julilili42/papers huggingface dataset:
Risk of moderate or severe hypoxic ischemic encephalopathy does not correlate with prenatally known risk factors
2025-09-16

Abstract Infants with perinatal asphyxia require immediate support in order to prevent further damage. If asphyxia progresses towards hypoxic ischemic encephalopathy, therapeutic hypothermia (TH) in a specialised NICU is indicated. In order to provide evidence-based recommendations for an appropriate perinatal care structure, data for Germany are needed. German NICUs which offer TH (cooling centres) provided data in order to analyse how many neonates were treated with TH and how many of them were transferred for TH. Furthermore, for transferred infants the level of care of birth hospital was analysed and the rate of neonates with TH per 1,000 deliveries was calculated for each hospital. Data for 1,431 neonates with TH was obtained from 20 cooling centres. The average annual rate of neonates receiving TH in each cooling centre varied between 3 and 12 neonates. In only 13% of the analysed hospital years was the annual rate of neonates receiving TH equal to or more than 12. For 19 out of the 20 cooling centres, detailed information on the place of birth was available. Out of these 1,390 neonates, 46% (n=637) were transferred for TH. 4.7% of the transferred neonates were born out-of-hospital, whereas 95.3% (n=607) were born in 111 different hospitals, with a total of 1,298,058 deliveries during the respective data reporting period. Altogether, 55.3%, 18.5%, and 26.2% were born in hospitals caring for high-, medium-, or low-risk pregnancies, respectively. For each hospital, the respective rate of neonates with TH per 1,000 deliveries was calculated and showed variations between different hospitals. However, the median rate was similar among hospitals caring for high-, medium-, or low-risk pregnancies. Our findings could be used for subsequent planning of perinatal care. Since the annual number of neonates treated with TH is rather low in the majority of participating cooling centres, more centralisation is needed. Furthermore, the relative rate of newborns requiring TH is similar in hospitals providing care for high-, medium-, or low-risk pregnancies. In order to provide immediate resuscitation to asphyxiated infants, paediatric expertise should be available in each hospital where infants are born.
Fungal infections in focus: accelerating non-invasive imaging from preclinical insights to clinical breakthroughs
2025-09-16

Invasive fungal diseases (IFDs) present a growing clinical challenge, underscoring the urgent need for improved diagnostics, therapeutics and mechanistic understanding. This review highlights the key role of innovative imaging techniques across all scales - ranging from whole-body-level diagnostics and therapy monitoring to host-pathogen interactions at cellular resolution in both clinical and preclinical settings. These imaging modalities facilitate translation of preclinical innovations into clinical applications, accelerating research and advancing IFD management.
Reconstructing flexible pathways of Aurignacian blade and bladelet production at Vogelherd
2025-09-16

The beginning of the Upper Paleolithic represents a key period in human history. At this time, we can grasp the technological concepts that Homo sapiens used in the early Upper Paleolithic. The age of the Aurignacian in combination with the three-dimensional ivory artworks, musical instruments and personal ornaments in the Swabian Jura sites emphasize the importance of this region for understanding and defining the Upper Paleolithic. During that time blade and bladelet production became the central interest of lithic production. The study of these lithic reduction sequences is essential for understanding technological inventions and socio-economic behaviors of early anatomically modern humans in Central Europe. So far, however, the lithic technology from the Aurignacian of the Swabian Jura has only been studied in detail at the site of Geißenklösterle. In this paper, we provide an exhaustive study based on the rich lithic assemblage from Vogelherd Cave combining both the chaîne opératoire approach and attribute analysis. This work highlights the importance of carefully sorting minimal raw material units and engaging in systematic refitting. These observations allow us to reconstruct entire reduction sequences including the biographies of both cores and tools. The source and physical characteristics of lithic raw materials greatly influenced decision-making during the reduction process. As in many other Paleolithic contexts, Aurignacian knappers thoroughly exploited imported raw materials while exhausting low quality local material to a lesser degree. Comparisons with other assemblages from the region help to facilitate the characterization of the Swabian Aurignacian. This comparison allows us to separate regional adaptations from more site-specific behaviors.
Exploring the impact of visual function degradation on manual prehension movements in normal-sighted individuals
2025-09-16

