bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soleus H-Reflex Up-Conditioning during Sciatic Nerve Regeneration in Rats Improves Recovery of Locomotion
Authors: Chen Yi , Wang Yu , Chen Lu , Yang Xinxin , Gemoets Darren E. , Chen Xiang Yang , Wolpaw Jonathan R. 
Published: December 2024

ABSTRACTOperant conditioning of the spinal stretch reflex or its electrical analog, the H-reflex, induces plasticity in the brain and spinal cord that increases (up-conditioning) or decreases (down-conditioning) the reflex elicited by primary afferent input to the spinal motoneuron. In rats in which the sciatic nerve is transected and repaired, soleus (SOL) H-reflex up-conditioning during regeneration strengthens primary afferent reinnervation of SOL motoneurons and improves recovery of the SOL H-reflex. This suggests that H-reflex up-conditioning could improve functional recovery after nerve injury and repair. To explore this possibility, we examined the impact of SOL H-reflex up- or down-conditioning during sciatic regeneration on recovery of locomotor symmetry. Sprague-Dawley rats were implanted with EMG electrodes in right SOL and a stimulating cuff on right posterior tibial nerve. After control data collection, right sciatic nerve was transected and repaired. Control EMG and H-reflex data collection continued for 20 more days. The rat was then exposed for 100 days to either: continued control data collection; SOL H-reflex up-conditioning; or SOL H-reflex down-conditioning. Locomotor EMG, H-reflex, and kinematics were assessed before nerve transection and 120 days after transection. H-reflex up-conditioning improved H-reflex recovery and also restored right/left step symmetry. H-reflex down-conditioning did not worsen H-reflex recovery or right/left step asymmetry. These results suggest that H-reflex up-conditioning might enhance functional recovery after nerve injury in humans. They also confirm previous results indicating that compensatory plasticity prevents inappropriate H-reflex conditioning (i.e., down-conditioning) from further impairing function.
Transcription factors associated with regulation of transcriptome in human thigh and calf muscles at baseline and after six days of disuse
Authors: Borzykh Anna A. , Makhnovskii Pavel A. , Ponomarev Ivan I. , Vepkhvadze Tatiana F. , Lednev Egor M. , Rukavishnikov Ilya V. , Orlov Oleg I. , Tomilovskaya Elena S. , Popov Daniil V. 
Published: December 2024

AbstractDisuse has a negative impact on the postural muscles of the trunk and legs. Different leg muscles demonstrate a differentiated and conservative response to disuse, in terms of a decrease in muscle mass, strength, aerobic performance, and changes in gene expression. We aimed to identify transcription factors regulating gene expression at baseline and after disuse in humanm. soleus– a “slow” muscle with a strong postural function, and “mixed”m. vastus lateralis. Biopsies were taken from these muscles prior to and after 6 days of strict disuse (dry immersion). The enriched transcription factor binding sites (and corresponding factors) in the individual promoter regions of co-expressed genes were examined using the positional weight matrix approach. The baseline transcriptomic profiles and the disuse-induced changes (RNA-seq) differ significantly between muscles. In particular, the specific and significant response to disuse inm. soleuswas found to be strongly related to the suppression of genes regulating the mitochondrial energy metabolism, the activation of the inflammatory response and the ubiquitin-proteasome system. This response is associated with the proinflammatory transcription factors such as families IRF, STAT, and other. The validity of approximately two-thirds of the predicted transcription factors was indirectly confirmed by the analysis of their function described in the literature. These identified transcription factors appear to be promising candidates for future targeted studies that mechanistically investigate gene expression regulation in various muscles at baseline, following disuse or inactivity.HighlightsDisuse has a different negative impact on the different human postural leg muscles.The transcriptome regulation inm. soleusandm. vastus lateralisdiffers markedly.The gene response to disuse inm. soleusis greater than inm. vastus lateralis.This partially related to activation of inflammation-induced transcription factors.
Gestational diabetes mellitus and hypertension causally increased the risk of postpartum depression: a Mendelian randomization analysis
Authors: Jia Jia , Liu Haojie , Cao Liying , Xing Ying 
Published: December 2024

