bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of publicly available transcriptomic data to identify key genes and pathways associated with osteosarcoma metastasis
Authors: Horak Iryna 
Published: November 2024

AbstractOsteosarcoma is the most common bone tumor occurring in children and adolescents. The prognosis of osteosarcoma patients with metastasis is rather poor, availability of prognostic molecular markers would thereby help to distinguish patients with a worse prognosis and to choose appropriate treatment. This study aimed to analyze data from publicly available datasets to identify genes and pathways associated with osteosarcoma onset and metastasis.A total of 8 datasets were analyzed (TARGET-OS, GSE220538, GSE21257, GSE9508, GSE87624, GSE14359, GSE19276, and GSE36001), and common deregulated genes and abundant pathways were searched. Three downregulated genes,TMBIM4, PKIBandIGKC, were common between metastatic and non-metastatic osteosarcoma tumors. Several abundant GO terms and pathways were identified, including Apoptotic Process (GO:0006915), Regulation Of Phosphatidylinositol 3-Kinase Signaling (GO:0014066), Regulation Of Cell Adhesion Molecule Production (GO:0060353), Positive Regulation Of MAP Kinase Activity (GO:0043406), and KEGG pathway Adherens junction.Analysis of metastasisversusprimary tumor revealed 231 common deregulated genes, identified hub genes involved in the organization of cell-cell junctions and surfactant metabolism. Significant enrichment was found in tight junctions, actin cytoskeleton, focal adhesion, muscle contraction proteins, NF-κB, PIK3/Akt/mTOR, AMPK, TNF, and MAPK signaling.335 common deregulated genes were found between tumor and normal bone, network analysis revealed two clusters involved in cell cycle progression and G2/M transition, and immune response regulation. Abundance was found in p53, TNF, MAPK, and JAK-STAT pathways.Taken together, this study consolidated transcriptomic data from 8 publicly available datasets to identify common deregulated genes and pathways in osteosarcoma development and metastasis.
The Lifespan Evolution of Individualized Neurophysiological Traits
Authors: da Silva Castanheira Jason , Wiesman Alex I. , Taylor Margot J. , Baillet Sylvain 
Published: November 2024

AbstractHow do neurophysiological traits that characterize individuals evolve across the lifespan? To address this question, we analyzed brief, task-free magnetoencephalographic recordings from over 1,000 individuals aged 4-89. We found that neurophysiological activity is significantly more similar between individuals in childhood than in adulthood, though periodic patterns of brain activity remain reliable markers of individuality across all ages. The cortical regions most critical for determining individuality shift across neurodevelopment and aging, with sensorimotor cortices becoming increasingly prominent in adulthood. These developmental changes in neurophysiology align closely with the expression of cortical genetic systems related to ion transport and neurotransmission, suggesting a growing influence of genetic factors on neurophysiological traits across the lifespan. Notably, this alignment peaks in late adolescence, a critical period when genetic factors significantly shape brain individuality. Overall, our findings highlight the role of sensorimotor regions in defining individual brain traits and reveal how genetic influences on these traits intensify with age. This study advances our understanding of the evolving biological foundations of inter-individual differences.Lay summaryThis study examines how brain activity reflects the development of individuality across a person’s life. Using magnetoencephalography to capture brief recordings of spontaneous brain activity, the researchers distinguished between over 1,000 individuals, spanning ages 4 to 89. They found that the brain regions most associated with individuality change with age: sensory and motor regions become increasingly distinctive in early adulthood, highlighting their role in shaping a person’s unique characteristics of brain activity. The study also revealed that changes in brain activity across different ages correspond to specific patterns of gene expression, shedding light on how genetics influence brain individuality. These findings deepen our understanding of the biological foundations of inter-individual differences and how it evolves over the lifespan.
Rab2B promotes chaperonin-mediated actin folding and prevents developmental transcription reprogramming and quiescence in trypanosomes
Authors: Li Feng-Jun , Dong Xiaoduo , Huang Yameng , Hu Donghui , Chae Eunyoung , He Cynthia Y. 
Published: November 2024

