bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal Dynamics of Stemphylium Leaf Blight and Potential Inoculum Sources in New York Onion Fields
Authors: Hay Frank , Heck Daniel W. , Klein Audrey , Sharma Sandeep , Hoepting Christy , Pethybridge Sarah J. 
Published: August 2021

AbstractStemphylium leaf blight (SLB) caused byStemphylium vesicariumis the dominant foliar disease affecting large-scale onion production in New York. The disease is managed by fungicides, but control failures are prevalent and recently attributed to fungicide resistance. Little is known of the relative role of inoculum sources in initiation and spread of SLB epidemics. The spatial and spatiotemporal dynamics of SLB epidemics in six onion fields were evaluated along linear transects in 2017 and 2018. Average SLB incidence increased from 0 to 100% throughout the cropping seasons with an average final lesion length of 28.3 cm. Disease progress was typical of a polycyclic epidemic and the logistic model provided the best fit to 83.3% of the datasets. Spatial patterns were better described by the beta-binomial than binomial distribution in half of the datasets and random patterns were more frequently observed by the index of dispersion. Geostatistical analyses of spatial pattern also found a low frequency of datasets with aggregation. Spatiotemporal analysis of epidemics detected that the aggregation was influenced by disease incidence. However, diseased units were not associated with the previous time period according to the spatiotemporal association function ofSADIE. Variable spatial patterns suggested mixed inoculum sources dependent upon location, and likely an external inoculum source at the sampling scale used in this study. Plate testing of 28 commercially available organic onion seedlots from 2017 and 2018 did not detectS. vesicarium. This finding suggests that althoughS. vesicariumhas been reported as seed transmitted, this is unlikely to be a significant inoculum source in commercially available organic seed lots and even less so in fungicide-treated seed used to establish conventional fields. A small-plot replicated trial was also conducted in each of two years to quantify the effect ofS. vesicarium-infested onion residue on SLB epidemics in a field isolated from other onion fields. SLB incidence was significantly reduced in plots without residue compared to those in which residue remained on the soil surface. Burial of infested residue also significantly reduced epidemic progress in one year. The effect of infested onion residue on SLB epidemics in the subsequent onion crop suggests rotation or residue management may have a substantial effect on epidemics. However, the presence of an inoculum source external to fields in onion production regions as indicated by a lack of spatial aggregation may reduce the efficacy of in-field management techniques.
Deliberation gated by opportunity cost adapts to context with urgency
Authors: Touzel Maximilian Puelma , Cisek Paul , Lajoie Guillaume 
Published: August 2021

AbstractFinding the right amount of deliberation, between insufficient and excessive, is a hard decision making problem that depends on the value we place on our time. Average-reward, putatively encoded by tonic dopamine, serves in existing reinforcement learning theory as the stationary opportunity cost of time, and of deliberation in particular. However, this cost often varies with environmental context that can change over time. Here, we introduce an opportunity cost of deliberation estimated adaptively on multiple timescales to account for non-stationary contextual factors. We use it in a simple decision-making heuristic based on average-reward reinforcement learning (AR-RL) that we callPerformance-Gated Deliberation(PGD). We propose PGD as a strategy used by animals wherein deliberation cost is implemented directly as urgency, a previously characterized neural signal effectively controlling the speed of the decision-making process. We show PGD outperforms AR-RL solutions in explaining behaviour and urgency of non-human primates in a context-varying random walk prediction task and is consistent with relative performance and urgency in a context-varying random dot motion task. We make readily testable predictions for both neural activity and behaviour and call for an integrated research program in cognitive and systems neuroscience around the value of time.
LEVELNET to Visualise, Explore and Compare Protein-Protein Interaction Networks
Authors: Mohseni Behbahani Yasser , Saighi Paul , Corsi Flavia , Laine Elodie , Carbone Alessandra 
Published: August 2021

