bluuebunny/crossref_metadata_2025_split huggingface dataset:
Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance
Authors: Najar Fares Z. , Linde Evan , Murphy Chelsea , Borin Veniamin A. , Wang Huan , Haider Shozeb , Agarwal Pratul K. 
Published: September 2022

ABSTRACTCOVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate, combined with high rates of transmission and fatality can cause a deadly world-wide pandemic in a matter of weeks.1 Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections (“surges”) before they occur. We describe here real time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens.
A neural framework for spontaneous development of orientation selectivity in the primary visual cortex
Authors: Davey Catherine E. , Lloyd Errol K.J. , Kuhlmann Levin , Burkitt Anthony N. , Vidyasagar Trichur R. 
Published: September 2022

AbstractThe mechanism or microcircuitry behind orientation selectivity in primary visual cortex (V1), and the means by which it develops without supervision or visual input, both remain unresolved questions. Work on the developmental question has assumed the prevalent spatial convergence model of orientation selectivity as the target mechanism. Encouraged by growing evidence challenging both the completeness of this model and its developmental viability, we investigated an alternative scheme. Accordingly, we demonstrate computationally how a scheme in which orientation selectivity originates from the orientation biases already in the retina and lateral geniculate nucelus (LGN) can answer both the mechanistic and developmental questions. In this scheme, the divergence of outputs from the retina allows retinal spontaneous activity to create correlations within the LGN. These correlations in turn allow a Hebbian plasticity mechanism to strengthen those LGN inputs to V1 which carry similar orientation biases and thus provide an orientation tuned excitatory input.
Cognition through internal models: Mirror neurons as one manifestation of a broader mechanism
Authors: Aflalo Tyson , Chivukula Srinivas , Zhang Carey , Rosario Emily R. , Pouratian Nader , Andersen Richard A. 
Published: September 2022

AbstractCognition relies on transforming sensory inputs into a more generalizable understanding. Mirror neurons are proposed to underlie this process, yet they fail to explain many key features of human thinking and learning. Here we hypothesize that mirror-like responses are one limited view into a more general framework by which internal models of the world are built and used. We recorded populations of single neurons in the human posterior parietal cortex as a participant felt or observed diverse tactile stimuli. We found that mirror-like responses were fragile and embedded within a richer population response that encoded generalizable and compositional features of the stimuli. We speculate that populations of neurons support versatile understanding, not through mirroring, but instead by encoding representational building blocks of cognition.One-Sentence SummarySimilar neural responses during observed and experienced sensations are mediated by shared compositional building blocks, not mirror neurons.
GOAT: Deep learning-enhanced Generalized Organoid Annotation Tool
Authors: Bremer Jan P. , Baumdick Martin E. , Knorr Marius S. , Wegner Lucy H.M. , Wesche Jasmin , Jordan-Paiz Ana , Jung Johannes M. , Highton Andrew J. , Jäger Julia , Hinrichs Ole , Brias Sebastien , Niersch Jennifer , Müller Luisa , Schreurs Renée R.C.E. , Koyro Tobias , Löbl Sebastian , Mensching Leonore , Konczalla Leonie , Niehrs Annika , Vondran Florian W. R. , Schramm Christoph , Hölzemer Angelique , Oldhafer Karl , Königs Ingo , Kluge Stefan , Perez Daniel , Reinshagen Konrad , Pals Steven T. , Gagliani Nicola , Joosten Sander P. , Topf Maya , Altfeld Marcus , Bunders Madeleine J. 
Published: September 2022

AbstractOrganoids have emerged as a powerful technology to investigate human development, model diseases and for drug discovery. However, analysis tools to rapidly and reproducibly quantify organoid parameters from microscopy images are lacking. We developed a deep-learning based generalized organoid annotation tool (GOAT) using instance segmentation with pixel-level identification of organoids to quantify advanced organoid features. Using a multicentric dataset, including multiple organoid systems (e.g. liver, intestine, tumor, lung), we demonstrate generalization of the tool to annotate a diverse range of organoids generated in different laboratories and high performance in comparison to previously published methods. In sum, GOAT provides fast and unbiased quantification of organoid experiments to accelerate organoid research and facilitates novel high-throughput applications.
A parabrachial-to-amygdala circuit that determines hemispheric lateralization of somatosensory processing
Authors: Allen Heather N. , Chaudhry Sarah , Hong Veronica M. , Lewter Lakeisha A. , Sinha Ghanshyam P. , Carrasquillo Yarimar , Taylor Bradley K. , Kolber Benedict J. 
Published: September 2022

