bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel MRI-based Biotypes of Human Neurodevelopment associated with Impulsivity performance
Authors: Zhou Zicong , Rivas-Fernandez Miguel A. , Adise Shana , Colon-Perez Luis 
Published: November 2024

AbstractIntroductionAdequate neurodevelopment is critical to the proper advancement of cognitive and emotional processing; however, variation in neurodevelopment has emerged as a potential risk factor for subsequent drug use. The Adolescent Brain Cognitive Development (ABCD) Study is an ongoing and longitudinal study to determine the developmental trajectories of the brain and how experiences impact brain development, which makes it an ideal framework study to determine proper neurodevelopmental trajectories associated with healthy executive function behavioral development and their neurobiology.MethodBased on the availability of ABCD (Release 5.1) tabulated data, we selected 1368 subjects with neuroimaging records on multiple time points. To focus on the frontal cortex, we preprocess 20 ROIs (including ten regions with right and left cerebral hemispheres) cortical thickness measurements for SuStaIn. Once SuStaIn determined the potential control and phenotype (subtypes) group, we conducted t-tests between the control and phenotype groups on their delay discounting measurements. To overserve possible trajectories, we also investigated the correlation of the thickness measurements with delay discounting under the suggested phenotype by SuStaIn.ResultsSuStaIn identified four subtypes and one potential control group, validated by cross-validation test as the optimal solution for balancing model accuracy and complexity. Among the t-tests on delay discounting results between the control group and each subtype, subtype1 tends to show low significance on the 3-month indifference point (p=0.067), subtype 2 identifies a significant reduction in impulsivity on the 1-month indifference point (p=0.017), subtype 4 stands significant reduction at on 3-month indifference point (p=0.0092) and significance on 1-year indifference point (p=0.00418). For the correlations between each selected ROI, we identified a negative correlation (R=-0.18, p=0.0095) between the thickness of the left hemisphere caudal-anterior-cingulate and delay discounting indifference point at 3 months.ConclusionWe successfully identified four subtypes of the ABCD, which may be putative abnormal trajectories of executive function accelerated development. Three of the four subtypes reflect impulsive behavioral phenotype, and one displays an association with cortical thinning. Overall, we present evidence that there are putative neurobiological signs of potential executive function disruption as early as nine years of age.
Multi-objective computational optimization of human 5′ UTR sequences
Authors: Yamada Keisuke , Suga Kanta , Abe Naoko , Hashimoto Koji , Tsutsumi Susumu , Inagaki Masahito , Hashiya Fumitaka , Abe Hiroshi , Hamada Michiaki 
Published: November 2024

AbstractThe computational design of mRNA sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of 5′ UTR sequences, key upstream elements of mRNA. However, fully automated design of 5′ UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human 5′ UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.
Social Anxiety Alters Theory of Mind Activation and Intersubject Neural Variability During Movie Viewing
Authors: Mangnus Margot , Koch Saskia B. J. , Devillers Robin , Hagoort Peter , Bašnáková Jana , Stolk Arjen 
Published: November 2024

AbstractSocial anxiety is characterized by an intense fear of judgment in social situations, yet the underlying mechanisms driving this condition remain poorly understood. One hypothesis holds that specific alterations in Theory of Mind (ToM) affect the ability to interpret others’ thoughts and emotions. Another hypothesis proposes that broader interpretive biases lead individuals to perceive social cues as overly significant, even in neutral settings. We investigated these possibilities by measuring brain activity, pupil responses, and heart rates in socially anxious individuals and matched controls as they viewed ‘Partly Cloudy’, an animated film known to engage the ToM network during specific scenes. While overall brain activity during ToM-related scenes was similar across groups, socially anxious participants exhibited reduced activation in the left posterior superior temporal sulcus (pSTS), a key area for ToM processing. Additionally, intersubject correlation analysis revealed a distinct neural response pattern in the socially anxious group, marked by uniform responses in sensory regions and heightened variability in higher-order cortical areas. This pattern persisted throughout the film and occurred without changes in heart rate or pupil responses, indicating a neural processing bias that manifests even in non-evaluative settings. These findings provide a neural basis for ToM alterations and broader interpretive biases in social anxiety, supporting cognitive-behavioral models and suggesting novel targets for intervention.
WMH-DualTasker: A Dual-Task Deep Learning Model with Self-supervised Consistency for Automated Segmentation and Visual Rating of White matter Hyperintensities - a Multicentre study
Authors: Wu Yilei , Dong Zijian , Li Hongwei Bran , Chong Yao Feng , Ji Fang , Xian Chong Joanna Su , Jie Tang Nathanael Ren , Hilal Saima , Fu Huazhu , Chen Christopher Li-Hsian , Zhou Juan Helen ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2024