AbstractPhysical interactions between proteins are central to all biological processes. Yet, the current knowledge of who interacts with whom in the cell and in what manner relies on partial, noisy, and highly heterogeneous data. Thus, there is a need for methods comprehensively describing and organising such data. LEVELNET is a versatile and interactive tool for visualising, exploring and comparing protein-protein interaction (PPI) networks inferred from different types of evidence. LEVELNET helps to break down the complexity of PPI networks by representing them as multilayered graphs and by facilitating the direct comparison of their subnetworks toward biological interpretation. It focuses primarily on the protein chains whose 3D structures are available in the Protein Data Bank. We showcase some potential applications, such as investigating the structural evidence supporting PPIs associated to specific biological processes, assessing the co-localisation of interaction partners, comparing the PPI networks obtained through computational experiments versus homology transfer, and creating PPI benchmarks with desired properties.Availability: LEVELNET is freely available to the community athttp://www.lcqb.upmc.fr/levelnet/.
Near-infrared spectroscopy calibration strategies to predict multiple nutritional parameters of pasture species from different functional groups
Authors: Catunda Karen L. M. , Churchill Amber C. , Power Sally A. , Moore Ben D. 
Published: August 2021

AbstractNear-infrared reflectance spectroscopy (NIRS) has been used by the agricultural industry as a high-precision technique to quantify nutritional chemistry in plants both rapidly and inexpensively. The aim of this study was to evaluate the performance of NIRS calibrations in predicting the nutritional composition of ten pasture species that underpin livestock industries in many countries. These species comprised a range of functional diversity (C3 legumes; C3/C4 grasses; annuals/perennials) and origins (tropical/temperate; introduced/native) that grew under varied environmental conditions (control and experimentally induced warming and drought) over a period of more than 2 years (n = 2,622). A maximal calibration set including 391 samples was used to develop and evaluate calibrations for all ten pasture species (global calibrations), as well as for subsets comprised of the plant functional groups. We found that the global calibrations were appropriate to predict the six key nutritional quality parameters studied for our pasture species, with the highest accuracy found for ash (ASH), crude protein (CP), neutral detergent fibre and acid detergent fibre (ADF), and the lowest for ether extract (EE) and acid detergent lignin parameters. The plant functional group calibrations for C3 grasses performed better than the global calibrations for ASH, CP, ADF and EE parameters, whereas for C3 legumes and C4 grasses the functional group calibrations performed less well than the global calibrations for all nutritional parameters of these groups. Additionally, our calibrations were able to capture the range of variation in forage quality caused by future climate scenarios of warming and severe drought.
Gene regulatory networks controlling temporal patterning, neurogenesis, and cell fate specification in the mammalian retina
Authors: Lyu Pin , Hoang Thanh , Santiago Clayton P. , Thomas Eric D. , Timms Andrew E. , Appel Haley , Gimmen Megan , Le Nguyet , Jiang Lizhi , Kim Dong Won , Chen Siqi , Espinoza David , Telger Ariel E. , Weir Kurt , Clark Brian S. , Cherry Timothy J. , Qian Jiang , Blackshaw Seth 
Published: August 2021

AbstractGene regulatory networks (GRNs), consisting of transcription factors and their target cis- regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized. In this study, we performed integrated single-cell RNA- and scATAC-seq analysis in both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis. We identified multiple interconnected, evolutionarily-conserved GRNs consisting of cell type-specific transcription factors that both activate expression of genes within their own network and often inhibit expression of genes in other networks. These GRNs control state transitions within primary retinal progenitors that underlie temporal patterning, regulate the transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirmed the prediction of this analysis that the NFI transcription factors Nfia, Nfib, and Nfix selectively activate expression of genes that promote late-stage temporal identity in primary retinal progenitors. We also used GRNs to identify additional transcription factors that promote (Insm1/2) and inhibit (Tbx3, Tcf7l1/2) rod photoreceptor specification in postnatal retina. This study provides an inventory of cis- and trans-acting factors that control retinal development, identifies transcription factors that control the temporal identity of retinal progenitors and cell fate specification, and will potentially guide cell-based therapies aimed at replacing retinal neurons lost due to disease.
Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk
Authors: Thomas Eric D. , Timms Andrew E. , Giles Sarah , Harkins-Perry Sarah , Lyu Pin , Hoang Thanh , Qian Jiang , Jackson Victoria , Bahlo Melanie , Blackshaw Seth , Friedlander Martin , Eade Kevin , Cherry Timothy J. 
Published: August 2021

