julilili42/papers huggingface dataset:
Responsible research assessment in the area of quantitative methods research: A comment on Gärtner et al.
2024-03-17

In this commentary, we discuss the proposed criteria in Gärtner et al. (2022) for hiring or promoting quantitative methods researchers. We argue that the criteria do not reflect aspects that are relevant to quantitative methods researchers and typical publications they produce. We introduce a new set of criteria that can be used to evaluate the performance of quantitative methods researchers in a more valid fashion. We discuss the necessity to balance scientific expertise and open science commitment in such ranking schemes.
Reducing the global burden of cerebral venous thrombosis: An international research agenda
2024-03-18

Background: Due to the rarity of cerebral venous thrombosis (CVT), performing high-quality scientific research in this field is challenging. Providing answers to unresolved research questions will improve prevention, diagnosis, and treatment, and ultimately translate to a better outcome of patients with CVT. We present an international research agenda, in which the most important research questions in the field of CVT are prioritized. Aims: This research agenda has three distinct goals: (1) to provide inspiration and focus to research on CVT for the coming years, (2) to reinforce international collaboration, and (3) to facilitate the acquisition of research funding. Summary of review: This international research agenda is the result of a research summit organized by the International Cerebral Venous Thrombosis Consortium in Amsterdam, the Netherlands, in June 2023. The summit brought together 45 participants from 15 countries including clinical researchers from various disciplines, patients who previously suffered from CVT, and delegates from industry and non-profit funding organizations. The research agenda is categorized into six pre-specified themes: (1) epidemiology and clinical features, (2) life after CVT, (3) neuroimaging and diagnosis, (4) pathophysiology, (5) medical treatment, and (6) endovascular treatment. For each theme, we present two to four research questions, followed by a brief substantiation per question. The research questions were prioritized by the participants of the summit through consensus discussion. Conclusions: This international research agenda provides an overview of the most burning research questions on CVT. Answering these questions will advance our understanding and management of CVT, which will ultimately lead to improved outcomes for CVT patients worldwide.
Unraveling TPACK: Investigating the inherent structure of TPACK from a subject-specific angle using test-based instruments
2024-03-18

Against the backdrop of digitalization, it is imperative to provide pre-service teachers with adequate training opportunities to foster their professional knowledge regarding technology integration in teaching-learning situations. However, to date, only limited insights into the empirical nature of such knowledge – often subsumed under the term Technological Pedagogical and Content Knowledge (i.e., TPCK) – are possible given the heterogeneity of prior research investigating the empirical relationship between different knowledge components. This heterogeneity is likely due to the predominant use of self-reports in previous studies. Against this background, the present study pursued two goals. The first goal was to investigate the empirical nature of TPCK among pre-service teachers, utilizing test-based instruments to explore TPCK's nature from a subject-specific angle, that is, its relationship with Pedagogical Content Knowledge (PCK) and Technological Knowledge (TK). Given the widespread use of self-reports, the study's second goal was to examine the relationship between test-based and self-reported TPCK, exploring possible associated factors (e.g., pre-service teachers' gender, prior experience in teaching with technologies in school, or metacognitive accuracy) that may explain why both measures are linked only weakly. Findings reveal that both PCK and TK statistically predicted TPCK to a similar extent highlighting the integrated nature of TPCK. The relationship between test-based and self-reported TPCK was moderated by pre-service teachers' metacognitive accuracy, but not by their gender or prior experience. Together, these insights offer valuable guidance for refining teacher training regarding effective technology integration by indicating the need to target not only PCK and TK but also TPCK.
Optimal Ownership and Firm Performance: An Analysis of China's FDI Liberalization
2024-03-18

Abstract Seminal theories of the firm posit that firm ownership is allocated to minimize contractual inefficiencies. Yet, it remains unclear how much the optimal ownership choice affects firm performance in practice. This paper provides a first quantification of the gains from optimal ownership within multinational firms, by exploiting a major liberalization of China's policy restrictions on foreign ownership. The liberalization allowed previously restricted firms to become fully foreign owned. We find that these reoptimized ownership choices raise firm output by 40% and productivity by 7.5% on average. An extended property-rights theory of the multinational firm rationalizes these effects and their heterogeneity.
Neural dynamics of semantic control underlying generative storytelling
2024-03-18

