bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes
Authors: Tovar Adelaide , Kyono Yasuhiro , Nishino Kirsten , Bose Maya , Varshney Arushi , Parker Stephen C.J. , Kitzman Jacob O. 
Published: October 2023

AbstractRecent genome-wide association studies have established that most complex disease-associated loci are found in noncoding regions where defining their function is nontrivial. In this study, we leverage a modular massively parallel reporter assay (MPRA) to uncover sequence features linked to context-specific regulatory activity. We screened enhancer activity across a panel of 198-bp fragments spanning over 10k type 2 diabetes- and metabolic trait-associated variants in the 832/13 rat insulinoma cell line, a relevant model of pancreatic beta cells. We explored these fragments’ context sensitivity by comparing their activities when placed up-or downstream of a reporter gene, and in combination with either a synthetic housekeeping promoter (SCP1) or a more biologically relevant promoter corresponding to the human insulin gene (INS). We identified clear effects of MPRA construct design on measured fragment enhancer activity. Specifically, a subset of fragments (n = 702/11,656) displayed positional bias, evenly distributed across up- and downstream preference. A separate set of fragments exhibited promoter bias (n = 698/11,656), mostly towards the cell-specificINSpromoter (73.4%). To identify sequence features associated with promoter preference, we used Lasso regression with 562 genomic annotations and discovered that fragments withINSpromoter-biased activity are enriched for HNF1 motifs. HNF1 family transcription factors are key regulators of glucose metabolism disrupted in maturity onset diabetes of the young (MODY), suggesting genetic convergence between rare coding variants that cause MODY and common T2D-associated regulatory variants. We designed a follow-up MPRA containing HNF1 motif-enriched fragments and observed several instances where deletion or mutation of HNF1 motifs disrupted theINSpromoter-biased enhancer activity, specifically in the beta cell model but not in a skeletal muscle cell line, another diabetes-relevant cell type. Together, our study suggests that cell-specific regulatory activity is partially influenced by enhancer-promoter compatibility and indicates that careful attention should be paid when designing MPRA libraries to capture context-specific regulatory processes at disease-associated genetic signals.
PSEN1M146Vand PSEN1A246Emutations associated with Alzheimer’s disease impair proper microglia differentiation
Authors: Aubert Antoine , Mendoza-Ferri Maria Grazia , Bramoulle Aude , Stüder François , Colombo Bruno Maria , Mendoza-Parra Marco Antonio 
Published: October 2023

ABSTRACTGenetic variants associated with the late onset of Alzheimer’s disease (AD), were correlated with genes known to be expressed in microglia, suggesting for an AD-genetic component directly influencing microglia behavior. Instead, the role of the familial AD (fAD) genetic mutations was systematically studied from the angle of the Amyloid-Beta pathway; leaving their participation in microglia homeostasis unexplored.Here we demonstrate that two previously described fAD-related PSEN1 mutations directly impair proper microglia differentiation. While human induced pluripotent stem cells harboring the PSEN1-M146V mutation did not give rise to hematopoietic precursor (HPC) intermediate during microglia differentiation, a PSEN1-A246E mutant line managed to produce HPCs, but died within the first days of microglia differentiation.Detailed transcriptomics/epigenomics and functional assays revealed the setup of a pro-apoptotic program in the PSEN1-A246E mutant, which was circumvented when HPCs were grafted in brain organoids (BORGs). Microglia obtained in BORGs presented preferentially pro-inflammatory signatures, further supported by their correlation with recent data providing a detailed stratification of the various microglia populations within AD-patient samples.Overall, this study contributes to reconsider the influence of the previously identified familial mutations in the homeostasis of this immune component of the central nervous system.
PRIME-BSPre: A genome-wide protein-RNA binding sites prediction method based on templates
Authors: Wei Xinhang , Duan Yingtian , Li Danyang , Liu Xudong , Xie Juan , Liu Shiyong 
Published: October 2023

