bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bright light therapy and early morning attention, mathematical performance, electroencephalography and brain connectivity in adolescents with morning sleepiness
Authors: Teicher Martin H. , Bolger Elizabeth , Hernandez Garcia Laura C. , Hafezi Poopak , Weiser Leslie P. , McGreenery Cynthia E. , Khan Alaptagin , Ohashi Kyoko 
Published: August 2022

AbstractAdolescents typically sleep too little and feel drowsy during morning classes. We assessed whether early morning use of an LED bright light device could increase alertness in school students. Twenty-six (8M/18F) healthy, unmedicated participants, ages 13-18 years, (mean 17.1±1.4) were recruited following screenings to exclude psychopathology. Baseline assessments were made of actigraph-assessed sleep, attention, math solving ability, electroencephalography and structural and functional MRI (N=10-11, pre-post). Participants nonrandomly received 3-4 weeks of bright light therapy (LiteBook Edge™) for 30 minutes each morning and used blue light blocking glasses for 2 hours before bedtime. LiteBooks™ were modified to surreptitiously record degree of use so that the hypothesis tested was whether there was a significant relationship between degree of use and outcome. LiteBooks™ were used 57±18% (range 23%–90%) of recommended time. There was a significant association between degree of use and: (1) increased beta spectral power in frontal EEG leads (primary measure); (2) greater post-test improvement in math performance and reduction in errors of omission on attention test; (3) earlier rise times on non-school days and reduced day-to-day variability in rise times; (4) increased dentate gyrus volume and (5) enhanced frontal connectivity with temporal, occipital and cerebellar regions during Go/No-Go task performance. Degree of bright light therapy use was associated with improvement in sleep cycle consistency, arousal, attention and functional connectivity, but not sleep onset or duration (primary measures). Although this was an open study, it suggests that use of bright morning light and blue light blocking glasses before bed may benefit adolescents experiencing daytime sleepiness.
Astrocytes in the retinorecipient superior colliculus display unique cellular and structural properties
Authors: Visser Josien , Ribot Jérôme , Pauletti Alberto , Mazaud David , Henneberger Christian , Rouach Nathalie 
Published: August 2022

AbstractAstrocytes have long been considered to be a largely homogeneous cell population. Recent studies however suggest that astrocytes are highly adapted to the local neuronal circuitry. Glucose utilization in the retinorecipient superior colliculus (SC) is one of the highest in the brain. Since metabolic support to neurons is a major function of astrocytes, they could be of particular relevance in this region and display specific features. However, little is known about astrocytes and their interactions with neurons in this multisensory brain area. We thus here investigated region-specific cellular and structural properties of astrocytes in the visual layer of the SC. Using morphological reconstructions, fluorescent recovery after photobleaching (FRAP) and superresolution imaging, we found that astrocytes from the visual layers of the SC are highly distinct with a higher cellular density, a more complex morphology and a stronger proximity to synapses compared to astrocytes from the primary visual cortex and the hippocampus. These data point to astroglial diversity and specialization within neural circuits integrating sensory information in the adult brain.
Beyond Linear Neural Envelope Tracking: A Mutual Information Approach
Authors: De Clercq Pieter , Vanthornhout Jonas , Vandermosten Maaike , Francart Tom 
Published: August 2022

AbstractThe human brain tracks the temporal envelope of speech, which contains essential cues for speech understanding. Linear models are the most common tool to study neural envelope tracking. However, information on how speech is processed can be lost since nonlinear relations are precluded. As an alternative, mutual information (MI) analysis can detect both linear and nonlinear relations. Yet, several different approaches to calculating MI are applied without consensus on which approach to use. Furthermore, the added value of nonlinear techniques remains a subject of debate in the field. To resolve this, we applied linear and MI analyses to electroencephalography (EEG) data of participants listening to continuous speech. Comparing the different MI approaches, we conclude that results are most reliable and robust using the Gaussian copula approach, which first transforms the data to standard Gaussians. With this approach, the MI analysis is a valid technique for studying neural envelope tracking. Like linear models, it allows spatial and temporal interpretations of speech processing, peak latency analyses, and applications to multiple EEG channels combined. Finally, we demonstrate that the MI analysis can detect nonlinear components on the single-subject level, beyond the limits of linear models. We conclude that the MI analysis is a more informative tool for studying neural envelope tracking.Significance statementIn the present study, we addressed key methodological considerations for MI applications. Traditional MI methodologies require the estimation of a probability distribution at first. We show that this step can introduce a bias in the results and, consequently, severely impact interpretations. As an alternative, we propose using the parametric Gaussian copula method, which we demonstrated to be robust against biases. Second, using the parametric MI analysis, we show that there is nonlinear variance in the EEG data that the envelope of speech can explain at the single-subject level, proving its added value to neural envelope tracking. We conclude that the MI analysis is a statistically more powerful tool for studying neural envelope tracking than linear models. In addition, it retains spatial and temporal characteristics of speech processing which are lost when using more complex deep neural networks.
Modulation of spinal circuits following phase-dependent electrical stimulation of afferent pathways
Authors: Pascual-Valdunciel Alejandro , Kurukuti Nish Mohith , Montero-Pardo Cristina , Barroso Filipe Oliveira , Pons José Luis 
Published: August 2022