Storytelling has been pivotal for the transmission of knowledge and cultural norms across human history. A crucial process underlying the generation of narratives is the exertion of cognitive control on the semantic representations stored in memory, a phenomenon referred as semantic control. Despite the extensive literature investigating the neural mechanisms of semantic control in generative language tasks, little effort has been done towards storytelling under naturalistic conditions. Here, we probed human participants to generate stories in response to a set of instructions which triggered a narrative that was either appropriate (ordinary), novel (random), or balanced (creative), while recording functional magnetic resonance imaging (fMRI) signal. By leveraging deep language models, we demonstrated how participants ideally balanced the level of semantic control during story generation. At the neural level, creative stories were differentiated by a multivariate pattern of neural activity in frontal cortices compared to ordinary ones and in fronto- temporo-parietal cortices with respect to randomly generated stories. Crucially, similar brain regions were also encoding the features that distinguished the stories behaviourally. Moreover, we decomposed the neural dynamics into connectome harmonic modes and found specific spatial frequency patterns underlying the modulation of semantic control during story generation. Finally, we found different functional coupling within and between the default mode, salience and control networks when contrasting creative stories with their controls. Together, our findings highlight the neural mechanisms underlying the regulation of semantic exploration during narrative ideation and contribute to a deeper understanding of the neural dynamics underpinning the role of semantic control in generative storytelling.
Magnetospheric flows in X-ray pulsars – I. Instability at super-Eddington regime of accretion
2024-03-18

ABSTRACT Within the magnetospheric radius, the geometry of accretion flow in X-ray pulsars is shaped by a strong magnetic field of a neutron star. Starting at the magnetospheric radius, accretion flow follows field lines and reaches the stellar surface in small regions located close to the magnetic poles of a star. At low mass accretion rates, the dynamics of the flow is determined by gravitational attraction and rotation of the magnetosphere due to the centrifugal force. At the luminosity range close to the Eddington limit and above it, the flow is additionally affected by the radiative force. We construct a model simulating accretion flow dynamics over the magnetosphere, assuming that the flow strictly follows field lines and is affected by gravity, radiative, and centrifugal forces only. The magnetic field of a neutron star is taken to be dominated by the dipole component of arbitrary inclination with respect to the accretion disc plane. We show that accretion flow becomes unstable at high mass accretion rates and tends to fluctuate quasi-periodically with a typical period comparable to the free-fall time from the inner disc radius. The inclination of a magnetic dipole with respect to the disc plane and strong anisotropy of X-ray radiation stabilize the mass accretion rate at the poles of a star, but the surface density of material covering the magnetosphere fluctuates even in this case.
What Fires Together, Wires Together: The Effect of Idiomatic Co-Occurrence on Lexical Networks
2024-03-18

This study investigated the processing of lexical elements of idioms in isolation. Using visual word priming, spreading activation for idiomatically related word pairs (e.g., pop–question) was compared to that for semantically related (e.g., answer–question) and unrelated word pairs (e.g., trim–question) in two experiments varying in SOA (500 ms and 350 ms). In line with hybrid theories of idiom representation and processing, facilitatory priming was found in both experiments for idiomatic primes, suggesting a tight link between the words of an idiom that is mediated by a common idiom representation. While idiomatic priming was stable across SOAs, semantic priming was stronger for the short SOA, implying fast and early activation. In conclusion, one lexical element of an idiom can facilitate the processing of another, even if the elements are not presented within a phrasal context (i.e., within an idiom), and without the words being semantically related. We discuss our findings in light of theories about idiom processing, as well as current findings in the field of semantic priming.
CLAUDIO: automated structural analysis of cross-linking data
2024-03-18