SUMMARYCis-regulatory elements (CREs) play a critical role in the development, maintenance, and disease-states of all human cell types. In the human retina, CREs have been implicated in a variety of inherited retinal disorders. To characterize cell-class-specific CREs in the human retina and elucidate their potential functions in development and disease, we performed single-nucleus (sn)ATAC-seq and snRNA-seq on the developing and adult human retina and on human retinal organoids. These analyses allowed us to identify cell-class-specific CREs, enriched transcription factor binding motifs, putative target genes, and to examine how these features change over development. By comparing DNA accessibility between the human retina and retinal organoids we found that CREs in organoids are highly correlated at the single-cell level, validating the use of organoids as a model for studying disease-associated CREs. As a proof of concept, we studied the function of a disease-associated CRE at 5q14.3 in organoids, identifying its principal target gene as the miR-9-2 primary transcript and demonstrating a dual role for this CRE in regulating neurogenesis and gene regulatory programs in mature glia. This study provides a rich resource for characterizing cell-class-specific CREs in the human retina and showcases retinal organoids as a model in which to study the function of retinal CREs that influence retinal development and disease.HIGHLIGHTSSingle-cell map of cis-regulatory elements in developing and adult human retina.Correlation of single-cell DNA accessibility between human retina and retinal organoids.Association of disease risk loci with cell-class-specific accessibility.Modeling of enhancer function at the 5q14.3 retinal disease-risk locus.
Selective ablation of adult GFAP-expressing tanycytes leads to hypogonadotropic hypogonadism in males
Authors: Butruille Lucile , Batailler Martine , Cateau Marie-Line , Sharif Ariane , Leysen Valérie , Prévot Vincent , Vaudin Pascal , Pillon Delphine , Migaud Martine 
Published: August 2021

ABSTRACTIn adult mammals, neural stem cells emerge in three neurogenic regions, the subventricular zone of the lateral ventricle (SVZ), the subgranular zone of the dentate gyrus of the hippocampus (SGZ) and the hypothalamus. In the SVZ and the SGZ, neural stem/progenitor cells (NSPCs) express the glial fibrillary acidic protein (GFAP) and selective ablation of these NSPCs drastically decreases cell proliferation in vitro and in vivo. In the hypothalamus, GFAP is expressed by α-tanycytes, which are specialized radial glia-like cells in the wall of the third ventricle. To explore the role of these hypothalamic GFAP-positive tanycytes, we used transgenic mice expressing herpes simplex virus thymidine kinase (HSV-Tk) under the control of the mouse Gfap promoter and 4-week intracerebroventricular infusion of the antiviral agent ganciclovir (GCV) that kills dividing cells expressing Tk. While GCV drastically reduced the number and growth of hypothalamus-derived neurospheres from adult transgenic mice in vitro, it caused hypogonadism in vivo. The selective death of dividing tanycytes expressing GFAP indeed caused a marked decrease in testosterone levels and testicular weight, as well as vacuolization of the seminiferous tubules and loss of spermatogenesis. In addition, GCV-treated GFAP-Tk mice showed impaired sexual behavior, but no alteration in food intake or body weight. Our results also show that the selective ablation of GFAP-expressing tanycytes leads to a sharp decrease in the number of gonadotropin-releasing hormone (GnRH)-immunoreactive neurons and blunted LH secretion. Altogether, our data show that GFAP-expressing tanycytes play a central role in the regulation of male reproductive function.Main pointsKilling adult hypothalamic GFAP-expressing cells blunts neurosphere formation in vitro and leads to GnRH deficiency and hypogonadism in vivo. This work pinpoints an unreported role of dividing GFAP-expressing tanycytes in reproductive function.
Deep learning-enhanced morphological profiling predicts cell fate dynamics in real-time in hPSCs
Authors: Ren Edward , Kim Sungmin , Mohamad Saad , Huguet Samuel F. , Shi Yulin , Cohen Andrew R. , Piddini Eugenia , Salas Rafael Carazo 
Published: August 2021