Impairments of visual function abilities, such as visual acuity and contrast sensitivity, can negatively impact our ability to perform manual prehension tasks. Despite the clear link between visual input and motor output, there is still limited understanding of how visual function deficits affect hand motor behavior. This study aimed to explore the impact of different levels of visual function degradation, specifically in terms of visual acuity and contrast sensitivity, on the reach and grasp components of manual prehension. To this end, visual function degradation was induced in young participants with normal vision using five different densities of Bangerter occlusion foils. Participants were instructed to perform a natural and accurate reach-to-grasp task towards a cylindrical object with two different diameters (3.5 or 7 cm) and positioned at two distances (25 or 50 cm). The effects of visual function degradation, object size, and distance were evaluated by recording the position and trajectory of the right hand using an optoelectronic motion capture system. Three-dimensional kinematic analysis revealed that visual function degradation in normal-sighted individuals directly altered the reach and grasp components of prehension movements. These alterations included longer movement durations, lower velocity and acceleration profiles, slower deceleration phases, over-scaled hand grip apertures, and greater trajectory deviations. The effects were dependent on the level of visual degradation induced and the intrinsic (size) and extrinsic (distance) object properties. Reductions exceeding 70% in visual acuity and 55% in CS had the most pronounced impact on prehension components. However, subtle reductions greater than 30% in visual acuity and 15% in contrast sensitivity were sufficient to trigger compensatory mechanisms. These findings provide further understanding of how visual function degradation affects prehension movement strategies, highlighting the crucial relationship between visual feedback quality and object properties in the motor online control of the transport, manipulation and spatial components. Our results offer new insights into the implications of visual impairments on manual prehension movements.
Opportunities and Challenges of the Application of Nuclear Magnetic Resonance‐Based Cerebrospinal Fluid Metabolomics for Clinical Research
2025-09-16

Cerebrospinal fluid (CSF) is an important human biofluid studied within neurological implications. The objective of this literature review is to explore the potential of quantitative nuclear magnetic resonance (NMR) spectroscopy for a precise and reproducible measurement of metabolites in CSF. A two‐source‐based literature search is conducted among entries from a Web of Science Core Collection (owned by Clarivate) and the PubMed library, with the objective of researching NMR‐based investigations of human CSF. The query results are then rerouted toward key summaries pertaining to NMR experiments, sample preparation, and identified metabolites. 94 papers focusing on sample preparation and NMR methods and 49 papers that reported about CSF metabolite concentrations with an overall total of 114 different metabolites that can be detected by NMR are identified. The findings are summarized in comprehensive tables to facilitate future research and use of harmonized protocols regarding sample preparation and measurement. While a large set of metabolites can be measured in CSF, many different sample preparation protocols and analytical settings are used. This is a major drawback for the translation of CSF NMR spectroscopy to a clinical setting, so future studies should try to harmonize preanalytical and analytical conditions and apply absolute quantitation.
Altered thymic niche synergistically drives the massive proliferation of malignant thymocytes
2025-09-16

The discovery of genetic alterations in patient samples over the last decades has reinforced a cell-autonomous view of proliferative expansion during T-cell acute lymphoblastic leukemia (T-ALL) development in the thymus. However, the potential contribution of non-cell-autonomous factors, particularly the impact of thymic epithelial cells (TECs) within the thymic niche during the initiation phase, remains unexplored. In this study, we combine a cell-based computational model of the thymus with complementary in vivo experiments in medaka ( Oryzias latipes ) to systematically analyze the impact of 12 cell-autonomous and non-autonomous factors, individually and in combination, on the proliferation of normal and malignant thymocytes carrying interleukin-7 receptor (IL7R) gain-of-function mutations or elevated IL7R levels, as observed in T-ALL patients. By simulating over 1500 scenarios, we show that while a dense TEC network favored the proliferation of normal thymocytes, it inhibited the proliferation of malignant lineages, which achieved their maximal proliferative capacity when TECs were sparsely distributed. Our in silico model further predicts that specific mutations could accelerate proliferative expansion within a few days. This prediction was experimentally validated, revealing the rapid onset of thymic lymphoma and systemic infiltration of malignant T cells within just 8 days of embryonic development. These findings demonstrate that synergistic interaction between oncogenic alterations and modifications in the thymic niche can significantly accelerate disease progression. Our results also suggest that negative feedback from the proliferative state suppresses thymocyte differentiation. Overall, this multidisciplinary work reveals the critical role of TEC-thymocyte interactions in both the initiation and progression of T-ALL, highlighting the importance of the thymic microenvironment in early leukemogenesis.
Bioavailability and phyto-extractability of metals in a peat-amended agricultural soil under climate stress
2025-09-16

