bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatosensory cortex microstimulation modulates primary motor and ventral premotor cortex neurons with extensive spatial convergence and divergence
Authors: Ruszala Brandon , Mazurek Kevin A. , Schieber Marc H. 
Published: August 2023

AbstractIntracortical microstimulation (ICMS) is known to affect distant neurons transynaptically, yet the extent to which ICMS pulses delivered in one cortical area modulate neurons in other cortical areas remains largely unknown. Here we assessed how the individual pulses of multi-channel ICMS trains delivered in the upper extremity representation of the macaque primary somatosensory area (S1) modulate neuron firing in the primary motor cortex (M1) and in the ventral premotor cortex (PMv). S1-ICMS pulses modulated the majority of units recorded both in the M1 upper extremity representation and in PMv, producing more inhibition than excitation. Effects converged on individual neurons in both M1 and PMv from extensive S1 territories. Conversely, effects of ICMS delivered in a small region of S1 diverged to wide territories in both M1 and PMv. The effects of this direct modulation of M1 and PMv neurons produced by multi-electrode S1-ICMS like that used here may need to be taken into account by bidirectional brain-computer interfaces that decode intended movements from neural activity in these cortical motor areas.Significance StatementAlthough ICMS is known to produce effects transynaptically, relatively little is known about how ICMS in one cortical area affects neurons in other cortical areas. We show that the effects of multi-channel ICMS in a small patch of S1 diverge to affect neurons distributed widely in both M1 and PMv, and conversely, individual neurons in each of these areas can be affected by ICMS converging from much of the S1 upper extremity representation. Such direct effects of ICMS may complicate the decoding of motor intent from M1 or PMv when artificial sensation is delivered via S1-ICMS in bidirectional brain-computer interfaces.
Tissue-wide scRNA-seq analysis reveals enrichment of imprinted genes in stem and endocrine cell-types in mice
Authors: Higgs Matthew J. , Hill Matthew J. , John Rosalind M. , Isles Anthony R. 
Published: August 2023

ABSTRACTEnriched expression of imprinted genes may provide evidence of convergent function. Here we interrogated five single-cell RNA sequencing datasets to identify imprinted gene over-representation in the embryonic and adult mouse focusing on tissues including the bladder, pancreas, mammary gland and muscle. We identify a consistent enrichment of imprinted genes in stromal cell and mesenchymal stem cell populations across these tissues, suggesting a role in tissue maintenance. Furthermore, we identify a distinct enrichment in the endocrine islets of the mouse pancreas, over and above the stromal/stem cells from this tissue. Taken together with our previous work examining imprinted gene expression in cell subpopulations of the adult mouse brain and pituitary gland, these data suggest that genomic imprinting influences physiology largely via separate systems of cell populations either involved in hormonal signalling or in stemness and cell-fate co-ordination.
Decoding Visual Spatial Attention Control
Authors: Meyyappan Sreenivasan , Rajan Abhijit , Yang Qiang , Mangun George R , Ding Mingzhou 
Published: August 2023

