julilili42/papers huggingface dataset:
Expressing experiences: Sensorimotor activations and interoceptive sensibility influence which words we choose when speaking
2025-09-08

During language production we translate thoughts into articulated speech. While we know much about how different aspects of our thoughts are co-activated during lexical-semantic processing, the range of meaning dimensions that influence which words we choose to express our thoughts and experiences remains largely unknown. Here, we investigated whether (re)activations of bodily experiences have an impact on language production. Participants performed up- and downward head movements while listening to sentence fragments describing situations (e.g. 'You are at the beach and you see...'). When reaching the upward/downward head position they completed the sentence with a freely chosen noun. We found that the activation of experiential traces of space via head movement/position influenced participant's lexical choices. The referents of the produced words were classified by a different group of participants to be located higher up in space after upward movements compared to downward movements. Furthermore, higher levels of interoceptive sensibility as measured using the attention regulation scale from the Multidimensional Assessment of Interoceptive Awareness questionnaire (Mehling, Acree, Stewart, Silas, & Jones, 2018) le d to an increased reflection of the sensory and bodily experience in the spatial properties of the produced nouns. We conclude that sensorimotor activations are among the meaning facets that guide which words we chose when speaking. In addition, the tendency to verbally express embodied meaning is enhanced with higher levels of interoceptive sensibility, suggesting that interoception may be a key to understand interindividual differences in how we express our experiences and feelings when we speak or write.
MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads
2025-09-08

Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open source software platform for the real-time analysis and visualization of metagenomic Oxford Nanopore Technologies (ONT) sequencing data. MMonitor includes two components: a desktop application for running bioinformatics pipelines through a graphical user interface (GUI) or command-line interface (CLI), and a web-based dashboard for interactive result inspection. The dashboard provides taxonomic composition over time, quality scores, diversity indices, and taxonomy-metadata correlations. Integrated pipelines enable automated de-novo assembly and reconstruction of metagenome-assembled genomes (MAGs). To validate MMonitor, we tracked human gut microbial populations in three bioreactors using 16S rRNA gene sequencing, and applied it to whole-genome sequencing (WGS) data to generate high-quality annotated MAGs and reveal functional insights. We also compare MMonitor to other software for real-time metagenomic analysis, highlighting the strengths and limitations of each tool for this use case. By performing automated time-series analyzes, sample management, and updating of reference databases, MMonitor addresses current limitations and supports dynamic microbiome research in various fields.
Nested Melanoma and Superficial Spreading Melanoma with Prominent Nests—A Retrospective Study on Clinical Characteristics and PRAME Expression
2025-09-08

Background: Nested melanoma is a rare subtype of superficial spreading melanoma. Due to its typical histology, characterized by the predominance of large melanocytic nests in an extensive horizontal spread, it is challenging to distinguish it from other benign nested melanocytic lesions. There is a need to identify additional histopathological parameters that can support the diagnosis of nested melanoma. Methods: In this retrospective case-control study, we analyzed immunohistochemical staining for PRAME in 10 cases of superficial spreading melanoma with prominent nests and 26 nested melanomas. Dysplastic melanocytic nevi were used as the control group. Results: We found a diffuse PRAME positivity (&gt;75% of melanocytes) in 60% of superficial spreading melanoma with prominent nests and 19% of nested melanoma cases, whereas the control group showed no diffuse PRAME positivity. Furthermore, using Melan A immunohistochemistry, we found an absence of pagetoid spread in 31% of nested melanoma and single cells in suprabasal epidermal layers in 69% of cases. All cases with no pagetoid spread were PRAME negative, whereas 28% of cases with a mild pagetoid spread demonstrated diffuse PRAME positivity. Conclusions: We found lower PRAME positivity in nested melanoma compared to superficial spreading melanoma with prominent nests. Particularly in cases without pagetoid intraepidermal spread of melanocytes, negative PRAME staining does not rule out the possibility of nested melanoma. The diagnosis should be made based on typical histomorphological and clinical criteria.
Flexible use of multimodal communicative strategies in adult chimpanzees
2025-09-09

