bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Sudarshan Kriya Yoga (SKY) Breath Meditation on Heart Rate Variability, Sleep and Mental Health in Healthy Individuals : A Pilot and Feasibility Randomized Controlled Trial
Authors: Ganesan Vinitha , Fowler Lauren A , Bajaj Sahil , Qu Haiyan , Singh Priyam , Krishnan Snehaa D , McGregor Keith M , Nolan Timiya S , Baidwan Navneet , Mehta Tapan S , Aneja Ritu 
Published: January 2025

AbstractEffective interventions are needed to address increasing mental health challenges that affect wellbeing. Sudarshan Kriya Yoga (SKY), a breath-based meditation, has previously shown to improve mental health. We conducted a pilot randomized controlled trial (RCT) in healthy individuals, to evaluate the feasibility of SKY intervention with an eight-week followup for studying its immediate and sustained effects on psychophysiological outcomes in real-world settings. 187 healthy individuals (>21 years old) were assessed for eligibility through telephone interviews and 45 consented individuals were randomized (2:1) to either receive three-day SKY intervention with eight-week followup or waitlist control group. The mean age was 40.9 years (SD = 11.3), and 35 (77.8%) were female. Adherence (≥ three-times/week) to 30-minute daily (75.9%) and (≥ six-times/week) 75-minute (89.7%) SKY practice were high. Compared to controls, SKY participants exhibited significantly higher resting heart rate variability (mean difference = 6.47 ([95% CI [0.95, 11.98]) at the end of three-days, and at eight-week followup (mean difference = 5.55 (90% CI [0.46, 10.64]) relative to baseline. At eight-week followup, SKY participants had significant improvements in resting heart rate, overall sleep score, anxiety and social connectedness compared to controls. These results demonstrate feasibility that consistent SKY practice can impact physiology. ClinicalTrials.gov,NCT05523414.
Thermodynamic uncertainty relation constraints information transmission through cell signaling systems
Authors: Verma Shreyansh , Saravanan R Vishva , Ghosh Bhaswar 
Published: January 2025

ABSTRACTBiological systems in general operates out of equilibrium which demands the requirement for constant supply of energy due to non-equilibrium entropy production. The thermodynamic uncertainty relation (TUR) essentially imposes a bound on minimum current fluctuation the system can have given a entropy production rate. The fluctuation eventually impacts the signal to noise ratio imposing an upper bound on information transmission accuracy. In this study, we explored the role of TUR on the information transmission capacity of a set of cellular signaling systems using a coupled mathematical and machine learning approaches to experimental data in yeast under several stress conditions. Cell signaling systems are involved in sensing the changes in environment by activating a set of transcription factors which typically diffuse inside the nucleus to trigger transcription of the required genes. However, the inherent stochasticity of the biochemical pathways associated with signaling processes severely limits the accuracy of estimating the environmental input by the transcription factors. Application of TUR reveals a general picture about the working principle of the transcription factors. We found that the the activation followed by biased diffusion of transcription factors (TF) towards the nucleus triggers entropy production which amplifies magnitude of the overall TF currents towards the nucleus as well as reduces the fluctuations. These outcomes significantly improve the accuracy of information transmission carried out by the transcription factors following the bound imposed by TUR. Thus, experimental observations coupled with TUR based theoretical models demonstrate the role of thermodynamic fluctuation and entropy production on cellular information processing.
Rational engineering of lipid-binding probes via high-throughput protein-lipid interaction screening
Authors: Nishimura Taki , Tsuboyama Kotaro , Nakagaki Yuki , Yamamoto Eiji , Mizushima Noboru 
Published: January 2025