SUMMARYPredicting how stem cells become patterned and differentiated into target tissues is key for optimising human tissue design. Here, we established DEEP-MAP - for deep learning-enhanced morphological profiling - an approach that integrates single-cell, multi-day, multi-colour microscopy phenomics with deep learning and allows to robustly map and predict cell fate dynamics in real-time without a need for cell state-specific reporters. Using human pluripotent stem cells (hPSCs) engineered to co-express the histone H2B and two-colour FUCCI cell cycle reporters, we used DEEP-MAP to capture hundreds of morphological- and proliferation-associated features for hundreds of thousands of cells and used this information to map and predict spatiotemporally single-cell fate dynamics across germ layer cell fates. We show that DEEP-MAP predicts fate changes as early or earlier than transcription factor-based fate reporters, reveals the timing and existence of intermediate cell fates invisible to fixed-cell technologies, and identifies proliferative properties predictive of cell fate transitions. DEEP-MAP provides a versatile, universal strategy to map tissue evolution and organisation across many developmental and tissue engineering contexts.
Three conserved hydrophobic residues in the CC domain of Pit contribute to its plasma membrane localization and immune induction
Authors: Wang Qiong , Li Yuying , Kosami Ken-ichi , Liu Chaochao , Li Jing , Zhang Dan , Miki Daisuke , Kawano Yoji 
Published: August 2021

ABSTRACTNucleotide-binding leucine-rich repeat (NLR) proteins work as crucial intracellular immune receptors. N-terminal domains of NLRs fall into two groups, namely coiled-coil (CC) and Toll-interleukin 1 receptor (TIR) domains, which play critical roles in signal transduction and disease resistance. However, the activation mechanisms of NLRs, and how their N-termini are involved in immune induction, remain largely unknown. Here, we revealed that the rice NLR Pit self-associates through its CC domain. The CC domain of Pit possesses three conserved hydrophobic residues that are known to be involved in homodimer formation in two NLRs, barley MLA10 and Arabidopsis RPM1. Interestingly, the function of these residues in Pit is different from that in MLA10 and RPM1. Although the three hydrophobic residues are important for Pit-induced disease resistance against rice blast fungus, they do not participate in self-association or in binding to downstream signaling molecules. Based on homology modeling of Pit using the structure of the Arabidopsis NLR ZAR1, we tried to clarify the role of the three conserved hydrophobic residues and found that they are involved in the plasma membrane localization. Our findings provide novel insights for understanding the mechanisms of NLR activation as well as the relationship between subcellular localization and immune induction.
Transcriptomic analysis of ribosome biogenesis and pre-rRNA processing during growth stress in Entamoeba histolytica
Authors: Naiyer Sarah , Singh Shashi Shekhar , Kaur Devinder , Singh Yatendra Pratap , Mukherjee Amartya , Bhattacharya Alok , Bhattacharya Sudha 
Published: August 2021