Abstract Human communication is remarkable for its flexibility, a trait largely reflected in its multimodal nature and shared to some extent with nonhuman primates. Although individual differences in social behaviour are known to have evolutionary implications, their role in shaping primate communication remains largely unexplored. This study adopts a multimodal framework to partition variation in chimpanzees’ use of multicomponent and multisensory communicative strategies into socio-environmental, between-individual, and within-individual sources. Results showed that research setting and signaller’s sex affected communicative expression. Importantly, we also detected consistent between-individual differences in both strategies, independent of age, sex, or setting. While only multicomponent signal use was predicted by behavioural context at the population level, individuals varied in how they adjusted to context only in their use of multisensory acts. These findings reveal substantial flexibility in chimpanzee communication, highlighting individual-specific patterns and supporting a gradual evolutionary pathway toward the complexity of human multimodal communication.
Nigral stimulation for freezing of gait: kinematic gait parameters inform optimization of stimulation frequency
2025-09-09

Abstract Innovative technology allows for personalization of stimulation frequency in dual-site deep brain stimulation (DBS), offering promise for challenging symptoms in advanced Parkinson’s disease (PD), particularly freezing of gait (FoG). Early results suggest that combining standard subthalamic nucleus (STN) stimulation with substantia nigra pars reticulata (SNr) stimulation may improve FoG outcomes. However, patient response and the optimal SNr stimulation frequency vary. Our randomized controlled trial studied patients with advanced PD and persistent FoG, while recording gait kinematics through wearable inertial sensors, along with clinical assessments and patient-reported outcomes. In a with-subjects design, we compared a no-stimulation control with four stimulation conditions: Mono-site STN stimulation at 119 Hz and three dual-site protocols (STN + SNr) with SNr stimulation at 119 Hz, 71 Hz, or 30 Hz, keeping total electrical energy delivered (TEED) constant between SNr conditions. Significant interindividual variability was observed for the optimal stimulation protocol, with comparable proportions favoring STN, STN + SNr119, and STN + SNr71. Changes in spatial and temporal gait parameters, such as stride length and swing time, correlated significantly with FoG clinical improvements, with high correlation coefficients (&gt; 0.8). Optimized stimulation parameters also led to improvements in patient-reported outcomes, highlighting the potential of digital biomarkers in tailoring DBS protocols for individualized outcomes.
A Systematic Literature Review of Reproductive Toxicological Studies on Phthalates
2025-09-09

Phthalates are widely used plasticizers recognized as endocrine-disrupting chemicals (EDCs) with well-documented adverse effects on reproductive health. These compounds act either directly or through their metabolites and can influence various biochemical pathways. Key phthalates that have been associated with potential toxic outcomes include di(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), butyl benzyl phthalate (BBP), diisononyl phthalate (DiNP), and diisodecyl phthalate (DiDP). The presence of these compounds in everyday consumer products has been associated with various adverse effects on human reproductive health, including hormonal disruption, issues in gonadal function, and other hormone related problems. This systematic review provides an overview and critical synthesis of the most recent research regarding phthalate reproductive toxicity. The scope is to summarize and aggregate correlations between phthalate exposure and reproductive health outcomes and highlight factors, such as age, sex, and extent of exposure, that have the most significant impacts on clinical outcomes. The reported studies focus on the gender-specific outcomes of various phthalates, while the epidemiological data reveal the importance of exposure duration and age. The reported results highlight the need for strict regulations regarding phthalate usage and the importance of developing safer alternatives.
Tribenzoylarsine – A Benign Arsenic Precursor for InAs Nanocrystals
2025-09-10

