julilili42/papers huggingface dataset:
Anti-Pelagian Theology in Augustine’s Non-Anti-Pelagian Works
2025-07-22

Abstract Major works of Augustine such as De ciuitate Dei, De trinitate, or De Genesi ad litteram cannot be understood appropriately if not related to the Pelagian debate. The high occurrence of anti-Pelagian arguments in works that are not primarily directed against Pelagians shows how deeply Augustine’s thought was shaped by his doctrine of grace. His doctrine of grace was linked to fundamental observations on how God dealt with His creation (predestination, presence in the universe), on anthropology (human nature, emotions, concupiscence, death), and on soteriology (perseverance, comparison of beatitude before the Fall and in the final state, Christ being the mediator). These themes shaped even Augustine’s piety (especially prayer as a fundamental behaviour of the believer) and self-representation (as somebody who was led himself to a proper understanding of grace by God in the Retractationes). Pelagianism was not just another heresy against which Augustine polemicized, but seemed—from his point of view—to threaten the core intentions of his thought and of Christian faith in general.
Increased feelings of external influence during instructed imaginations in patients with psychotic disorder
2025-07-22

Abstract Feelings of external influence are a hallmark of psychotic disorders, but mitigated forms can also be observed in healthy persons. A newly developed paradigm designed to induce feelings of external influence through verbal information (influence will be attempted/not-attempted) and physical setup (presence of tDCS-device or hand touch) was carried out in a pilot study in 21 patients with psychosis and in 22 healthy controls. A higher prevalence of induced feelings of external influence was observed in patients with psychosis. Furthermore, in healthy controls the impact of verbal information outweighed the impact of physical setup, whereas in patients the setup had a stronger influence. Moreover, the intensity of induced feelings of external influence correlated with measures of psychotic symptom severity (PANSS positive score, SAPS, AMDP ego-disorder) as well as response latencies during the estimation process. These findings indicate that feelings of external influence can be reliably induced in healthy controls and in patients with psychotic disorders. Stronger effects of physical setup in patients might be related to disorder-specific biases regarding the impact of initial perceptual impressions of features of the physical environment on belief formation, whereas the attenuated response to explicit verbal information about attempted influence might reflect reduced trust in other people’s statements.
Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli
2025-07-22

In Gram-negative bacteria, the uptake and export of a wide range of molecules, including antibiotics, is facilitated by porins and efflux pumps. Because of their role in regulating small molecule permeability of the outer and inner membrane, these transport machineries are tightly regulated at the transcriptional and post-transcriptional levels. However, regulation of transport by external chemical cues remains poorly understood. Here we investigated transcriptional regulation of three prominent transporter genes in Escherichia coli across 94 defined chemical cues, and simultaneously mapped the contributions of the key regulators MarA, SoxS and Rob to promoter activity. One third of all tested compounds triggered transcriptional changes, the majority of which were previously unknown. Importantly, we exposed main drivers of transport control in E. coli , e.g., bacteriostatic but not bactericidal antibiotics trigger the expression of efflux pumps, and Rob contributes to ~1/3 of all measured transcriptional changes, thereby emerging as a more prominent regulator of transport than previously thought. We showcase the potential of our resource by elucidating the molecular mechanism of antibiotic antagonisms with widely consumed caffeine in E. coli . Altogether, our analysis provides a quantitative overview of how different regulators orchestrate the transcriptional response of major transport determinants to environmental chemical cues.
Targeting Treg–fibroblast interaction to enhance immunotherapy in steatotic liver disease-related hepatocellular carcinoma
2025-07-22

