bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of combined virtual reality combined with standing balance training vs. standard practice in patients with hemiplegia: A single-blinded, randomized controlled trial.
Authors: Xu Yan , Yao Jiajia , Ni Jiadong , Yang Yajing , Fu Lianhui , Xu Cong 
Published: July 2024

Abstract

Objective
To determine whether virtual reality (VR)-based dynamic standing balance training improves three elements of sensory integration and investigate whether VR-based dynamic standing balance training results in improved outcomes, especially regarding balance and gait, compared to the standard training method.

Design
This single-blinded, randomized, controlled trial involved 30 patients with hemiplegia. The experimental (EG, n = 15) and control (CG, n = 15) groups received VR augmented-standing balance training or standard standing balance training, respectively, for 20 minutes, 5 days a week, for 3 weeks. The patients were assessed for primary (Sensory Organization Test [SOT] and the Berg balance scale [BBS]) and secondary (the functional reaching test and timed up-and-go test [TUG]) outcomes before and after training.

Results
From preintervention to postintervention, the BBS score (F = 26.295, p < 0.05), TUG score (F = 18.12, p < 0.05), mean score of conditions 2 (F = 4.36, p < 0.05) and 6 (F = 5.61, p < 0.05), and composite score of the SOT (F = 5.385, p < 0.05) in both groups were significantly improved. However, there was no significant difference between EG and CG (time*group p > 0.05).

Conclusion
VR combined with standing balance training improved sensory integration, postural control, balance, and gait ability in patients with hemiplegia, reducing fall risk. However, outcomes were comparable to general balance training regarding balance and gait.
Selection for early reproduction leads to accelerated aging and extensive metabolic remodeling inDrosophila melanogaster
Authors: Hubert David L. , Arnold Kenneth R. , Greenspan Zachary G. , Pupo Anastasia , Robinson Ryan D. , Chavarin Valeria V. , Barter Thomas B. , Djukovic Danijel , Raftery Daniel , Vue Zer , Hinton Antentor , McReynolds Melanie R. , Harrison Benjamin R. , Phillips Mark A. 
Published: July 2024

AbstractExperimental evolution studies that feature selection on life-history characters are a proven approach for studying the evolution of aging and variation in rates of senescence. Recently, the incorporation of genomic and transcriptomic approaches into this framework has led to the identification of hundreds of genes associated with different aging patterns. However, our understanding of the specific molecular mechanisms underlying these aging patterns remains limited. Here, we incorporated extensive metabolomic profiling into this framework to generate mechanistic insights into aging patterns inDrosophila melanogaster. Specifically, we characterized metabolomic change over adult lifespan in populations ofD. melanogasterwhere selection for early reproduction has led to an accelerated aging phenotype relative to their controls. Using these data we: i) evaluated evolutionary repeatability across the metabolome; ii) assessed the value of the metabolome as a predictor of “biological age” in this system; and iii) identified specific metabolites associated with accelerated aging. Generally, our findings suggest that selection for early reproduction resulted in highly repeatable alterations to the metabolome and the metabolome itself is a reliable predictor of “biological age”. Specifically, we find clusters of metabolites that are associated with the different rates of senescence observed between our accelerated aging population and their controls, adding new insights into the metabolites that may be driving the accelerated aging phenotype.SignificanceWhile experimental evolution studies featuringDrosophila melanogasterhave generated significant insights into the forces that shape aging and life history patterns, more recent efforts incorporating genomic and transcriptomic data have had comparatively little success identifying the molecular mechanisms underlying these patterns. Here we work to incorporate molecular phenotyping into this general framework as a way forward. Specifically, we characterize how the metabolome changes with age in populations ofD. melanogasterwhere hundreds of generations of selection for early reproduction have led to enrichment for an accelerated aging phenotype. By comparing to control populations, we show that the metabolome does appear to capture true signals of “biological age” and provides a new avenue for understanding the factors that underlie complex trait variation in real populations.
Revolutionizing Molecular Cloning: Introducing FastCloneAssist, a Streamlined Python Tool for Optimizing Primer Design in Restriction & Ligation-Independent PCR Cloning
Authors: Singh Pradip Kumar , Donnenberg Michael S. 
Published: July 2024