ABSTRACTIdentification of RNA binding sites that potentially interact with RNA-binding proteins facilitates a comprehensive analysis of protein-RNA interactions and enables further investigation into the mechanisms underlying RNA splicing and modification. However, the current experimental data remains limited in comparison to the vast family of RBPs, and deep learning prediction methods are inadequate for those RBPs lacking sufficient interaction data for training. Therefore, we present PRIME-BSPre, a genome-wide method for predicting protein-RNA binding sites based on templates that incorporate both RNA sequence and secondary structure as well as the tertiary structure of corresponding RBPs. We have successfully benchmarked our method on the human genome, demonstrating excellent prediction performance on RBP datasets beyond our library and robustness across cell lines. Additionally, we are pioneers in introducing the low Shannon entropy algorithm to describe binding preferences of RNA motifs. Our predicted results further support the hypothesis that RBPs preferentially bind RNA motifs with low complexity.
TAF7L REGULATES EARLY STAGES OF MALE GERM CELL DEVELOPMENT
Authors: Moreno-Irusta Ayelen , Dominguez Esteban M. , Iqbal Khursheed , Zhang Xiaoyu , Wang Ning , Soares Michael J. 
Published: October 2023

ABSTRACTMale germ cell development is dependent on the orchestrated regulation of gene networks. TATA-box binding protein associated factors (TAFs) facilitate interactions of TATA-binding protein with the TATA element, which is known to coordinate gene transcription during organogenesis. TAF7 like (Taf7l) is situated on the X chromosome and has been implicated in testis development. We examined the biology of TAF7L in testis development using the rat.Taf7lwas prominently expressed in preleptotene to leptotene spermatocytes. To study the impact of TAF7L on the testis we generated a globalloss-of-functionrat model using CRISPR/Cas9genome editing. Exon 3 of theTaf7lgene was targeted. A founder was generated possessing a 110 bp deletion within theTaf7l locus, which resulted in a frameshift and the premature appearance of a stop codon. The mutation was effectively transmitted through the germline. Deficits in TAF7L did not adversely affect pregnancy or postnatal survival. However, theTaf7ldisruption resulted in male infertility due to compromised testis development and failed sperm production. Mutant germ cells suffer meiotic arrest at the zygotene stage, with defects in sex body formation and meiotic sex chromosome inactivation. This testis phenotype was more pronounced than previously described for the subfertileTaf7lnull mouse. We conclude that TAF7L is essential for male germ cell development in the rat.
Diverse stimuli induce piloerection and yield varied autonomic responses in humans
Authors: McPhetres Jonathon 
Published: October 2023

AbstractThis research provides an in-depth exploration into the triggers and corresponding autonomic responses of piloerection, a phenomenon prevalent across various species. In non-human species, piloerection occurs in reaction to a variety of environmental changes, including social interactions and temperature shifts. However, its understanding in humans has been confined to emotional contexts. This is problematic because it reflects solely upon subjective experience rather than an objective response to the environment, and because, given our shared evolutionary paths, piloerection should function similarly in humans and other animals. We observed 1,198 piloerection episodes from eight participants while simultaneously recording multiple autonomic and body temperature indices, finding that piloerection in humans can indeed be elicited by thermal, tactile, and audio-visual stimuli. The data also revealed variations in cardiac reactivity measures: audio-visual piloerection was associated with greater sympathetic arousal, while tactile piloerection was linked to greater parasympathetic arousal. Despite prevailing notions of piloerection as a vestigial response in humans, it does respond to decreases in skin temperature and induces a rise in skin temperature during episodes. This research underscores that piloerection in humans is not solely an affective response to emotional stimuli. Rather, it is best understood as a reflexive response to environmental changes, suggesting a shared functional similarity with other species.
Motion Blur Microscopy
Authors: Goreke Utku , Gonzales Ayesha , Shipley Brandon , Tincher Madeleine , Sharma Oshin , Wulftange William , Man Yuncheng , An Ran , Hinczewski Michael , Gurkan Umut A. 
Published: October 2023