AbstractThe Rab family of small GTPases are regulators of intracellular membrane trafficking. Rab2B, a Golgi-resident Rab GTPase, has been shown to function in ER-Golgi transport and autophagosome-lysosome fusion in mammalian cells andDrosophila. InTrypanosoma brucei, the autophagy-related function of Rab2B was conserved and depletion of Rab2B blocked autophagosome-lysosome fusion. Intriguingly, depletion of Rab2B induced differentiation ofT. bruceifrom a proliferative slender form to a quiescent stumpy form, a step crucial for parasite transmission. Chaperonin CCT/TRiC was identified as an effector of Rab2B. Depletion of CCT/TRiC subunits or actin (a known CCT/TRiC substrate), or blocking actin polymerisation with Latrunculin A all triggered differentiation, suggesting a role of Rab2B on CCT/TRiC-mediated actin folding. Using an actin chromobody, we identified a pool of nuclear actin that is crucial for transcription reprogramming and life cycle differentiation inT. brucei.The study revealed a function of Rab2B and actin inT. bruceitranscription reprogramming leading to cell differentiation, and an unexpected role of Rab2B and CCT/TRiC mediated actin folding.
Immortalized Intestinal Telocytes - A Stem Cell Niche In Vitro
Authors: Canella Marco , Gharbi Amal , Duran Deborah , Corem Noa , Ben-Neriah Yinon , Birimberg-Schwartz Liron , Ben-Porath Ittai , Grunewald Myriam , Shoshkes-Carmel Michal 
Published: November 2024

SummaryTelocytes, a distinct type of mesenchymal cell, have recently emerged as crucial components of the intestinal stem cell niche, primarily by providing essential Wnt proteins that drive stem cell function. However, their detailed biology and the specific mechanisms by which they regulate stem cell activity remain largely unexplored. Here, we established an immortalized intestinal telocyte cell line that retains the key cellular and molecular characteristics of native telocytes. Remarkably, this cell line, unlike telocyte-depleted immortalized mesenchyme, supports the growth of both mouse and human organoids in co-culture without the need for external factor supplementation. These findings indicate that telocytes are not only essential but are also sufficient to maintain stem cell activity. This immortalized telocyte line provides a valuable source of factors that support stem cell activity in vitro, offering a powerful tool for advancing our understanding of telocyte biology and the reciprocal communication between stem cells and their niche.
White matter microstructure links with brain, bodily and genetic attributes in adolescence, mid- and late life
Authors: Korbmacher Max , Tranfa Mario , Pontillo Giuseppe , van der Meer Dennis , Wang Meng-Yun , Andreassen Ole A. , Westlye Lars T. , Maximov Ivan I. 
Published: November 2024

AbstractAdvanced diffusion magnetic resonance imaging (dMRI) allows one to probe and assess brain white matter (WM) organization and microstructurein vivo. Various dMRI models with different theoretical and practical assumptions have been developed, representing partly overlapping characteristics of the underlying brain biology with potentially complemen-tary value in the cognitive and clinical neurosciences. To which degree the different dMRI metrics relate to clinically relevant geno-and phenotypes is still debated. Hence, we inves-tigate how tract-based and whole WM skeleton parameters from different single- and multi-compartment dMRI approaches associate with clinically relevant and white matter-related phenotypes (sex, age, pulse pressure (PP), body-mass-index (BMI), brain asymmetry) and genetic markers in the UK Biobank (UKB, n=52, 140) and the Adolescent Brain Cognitive Development (ABCD) Study (n=5, 844). Multi-compartment dMRI approaches provided the strongest WM associations with age, and unique insights into brain asymmetry. Kurto-sis was most indicative of PP and BMI. WM-based sex classifications and polygenic score associations for common psychiatric disorders and Alzheimer’s disease were similar across diffusion approaches. We conclude that WM microstructure is differentially associated with clinically relevant pheno- and genotypes at different points in life. Multi-compartment dMRI approaches, and particularly the examined Bayesian approach, provide additional information to conventional approaches in such examinations.
Individual differences in the effects of musical familiarity and musical features on brain activity during relaxation
Authors: Scarratt Rebecca Jane , Dietz Martin , Vuust Peter , Kleber Boris , Jespersen Kira Vibe 
Published: November 2024

