bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two types of hand withdraw movement to place food in the mouth mediated by somatosensation in 22-species of strepsirrhines
Authors: Peckre Louise R , Fabre Anne-Claire , Wall Christine E , Pouydebat Emanuelle , Whishaw Ian Q 
Published: March 2022

AbstractThe evolution of visual control of the hand to assist feeding by primates is uncertain but in anthropoid primates vision contributes not only to reaching for food and grasping it but also to the withdraw movement that brings food to the mouth. The strepsirrhines are a relatively large monophyletic group of Euarchontoglires near the base of the primate cladogram that are described as using vision to reach for food, but it is not known whether they use vision to assist the withdraw movement. The present study answere this question in 22 species of captive strepsirrhines from 6 of the seven strepsirrhine families, Daubentoniidae, Cheirogaleidae, Indriidae, Lemuridae, Lorisidae and Galagidae. Animals were videorecorded as they ate their normal food provisions. Dependent measures for analyses were ground withdraw movements, bringing grasped food to the mouth, and inhand withdraw movements, brining food held in the hand to the mouth, as well as the posture and head movements associated with each type of withdraw. Frame-by-frame scores from the video record showed that there were large differences between and within strepsirrhine families in these movements. Nevertheless, for all species, the withdraw movement was mediated by somatosensation, with mouth reaching and perioral contact with food determining how food was eventually eaten. Nonvisual behavior also contributed to food grasping as many species sniffed food before or during grasping. Even amongst species that made most use of the hand for their withdraws, the insectivoresLoris lydekkerianusandGalago senegalensis, and herbivores,Hapalemur simusandEulemur flavifrons, perioral contact was used to orient food for biting. The use of somatosensation and the absence of vision in mediating getting food in strepsirrhines suggests that visual mediation of the withdraw is an anthropoid innovation.
New β-propellers are continuously amplified from single blades in all major lineages of the β-propeller superfamily
Authors: Pereira Joana , Lupas Andrei N. 
Published: March 2022

Abstractβ-Propellers are toroidal folds, in which consecutive supersecondary structure units of four anti-parallel β-strands – called blades – are arranged radially around a central axis. Uniquely among toroidal folds, blades span the full range of sequence symmetry, from near identity to complete divergence, indicating an ongoing process of amplification and differentiation. We have proposed that the major lineages of β-propellers arose through this mechanism and that therefore their last common ancestor was a single blade, not a fully formed β-propeller. Here we show that this process of amplification and differentiation is also widespread within individual lineages, yielding β-propellers with blades of more than 60% median pairwise sequence identity in most major β-propeller families. In some cases, the blades are nearly identical, indicating a very recent amplification event, but even in cases where such recently amplified β-propellers have more than 80% overall sequence identity to each other, comparison of their DNA sequence shows that the amplification occurred independently.
iSparse kmeans: a two-step clustering approach for big dynamic functional network connectivity data
Authors: Sendi Mohammad S. E. , Salat David H , Miller Robyn L , Calhoun Vince D 
Published: March 2022