Abstract III‐V semiconductor nanocrystals (NCs) have emerged as a benign alternative to II‐VI and IV‐VI NCs, which are restricted due to the toxicity of the comprising elements. While InP NCs advanced significantly, the development of infrared‐emitting InAs NCs has been relatively slow‐paced. This is due to the synthetic challenges arising from the highly covalent bonding in InAs and the limited range of available arsenic sources. Most importantly, current syntheses rely on hazardous pyrophoric and costly reagents, which hampers their wider adoption. In this work, the synthesis of tribenzoylarsine is reported, which can be used as a novel nonvolatile, nonpyrophoric, and hence safer precursor for metal arsenide nanoparticles. Tribenzoylarsine reacts with indium oleate without additional reducing agents yielding small (≈2 nm) InAs NCs. By tuning synthesis parameters (e.g., the addition of zinc oleate or using continuous injection) it is possible to cover the photoluminescence range of 630–780 nm with full width at half maximum as low as 170–210 meV, which is a very competitive value to the existing synthetic approaches. Along with the significantly safer nature of tribenzoylarsine and the great potential for synthesis optimization, this makes it a very promising alternative to the currently used arsenic precursors.
KIF13B controls ciliary protein content by promoting endocytic retrieval and suppressing release of large extracellular vesicles from cilia
2025-09-10

Dynamic control of ciliary membrane protein content is crucial for the organelle's homeostasis and signaling function and involves removal of ciliary components by intraflagellar transport (IFT) and BBSome-mediated export, endocytic retrieval, and/or extracellular vesicle (EV) shedding. We report that the kinesin-3 motor KIF13B regulates ciliary protein composition and EV shedding in cultured kidney epithelial cells, with effects that vary over time. In early stages of ciliation, Kif13b<sup>-/-</sup> cells aberrantly accumulate polycystin-2 (PC2) within cilia and release large EVs enriched with CCDC198 and the centriole distal appendage protein CCDC92, which also localizes to the ciliary tip. These cells also produce fewer small EVs through the neutral sphingomyelinase 2 pathway. Upon cilia maturation, Kif13b<sup>-/-</sup> cells accelerate large EV release of numerous ciliary proteins, including PC2, BBSome, and IFT components, which correlates with gradual depletion of CCDC92 and PC2 from the ciliary tip and shaft, respectively. Furthermore, over time, Kif13b<sup>-/-</sup> cells show an upregulation in the release of small EVs, which differ in composition from wild-type small EVs. Specifically, mutant small EVs lack several proteins that are enriched in small EVs from BBSome-deficient cells, including palmitoyl transferase ZDHHC5, which localizes to cilia where it accumulates upon BBSome dysfunction and regulates ciliary length and PC2 levels. Our results suggest that KIF13B acts at the level of centriole distal appendages to limit ciliary protein entry and promote endocytic retrieval downstream of the BBSome, thereby suppressing EV release from cilia. Furthermore, the ciliary localization of CCDC198 and ZDHHC5 indicates they are potential novel ciliopathy candidates.
A neuronal correlate for time interval estimation in the crow’s telencephalon
2025-09-10

Abstract Interval timing, the ability to perceive and estimate durations between events, is essential for many animal behaviors. In mammals, it is linked to specific cortical and sub-cortical brain regions, but its neural basis in birds remains unclear. We trained two male carrion crows on a time estimation task using visual stimuli, cueing them to wait for a minimum duration of 1500 ms, 3000 ms, or 6000 ms before responding to receive a reward. During the task, we recorded activity from single neurons in the nidopallium caudolaterale (NCL), the avian executive telencephalon. Many neurons showed tuning to specific durations, suggesting that time intervals are encoded as abstract magnitudes along an ordered scale. Population-level decoding revealed that NCL activity predicted the crows’ intended wait time, independent of the sensory properties of the cues. These findings show that abstract time estimation can emerge from neural architectures different from the mammalian neocortex.
Metacognitive antecedents to states of mental ill-health: Drops in confidence precede symptoms of OCD
2025-09-10