ABSTRACTImaging and characterizing the dynamics of cellular adhesion in blood samples is of fundamental importance in understanding biological function.In vitromicroscopy methods are widely used for this task, but typically require diluting the blood with a buffer to allow for transmission of light. However whole blood provides crucial mechanical and chemical signaling cues that influence adhesion dynamics, which means that conventional approaches lack the full physiological complexity of living microvasculature. We propose to overcome this challenge by a newin vitroimaging method which we call motion blur microscopy (MBM). By decreasing the source light intensity and increasing the integration time during imaging, flowing cells are blurred, allowing us to identify adhered cells. Combined with an automated analysis using machine learning, we can for the first time reliably image cell interactions in microfluidic channels during whole blood flow. MBM provides a low cost, easy to implement alternative to intravital microscopy, thein vivoapproach for studying how the whole blood environment shapes adhesion dynamics. We demonstrate the method’s reproducibility and accuracy in two example systems where understanding cell interactions, adhesion, and motility is crucial—sickle red blood cells adhering to laminin, and CAR-T cells adhering to E-selectin. We illustrate the wide range of data types that can be extracted from this approach, including distributions of cell size and eccentricity, adhesion durations, trajectories and velocities of adhered cells moving on a functionalized surface, as well as correlations among these different features at the single cell level. In all cases MBM allows for rapid collection and processing of large data sets, ranging from thousands to hundreds of thousands of individual adhesion events. The method is generalizable to study adhesion mechanisms in a variety of diseases, including cancer, blood disorders, thrombosis, inflammatory and autoimmune diseases, as well as providing rich datasets for theoretical modeling of adhesion dynamics.
Modeling dry eye with an air-liquid interface in corneal epithelium-on-a-chip
Authors: Abdalkader Rodi Kado , Chaleckis Romanas , Fujita Takuya , Kamei Ken-ichiro 
Published: October 2023

ABSTRACTDry eye syndrome (DES) is a complex ocular condition characterized by an unstable tear film and inadequate tear production, leading to tissue damage. Despite its common occurrence, there is currently no comprehensivein vitromodel that accurately reproduce the cellular characteristics of DES. Here we modified a corneal epithelium-on-a-chip (CEpOC) model to recapitulate DES by subjecting HCE-T human corneal epithelial cells to an air-liquid (AL) interface stimulus. We then assessed the effects of AL stimulation both in the presence and absence of diclofenac (DCF). Transcriptomic analysis revealed distinct gene expression changes in response to AL and AL_DCF, affecting pathways related to development, epithelial structure, inflammation, and extracellular matrix remodeling. Both treatments upregulatedPIEZO2, linked to corneal damage signaling, while downregulatingOCLN, involved in cell-cell junctions. They increased the expression of inflammatory genes (e.g.,IL6) and reduced mucin production genes (e.g.,MUC16), reflecting dry eye characteristics.TGFB1, crucial for corneal wound healing, was slightly downregulated in AL_DCF, potentially affecting wound healing processes rather than reducing inflammation by DCF. Metabolomic analysis showed increased secretion of metabolites associated with cell damage and inflammation (e.g., methyl-2-oxovaleric acid, 3-methyl-2-oxobutanoic acid, lauroyl-carnitine) in response to AL and even more with AL_DCF, indicating a shift in cellular metabolism. This study showcases the utilization of AL stimulus within the CEpOC as a comprehensive approach to faithfully reproduce the cellular characteristics of DES.
Can lateral tenodesis improve the rotational stability of the ACL reconstruction? A finite element analysis
Authors: Risvas Konstantinos , Stanev Dimitar , Moustakas Konstantinos 
Published: October 2023