AbstractIn models of visual spatial attention control, it is commonly held that top-down control signals originate in the dorsal attention network, propagating to the visual cortex to modulate baseline neural activity and bias sensory processing. However, the precise distribution of these top-down influences across different levels of the visual hierarchy is debated. In addition, it is unclear whether these changes in baseline neural activity directly translate into improved performance. We analyzed attention-related baseline activity during the anticipatory period of a trial-by-trial voluntary spatial attention task, using two independent fMRI datasets, and two different analytic approaches. First, as in prior studies, univariate analysis showed that covert attention significantly enhanced baseline neural activity in higher-order visual areas contralateral to the attended visual hemifield, while effects in lower-order visual areas (e.g., V1) were weaker and more variable. Second, in contrast, multivariate pattern analysis (MVPA) revealed significant decoding of attention conditions across all visual cortical areas, with lower-order visual areas exhibiting higher decoding accuracies than higher-order areas. Third, decoding accuracy, rather than the magnitude of univariate activation, was a better predictor of a subject’s stimulus discrimination performance. Finally, the MVPA results were replicated across two experimental conditions, where the direction of spatial attention was either externally instructed by a cue or based on the participants free choice decision about where to attend. Together, these findings offer new insights into the extent of attentional biases in the visual hierarchy under top-down control, and how these biases influence both sensory processing and behavioral performance.HighlightsMultivariate pattern analysis revealed the presence of top-down attentional biasing signals in all areas of the visual hierarchy whereas univariate analysis was not able to reveal the full extent of attentional biasing in the visual cortex.The decoding accuracy derived from the MVPA analysis but not the magnitude difference derived from the univariate analysis predicted the subject’s behavioral performance in stimulus discrimination.The MVPA results were consistent across two experimental conditions where the direction of spatial attention was driven either by external instructions or from purely internal decisions.
Targeted decontamination of sequencing data with CLEAN
Authors: Lataretu Marie , Krautwurst Sebastian , Huska Matthew R. , Marquet Mike , Viehweger Adrian , Braun Sascha D. , Brandt Christian , Hölzer Martin 
Published: August 2023

ABSTRACTMany biological and medical questions are answered based on the analysis of sequence data. However, we can find contamination, artificial spike-ins, and overrepresented rRNA sequences in various read collections and assemblies. In particular, spike-ins used as controls, as those known from Illumina or Nanopore data, are often not considered as contaminants and also not appropriately removed during analyses. Additionally, removing human host DNA may be necessary for data protection and ethical considerations to ensure that individuals cannot be identified.We developed CLEAN, a pipeline to remove unwanted sequences from both long- and short-read sequencing techniques. While focusing on Illumina and Nanopore data with their technology-specific control sequences, the pipeline can also be used for host decontamination of metagenomic reads and assemblies, or the removal of rRNA from RNA-Seq data. The results are the purified sequences and sequences identified as contaminated with statistics summarized in a report.The output can be used directly in subsequent analyses, resulting in faster computations and improved results. Although decontamination seems mundane, many contaminants are routinely overlooked, cleaned by steps that are not fully reproducible or difficult to trace. CLEAN facilitates reproducible, platform-independent data analysis in genomics and transcriptomics and is freely available athttps://github.com/rki-mf1/cleanunder a BSD3 license.GRAPHICAL ABSTRACT
Microplastics reach the brain and interfere with honey bee cognition
Authors: Pasquini Elisa , Ferrante Federico , Passaponti Leonardo , Pavone Francesco Saverio , Costantini Irene , Baracchi David 
Published: August 2023

AbstractScientific research exploring the impact of microplastics (MPs) in terrestrial systems is still at an early stage but has already confirmed that exposure to plastics leads to various detrimental health effects in several organisms. Although recent studies have shown the toxicological effects of single MP polymers on honey bees, the effects of different polymer combinations and their consequences on cognitive and behavioural performance remain unknown. To fill this knowledge gap, we investigated the effects of MPs, both individually and in combination, on the cognitive abilities of the honey beeApis mellifera. We evaluated the acute oral toxicity of Polystyrene (PS) and Plexiglass (PMMA) MPs, as well as a combination of the two (MIX), at three different concentrations (0.5, 5 and 50 mg/L-1) and analysed their effects on sucrose responsiveness and appetitive olfactory learning and memory. We also explored whether these MPs could reach and accumulate in the insect brain using Two-Photon Fluorescence Microscopy (TPFM) in combination with an optimized version of the DISCO clearing technique. The results revealed that PS reduced the responsiveness of foragers to sucrose, whereas PMMA had no significant impact; however, the combination of PMMA and PS had a pronounced negative effect on sucrose responsiveness. In addition, both PMMA and PS, as well as MIX, impaired bee learning formation and memory retrieval, with PS exhibiting the most severe effects. Regarding our brain imaging analysis performed with TFPM, we found that after only three days of oral exposure, MPs could penetrate and accumulate in the brain. These results raise concerns about the potential mechanical, cellular, and biochemical damage that MPs may cause to the central nervous system.
Sex-Specific Developmental Gene Expression Atlas Unveils Dimorphic Gene Networks inC. elegans
Authors: Haque Rizwanul , Kurien Sonu Peedikayil , Setty Hagar , Salzberg Yehuda , Stelzer Gil , Litvak Einav , Gingold Hila , Rechavi Oded , Oren-Suissa Meital 
Published: August 2023