<title>Abstract</title> Mental health symptoms, like those in obsessive-compulsive disorder (OCD), show pronounced fluctuations over time. However, little is known about the underlying factors driving these fluctuations. Whilst theoretical accounts propose that cognitive processes drive symptom variability, cross-sectional work is unable to effectively probe these mechanisms. Based on prevailing notions of doubt and underconfidence being cognitive hallmarks of OCD, we investigated whether metacognitive processes correspond to OCD symptoms. We employed a novel smartphone-based momentary assessment design wherein participants with OCD (N = 137) logged instances of experiencing OCD symptoms across 2-weeks. Participants also completed daily scheduled assessments, and played a perceptual metacognitive task every two days. Our results showcase the validity of our novel approach and, importantly, reveal that metacognition drives OCD symptoms. Concretely, we found directional effects whereby reductions in both self-confidence and task-based metacognition preceded occurrences of OCD symptom logs, but not vice versa. Thus, our novel micro-longitudinal study design provides compelling evidence for cognitive distortions (both self-reported and task-based) preceding symptom escalations, signifying the potential for designing novel, just-in-time interventions.
High Adherence to Adjuvant Endocrine Therapy Improves Outcome in Early Breast Cancer – Results from a Large Real-World Claims Data Analysis in Germany
2025-09-10

Abstract In hormone-receptor positive (HR+) early breast cancer (EBC), adjuvant endocrine therapy (ET) significantly reduces recurrence and mortality. A common means of estimating therapy adherence is to use patient-reported outcome measures. Yet, this method is inaccurate due to social-desirability bias. We therefore aimed to analyze adherence to ET over the first five years of treatment by using claims data from a large health insurance provider in Germany (AOK Baden-Wuerttemberg).Female patients diagnosed with HR+ EBC who received inpatient treatment and breast cancer surgery between 1 July 2010 and 31 December 2019 were included in the analysis. Adherence to ET was defined as the ratio between the sum of the number of pills from filled prescriptions and the duration of ET in days (from the start of the first prescription after completing surgery and chemotherapy). ET use was observed over five years. Low adherence was defined as a ratio smaller than 0.8 and high adherence as a ratio larger than or equal to 0.8. Distant recurrence-free survival (DRFS) was calculated from the day of the first diagnosis of EBC until onset of distant recurrence. Overall survival (OS) was defined as the period between first diagnosis of EBC until death of any cause.In total, 16642 patients with EBC were included. Of these patients, 4303 (86%) showed high adherence to ET in the first year after initiating treatment. After five years, high adherence persisted in 68% of patients. Continuous high adherence to ET had a significant impact on DRFS (HR: 0.66; 95% CI: 0.58–0.76, p &gt; 0.0001) and OS (HR 0.52, 95% CI: 0.47–0.57, p &lt; 0.0001).In conclusion, adherence to ET is an independent risk factor that significantly influences DRFS and OS. Further real-world studies should explore the factors contributing to treatment discontinuation and evaluate prospective strategies to enhance adherence.
Incretin Signaling Neighborhoods and Adverse Drug Reactions
2025-09-10

In light of the success of blockbuster drugs for type 2 diabetes and obesity based on the GLP-1 hormone, drugmakers have concentrated their efforts on developing new and improved variations that address the route of administration, dosing, pathway selectivity, or polypharmacology. While some of these modifications have demonstrated improved efficacy in clinical studies and offered exciting opportunities for treating other diseases, drug-induced shifts to the conformational landscape of target receptors may have consequences for side effects. Our review summarizes advances in the understanding of the biochemistry, pharmacogenomics, and molecular pharmacology of incretins and their cognate receptors. We further highlight the current landscape of incretin mimetics and discuss how differences in compartmentalized pathway selectivity affect drug action and outcomes.
Physician-led versus questionnaire-based psychosocial screening in adults with high-grade glioma: a cluster-randomized controlled trial (GLIOPT)
2025-09-10

