julilili42/papers huggingface dataset:
Functional connectivity of thalamic nuclei during sensorimotor task-based fMRI at 9.4 Tesla
2025-05-13

The thalamus is the brain’s central communication hub, playing a key role in processing and relaying sensorimotor and cognitive information between the cerebral cortex and other brain regions. It consists of specific and non-specific nuclei, each with a different role. Specific thalamic nuclei relay sensory and motor information to specific cortical and subcortical regions to ensure precise communication. In contrast, non-specific thalamic nuclei are involved in general functions such as attention or consciousness through broader and less targeted connections. In the present study, we aimed to investigate the functional connectivity patterns of the thalamic nuclei identified in our previous study as being involved in motor (finger-tapping) and sensory (finger-touch) tasks. The results of this study show that thalamic nuclei are not static hubs with a predefined role in neural signal processing, as they show different task-specific functional connectivity patterns in the anterior, middle, lateral, and posterior thalamic nuclei. Instead, they are all functional hubs that can flexibly change their connections to other brain regions in response to task demands. This work has important implications for understanding task-dependent functional connectivity between thalamic nuclei and different brain regions using task-based fMRI at 9.4 Tesla.
Using post-regularization distribution regression to measure the effects of a minimum wage on hourly wages, hours worked, and monthly earnings
2025-05-13

Summary We evaluate the distributional effects of a minimum wage introduction based on a dataset with a moderate sample size, but a large number of potential covariates. In this context, the selection of relevant control variables at each distributional threshold is crucial to test hypotheses about the impact of the continuous treatment variable. To this end, we use a post-double-selection logistic distribution regression approach, which allows for uniformly valid inference about the target coefficients of our low-dimensional treatment variables across the entire outcome distribution. Our empirical results show that the minimum wage replaced hourly wages below the minimum threshold, increased monthly earnings in the lower-middle segment, but not at the very bottom of the distribution, and did not significantly affect the distribution of working hours.
Kinesin-12 POK2 polarization is a prerequisite for a fully functional division site and aids cell plate positioning
2025-05-14

Division plane positioning in plants relies on the remarkably accurate selection of the cortical division zone (CDZ), earmarked by the preprophase band of microtubules. The PHRAGMOPLAST ORIENTING KINESIN 1 and 2 (POK1/2) play pivotal roles in CDZ maintenance in mitosis and guide the approaching phragmoplast during cytokinesis. Our knowledge regarding the mechanism of POK recruitment and subsequent maintenance is hitherto limited. Here, we report that POK2 arrives at the preprophase band utilizing a secondary microtubule-binding site within its carboxy-terminus. Effective tethering to the plasma membrane is achieved through non-specific electrostatic interactions with phospholipids. Reaching the cortex via premitotic cortical microtubules emerges as a prerequisite for POK2 polarization, as the order and the density of prophase microtubules become particularly relevant in the preprophase band-compromised mutant trm678. POK2 binding to cortical microtubules templates its future position at the cortex and appears critical for adequate division site setup and consequently tissue architecture.
Mental association of time and valence revealed with a novel chronometric approach: The positive-future effect
2025-05-14

Abstract Two recent studies utilized indirect response procedures (i.e., a sentence completion task and the Implicit Association Test) and suggest that people evaluate the future more positively than the past (Kaup et al., Frontiers in Psychology, 12, 612,720, 2021; Ulrich et al., Memory &amp; Cognition, 52, 444–458, 2024). This present article reports a novel chronometric approach and a self-report study examining whether this relationship can be observed consistently. In one part of the chronometric study, participants were instructed to respond verbally with the words “past” and “tomorrow” to negatively and positively connotated words. In the positive-future condition, participants responded with “tomorrow” to positive and “yesterday” to negative words; in the positive-past condition, they responded with “yesterday” to positive and “tomorrow” to negative words. In the other part, participants responded verbally with “good” and “bad” to time-related words. In the positive-future condition, they responded with “good” to future-related and “bad” to past-related words; in the positive-past condition, they responded with “good” to past-related and “bad” to future-related words. Response times were shorter in the positive-future than in the positive-past condition, suggesting that participants consistently evaluate the future more positively than the past (i.e., the positive-future effect). This strengthens the view that the positive-future effect is robust and general. Several possible mechanisms of why this effect emerges are discussed. The self-report study, in contrast, indicated no significant difference in individuals' perceptions of the past compared to the future. This may be attributed to a positivity bias in recalling past events, which may mask the differences in how people perceive the past versus the future.
The endocranial anatomy of protocetids and its implications for early whale evolution
2025-05-14

