bluuebunny/crossref_metadata_2025_split huggingface dataset:
BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification
Authors: Coulter Max , Entizne Juan Carlos , Guo Wenbin , Bayer Micha , Wonneberger Ronja , Milne Linda , Schreiber Miriam , Haaning Allison , Muehlbauer Gary , McCallum Nicola , Fuller John , Simpson Craig , Stein Nils , Brown John W. S. , Waugh Robbie , Zhang Runxuan 
Published: September 2021

ABSTRACTAccurate characterization of splice junctions as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data and enable detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset (RTD) from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the splice junctions and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared to an earlier version, BaRTv1.0. The accuracy of transcript level quantification, splice junctions and transcript start and end sites has been validated extensively using parallel technologies and analysis, including high resolution RT PCR and 5’ RACE. BaRTv2.18 contains 39,434 genes and 148,260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.
Identification of hub genes and pathways in nonalcoholic steatohepatitis by integrated bioinformatics analysis
Authors: Einaliyan Pegah , Owfi Ali , Mahmanzar Mohammadamin , Aghajanzadeh Taha , Hadizadeh Morteza , Sharifi-Zarchi Ali , Hatami Behzad , Aghdaei Hamid Asadzadeh , Zali Mohammad Reza , Baghaei Kaveh 
Published: September 2021

AbstractBackgroundCurrently, non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases in the world. Forecasting the short-term, up to 2025, NASH due to fibrosis is one of the leading causes of liver transplantation. Cohort studies revealed that non-alcoholic steatohepatitis (NASH) has a higher risk of fibrosis progression among NAFLD patients. Identifying differentially expressed genes helps to determine NASH pathogenic pathways, make more accurate diagnoses, and prescribe appropriate treatment.Methods and ResultsIn this study, we found 11 NASH datasets by searching in the Gene Expression Omnibus (GEO) database. Subsequently, NASH datasets with low-quality control scores were excluded. Four datasets were analyzed with packages of R/Bioconductor. Then, all integrated genes were Imported into Cytoscape to illustrate the protein-protein interactions network. All hubs and nodes degree has been calculated to determine the hub genes with critical roles in networks.Possible correlations between expression profiles of mutual DEGs were identified employing Principal Component Analysis (PCA). Primary analyzed data were filtered based on gene expression (logFC > 1, logFC < −1) and adj-P-value (<0.05). Ultimately, among 379 DEGs, we selected the top 10 genes (MYC, JUN, EGR1, FOS, CCL2, IL1B, CXCL8, PTGS2, IL6, SERPINE1) as candidates among up and down regulated genes, and critical pathways such as IL-6, IL-17, TGF β, and TNFα were identified.ConclusionThe present study suggests an important DEGs, biological processes, and critical pathways involved in the pathogenesis of NASH disease. Further investigations are needed to clarify the exact mechanisms underlying the development and progression of NASH disease.
A modular toolset for electrogenetics
Authors: Lawrence J. M. , Yin Y. , Bombelli P. , Scarampi A. , Storch M. , Wey L. T. , Climent-Catala A. ,   PixCell iGEM team, Baldwin G. S. , O’Hare D. , Howe C. J. , Zhang J. Z , Ouldridge T. E. , Ledesma-Amaro R. 
Published: September 2021

AbstractSynthetic biology research and its industrial applications rely on the deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and an electrode), allowing for the direct integration of electronics with complex biological processes for a variety of new applications. However, the use of electrogenetic systems is limited by poor activity, tunability and standardisation. Here, we have developed a variety of genetic and electrochemical tools that facilitate the design and vastly improve the performance of electrogenetic systems. We developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We then constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Finally, we demonstrated electrochemical activation of gene expression in aerobic conditions utilising a novel, modular bioelectrochemical device. This toolset provides researchers with all the elements needed to design and build optimised electrogenetic systems for specific applications.
Streamlined use of protein structures in variant analysis
Authors: Kaur Sandeep , Sikta Neblina , Schafferhans Andrea , Bordin Nicola , Cowley Mark J. , Thomas David M. , Ballinger Mandy L. , O’Donoghue Seán I. 
Published: September 2021