Abstract Motivation Cross-linking mass spectrometry has made remarkable advancements in the high-throughput characterization of protein structures and interactions. The resulting pairs of cross-linked peptides typically require geometric assessment and validation, given the availability of their corresponding structures. Results CLAUDIO (Cross-linking Analysis Using Distances and Overlaps) is an open-source software tool designed for the automated analysis and validation of different varieties of large-scale cross-linking experiments. Many of the otherwise manual processes for structural validation (i.e. structure retrieval and mapping) are performed fully automatically to simplify and accelerate the data interpretation process. In addition, CLAUDIO has the ability to remap intra-protein links as inter-protein links and discover evidence for homo-multimers. Availability and implementation CLAUDIO is available as open-source software under the MIT license at https://github.com/KohlbacherLab/CLAUDIO.
Nonlinear Mixed‐Effects Model of Z‐Endoxifen Concentrations in Tamoxifen‐Treated Patients from the CEPAM Cohort
2024-03-18

Tamoxifen is widely used in patients with hormone receptor‐positive breast cancer. The polymorphic enzyme CYP2D6 is primarily responsible for metabolic activation of tamoxifen, resulting in substantial interindividual variability of plasma concentrations of its most important metabolite, Z‐endoxifen. The Z‐endoxifen concentration thresholds below which tamoxifen treatment is less efficacious have been proposed but not validated, and prospective trials of individualized tamoxifen treatment to achieve Z‐endoxifen concentration thresholds are considered infeasible. Therefore, we aim to validate the association between Z‐endoxifen concentration and tamoxifen treatment outcomes, and identify a Z‐endoxifen concentration threshold of tamoxifen efficacy, using pharmacometric modeling and simulation. As a first step, the CYP2D6 Endoxifen Percentage Activity Model (CEPAM) cohort was created by pooling data from 28 clinical studies (&gt; 7,000 patients) with measured endoxifen plasma concentrations. After cleaning, data from 6,083 patients were used to develop a nonlinear mixed‐effect (NLME) model for tamoxifen and Z‐endoxifen pharmacokinetics that includes a conversion factor to allow inclusion of studies that measured total endoxifen but not Z‐endoxifen. The final parent‐metabolite NLME model confirmed the primary role of CYP2D6, and contributions from body weight, CYP2C9 phenotype, and co‐medication with CYP2D6 inhibitors, on Z‐endoxifen pharmacokinetics. Future work will use the model to simulate Z‐endoxifen concentrations in patients receiving single agent tamoxifen treatment within large prospective clinical trials with long‐term survival to identify the Z‐endoxifen concentration threshold below which tamoxifen is less efficacious. Identification of this concentration threshold would allow personalized tamoxifen treatment to improve outcomes in patients with hormone receptor‐positive breast cancer.
Innexin hemichannel activation by Microplitis bicoloratus ecSOD monopolymer reduces ROS
2024-03-18

The extracellular superoxide dismutases (ecSODs) secreted by <i>Microplitis bicoloratus</i> reduce the reactive oxygen species (ROS) stimulated by the <i>Microplitis bicoloratus bracovirus</i>. Here, we demonstrate that the bacterial transferase hexapeptide (hexapep) motif and bacterial-immunoglobulin-like (BIg-like) domain of ecSODs bind to the cell membrane and transiently open hemichannels, facilitating ROS reductions. RNAi-mediated ecSOD silencing <i>in vivo</i> elevated ROS in host hemocytes, impairing parasitoid larva development. <i>In vitro</i>, the ecSOD-monopolymer needed to be membrane bound to open hemichannels. Furthermore, the hexapep motif in the beta-sandwich of ecSOD49 and ecSOD58, and BIg-like domain in the signal peptides of ecSOD67 were required for cell membrane binding. Hexapep motif and BIg-like domain deletions induced ecSODs loss of adhesion and ROS reduction failure. The hexapep motif and BIg-like domain mediated ecSOD binding via upregulating innexins and stabilizing the opened hemichannels. Our findings reveal a mechanism through which ecSOD reduces ROS, which may aid in developing anti-redox therapy.
Rendering the European Neutron Research Landscape
2024-03-18