AbstractFastCloning, a paradigm shift in PCR cloning, has streamlined the process by eliminating laborious, multi-step traditional methods. This innovative technique, pioneered by Li et al. (2011), utilizes overlapping PCR primers and DpnI digestion for seamless integration of insert DNA into any desired vector position, regardless of restriction sites. This versatility makes FastCloning ideal for constructing fusion proteins, chimeric cDNAs, and manipulating genes with unparalleled ease.However, efficient primer design remains a critical hurdle, particularly for newcomers, as errors can lead to failed cloning attempts. To address this bottleneck, we present FastCloneAssist, a user-friendly Python program that automates FastCloning primer design with minimal user input. Users simply provide vector and insert sequences, along with the desired melting temperature (Tm), and FastCloneAssist provides best primer pairs after calculating optimal primer parameters for efficient PCR amplification and seamless DNA integration using established bioinformatics libraries. This open-source, freely available tool simplifies and accelerates cloning, making this powerful technique accessible to researchers of all levels and expediting scientific discovery.
Self-organizing recruitment of compensatory areas maximizes residual motor performance post-stroke
Authors: Lee Kevin , Barradas Victor , Schweighofer Nicolas 
Published: July 2024

AbstractWhereas the orderly recruitment of compensatory motor cortical areas after stroke depends on the size of the motor cortex lesion affecting arm and hand movements, the mechanisms underlying this reorganization are unknown. Here, we hypothesized that the recruitment of compensatory areas results from the motor system’s goal to optimize performance given the anatomical constraints before and after the lesion. This optimization is achieved through two complementary plastic processes: a homeostatic regulation process, which maximizes information transfer in sensory-motor networks, and a reinforcement learning process, which minimizes movement error and effort. To test this hypothesis, we developed a neuro-musculoskeletal model that controls a 7-muscle planar arm via a cortical network that includes a primary motor cortex and a premotor cortex that directly project to spinal motor neurons, and a contra-lesional primary motor cortex that projects to spinal motor neurons via the reticular formation. Synapses in the cortical areas are updated via reinforcement learning and the activity of spinal motor neurons is adjusted through homeostatic regulation. The model replicated neural, muscular, and behavioral outcomes in both non-lesioned and lesioned brains. With increasing lesion sizes, the model demonstrated systematic recruitment of the remaining primary motor cortex, premotor cortex, and contra-lesional cortex. The premotor cortex acted as a reserve area for fine motor control recovery, while the contra-lesional cortex helped avoid paralysis at the cost of poor joint control. Plasticity in spinal motor neurons enabled force generation after large cortical lesions despite weak corticospinal inputs. Compensatory activity in the premotor and contra-lesional motor cortex was more prominent in the early recovery period, gradually decreasing as the network minimized effort. Thus, the orderly recruitment of compensatory areas following strokes of varying sizes results from biologically plausible local plastic processes that maximize performance, whether the brain is intact or lesioned.
Linker histone H1-0 is a specific mediator of the repressive ETV6::RUNX1 transcriptional landscape
Authors: Jepsen Vera H. , Hanel Andrea , Picard Daniel , Mehtonen Juha , Hasselmann Rebecca , Schliehe-Diecks Julian , Scharov Katerina , Tu Jia-Wey , Bhave Rigveda , Kameri Ersen , Qin Nan , Wang Herui , Zhuang Zhengping , Wagener Rabea , Blümel Lena , Lautwein Tobias , Hein Daniel , Kögler Gesine , Remke Marc , Bhatia Sanil , Heinäniemi Merja , Borkhardt Arndt , Fischer Ute 
Published: July 2024