AbstractBackgroundDynamic functional network connectivity (dFNC) estimated from resting-state functional magnetic imaging (rs-fMRI) studies the temporally varying of functional integration between brain networks. In a typical dFNC pipeline, a clustering stage to summarize the connectivity patterns that are transiently but reliably realized over the course of a scanning session. However, identifying the right number of clusters through a conventional clustering criterion computed by running the algorithm repeatedly, over a large range of cluster numbers is time-consuming and requires substantial computational power even for typical dFNC datasets, and the computational demands become prohibitive as datasets become larger and scans longer. Here we developed a new dFNC pipeline, called iterative sparse kmeans or iSparse kmeans, to analyze large dFNC data without having access to huge computational power.MethodIn iSparse kmeans, we implement two-step clustering. In the first step, we randomly use a sub-sample dFNC data and identify several sets of states at different model orders. In the second step, we aggregate all dFNC states estimated from all iterations in the first step and use this to identify the optimum number of clusters using the elbow criteria. Additionally, we use this new reduced dataset and estimate a final set of states by performing a second kmeans clustering on the aggregated dFNC states from the first k-means clustering. To validate the reproducibility of iSparse kmeans, we analyzed four dFNC datasets from the human connectome project (HCP).ResultsWe found that both conventional kmeans and iSparse kmeans generate similar brain dFNC states while iSparse kmeans is 27 times faster than the traditional method in finding the optimum number of clusters. We show that the results are replicated across four different datasets from HCP.ConclusionWe developed a new analytic pipeline which facilitates analysis of large dFNC datasets without having access to a huge computational power source. We validated the reproducibility of the result across multiple datasets.
Lipid-correlated alterations in the transcriptome are enriched in several specific pathways in the postmortem prefrontal cortex of Japanese patients with schizophrenia
Authors: Arihisa Wataru , Kondo Takeshi , Yamaguchi Katsushi , Matsumoto Junya , Nakanishi Hiroki , Kunii Yasuto , Akatsu Hiroyasu , Hino Mizuki , Hashizume Yoshio , Sato Shumpei , Sato Shinji , Niwa Shin-Ichi , Yabe Hirooki , Sasaki Takehiko , Shigenobu Shuji , Setou Mitsutoshi 
Published: March 2022

AbstractBackgroundSchizophrenia is a chronic relapsing psychiatric disorder that is characterized by many symptoms and has a high heritability. A previous study showed that specific lipid molecules belong to phosphatidylinositol (PI) and phosphatidylserine (PS) was reduced in the postmortem prefrontal cortex of patients with schizophrenia1. However, signaling pathways contributing to the lipid changes remain unknown. Here we performed two types of transcriptome analyses in patients with schizophrenia: an un-biased transcriptome analysis solely based on RNA-seq data and a correlation analysis between levels of gene expression and lipids.Methodology/Principal FindingsRNA-Seq analysis was performed in the postmortem prefrontal cortex from 10 subjects with schizophrenia and 5 controls. Correlation analysis between the transcriptome and lipidome from 9 subjects which are the same samples in the previous lipidomics study1 (Table 1). Extraction of differentially expressed genes (DEGs) and further sequence and functional group analysis revealed changes of gene expression levels in phosphoinositide 3-kinase (PI3K)-Akt signaling and the complement system. In addition, a correlation analysis clarified alterations in several signaling/metabolic pathways including lipid-correlated genes, most of which are not found as DEGs in transcriptome analysis alone.Table 1.Characteristics of patients from whom postmortem brain samples were obtained.Abbreviations: PMI, postmortem interval, the time that has elapsed since a person has died; DOI, duration of illness, The samples used in correlation analysis are shown by black circles.ConclusionsThis study provided results of the first integrated analysis of the schizophrenia-associated transcriptome and lipidome within the PFC and revealed that lipid-correlated alterations in the transcriptome are enriched in specific pathways including PI3K-Akt signaling.
Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors
Authors: Pekkarinen Meeri , Nordfors Kristiina , Uusi-Mäkelä Joonas , Kytölä Ville , Rauhala Minna , Urhonen Henna , Huhtala Laura , Häyrynen Sergei , Afyounian Ebrahim , Yli-Harja Olli , Zhang Wei , Helen Pauli , Lohi Olli , Haapasalo Hannu , Haapasalo Joonas , Nykter Matti , Kesseli Juha , Rautajoki Kirsi J. 
Published: March 2022

AbstractAtypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness, exceptionally low mutation rate, and aberrant but still unresolved epigenetic regulation. To evaluate methylation associated regulation in AT/RTs, we compared them to medulloblastomas and choroid plexus tumors by integrating DNA methylation (507 samples), gene expression (120 samples), and public transcription factor (TF) binding data. We showed that elevated DNA methylation masks the binding sites of TFs driving neural development and is associated with reduced transcription for specific neural regulators in AT/RTs. Part of the hypermethylated sites behaved similarly in AT/RTs and pluripotent stem cells, revealing DNA methylation -driven halted cell differentiation. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 members, like EZH2, and linked to suppressed genes with a role in neural development and tumorigenesis. The obtained results highlight and characterize these DNA methylation programs as drivers of AT/RT malignancy.
Concurrent separation of phase-locked and non-phase-locked activity
Authors: Singhal Shubham , Ghosh Priyanka , Kumar Neeraj , Banerjee Arpan 
Published: March 2022

