bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear RNA exosome targeting onto chromatin loci in the degradation of unstable transcripts affects transcriptional programs in liver cells
Authors: Souaifan Hiba , Costallat Mickael , Sitkiewicz Laura , Godest Kylian , Cammas Florence , Mann Carl , Muchardt Christian , Rachez Christophe 
Published: February 2025

AbstractThe regulation of RNA maturation and degradation processes is crucial for maintaining cellular homeostasis, with defective regulation potentially leading to cancer or cellular senescence. RNA homeostasis occurs co-transcriptionally and is influenced by chromatin-associated factors, highlighting the need for further exploration in this area. HP1 proteins, originally identified as markers of pericentromeric heterochromatin, play significant roles in co-transcriptional processes occuring on chromatin. This study investigates the role of HP1 proteins in the maturation and degradation of non-coding RNAs, specifically focusing on their interaction with the RNA exosome, a key machinery for RNA degradation.The effects of depleting all three HP1 isoforms were investigated in mouse embryonic liver (BMEL) cell lines. Our results demonstrate that the RNA exosome interacts with HP1 proteins and is targeted to chromatin loci through HP1-dependent mechanisms. Furthermore, the absence of HP1 proteins alters various RNA species genome-wide, reactivating transposon-like repeat elements and stabilizing certain gene-associated transcripts thereby found in cytoplasm. In human cells, patients with highest levels of inflammation show reduced HP1 levels and less RNA degradation. This reduction leads to tumors with unique characteristics, being more rigid and exhibiting lower proliferation, which makes them less deadly than tumors with high HP1 levels.These findings illustrate the role of HP1 proteins in regulating RNA homeostasis through their interaction with the RNA exosome, suggesting important implications for cancer biology.
Organo-metal coprecipitation contributes to stable organic carbon fraction in mangrove soil
Authors: Hamada Kota , Yimatsa Nada , Ohtsuka Toshiyuki , Fujitake Nobuhide , Miyajima Toshihiro , Yokoyama Yusuke , Miyairi Yosuke , Kida Morimaru 
Published: February 2025

AbstractPrediction of the impact of anthropogenic disturbances and global change on organic carbon (OC) pools in mangrove soils requires a detailed understanding of the mechanisms underlying OC stabilization. Using density fractionation to physically separate OC fractions with varying degrees of mineral association and protection, this study aimed to assess distributions of these fractions and the geochemical factors influencing the most dominant and refractory mineral-associated, high-density fraction (HF) in mangrove soil. We conducted forest-wide soil sampling in the Gaburumata mangrove forest on Ishigaki Island, Japan, along three transects (upstream, midstream, downstream) and at five depths (until 100 cm). The OC in HF (OCHF) was the oldest (median Δ14C value of -13.81‰) and contributed most significantly to total soil OC (43%-63%) and nitrogen (64%-85%). Among the extractable metals analyzed (aluminum [Al], iron [Fe], calcium [Ca], and magnesium [Mg]) with different crystallinity, only organically complexed Al and Fe showed strong positive correlations with OCHF. Together with high OCHF:Fe ratios that surpassed the maximum sorptive capacity of Fe oxides, these results indicate that co-precipitation of OC and Fe was the dominant mode of organo-mineral associations. The low clay content reduced the importance of Ca and Mg on OCHF, as these divalent cations typically facilitate OC stabilization through cation bridging between negatively charged clay surfaces and organic matter. Furthermore, the Δ14C–OC relationship suggested efficient incorporation of mangrove-derived modern C into HF, in addition to the pre-existing old C. Thus, mangrove expansion is likely to enhance stable soil OC pools in addition to increasing plant biomass and litter. Overall, this study proposes a biogeochemical mechanism for how stable mangrove OC is newly formed, as well as maintained, with ramifications for global mangrove expansion and plantation efforts.
Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response
Authors: Felipe CJ San , Batra Jyoti , Muralidharan Monita , Malpotra Shivali , Anand Durga , Bauer Rachel , Verba Kliment A , Swaney Danielle L. , Krogan Nevan J. , Grabe Michael , Fraser James S. 
Published: February 2025

