julilili42/papers huggingface dataset:
Putting the pieces of the puzzle together in modeling gendered educational choices
2025-07-28

Abstract Background The underrepresentation of women in science, technology, engineering, and mathematics (STEM) remains a persistent international challenge with complex causes. This study draws on five complementary theoretical perspectives—theory of circumscription and compromise, situated expectancy-value theory, the internal/external frame of reference model, the differential effects model, and the goal congruity model—to identify the strongest predictors of women's entry into STEM fields in higher education from 21 variables and their up to 441 nonlinear pairwise interactions. No previous study has included such a comprehensive set of variables and interactions. To address this gap, we applied Prediction Rule Ensembles, a machine-learning technique that balances interpretability and predictive accuracy, capturing complex, nonlinear interactions between variables. We used a nationally representative longitudinal German NEPS sample of 4,383 academic-track students (53% female, 25% second-generation immigrants). Results Our analyses showed that high-school students' career aspirations with a higher proportion of female than male incumbents (gendered career aspirations), along with their self-concept of math and verbal ability, were the strongest predictors of STEM major choice. Gendered career aspirations accounted for between 71% and 77% of the gender gap in STEM major choice, while students’ achievement variables had a much lower importance for the STEM major choice prediction. Notably, the association between math self-concept and STEM major choice was stronger for students with higher male-dominated career aspirations, highlighting the interplay between gendered career aspirations and domain-specific self-concepts. The application of prediction rule ensembles allowed us to uncover nonlinear interactions between predictors that had not previously been identified, demonstrating the potential of machine-learning approaches in educational research. Conclusions Our findings highlight the importance of considering complex, nonlinear interactions between theory-driven predictors to better understand the gender gap in STEM. These findings have significant implications for both theory and practice, suggesting that interventions targeting the perceived gender typicality of STEM careers and students' math self-concepts may be effective in increasing women's participation in STEM. Furthermore, the methodological approach adopted in this study offers a promising framework for future research, paving the way for more nuanced investigations of the multiple factors that influence educational and career choices in STEM.
Local environment and fire history of a potential Lower Palaeolithic refugium in the Megalopolis Basin, southern Greece, during Marine Isotope Stage 12
2025-07-28

Abstract The Balkan Peninsula is considered to have acted as a glacial refugium as well as a biogeographic crossroads during the Pleistocene, playing an important role in the survival of biota and population dynamics through time. Furthermore, rather than being a homogeneous habitat, it is thought to have hosted a number of diverse, isolated “refugia within refugia,” providing suitable conditions for the persistence of different plant and animal species, as well as, potentially, Pleistocene hominins. We present the first palynological and charcoal record, although discontinuous, from the middle Pleistocene archaeological site Marathousa 1 (MAR-1; Megalopolis Basin) to reconstruct the local environment along with the first multispecies record of coprophilous fungal spores from Greece to track herbivore activity during the Marine Isotope Stage (MIS) 12. Our data show that during the early and late MIS 12, when the forest cover substantially decreased, mesophilous trees and aquatic vegetation persisted, reflecting wetter and milder conditions at MAR-1. Herbivore presence is documented by ∼473 ka, while its intensification coincides with increased vegetation biomass and local fire activity during the late MIS 12. Our findings suggest that MAR-1 likely served as a glacial refugium for middle Pleistocene hominins, providing essential resources for their survival during MIS 12.
Impact of Bulky Substituents on the Singlet Arylnitrene Ring Enlargement
2025-07-28

Substituents of the hydrindacene type allow the isolation of crystalline stable triplet arylnitrenes from photodecomposition of the corresponding aryl azides, while phenyl azide is known to produce singlet phenylnitrene that reacts to didehydroazepine via benzazirine. Comparison of computed potential energy surfaces for ring enlargement of singlet arylnitrenes suggests that bulky groups of the hydrindacene type should not significantly change the rates of formation of didehydroazepines compared to phenylnitrene. Thus, didehydroazepines could be trappable intermediates en route to stable triplet arylnitrenes.
Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships
2025-07-28

Abstract Advancing spatially resolved in vivo functional genomes will link complex genetic alterations prevalent in cancer to critical disease phenotypes within tumour ecosystems. To this end, we developed PERTURB-CAST, a method to streamline the identification of perturbations at the tissue level. By adapting RNA-templated ligation probes, PERTURB-CAST leverages commercial 10X Visium spatial transcriptomics to integrate perturbation mapping with transcriptome-wide phenotyping in the same tissue section using a widely available single-readout platform. In addition, we present CHOCOLAT-G2P, a scalable framework designed to study higher-order combinatorial perturbations that mimic tumour heterogeneity. We apply it to investigate tissue-level phenotypic effects of combinatorial perturbations that induce autochthonous mosaic liver tumours.
Ipsilateral motor cortex regulates distinctly via interhemispheric inhibition force production versus force control in isometric unimanual contraction
2025-07-28