AbstractBackgroundWhite matter hyperintensities (WMH) are neuroimaging markers linked to an elevated risk of cognitive decline. WMH severity is typically assessed via visual rating scales and through volumetric segmentation. While visual rating scales are commonly used in clinical practice, they offer limited descriptive power. In contrast, supervised volumetric segmentation requires manually annotated masks, which is labor-intensive and challenging to scale for large studies. Therefore, our goal was to develop an automated deep learning model that can provide accurate and holistic quantification of WMH severity with minimal supervision.MethodsWe developed WMH-DualTasker, a deep learning model that simultaneously performs voxel-wise segmentation and visual rating score prediction. The model leverages self-supervised, transformation-invariant consistency constraints, using WMH visual ratings from clinical settings as the sole supervisory signal. Additionally, we assessed its clinical utility by applying it to identify individuals with mild cognitive impairment (MCI) and to predict dementia conversion.FindingsThe volumetric quantification performance of WMH-DualTasker was either superior to or on par with existing supervised methods, as demonstrated on the MICCAI-WMH dataset (N=60, Dice=0.602) and the SINGER dataset (N=64, Dice=0.608). Furthermore, the model exhibited strong agreement with clinical visual rating scales on an external dataset (SINGER, MAE=1.880, K=0.77). Importantly, WMH severity metrics derived from WMH-DualTasker improved predictive performance beyond conventional clinical features for MCI classification (AUC=0.718, p<0.001), MCI conversion prediction (AUC=0.652, p<0.001) using the ADNI dataset.InterpretationsWMH-DualTasker substantially reduces the reliance on labor-intensive manual annotations, facilitating more efficient and scalable quantification of WMH severity in large-scale population studies. This innovative approach has the potential to advance preventive and precision medicine by enhancing the assessment and management of vascular cognitive impairment associated with WMH. Code and model weights are publicly available athttps://github.com/hzlab/WMH-DualTasker.
VIRALpre: Genomic Foundation Model Embedding Fused with K-mer Feature for Virus Identification
Authors: Wang Zanyi , Yu Qinze , Li Yu 
Published: November 2024

AbstractVirus, a submicroscopic infectious agent, influences all life forms. Identifying viral sequences is essential to understand their biological functions and then analyze their impacts on public health, and the development of microbial communities. For its significance, tools are developed based on various mathematical methods and algorithms. However, previous methods struggle to identify viral sequences, especially short contigs accurately since the limited information and small-scale close-set dataset. Here we propose VIRALpre, a hybrid framework combined with genomic foundation model (GFM) embedding and K-mer feature of sequences to precisely recognize viral genomic fragments. VIRALpre is empowered by the generalization competencies of GFMs, which have proven their strength in various downstream tasks, thanks to newly established large-scale training databases and Attention mechanism. On the other hand, K-mer features provide additional biological information to bridge the limitation of GFMs in classification tasks. Comprehensive experimental results demonstrate that VIRALpre significantly outperforms all the previous methods on virus identification performance by 4% in accuracy. To prove that this model is qualified when facing unique contigs to training data, BLASTn-based similarity cut-off test(setting e-value as 10−5) is done and it achieves about 10% F1-score improvement. More than well-built test datasets, new zero-shot cross-dataset tests on benchmark datasets sampling from natural environments are conducted, VIRALpre performs identify almost most viral sequences while keeping a very low False Positive Rate. Based on these solid experiments, VIRALpre has the ability to manage short-contig virus identification by truly learning the distinctions of viral sequences and hopefully act as an adviser to promote virus-related research.
Seed dispersal effectiveness and plant-bird interaction networks in the Tehuacán Valley
Authors: Contreras-González Ana María , González-Montes Mónica Beatriz , Jair Ortega-Jiménez E. , Herrera-Serrano Pamela , Rivera-Ortiz Francisco Alberto , Valiente-Banuet Alfonso 
Published: November 2024