AbstractFinding a way to relax is increasingly difficult in our overstimulating modern society and chronic stress can have severe psychological and physiological consequences. Music is a promising tool to promote relaxation by lowering heart rate, modulating mood and thoughts, and providing a sense of safety. Here, we used functional magnetic resonance imaging (fMRI) to investigate how music influence brain activity during relaxation with a particular focus on the participants’ experience of different types of music. In a 2×2 design, 57 participants were scanned while rating how relaxed they felt after listening to 28-second excerpts of either familiar or unfamiliar relaxation music with calm or energetic features. Behaviourally, calm music was the strongest predictor of relaxation, followed by familiar music. fMRI results revealed activations of auditory, motor, emotion, and memory areas, for listening to familiar compared to unfamiliar music. This suggests increased audio-motor synchronization and participant engagement of known music. Listening to unfamiliar music was correlated with attention-related brain activity, suggesting increased attentional load for this music. Behaviourally, we identified four clusters of participants based on their relaxation response to the different types of music. These groups also displayed distinct auditory and motor activity patterns, suggesting that the behavioural responses are linked to changes in music processing. Interestingly, some individuals found energetic music to be relaxing if it is familiar, whereas others only found calm music to be relaxing. Such individual behavioural and neurological differences in relaxation responses to music emphasise the importance of developing personalised music-based interventions.Graphical AbstractHighlights:- Participants listen to relaxation tracks varying in familiarity and energy levels- Sedative music followed by familiar music increased relaxation ratings the most- Auditory, motor, memory and attention activations depending on the music type- 4 distinct clusters of behavioural responses to familiar or sedative music- These groups are also present in brain activity
Pupil size variations reveal Bayesian inference in cognitive arithmetic
Authors: Zénon Alexandre , Salvaggio Samuel , Andres Michael 
Published: November 2024

AbstractThe assumption that the brain relies on Bayesian inference has been successful in accounting for many behavioural and neurophysiological observations, but to date, dependence on such mechanism has not been assessed in the context of arithmetic. Bayesian inference implies the representation of uncertainty and reliance on prior beliefs. In arithmetic problem solving, it would consist in refining prior knowledge about the response range as the system progressively integrates the numerical information conveyed by the operands. Within this framework, the amount of information needed to progress from a prior to a posterior probability distribution over responses can be quantified by the information gain, which would relate to the cognitive workload of the task. To test this hypothesis, we designed three experiments in which participants computed the sum of two numbers presented one after another through headphones. In each experiment, the information about response predictability conveyed by the first operand was manipulated. The first operand was either highly informative and contributed to narrow down the response range, or poorly informative and conveyed little information about a plausible response. Throughout all experiments, we found that pupil-related arousal signalled the information gain associated with the first operand, indicating that participants already updated the probability distribution of possible responses upon hearing that first stimulus. This finding shows that Bayesian inference is central to arithmetic problem solving and that information gains consecutive to the integration of the operands can be tracked over time through pupillometry.Public significance statement–This study suggests that when we do arithmetic, our brain uses Bayesian inference, a method similar to how scientists update their theories based on new evidence. This means that when doing math, we start with hypotheses about the result and progressively narrow down possible solutions.–By observing the eye of the participants while they were solving arithmetic problems, the authors showed that their pupil size increased in proportion to the amount of processed information.–The authors also found that when participants received more informative first operands in the math problem, and when their pupil size increased more during this presentation, they were also faster to respond, indicating that greater initial information processing facilitated quicker problem-solving.
Born Connected: Do Infants Already Have Adult-Like Multi-Scale Connectivity Networks?
Authors: Bajracharya Prerana , Mirzaeian Shiva , Fu Zening , Calhoun Vince , Shultz Sarah , Iraji Armin 
Published: November 2024