AbstractOpen Reading Frame 9b (Orf9b), an accessory protein of SARS-CoV and –2, is involved in innate immune suppression through its binding to the mitochondrial receptor Translocase of Outer Membrane 70 (Tom70). Previous structural studies of Orf9b in isolation revealed a β-sheet-rich homodimer, however, structures of Orf9b in complex with Tom70 revealed a monomeric helical fold. Here, we developed a biophysical model that quantifies how Orf9b switches between these conformations and binds to Tom70, a requirement for suppressing the type 1 interferon response. We used this model to characterize the effect of lipid binding and mutations in variants of concern to the Orf9b:Tom70 equilibrium. We found that the binding of a lipid to the Orf9b homodimer biases the Orf9b monomer:dimer equilibrium towards the dimer by reducing the dimer dissociation rate ∼100-fold. We also found that mutations in variants of concern can alter different microscopic rate constants without significantly affecting binding to Tom70. Together our results highlight how perturbations to different steps in these coupled equilibria can affect the apparent affinity of Orf9b to Tom70, with potential downstream implications for interferon signaling in coronavirus infection.
Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans
Authors: Zhou Yi , Su Yijing , Yang Qian , Li Jiaqi , Hong Yan , Gao Taosha , Zhong Yanqing , Ma Xueting , Jin Mengmeng , Liu Xinglan , Yuan Nini , Kennedy Benjamin C. , Wang Lizhou , Yan Longying , Viaene Angela N. , Helbig Ingo , Kessler Sudha K. , Kleinman Joel E. , Hyde Thomas M. , Nauen David W. , Liu Cirong , Liu Zhen , Shen Zhiming , Li Chao , Xu Shengjin , He Jie , Weinberger Daniel R. , Ming Guo-li , Song Hongjun 
Published: February 2025

AbstractImmature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development. We further identified human-specific transcriptomic features of imGCs and demonstrated functional roles of human imGC-enriched expression of a family of proton-transporting vacuolar-type ATPase subtypes in development of imGCs derived from human pluripotent stem cells. Our study reveals divergent gene expression patterns but convergent biological processes in the molecular characteristics of imGCs across species, highlighting the importance of conducting independent molecular and functional analyses for adult neurogenesis in different species.
Correlating High-dimensional longitudinal microbial features with time-varying outcomes with FLORAL
Authors: Fei Teng , Donovan Victoria , Funnell Tyler , Baichoo Mirae , Waters Nicholas R. , Paredes Jenny , Dai Anqi , Castro Francesca , Haber Jennifer , Gradissimo Ana , Raj Sandeep S. , Lesokhin Alexander M. , Shah Urvi A. , van den Brink Marcel R. M. , Peled Jonathan U. 
Published: February 2025

AbstractCorrelating time-dependent patient characteristics and matched microbiome samples can be helpful to identify biomarkers in longitudinal microbiome studies. Existing approaches typically repeat a pre-specified modeling approach for all taxonomic features, followed by a multiple testing adjustment step for false discovery rate (FDR) control. In this work, we develop an alternative strategy of using logratio penalized generalized estimating equations, which directly models the longitudinal patient characteristic of interest as the outcome variable and treats microbial features as high-dimensional compositional covariates. A cross validation procedure is developed for variable selection and model selection among different working cor-relation structures. In extensive simulations, the proposed method achieved superior sensitivity over the state-of-the-art methods with robustly controlled FDR. In the analyses of correlating longitudinal dietary intake and microbial features from matched samples of cancer patients, the proposed method effectively identified gut health indicators and clinically relevant microbial markers, showing robust utilities in real-world applications. The method is implemented under the open-source R packageFLORAL, which is available at (https://vdblab.github.io/FLORAL/).
Shared brain basis of aggression in clinical, forensic, and healthy samples: A meta-analysis
Authors: Harju Harri , Tuisku Jouni , Nummenmaa Lauri 
Published: February 2025