AbstractLipid-binding domains, originally isolated from natural proteins, are useful tools essential for analyzing membrane lipids in cells, and their applications are varied. Yet, there is no general strategy for engineering lipid-binding domains. Here, we present a robust method for monitoring protein-lipid interactions, named the Cell surface Liposome Binding (CLiB) assay. Using this technique, we isolated high-affinity lipid-binding domains and nanobodies that preferentially bind to phosphatidylinositol phosphates. Furthermore, by combining the CLiB assay with next-generation sequencing, allowing the analysis of more than 10,000 clones in parallel, we identified novel variants with enhanced binding to phosphatidylinositol phosphates and uncovered a common structural feature: a positively charged pocket necessary for binding, formed by the three loop regions. This study opens a new avenue for the rational design and generation of lipid-binding probes on demand.
Lack of ADAP1/Centaurin-α1 Ameliorates Cognitive Impairment and Neuropathological Hallmarks in Mouse Alzheimer Model
Authors: Szatmari Erzsebet M. , Moran Corey , Cohen Sarah J. , Bashtovyy Denys , Jacob Amanda , Bunner Wyatt , Phipps Mary , Lora Joan Cristino , Stackman Robert W. , Yasuda Ryohei 
Published: January 2025

ABSTRACTArfGAP, with dual PH domain-containing protein 1/Centaurin-α1 (ADAP1CentA1), is a brain-enriched and highly conserved Arf6 GTPase-activating and Ras-anchoring protein. ADAP1 is involved in dendritic outgrowth and arborization, synaptogenesis, and axonal polarization by regulating the dynamics of the actin cytoskeleton. An increased level of ADAP1 and its association with amyloid plaques in the human Alzheimer’s disease (AD) brain suggest a role for this protein in AD progression. To understand the role of ADAP1/CentA1 in neurodegeneration, we crossbred CentA1 KO mice with the hAPP-J20 mouse model of AD (J20 x CentA1 KO). We then evaluated the gene expression profile and the behavioral and neuropathological hallmarks of AD to determine the impact of eliminating ADAP1/CentA1 expression on AD-related phenotypes. Spatial memory assessed by the Morris Water Maze test showed significant impairment in J20 mice, which was rescued by the deletion of CentA1. Neuropathological hallmarks of AD, such as deposits of amyloid plaques and neuroinflammation, were significantly reduced in the AD model mice with CentA1 KO background. To identify potential mediators of AD phenotype rescue, we analyzed differentially expressed genes (DEGs) between genotypes, by employing transcriptome profiling with Nanostring nCounter Neuropathology and Neuroinflammation panels. We found significant upregulation of genes associated with apoptosis and gliosis in the brain of J20 mice. However, many of these genes, including the pro-apoptotic gene,Bid, were restored in the brains of J20 x CentA1 KO mice compared to J20 mice. In summary, our data indicate that CentA1 is required for the progression of AD phenotypes and that targeting CentA1 signaling at mitochondria might have therapeutic potential for AD prevention or treatment.SIGNIFICANCE STATEMENTADAP1/Centaurin-α1 (CentA1) is highly enriched in the brain and increased CentA1 level has been linked to Alzheimer’s disease (AD). However, the precise role of ADAP1 in the pathogenesis of AD is poorly understood. We found that genetic deletion of CentA1 in the AD model mice rescues the pathological hallmarks of AD, including loss of dendritic spines in the hippocampus, amyloid plaque deposition, neuroinflammation and spatial memory deficits. Transcriptome analysis of forebrain samples using NanoString nCounter panels for 880 genes, identified the pro-apoptotic protein, Bid, with significantly reduced expression in the J20 mice on ADAP1 KO background. These findings point towards a role of ADAP1 in the activation of the mitochondrial pathways of death associated with the progression of neurodegeneration.
Changes in free-roaming dog population demographics and health associated with a catch-neuter-vaccinate-release program in Jamshedpur, India
Authors: Smith Lauren , Kartal Tamara , Rawat Sanjay , Chaudhari Amit , Kumar Ashok , Pandey Rajesh Kumar , Quinnell Rupert J. , Collins Lisa 
Published: January 2025