ABSTRACTSex-specific traits and behaviors emerge during development by the acquisition of unique properties in the nervous system of each sex. However, the genetic events responsible for introducing these sex-specific features remain poorly understood. In this study, we created a comprehensive gene expression atlas for both sexes of the nematodeCaenorhabditis elegansacross development. By comparing the transcriptome of pure populations of hermaphrodites and males from early larval stages to adulthood, we discovered numerous differentially expressed genes, including neuronal gene families like transcription factors, neuropeptides, and GPCRs. We identified INS-39, an insulin-like peptide, as a prominent male-biased gene expressed specifically in ciliated sensory neurons. We show that INS-39 serves as an early-stage male marker, facilitating the effective isolation of males in high-throughput experiments. Through complex and sex-specific regulation,ins-39plays pleiotropic sexually-dimorphic roles in temperature sensation, survival in cold temperatures, resilience against high hydrogen peroxide levels, and dauer entry, while also playing a shared, dimorphic role in early life stress. This study offers a comparative sexual and developmental gene expression database forC. elegans, which will facilitate research into the genetic regulation of the sexual development of other organisms. Furthermore, it highlights conserved candidate genes that may underlie the sexually-dimorphic manifestation of different human diseases.
Using social information improves individual foraging efficiency in sheep
Authors: Vartparonian Vartan E , Leu Stephan T 
Published: August 2023

AbstractKnowledge about the environment is fundamentally important to move, find resources and forage efficiently. This information can either be acquired through individual exploration (personal information) or from other group members (social information). We experimentally assessed the use of social information and its influence on foraging efficiency in sheep,Ovis aries. Naïve individuals paired with an informed partner that knew the food patch location, found the patch significantly faster compared to naïve individuals paired with another naïve individual. Similarly, they spent a significantly lower proportion of time exploring areas away from the food patch. We further found that the previous outcome of using social information (success = access to feed vs failure = no access to feed) had no impact and sheep continued to use social information in subsequent foraging trials and foraged similarly efficient. Our results suggest, naïve sheep that are unfamiliar with resource locations, forage more efficiently when informed individuals are present compared to when all individuals are naïve. If informed individuals play a similar role in larger groups, new management practices could be developed to improve foraging efficiency when sheep are moved to new paddocks or in paddocks with heterogenous and dynamic resource distribution.
Dissociation of attentional state and behavioral outcome using local field potentials
Authors: Prakash Surya S , Mayo J Patrick , Ray Supratim 
Published: August 2023

AbstractSuccessful behavior depends on attentional state and other factors related to decision-making, which may modulate neuronal activity differently. Here, we investigated whether attentional state and behavioral outcome (i.e., whether a target is detected or missed) are distinguishable using the power and phase of local field potential (LFP) recorded bilaterally from area V4 of monkeys performing a cued visual attention task. To link each trial’s outcome to pairwise measures of attention that are typically averaged across trials, we used several methods to obtain single-trial estimates of spike count correlation and phase consistency. Surprisingly, while attentional location was best discriminated using gamma and high-gamma power, behavioral outcome was best discriminated by alpha power and steady-state visually evoked potential. Power outperformed absolute phase in attentional/behavioral discriminability, although single-trial gamma phase consistency provided reasonably high attentional discriminability. Our results suggest a dissociation between the neuronal mechanisms that regulate attentional focus and behavioral outcome.
Feed-forward metabotropic signaling by Cav1 Ca2+channels supports pacemaking in pedunculopontine cholinergic neurons
Authors: Tubert C. , Zampese E. , Pancani T. , Tkatch T. , Surmeier D. J. 
Published: August 2023