AbstractBackgroundAggression, violence, and antisocial behaviour constitute a large-scale societal problem. Aggression is common in incarcerated offenders and psychiatric conditions, but also healthy and noninstitutionalized populations vary in violent and aggressive behaviour. The brain basis of aggression has been studied extensively in the past, but the similarities between criminal, pathological and everyday aggression in the brain remain elusive.MethodsWe conducted an activation likelihood estimation (ALE) meta-analysis of 406 neuroimaging studies with 28 968 subjects using structural magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), positron emission tomography (PET) and single photon emission tomography (SPECT). The included studies had either i) measured haemodynamic responses during aggression-related functional tasks, ii) compared the brain structure, molecular organization, or function between aggressive forensic and psychiatric populations and control groups, or iii) addressed the effects of trait aggression on brain structure or function.ResultsAggression was consistently associated with altered function and structure in the amygdala, hippocampus, basal ganglia, anterior cingulate cortex, and the dorsolateral and orbitofrontal cortices. Functional coactivation analysis suggested that these regions are most consistently associated with emotional and reward function as well as their regulation. The results were comparable in healthy subjects as well as forensic and psychiatric populations.ConclusionsAggression is linked with alterations in multiple neurocognitive systems forming a common network for aggressiveness. Particularly the neural systems implicated in reward, emotions and regulation were commonly associated with aggression. The established network is involved in the whole continuum of aggression from benign variations in healthy volunteers to forensic subjects and violent clinical populations, suggesting a common aggression network whose severe perturbations may be linked with criminal behaviour or pathological aggression.
Remote sensing reveals inter- and intraspecific variation in riparian cottonwood (Populusspp) response to drought
Authors: Seeley M. M. , Wiebe B. C. , Gehring C. A. , Hultine K. R. , Posch B. C. , Cooper H. F. , Schaefer E. , Bock B. , Abraham A. J. , Moran E. M. , Keith A. , Allan G. J. , Scull M. , Whitham T. G. , Martin R. M. , Asner G. P. , Doughty C. E. 
Published: February 2025

AbstractUnderstanding how vegetation responds to drought is fundamental for understanding the broader implications of climate change on foundation tree species that support high biodiversity. Leveraging remote sensing technology provides a unique vantage point to explore these responses across and within species.We investigated interspecific drought responses of twoPopulusspecies (P.fremontii,P.angustifolia) and their naturally occurring hybrids using leaf-level visible through shortwave infrared (VSWIR; 400-2500 nm) reflectance. As F1hybrids backcross with either species, resulting in a range of backcross genotypes, we heretofore refer to the two species and their hybrids collectively as “cross types.” We additionally explored intraspecific variation inP. fremontiidrought response at the leaf and canopy levels using reflectance data and thermal unmanned aerial vehicle (UAV) imagery. We employed several analyses to assess genotype-by-environment (GxE) interactions concerning drought, including principal component analysis, support vector machine, and spectral similarity index.Five key findings emerged: (1) Spectra of all three cross types shifted significantly in response to drought. The magnitude of these reaction norms can be ranked from hybrids>P. fremontii>P. angustifolia,suggesting differential variation in response to drought; (2) Spectral space among cross types constricted under drought, indicating spectral—and phenotypic—convergence; (3) Experimentally, populations ofP. fremontiifrom cool regions had different responses to drought than populations from warm regions, with source population mean annual temperature driving the magnitude and direction of change in VSWIR reflectance. (4) UAV thermal imagery revealed that watered, warm-adapted populations maintained lower leaf temperatures and retained more leaves than cool-adapted populations, but differences in leaf retention decreased when droughted. (5) These findings are consistent with patterns of local adaptation to drought and temperature stress, demonstrating the ability of leaf spectra to detect ecological and evolutionary responses to drought as a function of adaptation to different environments.Synthesis.Leaf-level spectroscopy and canopy-level UAV thermal data captured inter- and intraspecific responses to water stress in cottonwoods, which are widely distributed in arid environments. This study demonstrates the potential of remote sensing to monitor and predict the impacts of drought on scales varying from leaves to landscapes.
Autism-associatedASPMvariant causes macrocephaly and social-cognitive deficits in mice
Authors: Singh Sonu , Kim Hyopil , Ecevitoglu Alev , Chasse Renee , Ludko Alexis M. , Sanganahalli Basavaraju , Gangasandra Vishaak , Park Sung Rye , Yee Siu-Pok , Grady James , Salamone John , Holly Fitch R. , Spellman Timothy , Hyder Fahmeed , Bae Byoung-Il 
Published: February 2025