AbstractOne of the most common knee injuries is the Anterior Cruciate Ligament (ACL) rupture with severe implications on knee stability. The usual treatment is the ACL Reconstruction (ACLR) surgery where the surgeon replaces the torn ligament with a graft in an effort to restore knee kinematics. In case of excessive rotatory instability, Lateral Extra - Articular Tenodesis (LET) can be performed in combination with ACLR. Additionally, LET appears to reduce ACLR graft forces reducing graft failure chances. However, there are concerns about overconstraining physiological rotation. To gain insight in this controversial topic, we developed an automatic, open-source tool to create a series of Finite Element (FE) models attempting to investigate the interactions of ACLR and LET through simulation. We started by creating a validated model of the healthy knee joint that served as reference for subsequent FE simulations. Then, we created FE models of standalone ACLR and combined ACLR - LET. Each model was assessed by applying a loading profile that resembles the Pivot - Shift clinical exam. We measured the External Tibia Rotation (ETR), the Anterior Tibia Translation (ATT) of the lateral tibial compartment, and the ACLR graft stress developed around the femoral tunnel insertion site. We observed the following: a) LET reduces ETR and ATT compared to isolated ACLR, b) combined ACLR - LET is more sensitive to LET graft pretension with lower values showcasing performance closer to the healthy joint, c) LET reduces ACLR graft forces for the same pretension values, d) LET exhibits significant overconstraint for higher pretension values. In general, these findings are in agreement with relevant clinical studies and accentuate the potential of the developed framework as a tool that can assist orthopaedists during surgery planning. We provide open access for the FE models of this study to enhance research transparency, reproducibility and extensibility.
The Rho GTPase Rac1 mediates exercise training adaptations
Authors: Raun Steffen H. , Henriquez-Olguín Carlos , Frank Emma , Knudsen Jonas Roland , Ali Mona S. , Andersen Nicoline R. , Møller Lisbeth L. V. , Davey Jonathan , Qian Hongwei , Coelho Ana , Carl Christian S. , Voldstedlund Christian T. , Kiens Bente , Holmdahl Rikard , Gregorevic Paul , Jensen Thomas E. , Richter Erik A. , Sylow Lykke 
Published: October 2023

AbstractExercise training elicits tremendous health benefits; however, the molecular underpinnings are poorly understood. As one of the most regulated groups of proteins following acute exercise in human muscle, Rho GTPases are unexplored candidates for mediating the beneficial effects of exercise. The Rho GTPase Rac1 was activated during multiple exercise modalities and remained elevated hours after resistance exercise in human muscle. Inducible muscle-specific Rac1 knockout (Rac1 imKO) mice, displayed attenuated muscle protein synthesis, glycogen resynthesis and p38 MAPK signaling in recovery from contractions. Exercise training upregulated Rac1 protein content in human and mouse muscle. Overexpression of hyperactive Rac1 elevated reactive oxidant species production during exercise yet did not induce a trained muscle phenotype. In Rac1 imKO mice, the improvements in running capacity and muscle mass after exercise training were diminished. Using gain- and loss-of-function mouse models and human muscle biopsies, we identify Rac1 as a regulator of exercise training adaptions.HighlightsVarious exercise modalities activate Rac1 signaling in human skeletal muscle.HSP27, MNK1, and CREB are Rac1-dependent contraction-responsive targets in muscle.Post-contraction protein synthesis requires Rac1 but not NOX2.Rac1-NOX2 signaling is necessary for post-contraction glycogen resynthesis.Exercise training increases Rac1 protein content in human and mouse muscles.Rac1 mediates critical adaptations to exercise training.
To touch or to be touched? Comparing pleasantness of vicarious execution and reception of interpersonal touch
Authors: Butti Niccolò , Urgesi Cosimo , McGlone Francis P. , Oldrati Viola , Montirosso Rosario , Cazzato Valentina 
Published: October 2023