AbstractThe maintenance of biodiversity in communities is mediated by interactions that influence community structure, including seed dispersal. The aim of this study was to evaluate the seed dispersal effectiveness of fruit-eating bird species in the Tehuacán Valley and assess the extinction risk of both bird and plant species through interaction networks. From June 2022 to July 2024, we conducted monthly observations of bird foraging on 12 plant species in San Juan Raya and 13 plant species in Zapotitlán Salinas. We calculated the seed dispersal effectiveness and constructed quantitative and qualitative interaction networks for both locations. For both sites, we found that few birds were effective seed dispersers. The most effective dispersers in San Juan Raya wereMelanerpes hypopolius,Toxostoma curvirostre, andPhainopepla nitens, while in Zapotitlán Salinas, the main dispersers wereMimus polyglottos,T. curvirostre, andP. nitens. Through qualitative analysis of the interaction networks, we determined that plant communities in both locations are moderately fragile. Quantitative network analyses revealed that plants in Zapotitlán Salinas are particularly vulnerable, as most species could face local extinction if they lose their disperser species, potentially disrupting the community structure. In contrast, bird species exhibited a lower degree of specialization. Thus, even if certain plant species are lost, birds could continue to interact with other species or migrate to areas with a greater availability of resources. The extraction of plant species, many of which are used for firewood, could negatively impact seed dispersal, as these plants serve as facilitators for many of the species studied. This could reduce the number of available sites where birds can deposit seeds, decreasing the likelihood of seed germination and the establishment of new individuals, which, in turn, may compromise community structure.
Impacts of Structural Properties of Myosin II Filaments on Force Generation
Authors: Ding Shihang , Chou Pei-En , Deguchi Shinji , Kim Taeyoon 
Published: November 2024

ABSTRACTCells need intracellular forces for their physiological functions, such as migration, cytokinesis, and morphogenesis. The actin cytoskeleton generates a large fraction of the forces via interactions between cytoskeletal components, such as actin filament (F-actin), myosin, and actin cross-linking proteins (ACPs). Myosin II plays the most important role in cellular force generation. Myosin II molecules self-assemble into filaments with different structures depending on myosin II isoforms and other conditions such as pH and ionic concentration. It has remained elusive how force generation in actomyosin structures is affected by the architecture of myosin II filaments. In this study, we employed an agent-based model to investigate the effects of the structural properties of myosin II filaments on force generation in disorganized actomyosin structures. We demonstrated that the magnitude of forces and the efficiency of force generation can vary over a wide range depending on the number and spatial distribution of myosin II filaments. Further, we showed that the number of myosin heads and the length of a bare zone at the center of myosin II filaments without heads highly affect the force generation process in bundles and networks. Our study provides insights into understanding the roles of the structural properties of myosin II filaments in actomyosin contractility.
Dynamic prioritisation of sensory and motor contents in working memory
Authors: Echeverria-Altuna Irene , Boettcher Sage E.P , van Ede Freek , Nobre Anna C. 
Published: November 2024