AbstractMotivationVariant analysis is a core task in bioinformatics that requires integrating data from many sources. This process can be helped by using 3D structures of proteins, which can provide a spatial context that can provide insight into how variants affect function. Many available tools can help with mapping variants onto structures; but each has specific restrictions, with the result that many researchers fail to benefit from valuable insights that could be gained from structural data.ResultsTo address this, we have created a streamlined system for incorporating 3D structures into variant analysis. Variants can be easily specified via URLs that are easily readable and writable, and use the notation recommended by the Human Genome Variation Society (HGVS). For example, ‘https://aquaria.app/SARS-CoV-2/S/?N501Y’ specifies the N501Y variant of SARS-CoV-2 S protein. In addition to mapping variants onto structures, our system provides summary information from multiple external resources, including COSMIC, CATH-FunVar, and PredictProtein. Furthermore, our system identifies and summarizes structures containing the variant, as well as the variant-position. Our system supports essentially any mutation for any well-studied protein, and uses all available structural data — including models inferred via very remote homology — integrated into a system that is fast and simple to use. By giving researchers easy, streamlined access to a wealth of structural information during variant analysis, our system will help in revealing novel insights into the molecular mechanisms underlying protein function in health and disease.AvailabilityOur resource is freely available at the project home page (https://aquaria.app). After peer review, the code will be openly available via a GPL version 2 license at https://github.com/ODonoghueLab/Aquaria. PSSH2, the database of sequence-to-structure alignments, is also freely available for download at https://zenodo.org/record/4279164.Contactsean@odonoghuelab.orgSupplementary informationNone.
Newly developed MAGIC population allows identification of strong associations and candidate genes for anthocyanin pigmentation in eggplant
Authors: Mangino Giulio , Arrones Andrea , Plazas Mariola , Pook Torsten , Prohens Jaime , Gramazio Pietro , Vilanova Santiago 
Published: September 2021

SummaryMAGIC populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3MEGGIC; 8-way), constituted by 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanins presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-sensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence SNPs confirmed a low residual heterozygosity (6.87%) and a lack of genetic structure in the S3MEGGIC population, including no differentiation among subpopulations carrying cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of founder genomes, suggesting cryptic selection in favour or against specific parental genomes. GWAS analysis for PA, FA and PUC detected strong associations with two MYB genes similar to MYB113 involved in the anthocyanin biosynthesis pathway and with a COP1 gene, which encodes for a photo-regulatory protein and may be responsible for the PUC phenotype. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1. Parental genotypes for the three genes were in agreement with the candidate genes identification performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.
What ecological factors favor parthenogenesis over sexual reproduction? A study on the facultatively parthenogenetic mayfly Alainites muticus in natural populations
Authors: Liegeois Maud , Sartori Michel , Schwander Tanja 
Published: September 2021

AbstractDifferent reproductive modes are characterized by costs and benefits which often depend on ecological contexts. Benefits of sex are expected to increase under complex biotic interactions, whereas parthenogenesis can be beneficial for reproductive assurance when females are mate limited. Here, we study how different ecological contexts influence the frequency of sex or parthenogenesis in the facultatively parthenogenetic mayfly Alainites muticus. We first verified that high parthenogenetic frequencies translate into female-biased population sex ratios. We then measured the population sex ratio (a proxy for parthenogenetic capacities), density of individuals (mate limitation) and community diversity (biotic interaction complexity) for 159 A. muticus populations, and used structural equation modeling to investigate their direct and indirect influences on sex ratios. We found no effect of community diversity or altitude on sex ratios. Furthermore, even when females can reproduce parthenogenetically, they generally reproduce sexually, indicating that the benefits of sex exceed its costs in most situations. Sex ratios become female-biased in low population densities, as expected if mate limitation selects for parthenogenesis. Mate limitation might be widespread in mayflies because of their very short adult lifespan and limited dispersal, which can generate strong selection for reproductive assurance and may provide a steppingstone towards obligate parthenogenesis.
Learning neural decoders without labels using multiple data streams
Authors: Peterson Steven M. , Rao Rajesh P. N. , Brunton Bingni W. 
Published: September 2021

AbstractRecent advances in neural decoding have accelerated the development of brain-computer interfaces aimed at assisting users with everyday tasks such as speaking, walking, and manipulating objects. However, current approaches for training neural decoders commonly require large quantities of labeled data, which can be laborious or infeasible to obtain in real-world settings. One intriguing alternative uses self-supervised models that share self-generated pseudo-labels between two data streams; such models have shown exceptional performance on unlabeled audio and video data, but it remains unclear how well they extend to neural decoding. Here, we learn neural decoders without labels by leveraging multiple simultaneously recorded data streams, including neural, kinematic, and physiological signals. Specifically, we apply cross-modal, self-supervised deep clustering to decode movements from brain recordings; these decoders are compared to supervised and unimodal, self-supervised models. We find that sharing pseudo-labels between two data streams during training substantially increases decoding performance compared to unimodal, self-supervised models, with accuracies approaching those of supervised decoders trained on labeled data. Next, we develop decoders trained on three modalities that match or slightly exceed the performance of supervised models, achieving state-of-the-art neural decoding accuracy. Cross-modal decoding is a flexible, promising approach for robust, adaptive neural decoding in real-world applications without any labels.
Predictors of taxonomic splitting and its role in primate conservation
Authors: Creighton Maria J.A. , Luo Alice Q. , Reader Simon M. , Mooers Arne Ø. 
Published: September 2021