AbstractPeripheral electrical stimulation (PES) of afferent pathways is a tool commonly used to induce neural adaptations in some neural disorders such as pathological tremor or stroke. However, the neuromodulatory effects of stimulation interventions synchronized with physiological activity (closed-loop strategies) have been scarcely researched in the upper-limb. Here, the short-term spinal effects of a 20-minute stimulation of afferent pathways protocol applied with a closed-loop strategy named Selective and Adaptive Timely Stimulation (SATS) was explored. The SATS strategy was applied to the radial nerve in-phase (INP) or out-of-phase (OOP) with respect to the muscle activity of the extensor carpi radialis (ECR). The neural adaptations at the spinal cord level were assessed for the flexor carpi radialis (FCR) by measuring disynaptic Group I inhibition, Ia presynaptic inhibition, and Ib facilitation from the H-reflex, and estimation of the neural drive before, immediately after, and 30 minutes after the intervention. SATS strategy was proved to deliver synchronous stimulation with the real-time measured muscle activity with an average delay of 17±8 ms. SATS-INP induced an increase of the disynaptic Group I inhibition (77±23 % of baseline conditioned FCR H-reflex), while SATS-OOP elicited the opposite effect (125±46 %). Not all the subjects maintained the changes after 30 minutes. Additionally, no other significant specific neural adaptations were found for the rest of measurements. These results suggest that the short-term modulatory effects of phase-dependent PES occur at the specific targeted spinal pathways for the wrist muscles in healthy individuals. Overall, timely recruitment of afferent pathways with the muscle activity is a fundamental principle which should be considered in tailoring PES protocols for the specific neural circuits to be modulated.
Bayesian Tests for Random Mating in Polyploids
Authors: Gerard David 
Published: August 2022

AbstractHardy-Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations, and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of the hwep R package on the Comprehensive R Archive Networkhttps://cran.r-project.org/package=hwep.
Aldy 4: An efficient genotyper and star-allele caller for pharmacogenomics
Authors: Hari Ananth , Zhou Qinghui , Gonzaludo Nina , Harting John , Scott Stuart A. , Sahinalp S. Cenk , Numanagić Ibrahim 
Published: August 2022

AbstractHigh-throughput sequencing provides sufficient means for determining genotypes of clinically important pharmacogenes that can be used to tailor medical decisions to individual patients. However, pharmacogene genotyping, also known as star-allele calling, is a challenging problem that requires accurate copy number calling, structural variation discovery, variant calling and phasing within each pharmacogene copy present in the sample.Here we introduce Aldy 4, a fast and efficient tool for genotyping pharmacogenes that utilizes combinatorial optimization for accurate star-allele calling across different sequencing technologies. Aldy 4 adds support for long reads and ships with a novel phasing model and improved copy number and variant calling models.We compare Aldy 4 against the current state-of-the-art star-allele callers on a large and diverse set of samples and genes sequenced by various sequencing technologies, such as whole-genome and targeted Illumina sequencing, barcoded 10X Genomics and PacBio HiFi. We show that Aldy 4 is the most accurate star-allele caller with near-perfect accuracy in all evaluated contexts. We hope that Aldy remains an invaluable tool in the clinical toolbox even with the advent of long-read sequencing technologies.AvailabilityAldy 4 is available at https://github.com/0xTCG/aldy.
The addiction-susceptibility TaqIA/Ankyrin repeat and kinase domain containing 1 kinase (ANKK1) controls reward and metabolism through dopamine receptor type 2 (DR2)-expressing neurons
Authors: Montalban Enrica , Walle Roman , Castel Julien , Ansoult Anthony , Hassouna Rim , Foppen Ewout , Fang Xi , Hutelin Zach , Mickus Sophie , Perszyk Emily , Petitbon Anna , Berthelet Jérémy , Rodrigues-Lima Fernando , Cebrian-Serrano Alberto , Gangarossa Giuseppe , Martin Claire , Trifilieff Pierre , Bosch-Bouju Clémentine , Small Dana. M , Luquet Serge 
Published: August 2022