This study reveals a dual regulatory mechanism by which the ipsilateral M1 optimizes unimanual force production and control through dynamic modulation of SIHI. We demonstrate that ipsilateral M1 facilitates force generation by attenuating SIHI, whereas persistent SIHI during isometric contraction correlates with precision during sustained contractions.
Factors Driving Background Choice in Scorpionfish
2025-07-28

ABSTRACT For a successful hunt, marine ambush predators such as scorpionfish need to be well camouflaged to deceive their prey. When the natural environment is heterogeneous, one strategy to maintain camouflage is choosing backgrounds to achieve better crypsis. We tested if two Mediterranean scorpionfish species, Scorpaena maderensis and S. porcus , select backgrounds according to this strategy. By using visual modelling on data extracted from standardised photography of natural substrates, we show that scorpionfish should be able to visually distinguish between different substrates using achromatic rather than chromatic contrast information. We then conducted a behavioural experiment where scorpionfish could choose between backgrounds that were similar or different (lighter and darker) to their own average body luminance, as measured in previous studies. Unexpectedly, scorpionfish did not choose backgrounds of luminance similar to their own but instead settled preferentially on darker backgrounds. To investigate these results further, we characterised the colouration of scorpionfish's distinct pattern components after their choice using calibrated image analysis. We show that the darker parts of the fish pattern best matched the dark background for both species, and that S. porcus increased internal pattern contrast when choosing the darker background. We therefore propose that the preference for dark backgrounds enhances camouflage via disruptive colouration. The choice for specific backgrounds, in addition to their ability to rapidly change colour and intensify disruptive colouration, can potentially allow scorpionfish to camouflage in a broad range of microhabitats.
Risk-adapted therapy in pediatric thyroid cancer: initial experience from a national reference program by the MET group
2025-07-28

Background Pediatric differentiated thyroid carcinoma (pedDTC) is rare but increasingly prevalent, requiring multidisciplinary care to ensure optimal outcomes. In 2021, the pediatric national reference program of the German Malignant Endocrine Tumor (MET) registry was established to standardize the management of pedDTC, with a particular focus on radioactive iodine (RAI) use and minimizing treatment variability. Methods This study evaluated the program’s first 3.5 years, including 43 inquiries concerning 39 patients with confirmed or suspected pedDTC. A weekly national expert tumor board provided individualized recommendations based on multidisciplinary input and risk stratification. Data were analyzed for demographic trends, therapeutic decisions, and short-term outcomes. Results Among 34 patients with confirmed pedDTC, RAI use was reduced or omitted in 70.6% of cases, particularly among low-risk patients, in alignment with the American Thyroid Association 2015 guidelines. Surgical strategies were modified in 61.5% of cases to balance disease control with treatment-related morbidity. No systemic medical therapy was recommended during initial management. At a mean follow-up of 0.7 years, all patients were alive; persistent disease was observed in 15.4%. Conclusions The national reference program has successfully introduced a structured, individualized approach to the management of pedDTC in Germany. Ongoing data collection and longer follow-up will be essential to assess the long-term impact of this centralized, risk-adapted model.
Does pharma R&D need a strategic reset? Adapting to a changing US landscape
2025-07-28

R&D productivity has long challenged research-based pharmaceutical companies, raising concerns about the sustainability of their research-driven business models. These firms have traditionally relied on the U.S. as a stable hub for biomedical innovation, skilled talent, and high-price markets-supporting the biotech-leveraged pharma company (BIPCO) model However, recent geopolitical shifts-especially under the new Trump administration, including FDA budget cuts, reduced U.S. research funding, and pharmaceutical tariffs-are destabilizing this foundation. The once-reliable "safe harbor" is no longer secure. As a result, pharma R&D now faces strategic risks beyond its prior scope. With the weakening of the U.S.-centered innovation model, companies must rethink R&D pipelines, secure key technologies, maintain global clinical networks, and adjust supply chain and tax strategies. The viability of the current R&D model-rooted in U.S. leadership and premium markets-is now uncertain, requiring urgent strategic realignment.
Counting Tropical Curves in ℙ1 × ℙ1 : Computation and Polynomiality Properties
2025-07-28