Abstract Extant whales, dolphins, and porpoises result from a major macroevolutionary lifestyle transition that transformed land-dwelling cetaceans into fully aquatic species. This involved significant changes in sensory systems. The increase in brain size relative to body size (encephalization quotient) is an outstanding feature of modern cetaceans, especially toothed whales. Conversely, olfactory capabilities are assumed to have diminished along this transition, with airborne olfaction becoming less relevant. The extent and timing of olfactory reduction remain obscure due to challenges in accessing well-preserved fossil endocranial anatomy. This study shows that early cetaceans had already evolved an increased encephalization quotient, and that their olfactory apparatus was likely not yet under selective pressure leading to its reduction. We demonstrate this through an analysis of the extinct whale, Protocetus atavus, a member of the middle Eocene semiaquatic cetacean group Protocetidae. We provide the first documentation of its endocranial anatomy using high-resolution computed tomography and compare it to other early cetaceans as well as extant mammals. We conclude that cetaceans increased their brain size earlier than previously thought, while relying on a well-developed olfactory system at a time when they were still partly terrestrial.
Exploration Into Lived Experiences of Multiple Sulfatase Deficiency–Affected Individuals and Their Families
2025-05-14

Despite their importance, rare diseases’ impact on patients and families is understudied. This is particularly true for ultrarare disorders, such as multiple sulfatase deficiency (MSD), a pediatric neurodegenerative disorder. To address this gap, we captured caregiver perspectives on how multiple sulfatase deficiency affects their child, themselves, and their families regarding adaptive behaviors and health-related quality of life. Overall, 19 multiple sulfatase deficiency caregivers participated in assessments capturing health outcomes related to daily functional abilities (Vineland Adaptive Behavior Scale–Third Edition [VABS-3]: n = 19), child health-related quality of life (Caregiver Priorities and Child Health Index of Life with Disabilities: n = 12; Pediatric Quality of Life Inventory–generic core scales: n = 13), and caregiver health-related quality of life (Pediatric Quality of Life Inventory–family impact module: n = 12; Traumatic Brain Injury Caregiver Quality of Life: n = 15). The Pediatric Quality of Life Inventory–family impact module results were compared to a data set from metachromatic leukodystrophy (n = 30), a rare disease with an overlapping sulfatase deficiency. The Vineland Adaptive Behavior Scale–Third Edition captured global impairment across domains in multiple sulfatase deficiency. Despite these functional limitations, the Caregiver Priorities and Child Health Index of Life with Disabilities and Pediatric Quality of Life Inventory–generic core scales captured relative preservation of health-related quality of life, especially related to emotional well-being. Compared with the Pediatric Quality of Life Inventory–generic core scales, the Caregiver Priorities and Child Health Index of Life with Disabilities captured a broader spectrum of health-related quality of life across all domains and caregivers’ top priorities in disease management and care coordination. The health-related quality of life of caregivers was severely impacted, with caregivers reporting profound feelings of grief and entrapment. Additionally, there was a similar caregiver burden between multiple sulfatase deficiency and metachromatic leukodystrophy. Our results will help inform psychosocial outcome measures for rare disease families and patient-centered endpoints in impending multiple sulfatase deficiency clinical trials.
Mechanisms of mistrust: A Bayesian account of misinformation learning
2025-05-14

From the intimate realm of personal interactions to the sprawling arena of political discourse, discerning the trustworthy from the dubious is crucial. Here, we present a novel behavioral task and accompanying Bayesian models that allow us to study key aspects of this learning process in a tightly controlled setting. In our task, participants are confronted with several different types of (mis-)information sources, ranging from ones that lie to ones with biased reporting, and have to learn these attributes under varying degrees of feedback. We formalize inference in this setting as a doubly Bayesian learning process where agents simultaneously learn about the ground truth as well as the qualities of an information source reporting on this ground truth. Our model and detailed analyses reveal how participants can generally follow Bayesian learning dynamics, highlighting a basic human ability to learn about diverse information sources. This learning is also reflected in explicit trust reports about the sources. We additionally show how participants approached the inference problem with priors that held sources to be helpful. Finally, when outside feedback was noisier, participants still learned along Bayesian lines but struggled to pick up on biases in information. Our work pins down computationally the generally impressive human ability to learn the trustworthiness of information sources while revealing minor fault lines when it comes to noisier environments and news sources with a slant.
Actionable heterogeneity of hepatocellular carcinoma therapy-induced senescence
2025-05-15