AbstractIndia’s large free-roaming dog populations contribute to significant human health, environmental, and social challenges. Population management strategies, such as capture-neuter-vaccinate-return (CNVR), aim to reduce dog numbers, improve their welfare, and reduce human-animal conflict. The Humane Society International, in partnership with the Animal Health Foundation, implemented a CNVR program in Jamshedpur, neutering and vaccinating over 20,000 dogs. This study evaluates the impact of this program on dog health, population structure and size. The study areas encompassed 10 sites within the Jamshedpur Metropolitan Region, including both intervention sites where CNVR was directly applied and sites without direct intervention. Data was collected from May 2014 until December 2018, including bi-annual street surveys, as well as clinical data from the dogs captured and treated. We fit logistic regression, negative binomial, and binomial mixed effects models to assess changes in dog population characteristics, health, and reproductive conditions over time in relation to the CNVR intervention. We found that, over time, the CNVR program significantly reduced the probability of dogs entering the clinic with mange, transmissible venereal tumours, and pregnant. Street surveys showed an increase in sterilised dogs, with higher proportions observed in CNVR-treated sites, although the counts of dogs observed increased overall. The age-structure of free-roaming dogs remained stable over time. In CNVR-treated areas, the probability of observing lactating female dogs decreased, whereas it increased in untreated sites. This work contributes to the growing body of knowledge investigating the impact of dog population management interventions. Continued monitoring and evaluation of CNVR programs are required to identify optimal coverage required to reduce population size effectively.
Populations of the Australian saltmarsh mosquitoAedes vigilaxvary between panmixia and temporally stable local genetic structure
Authors: Schmidt Thomas L , Endersby-Harshman Nancy , Mills Toby , Rane Rahul , Pandey Gunjan , Hardy Chris , Court Leon , Webb Cameron , Trewin Brendan , Neilan Brett , Hoffmann Ary A 
Published: January 2025

AbstractPest management programs can operate more effectively when movement patterns of target species are known. As individual insects are difficult to track, genomic data can instead be used to infer movement patterns based on pest population structure and connectivity. These data can also provide critical information about cryptic taxa relevant to management. Here we present the first genomic investigation ofAedes vigilax, the Australian saltmarsh mosquito, a major arbovirus vector across Australasia. We used a ddRAD pool-seq approach and a draft genome assembly to investigate genetic variation in 60Ae. vigilaxpools from across Australia but with a focus on urban Newcastle and Sydney, NSW. There was strong genetic structure between samples from the west and east coasts of Australia, and additional structure that differentiated east coast populations. Within Newcastle and Sydney, contrasting patterns of genetic structure were evident. In Newcastle, there was no differentiation among subregions up to 60 km apart. In Sydney, samples from one urban subregion were differentiated from others < 3 km apart, and this structure was stable across sampling years. Heterozygosity and Tajima’s D indicated no bottlenecks in Newcastle or Sydney populations, suggesting this structure represents a gene flow barrier. Nuclear differentiation patterns contrast with previous mtDNA data indicating two COI clades in the east coast, one of which was also present in Western Australia. The panmixia over 60 km across the Newcastle region corroborates previous field observations of high dispersal capacity in this mosquito. These findings indicate specific challenges that may hinder local suppression strategies for this species.
Spectral acoustic contributions to musical pleasure are dynamically shaped by autonomic neural inputs
Authors: Cheung Vincent K.M. , Harada Tamaka , Sakamoto Shu , Furuya Shinichi 
Published: January 2025

AbstractMost people enjoy music and often use music to regulate their emotions. Although pleasure derived from music-listening has been shown to be mediated by dopaminergic signals in the mesolimbic reward network, its relationship with physiology is still poorly understood. Here, we introducedtime-warped representational similarity analysis(twRSA) to directly map dynamic representations of multiple modalities across variable-duration stimuli. Our method revealed that although time-varying spectral and tonal acoustic features predicted changes in autonomic neural responses (measured via cardiac, pupil, and respiratory activity) during music-listening, only a small subset was in fact relevant to listeners’ on-line pleasure ratings. Despite that, we identified a weak mediation effect of physiology on shaping musical pleasure. Our results thus indicate that whilst musical pleasure may be embodied in bodily responses, the mapping between subjective experience and physiology is likely one-to-many—in line with psychological construction theories of emotion—and not one-to-one as is commonly assumed in classical basic emotion theories.
Design of an exclusive obligate symbiosis for organism-based biological containment
Authors: Forti Amanda M. , Jones Michaela A. , Elbeyli Defne N. , Butler Neil D. , Kunjapur Aditya M. 
Published: January 2025