Climate-induced mobilization of harmful metals in soils with a pH below 7 threatens food safety through plant uptake. While organic amendments like peat are known to immobilize metals, it remains unclear how their immobilization effectiveness changes under future climate scenarios and whether there is an optimal amendment threshold before immobilization turns into re-mobilization. This study assessed how varying peat input levels (3, 5 and 8 %) and projected climatic conditions (+4 °C, +320 ppm<sub>v</sub> CO<sub>2</sub>) affect metal fractionation, bioavailability, and uptake by a metal-tolerant plant in historically contaminated soils. Intermediate 5 % peat levels enhanced metal immobilization via organic matter complexation, reducing exchangeable Zn and Cd ∼2-fold compared to 3 % peat, despite acidification. At high 8 % peat input, a 0.65-unit pH decline and increased dissolved organic matter reversed this trend, increasing exchangeable Zn and Cd > 2-fold relative to 5 % peat. Chemical equilibrium modeling (WHAM VII) confirmed greater metal complexation with dissolved organic matter at higher 5-8 % peat levels. Under future climatic conditions-elevated temperature and CO<sub>2</sub>-metal immobilization improved at low 3 % peat input, likely due to stable organic matter and functional group buffering. Nevertheless, metal re-mobilization occurred at higher peat inputs, likely due to enhanced peat decomposition. Despite these variations, plant Cd uptake remained low across peat and climate treatments. This emphasizes peat's protective role against Cd while maintaining the plant's nutritional status for Zn. This study highlights the dual effects of peat amendments: intermediate levels optimize metal immobilization, but excessive amendments may destabilize harmful metals, especially under future conditions.
Effects of Au Nanoparticles Suspended in Chlorobenzene Antisolvent on Mixed-Halide Perovskites
2025-09-16

In this work, Au nanoparticles (NPs) were synthesized by laser ablation in liquids (LASiS) by using chlorobenzene, resulting in a stable suspension with a plasmon resonance band around 560 nm. This Au NPs suspension was subsequently used in the antisolvent step for the preparation of the CsFAMA perovskite films. Morphological analyses revealed an increase in the grain size in the Au NPs-modified films, attributed to Au NPs-assisted heterogeneous nucleation. In situ GIWAXS measurements were conducted during film crystallization, pointing out that in the Au NPs-modified films prepared with diluted suspension, the peaks corresponding to the cubic α-phase formed faster and with reduced PbI<sub>2</sub> content, when compared to the control film produced without Au NPs. The characterization of solar cell devices fabricated with Au NPs-modified CsFAMA films presented the influence of the NPs concentration on photovoltaic performance. Devices prepared with diluted Au NPs suspensions exhibited a higher power conversion efficiency (PCE) over time, improved stability, and a reduced hysteresis index.
The metacognitive paradox of OCD: confidence is globally reduced but shows increasedsensitivity to local evidence
2025-09-16

<title>Abstract</title> Confidence is a critical metacognitive signal that guides performance. Biases in confidence, such as excessive doubt, are hallmark features of mental health disorders, especially obsessive- compulsive disorder (OCD). Yet, the underlying neurocognitive mechanisms and how they link to learning and decision-making remain elusive. We asked patients with OCD and matched healthy controls to perform a novel rule-shifting task incorporating trial-by-trial confidence ratings. Using a Bayes-optimal model, we identified two distinct confidence biases: while patients with OCD indicated lower overall confidence, their trial-by-trial confidence ratings more accurately tracked task-relevant information, rendering their confidence reports more Bayes-optimal than those of controls. These findings challenge the idea of a simple, unified metacognitive impairment in OCD. Instead, they suggest that OCD is linked to an enhanced responsiveness to environmental evidence and feedback during decision-making.
Learning the natural history of human disease with generative transformers
2025-09-17

Abstract Decision-making in healthcare relies on understanding patients’ past and current health states to predict and, ultimately, change their future course 1–3 . Artificial intelligence (AI) methods promise to aid this task by learning patterns of disease progression from large corpora of health records 4,5 . However, their potential has not been fully investigated at scale. Here we modify the GPT 6 (generative pretrained transformer) architecture to model the progression and competing nature of human diseases. We train this model, Delphi-2M, on data from 0.4 million UK Biobank participants and validate it using external data from 1.9 million Danish individuals with no change in parameters. Delphi-2M predicts the rates of more than 1,000 diseases, conditional on each individual’s past disease history, with accuracy comparable to that of existing single-disease models. Delphi-2M’s generative nature also enables sampling of synthetic future health trajectories, providing meaningful estimates of potential disease burden for up to 20 years, and enabling the training of AI models that have never seen actual data. Explainable AI methods 7 provide insights into Delphi-2M’s predictions, revealing clusters of co-morbidities within and across disease chapters and their time-dependent consequences on future health, but also highlight biases learnt from training data. In summary, transformer-based models appear to be well suited for predictive and generative health-related tasks, are applicable to population-scale datasets and provide insights into temporal dependencies between disease events, potentially improving the understanding of personalized health risks and informing precision medicine approaches.
Serum NfL, but not GFAP, differentiates primary lateral sclerosis from adrenomyeloneuropathy and hereditary spastic paraplegia type 4
2025-09-17