AbstractUnmyelinated C-Tactile (CT) fibres are activated by caress-like touch, eliciting a pleasant feeling that decreases for static and faster stroking. Previous studies documented this effect also for vicarious touch, hypothesising ‘mirror-neurons’ mechanisms driving the perception and appreciation of observed interpersonal touch. Notably, less is known about appreciation of vicarious execution of touch, that is as referred to the one giving gentle touch. To address this issue, 53 healthy participants were asked to view and rate a series of videoclips displaying an individual being touched by another on hairy (i.e., hand dorsum) or glabrous (i.e., palm) skin sites, with touch being delivered at CT-optimal (5 cm/s) or non-CT optimal velocities (0 cm/s or 30 cm/s). Following the observation of each clip, participants were asked to complete self- and other-directed ratings of the pleasantness of touch for both executer (toucher-referred) and receiver (touchee-referred). Consistent with the CT fibres properties, for both self- and other-directed judgements of touch execution and reception, participants provided higher ratings for touch delivered at CT-optimal than other velocities, and when CT-optimal touch was delivered to the hand-dorsum compared to the palm. However, higher ratings were attributed to reception compared to execution of CT-optimal touch. Notably, individual differences in interoceptive trusting and attitude to interpersonal touch were positively correlated with, respectively, toucher- and touchee-related overall pleasantness of touch. These findings suggest that the appreciation of both toucher- and touchee-referred vicarious touch is specifically attuned to CT-optimal touch, even though they might rely on different neurocognitive mechanisms to understand affective information conveyed by interpersonal tactile interactions.
In silico MS/MS prediction for peptidoglycan profiling uncovers novel anti-inflammatory peptidoglycan fragments of the gut microbiota
Authors: Kwan Jeric Mun Chung , Liang Yaquan , Ng Evan Wei Long , Sviriaeva Ekaterina , Li Chenyu , Zhao Yilin , Zhang Xiao-Lin , Liu Xue-Wei , Wong Sunny H. , Qiao Yuan 
Published: October 2023

AbstractPeptidoglycan is an essential exoskeletal polymer present across all bacteria. The gut microbiota-derived peptidoglycan fragments (PGNs) are increasingly recognized as key effector molecules that impact host biology, offering attractive yet untapped potential to combat microbiome-associated diseases in humans. Unfortunately, comprehensive peptidoglycan profiling of gut bacteria has been hampered by the lack of a robust and automated analysis workflow. Currently, PGN identification still relies on manual deconvolutions of acquired tandem mass spectrometry (MS/MS) data, which are highly laborious and inconsistent. Recognizing the unique sugar and amino acid makeup of bacterial peptidoglycan and guided by the experimental MS/MS fragmentation patterns of known PGNs, we developed a computational tool PGN_MS2 that reliably simulates MS/MS spectra of PGNs. Integrating PGN_MS2 into the customizablein silicoPGN database, we built an open-access PGN MS library of predicted MS/MS spectra for all molecules in the user-definedin silicoPGN search space. With this library, automated searching and spectral matching can be used to identify PGN. We then performed comprehensive peptidoglycan profiling for several gut bacteria species, revealing distinct PGN structural features that may be implicated in microbiota-host crosstalk. Strikingly, the probioticBifidobacteriumspp. has an exceedingly high proportion of anhydro-PGNs, which exhibit anti-inflammatory effectsin vitro. We further identified MltG and RfpB homologs inBifidobacteriumas lytic transglycosylases (LTs), which demonstrate distinct substrate preferences to produce anhydro-PGNs. Overall, our novel PGN_MS2 prediction tool contributes to the robust and automated peptidoglycan analysis workflow, advancing efforts to elucidate the structures and functions of gut microbiota-derived PGNs in the host.
Variability in radiocesium activity concentration in growing hardwood shoots in Fukushima, Japan
Authors: Itô Hiroki , Miura Satoru , Komatsu Masabumi , Kanasashi Tsutomu , Nagakura Junko , Hirai Keizo 
Published: October 2023

AbstractThe radiocesium contamination caused by the Fukushima Daiichi Nuclear Power Plant accident has made it difficult to use coppice woods as bed logs for mushroom cultivation. Evaluating the variability in the radiocesium activity concentration of logs is necessary in order to predict how many coppice woodlands are available for producing mushroom bed logs. To clarify the variability in radiocesium activity concentrations and to estimate the sample size required to estimate these concentrations with sufficient accuracy, we modeled the log-transformed radiocesium activity concentrations in growing shoots of hardwoods. We designed two models: (1) a model with mean concentrations that varied among stands with a standard deviation that was the same among stands, and (2) a model with varying means and standard deviations. We fit the data pertaining to onlyQuercus serratato both models and calculated the widely applicable information criterion values. Consequently, we adopted the simpler model (1). Applying the selected model to data for all species, we examined the relationship between the number of measurement individuals and the predictive distribution of the expected concentration. Based on previous recommendations and measurement costs, we proposed that five individuals would be appropriate for estimating radiocesium activity concentration in a stand.