AbstractBackgroundObservational studies have presented inconsistent findings on the association between gestational diabetes mellitus, gestational hypertension, and postpartum depression. This study used Mendelian randomization to examine the potential causal relationship between gestational diabetes mellitus, gestational hypertension, and postpartum depression.MethodsWe obtained data from genome-wide association study databases. Single nucleotide polymorphisms associated with gestational diabetes mellitus (5,687 cases; 117,892 controls), gestational hypertension (7,686 cases; 115,893 controls), and postpartum depression (7,604 cases; 59,601 controls) were analyzed. Various Mendelian randomization methods were applied, including inverse variance weighted, weighted median, MR-Egger, simple mode, and weighted mode. Sensitivity analyses such as the MR-Egger intercept test, funnel plot, MR-PRESSO analysis, Cochran’s Q test, and leave-one-out tests confirmed the robustness of our findings. The MR-Steiger test was applied to verify the causal direction from exposure to outcome.ResultsGenetically predicted gestational diabetes mellitus was significantly associated with increased postpartum depression risk (IVW OR = 1.09; 95% CI: 1.03- 1.14; p = 1.24×10⁻³), as was gestational hypertension (IVW OR = 1.08; 95% CI: 1.01- 1.15; p = 0.01). Multiple sensitivity analyses further reinforced the validity of these findings. Multivariable Mendelian randomization adjusting for gestational hypertension confirmed the independent effect of gestational diabetes mellitus on postpartum depression and vice versa for gestational hypertension.ConclusionBoth gestational diabetes mellitus and gestational hypertension increase the incidence of postpartum depression. By focusing on interventions to manage these prenatal conditions, nursing professionals can play a crucial role in potentially reducing the incidence of postpartum depression.
Structurally distinct manganese-sensing riboswitch aptamers regulate diverse expression platform architectures
Authors: Stephen Christine N. , Palmer Danea E. , Bautista Clarisa , Mishanina Tatiana V. 
Published: December 2024

ABSTRACTManganese (Mn)-sensing riboswitches protect bacteria from Mn toxicity by upregulating expression of Mn exporters. The Mn aptamers share key features but diverge in other important elements, including within the metal-binding core. Although X-ray crystal structures of isolated aptamers exist, these structural snapshots lack crucial details about how the aptamer communicates the presence or absence of ligand to the expression platform. In this work, we investigated the Mn-sensing translational riboswitches inE. coli(mntPandalx), which differ in aptamer secondary structure, nucleotide sequence, and pH-dependence of Mn response. We performed co-transcriptional RNA chemical probing, allowing us to visualize RNA folding intermediates that form and resolveen routeto the final folded riboswitch. For the first time, we report that sampling of metal ions by the RNA begins before the aptamer synthesis and folding are complete. At a single-nucleotide resolution, we pinpoint the transcription window where “riboswitching” occurs in response to Mn binding and uncover key differences in how thealxandmntPriboswitches fold. Finally, we describe riboswitch-specific effects of pH, providing insights into how two members of the same riboswitch family differentially sense two distinct environmental cues: concentration of Mn and pH.GRAPHICAL ABSTRACT
Aperiodic parameters of the fMRI power spectrum associate with preterm birth and neonatal age
Authors: Suuronen Ilkka , Luotonen Silja , Railo Henry , Airola Antti , Bano Wajiha , Merisaari Harri , Pulli Elmo P. , Mariani Wigley Isabella L.C , Vartiainen Elena , Hashempour Niloofar , Karlsson Hasse , Karlsson Linnea , Kringelbach Morten L. , Batalle Dafnis , Tuulari Jetro J. 
Published: December 2024

