bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Language Lateralization Using Spectral Analysis of EEG
Authors: Nix Kerry C. , Oh Ahyuda , Goad Beattie S. , Wu Wei , Lucas Molly V. , Baumer Fiona M. 
Published: May 2024

Purpose:
Language lateralization relies on expensive equipment and can be difficult to tolerate. We assessed if lateralized brain responses to a language task can be detected with spectral analysis of electroencephalography (EEG).

Methods:
Twenty right-handed, neurotypical adults (28 ± 10 years; five males) performed a verb generation task and two control tasks (word listening and repetition). We measured changes in EEG activity elicited by tasks (the event-related spectral perturbation [ERSP]) in the theta, alpha, beta, and gamma frequency bands in two language (superior temporal and inferior frontal [ST and IF]) and one control (occipital [Occ]) region bilaterally. We tested whether language tasks elicited (1) changes in spectral power from baseline (significant ERSP) at any region or (2) asymmetric ERSPs between matched left and right regions.

Results:
Left IF beta power (−0.37±0.53, t = −3.12, P = 0.006) and gamma power in all regions decreased during verb generation. Asymmetric ERSPs (right > left) occurred between the (1) IF regions in the beta band (right vs. left difference of 0.23±0.37, t(19) = -2.80, P = 0.0114) and (2) ST regions in the alpha band (right vs. left difference of 0.48±0.63, t(19) = -3.36, P = 0.003). No changes from baseline or hemispheric asymmetries were noted in language regions during control tasks. On the individual level, 16 (80%) participants showed decreased left IF beta power from baseline, and 16 showed ST alpha asymmetry. Eighteen participants (90%) showed one of these two findings.

Conclusions:
Spectral EEG analysis detects lateralized responses during language tasks in frontal and temporal regions. Spectral EEG analysis could be developed into a readily available language lateralization modality.
Endothelial ERG programs neutrophil transcriptome for sustained anti-inflammatory vascular niche
Authors: Vellingiri Vigneshwaran , Balaji Ragunathrao Vijay Avin , Joshi Jagdish Chandra , Akhter Md Zahid , Anwar Mumtaz , Banerjee Somenath , Dudek Steven , Tsukasaki Yoshikazu , Pinho Sandra , Mehta Dolly 
Published: May 2024

AbstractNeutrophils (PMNs) reside as a marginated pool within the vasculature, ready for deployment during infection. However, how endothelial cells (ECs) control PMN extravasation and activation to strengthen tissue homeostasis remains ill-defined. Here, we found that the vascular ETS-related gene (ERG) is a generalized mechanism regulating PMN activity in preclinical tissue injury models and human patients. We show that ERG loss in ECs rewired PMN-transcriptome, enriched for genes associated with the CXCR2-CXCR4 signaling. Rewired PMNs compromise mice survival after pneumonia and induced lung vascular inflammatory injury following adoptive transfer into naïve mice, indicating their longevity and inflammatory activity memory. Mechanistically, EC-ERG restricted PMN extravasation and activation by upregulating the deubiquitinase A20 and downregulating the NFκB-IL8 cascade. Rescuing A20 inEC-Erg-/-endothelium or suppressing PMN-CXCR2 signaling rescued EC control of PMN activation. Findings deepen our understanding of EC control of PMN-mediated inflammation, offering potential avenues for targeting various inflammatory diseases.HighlightsERG regulates trans-endothelial neutrophil (PMN) extravasation, retention, and activationLoss of endothelial (EC) ERG rewires PMN-transcriptomeAdopted transfer of rewired PMNs causes inflammation in a naïve mouseERG transcribesA20and suppresses CXCR2 function to inactivate PMNsIn brief/blurbThe authors investigated how vascular endothelial cells (EC) control polymorphonuclear neutrophil (PMN) extravasation, retention, and activation to strengthen tissue homeostasis. They showed that EC-ERG controls PMN transcriptome into an anti-adhesive and anti-inflammatory lineage by synthesizingA20and suppressing PMNs-CXCR2 signaling, defining EC-ERG as a target for preventing neutrophilic inflammatory injury.
Effects of Classical Psychedelics on Implicit and Explicit Emotional Empathy and Cognitive Empathy: A Meta-analysis of MET task
Authors: Olami Amit , Peled-Avron Leehe 
Published: May 2024

