provide a quantitative metric by which to compare the visual similarity between shapes. Our results showed that a model of skeletal similarity explained the greatest amount of variance in participants’ object dissimilarity judgments when compared with other computational models of visual similarity (Experiment 1). Moreover, parametric changes to an object’s skeleton led to proportional changes in perceived similarity, even when controlling for another model of structure (Experiment 2). Importantly, participants preferentially categorized objects by their skeletons across changes to local shape contours and non-accidental properties (Experiment 3). Our findings highlight the importance of skeletal structure in vision, not only as a shape descriptor, but also as a diagnostic cue of object identity.
Genomic evidence of genetic variation with pleiotropic effects on caterpillar fitness and plant traits in a model legume
Authors: Gompert Zachariah , Brady Megan , Chalyavi Farzaneh , Saley Tara C. , Philbin Casey S. , Tucker Matthew J. , Forister Matt L. , Lucas Lauren K. 
Published: January 2019

AbstractPlant-insect interactions are ubiquitous, and have been studied intensely because of their relevance to damage and pollination in agricultural plants, and to the ecology and evolution of biodiversity. Variation within species can affect the outcome of these interactions, such as whether an insect successfully develops on a plant species. Whereas specific genes and chemicals that mediate these interactions have been identified, studies of genome-or metabolome-wide intraspecific variation might be necessary to better explain patterns of host-plant use and adaptation often observed in the wild. Here, we present such a study. Specifically, we assess the consequences of genome-wide genetic variation in the model plantMedicago truncatulaforLycaeides melissacaterpillar growth and survival (i.e., larval performance). Using a rearing experiment and a whole-genome SNP data set (>5 million SNPs), we show that polygenic variation inM. truncatulaexplains 9–41% of the observed variation in caterpillar growth and survival. We detect genetic correlations among caterpillar performance and other plant traits, such as structural defenses and some anonymous chemical features; these genetic correlations demonstrate that multipleM. truncatulaalleles have pleiotropic effects on plant traits and caterpillar growth or survival (or that there is substantial linkage disequilibrium among loci affecting these traits). We further show that a moderate proportion of the genetic effect ofM. truncatulaalleles onL. melissaperformance can be explained by the effect of these alleles on the plant traits we measured, especially leaf toughness. Taken together, our results show that intraspecific genetic variation inM. truncatulahas a substantial effect on the successful development ofL. melissacaterpillars (i.e., on a plant-insect interaction), and further point toward traits mediating this genetic effect.
Acoustic community structure and seasonal turnover in tropical South Asian birds
Authors: Krishnan Anand 
Published: January 2019

AbstractBirds produce diverse acoustic signals, with coexisting species occupying distinct ‘acoustic niches’ to minimize masking, resulting in overdispersion within acoustic space. In tropical regions of the world, an influx of migrants from temperate regions occurs during winter. The effects of these migrants on acoustic community structure and dynamics remain unstudied. Here, I show that in a tropical urban bird community, the influx of winter migrants is accompanied by a turnover of the acoustic community. However, in spite of this turnover, the acoustic community remains overdispersed in acoustic niche space. The winter acoustic community additionally exhibits lower frequency-band diversity, consistent with species singing less continuously, as well as lower phylogenetic diversity. My data thus suggests that acoustic niches and community structure are stable across seasons in spite of species turnover. Migrants occupy similar regions of acoustic space as residents, and are relatively closely related to some of these species. Their arrival therefore leads to greater phylogenetic clustering in the winter, and thus lower phylogenetic diversity, although the acoustic community remains overdispersed. Studying seasonal dynamics of acoustic communities thus provides valuable insight into assembly processes, as well as a potential framework for long-term monitoring of urban ecosystems.
Physiological Growth Indices of Maize (Zea mays L.) Genotypes in Sylhet
Authors: Islam M. Tazul , Islam A.F.M. Saiful , Sharaf Uddin M. 
Published: January 2019