AbstractRibosome biogenesis, a multi-step process involving the transcription, modification, folding and processing of rRNA is the major consumer of cellular energy. It involves the sequential assembly of ribosomal proteins (RP)s via more than 200 ribogenesis factors. Unlike model organisms where transcription of rRNA and RP genes slows down during stress, in Entamoeba histolytica, pre-rRNA synthesis continues, and unprocessed pre-rRNA accumulates. To gain insight into the vast repertoire of ribosome biogenesis factors and understand the major components playing role during stress we computationally identified the ribosome biogenesis factors in E. histolytica. Of the total ∼279 S. cerevisiae proteins, we could only find 188 proteins in E. histolytica. Some of the proteins missing in E. histolytica were also missing in humans. A number of proteins represented by multiple genes in S. cerevisiae had only a single copy in E. histolytica. It was interesting to note that E. histolytica lacked mitochondrial ribosome biogenesis factors and had far less RNase components as compared to S. cerevisiae. Northern hybridization using probes from different spacer regions depicted the accumulation of unprocessed intermediates during stress. Transcriptomic studies revealed the differential regulation of a number of ribosomal factors both in serum-starved and RRP6KD conditions. The ARB1 protein involved at multiple steps of ribosome biogenesis and NEP1 and TSR3 involved in chemical modification of 18S rRNA previously shown to accumulate pre-rRNA precursors upon downregulation in S. cerevisiae and humans were included. The data reveals the importance of some of the major factors required for regulating pre-rRNA processing during stress. This is the first report on the complete repertoire of ribosome biogenesis factors in E. histolytica.
Connectome-based predictions reveal developmental change in the functional architecture of sustained attention and working memory
Authors: Kardan Omid , Stier Andrew J. , Cardenas-Iniguez Carlos , Pruin Julia C. , Schertz Kathryn E. , Deng Yuting , Chamberlain Taylor , Meredith Wesley J. , Zhang Xihan , Bowman Jillian E. , Lakhtakia Tanvi , Tindel Lucy , Avery Emily W. , Lin Qi , Yoo Kwangsun , Chun Marvin M. , Berman Marc G. , Rosenberg Monica D. 
Published: August 2021

AbstractSustained attention (SA) and working memory (WM) are critical processes, but the brain networks supporting these abilities in development are unknown. We characterized the functional brain architecture of SA and WM in 9–11-year-old children and adults. First, we found that adult network predictors of SA generalized to predict individual differences and fluctuations in SA in youth. A WM network model predicted WM performance both across and within children—and captured individual differences in later recognition memory—but underperformed in youth relative to adults. We next characterized functional connections differentially related to SA and WM in youth compared to adults. Results revealed two network configurations: a dominant architecture predicting performance in both age groups and a secondary architecture, more prominent for WM than SA, predicting performance in one. Thus, functional connectivity predicts SA and WM in youth, with networks predicting WM changing more from preadolescence to adulthood than those predicting SA.
Multidimensional encoding of movement and contextual variables by rat globus pallidus neurons during a novel environment exposure task
Authors: Peer Noam D. , Yamin Hagar G. , Cohen Dana 
Published: August 2021

SummaryThe basal ganglia (BG) play a critical role in a variety of functions that are essential for animal survival. Information from different cortical areas propagates through the BG in anatomically segregated circuits along the parallel direct and indirect pathways. We examined how the globus pallidus (GP), a central nucleus within the indirect pathway, encodes input from the motor and cognitive domains. We chronically recorded and analyzed neuronal activity in the GP of rats engaged in a novel environment exposure task. GP neurons displayed multidimensional responses to movement and contextual information. A model predicting single unit activity required many task-related variables, thus confirming the multidimensionality of GP neurons. In addition, populations of GP neurons, but not single units, reliably encoded the animals’ locomotion speed and the environmental novelty. We posit that the GP independently processes information from different domains, effectively compresses it and collectively conveys it to successive nuclei.
Evolutionary conservation of maternal RNA localization in fishes and amphibians revealed by TOMO-Seq
Authors: Naraine Ravindra , Iegorova Viktoriia , Abaffy Pavel , Franek Roman , Soukup Vladimír , Psenicka Martin , Sindelka Radek 
Published: August 2021

AbstractAsymmetrical localization of biomolecules inside the egg, results in uneven cell division and establishment of many biological processes, cell types and the body plan. However, our knowledge about evolutionary conservation of localized mRNAs is still limited to a few candidates. Our goal was to compare localization profiles along the animal-vegetal axis of mature eggs from four models, Xenopus laevis, Danio rerio, Ambystoma mexicanum and Acipenser ruthenus using the spatial expression method called TOMO-Seq. We revealed that RNAs of many known important genes such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models. There was also a poor correlation between vegetally localized genes but a relatively good correlation between animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.