AbstractBiological containment is a critical safeguard for genetically engineered microbes prior to their environmental release to prevent proliferation in unintended regions. However, few biocontainment strategies can support the longer-term microbial survival that may be desired in a target environment without repeated human intervention. Here, we introduce the concept of an orthogonal obligate commensalism for the autonomous creation of environments that are permissive for survival of a biocontained microbe. We engineer one microbe to produce a non-standard amino acid (nsAA), and we engineer synthetic auxotrophy in a second microbe via reliance on this nsAA for growth. We show that this obligate commensalism is highly effective, with the survival of our commensal organism during co-culture dependent on the presence of our producer strain. We also show that this commensalism is orthogonal to a small microbial consortium isolated from maize roots, with survival of the synthetic auxotroph conditional upon the presence of the nsAA-producing strain in the consortium. Overall, our study demonstrates a transition from a chemical to a biological dependence for biocontained organisms that could lay the groundwork for biocontained synthetic ecologies.
Gait Adaptations in Step Length and Push-off Force during Walking with Functional Asymmetry
Authors: Baček Tomislav , Xu Yufan , Peng Liuhua , Oetomo Denny , Tan Ying 
Published: January 2025

AbstractHuman walking is remarkably adaptable, allowing individuals to maintain efficiency and stability across diverse conditions. This study investigates how healthy young adults adapt step length and push-off force to varying speeds and cadences under functional asymmetry induced by a unilateral knee constraint, simulating hemiparetic gait. A dataset of 19 participants walking across 30 conditions was used to examine these adaptations in both absolute terms and symmetry metrics. Results reveal that functional asymmetry disproportionately impacts propulsion, with constrained-leg force decreasing significantly at higher speeds. Step length symmetry remains stable, suggesting a prioritisation of spatial over kinetic symmetry, likely to optimise walking energetics and maintain anterior-posterior balance. Statistical models demonstrated good within-dataset performance but limited generalisability in cross-dataset predictions, where differences in population cohorts and experimental designs reduced accuracy. These findings provide insights into the mechanisms driving gait adaptations and highlight critical limitations in applying statistical models to patient populations, underscoring the importance of representative datasets and caution when extrapolating findings across populations.
A High Sensitivity Assay of UBE3A Ubiquitin Ligase Activity
Authors: Han Linna , Yagci Z. Begum , Keung Albert J. 
Published: January 2025

AbstractUBE3A is an E3 ubiquitin ligase associated with several neurodevelopmental disorders. The development of several preclinical therapeutic approaches involving UBE3A, such as gene therapy, enzyme replacement therapy, and epigenetic reactivation, require the detection of its ubiquitin ligase activity. Prior commercial assays leveraged Western Blotting to detect shifts in substrate size due to ubiquitination, but these suffered from long assay times and have also been discontinued. Here we develop a new assay that quantifies UBE3A activity. It measures the fluorescence intensity of ubiquitinated p53 substrates with a microplate reader, eliminating the need for Western Blot antibodies and instruments, and enables detection in just 1 hour. The assay is fast, cost-effective, low noise, and uses components with long shelf lives. Importantly, it is also highly sensitive, detecting UBE3A levels as low as 1nM, similar to that observed in human and mouse cerebrospinal fluid. It also differentiates the activity of wild-type UBE3A and catalytic mutants. We also design a p53 substrate with a triple-epitope tag HIS-HA-CMYC on the N terminus, which allows for versatile detection of UBE3A activity from diverse natural and engineered sources. This new assay provides a timely solution for growing needs in preclinical validation, quality control, endpoint measurements for clinical trials, and downstream manufacturing testing and validation.
Non-invasive characterization of oocyte deformability in micro-constrictions
Authors: Barbier Lucie , Bulteau Rose , Rezaei Behnam , panier Thomas , Labrune Elsa , Verlhac Marie-Hélène , Vernerey Franck , Campillo Clement , Terret Marie-Emilie 
Published: January 2025