Abstract Purpose Patients diagnosed with high-grade gliomas (HGG) often experience substantial psychosocial dis-tress. However, due to neurological and neurocognitive deficits its assessment remains challenging, and needs remain unmet. We compared a novel face-to-face assessment during doctor-patient conversations with questionnaire-based screening. Methods In this multicenter, two-arm cluster-randomized study involving 13 centers patients in the interven-tion group (IG) were screened for distress via physician-patient conversations, while the control group (CG) completed the Distress Thermometer. Primary outcome was the proportion of patients with poor emotional functioning (measured with the EORTC Quality of Life Questionnaire) who received specialized psychosocial care (PC) within 3 months. Data were collected via patient and physician reports and medical records. Analysis employed mixed models logistic regression. Results In total, 763 patients were enrolled at baseline, and 506 completed the follow-up. The emotional functioning was poor in 302/506 (59.7%). The frequency of patients reporting PC utilization was comparable between groups (IG 93/168, 55.4% vs. CG 87/134, 64.9%, odds ratio (OR) =0.67, 95% confidence interval (CI)=0.40-1.11, p=0.115). Likewise, the provision of information about special-ized psycho-oncological care was similar (IG 112/168, 66.7% vs. CG 94/134, 70.1%, OR=0.95, 95%CI=0.39-2.29, p=0.904). Conclusion Physician-led, face-to-face distress screening was not superior to questionnaire-based screening in facilitating psychosocial care referrals. Nonetheless, it represents a feasible and patient-centered alternative, particularly for patients with high-grade gliomas suffering from neurocognitive or func-tional deficits.
Tips and Tricks to Study Mudbricks. Experiences from the Protohistoric Site of Casas del Turuñuelo, Spain
2025-09-10

The main construction technique during the Protohistory in the southwest of the Iberian Peninsula was adobe. However, to date, there have been few sites with the necessary state of preservation to conduct studies that provide a holistic view of the architecture. In contrast, the discovery of the Tartessian building at Casas del Turuñuelo (Guareña, Badajoz, Spain) with its exceptional state of preservation has enabled the application of a wide range of interdisciplinary analytical techniques and methodologies—many of which have never before been used together at a single site. In this paper, we present a detailed synthesis of all the strategies, techniques and analyses applied over ten years of excavation, as well as those currently under development. Our aim is to share the insights gained from this specific case study and, more importantly, to provide methodological tools that can be applied to other adobe-using sites, regardless of their chronology or cultural context.
Incidence and risk factors for portal vein complications after pediatric liver transplantation: A retrospective cohort analysis from the PORTAL registry
2025-09-10

Portal vein complications (PVCs) are recognized but infrequent complications following pediatric liver transplantation (pLT), particularly in young patients with biliary atresia (BA). However, the exact incidence of PVCs remains unclear. This study aimed to determine the overall incidence of PVCs after pLT and to explore variations within specific subgroups defined by indication for pLT, age at pLT, donor type, transplant era, and center volume. Differences between portal vein stenosis (PVS) and portal vein occlusion (PVO) were also examined. The Portal Vein Obstruction Revascularization Therapy After Liver Transplantation (PORTAL) registry, a multicenter, retrospective, observational database, collected data on PVCs from 21 pLT centers. Analysis of 6035 pLT procedures performed over a 19-year period identified 385 cases of PVCs, yielding an overall incidence of 6.3%. PVS and PVO most commonly occurred within the first year post-pLT, with PVO peaking in the first week and PVS cases distributed more evenly throughout the year. The incidence was highest following pLT for BA performed before the age of 1 year (13.0%). PVC rates increased over time, rising from 4.3% during 2001–2006 to 6.9% during 2016–2020. The highest rates of PVS and the lowest rates of PVO were observed in high-volume centers. These findings clarify the incidence of PVCs among pLT recipients and provide critical insights to improve prevention, early detection, and management strategies for these complications.