AbstractInternal selective attention prioritises both sensory and motor contents in working memory to guide prospective behaviour. Prior research has shown how attention modulation of sensory contents is flexible and temporally tuned depending on access requirements, but whether the prioritisation of motor contents follows similar flexible dynamics remains elusive. Also uncharted is the degree of co-dependence of sensory and motor modulation, which gets at the nature of both working-memory representations and internal attention functions. To address these questions, we independently tracked the prioritisation of sensory and motor working-memory contents as a function of dynamically evolving temporal expectations. The design orthogonally manipulated when an item location (left vs right side) and associated prospective action (left vs right hand) would be relevant. Contralateral modulation of posterior alpha (8-12 Hz) activity in electroencephalography (EEG) tracked prioritisation of the item location, while contralateral modulation of central mu/beta (8-30 Hz) activity tracked response prioritisation. Proactive and dynamic alpha and mu/beta modulation confirmed the flexible and temporally structured prioritisation of sensory and motor contents alike. Intriguingly, the prioritisation of sensory and motor contents was temporally uncoupled, showing dissociable patterns of modulation. The findings reveal multiple modulatory functions of internal attention operating in tandem to prepare relevant aspects of internal representations for adaptive behaviour.
PrP turnover in vivo and the time to effect of prion disease therapeutics
Authors: Corridon Taylor L , O’Moore Jill , Lian Yuan , Laversenne Vanessa , Noble Briana , Kamath Nikita G , Serack Fiona E , Shaikh Abdul Basit , Erickson Brian , Braun Craig , Lenz Kenney , Howard Michael , Chan Nathan , Reidenbach Andrew G , Cabin Deborah E , Vallabh Sonia M , Grindeland Andrea , Oberbeck Nina , Zhao Hien T , Minikel Eric Vallabh 
Published: November 2024

AbstractPrP lowering is effective against prion disease in animal models and is being tested clinically. Therapies in the current pipeline lower PrP production, leaving pre-existing PrP to be cleared according to its own half-life. We hypothesized that PrP’s half-life may be a rate-limiting factor for the time to effect of PrP-lowering drugs, and one reason why late treatment of prion-infected mice is not as effective as early treatment. Using isotopically labeled chow with targeted mass spectrometry, as well as antisense oligonucleotide treatment followed by timed PrP measurement, we estimate a half-life of 5-6 days for PrP in the brain. PrP turnover is not affected by over- or under-expression. Mouse PrP and human PrP have similar turnover rates measured in wild-type or humanized knock-in mice. CSF PrP appears to mirror brain PrP in real time in rats. PrP is more readily quantifiable in colon than in other peripheral organs, and appears to have a shorter half-life in colon than in brain. Our data may inform the design of both preclinical and clinical studies of PrP-lowering drugs.
Chronic inflammation drives epididymal tertiary lymphoid structure formation and autoimmune fertility disorders
Authors: Elizagaray Maia L. , Barrachina Ferran , Avenatti Maria C. , Bastepe Isinsu , Chen Angela , Odriozola Ainize , Ukairo Oluchi , Ros Vanina Da , Ottino Kiera , Subiran Nerea , Battistone Maria A. 
Published: November 2024

AbstractThe incomplete understanding of epididymal mucosal immunity is a significant contributing factor to the classification of many male infertility cases as idiopathic. Conditions that disrupt the immune balance in the male reproductive tract, such as vasectomy and infections, can expose sperm to the immune system, leading to increased production of anti-sperm antibodies (ASAs) and subsequent reproductive challenges. Regulatory T cells (Tregs) regulate inflammation and maintain sperm tolerance. In a murine model, we demonstrated that disrupting sperm immunotolerance induces chronic autoimmune responses characterized by antibody production targeting sperm and reproductive tissue autoantigens and unique tissue-specific immune cell signatures in the epididymis and testis. Such inflammatory features impair sperm function, contribute to epididymal damage, and drive sustained male subfertility. Tertiary lymphoid structures (TLSs) were formed within the epididymis after Treg depletion, defined by clusters of heterogenous B and T cells, fibroblasts, and endothelial cells. These ectopic structures perpetuate inflammation and lower the activation threshold for future immune threats. Similar isotypes of autoantibodies were detected in the seminal plasma of infertile patients, suggesting shared mechanistic pathways between mice and humans. Overall, we provide an in-depth understanding of the diverse B- and T-cell dynamics and TLS formation during epididymitis to develop precision-targeted therapies for infertility and chronic inflammation. Additionally, this immunological characterization of the epididymal microenvironment has the potential to identify novel targets for the development of male contraceptives.One Sentence SummaryUnderstanding the epididymal immune cell landscape dynamics aids in developing targeted therapies for infertility and contraception.
Lipid polymorphism of the marginal region of plant thylakoid membranes
Authors: Böde Kinga , Dlouhý Ondřej , Javornik Uroš , Domonkos Ildikó , Zsiros Ottó , Plavec Janez , Špunda Vladimír , Garab Győző 
Published: November 2024