Abstract Counts of curves in with transverse contact along the zero and infinity sections but fixed contact orders along the zero and infinity fibers have been shown to piecewise polynomial in the entries of the contact order conditions. The result was proved by using tropical methods [36], and in particular the technique of floor diagrams [3]. We expand the tropical tools to determine counts of curves in . We provide a computational tool (building on Polymake [22]) that determines such numbers of tropical curves for any genus and any contact orders via a straightforward generalization of Mikhalkin’s lattice path algorithm. The tool can also be used for other toric surfaces. To enable efficient computations by hand, we introduce a new counting tool (for the case of rational curves with transverse contacts with the infinity section) which can be seen as a combination of the floor diagram and the lattice path approach: subfloor diagrams. We use both our computational tool and the subfloor diagrams for experiments revealing structural properties of these counts. We obtain new results on the (piecewise) polynomial structure of counts of rational curves in with arbitrary contact orders on the zero and infinity fiber and certain restricted, non-transverse choices for the contact orders on the zero and infinity section.
Empowering bioinformatics communities with Nextflow and nf-core
2025-07-29

Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.
Genome of Rhodovulum iodosum , a marine photoferrotroph
2025-07-29

ABSTRACT Photoferrotrophs drove primary production in the Earth’s early oceans and are still abundant in modern environments. We present a draft genome sequence of a model photoferrotroph, Rhodovulum iodosum UT/N1. By comparing it with its close relative Rhodovulum robiginosum DSM 12329, we identify that these cultures were likely swapped during their history.
Current Practices for Analyzing Soils and Sediments via Mössbauer Spectroscopy
2025-07-29

ABSTRACT Environmental scientists are increasingly returning to Mössbauer spectroscopy (MBS) to reveal details about iron (Fe)‐bearing phases in soils and sediments. MBS is particularly powerful at distinguishing between Fe(II) and Fe(III) and, given appropriate background information, can offer exceptionally precise information on Fe speciation in compositionally complex environmental samples. However, there are relatively few accessible guides for analyzing environmental samples by MBS. In this review, we seek to distill the essential understanding of MBS for earth scientists and provide guidance on analysis, spectral fitting, and interpretation for new practitioners and a consolidation of approaches for experienced users. As a rule, Fe phases in soils and sediments are more disordered and complex than synthetic or geogenic Fe minerals. We cover the most successful ways MBS can be applied to soils, including the determination of Fe(II)/Fe(III) ratios, characterization of Fe (oxyhydr)oxide crystallinity, and the use of 57 Fe isotope spikes, as well as highlighting how to avoid common pitfalls and arrive at Fe phase identification and quantification by leveraging complimentary data and environment context. We outline procedures for sample preparation, analysis, and spectral fitting using decision trees based on the analytical goals and sample conditions. The fitting and interpretation of magnetically ordered ferrous phases at low temperature is lacking in the literature and so we offer an expanded discussion of approaches to these challenging spectra. We provide a discussion and fitting guidance for the most common Fe phases in soils and sediments organized around environmental contexts: young soils (and sediments derived from them) dominated by aluminosilicates, highly weathered soils rich in Fe oxides, organic‐rich soils, soils in sulfur‐rich environments, and soils exposed to anoxia. For each context, we describe expected Fe phases and their characteristic spectral features while emphasizing the importance of complementary analyses for reliable interpretation. Finally, we identify two critical needs in the field: improved theoretical frameworks for fitting low‐temperature ferrous octets and Fe–sulfur phases and a need for standardization of parameter reporting and data sharing within the environmental MBS community. This review aims to both facilitate broader adoption of MBS in the environmental sciences and advance the technique's application to complex natural samples.
Casein kinase 1α essentially regulates thrombopoiesis by driving megakaryocyte maturation and cytoskeleton organization
2025-07-29

Abstract Throughout thrombopoiesis megakaryocytes (MKs) form proplatelets within the bone marrow (BM) and release platelets into BM sinusoids. Casein kinase 1α (CK1α) is a major player and thus, an important therapeutic target in several hematological malignancies. This study aimed to define the role of CK1α for the essential steps of thrombopoiesis and to dissect potential mechanisms of thrombocytopenia. MK-specific CK1α-deficiency resulted in a macrothrombocytopenia. Ck1αPf4Δ/Pf4Δ mice displayed a substantial BM hyperplasia with pivotal changes in MK nuclear lobulation and reduced contact to BM sinusoids. Ck1αPf4Δ/Pf4Δ MKs displayed a defective cytoskeleton organization reflected by a decreased amount of polymerized filamentous actin and disturbed microtubule dynamics due to p21/p53 accumulation and impaired Rho-associated protein kinase (ROCK)/LIM domain kinase (LIMK)/cofilin signaling. Further, pronounced defects in DMS (demarcation membrane system) polarization and proplatelet formation of Ck1αPf4Δ/Pf4Δ MKs, unraveled CK1α as a prerequisite for thrombopoiesis. Our findings could be translated into a human approach, because a CRISPR/Cas9–mediated genetic deletion of CSNK1A1 in MKs derived from human CD34+ progenitor cells resulted in a substantial defect in human MK maturation and platelet production. The present observations elucidated CK1α as an important signaling molecule in MK cytoskeletal dynamics and polarization, proplatelet formation, and polyploidization, thus highlighting the crucial role of CK1α in platelet biogenesis.
The transcription factor WRKY25 can act as redox switch to drive the expression of WRKY53 during leaf senescence in arabidopsis
2025-07-29