AbstractOocytes naturally present mechanical defects that hinder their development after fertilization. Thus, in the context of assisted reproduction, oocyte selection based on their mechanical properties has great potential to improve the quality of the resulting embryos and the success rate of these procedures. However, the use of mechanical properties as a quantifiable selective criterion requires robust and non-destructive measurement tools. This study developed a constriction-based microfluidic device that monitors the deformation of mouse oocytes under controlled pressure. The device can distinguish mechanically aberrant oocyte groups from healthy control ones. Based on a mathematical model, we propose that deformability measurements infer both oocyte tension and elasticity, elasticity being the most discriminating factor in our geometry. Despite force transmission during oocyte deformation, no long-term damage was observed. This non-invasive characterization of mouse oocyte deformability in micro-constrictions allows for a significant advance in assessing the mechanical properties of mammalian oocytes and has potential application as a quantifiable selective criterion in medically assisted reproduction.TeaserA measurement method for translating advances in oocyte mechanics into selection criteria for improving medically assisted reproduction.
High genetic diversity and no detectable founder effects following a rapid range expansion of a long-distance migrant (Acrocephalus scirpaceus)
Authors: Bergman Nora M. , Lehikoinen Petteri , Kluen Edward , Bensch Staffan , Lo Cascio Sætre Camilla , Eroukhmanoff Fabrice , Fossøy Frode , Procházka Petr , Smith William J. , Stokke Bård G. , Primmer Craig R. , Thorogood Rose , Rönkä Katja 
Published: January 2025

AbstractMany species are currently experiencing range shifts in response to climate change. The colonisation of new regions can have serious genetic consequences for the shifting population, given that repeated founder events and strong genetic drift are expected to erode genetic variation along the expansion axis. Such a loss of genetic diversity could reduce adaptive potential, slowing or even halting the expansion. These genetic consequences are known to be particularly acute in species with low dispersal capabilities and therefore low levels of gene flow. Whether highly mobile species experience similar genetic bottlenecks as they undergo environment-driven range shifts is, however, less clear. Here we combined ecological and genomic evidence to (1) infer the origin and (2) quantify the genetic consequences of a recent and rapid northward range expansion of the common reed warbler (Acrocephalus scirpaceus), a philopatric long-distance migratory passerine capable of high dispersal. Together, historical observations, ringing data, and genomic RAD-seq data covering the species’ European breeding range support an expansion origin from southwest. There were no reductions in levels of nucleotide diversity or allelic richness along the colonisation route, and no detectable allele frequency clines persisting from potential past founder effects. The genomic dataset confirmed the occurrence of low but significant levels of geographically continuous population structure across the European range. These results suggest that high dispersal capabilities can help even strongly philopatric species to escape the genetic costs of rapid range expansions. The lack of genetic patterns also highlights the value of combining multiple lines of evidence to reveal range shifts as genomic data alone was not sufficient to detect the occurrence of this large-scale range expansion.
Investigation of the effect of interactive art activity program on repetitive behaviors, social skills and parents’ emotions in children with autism spectrum disorder
Authors: İnci Ramazan , Sağlam Mehmet 
Published: January 2025

Purpose
The purpose of this study was to examine the effects of an interactive art activity program on repetitive behaviors, social skills and parents’ emotions in children with autism spectrum disorder.

Design/methodology/approach
The research was carried out in autism classes and special education and rehabilitation centers of children diagnosed with autism in Batman city center between September 2021 and March 2022. The study was concluded with 28 children with Autism spectrum disorder (5–17 years old) and their mothers (13 experiments, 15 controls). Data were collected using the Personal Information Form, the ASSP-T Form, the Quality of Life in Autism Questionnaire-Parent Edition and the Social Impact Form of the Repetitive Behaviors in Children with Autism Scale. In the analysis, in the comparison of the pretest, posttest and retention data in the application group, repeated measures ANOVA was used if the data were suitable for normal distribution, and Friedman analysis was used if not. In the comparison of the data in the control group, the Paired T test was used if the data were suitable for normal distribution, and the Wilcoxon test was used if it was not.

Findings
After the training, it was concluded that there was a significant difference p < 0.05 on social skills, repetitive behaviors and quality of life of the children and mothers in the experimental group, and there was no significant difference in the control group in general.

Research limitations/implications
It was determined that the interactive art activity program of children with autism had a positive effect on repetitive behaviors, social skills and parents’ emotions.

Originality/value
Considering the positive effect of art activities on children’s social skills and repetitive behaviors, educational programs for children with autism can be integrated with art and sports activities, and the use of different areas of art and sports can be expanded, taking into account the interests and readiness of the children.