AbstractLike a handful of other neuronal types in the brain, cholinergic neurons (CNs) in the pedunculopontine nucleus (PPN) are lost in the course of Parkinson’s disease (PD). Why this is the case is unknown. One neuronal trait implicated in PD selective neuronal vulnerability is the engagement of feed-forward stimulation of mitochondrial oxidative phosphorylation (OXPHOS) to meet high bioenergetic demand, leading to sustained oxidant stress and ultimately degeneration. The extent to which this trait is shared by PPN CNs is unresolved. To address this question, a combination of molecular and physiological approaches were used. These studies revealed that PPN CNs are autonomous pacemakers with modest spike-associated cytosolic Ca2+transients. These Ca2+transients were attributable in part to the opening of high-threshold Cav1.2 Ca2+channels, but not Cav1.3 channels. Nevertheless, Cav1.2 channel signaling through endoplasmic reticulum ryanodine receptors stimulated mitochondrial OXPHOS to help maintain cytosolic adenosine triphosphate (ATP) levels necessary for pacemaking. Inhibition of Cav1.2 channels led to recruitment of ATP-sensitive K+channels and slowing of pacemaking. Cav1.2 channel-mediated stimulation of mitochondria increased oxidant stress. Thus, PPN CNs have a distinctive physiological phenotype that shares some, but not all, of the features of other neurons that are selectively vulnerable in PD.
Resource-combining costs of being a diet generalist in the super-generalist protist predatorDictyostelium discoideum
Authors: Shreenidhi P. M. , Brock Debra A. , McCabe Rachel I. , Strassmann Joan E. , Queller David C. 
Published: August 2023

AbstractConsumers lie on a continuum between diet specialization on few resources to being generalist feeders on many resources. Generalism has the clear advantage of having more resources to exploit, but the costs that limit generalism are less clear. We explore two understudied costs of generalism in a super-generalist amoeba predator,Dictyostelium discoideum, feeding on naturally co-occurring bacterial prey. Both involve costs of combining different prey. First, amoebas exhibit a reduction in growth rate when they switch from one species of prey bacteria to another, something we call resource-switching costs. These switching costs typically disappear within a day, indicating adjustment to new prey bacteria. Second, amoebas usually divide more slowly on mixtures of bacteria compared to on single bacteria, something we call resource-mixing costs. Both results support that idea that, although amoebas can consume a huge variety of prey, they must use partially different methods and thus must pay costs to handle multiple prey, either sequentially or simultaneously.Significance StatementPerhaps the most fundamental conflict in nature occurs when one organism consumes another. Diet generalists benefit from the advantage of eating many prey but then must deal with many prey defences. We explore costs associated with a broad diet in a protist microbial predator,Dictyostelium discoideum. These predators of bacteria show a delay in growth when switched from one bacteria to another, supporting the hypothesis that they must deploy different strategies. They also experience costs when grown on many bacteria at once, suggesting that the alternative strategies for consuming different prey are partly incompatible with each other. Our findings shed light on the nature of diet generalism and highlight the complexity of predation in the microbial world.
HIV-1 Capsid Shape, Orientation, and Entropic Elasticity Regulate Translocation into the Nuclear Pore Complex
Authors: Hudait Arpa , Voth Gregory A. 
Published: August 2023

ABSTRACTNuclear import of the viral capsid is a critical step in the HIV-1 life cycle that serve to transport and release genomic material into the nucleus. Nuclear Pore Complex (NPC) allows passage of intact capsid, though mechanistic details of the process remain to be fully understood. Here we investigate the factors regulating HIV-1 capsid translocation into the NPC central channel using coarse-grained molecular dynamics simulations. We find that successful translocation is contingent on the compatibility of the capsid morphology and channel dimension and the proper orientation of the capsid approach to the channel. The central channel dynamically expands to allow capsid passage, demonstrating the pleomorphic nature of the channel necessary for transporting large cargoes. Structural analysis shows that stress induced by the central channel confinement and uncondensed internal genomic material generates correlated striated patterns of lattice disorder across the viral capsid surface which is an indicator of its lattice “elasticity”. Our results suggest that the “elasticity” can aid the capsid to adapt to the stress and remain structurally intact during translocation.TeaserComputer Simulations identify capsid elasticity as a key factor for successful nuclear entry.
Scoping Review of One-Dimension Statistical Parametric Mapping in Lower Limb Biomechanical Analysis
Authors: Yona Tomer , Kamel Netanel , Cohen-Eick Galya , Ovadia Inbar , Fischer Arielle 
Published: August 2023