AbstractSignificant evidence highlights the importance of genetic variants in the development of psychiatric and metabolic conditions. Among these, the Taq1A polymorphism is one of the most commonly studied in psychiatry. TaqIA is located in the gene that codes for the Ankyrin repeat and kinase domain containing 1 kinase (ANKK1) near the dopamine D2 dopamine receptor (DR2) gene. Depending on race it affects 30 to 80% of the population and its homozygous expression of the A1 allele correlates with a 30 to 40% reduction of striatal DR2, a typical feature of addiction, over-eating and other psychiatric pathologies. The mechanisms by which the variant influences dopamine signaling and behavior is unknown. Here we used transgenic and viral-mediated strategies to reveal the role of ANKK1 in the regulation of activity and functions of the striatum. We found that Ankk1 is preferentially enriched in striatal DR2 expressing neurons and that Ankk1 loss-of-function in dorsal and ventral striatum leads to alteration in learning, impulsive, and flexible behaviors resembling the endophenotypes described in A1 carriers. We also observed an unsuspected role of ANKK1 in striatal DR2-expressing neurons in the ventral striatum in the regulation of energy homeostasis and documented differential nutrient partitioning in humans with versus without the A1 allele. Overall, our data demonstrate that the Ankk1 gene is necessary for the integrity of striatal functions and reveal a new role for ANKK1 in the regulation of body metabolism.
Egocentric Bias in Effort Comparison Tasks Is Driven by Sensory Asymmetries, Not Attribution Bias
Authors: Stinson Caedyn , Kagan Igor , Pooresmaeili Arezoo 
Published: August 2022

AbstractWhen comparing themselves with others, people often perceive their own actions and behaviour favourably. This phenomenon is often categorised as a bias of attribution, with favourable self-evaluation resulting from differing explanations of one’s own behaviour and that of others. However, studies on availability biases offer an alternative explanation, ascribing egocentric biases to the inherent sensory asymmetries between performing an action and merely observing it. In this study, we used a paradigm that allowed us to directly compare these two distinct sources of bias. Participants perceived the tasks they performed to be harder than the tasks they observed, but demonstrated no bias driven by favourable self-evaluation. Furthermore, the degree of overestimation of the difficulty of performed tasks was magnified as overall task difficulty increased. These findings suggest that egocentric biases are in part derived from sensory asymmetries inherent to the first-person perspective.
rRNA depletion for holobiont metatranscriptome profiling across demosponges
Authors: Vargas Sergio , Rivera-Vicéns Ramón E. , Eitel Michael , Leiva Laura , Büttner Gabrielle , Wörheide Gert 
Published: August 2022

AbstractDespite the extensive knowledge of sponge microbiome diversity, a critical knowledge gap persists concerning the molecular mechanisms that govern host-symbiont interactions. Deciphering these mechanisms is crucial for understanding how sponge holobionts respond to environmental changes and identifying potential disruptions in sponge-microbe associations. A hindrance to progress in characterizing these molecular crosstalk mechanisms is the scarcity of broadly applicable molecular methods for efficiently sequencing meta-transcriptomes across a diverse array of sponge species. To tackle this challenge, we have introduced a hybrid-capture strategy capable of selectively depleting sponge and bacterial rRNA from total RNA extracts obtained from highly divergent demosponges with varying microbiome complexities. Our innovative pan-demosponge rRNA depletion approach streamlines the efficient characterization of metatranscriptomes within diverse demosponge holobionts, concurrently facilitating the quantification of gene expression in both the host and its microbiome. This methodological advancement represents a significant stride in unraveling the molecular intricacies of sponge-microbe interactions, providing a robust platform for future investigations across a broad spectrum of sponge species.
Multi-sugar fermentation of lignocellulosic hydrolysate under industrially relevant conditions: comparison of several yeast strains
Authors: Froehlich Allan , Covalla Sean , Fromanger Romain , Hämäläinen Joonas , Kaartinen Tarja , Mastel Beth , Laine M. Minna 
Published: August 2022

ABSTRACTBoth hexose- and pentose-fermenting yeasts are commercially available. The aim of this study was to test several yeast strains for their ability to ferment lignocellulosic feedstock and to evaluate their usability in a bioethanol production process based on the Cellunolix® concept. The Cellunolix® bioethanol demonstration plant of St1 uses sawdust to produce second-generation lignocellulosic ethanol. The study was performed in collaboration with yeast providers using two types of pretreated and filtered lignocellulosic ethanol hydrolysate originating from pine and willow. Ten pentose- and three hexose-fermenting yeast strains were tested. They all performed well under industrial conditions but differed in the rate of detoxification and profile for utilization of different sugars. A satisfactory 82–97% fermentation yield of a multi-sugar hydrolysate containing glucose, mannose, galactose, arabinose and xylose was achieved within 48 h. The results indicate significant potential for the usability of pentose-fermenting strains with real industrial hydrolysates and settings.
Zebrafish Slit2 and Slit3 act together to regulate retinal axon crossing at the midline
Authors: Davison Camila , Bedó Gabriela , Zolessi Flavio R. 
Published: August 2022

