julilili42/papers huggingface dataset:
Brain-wide representations of prior information in mouse decision-making
2025-09-03

Abstract The neural representations of prior information about the state of the world are poorly understood 1 . Here, to investigate them, we examined brain-wide Neuropixels recordings and widefield calcium imaging collected by the International Brain Laboratory. Mice were trained to indicate the location of a visual grating stimulus, which appeared on the left or right with a prior probability alternating between 0.2 and 0.8 in blocks of variable length. We found that mice estimate this prior probability and thereby improve their decision accuracy. Furthermore, we report that this subjective prior is encoded in at least 20% to 30% of brain regions that, notably, span all levels of processing, from early sensory areas (the lateral geniculate nucleus and primary visual cortex) to motor regions (secondary and primary motor cortex and gigantocellular reticular nucleus) and high-level cortical regions (the dorsal anterior cingulate area and ventrolateral orbitofrontal cortex). This widespread representation of the prior is consistent with a neural model of Bayesian inference involving loops between areas, as opposed to a model in which the prior is incorporated only in decision-making areas. This study offers a brain-wide perspective on prior encoding at cellular resolution, underscoring the importance of using large-scale recordings on a single standardized task.
Added Diagnostic Value of Intravascular Ultrasound over Venography in “High Risk for Dialysis Circuit Vascular Access Failure” ESRD Patients
2025-09-03

In no-option ESRD patients, IVUS revealed changes in stenosis severity in half of the cases compared to standard two-dimensional venography, resulting in permanent dialysis circuit vascular access creation in more than half of the assessed patients, with 63% of these patients reaching vascular access maturation. Routine incorporation of IVUS into salvage central venous mapping may expand durable vascular access options and reduce dialysis catheter dependency.
The Lowest Excited State of Heptacenes Is Dark
2025-09-03

Understanding the electronic structure of polycyclic aromatic compounds is of fundamental importance for their potential applications. The optoelectronic properties of shorter acenes such as tetracene and pentacene have been extensively studied with regard to excitation, emission, and nonlinear effects such as singlet fission. The longer homologues present a unique challenge due to their low stability both in the solid state and in solution. In this work, we synthesized persistent 6,8,15,17-tetrakis((triisopropylsilyl)ethynyl)heptacene and investigated its photophysical properties as well as those of the parent heptacene. Our steady-state electronic absorption and emission experiments combined with transient absorption spectroscopy show that the Franck-Condon electric-dipole-forbidden ("dark") transition to the 2<sup>1</sup>A<sub>g</sub> singlet state is the lowest-energy excited state of heptacene. This contrasts with the optical properties of the well-known shorter acenes. Transient absorption data further suggest singlet fission or intersystem crossing as potential pathways to rapid population of the triplet state facilitated by the dark singlet state.
Towards a FHIR Specification for Research in Ophthalmology: Designing the EyeMatics Core Data Set for Multi-Centric Data Integration
2025-09-03

Introduction: EyeMatics (Eye disease “treated” with interoperable medical informatics) is a clinical use case in Germany’s Medical Informatics Initiative (MII). The objective of EyeMatics is to improve the understanding of the treatment effects of intravitreal injections, the most frequent procedure to treat retinal diseases. To achieve this, as part of the efforts, medical data of multiple hospital sites must be integrated into a local FHIR repositories using a common set of FHIR profiles. Methods: A panel of medical and technical experts was formed to create a project-specific core data set. The core data set is compiled from different preliminary work like previously existing data models, the data donation of a synthetic patient encounter scenario, screenshots of UI forms used at the local sites and relevant MII profiles. Results: Complex profiling and custom code systems were required to represent central ophthalmic concepts such as visual acuity using FHIR. A common pattern for representing eye laterality in FHIR Observation resources was established. The resulting profiles are available in a public GitHub repository. Conclusion: While our FHIR profiles will be sufficient for EyeMatics, our experience shows that the clinical complexity of basic ophthalmological observations requires some deviations from standard FHIR modelling patterns and would be limited by gaps in terminology if deployed elsewhere. Our experience indicates that project-specific FHIR profile development is possible within a short time frame but may harbor risks of contributing to a growing number of fragmented implementations unless closely coordinated or based on common data models. To counteract this, future ophthalmic MII extension modules should attempt to integrate both profiles described here and international standard data models for ophthalmology.
Influence of Sex and Diagnosis on Clinical Variables and Neurocognitive Performance in Severe Mental Illness. Results From the PsyCourse Study
2025-09-03

