julilili42/papers huggingface dataset:
Recovering lost time in Syria: a new Eocene stereogenyin turtle from the Aleppo Plateau
2025-07-01

Abstract Across the Arabian Platform, fossil turtles have been recovered from deposits dating back to the Cretaceous. In Syria, such remains are mostly fragmentary, recovered from the phosphatic deposits around Palmyra, as well as from the Pleistocene Nadaouiyeh Aïn Askar archaeological site. Here we report a new genus and species, Syriemys lelunensis , represented by a fully preserved inner cast of the shell, plus some plastral, pelvic and hind‐limb bones, some enclosed within the cast. The specimen was collected from the Al‐Zarefeh Quarry, near Afrin, in Aleppo Governorate, with foraminifera extracted from the surrounding rock indicating an early Eocene age. Syriemys lelunensis can be ascribed to the pleurodiran clade Stereogenyini based on a short cranial lobe of the plastron, which does not extend beyond the cranial margin of the carapace, a short epiplastral symphysis, and very reduced gular, extragular and humeral scutes. Syriemys lelunensis also differs from all other known members of the group that have a preserved shell by the presence of three autapomorphic traits: seven neural bones extending at least to costal bone 7, a nuchal bone with a cranial edge half the lateromedial breadth of its widest part, and a shallow anal notch formed by short xiphiplastral processes. This discovery pushes the origin of Stereogenyini back at least to the early Eocene, providing further support for a Mediterranean ancestral geographical range for the group. Finally, Sy . lelunensis represents the first new species of extinct vertebrate ever described from Syria.
Food-Related Inhibitory Control and Transcranial Direct Current Stimulation: Bilateral Prefrontal or Excitatory Right-Hemispheric Stimulation?
2025-07-01

Possible effects of tDCS are subtle and transient. For more robust results, individual targeting might be considered. Reaching inferior frontal regions might be crucial for modulating inhibitory control. The neural and behavioral consequences of bilateral vs unilateral tDCS should be critically considered in future research.
Identifying Risk Factors for Metachronous Colorectal Cancer in Lynch Syndrome
2025-07-01

This study identifies important risk factors for metachronous CRC in patients with LS, which may support personalized counseling regarding surgical strategies. The findings highlight the complexity of surgical decision-making and the need for individualized approaches. Further studies are required to refine risk stratification and evaluate long-term outcomes to optimize patient care.
Standing giants: a digital biomechanical model for bipedal postures in sauropod dinosaurs
2025-07-01

ABSTRACT Here we explore the potential of sauropod dinosaurs to adopt a bipedal or tripodal stance using digital biomechanical modelling and finite element analysis (FEA). Seven sauropod species from diverse lineages and sizes were sampled, and 3D models of their femora were analysed under both extrinsic (body weight distribution) and intrinsic (muscular force) functional scenarios. The results indicate that smaller sauropods, like the saltasaurid titanosaur Neuquensaurus , were more capable of sustaining bipedal postures, probably due to their robust femora combined with advantageous muscle attachment areas. In contrast, larger sauropods such as Dreadnoughtus experienced higher stress levels, making bipedal postures less likely for extended periods. Our analysis provides new insights into sauropod functional evolution, highlighting that species size and morphology significantly influenced their ability to rear up, which could have played a role in behaviours such as feeding, defence and reproduction.
Prospective first-in-human clinical investigation to evaluate the safety of the fracture monitor T1 in patients with femur fractures treated with a locking compression plate: a study protocol
2025-07-01

Introduction An objective way to monitor bone healing in real time could provide major benefits for the rehabilitation of fracture patients. The fracture monitor T1 is a novel biofeedback sensor system designed to provide continuous data of the relative implant load, that is, a measure inversely correlated to bone healing progression as well as patient’s physical activities. The primary objective of this first-in-human study is to evaluate the safety, that is, the incidence of adverse device effects (ADEs), of the investigational device fracture monitor T1 in femoral fracture patients within the first 6-months postsurgery. Secondary objectives are to collect information on clinical performance, other safety parameters and device handling and usability. Methods and analysis 37 adult patients with femoral fractures to be treated with a plate, which is compatible with having the fracture monitor T1 mounted on it, will be prospectively enrolled in this multicentre, interventional first-in-human study. The fracture monitor T1 will be implanted together with the osteosynthesis plate for femoral fracture fixation as well as femoral instabilities, such as post-traumatic non-unions. Standard of care will be followed for femoral fracture treatment and patients will be followed up for 6-months. Demographic data, comorbidities, prior medication, prior treatment details, injury details, treatment details and outcome measures will be documented in a cloud-based database. The primary outcome measure is ADEs. Secondary outcome measures include clinical and functional outcomes, safety outcomes, device removal, patient-reported outcomes (pain, Numeric Rating Scale, EQ-5D-5L), device handling and usability, number of visits and radiographic assessments, radiographic outcomes, relative implant load and technical performance parameters. A statistical analysis plan will be prepared before final analysis. Ethics and dissemination Ethics approval is obtained at each site before patient enrolment, which follows an informed consent process approved by the responsible ethics committee. Data from this first-in-human study will be compiled into a clinical evaluation report for the application of CE (Conformité Européenne, certification mark indicating conformity with European Union health, safety and environmental protection standards) marking of the device. The results of this first-in-human study will be published in a peer-reviewed journal. Trial registration number NCT05410587
A Note on Spurious Correlations and Explainable Machine Learning in Digital Soil Mapping
2025-07-01