Background Steatotic liver disease-related hepatocellular carcinoma (SLD-HCC), a rising global challenge, is characterised by unique tumour microenvironment (TME) adaptations. Objective This study investigates the immune microenvironment and interactions driving immunosuppression and potential resistance to immunotherapy in SLD-HCC. Design We employed single-cell transcriptomics, cytometry by time-of-flight (CyTOF) and two independent spatial transcriptomics platforms to study the TME of 22 SLD-HCC and 31 non-SLD-HCC cases. Findings were further validated using multiplex immunohistochemistry in an independent cohort of 103 patients, an HCC model and an immunotherapy-treated patient cohort to evaluate clinical relevance. Results Our findings revealed significant alterations in immune and lipid metabolism pathways, particularly in regulatory T cells (Tregs) and cancer-associated fibroblasts (CAFs), suggesting distinct cellular adaptations to a high-fat TME and general immunosuppression. CyTOF revealed a cold, immunosuppressive TME with reduced CD8 + T cells and increased Tregs. Spatial transcriptomics further highlighted distinct Treg–CAF clusters localised at tumour margins, suggesting a spatially organised immunosuppressive niche. Mechanistically, tumour necrosis factor superfamily member 14 (TNFSF14)-tumour necrosis factor receptor superfamily member 14 (TNFRSF14)-mediated Treg–CAF interaction was identified as a critical driver of immunotherapy resistance in SLD-HCC. Blocking TNFRSF14 in an HCC model fed with a high-fat diet resulted in reduced Tregs, increased active CD8 + and memory CD4 + T cells, and a synergistic effect with anti-programmed cell death protein 1 therapy to enhance antitumour immunity and overcome immunotherapy resistance in SLD-HCC. Conclusion This study uncovers critical immune and metabolic adaptations in SLD-HCC, identifying TNFSF14-TNFRSF14 signalling as a key driver of immunotherapy resistance. Targeting this signalling axis enhances antitumour immunity and improves immunotherapy efficacy, offering a promising therapeutic strategy for SLD-HCC.
Altered Functional Activation Is Associated With Speech Dysfunction in People With Multiple Sclerosis
2025-07-22

Abstract Dysarthria is a motor speech disorder that is a common symptom of cerebellar dysfunction in people with multiple sclerosis (pwMS). Despite its prevalence, little is known regarding changes in brain functioning associated with dysarthria in this cohort. Management strategies for cerebellar symptoms such as dysarthria are also limited. Fifty-five pwMS and 14 healthy controls participated in this study. We used fMRI to assess changes in speech related functional activation associated with MS, and split our MS cohort into people with and without dysarthria, and with and without cerebellar dysfunction clinically evident as upper limb action tremor. We found that pwMS performed worse on speech production tasks and had overall lower functional activation while preparing for speech than controls. Furthermore, pwMS require additional recruitment of the left Brodmann areas 45 and 46, key motor speech regions, during speech production compared to healthy controls. MS participants presenting with both dysarthria and action tremor performed worst on speech production tasks. These participants had lower functional activation during speech production compared to other MS participants. People with multiple sclerosis display altered functional activation of motor speech areas during speech production, either due to MS injury or reduced activity during preparation. Compensatory activation is reduced in those with both clinical dysarthria and action tremor compared to MS controls and those with tremor only, likely due to more advanced MS.
Island bioarchaeology and ritual knowledge transfer at Biniadrís cave (Menorca, Spain): a longue durée perspective
2025-07-22

The Biniadrís cave is located in the southern part of the island of Menorca (Spain). It is the fourth funerary cave with preserved materials discovered in Menorca up to now, along with Es Càrritx, Es Mussol, and Es Pas. However, the chronology of Biniadrís is more extensive, covering more than seven centuries, allowing for a study of human practices over the “longue durée”. What makes Biniadrís unique is its large number of bioarchaeological remains, mainly human remains and other organic and inorganic material, in an extraordinary state of preservation. The main goal of this paper is to reconstruct the burial ritual using comprehensive bioarchaeological methods, including 14 C radiocarbon dating, to understand the modality and temporality of use of the Biniadrís cave during the pre- and protohistory of the Balearic Islands. The palaeodemographic data derived from our ongoing excavation are described here in detail and point to interesting patterns, such as the equal representation of female and male individuals across all ages, including very young and older individuals. The fact that all individuals are equally represented and integrated into the community in the funerary settings provides insights into the group ideology, which are discussed further. These burial practices are interpreted as a strong expression of community identity at Biniadrís linked to its island setting, as seen from the preservation of the funerary memory over such a long period, which is unique for this cave. The multi-proxy approach employed here to study the bioarchaeological and organic remains contributes to a better understanding of the “longue durée” of the funerary ritual and the reconstruction of human behavior during the Late Bronze and Iron Ages of an island community in the western Mediterranean.
Time‐Resolved Intrinsic and Extrinsic Photoresponse of Colloidal Short‐Wavelength Infrared‐Active Indium Antimonide Quantum Dot Photodetectors
2025-07-22