AbstractETV6::RUNX1is the most common oncogenic fusion in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL). It induces a clinically silent preleukemic state that requires secondary mutations for progression to leukemia. However, the molecular mechanisms contributing to the characteristic quiescence ofETV6::RUNX1+ preleukemic cells remain elusive. Here, we detect factors involved in the preleukemic state by generating human induced pluripotent stem cell (hiPSC) models using CRISPR/Cas9 gene editing. We identified upregulation of linker histoneH1-0in our preleukemic models, which was preserved upon hematopoietic differentiation and transformation to BCP-ALL. ETV6::RUNX1 inducesH1-0promoter activity whereas depletion of H1-0 specifically inhibited ETV6::RUNX1 signature genes, indicating its role as a key mediator of the ETV6::RUNX1 transcriptome. Single-cell gene expression analysis revealed highH1-0levels in quiescent cells during hematopoiesis and inverse correlation with transcriptional activity. Pharmacologically, H1-0 protein levels correspond to susceptibility of BCP-ALL towards histone deacetylase inhibitors (HDACi). Altogether, our study provides novel insights into ETV6::RUNX1-induced quiescence and suggests that further investigation into combinatorial treatment of BCP-ALL using the H1-0- inducing HDACi Quisinostat may be worthwhile.
Tracking spatial patterns and nocturnal arousal in an undisturbed natural population of the pulse-type weakly electric fishGymnotus omarorum
Authors: Migliaro Adriana , Pedraja Federico , Mucha Stefan , Benda Jan , Silva Ana 
Published: July 2024

SUMMARYAssessing animals’ locomotor and activity-rest patterns in natural populations is challenging. It requires individual identification and behavioral tracking in sometimes complex and inaccessible environments. Weakly electric fish are advantageous models for remote monitoring due to their continuous emission of electric signals (EODs).Gymnotus omarorumis a South American freshwater pulse-type weakly electric fish. Previous manual recordings of restrained individuals in the wild showed a spatial distribution compatible with territoriality and a nocturnal increase in EOD rate interpreted as arousal. This interdisciplinary study presents the development of low-cost amplifiers for remote EOD recordings and the refinement of tracking algorithms that provide individual recognition ofGymnotus omarorumin the wild. We describe natural daily spacing patterns of undisturbed individuals that are compatible with territoriality, although heterogeneous across sampling sites, and confirm that all resident fish showed a robust nocturnal increase of EOD rate likely associated with daily variations of water temperature.HIGHLIGHTSSuccessful remote individual tracking of wild pulse type weakly electric fishG. omarorumspacing patterns are compatible with known nocturnality and territorialityResidents keep their diurnal resting sites and move within small areas during the nightThe robust nocturnal electric arousal of residents is linked to water temperature peak
Are circulating levels of the myokine irisin linked to type 2 diabetes? A systematic review and meta-analysis
Authors: Aminov E. , Folan P. , Pisconti A. 
Published: July 2024

ABSTRACTBackgroundType II diabetes (T2DM) is one of the most prevalent metabolic disorders, and its multisystemic health consequences are widely known. Due to skeletal muscle’s ability to sequester a vast amount of glucose, muscle function and exercise have become a subject of much research into strategies to prevent and treat T2DM. Myokines are bioactive molecules released by muscle during contraction and involved in several biological processes such as metabolism, inflammation and behavior. Irisin, a recently discovered myokine, has been implicated in a vast array of physiological roles, including the ability to induce fat beiging. Since beige and brown fat both serve important roles in metabolic regulation, irisin’s role in the context of T2DM is the subject of ongoing investigations.MethodsWe systematically reviewed articles indexed in PubMed, Scopus and Web of Science that were published between 2011 and 2024, and compared circulating irisin levels in patients affected by T2DM and healthy subjects. As part of our systematic review of the literature, we performed meta-analysis of the data across all included articles, as well as stratified by body mass index (BMI), country of origin and by average irisin concentration in the control group.ResultsWe discovered great variability across the included studies in the average irisin levels detected, which spanned four orders of magnitude, hence the attempt at reducing variability by stratifying based on average levels in the control group. While the statistical power of our meta-analysis was decreased by the great variability in reported irisin concentrations, we nonetheless detected a consistent trend of decreased irisin concentration in T2DM patients compared with healthy controls, regardless of BMI, country of origin or average irisin concentration in the control group.ConclusionWith almost 60 articles included, ours is the first extensive systematic review and meta-analysis of irisin in T2DM, yet a highly statistically significant association between circulating irisin levels and T2DM could not be established due to the great variability of the data across include articles. Nonetheless we noticed a trend that is independent of BMI, suggesting a direct relationship between T2DM and irisin that is likely not secondary to diabetic sarcopenia. While our work encourages further research into irisin’s potential role in T2DM pathogenesis, the reproducibility of irisin detection methods in biological samples should be determined and standardized protocols should be made available to the research and clinical communities.
Modular organization of synapses within a neuromere for distinct axial locomotion inDrosophilalarvae
Authors: Fukumasu Kazushi , Nose Akinao , Kohsaka Hiroshi 
Published: July 2024