ABSTRACT The use of machine learning as a method for knowledge discovery is often critically discussed in soil science and related environmental disciplines. Reviews of the use of machine learning in digital soil mapping identified few studies that incorporated existing soil knowledge of transformation and translocation processes in soils and mechanistic relationships between covariates in the modelling process. Even models trained with predictors that are meaningless from a soil science perspective can have high accuracies. To test and widen this perspective, we expanded the setup of a previous study by Wadoux, Samuel‐Rosa, et al. (2020) from one hypothetical case study to a larger set of 668 hypothetical case studies in 334 study areas. We found that the high accuracy of one single model for a specific area was part of a wide range of possible accuracy metrics (concordance correlation coefficient: 0.16–0.91) when applying the same set of meaningless predictors to all study areas. We discuss these spurious correlations in the context of explainable machine learning and highlight how the important elements of model explainability, model input and model output largely depend on discipline‐specific domain knowledge. As soil science knowledge is often incorporated implicitly, we argue that the motivation behind covariate selection should be discussed more explicitly to achieve soil science knowledge beyond spatial prediction.
Functional Traits and Phylogeny Explain Plant Phenological Variations Among Native and Non‐Native Species in Botanical Gardens
2025-07-01

ABSTRACT Aim Phenological shifts are regarded to be the most pronounced indicators of global climate change. Worldwide, native species pools are being increasingly colonised by non‐native species, thus shaping novel communities. Here, we investigate whether, and how, phenology varies between native and non‐native species. We also examine whether functional traits and/or phylogeny can explain these phenological variations. Location Europe and Asia. Time Period 2022. Major Taxa Studied Perennial herbs. Methods We studied multiple phenophases and functional traits of 427 plant species across 13 botanical gardens using the PhenObs monitoring protocol. We used linear mixed models to test for phenology and functional trait differences between native and non‐native species. Boosted regression trees were employed to identify the functional trait predictors of phenology variance between native and non‐native species. To test the effect of phylogeny on these phenological variations, we estimated phylogenetic signal using Pagel's λ. Results Native and non‐native species exhibited distinct phenological patterns and functional traits. Native species started vegetative phenophases earlier than non‐native species and senesced later. Similarly, reproductive phenophases varied, with native species flowering earlier and having longer flowering and fruiting durations. Native species also had higher specific leaf area, while non‐native species had higher seed mass and larger leaf area. The variations in phenology were explained by garden location, leaf area, plant height, and leaf nitrogen. Most phenophases and functional traits showed low phylogenetic conservatism, suggesting a more important role of local environmental factors in driving these variations. Main Conclusions Our findings suggest that the phenological differences between native and non‐native species, both in timing and magnitude, may change the community composition and structure under global change. Non‐native species likely occupy a subset of native phenological niches, and this overlap may alter biotic interactions and ecosystem functioning. Future research needs to substantiate our findings under natural field conditions.
Intravenous thrombolysis before percutaneous coronary intervention in patients with non-ST-elevation acute coronary syndrome and acute ischaemic stroke: a subanalysis of the PRAISE study
2025-07-01

Background In patients with acute ischaemic stroke (AIS) and concomitant non-ST-elevation acute coronary syndrome (NSTE-ACS), the role of intravenous thrombolysis (IVT) before percutaneous coronary intervention (PCI) is unclear. Methods We performed a subanalysis of the PRAISE (PRediction of Acute coronary syndrome in acute Ischemic StrokE) study, a multicentre, prospective observational study in 247 patients with AIS and elevated high-sensitivity cardiac troponin who underwent coronary angiography based on European Society of Cardiology guidelines. The impact of IVT prior to PCI on coronary artery flow (Thrombolysis in Myocardial Infarction (TIMI) score) and myocardial perfusion (TIMI myocardial perfusion score) was compared using Fisher’s exact test and logistic regression analysis, adjusting for time from stroke onset to PCI. Results Among 71 patients with AIS undergoing PCI, those who received IVT prior to PCI for NSTE-ACS (33 women; median age 77 (66–82 IQR)) achieved a TIMI grade 3 flow more frequently than those undergoing direct PCI (97% vs 79%; p=0.04). Regression analysis indicated a trend toward improved coronary artery flow with IVT (adjusted OR 8.5, 95% CI 0.9 to 75.3; p=0.05). Myocardial perfusion did not differ between groups (p=0.06). Conclusions This subanalysis suggests that IVT before PCI may enhance coronary artery flow in selected patients with NSTE-ACS with AIS. The results of this exploratory subanalysis warrant further investigation, particularly in patients with delayed access to PCI.
Delving into LLM-assisted writing in biomedical publications through excess vocabulary
2025-07-02