AbstractBackgroundThe central amygdala (CeA) is a bilateral hub of pain and emotional processing with well-established functional lateralization. We reported that optogenetic manipulation of neural activity in the left and right CeA has opposing effects on bladder pain.MethodsTo determine the influence of calcitonin gene-related peptide (CGRP) signaling from the parabrachial nucleus (PBN) on this diametrically opposed lateralization, we administered CGRP and evaluated the activity of CeA neurons in acute brain slices as well as the behavioral signs of bladder pain in the mouse.ResultsWe found that CGRP increased firing in both the right and left CeA neurons. Furthermore, we found that CGRP administration in the right CeA increased behavioral signs of bladder pain and decreased bladder pain-like behavior when administered in the left CeA.ConclusionsThese studies reveal a parabrachial-to-amygdala circuit driven by opposing actions of CGRP that determines hemispheric lateralization of visceral pain.
MultiOMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells
Authors: Pinto Sneha M. , Subbannayya Yashwanth , Kim Hera , Hagen Lars , Górna Maria W. , Nieminen Anni I. , Bjørås Magnar , Espevik Terje , Kainov Denis , Kandasamy Richard K. 
Published: September 2022

AbstractDespite the availability of vaccines and approved therapeutics, the COVID-19 pandemic continues to rise owing to the emergence of newer variants. Several multi-omics studies have made available extensive evidence on host-pathogen interactions and potential therapeutic targets. Nonetheless, an increased understanding of host signaling networks regulated by post-translational modifications and their ensuing effect on the biochemical and cellular dynamics is critical to expanding the current knowledge on the host response to SARS-CoV-2 infections. Here, employing unbiased global transcriptomics, proteomics, acetylomics, phosphoproteomics, and exometabolome analysis of a lung-derived human cell line, we show that SARS-CoV-2 Norway/Trondheim-S15 strain induces time-dependent alterations in the induction of type I IFN response, activation of DNA damage response, dysregulated Hippo signaling, among others. We provide evidence for the interplay of phosphorylation and acetylation dynamics on host proteins and its effect on the altered release of metabolites, especially organic acids and ketone bodies. Together, our findings serve as a resource of potential targets that can aid in designing novel host-directed therapeutic strategies.
DeepRetroMoCo: Deep neural network-based Retrospective Motion Correction Algorithm for Spinal Cord functional MRI
Authors: Mobarak-Abadi Mahdi , Mahmoudi-Aznave Ahmad , Dehghani Hamed , Zarei Mojtaba , Vahdat Shahabeddin , Doyon Julien , Khatibi Ali 
Published: September 2022

AbstractThere are unique challenges in the preprocessing of spinal cord fMRI data, particularly voluntary or involuntary movement artifacts during image acquisition. Despite advances in data processing techniques for movement detection and correction, there are challenges in extrapolating motion correction algorithm developments in the brain cortex to the brainstem and spinal cord. We trained a Deep Learning-based convolutional neural network (CNN) via an unsupervised learning algorithm, called DeepRetroMoCo, to detect and correct motions in axial T2*-weighted spinal cord data. Spinal cord fMRI data from 27 participants were used for training of the network (135 runs for training and 81 runs for testing). We used average temporal signal-to-noise-ratio (tSNR) and Delta Variation Signal (DVARS) of raw and motion-corrected images to compare the outcome of DeepRetroMoco with sct_fmri_moco implemented in the spinal cord toolbox. The average tSNR in the cervical cord was significantly higher when DeepRetroMoco was used for motion correction compared to sct_fmri_moco method. Average DVARS was lower in images corrected by DeepRetroMoco than those corrected by sct_fmri_moco. The average processing time for DeepRetroMoco was also significantly shorter than sct_fmri_moco. Our results suggest that DeepRetroMoCo improves motion correction procedures in fMRI data acquired from the cervical spinal cord.
Behavior shapes retinal motion statistics during natural locomotion
Authors: Muller Karl , Matthis Jonathan S. , Bonnen Kathryn , Cormack Lawrence K. , Huk Alexander C. , Hayhoe Mary 
Published: September 2022

AbstractWalking through an environment generates retinal motion, which humans rely on to perform a variety of visual tasks. Retinal motion patterns are determined by an interconnected set of factors, including gaze location, gaze stabilization, the structure of the environment, and the walker’s goals. The characteristics of these motion signals have important consequences for neural organization and behavior. However, to date, there are no empirical in situ measurements of how combined eye and body movements interact with real 3D environments to shape the statistics of retinal motion signals. Here, we collect measurements of the eyes, the body, and the 3D environment during locomotion. We describe properties of the resulting retinal motion patterns. We explain how these patterns are shaped by gaze location in the world, as well as by behavior, and how they may provide a template for the way motion sensitivity and receptive field properties vary across the visual field.
An extracellular vesicle targeting ligand that binds to Arc proteins and facilitates Arc transport in vivo
Authors: Lee Peter H. , Anaya Michael , Ladinsky Mark S. , Reitsma Justin M. , Zinn Kai 
Published: September 2022