AbstractSlit-Robo signaling regulates midline crossing of commissural axons in different systems. In the zebrafish, all retinofugal axons cross at the optic chiasm to innervate the contralateral tectum. Here, the mutant for the Robo2 receptor presents severe axon guidance defects, which were not completely reproduced in a Slit2 ligand null mutant. Since slit3 is also expressed around this area at the stage of axon crossing, we decided to analyze the possibility that it collaborates with Slit2 in this process. We found that the disruption of slit3 expression by sgRNA-Cas9 injection caused similar, albeit slightly milder, defects than those of the slit2 mutant, while the same treatment in the slit2-/- background caused much more severe defects, comparable to those observed in robo2 mutants. Tracking analysis of in vivo time-lapse experiments indicated differential but complementary functions of these secreted factors in the correction of axon turn errors around the optic chiasm. Interestingly, RT-qPCR analysis showed a mild increase in slit2 expression in slit3 deficient embryos, but not the opposite. Our observations support the previously proposed “repulsive channel” model for Slit-Robo action at the optic chiasm, with both Slits acting in different manners, most probably relating to their different spatial expression patterns.
Theoretical assessment of persistence and adaptation in weeds with complex life cycles
Authors: Lauenroth Dana , Gokhale Chaitanya S. 
Published: August 2022

AbstractHerbicide-resistant weeds pose a significant threat to global food security. Perennial weed species are particularly troublesome. Such perennials asSorghum halepensespread quickly and are difficult to manage due to their ability to reproduce sexually via seeds and asexually through rhizomes. Our theoretical study ofSorghum halepenseincorporates this complex life cycle with control measures of herbicide application and tillage. Rooted in the biology and experimental data ofSorghum halepense, our population-based model predicts population dynamics and target-site resistance evolution in this perennial weed. We found that the resistance cost determines the standing genetic variation for herbicide resistance. The sexual phase of the life cycle, including self-pollination and seed bank dynamics, contributes substantially to the persistence and rapid adaptation ofSorghum halepense. While self-pollination accelerates target-site resistance evolution, seed banks significantly increase the probability of escape from control strategies and maintain genetic variation. Combining tillage and herbicide application effectively reduces weed densities and the risk of control failure without delaying resistance adaptation. We also show how mixtures of different herbicide classes are superior to rotations and monotreatment in controlling perennial weeds and resistance evolution. Thus, by integrating experimental data and agronomic views, our theoretical study synergistically contributes to understanding and tackling the global threat to food security from resistant weeds.
Automated cell type annotation and exploration of single cell signalling dynamics using mass cytometry
Authors: Kleftogiannnis Dimitrios , Gavasso Sonia , Tislevoll Benedicte Sjo , van der Meer Nisha , Motzfeldt Inga K. F. , Hellesøy Monica , Gullaksen Stein-Erik , Griessinger Emmanuel , Fagerholt Oda , Lenartova Andrea , Fløisand Yngvar , Gjertsen Bjørn Tore , Jonassen Inge 
Published: August 2022

AbstractMass cytometry by time-of-flight (CyTOF) is an emerging technology allowing for in-depth characterisation of cellular heterogeneity in cancer and other diseases. However, computational identification of cell populations from CyTOF, and utilisation of single cell data for biomarker discoveries faces several technical limitations, and although some computational approaches are available, high-dimensional analyses of single cell data remains quite demanding. Here, we deploy a bioinformatics framework that tackles two fundamental problems in CyTOF analyses namely: a) automated annotation of cell populations guided by a reference dataset, and b) systematic utilisation of single cell data for more effective patient stratification. By applying this framework on several publicly available datasets, we demonstrate that the Scaffold approach achieves good tradeoff between sensitivity and specificity for automated cell type annotation. Additionally, a case study focusing on a cohort of 43 leukemia patients, reported salient interactions between signalling proteins that are sufficient to predict short-term survival at time of diagnosis using the XGBoost algorithm. Our work introduces an automated and versatile analysis framework for CyTOF data with many applications in future precision medicine projects. Datasets and codes are publicly available at:https://github.com/dkleftogi/singleCellClassification