AbstractThe ability to generate diverse patterns of behavior is advantageous for animal survival. However, it is still unclear how interneurons in a single nervous system are organized to exhibit distinct motions by coordinating the same set of motor neurons. In this study, we analyze the populational dynamics of synaptic activity when fly larvae exhibit two distinct fictive locomotion, forward and backward waves. Based on neurotransmitter phenotypes, the hemi-neuromere is demarcated into ten domains. Calcium imaging analysis shows that one pair of the domains exhibits a consistent recruitment order in synaptic activity in forward and backward waves, while most other domains show the opposite orders in the distinct fictive locomotion. Connectomics-based mapping indicates that these two domains contain pre- and post-synaptic terminals of interneurons involved in motor control. These results suggest that the identified domains serve as a convergence region of forward and backward crawling programs.
Color-barcoded Super-multiplex RNA FISH in Three-dimensional Tissues through Single-round Imaging
Authors: Chang Tianyi , Zhao Shihui , Deng Kunyue , Liao Zhizhao , Tang Mingchuan , Zhu Yanxi , Han Wuji , Yu Chenxi , Fan Wenyi , Jiang Mengcheng , Wang Guanbo , Liu Dongfang , Peng Jirun , Pang Yuhong , Fei Peng , Wang Jianbin , Zheng Chunhong , Huang Yanyi 
Published: July 2024

AbstractTo resolve diverse RNA species in situ, cyclic reactions are often required to increase multiplexity, as conventional fluorescence microscopy is limited to only a few channels. This typically necessitates sophisticated instrumentation for techniques such as in-situ sequencing or sequential fluorescence in-situ hybridization (FISH) imaging, which has hindered the widespread adoption of spatial RNA imaging in biological research. Here, we introduce ‘Profiling of RNA In-situ through Single-round iMaging’ (PRISM), a method that expands coding capacity by leveraging color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validated PRISM’s versatility across various tissues, including mouse brains, mouse embryos, and human hepatocellular carcinoma (HCC) samples, collectively annotating over 5.6 million cells. Through quasi-3D spatial landscapes, we tracked major cell types in multiple organs during embryonic development from E12.5 to E14.5. Additionally, we uncovered the critical role of cancer-associated fibroblasts (CAFs) in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments. PRISM was further applied to 100-µm-thick mouse brain slices, generating an accurate 3D cell atlas and subcellular RNA localization landscapes. Robust, user-friendly, and capable of fast turnaround times with sub-cellular resolution, PRISM provides biologists with a powerful super-multiplex FISH toolkit.
WITHDRAWN: Unveiling the Family of Optimal Accelerations in Minimax Optimization and Fixed-Point Algorithms
Authors: Li Chris Junchi 
Published: July 2024

WITHDRAWAL STATEMENTbioRxiv has withdrawn this manuscript because it inappropriately listed Peter L. Bartlett, Jingfeng Wu, and Bin Yu as authors. Therefore, this work should not be cited as reference for the project. If you have any questions, please contact the corresponding author.
Maternal dietary deficiencies in folic acid and choline change metabolites levels in offspring after ischemic stroke
Authors: Anwar Fazian , Mosley Mary-Tyler , Jasbi Paniz , Chi Jinhua , Gu Haiwei , Jadavji Nafisa M. 
Published: July 2024