Colloidal indium antimonide (InSb) quantum dots (QDs) are highly promising nanomaterials for short‐wavelength infrared (SWIR) photodetectors due to their optical properties, solution processability, and low toxicity. Here, surface engineering of colloidal InSb QDs and an investigation of the intrinsic and extrinsic photoresponse time ( τ In and t Ex ) of InSb QD photodetectors is presented. Chloride (Cl − ) ligands are chosen for surface engineering and their effect is studied by X‐ray photoelectron spectroscopy. Using a pump‐probe technique based on asynchronous optical sampling (ASOPS), we find that τ In of Cl‐capped InSb QDs (InSb‐Cl QDs) can be described by two components of 1.5 ns and 200 ps. By studying the dependence of these components on the voltage, the excitation power, and the temperature, we assign them to trap‐assisted Auger recombination and carrier trapping. For t Ex , much faster rise times (9.77 μs) than fall times (635 μs) indicate prolonged recovery due to slow release of trapped carriers is obtained. We devise measures to partially mitigate this drawback, enabling submicrosecond photo switching and a 3 dB bandwidth of 5 MHz. These findings highlight the potential of environmentally benign and high‐speed SWIR photodetectors based on colloidal III‐V semiconductor nanomaterials.
Effects of ethylenediamine on the intrinsic photoresponse of PbS quantum dots
2025-07-22

We examine the intrinsic recombination dynamics of PbS quantum dots (QDs) functionalized with ethylenediamine (EDA) and compare it to the same QDs functionalized with ethane-1,2-dithiol (EDT). The recombination dynamics were studied as a function of temperature, pressure, and excitation intensity using asynchronous optical sampling (ASOPS). Only for EDA functionalization, we find that under vacuum at room temperature roughly 40 % of the total photocurrent decay with a fast lifetime of approximately 100 picoseconds. Intensity-dependent studies indicate that the remaining recombination processes are consistent with trap-assisted Auger recombination mechanisms. Temperature-dependent measurements suggest that the fast 100 ps component is governed by a phonon-assisted decay process. Exploiting such processes could be beneficial in realizing GHz photodetection with PbS QDs.
Expression of LTR and LINE1 transposable elements defines atypical teratoid/rhabdoid tumor subtypes
2025-07-22

Abstract Atypical teratoid rhabdoid tumors (ATRTs) are aggressive central nervous system tumors mainly affecting young children. Extensive molecular characterization based on gene expression and DNA methylation patterns has solidly established three major ATRT subtypes (MYC, SHH and TYR), which show distinct clinical features, setting the basis for more effective, targeted treatment regimens. Transcriptional activity of transposable elements (TEs), like LINE1s and LTRs, is tightly linked with human cancers as a direct consequence of lifting epigenetic repression over TEs. The sole recurrent biallelic loss-of-function mutation in SMARCB1 in ATRTs, a core component of the SWI/SNF chromatin remodeling complex, raises the question of how TE transcription contributes to ATRT development. Here, we comprehensively investigate the transcriptional profiles of 1.9M LINE1 and LTR elements across ATRT subtypes in primary human samples. We find TE transcription profiles allow sample stratification into ATRT subtypes. The TE activity signature in the ATRT-MYC subtype is unique, setting these tumors apart from SHH and TYR ATRTs. More specifically, ATRT-MYC show broadly reduced transcript levels of LINE1 and ERVL-MaLR subfamilies. ATRT-MYC also displayed significantly less LTR and LINE1 loci with bidirectional promoter activity. Furthermore, we identify 849 differentially transcribed TEs in primary samples, which are predictive towards established ATRT-SHH and -MYC cell line models. In summary, including TE transcription profiles into the molecular characterization of ATRTs might reveal new tumor vulnerabilities leading to novel therapeutic interventions, such as immunotherapy.
Intravenous Thrombolysis in Patients With Recent Intake of Direct Oral Anticoagulants: A Target Trial Analysis and Comparison With Reversal Agent Use
2025-07-22