Abstract Senescence requires high plasticity and, therefore, must be coordinated by a complex regulatory network. Notably, WRKY transcription factors highly impact senescence regulation. WRKYs can form homo- and heterodimers and contain the binding motifs of WRKY factors in their promoters already forming a complex regulatory network between themselves. For the Arabidopsis hub gene WRKY53 , WRKY18 acts as a strong negative while WRKY25 serves as strong positive regulator, creating a smaller subnetwork with high complexity, which we analyzed in detail. Activation of WRKY53 expression by WRKY25 is redox sensitive while repression by WRKY18 was not. Deletions and domain-swapping between WRKY18 and WRKY25 revealed that the N-terminal domain of WRKY25 is crucial for its activator effect on WRKY53 expression. Moreover, WRKY25 does not form homodimers but is able to heterodimerize with WRKY18 also requiring its N-terminal domain. The impact on senescence regulation and on WRKY53 expression was validated in planta using transgenic complementation lines of the wrky25 mutant. Modeling WRKY25 in silico indicated a putative covalent lysine-cysteine NOS redox switch. LC–MS analyses suggest that the NOS bridges really exist. We propose that WRKY25 acts as a redox sensor, balancing the expression and interactions of the WRKY53/WRKY25/WRKY18 network to ensure progressive senescence induction.
Attributing coordinated social media manipulation: A theoretical model and typology
2025-07-29

Social media are key arenas for public opinion formation, but are susceptible to coordinated social media manipulation (CSMM), that is, the orchestrated activity of multiple accounts to increase content visibility and deceive audiences. Despite advances in detecting and characterizing CSMM, the attribution problem—identifying the principals behind CSMM campaigns—has received little scholarly attention. In this article, we address this gap by synthesizing existing research and developing a theoretical model for understanding CSMM. We propose a consolidated definition of CSMM, identify its key observable and hidden characteristics, and present a rational choice model for inferring principals’ strategic decisions from campaign features. In addition, we present a typology of CSMM campaigns, linking variations in scale, elaborateness, and disguise to principals’ resources, stakes, and influence strategies. Our contribution provides researchers with conceptual and heuristic tools for attribution and invites interdisciplinary and comparative research on CSMM campaigns.
Sex-specific survival in advanced metastatic melanoma – a DeCOG study on 2032 patients of the multicenter prospective skin cancer registry ADOREG
2025-07-29

No overall sex-specific survival differences were detected for metastatic melanoma patients in the first-line therapy setting. According to subgroup analyses males show a trend towards a survival advantage over females.
Disease risk but not remission status determines transplant outcomes in AML: long-term outcomes of the ASAP trial
2025-07-30

Attempting to induce a complete remission (CR) prior to allogeneic hematopoietic cell transplantation (alloHCT) is current practice in patients with AML. A benefit of remission induction prior to alloHCT, however, has never been proven in a prospective trial. Potent conditioning regimens exist which allow for successful alloHCT in patients with active AML. Therefore, the ASAP trial was conducted to test remission induction by salvage chemotherapy prior to alloHCT against immediate transplantation after intensified conditioning. In total 281 patients with AML with poor response after first induction or untreated first relapse were randomized 1:1 to remission induction (RIST) with high-dose cytarabine plus mitoxantrone versus immediate alloHCT with sequential conditioning after non-intensive disease control measures (DisC) preferentially watchful waiting only. Overall survival (OS) at 5 years from randomization analyzed according to ITT was 46.1% for DisC versus 47.5% for RIST (p=0.82). In multivariable Cox regression analysis, genetic AML risk according to ELN (p&amp;lt;0.0001), age (p=0.001) and comorbidities (p=0.046) predicted survival, but not treatment arm (HR 1.08 for DisC versus RIST, p=0.67). In conclusion, long-term follow-up of the ASAP trial showed no survival advantage for standard salvage chemotherapy prior to alloHCT as opposed to immediate alloHCT. The trial results question the general concept of remission induction with intensive standard salvage therapy prior to alloHCT for all patients, since immediate alloHCT may reduce time in hospital and health care expenses. Well tolerable novel bridging therapies and post-transplant maintenance with targeted drugs are urgently warranted, especially for adverse-risk AML, to improve outcome after alloHCT. NCT02461537