ABSTRACT Introduction Bipolar disorder (BD) and schizophrenia (SZ) are serious mental illnesses (SMI) with overlapping symptoms but distinct differences in onset and course. Sex differences are an area of growing interest in SMI. This study aims to examine potential interactions between sex and diagnosis across a broad range of variables, to compare males and females within SZ and BD, and to investigate sex‐specific group differences. Methods A total of 1516 individuals were included in a cross‐sectional study using baseline data from the multicenter PsyCourse Study, including BD ( n = 543), SZ ( n = 517), and healthy controls (HC) ( n = 456). Sociodemographic characteristics, clinical symptoms, psychosocial functioning, quality of life, neurocognitive performance, and somatic comorbidities were assessed. Generalized linear models were used to analyze differences between groups and sexes. False Discovery Rate (FDR) and Bonferroni post hoc comparisons were performed. Results Significant interactions were identified in age ( p = 0.001), age at treatment ( p = 0.05), illness duration ( p = 0.03), illicit drug use ( p = 0.01), and smoking ( p = 0.05). Differences in substance use were observed across groups and sexes, with the highest rates found in males with SZ. The BD group showed better functioning and neurocognitive performance compared with the SZ group. Within the BD group, females reported better performance in verbal memory ( p = 0.003) and psychomotor speed ( p &lt; 0.001) than males. Moreover, both females and males with SMI showed higher rates of thyroid alterations compared with HC ( p = 0.01 for females and p = 0.002 for males). Conclusions Significant sex differences were observed in substance use and somatic comorbidities. Interactions between diagnosis and sex underscore the importance of considering both factors in clinical assessments. These findings highlight the need to tailor sex‐specific treatment for each patient. Further research is needed to explore the role of sex hormones and other biological and societal factors in the presentation and course of these disorders.
Predicting rainfall kinetic energy under forest canopies—A pilot study using ULS
2025-09-03

Abstract Rainfall erosivity, expressed in kinetic energy, is determined by intensity, velocity and drop size distribution. In natural precipitation, these properties vary and can be substantially altered by the vegetation before reaching the ground. The splash effect of impacting raindrops on the soil surface can initiate soil erosion. While research in this regard has focussed on relating plant characteristics to erosion processes, there is a lack of studies that attempt to reverse this by predicting throughfall kinetic energy from plant properties. This has been attempted by the Vegetation Splash Factor (VSF), a model solely based on the three‐dimensional distribution of vegetation surfaces derived from forest lidar forest data. We conducted a pilot study using the VSF model to validate it with in situ measurements and confirm its general suitability. We found a significant correlation between the observed and predicted effect of vegetation on the kinetic energy of rainfall, which demonstrates the suitability of the VSF, despite being solely based on structural traits. The observed effect of vegetation on rainfall kinetic energy exceeded literature reports, leading to systematic underestimation by the model. Our results showed that the VSF can be used to spatially continuously predict the effect of vegetation on the erosivity of rainfall from high‐resolution lidar data. These findings open new possibilities for research on splash erosion under vegetation, shifting the perspective from point‐based studies towards area‐wide approaches. The simplicity of the approach facilitates adaptation for wider use. The first application of the VSF in a field study has proved that the concept is functional and can illustrate zones of increased potential for soil loss under full vegetation cover. This adds to the methodological tool box for erosion studies and can support decision‐makers in forestry and agriculture in the future.
Funerary practices of cremation at the megalithic societies of South-Eastern Iberia: The cemetery of Los Milanes
2025-09-03

The archaeological excavations undertaken at the Chalcolithic necropolis of Los Milanes have revealed a previously unknown variability in funerary practices in the south-eastern Iberia. For the first time, a megalithic tomb housed a large funerary deposit (28,740 bone fragments) of exclusively cremated human bone remains. For a comprehensive characterization of the funerary ritual, a cutting-edge multi-proxy approach has been undertaken including the osteological study of cremated bone remains, radiocarbon chronology, Fourier-Transform Infrared spectroscopy in Attenuated Total Reflectance mode (FTIR-ATR), and carbon, oxygen and strontium isotope analyses. As a result, the cremation ritual consisted of multi-depositional events of at least 21 individuals chronologically concentrated in the first quarter of the third millennium, principally in the 28th century cal BC. The absence of charcoal/ashes in the funerary chamber and the underrepresentation of anatomical regions such as lower limb and trunk suggest that the cremation took place elsewhere and the bone remains were carefully collected and placed as secondary burial depositions. Different proxies including colour patterns, heat‐induced fractures, the presence of cyanamide in calcined bones would also suggest the cremation of principally complete corpses, burnt soon after death. The ritual of cremation coexisted with inhumations during the third millennium cal BC, suggesting a variability in the body manipulation that previously went unnoticed. Unlike inhumations, through cremation, bodies would have been reduced until being indistinguishable, transforming radically the nature of human beings and their ontological status.
Synergy between Enterobacteriaceae and dietary components shapes the competition between the dominant anaerobes of the human gut
2025-09-03