ABSTRACTIn autism spectrum disorder (ASD), a neurodevelopmental disorder with social-cognitive deficits, macrocephaly occurs in 20% of patients with severe symptoms. However, the role of macrocephaly in ASD pathogenesis remains unclear. Here, we address the mechanistic link between macrocephaly and ASD by investigating a novel ASD-associated gain-of-function A1877T mutation inASPM(abnormal spindle-like microcephaly-associated).ASPMis a key regulator of cortical size and cell proliferation expressed in both excitatory and inhibitory neuronal progenitors but not in differentiated neurons. We found thatAspmgain-of-function knock-in mice exhibit macrocephaly, excessive embryonic neurogenesis with expanded outer radial glia, an increased excitatory-inhibitory (E-I) ratio, brain hyperconnectivity, and social-cognitive deficits with male specificity. Our results suggest that macrocephaly in ASD is not a proportional expansion of excitatory and inhibitory neurons, but a shift in the E-I ratio, independent of the expression patterns of the causative gene. Thus, macrocephaly alone can cause a subset of ASD-like symptoms.
Developmental gene expression patterns driving species-specific cortical features
Authors: Javed Awais , Gomez Lucia , Pravata Veronica , Lo Giudice Quentin , Sarhadi Moein , Cappello Silvia , Klingler Esther , Jabaudon Denis 
Published: February 2025

AbstractThe cerebral cortex shows species-specific variations in size and organization, likely accounting for distinct behavioral abilities. These structural differences may reflect evolutionary changes in the developmental expression of shared genes. To investigate this possibility, we compared cell-type-specific gene expression across species in the developing mouse and human neocortex, and human cortical organoids, by generating a shared transcriptional reference framework. This identified genes with conserved/divergent expression patterns, providing a molecular foundation to interrogate species-specific cellular properties. Using this resource, we discovered that the transcription factor JUNB is expressed in human but not mouse progenitors. Through cell-type-specific gain- and loss-of-function experiments in mice and human organoids, we demonstrate that JUNB bidirectionally controls human cortical features, including progenitor proliferation rates, neuronal production timing, and total neuronal output. This reveals how cell-type-specific regulation of shared genes during development can drive species-specific cortical features, providing a framework for understanding the molecular basis of cortical evolution.
Morphological and functional alteration of light perception circuits in AD patients
Authors: Sanda Nicolae , Milea Dan , Kovari Eniko , Tong Yixin , Brügger Talayeh , Hannibal Jens , Egervari Kristof Levente , Lobrinus Johannes Alexander , Carrera Emmanuel , Thumann Gabriele , Kleinlogel Sonja , Adamantidis Antoine , Mure Ludovic S. 
Published: February 2025