AbstractMaize (Zea mays L.) is an important food and feed crop in Bangladesh as well as in the world. But its cultivation is limited in the soils of Sylhet, Bangladesh. To study the physiological growth indices of maize genotypes an experiment was carried out at the experimental field of Sylhet Agricultural University (SAU), Bangladesh during December 2014 to May 2015. The maize genotypes as the experimental materials were ZM 0001, ZM 0002, ZM 0003, ZM 0004, ZM 0005, ZM 0006 ZM 0007 and BARI Maize 6. The experiment was laid out in a Randomized Complete Block Design (RCBD) with three replications. Seeds were sown on 26 December 2014. Proper cultural management practices were followed as and when necessary during the growing period of the crop. Data were recorded on dry matter partitioning, different growth rate parameters and dry matter production of different plant parts at 30 days interval. The results indicated significant variations in almost all of the growth indices. Dry matter accumulation continued to increase from seedling to harvesting. The highest root dry matter was found in ZM 0007 (36.03 g) whereas the highest shoot and leaf dry matter was found in BARI Maize 6 (254.6 and 45.99 g, respectively) at harvest. The highest total dry matter (TDM) was produced in BARI Maize 6 at harvest (287.5 g) and AGR and CGR value was also highest in BARI Maize 6 (5.686 g day-1 and 45.48 g m-2 day-1) but at 60-90 days after germination (DAG). The highest RGR value was in ZM 0001 at seedling stage (114.1 mg g-1 day-1). A zigzag pattern graph was observed in all genotypes for RSR, RWR and SWR at different growth stages but a declining trend from seedling to harvesting was observed for LWR. Correlation between the growth rate parameters and kernel yield showed that shoot, leaf, total dry weight, AGR, CGR, RGR and SWR had significant positive correlation with yield.
Topographic organization of the “third tier” dorsomedial visual cortex in the macaque
Authors: Hadjidimitrakis Kostas , Bakola Sophia , Chaplin Tristan A. , Yu Hsin-Hao , Alanazi Omar , Chan Jonathan M. , Worthy Katrina H. , Rosa Marcello G.P. 
Published: January 2019

AbstractThe boundaries of the visual areas located anterior to V2 in the dorsomedial region of the macaque cortex remain contentious. This region is usually conceptualized as including two functional subdivisions: the dorsal component of area V3 (V3d), laterally, and another area, named the parietooccipital area (PO) or V6, medially. However, the nature of the putative border between V3d and PO/V6 has remained undefined. We recorded the receptive fields of multiunit clusters in adult male macaques, and reconstructed the locations of recording sites using histological sections and “unfolded” cortical maps. Immediately adjacent to dorsomedial V2 we observed a representation of the lower contralateral quadrant, which represented the vertical meridian at its rostral border. This region, corresponding to V3d of previous studies, formed a simple eccentricity gradient, from approximately <5° in the annectant gyrus, to >60° in the parietooccipital sulcus. However, there was no topographic reversal where one would expect to find the border between V3d and PO/V6. Rather, near the midline, this lower quadrant map continued directly into a representation of the peripheral upper visual field, without an intervening lower quadrant representation that could be unambiguously assigned to PO/V6. Thus, V3d and PO/V6 form a continuous topographic map, which includes parts of both quadrants. Together with previous observations that V3d and PO/V6 are both densely myelinated relative to adjacent cortex, and share similar input from V1, these results suggest that they are parts of a single area, which is distinct from the one forming the ventral component of the third tier complex.Significance statementThe primate visual cortex has a large number of areas. Knowing the extent of each visual area, and how they can be distinguished from each other, are essential for the interpretation of experiments aimed at understanding visual processing. Currently, there are conflicting models of the organization of the dorsomedial visual cortex rostral to area V2 (one of the earliest stages of cortical processing of vision). By conducting large-scale electrophysiological recordings, we found that what were originally thought to be distinct areas in this region (dorsal V3, and the parietooccipital area [PO/V6]), together form a single map the visual field. These results will help guide future functional studies, and the interpretation of the outcomes of lesions involving the dorsal visual cortex.
Benchmarking Database Systems for Genomic Selection Implementation
Authors: Nti-Addae Yaw , Matthews Dave , Ulat Victor Jun , Syed Raza , Sempéré Guil-hem , Pétel Adrien , Renner Jon , Larmande Pierre , Guignon Valentin , Jones Elizabeth , Robbins Kelly 
Published: January 2019