AbstractBrain dynamics recorded via electroencephalography (EEG) is conceptualized as a sum of two components, “phase-locked” and “non-phase-locked” to the stimulus. Both activities are understood to be stemming from different neuronal mechanisms and hence accurately characterizing them is of immense importance in neuroscientific studies. Here, we discuss the drawbacks of currently used methods to separate the phase-locked and non-phase-locked activity and propose a new method that decomposes the two components simultaneously. First, we demonstrate that single-trial separation of phase-locked and non-phase-locked power is an ill-posed problem. Second, using simulations where ground truth validation is possible, we elucidate the drawbacks of the widely used averaging method and efficacy of the proposed concurrent phaser method (CPM). Using two experimental datasets, audio oddball EEG data and auditory steady-state responses (ASSR) we show how the empirical signal-to-noise estimates warrant the usage of CPM to separate phase-locked and non-phase-locked activity.
Attentional effects on local V1 microcircuits explain selective V1-V4 communication
Authors: Katsanevaki Christini , Bastos André M. , Cagnan Hayriye , Bosman Conrado A. , Friston Karl J. , Fries Pascal 
Published: March 2022

ABSTRACTSelective attention implements preferential routing of attended stimuli, likely through increasing the influence of the respective synaptic inputs on higher-area neurons. As the inputs of competing stimuli converge onto postsynaptic neurons, presynaptic circuits might offer the best target for attentional top-down influences. If those influences enabled presynaptic circuits to selectively entrain postsynaptic neurons, this might explain selective routing. Indeed, when two visual stimuli induce two gamma rhythms in V1, only the gamma induced by the attended stimulus entrains gamma in V4. Here, we modeled induced responses with a Dynamic Causal Model for Cross-Spectral Densities and found that selective entrainment can be explained by attentional modulation of intrinsic V1 connections. Specifically, local inhibition was decreased in the granular input layer and increased in the supragranular output layer of the V1 circuit that processed the attended stimulus. Thus, presynaptic attentional influences and ensuing entrainment were sufficient to mediate selective routing.HIGHLIGHTSWe model selective visual attention in macaques using Dynamic Causal Modeling.Intrinsic V1 modulation can explain attention effects in V1-V4 communication.Modulation of superficial and granular inhibition is key to induce the effects.Those modulations increase V1-V4 communication in a feedforward manner.GRAPHICAL ABSTRACT
Beetles provide directed dispersal of viable spores of a keystone wood decay fungus
Authors: Lunde Lisa Fagerli , Boddy Lynne , Sverdrup-Thygeson Anne , Jacobsen Rannveig M. , Kauserud Håvard , Birkemoe Tone 
Published: March 2022

AbstractWood decay fungi are considered to be dispersed by wind, but dispersal by animals may also be important, and more so in managed forests where dead wood is scarce. We investigated whether beetles could disperse spores of the keystone species Fomitopsis pinicola. Beetles were collected on sporocarps and newly felled spruce logs, a favourable habitat for spore deposition. Viable spores (and successful germination) of F. pinicola were detected by dikaryotization of monokaryotic bait mycelium from beetle samples. Viable spores were on the exoskeleton and in the faeces of all beetles collected from sporulating sporocarps. On fresh spruce logs, nine beetle species transported viable spores, of which several bore into the bark. Our results demonstrate that beetles can provide directed dispersal of wood decay fungi. Potentially, it could contribute to a higher persistence of some species in fragmented forests where spore deposition by wind on dead wood is less likely.
MHC-I binding affinity derived metrics fail to predict tumor specific neoantigen immunogenicity
Authors: Nibeyro Guadalupe , Girotti Romina , Prato Laura , Moron Gabriel , Luján Hugo D. , Fernandez Elmer A. 
Published: March 2022