AbstractThis meta-analysis investigates the effect of classic psychedelic drugs on empathy and focuses on cognitive and emotional empathy measured using the Multifaceted Empathy Test (MET). Empathy entails the ability to understand and share the feelings of another and is a significant component of social interaction. Several studies have examined the effects of psychedelic drugs such as LSD, psilocybin and ayahuasca on empathy, yet their overall effect has not been studied so far. In this meta analysis, we reviewed data from studies up to November 2023 with the aim of examining the effects of various psychedelic drugs on empathic abilities broadly. Our findings suggest that classical psychedelics significantly enhance explicit and implicit emotional empathy without affecting measures of cognitive empathy. The results emphasize the need to continue testing the therapeutic potential of classic psychedelic drugs.
IRF7 from the black flying fox induces a STAT1-independent ISG response in unstimulated cell lines that protects against diverse RNA viruses
Authors: Cruz-Rivera Pamela C. De La , Eitson Jennifer L. , Schoggins John W. 
Published: May 2024

AbstractBats are considered unique in their ability to harbor large numbers of viruses and serve as reservoirs for zoonotic viruses that have the potential to spill over into humans. However, these animals appear relatively resistant to the pathogenic effects of many viruses. Mounting evidence suggests that bats may tolerate viral infections due to unique immune features. These include evolutionary innovations in inflammatory pathways and in the molecules involved in viral sensing, interferon induction, and downstream interferon-induced antiviral effectors. We sought to determine whether interferon-stimulated genes (ISGs) from the black flying fox (Pteropus alecto) encoded proteins with unique antiviral activity relative to their human orthologs. Accordingly, we compared the antiviral activity of over 50 ISG human-bat ortholog pairs to identify differences in individual effector functions. We identified IRF7 fromPteropus alecto(Pa.IRF7) as a potent and broad-acting antiviral molecule that provides robust antiviral protection without prior activation. We show that Pa.IRF7 uniquely induces a subset of protective ISGs independent of canonical IFN signaling, which leads to protection from alphaviruses, a flavivirus, a rhabdovirus, and a paramyxovirus. In uninfected cells, Pa.IRF7 partially localizes to the nucleus and can directly bind interferon-sensitive regulatory elements (ISREs). Compared to human IRF7, Pa.IRF7 also has additional serines in its C terminal domain that contribute to antiviral activity and may serve as unique phosphorylation hubs for activation. These properties constitute major differences between bat and human IRF7 that offer additional insight into the potential uniqueness of the black flying fox immune system.
Highly Effective Batch Effect Correction Method for RNA-seq Count Data
Authors: Zhang Xiaoyu 
Published: May 2024

AbstractRNA sequencing (RNA-seq) has become a cornerstone in transcriptomics, offering detailed insights into gene expression across diverse biological conditions and sample types. However, RNA-seq data often suffer from batch effects, which are systematic non-biological differences that compromise data reliability and obscure true biological variation. To address these challenges, we introduce ComBat-ref, a refined method of batch effect correction that enhances the statistical power and reliability of differential expression analysis in RNA-seq data. Building on the foundations of ComBat-seq, ComBat-ref employs a negative binomial model to adjust count data but innovates by using a pooled dispersion parameter for entire batches and preserving count data for the reference batch. Our method demonstrated superior performance in both simulated environments and real datasets, such as the growth factor receptor network (GFRN) data and NASA GeneLab transcriptomic datasets, significantly improving sensitivity and specificity over existing methods. By effectively mitigating batch effects while maintaining high detection power, ComBat-ref proves to be a robust tool for enhancing the accuracy and interpretability of RNA-seq data analyses.
Unraveling the proteome landscape of mouse hematopoietic stem and progenitor compartment with high sensitivity low-input proteomics
Authors: Üresin Nil , Petrosius Valdemaras , Aragon-Fernandez Pedro , Furtwängler Benjamin , Schoof Erwin M. , Porse Bo T. 
Published: May 2024