AbstractMotivationWith high-throughput genotyping systems now available, it has become feasible to fully integration genotyping information into breeding programs [22]. To make use of this information effectively requires DNA extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize them in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs one would need an efficient genotype data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems.ResultsWe found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix.Availabilityhttp://gobiinx1.bti.cornell.edu:6083/projects/GBM/repos/benchmarking/browseContactyn259@cornell.edu
Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
Authors: Wenger Aaron M. , Peluso Paul , Rowell William J. , Chang Pi-Chuan , Hall Richard J. , Concepcion Gregory T. , Ebler Jana , Fungtammasan Arkarachai , Kolesnikov Alexey , Olson Nathan D. , Töpfer Armin , Alonge Michael , Mahmoud Medhat , Qian Yufeng , Chin Chen-Shan , Phillippy Adam M. , Schatz Michael C. , Myers Gene , DePristo Mark A. , Ruan Jue , Marschall Tobias , Sedlazeck Fritz J. , Zook Justin M. , Li Heng , Koren Sergey , Carroll Andrew , Rank David R. , Hunkapiller Michael W. 
Published: January 2019

AbstractThe major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002/NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.
Growth Factor Independence (GFI) 1B-mediated transcriptional repression and lineage allocation require Lysine Specific Demethylase (LSD)1-dependent recruitment of the BHC complex
Authors: McClellan David , Casey Mattie J. , Bareyan Diana , Lucente Helena , Ours Christopher , Velinder Matthew , Singer Jason , Lone Mehraju Din , Sun Wenxiang , Coria Yunuen , Mason Clinton , Engel Michael E. 
Published: January 2019

ABSTRACTGrowth Factor Independence (GFI)1B coordinates assembly of transcriptional repressor complexes comprised of co-repressors and histone modifying enzymes to control gene expression programs governing lineage allocation in hematopoiesis. Enforced expression of GFI1B in K562 erythroleukemia cells favors erythroid over megakaryocytic differentiation, providing a platform to define molecular determinants of binary fate decisions triggered by GFI1B. We deployed proteome-wide proximity labeling to identify factors whose inclusion in GFI1B complexes depends upon GFI1B’s obligate effector, Lysine Specific Demethylase (LSD)1. We show that GFI1B preferentially recruits core and putative elements of the BRAF-histone deacetylase (HDAC) (BHC) chromatin remodeling complex (LSD1, RCOR1, HMG20A, HMG20B, HDAC1, HDAC2, PHF21A, GSE1, ZMYM2 and ZNF217) in an LSD1-dependent manner to control erythroid fate specification. Among these, depletion of both HMG20A and HMG20B, or GSE1 block GFI1B-mediated erythroid differentiation, phenocopying impaired differentiation brought on by LSD1 depletion or disruption of GFI1B—LSD1 binding. These findings demonstrate the central role of the GFI1B—LSD1 interaction as a determinant of BHC complex recruitment to enable cell fate decisions driven by GFI1B.
Repertoire-Based Diagnostics Using Statistical Biophysics
Authors: Arora Rohit , Kaplinsky Joseph , Li Anthony , Arnaout Ramy 
Published: January 2019