AbstractCommunication between distant cells can be mediated by extracellular vesicles (EVs) that deliver proteins and RNAs to recipient cells. Little is known about how EVs are targeted to specific cell types. Here we identify the Drosophila cell-surface protein Stranded at second (Sas) as a targeting ligand for EVs. Full-length Sas is present in EV preparations from transfected Drosophila Schneider 2 (S2 cells). Sas is a binding partner for the Ptp10D receptor tyrosine phosphatase, and Sas-bearing EVs preferentially target to cells expressing Ptp10D. We used co-immunoprecipitation and peptide binding to show that the cytoplasmic domain (ICD) of Sas binds to dArc1. dArc1 and mammalian Arc are related to retrotransposon Gag proteins. They form virus-like capsids which encapsulate Arc and other mRNAs and are transported between cells via EVs. The Sas ICD contains a motif required for dArc1 binding that is shared by the mammalian and Drosophila amyloid precursor protein (APP) orthologs, and the Sas and APP ICDs also bind to mammalian Arc. Sas facilitates delivery of dArc1 capsids bearing dArc1 mRNA into distant Ptp10D-expressing recipient cells in vivo.
Fibroblasts generate topographical cues that steer cancer cell migration
Authors: Baschieri Francesco , Illand Abigail , Barbazan Jorge , Zajac Olivier , Henon Clémence , Loew Damarys , Dingli Florent , Vignjevic Danijela Matic , Lévêque-Fort Sandrine , Montagnac Guillaume 
Published: September 2022

ABSTRACTFibroblasts play a fundamental role in tumor development. Among other functions, they regulate cancer cells migration through rearranging the extracellular matrix, secreting soluble factors and establishing direct physical contacts with cancer cells. Here, we report that migrating fibroblasts deposit on the substrate a network of tubular structures that serves as guidance cue for cancer cell migration. Such membranous tubular network, hereafter called tracks, is stably anchored to the substrate in a β5 integrin-dependent manner. We found that cancer cells specifically adhere to tracks by using clathrin-coated structures that pinch and engulf tracks. Tracks represent thus a spatial memory of fibroblast migration paths that is read and erased by cancer cells directionally migrating along them. We propose that fibroblast tracks represent a topography-based intercellular communication system capable of steering cancer cells migration.TEASERThe migration path of fibroblasts is marked by tubules that act as railways to direct following cancer cell migration.
Early life adversity and adult social relationships have independent effects on survival in a wild animal model of aging
Authors: Lange Elizabeth C. , Zeng Shuxi , Campos Fernando A. , Li Fan , Tung Jenny , Archie Elizabeth A. , Alberts Susan C. 
Published: September 2022

AbstractDoes social isolation in adulthood predict survival because socially isolated individuals are already unhealthy due to adversity earlier in life (health selection)? Or do adult social environments directly cause poor health and increased mortality risk (“social causation”)? These alternative hypotheses are difficult to disentangle in humans because prospective data on survival and the environment for both early life and adulthood are rarely available. Using data from the baboon population of Amboseli, Kenya, a model for human behavior and aging, we show that early adversity and adult social isolation contribute independently to reduced adult survival, in support of both health selection and social causation. Further, strong social bonds and high social status can buffer some negative effects of early adversity on survival. These results support a growing change in perspective, away from “either-or” hypotheses and towards a multi-causal perspective that points to multiple opportunities to mitigate the effects of social adversity.TeaserEarly life environments and adult social bonds have strong, but largely independent effects on survival in wild baboons.
Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification
Authors: Magbanua Zenaida V. , Hsu Chuan-Yu , Pechanova Olga , Arick Mark , Grover Corrinne E. , Peterson Daniel G. 
Published: September 2022