AbstractWhile strong associations of structural magnetic resonance imaging (sMRI) with preterm birth and post-menstrual age (PMA) have been reported, such associations for functional MRI (fMRI) have been considerably weaker. We studied the associations of the aperiodic parameters of neonatal fMRI Blood-oxygen-level-dependent (BOLD) signal power spectrum with preterm birth and PMA at scan using task-free fMRI data from the Developing Human Connectome Project (dHCP). First, we studied the associations of the aperiodic parameters of the BOLD signal from pre- and postcentral gyri with preterm birth and mapped the associations with PMA, postnatal age, and sex. Second, we used machine learning regression to predict PMA and postnatal age with 90 cortical and subcortical regions of interest (ROIs). We found clear differences between preterm and full-term groups, as well as males and females. Furthermore, our machine learning model predicted the age variables with relatively high accuracy (mean test R² = 0.20 – 0.41).
Prevalence of chlamydia, gonorrhoea, and trichomoniasis among male and female general populations in sub-Saharan Africa from 2000-2024: A systematic review and meta-regression analysis
Authors: Michalow Julia , Hall Lauren , Rowley Jane , Anderson Rebecca L. , Hayre Quinton , Chico R. Matthew , Edun Olanrewaju , Knight Jesse , Kuchukhidze Salome , Majaya Evidence , Reed Domonique M. , Stevens Oliver , Walters Magdalene K , Peters Remco PH , Cori Anne , Boily Marie-Claude , Imai-Eaton Jeffrey W. 
Published: December 2024

AbstractBackgroundSub-Saharan Africa (SSA) has the highest sexually transmitted infection (STI) prevalence globally, but information about trends and geographic variation is limited by sparse aetiologic studies, particularly among men. This systematic review assessed chlamydia, gonorrhoea, and trichomoniasis prevalence by sex, sub-region, and year, and estimated male-to-female prevalence ratios for SSA.MethodsWe searched Embase, MEDLINE, Global Health, PubMed, and African Index Medicus for studies measuring STI prevalence among general populations from January 1, 2000, to September 17, 2024. We adjusted observations for diagnostic test performance and used log-binomial mixed-effects meta-regressions to estimate prevalence trends and sex-prevalence ratios.FindingsOf 5202 records identified, we included 211 studies from 28 countries. In 2020, estimated prevalence among 15-49-year-olds in SSA for chlamydia was 6.6% (95%CI: 5.0-8.2%, n=169 observations) among females and 4.7% (3.4-6.1%, n=33) among males, gonorrhoea was 2.4% (1.4-3.3%, n=171) and 1.7% (0.7-2.6%, n=31), and trichomoniasis was 6.8% (3.6-9.9%, n=188) and 1.7% (0.7-2.7%, n=19). Male-to-female ratio estimates were 0.61 (0.53-0.71) for chlamydia, 0.81 (0.61-1.09) for gonorrhoea, and 0.23 (0.18-0.28) for trichomoniasis. From 2010-2020, chlamydia prevalence increased by 34.5% (11.1-62.9%) in SSA, while gonorrhoea and trichomoniasis trends were not statistically significant. Chlamydia and gonorrhoea prevalence were highest in Southern and Eastern Africa, whereas trichomoniasis was similar across sub-regions.InterpretationSSA has a high, geographically varied STI burden, with increasing prevalence of chlamydia. Region-specific sex-prevalence ratios differed from existing global ratios and should be considered in future burden estimates. Enhanced sex-stratified surveillance is crucial to guide national programmes and reduce STI prevalence in SSA.FundingGates Foundation, Imperial College London, NIH, UKRI
Dosage compensation of transposable elements in mammals
Authors: Wei Chunyao , Kesner Barry , Weissbein Uri , Wasserzug-Pash Peera , Das Priyojit , Lee Jeannie T. 
Published: December 2024

ABSTRACTIn mammals, X-linked dosage compensation involves two processes: X-chromosome inactivation (XCI) to balance X chromosome dosage between males and females, and hyperactivation of the remaining X chromosome (Xa-hyperactivation) to achieve X-autosome balance in both sexes. Studies of both processes have largely focused on coding genes and have not accounted for transposable elements (TEs) which comprise 50% of the X-chromosome, despite TEs being suspected to have numerous epigenetic functions. This oversight is due in part to the technical challenge of capturing repeat RNAs, bioinformatically aligning them, and determining allelic origin. To overcome these challenges, here we develop a new bioinformatic pipeline tailored to repetitive elements with capability for allelic discrimination. We then apply the pipeline to our recent So-Smart-Seq analysis of single embryos to comprehensively interrogate whether X-linked TEs are subject to either XCI or Xa-hyperactivation. With regards to XCI, we observe significant differences in TE silencing in parentally driven “imprinted” XCI versus zygotically driven “random” XCI. Chromosomal positioning and genetic background impact TE silencing. We also find that SINEs may influence 3D organization during XCI. In contrast, TEs do not undergo Xa-hyperactivation. Thus, while coding genes are subject to both forms of dosage compensation, TEs participate only in Xi silencing. Evolutionary and functional implications are discussed.
Oxidative stress drives potent bactericidal activity of pyrazinamide againstMycobacterium tuberculosis
Authors: Dillon Nicholas A. , Lamont Elise A. , Rather Muzafar A. , Baughn Anthony D. 
Published: December 2024