AbstractA fundamental challenge in immunology is diagnostic classification based on repertoire sequence. We used the principle of maximum entropy (MaxEnt) to build compact representations of antibody (IgH) and T-cell receptor (TCRβ) CDR3 repertoires based on the statistical biophysical patterns latent in the frequency and ordering of repertoires’ constituent amino acids. This approach results in substantial advantages in quality, dimensionality, and training speed compared to MaxEnt models based solely on the standard 20-letter amino-acid alphabet. Descriptor-based models learn patterns that pure amino-acid-based models cannot. We demonstrate the utility of descriptor models by successfully classifying influenza vaccination status (AUC=0.97, p=4×10-3), requiring only 31 samples from 14 individuals. Descriptor-based MaxEnt modeling is a powerful new method for dissecting, encoding, and classifying complex repertoires.
Direct Coupling Analysis of Epistasis in Allosteric Materials
Authors: Bravi Barbara , Ravasio Riccardo , Brito Carolina , Wyart Matthieu 
Published: January 2019

AbstractIn allosteric proteins, the binding of a ligand modifies function at a distant active site. Such al-losteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data. Currently, different methods lead to conflicting results, in particular on the existence of long-range evolutionary couplings between distant amino-acids mediating allostery. Here we propose a resolution of this conundrum, by studying epistasis and its inference in models where an allosteric material is evolved in silico to perform a mechanical task. We find four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range and have a simple mechanical interpretation. We perform a Direct Coupling Analysis (DCA) and find that DCA predicts well mutation costs but is a rather poor generative model. Strikingly, it can predict short-range epistasis but fails to capture long-range epistasis, in agreement with empirical findings. We propose that such failure is generic when function requires subparts to work in concert. We illustrate this idea with a simple model, which suggests that other methods may be better suited to capture long-range effects.Author summaryAllostery in proteins is the property of highly specific responses to ligand binding at a distant site. To inform protocols of de novo drug design, it is fundamental to understand the impact of mutations on allosteric regulation and whether it can be predicted from evolutionary correlations. In this work we consider allosteric architectures artificially evolved to optimize the cooperativity of binding at allosteric and active site. We first characterize the emergent pattern of epistasis as well as the underlying mechanical phenomena, finding four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range. The numerical evolution of these allosteric architectures allows us to benchmark Direct Coupling Analysis, a method which relies on co-evolution in sequence data to infer direct evolutionary couplings, in connection to allostery. We show that Direct Coupling Analysis predicts quantitatively mutation costs but underestimates strong long-range epistasis. We provide an argument, based on a simplified model, illustrating the reasons for this discrepancy and we propose neural networks as more promising tool to measure epistasis.
Genetic Risk for Rheumatoid Arthritis is Associated with Increased Striatal Volume in Healthy Young Adults
Authors: Avinun Reut , Nevo Adam , Hariri Ahmad R. 
Published: January 2019

AbstractRheumatoid arthritis (RA), an autoimmune disease, has recently been associated with increased striatal volume and decreased intracranial volume (ICV) in longstanding patients. As inflammation has been shown to precede the clinical diagnosis of RA and it is a known moderator of neuro- and gliogenesis, we were interested in testing whether these brain morphological changes appear before the clinical onset of disease in healthy young adult volunteers, as a function of relative genetic risk for RA. Genetic and structural MRI data were available for 516 healthy non-Hispanic Caucasian university students (275 women, mean age 19.78±1.24 years). Polygenic risk scores were computed for each individual based on a genome-wide association study of RA, so that higher scores indicated higher risk. Striatal volume (sum of caudate, putamen, and nucleus accumbens volumes) and ICV were derived for each individual from high-resolution T1-weighted images. After controlling for sex, age, genetic components of ethnicity, socioeconomic status, and depressive symptoms, we found that higher RA polygenic risk scores were associated with increased striatal volume, but not decreased ICV. Our findings suggest that increased striatal volume may be linked to processes that precede disease onset, such as inflammation, while decreased ICV may relate to disease progression.