ABSTRACTSpecies are the main unit used to measure biodiversity, but different preferred diagnostic criteria can lead to very different delineations. For instance, named primate species have more than doubled in number since 1982. Such increases have been attributed to a shift away from the ‘biological species concept’ (BSC) in favour of less inclusive species criteria. Critics of recent changes in primate taxonomy have suggested taxonomic splitting may be biased toward certain clades and have unfavourable consequences for conservation. Here, we explore predictors of taxonomic splitting across primate taxa since the initial shift away from the BSC nearly 40 years ago. We do not find evidence that diversification rate, the rate of lineage formation over evolutionary time, is significantly linked to splitting, contrary to expectations if new species concepts and taxonomic methods identify incipient species. We also do not find evidence that research effort in fields where work has been suggested to motivate splitting is associated with increases in species numbers among genera. To test the suggestion that splitting groups is likely to increase their perceived risk of extinction, we test whether genera that have undergone more splitting have also observed a greater increase in their proportion of threatened species since the initial shift away from traditional taxonomic methods. We find no cohesive signal of taxonomic splitting leading to higher threat probabilities across primate genera. Overall, this analysis sends a positive message: threat statuses of primate species are not being overwhelmingly affected by splitting. Regardless, we echo warnings that it is unwise for conservation to be reliant on taxonomic stability. Species (however defined) are not independent from one another, thus, monitoring and managing them as such may not meet the overarching goal of conserving biodiversity.
Dormancy Breaking Treatments in Northern Wild Rice (Zizania palustris L.) Seed Suggest a Physiological Source of Dormancy
Authors: McGilp Lillian , Semington Aaron , Kimball Jennifer 
Published: September 2021

AbstractDormancy is a limiting factor for breeding in northern wild rice (NWR; Zizania palustris L). This study developed a dormancy curve and tested a combination of scarification and hormone treatments, across three timepoints, for their ability to break dormancy in NWR and produce viable seedlings and plants. A dormancy curve was established across 9 months post-harvest, which showed maximum germination (95%) by 17 weeks post-harvest and high germination (≥81 %) through the rest of the testing period. Next, dormancy breaking treatments were tested. At 1 week post-harvest, few seeds germinated (≤ 15 %) across all treatment combinations. However, sulfuric acid increased germination shortly after harvest (5.8 %), compared to water (0.5 %) and NaClO (0 %) but resulted in stunted seedlings, all but one of which died shortly thereafter. At 7 weeks, sulfuric acid treated seeds did not result in significantly higher germination than water and maximum germination was still below 15%. By 11 weeks post-harvest, the water treatments had the highest germination and resulted in the most viable plants, indicating that dormancy had begun to break naturally and exceeded the effect of the other scarification treatments. Hormonal treatments had no significant effect on germination or seed viability and no strong conclusions could be drawn about their effect on seedling or plant health. Due to the inability of early germinated seed to consistently produce viable plants and the increase in germination following sufficient cold storage, it is likely that NWR seed has intermediate or deep physiological dormancy.
Deletion ofVhlinDmp1-expressing cells causes microenvironmental impairment of B cell lymphopoiesis
Authors: Chicana Betsabel , Abbasizadeh Nastaran , Burns Christian , Taglinao Hanna , Spencer Joel A. , Manilay Jennifer O. 
Published: September 2021

ABSTRACTThe contributions of skeletal cells to the processes of B cell development in the bone marrow (BM) have not been completely described. The von-Hippel Lindau protein (VHL) plays a key role in cellular responses to hypoxia. Previous work showed thatDmp1-Cre;Vhlconditional knockout mice (VhlcKO), which deleteVhlin late osteoblasts and osteocytes, display dysregulated bone growth and reduction in B cells. Here, we investigated the mechanisms underlying the B cell defects using flow cytometry and high-resolution imaging. In theVhlcKO BM, B cell progenitors were increased in frequency and number, whereas Hardy Fractions B-F were decreased.VhlcKO Fractions B-C cells showed increased apoptosis and quiescence. Reciprocal BM chimeras confirmed a B cell-extrinsic source of theVhlcKO B cell defects. In support of this,VhlcKO BM serum contained reduced CXCL12 and elevated EPO levels. Staining ofVhlcKO B cells with an intracellular hypoxic marker indicated the natural existence of distinct B cell microenvironments that differ in local oxygen tensions. Additionally, intravital and ex vivo imaging revealedVhlcKO BM blood vessels with increased diameter, frequency, volume, and a diminished blood-BM barrier. Our studies identify novel mechanisms linking altered bone homeostasis with drastic BM microenvironmental changes that dysregulate B cell development.
Benchmarking tools for DNA repeat identification in diverse genomes
Authors: Das Gourab , Ghosh Indira 
Published: September 2021