Our study suggests that serum NfL, but not GFAP, is a potential diagnostic biomarker in degenerative UMN diseases and may help to differentiate PLS from pure and complicated forms of HSP. Our results indicate that axonal degeneration-the source of NfL release-is predominant over astrocytic pathology-the source of GFAP release-in PLS, AMN, and SPG4.
Fluctuations of viti- and oleiculture traditions in the Bronze and Iron Age Levant
2025-09-17

Various researchers have demonstrated periods of instability in the cultivation of olives and grapes in the eastern Mediterranean, dating back at least to the Early Bronze Age. So far, pollen-based studies have focused primarily on olive cultivation in the southern Levant. Our research extends these studies to include both cash crops throughout the Levant and northern Mesopotamia, including several different climatic zones, to better understand the diversity of human strategies for maintaining agricultural stability. We analysed 1,514 charred olive ( Olea europaea ) and grape ( Vitis vinfera ) seed and wood samples from archaeological sites for their stable carbon isotope ratios to reconstruct Bronze and Iron Age growing conditions. The results, with generally 3.7‰ higher Δ 13 C values in grapevine than in olive, are consistent with the physiological characteristics of the two species, i.e., their water use efficiency, and with their different agronomic needs. Furthermore, higher values in charcoals than in fruits indicate the natural differences in the budgets of water availability associated with the period of formation of the measured plant tissue. Canonical correspondence analysis (CCA) of the complete data set shows clear correlation of the mean Δ 13 C values with reconstructed average precipitation (RAP) and the general north-south and west-east decline in precipitation of the region, as well as with chronology, including a gradual drying trend through time. Principal component analysis (PCA) based on these variables shows a highly diversified relationship between mean and maximum stress levels and RAP at different sites over time. An important trend is the significant accumulation of Iron Age sites in olive-growing and wine-producing regions above 500 mm RAP. However, there are considerable diachronic differences in the stress signals for the two tree crops. Interpolations of the mean Δ 13 C values of the crop species are in good agreement with the layout of the isohyets and visualize the PCA patterns of stable carbon isotope and precipitation relationships thereby confirming the major trends such as a better water availability in the Iron Age. The well-known major climatic fluctuations at 4.2 and 3.2 kyr BP correlate with likely irrigation of olive trees, while there are also drought patterns indicated in the Δ 13 C values at the end of the Middle Bronze Age. In general, the greater commitment to the establishment of agricultural niches and successful production for viticulture compared to oleiculture, which has already been observed in historical times, is confirmed, at least since the Middle Bronze Age and especially in the Iron Age.
Integrated e-Learning for Shoulder Anatomy and Clinical Examination Skills in First-Year Medical Students: Randomized Controlled Trial
2025-09-17

Abstract Background Applying functional anatomy to clinical examination techniques in shoulder examination is challenging for physicians at all learning stages. Anatomy teaching has shifted toward a more function-oriented approach and has increasingly incorporated e-learning. There is limited evidence on whether the integrated teaching of professionalism, clinical examination technique, and functional anatomy via e-learning is effective. Objective This study aimed to investigate the impact of an integrated blended learning course on the ability of first-year medical students to perform a shoulder examination on healthy volunteers. Methods Based on Kolb’s experiential learning theory, we designed a course on shoulder anatomy and clinical examination techniques that integrates preclinical and clinical content across all 4 stages of Kolb’s learning cycle. The study is a randomized, observer-blinded controlled trial involving first-year medical students who are assigned to one of two groups. Both groups participated in blended learning courses; however, the intervention group’s course combined clinical examination, anatomy, and professional behavior and included a peer-assisted practice session as well as a flipped classroom seminar. The control group’s course combined an online lecture with self-study and self-examination. After completing the course, participants uploaded a video of their shoulder examination. The videos were scored by 2 blinded raters using a standardized examination checklist with a total score of 40. Results Thirty-eight medical students were included from the 80 participants needed based on the power calculation. Seventeen intervention and 14 control students completed the 3-week study. The intervention group students scored a mean of 34.71 (SD 1.99). The control students scored a mean of 29.43 (SD 5.13). The difference of means was 5.3 points and proved to be statistically significant ( P &lt;.001; 2-sided Mann-Whitney U test). Conclusions The study shows that anatomy, professional behavior, and clinical examination skills can also be taught in an integrated blended learning approach. For first-year medical students, this approach proved more effective than online lectures and self-study.