Abstract The human gut microbiota is frequently dominated by the Bacteroidota phylum, with Bacteroidaceae and Prevotellaceae families prevailing in modern and traditional lifestyles, respectively. While these distinct profiles have been well-documented across cohorts, the underlying mechanisms remain poorly understood. Here, we combine defined gut community models and genetic tools to experimentally dissect the ecological principles that favor Prevotellaceae or Bacteroidaceae. Testing 94 dietary components in the community model shows these two families compete for overlapping nutritional niches. Notably, Segatella copri , a key Prevotellaceae representative, outcompetes Bacteroidaceae strains when preferred polysaccharides are available. Interestingly, this competitive advantage depends on the presence of Enterobacteriaceae, which synergize with dietary components to promote Segatella dominance. Accordingly, we observe that global Segatella -rich non-Westernized microbiomes correlate with higher Enterobacteriaceae content. Our results suggest a revised hypothesis in which the ecosystem-level dynamic interplay between dietary components and key commensals within the community contributes to distinct Bacteroidota family dominance.
Third-party imitation is not restricted to humans
2025-09-04

Abstract Imitation of cultural practices is ubiquitous in humans and often involves faithful copying of intransitive (i.e., non-object directed) gestures and societal norms which play a crucial role in human cumulative cultural evolution. Apart from learning these directly from a tutor, humans often learn passively as third-party observers from the interactions of two or more individuals. Whether third-party imitation has evolved outside humans remains unknown. In the current study, we investigated whether undomesticated blue-throated macaws ( Ara glaucogularis ) could imitate in a third-party setting. A naïve test group ( N = 6) passively observed a conspecific demonstrator performing rare intransitive actions in response to specific human gestural commands. Directly afterwards, the observer received the same gestural commands and performance-contingent rewards. An equally naïve control group ( N = 5) was tested correspondingly, in the absence of third-party demonstrations. The test group learned more target actions (mean = 4.16 versus mean = 2.2) in response to the specific commands, significantly faster and performed them more accurately than the control group. The test group also spontaneously imitated some of the actions even before they received any gestural commands or rewards. Our findings show that third-party imitation, even for intransitive actions, exists outside humans, allowing for rapid adaption to group specific behaviours and possibly cultural conventions in parrots.
Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers
2025-09-04

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.
Gene co-occurrence and its association with phage infectivity in bacterial pangenomes
2025-09-04

Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome sequences. Understanding the complex interactions between phages and their bacterial hosts is thus of considerable interest. We recently developed Goldfinder, a phylogenetic method to discover gene co-occurrences across bacterial pangenomes. Here, we expand Goldfinder to infer which gene presences or absences influence bacterial sensitivity to phages. By integrating a bacterial pangenome with an experimentally determined host range matrix, we infer associations between phage infectivity and the presence of accessory genes in bacterial pangenomes. The presented approach can be applied to predict bacterial genes that potentially enable phage infection, bacterial genes that prevent phage infection, and potential interactions between particular bacterial and phage accessory genes. Finally, the predicted interactions are clustered and visualized with the software Cytoscape. Here, we present a method to identify candidate genes within the pool of mobile accessory genes that may contribute to phage–host interactions. This approach will help to set up follow-up experiments and to understand the complex interactions between phages and bacteria. This article is part of the discussion meeting issue ‘The ecology and evolution of bacterial immune systems’.
Cerebrovascular Reactivity at Rest and Its Association With Cognitive Function in People With Genetic Frontotemporal Dementia
2025-09-04

CVR impairment in genetic FTD has a predilection for the middle frontal and posterior cortex, and its preservation may yield a cognitive benefit for at-risk individuals. Although findings do not provide causality and warrant replication, they support the notion that vascular dysfunction in familial FTD may be a target for biomarker identification and disease-modifying efforts.
SIN-1 Improves Cerebral Blood Flow and Reduces Deviation From Brain Homeostasis During Ischemia and Reperfusion in Rats
2025-09-04