AbstractTumor-specific antigens emerging through somatic genomic rearrangements, known as neoantigens, play a critical role in current anticancer immunotherapy. They may or may not elicit an immune response when presented on the tumor cell surface bound to the MHC-I molecule, whose strength has been assumed as an indicator of immunogenicity. Several in silico peptide-MHC-I binding affinity predictors are used to prioritize putative immunogenic neoantigens to be experimentally and clinically explored either as biomarkers or targets for anticancer vaccines. This claims for a fair evaluation of such predictors, making essential the development of appropriate databases with experimentally validated, immunogenic/non-immunogenic neoantigens. Thus far, such a database is lacking. We herein present ITSNdb, a new and curated immunogenic neoantigen database and use it to benchmark current neoantigen immunogenicity predictors. Benchmark results failed to support the application of the predicted peptide- MHC-I binding affinity or its derived metrics as a tool to estimate neoantigen immunogenicity and the tumor neoantigen burden as an immunotherapy response biomarker. Moreover, binding affinity based immunogenicity definition leads to identifying wild-type peptide counterparts as predictors of immunotherapy response. We demonstrate that MHC-I binding affinity is insufficient to define neoantigen immunogenicity, despite being necessary for neoantigen tumor cell presentation suggesting that a paradigm shift for the emergence of new rules to identify immunogenic neoantigens is required.
Eco-evolutionary dynamics of clonal multicellular life cycles
Authors: Ress Vanessa , Traulsen Arne , Pichugin Yuriy 
Published: March 2022

AbstractThe evolution of multicellular life cycles is a central process in the course of the emergence of multicellularity. The simplest multicellular life cycle is comprised from the growth of the propagule into a colony and its fragmentation to give rise to new propagules. The majority of theoretical models assume selection among life cycles to be driven by internal properties of multicellular groups resulting in growth competition. At the same time, the influence of interactions between groups on the evolution of life cycles is rarely even considered. Here, we present a model of colonial life cycles evolution taking into account group interactions. Our work shows that the outcome of evolution could be coexistence between multiple life cycles or that the outcome may depend on the initial state of the population – scenarios impossible without group interactions. At the same time, we found that some results of these simpler models remain relevant: Evolutionary stable strategies in our model are restricted to binary fragmentation – the same class of life cycles which contains all evolutionarily optimal life cycles in the model without interactions. Our results demonstrate that while models neglecting interactions can capture short-term dynamics, they fall short in predicting the population-scale picture of the evolution.
Brain Capillary Pericytes are Metabolic Sentinels that Control Blood Flow through KATP Channel Activity
Authors: Hariharan Ashwini , Robertson Colin D. , Garcia Daniela C.G. , Longden Thomas A. 
Published: March 2022

SUMMARYCapillary pericytes and their processes cover ∼90% of the total length of the brains capillary bed. Despite their abundance, little is known of pericyte function, and their contributions to the control of brain hemodynamics remain unclear. Here, we report that deep capillary pericytes possess a mechanistic ‘energy switch’ that, when activated by a decrease in glucose, elicits robust KATP channel activation to increase blood flow and protect energy substrate availability. We demonstrate that pharmacological activation of KATP channels profoundly hyperpolarizes capillary pericytes and leads to dilation of upstream penetrating arterioles and arteriole-proximate capillaries covered with contractile pericytes, leading to an increase in local capillary blood flow. Stimulation of a single capillary pericyte with a KATP channel agonist is sufficient to evoke this response, which is mediated via KIR channel-dependent retrograde propagation of hyperpolarizing electrical signals. Genetic inactivation of pericyte KATP channels via expression of a dominant-negative version of KIR6.1 eliminates these effects. Critically, we show that lowering extracellular glucose below 1 mM evokes dramatic KATP channel-mediated pericyte hyperpolarization. Inhibiting glucose uptake by blocking GLUT1 transporters in vivo also activates this energy switch to increase pericyte KATP channel activity, dilate arterioles and increase blood flow. Together, our findings recast capillary pericytes as metabolic sentinels that respond to local energy deficits by robustly increasing blood flow to protect metabolic substrate delivery to neurons and prevent energetic shortfalls.
Age-dependent lipid droplet-rich microglia worsen stroke outcome in old mice
Authors: Arbaizar-Rovirosa Maria , Gallizioli Mattia , Pedragosa Jordi , Lozano Juan J. , Casal Carme , Pol Albert , Planas Anna M. 
Published: March 2022