AbstractPyrazinamide (PZA) is a critical component of tuberculosis first-line therapy due to its ability to kill both growing and non-replicating drug-tolerant populations ofMycobacterium tuberculosiswithin the host. Recent evidence indicates that PZA acts through disruption of coenzyme A synthesis under conditions that promote cellular stress. In contrast to its bactericidal actionin vivo, PZA shows weak bacteriostatic activity againstM. tuberculosisin axenic culture. While the basis for this striking difference betweenin vivoandin vitroPZA activity has yet to be resolved, recent studies have highlighted an important role for cell-mediated immunity in PZA efficacy. These observations suggest that host-derived antimicrobial activity may contribute to the bactericidal action of PZA within the host environment. In this study we show that the active form of PZA, pyrazinoic acid (POA), synergizes with the bactericidal activity of host-derived reactive oxygen species (ROS). We determined that POA can promote increased cellular oxidative damage and enhanced killing ofM. tuberculosis. Further, we find that the thiol oxidant diamide is also able to potentiate PZA activity, implicating thiol oxidation as a key driver of PZA susceptibility. Using a macrophage infection model, we demonstrate the essentiality of interferon-γ induced ROS production for PZA mediated clearance ofM. tuberculosis. Based on these observations, we propose that thein vivosterilizing activity of PZA can be mediated through its synergistic interaction with the host oxidative burst leading to collateral disruption of coenzyme A metabolism. These findings will enable discovery efforts to identify novel host- and microbe-directed approaches to bolster PZA efficacy.
Spatially barcoding biochemical reactions using DNA nanostructures unveil a major contact mechanism in proximity labeling
Authors: Yang Zhe , Zhang Yu , Fang Yuxin , Zhang Yuan , Du Jiasheng , Shen Xiaowen , Zhang Kecheng , Zou Peng , Chen Zhixing 
Published: December 2024

AbstractProximity labeling techniques like TurboID and APEX2 have become pivotal tools in spatial omics research for studying protein interactions. However, the biochemical mechanisms underlying these reactive species-mediated labelings, particularly the spatial patterns of labeling methods within the sub-μm range, remain poorly understood. Here, we employed DNA nanostructure platforms to precisely measure the labeling radii of TurboID and APEX2 throughin vitroassays. Our DNA nanoruler design enables the deployment of oligonucleotide-barcoded labeling targets with nanometer precision near the enzymes. By quantifying labeling yields using quantitative PCR and mapping them against target distances, we uncovered surprising insights into the labeling mechanisms. Contrary to the prevailing diffusive labeling model, our results demonstrate that TurboID primarily operates through contact-dependent labeling. Similarly, APEX2 shows high labeling efficiency within its direct contact range. In parallel, it exhibits a low-level diffusive labeling towards more distant phenols. These findings reframe our understanding in the mechanism of proximity labeling enzymes, at the same time highlight the potential of DNA nanotechnology in spatially profiling reactive species.
Semantic mining of functionalde novogenes from a genomic language model
Authors: Merchant Aditi T. , King Samuel H. , Nguyen Eric , Hie Brian L. 
Published: December 2024