Large language models (LLMs) like ChatGPT can generate and revise text with human-level performance. These models come with clear limitations, can produce inaccurate information, and reinforce existing biases. Yet, many scientists use them for their scholarly writing. But how widespread is such LLM usage in the academic literature? To answer this question for the field of biomedical research, we present an unbiased, large-scale approach: We study vocabulary changes in more than 15 million biomedical abstracts from 2010 to 2024 indexed by PubMed and show how the appearance of LLMs led to an abrupt increase in the frequency of certain style words. This excess word analysis suggests that at least 13.5% of 2024 abstracts were processed with LLMs. This lower bound differed across disciplines, countries, and journals, reaching 40% for some subcorpora. We show that LLMs have had an unprecedented impact on scientific writing in biomedical research, surpassing the effect of major world events such as the COVID pandemic.
A foundation model to predict and capture human cognition
2025-07-02

Abstract Establishing a unified theory of cognition has been an important goal in psychology 1,2 . A first step towards such a theory is to create a computational model that can predict human behaviour in a wide range of settings. Here we introduce Centaur, a computational model that can predict and simulate human behaviour in any experiment expressible in natural language. We derived Centaur by fine-tuning a state-of-the-art language model on a large-scale dataset called Psych-101. Psych-101 has an unprecedented scale, covering trial-by-trial data from more than 60,000 participants performing in excess of 10,000,000 choices in 160 experiments. Centaur not only captures the behaviour of held-out participants better than existing cognitive models, but it also generalizes to previously unseen cover stories, structural task modifications and entirely new domains. Furthermore, the model’s internal representations become more aligned with human neural activity after fine-tuning. Taken together, our results demonstrate that it is possible to discover computational models that capture human behaviour across a wide range of domains. We believe that such models provide tremendous potential for guiding the development of cognitive theories, and we present a case study to demonstrate this.
Pre-sleep experiences shape neural activity and dream content in the sleeping brain
2025-07-02

Dreams incorporate recent experiences, and memory-related brain activity is reactivated during sleep, suggesting that dreaming, memory consolidation, and reactivation are tightly linked. We devised a paradigm to investigate whether memory reprocessing during sleep contributes to dreaming. Participants listened to different audiobooks before falling asleep, introducing dissimilar experiences to be processed at night. We show that audiobook content was reprocessed at the neural level using multivariate pattern analyses. Brain activity during rapid eye movement sleep, particularly in the beta range, carried information about the audiobook. While the amount of neural reinstatement did not correlate with memory retention, global beta power during REM sleep was associated with better memory performance. Moreover, blind raters could determine which audiobook participants had studied based on dream reports. Participants who dreamt of the audiobook also showed stronger neural reinstatement. Reprocessing of pre-sleep experiences during sleep may thus shape our brain activity, our dreams, and our memories.
Advances in understanding multifunctionality of Barley stripe mosaic virus γb protein
2025-07-02

Plant viruses usually encode versatile but limited number of proteins to reshape the cellular microenvironment, suppress or co-opt host pathways and proteins for their own benefit. Barley stripe mosaic virus (BSMV, Hordeivirus hordei ) is a positive single-stranded RNA virus that infects both monocots and dicots. Among its seven encoded proteins, the γb protein exhibits remarkable multifunctionality despite being the smallest one. By interacting with various viral and host proteins, γb acts as a master regulator participating in almost all steps of the viral life cycle, including replication, movement, virion morphogenesis and vertical transmission, in addition to counteracting several layers of host defenses. In this review, we systematically summarize current understanding of the γb protein multifunctionality and discuss its implications in the ongoing co-evolutionary battle between host plants and invading viruses.
State-of-the-Art: Somatic Cell Sources Used for the Generation of Human Induced Pluripotent Stem Cells
2025-07-02