BACKGROUND: Intravenous thrombolysis (IVT) in patients with recent ingestion of direct oral anticoagulants (DOACs) is a frequent challenge and remains controversial. The benefit of DOAC reversal before IVT is uncertain. METHODS: Using target trial methodology, we analyzed data from 28 comprehensive stroke centers. Patients on DOACs were included if they met IVT criteria, had a National Institutes of Health Stroke Scale score of ≥2, and last DOAC intake within 48 hours or was undeterminable. Safety and efficacy outcomes (symptomatic intracerebral hemorrhage, any intracerebral hemorrhage, major bleeding, 90-day mortality, and good functional outcome [modified Rankin Scale score of 0–2 or return to baseline]) were compared between those receiving IVT versus no IVT and IVT with versus without reversal. In addition, a comparison was made with patients from the New Zealand stroke registry, all of whom underwent reversal with idarucizumab. We adjusted for covariates known to be associated with safety and efficacy outcomes, including age, stroke severity, intended thrombectomy, blood glucose, blood pressure, DOAC reversal, and time from last intake. RESULTS: Overall, 1342 patients fulfilled the target trial criteria. The median age was 80 (interquartile range, 73–86) years, median National Institutes of Health Stroke Scale score was 11, 50% were female, and 52% of patients received endovascular therapy. IVT was given in 342 of 1342 (25%) patients. Of these, 141 (41.2%) had verified DOAC intake &lt;12 hours before admission, and 92 (26.9%) within 12 to 24 hours. Symptomatic intracerebral hemorrhage occurred in 10 of 328 (3.0%) of patients receiving IVT and 54 of 921 (5.9%) patients not receiving IVT (adjusted difference, −2.1% [95% CI, −5.3% to +1.2]). Patients receiving IVT were more likely to have good functional outcomes (adjusted difference, +14.4% [95% CI, +7.1% to +21.8%]). Comparing 289 patients with reversal (from the additional New Zealand registry) and 283 patients without reversal before IVT (from the target trial population), there was no significant difference in symptomatic intracerebral hemorrhage, major bleeding, or efficacy outcomes. CONCLUSIONS: This target trial confirms previous observational data regarding the safety of off-label IVT in patients with recent DOAC intake. More data and dedicated trials are needed for patients with confirmed high DOAC plasma levels and regarding the efficacy and safety of DOAC reversal before IVT.
Sharing a whole-/total-body [18F]FDG-PET/CT dataset with CT-derived segmentations: an ENHANCE.PET initiative
2025-07-23

<title>Abstract</title> We present a large whole-body and total-body curated dataset of dual-modality 2-deoxy-2-[18F]fluoro-D-glucose (FDG)-Positron Emission Tomography/Computed Tomography (PET/CT) studies, consisting of 1,597 PET/CT images and the corresponding CT-derived segmentations of over 100 target regions. This multi-center dataset includes images from individuals without overt disease and patients with different pathologies (lung cancer, lymphoma, and melanoma). Target regions were first automatically segmented from CT images using an in-house software, and subsequently verified and corrected by physicians. In total, the segmented regions encompass 130 volumes, including abdominal organs, muscles, bones, cardiac subregions, vessels, adipose tissue, and skeletal muscle around vertebra L3. PET/CT images and corresponding CT-derived segmentations are provided in anonymized NIfTI format. The dataset can be used for deep learning training, validation, or multi-modality image analysis and thus fills an important gap in available resources to advance the use of PET/CT data in clinical management.
Assessing flexibility in meaning and context in non‐human communication
2025-07-23