Abstract Therapy-induced senescence (TIS) is a stable cell cycle arrest in cancerous cells favoring immune control upon immune cell recruitment and activation via a senescence-associated secretory phenotype (SASP). Numerous studies have investigated the therapeutic applicability of TIS in hepatocellular carcinoma (HCC), a frequent cancer with high morbidity and mortality. Despite these efforts, a comprehensive understanding of how TIS may expose vulnerabilities specifically for immunotherapies, a potent means of cancer therapy, in HCC remains incomplete. Therefore, we conducted systematic studies to carefully characterize actionable and shared SASP- or other senescence-associated molecular parameters of TIS. We systematically compared the TIS inducers, etoposide and alisertib with a novel TIS inducer, CX5461, for their effects on SASP, surfaceome and innate immune clearance of representative human HCC cell lines. Surprisingly, all three compounds induced both metastasis surface antigens but also immunotherapeutically tractable antigens like CD95 (Fas), CD276 (B7-H3) and CD340 (Her2). This was verified in four representative HCC cell lines and publicly available datasets of HCC. Interestingly, alisertib, etoposide and CX5461 rendered senescent HCC vulnerable to be targeted by either T-cell-engaging bispecific antibodies or CAR NK cells. Collectively, our study indicates that heterogenous, but selective features of HCC senescence may be exploited by different immunotherapeutic approaches.
Development and validation of an AI algorithm to generate realistic and meaningful counterfactuals for retinal imaging based on diffusion models
2025-05-15

Counterfactual reasoning is often used by humans in clinical settings. For imaging based specialties such as ophthalmology, it would be beneficial to have an AI model that can create counterfactual images, illustrating answers to questions like “If the subject had had diabetic retinopathy, how would the fundus image have looked?”. Such an AI model could aid in training of clinicians or in patient education through visuals that answer counterfactual queries. We used large-scale retinal image datasets containing color fundus photography (CFP) and optical coherence tomography (OCT) images to train ordinary and adversarially robust classifiers that classify healthy and disease categories. In addition, we trained an unconditional diffusion model to generate diverse retinal images including ones with disease lesions. During sampling, we then combined the diffusion model with classifier guidance to achieve realistic and meaningful counterfactual images maintaining the subject’s retinal image structure. We found that our method generated counterfactuals by introducing or removing the necessary disease-related features. We conducted an expert study to validate that generated counterfactuals are realistic and clinically meaningful. Generated color fundus images were indistinguishable from real images and were shown to contain clinically meaningful lesions. Generated OCT images appeared realistic, but could be identified by experts with higher than chance probability. This shows that combining diffusion models with classifier guidance can achieve realistic and meaningful counterfactuals even for high-resolution medical images such as CFP images. Such images could be used for patient education or training of medical professionals.
Critical intelligence: Computing defensive behaviour
2025-05-15

Characterising the mechanisms underlying naturalistic defensive behavior remains a significant challenge. While substantial progress has been made in unravelling the neural basis of tightly constrained behaviors, a critical gap persists in our comprehension of the circuits that implement algorithms capable of generating the diverse defensive responses observed outside experimental restrictions. Recent advancements in neuroscience technology now allow for an unprecedented examination of naturalistic behaviour. To help provide a theoretical grounding for this nascent experimental programme, we summarise the main computational and statistical challenges of defensive decision making, encapsulated in the concept of critical intelligence. Next, drawing from an extensive literature in biology, machine learning, and decision theory, we explore a range of candidate solutions to these challenges. While the proposed solutions offer insights into potential adaptive strategies, they also present inherent trade-offs and limitations in their applicability across different biological contexts. Ultimately, we propose series of experiments designed to differentiate between these candidate solutions, providing a roadmap for future investigations into the fundamental defensive algorithms utilized by biological agents and their neural implementation. Thus, our work aims to provide a roadmap towards broader understanding of how complex defensive behaviors are orchestrated in the brain, with implications for both neuroscience research and the development of more sophisticated artificial intelligence systems.
Concepts for point-of-care ultrasound training in low resource settings: a scoping review
2025-05-15

Abstract Background Point-of-care ultrasound (POCUS) is a potent diagnostic tool especially in resource-limited settings. The implementation of POCUS diagnostics requires adequate training of POCUS operators. This scoping review aimed to identify and describe POCUS training concepts that have been applied in low-and middle-income countries (LMICs). Methods and findings All studies on diagnostic POCUS training in LMICs that could be found in the Cochrane, Embase, Google Scholar, and Medline databases up to July 6, 2023, were included and data was extracted for descriptive analysis. The review protocol was registered at OSF https://doi.org/10.17605/OSF.IO/8FQJW . A total of 53 publications were included with 59% of studies (n = 31) conducted in Africa and 23% (n = 12) in Asia. The majority of studies (n = 41, 81%) described short courses amongst which 40% were one-off sessions and 60% described longitudinal trainings. Curricula were mostly related to emergency medicine and obstetrics and organ-focused protocols (lung n = 29 (54%), cardiac n = 28 (53%), obstetric n = 23 (43%)). Trainees were largely medical doctors and clinical officers with minimal or absent ultrasound skills. Training challenges included resource constraints and lack of context adaptation. Best practice recommendations included focus on hands-on training, low trainer to trainee ratio, protected training time, online training options, use of local trainers, short and concise training manuals in print, continuous supervision and early and on-going evaluation, as well as tele-mentoring. Conclusions Context integration and focus on local needs, trainer availability and suitability, durable equipment and maintenance, as well as emphasis on hands on training including patients with relevant pathology, were key aspects for targeted and sustainable POCUS training in LMICs identified in this review.
Prognostic Value of a Multivariate Gut Microbiome Model for Progression from Normal Cognition to Mild Cognitive Impairment Within 4 Years
2025-05-15