BACKGROUND: Overall, 75% of patients with acute stroke have elevated mean arterial pressure (MAP). In randomized stroke trials, the indirect NO donor glyceryl trinitrate lowered MAP but improved neither regional cerebral blood flow (rCBF) nor functional outcomes. One probable reason is that the microcirculation cannot bioactivate glyceryl trinitrate. In contrast, the direct NO donor 3-morpholinosydnonimine (SIN-1), not requiring bioactivation, should also release NO in small vessels, where it supports eNOS (endothelial NO synthase)–derived NO in maintaining rCBF in the hypotensive portion of Lassen autoregulatory curve. In a meta-analysis, SIN-1 reduced infarct volume in ischemia models, but the effects of SIN-1 on early pathophysiology are unknown. METHODS: Here, we investigated SIN-1 during a 60-minute bilateral common carotid artery occlusion and reperfusion in forty-eight 12- to 14-week-old Wistar-Kyoto rat (WKY) controls and 48 stroke-prone spontaneously hypertensive rats. We calculated the difference between the median values of each variable in the last 5 minutes of bilateral common carotid artery occlusion and baseline and compared them between treatment (SIN-1/control) and strain (stroke-prone spontaneously hypertensive rat/WKY) using 2-way ANOVA. We proceeded in the same way regarding reperfusion. RESULTS: Strain×intervention interaction was only found for MAP during bilateral common carotid artery occlusion. SIN-1 lowered MAP within stroke-prone spontaneously hypertensive rats ( P &lt;0.001) and within WKY ( P &lt;0.001), whereas MAP increased only in untreated stroke-prone spontaneously hypertensive rats versus untreated WKY ( P =0.038). Across stroke-prone spontaneously hypertensive rat and WKY, SIN-1 increased rCBF ( P &lt;0.001), increased spontaneous brain activity ( P =0.002), lowered extracellular potassium concentration ( P =0.009) and area under the curve of potassium ( P =0.025), and reduced the direct current–amplitude ( P =0.028) and cumulative direct current–shift duration ( P =0.001), consistent with milder ischemia and less severe spreading depolarization load in SIN-1–treated animals. During reperfusion, SIN-1 lowered MAP ( P &lt;0.001), decreased the no-reflow area ( P =0.002), increased rCBF ( P &lt;0.001), increased spontaneous brain activity ( P &lt;0.001), and decreased extracellular potassium ( P =0.008) and direct current potential ( P =0.022) in both strains, consistent with less no-reflow and better recovery in SIN-1–treated animals. CONCLUSIONS: SIN-1 emerges as a promising antihypertensive in acute stroke as it paradoxically increases rCBF in ischemic tissue and reduces no-reflow.
Tailoring Adsorption Properties of Graphitic Surfaces: Toward Improved Anode Materials for Li‐ and Post‐Li Ion Batteries
2025-09-04

The adsorption of alkali metal (AM) atoms on graphitic surfaces is one of the processes that determine the performance of carbon‐based anode materials. In particular, when graphite derivatives such as hard carbon with increased surface area are considered, adsorption accounts for a significant amount of the AM storage capacity. While it is well known that the adsorption of Li and Na on pristine graphite is energetically unfavorable, this article shows how graphitic surfaces can be modified to tailor their adsorption properties. For this purpose, the adsorption of Li, Na, and K on graphitic model systems, containing defects and impurities as well as combinations thereof, is investigated by means of density functional theory. The results show that particular defects and impurity atoms can modify the adsorption strength of the surface such that Li and Na adsorption become energetically favorable, while at the same time, capacity loss via trapping of AM atoms is minimized.
Personalized real-time inference of momentary excitability from human EEG
2025-09-04

Abstract The efficacy of transcranial magnetic stimulation (TMS) is often limited by non-adaptive protocols that disregard instantaneous brain states, potentially constraining therapeutic outcomes. Current EEG-guided approaches are hindered by their reliance on motor-evoked potentials (MEPs), which confound cortical and spinal excitability and restrict applications to the motor cortex, and a dependence on static biomarkers that cannot adapt to changing neurophysiological patterns. We introduce PRIME (Personalized Real-time Inference of Momentary Excitability), a deep learning framework that predicts cortical excitability, quantified by TMS-evoked potential (TEP) amplitude, from raw EEG signals. By targeting cortical excitability directly, PRIME enables brain state-dependent stimulation across any cortical region. PRIME incorporates transfer learning and continual adaptation to automatically identify personalized biomarkers, allowing stimulation timing to be adapted across individuals and sessions. PRIME successfully predicts cortical excitability with minimal latency, providing a computational foundation for next-generation, personalized closed-loop TMS interventions.