AbstractDisruption of sleep and circadian rhythms is one of the earliest symptoms of Alzheimer’s disease (AD). Circadian entrainment and the modulation of alertness are non-visual responses to light driven by intrinsically photosensitive retinal ganglion cells (ipRGCs). However, little is known about ipRGCs in the context of AD. To explore structural and functional changes of ipRGCs and ipRGC circuits, we analyzed the retinas and brains of 13 elderly patients (9 males, 4 females, aged 69-103) ranging from normal to neuropathologically defined AD.We performed extracellular electrophysiological recordings on freshly harvested retinas using multi-electrode arrays. While rod and cone responses were moderately affected, we found a decreased density of ipRGCs in donors with advanced AD pathology, which was confirmed by immunostaining. The remaining ipRGCs displayed morphological alterations as well as abnormal responses to light, including hyperexcitability. These changes appeared to be subtype-specific and correlated with the advancement of the disease.Altered ipRGCs circuits and function could contribute to the disruption of sleep and circadian rhythms reported in AD patients. The measurement of ipRGC-dependent responses to light could constitute a promising tool to predict or monitor pathological changes in the brain.
Relative timing and coupling of neural population bursts in large-scale recordings from multiple neuron populations
Authors: Olarinre Motolani , Siegle Joshua H. , Kass Robert E. 
Published: February 2025

AbstractThe onset of a sensory stimulus elicits transient bursts of activity in neural populations, which are presumed to convey information about the stimulus to downstream populations. The time at which these synchronized bursts reach their peak is highly variable across stimulus presentations, but the relative timing of bursts across interconnected brain regions may be less variable, especially for regions that are strongly functionally coupled. We developed a simple analytical framework that obtains good estimates of population burst times on a trial-by-trial basis, and of the correlations in the timing of evoked population bursts across areas. We show that this method performs well on simulated data, and is 85 to 90% faster than an alternative, recently-published method while also being much easier to apply. Using this new approach, we examined the relative timing of the first two population bursts following the onset of a drifting grating stimulus in large-scale recordings of spiking activity from six cortical visual areas and one visual thalamic nucleus in thirteen mice. The new method allowed us to identify mouse-to-mouse variation in peak times and region-to-region functional coupling. While all results were consistent with known anatomy and physiology, we found some sequences of activity across areas to be the same across all mice, while others varied with the individual. The general approach can thus produce sensitive analyses of timing relationships across neural populations.Significant StatementCareful analysis can reveal strong and precisely-timed interactions across multiple brain areas from small populations of spiking neurons. We developed a computationally efficient procedure that allowed us to examine the relative timing and coupling of 7 visual areas (6 cortical and one thalamic) and compare results in over 10 mice. The method can be used to track the flow of information across the brain in response to stimuli or during a behavioral task.
Critical factors of change management in small and medium enterprises: an exploratory study using the best­ worst method in the Brazilian context
Authors: Miziara Thanus , Pinto Jefferson de Souza , Sigahi Tiago F.A.C. , Moraes Gustavo Hermínio Salati Marcondes de , Rampasso Izabela Simon , Zanon Lucas Gabriel , Anholon Rosley 
Published: February 2025

Purpose
This paper aims to investigate critical change management factors in small and medium enterprises (SMEs), shedding light on key aspects of resilient organizational strategies.

Design/methodology/approach
The research adopted a mixed-methods approach, including inductive content analysis to identify the drivers and the best-worst method with data collection from eight subject matter experts.

Findings
The drivers selected by the experts as most important were “the existence of a plan with clear guidelines and steps for organizational change” and “leadership engagement to motivate and support employees” (with weights of 0.31 and 0.25, respectively). Disparities in experts’ opinions arise concerning perceptions of management evolution, leadership styles and communication efficacy. The findings suggest that leadership needs to adopt a more inclusive and participatory approach to drive better outcomes in SMEs. Furthermore, flexibility and adaptability were identified as fundamental traits for maintaining competitiveness in the market.

Originality/value
The research’s originality lies in its focused and data-driven approach applied to the Brazilian context. This study offers a new methodological contribution by integrating the best-worst method with qualitative content analysis to prioritize and contextualize critical change management factors specific to SMEs. Unlike previous research that has mainly addressed general challenges or descriptive analyses, this study provides applied results for managers and policymakers. Also, it presents a replicable framework for exploring similar organizational challenges in other contexts.