AbstractProteins play a key role in defining cellular phenotypes, yet comprehensive proteomic analysis often requires substantial input material, posing challenges in studying rare populations in complex cell systems. Here, we present an accessible, label-free low-input proteomics workflow that allows for comprehensive proteome coverage reminiscent of classical bulk samples from only 500 cells and showcase its application in murine hematopoiesis. With this approach, we construct a proteomic map of hematopoietic stem and progenitor cell (HSPC) populations isolated by fluorescence-activated cell sorting (FACS) from the bone marrow of a single mouse, identifying approximately 7,000 proteins per cell population. Our study recapitulates the differentiation trajectories along the megakaryocytic-erythroid and granulocytic-monocytic lineages. We specifically focus on the dynamics of transcriptional regulators and provide insights into both known and novel population-specific factors. Furthermore, we extend our exploration to the most primitive stem and progenitor compartment, and identify ADP-Ribosyltransferase ART4 (CD297) as a novel cell surface marker that can potentially be used to enrich for long-term hematopoietic stem cells (LT-HSC). The low-input proteomics workflow presented here holds promise for overcoming the challenges associated with analyzing proteomes of rare cell populations, thereby paving the way for broader applications in biomedical research.
Protection of savings by reducing the salience of opposing errors
Authors: Javidialsaadi Mousa , Albert Scott T. , Al Mutairi Badr Moufarrej S , Wang Jinsung 
Published: May 2024

AbstractWhen humans encounter the same disturbance twice, they adapt to it faster during the second exposure. To examine how subconscious learning systems contribute to this savings process, previous studies have suppressed explicit awareness of the perturbation by gradually increasing its magnitude during initial learning. This has produced mixed effects, with some studies demonstrating faster relearning, and others observing no acceleration during relearning. Here we examined whether these differences might be due to the nature of a de-adaptation period that separates two learning periods. To test this idea, we manipulated the magnitude of washout errors by de-adapting participants abruptly, gradually, or by removing feedback entirely. Empirical analyses indicated that the different classes of washout errors had a profound effect on savings: large washout errors nullified the ability to save, whereas small errors or the absence of error protected savings. Model-based analyses suggested that changes in learning rates were mediated by an increase in sensitivity to error that could be reversed by experience with oppositely-oriented washout errors. This suggests that the experience of error produces both a facilitation of learning for similar errors and a reduction in learning for dissimilar errors. The latter can abolish the expression of savings following gradual adaptation.
Mechanical Analysis of Cell Migration Using Hybrid Structural Optimization
Authors: Havenhill Eric , Ghosh Soham 
Published: May 2024

ABSTRACTCell migration requires the dynamic formation and dissolution of mechanical structures inside the cytoplasm. Stress fibers are made of F-actin during cell migration driven by the strategic localization of focal adhesion complexes at the cell-substrate interface. The nucleus is also strategically positioned in the cell during the migration and the stress fibers wrap around the nucleus possibly to carry the nucleus with the cell. Cell migration is energetically demanding and should require strategic utilization of resources such as the F-actin stress fiber formation at specific locations so that they generate enough force by actomyosin contraction at the cell-matrix adhesion sites for a directed movement. In this work we propose a structural optimization based biophysical model to predict the strategic localization and sizes of F-actin fibers that supports the nucleus and the cytoplasm during migration. With the use of a nonlinear controller via a Newton-Euler-based model of the generated design, we further quantified the force in the stress fibers during migration, with results close to those obtained through experimental methods such as traction force microscopy. The predicted force decreases for a cell that migrates slowly due to a pharmacological perturbation. Such quantification of forces only require the information of the trajectory of the cell that can be readily obtained from time lapse microscopy. With novel microscopy techniques emerging, such biophysical model framework can be combined with traction force microscopy data to achieve unprecedented mechanical information inside and outside cells during migration, which is otherwise not possible by experiments only.SIGNIFICANCECell migration plays a critical role in biological functions. It requires the strategic formation of F-actin stress fibers at specific locations, to generate forces by actomyosin contraction for cells to migrate in a directed manner. The present study predicts the localization and force generated by stress fibers based on the trajectory of the cell, which can be obtained via time lapse microscopy. The technique can complement other techniques such as traction force microscopy to provide mechanical information inside and outside cells during cell migration.
Protein interactions, calcium, phosphorylation, and cholesterol modulate CFTR cluster formation on membranes
Authors: Wan Yimei , Hudson Rhea , Smith Jordyn , Forman-Kay Julie D. , Ditlev Jonathon A. 
Published: May 2024