In the original publications of Yamanaka et al. from 2006 to 2007, which were the basis for the Nobel Prize in medicine, murine, and human fibroblasts had been used as the primary cell source for the generation of induced pluripotent stem cells (iPSCs). Over time, four other types of somatic cells have been revealed to be suitable for pluripotency induction, namely blood cells, keratinocytes, urine-derived epithelial cells, and mesenchymal stem cells. Although mature cells have been frequently used for the generation of iPSCs, numerous primary cell types have also been reprogrammed successfully. In this review, we address the current state of research dealing with different sources of human somatic cells used for the generation of iPSCs. Our objective is to provide a comprehensive tabular summary of the sources of somatic cells, organized according to the four main types of tissue (connective tissue, epithelial tissue, muscle tissue, and neural tissue). This overview will serve as a guide for researchers new to the field looking for suitable sources to generate their own iPSCs, for those interested in generating patient-specific iPSCs, or for those seeking further literature on specific cell sources.
Missing what's right under your nose: Failed appetitive and aversive audio-olfactory conditioning in humans
2025-07-02

The comparison of physiological mechanisms underlying appetitive and aversive conditioning is often challenging due to the involvement of stimuli from different modalities with potentially disparate effective mechanisms (e.g., pain stimuli versus monetary rewards). The olfactory system offers a unique opportunity to examine both types of conditioning in humans, as isointense odors can serve as comparably pleasant and unpleasant stimuli. To study physiological and behavioral responses during appetitive and aversive learning, we employed odors as unconditioned stimuli (US) in a within-subjects design, measuring various conditioned physiological responses including skin conductance, heart rate, pulse wave amplitude, respiration, fear-potentiated startle, postauricular reflex, facial electromyography, as well as event-related potentials and auditory steady-state responses (ASSR) derived from electroencephalography. We conducted four experiments with a total of 95 participants, presenting three neutral sounds paired with either a pleasant odor, an unpleasant odor, or odorless air. The first experiment involved uninstructed participants and frequency-modulated conditioned stimuli (CS) for ASSR analysis. In the second experiment, we omitted the frequency modulation and startle probe. The third experiment included pre-experiment instruction on CS-US contingencies, while the fourth employed a delay conditioning paradigm in contrast to the other three experiments. Our results revealed differences between CS+ and CS- only in the fear-potentiated startle response in Experiment 3. No other effects were found. The minimal or absent learning effects observed across multiple peripheral and neural physiological measures may be attributed to the extra-thalamic nature of olfactory pathways and the subsequent difficulty in forming associations with auditory stimuli.
Hydrothermal Synthesis and Characterization of the Melamine‐Based Second‐Harmonic Generation Material HgCl2(C3N6H6)
2025-07-02

The pursuit of efficient nonlinear optical materials is critical for advancing optoelectronic applications. This study focuses on the synthesis and characterization of HgCl 2 (C 3 N 6 H 6 ), a melamine‐based hybrid metal halide. Structural analysis reveals a non‐centrosymmetric lattice facilitated by large asymmetric secondary building units and a π‐conjugated system. The compound exhibits a strong second‐harmonic generation efficiency. Density functional theory calculations, optical band gap measurements, and photoluminescence measurements specify the electronic properties. For completeness and analytical comparison, the centrosymmetric compound Hg 2 Cl 2 (C 3 N 6 H 6 ) 2 is also introduced.
Detecting single motor-unit activity in magnetomyography
2025-07-02

Abstract Objective. The study of motor unit (MU) discharge patterns is critical for understanding the mechanisms underlying human motor behavior. Intramuscular electromyography (iEMG) allows direct study of MU activity but is invasive. Surface electromyography offers a non-invasive alternative, but with lower spatial resolution. Recent advances in optically pumped magnetometers (OPMs) have sparked interest in the magnetic counterpart of EMG, magnetomyography (MMG), as an additional non-contact modality to study the neuromuscular system. However, it remains unclear whether MMG signals recorded with superconducting quantum interference devices (SQUIDs) or OPMs can be used to directly detect individual MUs. Approach. We addressed this question in a proof-of-principle study in which we recorded MMG signals from the abductor digiti minimi muscle using SQUIDs and OPMs. Critically, we simultaneously recorded iEMG from the same muscle as the ground truth to cross-validate the findings from the non-invasive measurements. Main results. We found that invasively recorded MUs can be detected in simultaneously recorded SQUID and OPM MMG signals. Furthermore, we found that individual MUs can be extracted directly from SQUID and OPM MMG and, importantly, validated this finding using the simultaneous iEMG recordings. These results provide converging evidence that individual MU activity is accessible using non-contact MMG. Significance. We demonstrate for the first time that individual MU activity is observable in MMG, paving the way for future research on MU decomposition using MMG. Our findings highlight the potential of MMG as a non-contact modality to study muscle activity in health and disease.