AbstractWe present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes optimally sized restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Library amplification and barcoding are completed in one PCR step, and magnetic beads are used to purify the genomic fragments from the ligation and library generation steps. Our protocol increases the efficiency and decreases the time to complete a ddRAD-Seq experiment. To demonstrate its utility, we compared SNPs from our protocol with those from whole genome resequencing data from Gossypium herbaceum and Gossypium arboreum. Principal component analysis demonstrated that the variability of the combined data was explained by the genotype (PC1) and methodology applied (PC2). Phylogenetic analysis showed that the SNPs from our method clustered with SNPs from the resequencing data of the corresponding genotype. Sequence alignments illustrated that for homozygous loci, more than 90% of the SNPs from the resequencing data were discovered by our method. Our analyses suggest that our ddRAD-Seq method is reliable in identifying SNPs suitable for phylogenetic and association genetic studies while reducing cost and time over known methods.
The native mussel Mytilus chilensis genome reveals adaptative molecular signatures facing the marine environment
Authors: Gallardo-Escárate Cristian , Valenzuela-Muñoz Valentina , Nuñez-Acuña Gustavo , Valenzuela-Miranda Diego , Tapia Fabian , Yévenes Marco , Gajardo Gonzalo , Toro Jorge E. , Oyarzún Pablo A. , Arriagada Gloria , Novoa Beatriz , Figueras Antonio , Roberts Steven , Gerdol Marco 
Published: September 2022

ABSTRACTThe blue mussel Mytilus chilensis is a key socioeconomic species inhabiting the southern coast of Chile. This endemic marine mussel supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to a diverse physical-chemical ocean conditions’ for farming. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4,795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis was conducted among M. chilensis and M. coruscus, revealing genic rearrangements distributed into the whole genome. Notably, Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative phylogenetic relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. Collectively, the evidence suggests that local genome adaptation can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex evolution and will help to understand how climate change can impact mussel biology.
Respiratory strategy at birth initiates distinct lung injury phenotypes in the preterm lamb lung
Authors: Pereira-Fantini Prue M. , Ferguson Kristin , McCall Karen , Oakley Regina , Perkins Elizabeth , Byars Sean , Williamson Nicholas , Nie Shuai , Tingay David G 
Published: September 2022

ABSTRACTBronchopulmonary disease is the chronic manifestation of the acute injury that may accompany ventilation following preterm birth. A lack of clear trial evidence often hampers clinical decision-making during support of the preterm lung at birth. Protein biomarkers have been used to define acute lung injury phenotypes and improve patient selection for specific interventions in adult respiratory distress syndrome. Here we present a mass spectrometry-based approach to profile the protein phenotype associated with three different aeration strategies known to cause different pathophysiological responses when applied at birth to preterm lambs. We were able to identify pathway enrichments specific to both ventilation strategy and lung regions based upon gravity-dependency. Ventilation strategy-specific phenotypes were further delineated by applying partial least square modelling to identify associations between specific proteins and clinical, physiological and morphological outcomes. This work highlights the specificity of lung injury responses to routinely applied birth interventions such as different respiratory support approaches and identified the molecular events associated with each. Furthermore, we demonstrate the capacity to subdivide preterm infants by the direct aetiology and response to lung injury; the first step towards true precision medicine in neonatology.
GRAS-1 is a conserved novel regulator of early meiotic chromosome dynamics inC. elegans
Authors: Martinez-Garcia Marina , Naharro Pedro Robles , Skinner Marnie W. , Baran Kerstin A. , Nadarajan Saravanapriah , Shin Nara , Silva-García Carlos G. , Saito Takamune T. , Beese-Sims Sara , Castaner Ana , Pacheco Sarai , Martinez-Perez Enrique , Jordan Philip W. , Colaiácovo Monica P. 
Published: September 2022

ABSTRACTChromosome movements and licensing of synapsis must be tightly regulated during early meiosis to ensure accurate chromosome segregation and avoid aneuploidy, although how these steps are coordinated is not fully understood. Here we show that GRAS-1, the worm homolog of mammalian GRASP/Tamalin and CYTIP, coordinates early meiotic events with cytoskeletal forces outside the nucleus. GRAS-1 localizes close to the nuclear envelope (NE) in early prophase I and interacts with NE and cytoskeleton proteins. Delayed homologous chromosome pairing, synaptonemal complex (SC) assembly, and DNA double-strand break repair progression are partially rescued by the expression of human CYTIP ingras-1mutants, supporting functional conservation. However,Tamalin, Cytipdouble knockout mice do not exhibit obvious fertility or meiotic defects, suggesting evolutionary differences between mammals.gras-1mutants show accelerated chromosome movement during early prophase I, implicating GRAS-1 in regulating chromosome dynamics. GRAS-1-mediated regulation of chromosome movement is DHC-1-dependent, placing it acting within the LINC-controlled pathway, and depends on GRAS-1 phosphorylation at a C-terminal S/T cluster. We propose that GRAS-1 serves as a scaffold for a multi-protein complex coordinating the early steps of homology search and licensing of SC assembly by regulating the pace of chromosome movement in early prophase I.