ABSTRACTThe Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride channel whose dysfunction leads to intracellular accumulation of chloride ions, dehydration of cell surfaces, and subsequent damage to airway and ductal organs. Beyond its function as a chloride channel, interactions between CFTR, ENaC, and SLC transporter family membrane proteins and cytoplasmic proteins, including calmodulin and NHERF-1, co-regulate ion homeostasis. CFTR has also been observed to form mesoscale membrane clusters. However, the biophysical mechanisms that regulate the formation of CFTR clusters are unknown. Using a combination of computational modeling and complex biochemical reconstitution assays, we demonstrate that multivalent protein-protein interactions with CFTR binding partners, calcium, and membrane cholesterol can induce CFTR cluster formation on model membranes. Phosphorylation of the intracellular domains of CFTR also promotes cluster formation in the absence of calcium, indicating that multiple mechanisms can regulate CFTR cluster formation. Our findings reveal that coupling of multivalent protein and lipid interactions promote CFTR cluster formation consistent with membrane-associated biological phase separation.SIGNIFICANCE STATEMENTMutations in the cystic fibrosis transmembrane conductance regulator (CFTR) membrane protein underlie cystic fibrosis. It is thought that molecular “hubs” of CFTR and its binding partners co-regulate ion homeostasis and that disruption of these clusters can result in disease. However, the physical basis for molecular hub formation is unclear. In this study, we present evidence that multivalent protein and lipid interactions drive the formation of mesoscale CFTR-containing clusters or “hubs” on model membranes in a manner consistent with biological phase separation. These data provide important insights into physical mechanisms that modulate CFTR membrane organization and offer a new lens for the development of corrective therapeutics.
DeepLeMiN: Deep-learning-empowered Physics-aware Lensless Miniscope
Authors: Tian Feng , Mattison Ben , Yang Weijian 
Published: May 2024

AbstractMask-based lensless fluorescence microscopy is a compact, portable imaging technique promising for biomedical research. It forms images through a thin optical mask near the camera without bulky optics, enabling snapshot three-dimensional imaging and a scalable field of view (FOV) without increasing device thickness. Lensless microscopy relies on computational algorithms to solve the inverse problem of object reconstruction. However, there has been a lack of efficient reconstruction algorithms for large-scale data. Furthermore, the entire FOV is typically reconstructed as a whole, which demands substantial computational resources and limits the scalability of the FOV. Here, we developed DeepLeMiN, a lensless microscope with a custom designed optical mask and a multi-stage physics-informed deep learning model. This not only enables the reconstruction of localized FOVs, but also significantly reduces the computational resource demands and facilitates real-time reconstruction. Our deep learning algorithm can reconstruct object volumes over 4×6×0.6 mm3, achieving lateral and axial resolution of ∼10 µm and ∼50 µm respectively. We demonstrated significant improvement in both reconstruction quality and speed compared to traditional methods, across various fluorescent samples with dense structures. Notably, we achieved high-quality reconstruction of 3D motion of hydra and the neuronal activity with cellular resolution in awake mouse cortex. DeepLeMiN holds great promise for scalable, large FOV, real-time, 3D imaging applications with compact device footprint.
The effect ofCitrus reticulatapeel extract containing hesperidin on inhibition of SARS-CoV-2 infection based on pseudovirus entry assays
Authors: Septisetyani Endah Puji , Harsan Hayfa Salsabila , Kumara Dennaya , Prasetyaningrum Pekik Wiji , Paramitasari Komang Alit , Cahyani Anisa Devi , Anam Khairul , Kastian Ria Fajarwati , Santoso Adi , Ikawati Muthi , Meiyanto Edy 
Published: May 2024