AbstractThylakoid membranes (TMs) of vascular plants exhibit a highly organized architecture comprising two main distinct functional domains which accommodate virtually all components of the photosynthetic machinery responsible for the light reactions: the stacked, appressed granum membranes and the unstacked stroma lamellae. A domain with distinct structural, compositional, and functional characteristics, the marginal region of grana (grana margin, GM) has also been identified, which includes the highly curved region at the periphery of the granum vesicles that is enriched in CURT1 proteins. It is also well established that plant TMs, in addition to the bilayer (or lamellar, L) phase, contain at least two isotropic (I) lipid phases and an inverted hexagonal (HII) phase. The I phases were shown to participate in membrane fusion and to be associated with the activity of the photoprotective water-soluble enzyme, the violaxanthin de-epoxidase (VDE); the HIIphase, for its trypsin sensitivity, was proposed to emerge from stroma-exposed lipid-protein assemblies. Considering the location of CURT1 in GM and that it possesses trypsin-sensitivity, it was hypothesized to participate in the formation of the HIIphase. The aim of the present study was to test this hypothesis – via fingerprinting the lipid phase behavior of GM particles isolated from spinach leaves. Our31P-NMR spectroscopy reveals that the GM fraction of TMs does not contain HIIphase signal; it exhibits an isotropic signature. This non-bilayer, isotropic lipid structure, together with CURT1 proteins, thus appear to promote the formation of the highly curved region of TMs.
Seedling recruitment after fire: Disentangling the roles of microsite conditions and seed availability
Authors: Beck Jared J. , Wagenius Stuart 
Published: November 2024

ABSTRACTPeriodic fire enhances seedling recruitment for many plant species in historically fire-dependent ecosystems. Fire is expected to promote recruitment by generating environmental conditions that promote seedling emergence and survival. However, fire may also increase flowering and seed production. This makes it difficult to distinguish the effects of microsite conditions from seed availability in observational studies of seedling recruitment. Experiments that manipulate seed inputs across a representative range of conditions are needed to elucidate how seed availability versus microsite conditions influence post-fire seedling recruitment and plant demography. We experimentally manipulated time since fire across 36 patches of remnant tallgrass prairie distributed across 6400 ha in western Minnesota (USA). Over two years, we sowed 11,057Echinacea angustifolia(Asteraceae) seeds across 84 randomly placed transects and tracked 974 experimentally sown seedlings to evaluate how time since fire influenced seedling emergence and survival after experimentally controlling for variation in seed inputs. We also quantified six environmental variables and evaluated whether these covariates were associated with seedling emergence and survival. Fire influenced both seedling emergence and seedling survival. Seedlings emerged from approximately 1 percent of all seeds sown prior to experimental burns. Seeds sown one year after experimental burns emerged at 15 times the rate of seeds sown in the fall before burns, but emergence then declined as time since fire increased. Sowing seeds at high densities reduced rates of seedling emergence but increased overall recruitment. Increases in litter depth were associated with reduced emergence. Meanwhile, the probability that seedlings survived to late summer was greatest when they emerged 0-1 years after fire. The probability of seedling survival decreased with litter depth and increased with the local density of conspecific seedlings. Our findings experimentally support widespread predictions that fire enhances seedling recruitment by generating microsite conditions favorable for seedling emergence and survival – especially by increasing the light available to newly emerged seedlings. Nevertheless, recruitment also increased with seed inputs indicating that both seed availability and microsite conditions influence post-fire recruitment. Explicitly discriminating between seed-limitation and microsite-limitation is critical for understanding the demographic processes that influence plant population dynamics in historically fire-dependent ecosystems.