AbstractThe human brain undergoes remarkable development with the first six postnatal months witnessing the most dramatic structural and functional changes, making this period critical for in-depth research. rsfMRI studies have identified intrinsic connectivity networks (ICNs), including the default mode network, in infants. Although early formation of these networks has been suggested, the specific identification and number of ICNs reported in infants vary widely, leading to inconclusive findings. In adults, ICNs have provided valuable insights into brain function, spanning various mental states and disorders. A recent study analyzed data from over 100,000 subjects and generated a template of 105 multi-scale ICNs enhancing replicability and generalizability across studies. Yet, the presence of these ICNs in infants has not been investigated.This study addresses this significant gap by evaluating the presence of these multi-scale ICNs in infants, offering critical insight into the early stages of brain development and establishing a baseline for longitudinal studies. To accomplish this goal, we employ two sets of analyses. First, we employ a fully data-driven approach to investigate the presence of these ICNs from infant data itself. Towards this aim, we also introduce burst independent component analysis (bICA), which provides reliable and unbiased network identification. The results reveal the presence of these multi-scale ICNs in infants, showing a high correlation with the template (rho > 0.5), highlighting the potential for longitudinal continuity in such studies.We next demonstrate that reference-informed ICA-based techniques can reliably estimate these ICNs in infants, highlighting the feasibility of leveraging the NeuroMark framework for robust brain network extraction. This approach not only enhances cross-study comparisons across lifespans but also facilitates the study of brain changes across different age ranges.In summary, our study highlights the novel discovery that the infant brain already possesses ICNs that are widely observed in older cohorts.
Changes in interlimb coordination induced by within-stride changes in treadmill speed
Authors: Hall Brooke L. , Roemmich Ryan T. , Banks Caitlin L. 
Published: November 2024

ABSTRACTDuring walking, interlimb coordination involves the right and left legs working together to achieve a desired movement. Previously, dynamic treadmill walking has been shown to drive asymmetric gait changes in healthy young adults through selectively changing the speed of the whole treadmill. Currently, the coordination demands of this novel walking environment are unknown and must be understood prior to assessing dynamic treadmill walking in clinical populations. We investigated the interlimb coordination requirements of dynamic treadmill walking in ten healthy young adults. We quantified interlimb coordination changes as phase shift (timing of maximum cross-correlation between limb angle trajectories of the left and right legs), center of oscillation (limb angle at midstance), and center of oscillation difference (oscillation angle difference between legs). We found that phase shift in the Fast trial (i.e., 1.0m/s treadmill speed in first 50% of gait cycle, 0.5m/s in latter 50%) was significantly more positive (i.e., the right leg oscillates ahead of the left leg in time) than in the Slow, Accelerate, and Decelerate trials (all p<0.01). The Fast trial produced significantly positive center of oscillation values on the right leg, indicating that the right leg is oscillating about a more flexed axis than the left. Center of oscillation difference was similarly more positive during the Fast trial than in the Decelerate (p<0.01) and Slow (p<0.01) trials. These results exemplify that some forms of dynamic treadmill walking change interlimb coordination to a greater extent than others. After several minutes of dynamic treadmill walking, interlimb coordination is changed relative to baseline walking in the spatial domain (Fast and Decelerate conditions) and the temporal domain (Fast and Slow). Therefore, dynamic treadmill walking is tunable in both biomechanical and interlimb coordination parameters, creating a variety of options for restoring gait symmetry in asymmetric populations.
p300/CBP-catalyzed acetylation safeguards minor zygotic genome activation via activating DUX
Authors: Xiao Lieying , Jin Hao , Dang Yanna , Zhao Panpan , Li Shuang , Shi Yan , Wang Shaohua , Zhang Kun 
Published: November 2024