<title>Abstract</title> Neutrons, owing to their unique properties, serve as indispensable probes for investigating the structure and dynamics of materials across various length scales. The scientific community utilizing neutron research infrastructures encompasses a diverse range of disciplines, making it challenging to quantify its scientific and societal impact. To address this challenge, we apply Natural Language Processing (NLP) and machine learning techniques to analyze the scientific output of the European neutron science community. Leveraging open-source software toolkits, our method allows for the quantitative assessment of community evolution and research focus. Our analysis reveals consistent growth in the neutron community despite a reduction in sources, underscoring the enduring significance of neutron methods in scientific research. Furthermore, an increase in unique authors and an even distribution of publications across diverse scientific topics highlight the community's interdisciplinary nature and collaborative spirit. Beyond neutron scattering, our methodology holds promise for a broad range of scientific communities reliant on Large Research Infrastructures (LRIs), offering opportunities for collaboration, optimization of experimental approaches, and informed decision-making by governmental and funding bodies.
Triple platelet inhibition in intracranial thrombectomy with additional acute cervical stent angioplasty due to tandem lesion: a retrospective single-center analysis
2024-03-18

Abstract Background Acute stroke treatment with intracranial thrombectomy and treatment of ipsilateral carotid artery stenosis/occlusion (“tandem lesion”, TL) in one session is considered safe. However, the risk of stent restenosis after TL treatment is high, and antiplatelet therapy (APT) preventing restenosis must be well balanced to avoid intracranial hemorrhage. We investigated the safety and 90-day outcome of patients receiving TL treatment under triple-APT, focused on stent-patency and possible disadvantageous comorbidities. Methods Patients receiving TL treatment in the setting of acute stroke between 2013 and 2022 were analyzed regarding peri-/postprocedural safety and stent patency after 90 days. All patients received intravenous eptifibatide and acetylsalicylic acid and one of the three drugs prasugrel, clopidogrel, or ticagrelor. Duplex imaging was performed 24 h after treatment, at discharge and 90 days, and digital subtraction angiography was performed if restenosis was suspected. Results 176 patients were included. Periprocedural complications occurred in 2.3% of the patients at no periprocedural death, and in-hospital death in 13.6%. Discharge mRS score was maintained or improved at the 90-day follow-up in 86%, 4.54% had an in-stent restenosis requiring treatment at 90 days. No recorded comorbidity considered disadvantageous for stent patency showed statistical significance, the duration of the endovascular procedure had no significant effect on outcome. Conclusion In our data, TL treatment with triple APT resulted in a low restenosis rate, low rates of sICH and a comparably high number of patients with favorable outcome. Aggressive APT in the initial phase may therefore have the potential to prevent recurrent stroke better than restrained platelet inhibition. Comorbidities did not influence stent patency.
GAA-FGF14 disease: defining its frequency, molecular basis, and 4-aminopyridine response in a large downbeat nystagmus cohort
2024-03-19

This work was supported by the Clinician Scientist program "PRECISE.net" funded by the Else Kröner-Fresenius-Stiftung (to CW, AT, and MSy), the grant 779257 "Solve-RD" from the European's Union Horizon 2020 research and innovation program (to MSy), and the grant 01EO 1401 by the German Federal Ministry of Education and Research (BMBF) (to MSt). This work was also supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) N° 441409627, as part of the PROSPAX consortium under the frame of EJP RD, the European Joint Programme on Rare Diseases, under the EJP RD COFUND-EJP N° 825575 (to MSy, BB and-as associated partner-SZ), the NIH National Institute of Neurological Disorders and Stroke (grant 2R01NS072248-11A1 to SZ), the Fondation Groupe Monaco (to BB), and the Montreal General Hospital Foundation (grant PT79418 to BB). The Care4Rare Canada Consortium is funded in part by Genome Canada and the Ontario Genomics Institute (OGI-147 to KMB), the Canadian Institutes of Health Research (CIHR GP1-155867 to KMB), Ontario Research Foundation, Genome Quebec, and the Children's Hospital of Eastern Ontario Foundation. The funders had no role in the conduct of this study.
Using local ensemble models and Landsat bare soil composites for large-scale soil organic carbon maps in cropland
2024-03-19