AbstractContinuous progression in genomics shows that repeats are important elements of genomes that perform many regulatory and other functions. Eventually, to date, many computational tools have been developed and frequently used for the identification and analysis of genomic repeats. A single tool cannot detect all different types of repeats in diverse species rather pipeline of tools is more effective. But, the choice of such rigorous and robust tools is highly challenging. A method has been implemented to select a set of optimal tools for finding all available classes of perfect and imperfect tandem repeats including microsatellites, minisatellites, and interspersed CRISPRs in genomes. A total of 11 tools have been shortlisted using rule-based selection and then ranked by analyzing rigorousness in searching in diverse species and execution time. Tool comparison shows consistency in perfect microsatellite detection performance but significantly differ for long and imperfect repeats. A web-server has been built which provides a generic platform for various classes of repeat identification from the diverse genome using multiple tools and comparison.
Canonical retinotopic shifts under an inverse force field explain predictive remapping
Authors: Adeyefa-Olasupo Ifedayo-EmmanuEL , Xiao Zixuan , Nandy Anirvan S. 
Published: September 2021

ABSTRACTPredictive remapping — the ability of cells in retinotopic brain areas to transiently exhibit spatio-temporal retinotopic shifts beyond the spatial extent of their classical receptive fields — has been proposed as a primary mechanism that stabilizes our percept of the visual world around the time of saccadic eye movements. Despite the well documented effects of predictive remapping, no study to date has been able to provide a mechanistic account of the neural computations and architecture that actively mediate this ubiquitous phenomenon. We propose a novel neurobiologically inspired general model of predictive remapping in which the underlying pre-saccadic attentional and oculomotor signals manifest as three temporally overlapping forces that act on retinotopic brain areas. These three forces – a centripetal one toward the center of gaze, a convergent one toward the saccade target and a translational one parallel to the saccade trajectory – act in an inverse force field and govern the spatio-temporal dynamics of predictive remapping of population receptive fields. The predictions of our model are borne out by the spatio-temporal changes in sensitivity to probe stimuli in human subjects around the time of an eye movement and are consistent with findings of predictive shifts in the receptive fields of cells in the superior colliculus, frontal eye fields, lateral intraparietal area, and visual area V4.
Construction of Disease-specific Cytokine Profiles by Associating Disease Genes with Immune Responses
Authors: Liu Tianyun , Wang Shiyin , Altman Russ B 
Published: September 2021

AbstractThe pathogenesis of many inflammatory diseases is a coordinated process involving metabolic dysfunctions and immune response—usually modulated by the production of cytokines and associated inflammatory molecules. In this work, we seek to understand how genes involved in pathogenesis which are often not associated with the immune system in an obvious way communicate with the immune system. We have embedded a network of human protein-protein interactions (PPI) from the STRING database with 14,707 human genes using feature learning that captures high confidence edges. We have found that our predicted Association Scores derived from the features extracted from STRING’s high confidence edges are useful for predicting novel connections between genes, thus enabling the construction of a full map of predicted associations for all possible pairs between 14,707 human genes. In particular, we analyzed the pattern of associations for 126 cytokines and found that the six patterns of cytokine interaction with human genes are consistent with their functional classifications. In order to define the disease-specific roles of cytokines we have collected gene sets for 11,944 diseases from DisGeNET. We used these gene sets to predict disease-specific gene associations with cytokines by calculating the normalized average Association Scores between disease-associated gene sets and the 126 cytokines; this creates a unique profile of inflammatory genes (both known and predicted) for each disease. We validated our predicted cytokine associations by comparing them to known associations for 171 diseases. The predicted cytokine profiles correlate (p-value<0.05) with the known ones in 147 diseases. We further characterized the profiles of each disease by calculating an “Inflammation Score” that summarizes different modes of immune responses. Finally, by analyzing subnetworks formed between disease-specific pathogenesis genes, hormones, receptors, and cytokines, we identified the key genes responsible for interactions between pathogenesis and inflammatory responses. These genes and the corresponding cytokines used by different immune disorders suggest unique targets for drug discovery.