AbstractGenerative genomics models can design increasingly complex biological systems. However, effectively controlling these models to generate novel sequences with desired functions remains a major challenge. Here, we show that Evo, a 7-billion parameter genomic language model, can perform function-guided design that generalizes beyond natural sequences. By learning semantic relationships across multiple genes, Evo enables a genomic “autocomplete” in which a DNA prompt encoding a desired function instructs the model to generate novel DNA sequences that can be mined for similar functions. We term this process “semantic mining,” which, unlike traditional genome mining, can access a sequence landscape unconstrained by discovered evolutionary innovation. We validate this approach by experimentally testing the activity of generated anti-CRISPR proteins and toxin-antitoxin systems, includingde novogenes with no significant homology to any natural protein. Strikingly, in-context protein design with Evo achieves potent activity and high experimental success rates even in the absence of structural hypotheses, known evolutionary conservation, or task-specific fine-tuning. We then use Evo to autocomplete millions of prompts to produce SynGenome, a first-of-its-kind database containing over 120 billion base pairs of AI-generated genomic sequences that enables semantic mining across many possible functions. The semantic mining paradigm enables functional exploration that ventures beyond the observed evolutionary universe.
New Constraints on the Melting Temperature and Phase Stability of Shocked Iron up to 270 GPa Probed by Ultrafast X-Ray Absorption Spectroscopy
Authors: Balugani S. , Hernandez J. A. , Sévelin-Radiguet N. , Mathon O. , Recoules V. , Kas J. J. , Eakins D. E. , Doyle H. , Ravasio A. , Torchio R. 
Published: December 2024

Studying the properties and phase diagram of iron at high-pressure and high-temperature conditions has relevant implications for Earth’s inner structure and dynamics and the temperature of the inner core boundary (ICB) at 330 GPa. Also, a hexagonal-closed packed to body-centered cubic (bcc) phase transition has been predicted by many theoretical works but observed only in a few experiments. The recent coupling of high-power laser with advanced x-ray sources from synchrotrons allows for novel approaches to address these issues. Here, we present a study on shock compressed iron up to 270 GPa and 5800 K probed by single-pulse (100 ps FWHM) x-ray absorption spectroscopy (XAS). Based on the analysis of the XAS spectra, we provide structural identification and bulk temperature measurements along the Hugoniot up to the melting. These results rule out the predicted transition to a high-temperature bcc phase and allow one to discriminate among existing equations of state models and melting curves. In particular, we report the first bulk temperature measurement in shock compressed iron on the melting plateau at 240(20) GPa and 5345(600) K. The melting curve resulting from our work extrapolates to a temperature of 6202(514) K at 330 GPa and represents a refined upper bound for the ICB temperature.

Published by the American Physical Society
2024
Personalized interactive urban maps for autism: an innovative approach involving persons with Level 1 autism spectrum disorder to user-centered design
Authors: Brighenti Stefania , Cena Federica , Keller Roberto 
Published: December 2024

Purpose
Because of social interaction difficulties, cognitive characteristics and sensory sensitivity, people with autism spectrum disorder (ASD) may struggle with independence and active participation in urban contexts. Through understanding how people with ASDs experience and perceive urban spaces, the Personalized Interactive Urban Maps for Autism (PIUMA) project’s purpose is to create a useful platform to support persons with ASD in their movements in the city, helping them in managing their daily lives, promoting their autonomy and active participation in urban contexts, taking in to account their direct point of view. This paper aim to present a user-centered approach involving autistic people.

Design/methodology/approach
The authors involved researchers with different backgrounds applying mixed research techniques such as semi-structured qualitative interviews, participatory design, exploiting user-adapted systems techniques, human–computer interaction techniques and interviews. The authors involved people with autism (PWA) from the beginning of the project to gain user requirements, as well as to assess the acceptability and effectiveness of our solution in the final stage. In specific phases of the project, the authors involved a group of parents of PWA and a group of neurotypical individuals as a control group.

Findings
The authors collected various data and created an App taking into account PWA needs, suggestions and points of view.

Research limitations/implications
Choosing different methodologies to allow participants to express their point of view, their needs and suggestions, the authors limited the quantitative data collected. The male-to-female ratio in the study, along with the sample size and participants’ age, can also be considered limitations.

Practical implications
The authors collected information about how autistic people move in urban contexts, represent the space of their cities, move independently and use technological devices. The data the author collected also provides suggestions about how to improve computer systems designed for them.

Social implications
The results suggest how to improve computer systems designed for autistic people and how to encourage their full participation in community life according to their cognitive and sensory characteristics.

Originality/value
The PIUMA project takes into account the direct input of PWA in all the different stages from conception and design to deployment of the device in a human-centered design approach.