National soil organic carbon (SOC) maps are essential to improve greenhouse gas accounting and support climate-smart agriculture. Large-scale SOC models based on wall-to-wall soil information from remote sensing remain a challenge due to the high diversity of natural soil conditions and the difficulty of accounting for the spatial location of the soil samples. In this study, we tested if the implementation of local ensemble models (LEM) can be used to improve the SOC predictions from Landsat-based soil reflectance composites (SRC) for Germany. For this, we divided the research area into 30 times 30 km tiles and calculated local generalized linear models (GLM) based on random, nearby observations. Based on the GLMs, local SOC maps were predicted and aggregated using a moving window approach. The local variable importance was analyzed to identify spatial dependencies in the correlation between the SRC and SOC. For the final SOC map, a Random Forest (RF) model was trained using the aggregated local SOC predictions, the SRC, and a full set of training samples from the agricultural soil inventory. The results show that the LEM was able to improve the accuracy (R2 = 0.68; RMSE = 5.6 g kg−1), compared to the maps based on a single, global model (R2 = 0.52; RMSE = 6.8 g kg−1). The local variable importance of the spectral bands showed clear spatial patterns throughout the research area. Differences can be explained by the local soil conditions, influencing the correlation between SOC and the spectral properties. Compared to the widely adopted integration of distance covariates such as geographical coordinates, the LEM was able the reduce the spatial autocorrelation to a greater extent and to improve the prediction accuracy, especially for underrepresented SOC values. The LEM presents a new method to integrate spatial information and increase the interpretability of DSM models.
Integration of Multijunction Absorbers and Catalysts for Efficient Solar‐Driven Artificial Leaf Structures: A Physical and Materials Science Perspective
2024-03-19

Artificial leaves could be the breakthrough technology to overcome the limitations of storage and mobility through the synthesis of chemical fuels from sunlight, which will be an essential component of a sustainable future energy system. However, the realization of efficient solar‐driven artificial leaf structures requires integrated specialized materials such as semiconductor absorbers, catalysts, interfacial passivation, and contact layers. To date, no competitive system has emerged due to a lack of scientific understanding, knowledge‐based design rules, and scalable engineering strategies. Herein, competitive artificial leaf devices for water splitting, focusing on multiabsorber structures to achieve solar‐to‐hydrogen conversion efficiencies exceeding 15%, are discussed. A key challenge is integrating photovoltaic and electrochemical functionalities in a single device. Additionally, optimal electrocatalysts for intermittent operation at photocurrent densities of 10–20 mA cm −2 must be immobilized on the absorbers with specifically designed interfacial passivation and contact layers, so‐called buried junctions. This minimizes voltage and current losses and prevents corrosive side reactions. Key challenges include understanding elementary steps, identifying suitable materials, and developing synthesis and processing techniques for all integrated components. This is crucial for efficient, robust, and scalable devices. Herein, corresponding research efforts to produce green hydrogen with unassisted solar‐driven (photo‐)electrochemical devices are discussed and reported.
Unveiling spatial complexity in solid tumor immune microenvironments through multiplexed imaging
2024-03-19

Deciphering cellular components and the spatial interaction network of the tumor immune microenvironment (TIME) of solid tumors is pivotal for understanding biologically relevant cross-talks and, ultimately, advancing therapies. Multiplexed tissue imaging provides a powerful tool to elucidate spatial complexity in a holistic manner. We established and cross-validated a comprehensive immunophenotyping panel comprising over 121 markers for multiplexed tissue imaging using MACSimaTM imaging cyclic staining (MICS) alongside an end-to-end analysis workflow. Applying this panel and workflow to primary cancer tissues, we characterized tumor heterogeneity, investigated potential therapeutical targets, conducted in-depth profiling of cell types and states, sub-phenotyped T cells within the TIME, and scrutinized cellular neighborhoods of diverse T cell subsets. Our findings highlight the advantage of spatial profiling, revealing immunosuppressive molecular signatures of tumor-associated myeloid cells interacting with neighboring exhausted, PD1 high T cells in the TIME of hepatocellular carcinoma (HCC). This study establishes a robust framework for spatial exploration of TIMEs in solid tumors and underscores the potency of multiplexed tissue imaging and ultra-deep cell phenotyping in unraveling clinically relevant tumor components.