SummaryZygotic genome activation (ZGA), the first transcriptional event at the onset of life, is crucial for early embryonic development. However, the mechanisms that initiate and regulate ZGA in mammals remain poorly understood. In this study, we demonstrate that p300/CBP-catalyzed acetylation plays a vital role in regulating ZGA. Inhibition of p300/CBP acetyltransferase activity results in impaired minor ZGA and a subsequent 2-cell arrest. By profiling the dynamic landscape of p300 during the ZGA stage, we elucidate the distinct patterns of p300 establishment in promoter and enhancer regions. Moreover, p300 recruits RNA polymerase (Pol II) to pre-configure in the promoter regions of ZGA genes, and orchestrates the gradual establishment of enhancer activity during the early 2-cell stage to activate ZGA. Furthermore, p300 enhances minor ZGA by promoting the expression of DUX. Restoring DUX levels, which are diminished due to p300/CBP inhibition, rescues ZGA and embryonic development by re-establishing Pol II enrichment on minor ZGA genes. Overall, our findings elucidate the mechanism by which p300/CBP regulates ZGA through acetylation and activation of the key transcription factor DUX.Highlightsp300/CBP plays a stage-specific role during preimplantation development phase.p300 displays distinctive dynamic changes in promoter and enhancer regions during ZGA stage.p300/CBP-catalyzed acetylation facilitates the pre-configuration and elongation of Pol II at ZGA gene regions.DUX recruits p300 and Pol II to activate minor ZGA genes independently of p300’s catalytic activity.
The inflammasome sensor NLRP3 interacts with REV7 to maintain genome integrity through homologous recombination
Authors: Burlet Delphine , Khan Md Muntaz , Hacot Sabine , Buthmann Hannes , Bardoulet Léa , Huber Anne-Laure , Gorry Julie , Lopez Bernard S , Couté Yohann , Geyer Matthias , Tissier Agnès , Petrilli Virginie 
Published: November 2024

ABSTRACTDNA double strand break (DSB) is a highly toxic lesion that can generate genome instability, a major source of tumorigenesis. DSBs are mainly repaired by non-homologous end joining (NHEJ) or homologous recombination (HR). The selection of the DSB repair pathway primarily depends on the DNA resection of the DSB ends. Indeed, HR is initiated by resection at the DSB generating 3’ single stranded extension. The shieldin complex prevents resection fostering DSB repair toward NHEJ. Here, we reveal that the inflammasome sensor NLRP3 facilitates DNA end resection to promote the HR pathway in an inflammasome-independent manner. Strikingly, NLRP3 silencing decreases HR efficiency, as evidenced by RAD51 foci and functional HR assays. Mechanistically, we describe that NLRP3 interacts with REV7, a subunit of the shieldin complex, and its depletion increases REV7 recruitment to IR-induced DSBs. Similar to cancer cells harboring HR mutated genes, we find that NLRP3 deficient cells are sensitive to PARP inhibitors (PARPi) and exhibit an epistatic relationship with BRCA1 deficiency. Remarkably, loss of REV7 in NLRP3-depleted cells induces PARPi resistance by restoring HR. This study unravels the crucial role of the innate immune receptor NLRP3 in regulating the selection of DSB repair pathways to maintain genome integrity.
Beer drinker perceptions of cannabis-infused beverages
Authors: Staples Aaron J. 
Published: November 2024

PurposeAs cannabis markets have expanded and nonalcoholic beer sales have grown, craft beverage manufacturers are increasingly interested in alternative beverage markets for product differentiation. This study evaluates consumer perceptions of nonalcoholic, cannabis-infused beverages to explore the market potential.Design/methodology/approachThe study used survey data from 1,094 US beer drinkers to identify consumer willingness to try and general perceptions of cannabis-infused beverages. First, we identified who is most likely to try cannabis-infused beverages using multinomial logistic regression analysis. Then, we identified perceptions of cannabis-infused beverages relative to conventional beer by asking respondents to rate the expected taste, nutrition, safety and price for one of three hypothetical product options: a traditional beer, a cannabidiol (CBD) beverage or a tetrahydrocannabinol (THC) beverage. Comparisons across products were then drawn using standard statistical tests.FindingsApproximately 53–56% of beer drinkers in our sample stated they were willing to try cannabis-infused beverages, with age, product knowledge and past purchasing behaviors correlating with this response. Additionally, consumers expected cannabis-infused beverage scores to have similar safety and nutrition metrics to traditional beer but at higher prices. On average, consumers expected CBD- and THC-infused beverages to be $0.33 and $0.98 more expensive per six-pack than a conventional beer, respectively.Originality/valueWith an evolving craft beverage and cannabis landscape, these results provide a glimpse into beer drinkers’ attitudes toward CBD- and THC-infused beverages. The results offer novel insights into the target audience and market potential for cannabis-infused beverages that manufacturers and entrepreneurs can use in their business strategies. Additionally, the findings can be useful to policymakers and public health officials in monitoring this emerging market, informing policy design and designing public health messaging. Lastly, the study opens avenues for future research on consumer perceptions of cannabis versus alcoholic products across academic disciplines.