Little is known about the dysbiosis of the gut microbiome in patients with mild cognitive impairment (MCI) potentially at risk for the development of Alzheimer’s disease (AD). So far, only cross-sectional differences and not longitudinal changes and their prognostic significance have been in the scope of research in MCI. Therefore, we investigated the ability of longitudinal taxonomic and functional gut microbiome data from 100 healthy controls (HC) to predict the progression from normal cognition to MCI over a 4-year follow-up period (4yFU). Logistic regression models were built with baseline features that best discriminated between the two groups using an ANOVA-type statistical analysis. The best model for the discrimination of MCI converters was based on functional data using Gene Ontology (GO), which included 14 features. This model achieved an area under the receiver operating characteristic curve (AUROC) of 0.84 at baseline, 0.78 at the 1-year follow-up (1yFU), and 0.75 at 4yFU. This functional model outperformed the taxonomic model, which included 38 genera features, in terms of descriptive performance and showed comparable efficacy to combined analyses integrating functional, taxonomic, and clinical characteristics. Thus, gut microbiome algorithms have the potential to predict MCI conversion in HCs over a 4-year period, offering a promising innovative supplement for early AD identification.
Evaluating the role of adjuvant therapy in improving outcomes for patients with lymph node-positive penile cancer following surgical management
2025-05-15

Penile squamous cell carcinoma (PeCa) is a rare malignancy with poor outcomes in pN+ cases. Prognosis is particularly poor in patients with extranodal extension (ENE) or pelvic lymph node (PLN) involvement. Despite advancements in surgical techniques, the role of adjuvant therapy (AT)-including radiotherapy (ART), chemotherapy (ACT), and chemoradiotherapy (ACRT)-following radical lymphadenectomy (LAD) remains undefined, and optimal strategies are yet to be established. This review evaluates the impact of AT on survival and recurrence in pN+ PeCa, assesses associated toxicities, and explores personalized treatment approaches. A systematic search of PubMed, Web of Science, Cochrane Library, and Scopus identified studies published between January 2000 and December 2024. Eligible studies focused on AT after LAD, including radiotherapy, chemotherapy, targeted therapies, or combination regimens. ART improves locoregional control in patients with ≥ 2 positive inguinal lymph nodes, particularly in HPV+ tumors. ACT with TIP or TPF regimens enhances disease-free and overall survival in high-risk pN+ patients, including those with PLN involvement. ACRT provides modest benefits in ENE cases but is associated with significant toxicity. Emerging biomarkers, such as HPV status and p53 mutations, show potential for predicting treatment response, while novel agents and immunotherapies represent promising investigational areas. AT improves outcomes in pN+ PeCa but requires individualized strategies based on risk factors and molecular profiles. Prospective, collaborative studies are essential to refine AT protocols, reduce toxicities, and integrate immunotherapies, targeted agents, and biomarkers into treatment algorithms. Multidisciplinary management and centralized care are critical for optimizing outcomes in this malignancy.
Soil microbial genomic responses to aridity-driven elemental imbalance across global biomes
2025-05-15

<title>Abstract</title> Aridification is known to disrupt soil biogeochemical cycles by altering the stoichiometry of key elements, such as carbon (C), nitrogen (N) and phosphorus (P). However, how soil microbiome metabolically responds to these imbalances, and the resulting implications for terrestrial ecosystem services, remain virtually unknown. By analyzing soil samples from 200 ecosystems across globally distributed biomes, our results revealed an overall microbial genomic adjustment to elemental imbalances driven by aridity. Genes involved in microbial anabolism were promoted with aridification, whereas those associated with catabolism were suppressed. Thus, while genes encoding extracellular enzymes responsible for the degradation of litter and organic matter decreased, genes related to RNA transcription and the synthesis and transport of intracellular proteins essential for microbial resistance and growth increased. Collectively, our findings highlighted that aridity-driven soil elemental imbalances are strongly associated with shifts in soil microbial metabolism from catabolism to anabolism, reflecting a microbial survival strategy that prioritizes growth over energy and nutrient acquisition under global-scale aridification.