AbstractIschemic stroke is a debilitating disease, with nutrition being a modifiable risk factor. Changes in levels of metabolites can be used to measure the alterations in the gut, a significant marker for the etiology of diseases. This study utilized untargeted metabolomics to investigate changes in fecal samples of offspring in response to maternal dietary deficiencies and ischemic stroke. Female mice were placed on control (CD), folic acid- (FADD), or choline-deficient (ChDD) diets prior to, during pregnancy, and lactation. Offspring were weaned on to CD and at 2 months of age an ischemic stroke was induced. Fecal samples were collected prior to ischemic stroke, and at 1- and 4-weeks post-stroke for analysis. Sex and maternal dietary differences in metabolites were observed at both the 1- and 4-week post-stroke timepoints. At the 1-week post-stroke, female FADD offspring had more changes in metabolites than males. Comparatively, at the 4-week post-stroke timepoint, female offspring on either FADD or ChDD demonstrated metabolite changes. This study demonstrates a long-lasting impact of maternal dietary deficiencies on central nervous system and gut microbiome function after ischemic stroke.Summary StatementOur study investigated metabolite changes in female and male offspring fecal samples from mothers maintained on folic acid or choline deficient diet. We report that female offspring metabolite levels were impacted.
Peering into the world of wild passerines with 3D-SOCS: synchronized video capture and posture estimation
Authors: Chimento Michael , Chan Alex Hoi Hang , Aplin Lucy M. , Kano Fumihiro 
Published: July 2024

1AbstractCollection of large behavioral data-sets on wild animals in natural habitats is vital in ecology and evolution studies. Recent progress in machine learning and computer vision, combined with inexpensive microcomputers, have unlocked a new frontier of fine-scale markerless measurements.Here, we leverage these advancements to develop a 3D Synchronized Outdoor Camera System (3D-SOCS): an inexpensive, mobile and automated method for collecting behavioral data on wild animals using synchronized video frames from Raspberry Pi controlled cameras. Accuracy tests demonstrate 3D-SOCS’ markerless tracking can estimate postures with a 3mm tolerance.To illustrate its research potential, we place 3D-SOCS in the field and conduct a stimulus presentation experiment. We estimate 3D postures and trajectories for multiple individuals of different bird species, and use this data to characterize the visual field configuration of wild great tits (Parus major), a model species in behavioral ecology. We find their optic axes at approximately±60◦azimuth and−5◦elevation. Furthermore, birds exhibit functional lateralization in their use of the right eye with conspecific stimulus, and show individual differences in lateralization. We also show that birds’ convex hulls predicts body weight, highlighting 3D-SOCS’ potential for non-invasive population monitoring.3D-SOCS is a first-of-its-kind camera system for wild research, presenting exciting potential to measure fine-scaled behavior and morphology in wild birds.
Layer-specific reorganization of mnemonic representations in primate retrosplenial cortex during learning
Authors: Kambi Niranjan A , Afrasiabi Mohsen , Phillips Jessica M , Kenchappa Shobha C , Cleveland Duncan , Redinbaugh Michelle , Mohanta Sounak , Wang Bekah , Fayyad Matt , Saalmann Yuri B 
Published: July 2024

ABSTRACTRapid learning of associations between co-occurring stimuli is essential for episodic memory formation. The retrosplenial cortex (RSC) is strongly interconnected with the hippocampus, and in rodents, the RSC has been shown to support spatial navigation and fear conditioning. Although lesion and neuroimaging studies in humans and macaques have further implicated the RSC in episodic memory, it is unclear how memory representations form and evolve in the RSC. Here we show that representations of memorized contexts in primate RSC form within minutes. These initial representations reorganize as the memory matures, with a shift in the weight of neuronal contributions from superficial to deep RSC layers across an hour and increased local connectivity between deep layer neurons. Because RSC superficial and deep layers represent input and output layers respectively, it suggests that hippocampal inputs provide context information to superficial layers during early learning, and this context information consolidates in deep RSC layers.