SummaryMicroglial cells of the aged brain manifest signs of dysfunction that could contribute to the worse neurological outcome of stroke in the elderly. Treatment with colony-stimulating factor-1 receptor antagonists enable transient microglia depletion that can be followed by microglia repopulation after interruption of the treatment, causing no known harm to mice. Using this strategy, we aimed to restore microglia function and ameliorate stroke outcome in aged mice. Cerebral ischemia/reperfusion induces strong innate immune responses in microglia highlighted by prominent type I interferon signaling, together with cellular metabolic perturbances and lipid droplet biogenesis in young mice. In aged mice, a subset of microglia accumulates lipid droplets under steady state and displays exacerbated innate immune responses after stroke. Microglia renewal in old mice reduces the lipid droplet content, prevents the ischemia-induced exaggerated type I interferon response, and improves the neurological outcome of stroke. This study shows that age-dependent lipid droplet-enriched microglia contribute to impair stroke outcome in old mice.
Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds
Authors: Hermawaty Dina , Cahn Jonathan , Chabikwa Tinashe G. , Lister Ryan , Considine Michael J. 
Published: March 2022

1.AbstractThe regulation of DNA accessibility by histone modification has emerged as a paradigm of developmental and environmental programming. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a versatile tool widely used to investigate in vivo protein-DNA interaction. The technique has been successfully demonstrated in several plant species and tissues; however, it has remained challenging in woody tissues. Here we developed a ChIP method specifically for mature dormant grapevine buds (Vitis vinifera cv. Cabernet Sauvignon). Each step of the protocol was systematically optimised, including crosslinking, chromatin extraction, sonication, and antibody validation. Analysis of histone H3-enriched DNA was performed to evaluate the success of the protocol and identify occupancy of histone H3 along grapevine bud chromatin. To our best knowledge, this is the first ChIP experiment protocol optimised for grapevine bud system.
Pre-Existing Comorbidities Diminish the Likelihood of Seropositivity After SARS-CoV-2 Vaccination
Authors: Amraotkar Alok R. , Bushau-Sprinkle Adrienne M. , Keith Rachel J. , Hamorsky Krystal T. , Palmer Kenneth E. , Gao Hong , Rai Shesh N. , Bhatnagar Aruni 
Published: March 2022

ABSTRACTBackgroundThe impact of chronic health conditions (CHC) on serostatus post-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is unknown.MethodsWe assessed serostatus post-SARS-CoV-2 vaccination among fully vaccinated adult residents of Jefferson County, Kentucky, USA from April 2021 through August 2021. Serostatus was determined by qualitative analysis of SARS-CoV-2 specific Spike IgG antibodies via enzyme-linked immunoassay (ELISA) in peripheral blood samples.ResultsOf the 5,178 fully vaccinated participants, 51 were seronegative and 5,127 were seropositive. Chronic kidney disease (CKD) and autoimmune disease showed highest association with negative serostatus in fully vaccinated individuals. The absence of any CHC was strongly associated with positive serostatus. The risk of negative serostatus increased as the total number of pre-existing CHCs increased. Similarly, use of 2 or more CHC related medications was associated with seronegative status.ConclusionsPresence of any CHC, especially CKD or autoimmune disease, increased the likelihood of seronegative status among individuals who were fully vaccinated to SAR-CoV-2. This risk increased with a concurrent increase in number of comorbidities, especially with multiple medications. Absence of any CHC was protective and increased the likelihood of a positive serological response. These results will help develop appropriate guidelines for booster doses and targeted vaccination programs.