ABSTRACTOrange (Citrus reticulataBlanco) peel contains a flavonoid glycoside hesperidin (HSD) as the primary component. HSD, upon enzymatic hydrolysis, forms hesperetin (HST) aglycone derivate. These two flavonoids have been predicted to havein-silicoaffinities for ACE2 and SARS-CoV-2 spike, crucial proteins in SARS-CoV-2 infection mechanisms. However,in vitroantiviral testing of orange peel extract, HSD, and HST has not been reported. This study presents for the first time a pseudovirus entry assay approach to test the anti-SARS-CoV-2 effect of HSD, HST, and orange peel extract prepared by hydrodynamic cavitation (HCV). We used a non-virulent pseudovirus model as an alternative to the original virus to target the entry point and enable research to be conducted outside the BSL-3 facility. Based on HPLC analysis, the test results showed that HCV contained HSD at about 4% w/w. Moreover, HSD 1 and 10 μM, HST 10 μM, and HCV 1 μg/ml showed inhibition of pseudovirus entry in 293/hACE2 cells with percentages inhibition 25.92, 37.40, 27.32, and 38.97 %, respectively. Despite HCV 1 μg/ml showing about 6 % lower inhibitory activity than HSD 1 μM in pseudovirus entry assay, it holds potential as a supplement or source of raw material for HSD as a SARS-CoV-2 antiviral.
Structural Basis for Intermodular Communication in Assembly-Line Polyketide Biosynthesis
Authors: Cogan Dillon P. , Soohoo Alexander M. , Chen Muyuan , Liu Yan , Brodsky Krystal L. , Khosla Chaitan 
Published: May 2024

ABSTRACTAssembly-line polyketide synthases are large multienzyme systems with considerable potential for genetic reprogramming. To investigate the mechanisms by which reactive biosynthetic intermediates are directionally channeled across a defined sequence of active sites in a naturally occurring assembly line, we employed a bifunctional reagent to crosslink transient domain-domain interfaces of the 6-deoxyerythronolide B synthase. Structural resolution of these crosslinked states by single-particle cryogenic electron microscopy (cryo-EM) together with statistical per-particle image analysis of cryo-EM data revealed ketosynthase – acyl carrier protein (KS-ACP) interactions that discriminate between intra- and inter-modular communication, while reinforcing the relevance of asymmetric conformations during the catalytic cycle. Our findings provide a new foundation for the structure-based design of hybrid polyketide synthases comprised of biosynthetic modules from different assembly lines.
KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription
Authors: Hyder Usman , Challa Ashwini , Thornton Micah , Nandu Tulip , Kraus W. Lee , D’Orso Iván 
Published: May 2024

AbstractSignal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
TrAQ: a novel, versatile, semi-automated, two-dimensional motor behavioural tracking software
Authors: Di Censo Davide , Rosa Ilaria , Ranieri Brigida , Di Lorenzo Tiziana , Alecci Marcello , Florio Tiziana M. , Galante Angelo 
Published: May 2024

AbstractWe present TrAQ, a new MATLAB-based two-dimensional tracking software for Open Field video analysis of unmarked single animal, featuring minimum user intervention. We developed TrAQ with the purpose to automatically count the in-plane rotations, an important parameter in the 6-hydroxydopamine hemiparkinsonian rat model and in many rodent models of neurodegenerative diseases, a very time-consuming manual task for highly trained human operators. In addition, TrAQ allows automatic recognition of the animal within a user defined arena providing a quantitative measurement of the body centroid and the two extremities positions. A full range of quantitative kinematic behavioral parameters are automatically calculated, and the optional shape erosion feature adds usage flexibility. TrAQ, free and non-species-specific application, was quantitively tested with rodents and on a qualitative basis with zebrafish, and invertebrate animal models. Quantitative results were successfully validated against a commercial software (for tracking) and manual annotation (for rotations in an hemiparkinsonian rat model). This is a widely used model in preclinical research to study postural instability and motor asymmetry. TrAQ allows the characterization of motor asymmetry using non-invasive tools, thus appreciating the spontaneous Open Field behaviour of unmarked single animal, with minimum user intervention.