ABSTRACT The concept of flexibility in communication is central to reconstructing the evolutionary history of language, and grappling with “contextual flexibility” in particular is pivotal to address implications for pragmatics‐first accounts of language evolution. Despite significant advances in the field, research is hindered by definitional inconsistencies and methodological gaps across modalities. We build on recent frameworks to propose further, detailed methods for studying contextual and functional variability, incorporating modality‐agnostic and standardised terminology to facilitate cross‐species comparisons. Our approach includes a detailed classification of communicative contexts and outcomes, offering practical methods to disentangle context from function and meaning. By integrating insights across behavioural ecology and comparative psychology, we aim to enhance the comparability of findings and provide a robust foundation for exploring the evolutionary trajectory of communicative flexibility and pragmatics.
Linguistic evolution minimizes the amount of syntactic hierarchy in grammar
2025-07-23

Abstract A core characteristic of language is the capacity for hierarchical syntax, but it remains debated to what extent languages favor hierarchical structure in their grammars, that is, the extent to which they favor hierarchical structures like “When driving, look ahead!” over concatenations like “You drive, you look ahead!”. Through phylogenetic modeling of the grammars of clause combining in three extensive language families (Tupí-Guaraní, Sino-Tibetan, and Indo-European), we find an overall bias towards minimizing hierarchy, with significant cultural variation. Our findings suggest that the computational and representational benefits of hierarchical structure tend not to be universally exploited in clause combinations, likely because they come with additional costs for learning. In consequence, the amount of hierarchy in language might differ from what is found in animal communication in a more graded way than commonly assumed.
Black feminism and Artificial Intelligence: the possibilities and limitations of contesting discriminatory AI from a critical social theory perspective
2025-07-23

Artificial Intelligence (AI) has been challenged in recent years by critical scholars inspired by American Black feminism and questions around diversity, inclusion, and justice in and through AI systems. This paper takes a closer look at the application of Black feminism as a critical social theory, which originated as a theory protesting the oppression of Black women as a group in the United States. The paper reveals the benefits and limitations of the theory in contesting AI-based sorting, classification, personalization, recommendation, and population-based predictions of different groups of technology stakeholders. Through conceptual analysis and reference to recent use cases of AI applications, the paper showcases the promise of an intersectional-type analysis and a structural perspective enabling the in-depth analysis of technology stakeholders' experiences with AI. The paper also highlights limitations of the theory in contesting AI, which inspires a discussion of constraints on critical scholarship on AI more broadly. The papers' findings and arguments are relevant to those engaging in critical conceptual, qualitative research on the design and implications of AI-based computer systems.
Optimizing the use of in vitro transcribed SGK1-mRNA as a therapeutic tool to treat female infertility
2025-07-23

Abstract Objectives Gene therapy has emerged as an encouraging therapeutic approach for several diseases. The use of plasmid DNA (pDNA) or viral vectors encoding proteins have yielded low efficacy in recent trials. Synthetic messenger RNA (mRNA), also known as in vitro transcribed mRNA (IVT-mRNA), is a highly potent alternative. However, the use of IVT-mRNA in reproductive conditions remains scarce. Our previous work has demonstrated the involvement of endometrial serum- and glucocorticoid kinase 1 (SGK1), where it influences pregnancy outcomes in murine models. On this basis, we investigated the expression and function of human SGK1 encoded by IVT-mRNA in vitro . Results We show using flow cytometry, quantitative RT-PCR and immunoblotting, that IVT-mRNA has a superior transfection efficiency compared with pDNA. At protein level, we show that the constitutively active SGK1 variant ( SGK1 S422D ) could increase protein levels and that the inactive SGK1 variant ( SGK1 K127A ) could reduce SGK1 levels. This effect of SGK1 activity modulation could contribute to reprogramming endometrial cells and support a conducive environment for pregnancy.
The Life‐Saving Benefit of the Living Donor Kidney Evaluation: A Mini Review
2025-07-23

ABSTRACT While there has been an appropriate focus on characterizing the risks associated with living kidney donation, little attention has been paid to the potential benefit to the donor of undergoing the living donor evaluation. This review highlights four studies from the United States and Europe across 30 years demonstrating that the living donor evaluation leads to the detection of previously undiagnosed medical problems in potential donors, including serious cancers. Potential donors should be counseled on the possible benefit of undergoing evaluation.