ABSTRACTBackgroundBiomechanics is crucial in enhancing sports performance and preventing injury. Traditionally, discrete point analysis is used to analyze important kinetic and kinematic data points, reducing continuous data to a single point. One-dimensional Statistical Parametric Mapping (spm1d) offers a more comprehensive approach by assessing entire movement curves instead of isolated peak values. Nevertheless, spm1d is still underutilized in various sports and sports-related injuries.PurposeTo summarize the existing literature on the application of spm1d in sports biomechanics, including the kinetics and kinematics of the hip, knee, and ankle joints, as well as to identify gaps in the literature that may require further research.MethodsA scoping review was conducted, searching PubMed, Embase, Web of Science, and ProQuest databases. English peer-reviewed studies using SPM to assess lower limb kinetics or kinematics in different sports or sports-related injuries were included. In contrast, reviews, meta-analyses, conference abstracts, grey literature, and studies focusing on non-kinetic or kinematic outcomes were excluded.ResultsThe review yielded 129 papers, with an increased number of studies published in the last three years. Of these studies, 81 examined healthy individuals (63%), and 48 focused on injured populations (37%). Running (n=28), cutting (n=21), and jumping/landing (n=14) were the most common activities. The most prevalent sport-related injuries examined were anterior cruciate ligament rupture (n=21), chronic ankle instability (n=16), and hip-related pain (n=9). Research gaps include the underrepresentation of common sports and movements, small sample size, lack of studies in non-laboratory settings and varied active age groups, and absence of evaluations on the effects of protective sports gear other than shoes.ConclusionThe application of spm1d in sports biomechanics demonstrates diverse uses in sports performance, injury reduction, and rehabilitation. While spm1d shows promise in improving our understanding of sports biomechanics, there are still significant gaps in the literature that present future research opportunities.
Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends
Authors: Sehgal Manas , R Soundharya , Vaz Joel Markus , Yogeshwar Raja G , Muralidharan Srinath , Venkatraghavan Sankalpa , Jolly Mohit Kumar 
Published: August 2023

AbstractColorectal cancer (CRC) is highly heterogenous with variable survival outcomes and therapeutic vulnerabilities. A commonly used classification system in CRC is the Consensus Molecular Subtypes (CMS) based on gene expression patterns. However, how these CMS categories connect to axes of phenotypic plasticity and heterogeneity remains unclear. Here, we analyze 101 bulk transcriptomic datasets, along with patient tumor samples from TCGA and single-cell RNA sequencing data, to evaluate the extent of variation among CMS subtypes across metabolic plasticity and EMT axes. Our results show that CMS2 and CMS3 samples were relatively more epithelial as compared to CMS1 and CMS4. Single-cell RNA-seq analysis of CMS1 revealed two subpopulations: one close to CMS4 (more mesenchymal) and the other closer to CMS2 or CMS3 (more epithelial), indicating a partial EMT-like behavior. Further, in our meta-analysis and in TCGA data, epithelial phenotype score was positively correlated with scores of glycolysis, OXPHOS and FAO pathways, while mesenchymal scores showed CMS subtype-specific associations with metabolic axes. PD-L1 activity scores, however, consistently correlated positively with mesenchymal signature ones and negatively with epithelial signature ones, across the four CMS categories. Together, our results quantify the patterns of two interconnected axes of phenotypic heterogeneity - EMT and metabolic reprogramming - at a CMS subtype level in CRC.