julilili42/papers huggingface dataset:
Using augmented reality to assess spatial neglect: The Free Exploration Test (FET)
2024-08-01

Abstract Background: To capture the distortion of exploratory activity typical of patients with spatial neglect, traditional diagnostic methods and new virtual reality applications use confined workspaces that limit patients’ exploration behavior to a predefined area. Our aim was to overcome these limitations and enable the recording of patients’ biased activity in real, unconfined space. Methods: We developed the Free Exploration Test (FET) based on augmented reality technology. Using a live stream via the back camera on a tablet, patients search for a (non-existent) virtual target in their environment, while their exploration movements are recorded for 30 s. We tested 20 neglect patients and 20 healthy participants and compared the performance of the FET with traditional neglect tests. Results: In contrast to controls, neglect patients exhibited a significant rightward bias in exploratory movements. The FET had a high discriminative power (area under the curve = 0.89) and correlated positively with traditional tests of spatial neglect (Letter Cancellation, Bells Test, Copying Task, Line Bisection). An optimal cut-off point of the averaged bias of exploratory activity was at 9.0° on the right; it distinguished neglect patients from controls with 85% sensitivity. Discussion: FET offers time-efficient (execution time: ∼3 min), easy-to-apply, and gamified assessment of free exploratory activity. It supplements traditional neglect tests, providing unrestricted recording of exploration in the real, unconfined space surrounding the patient.
The Early Jewish Abraham Tradition as a Primary Source of Theocentric Universalism in Romans: Paul’s Argument in Rom 4:2–17a; 8:32, and 15:7–12
2024-08-01

Abstract The Abraham tradition in the Old Testament is considered a source of Pauline universalism. The outstanding contribution made by early Jewish interpretations of Abraham, however, has been largely overlooked to date. Hymnal and liturgical texts of early Judaism provide further background about this character. Therefore, three central aspects of the apostle’s theocentric universalism will be discussed: ecclesiological (Rom 4:2–17a), christological-soteriological (8:32), and eschatological (15:7–12). The role that Gen 22 played in Jewish interpretation not only for Rom 8:32, but also for Rom 4, which has hardly been considered or discussed in detail to date, will be central. The Abraham tradition is also in the background in Rom 15:7–12 and 13, which is sometimes seen as the sum of Romans. Read in this context, a new approach to solving the linguistic problem of 15:8–9, which is often perceived as difficult, also emerges.
Inter-individual variability (but intra-individual stability) of overt versus covert rehearsal strategies in a digital Corsi task
2024-08-01

The Corsi (block-tapping) paradigm is a classic and well-established visuospatial working memory task in humans involving internal computations (memorizing of item sequences, organizing and updating the memorandum, and recall processes), as well as both overt and covert shifts of attention to facilitate rehearsal, serving to maintain the Corsi sequences during the retention phase. Here, we introduce a novel digital version of a Corsi task in which i) the difficulty of the memorandum (using sequence lengths ranging from 3 to 8) was controlled, ii) the execution of overt and/or covert attention as well as the visuospatial working memory load during the retention phase was manipulated, and iii) shifts of attention were quantified in all experimental phases. With this, we present behavioral data that demonstrate, characterize, and classify the individual effects of overt and covert strategies used as a means of encoding and rehearsal. In a full within-subject design, we tested 28 participants who had to solve three different Corsi conditions. While in condition A neither of the two strategies were restricted, in condition B the overt and in condition C the overt as well as the covert strategies were suppressed. Analyzing Corsi span, (eye) exploration index, and pupil size (change), data clearly show a continuum between overt and covert strategies over all participants (indicating inter-individual variability). Further, all participants showed stable strategy choice (indicating intra-individual stability), meaning that the preferred strategy was maintained in all three conditions, phases, and sequence lengths of the experiment.
Innenrücktitelbild: Radical‐Induced Changes in Transition Metal Interfacial Magnetic Properties: A Blatter Derivative on Polycrystalline Cobalt (Angew. Chem. 42/2024)
2024-08-01

Molecules deposited on polycrystalline cobalt are strongly hybridised with the inorganic surface and experience charge transfer from the cobalt. This is reflected in the modification of the interface electronic structure inducing a decrease in the magnetic moment of the cobalt atoms bonded to the molecules which, in turn, lose their radical character. In their Research Article (e202403495) M. Benedetta Casu et al. report a method, based on X-ray spectroscopies, that helps to screen in a simple way organic/ferromagnetic interfaces for applications in spintronics.
Stress response in Escherichia coli following sublethal phenalene-1-one mediated antimicrobial photodynamic therapy: an RNA-Seq study
2024-08-01

Abstract Since the molecular mechanisms behind adaptation and the bacterial stress response toward antimicrobial photodynamic therapy (aPDT) are not entirely clear yet, the aim of the present study was to investigate the transcriptomic stress response in Escherichia coli after sublethal treatment with aPDT using RNA sequencing (RNA-Seq). Planktonic cultures of stationary phase E. coli were treated with aPDT using a sublethal dose of the photosensitizer SAPYR. After treatment, RNA was extracted, and RNA-Seq was performed on the Illumina NextSeq 500. Differentially expressed genes were analyzed and validated by qRT-PCR. Furthermore, expression of specific stress response proteins was investigated using Western blot analysis.The analysis of the differential gene expression following pathway enrichment analysis revealed a considerable number of genes and pathways significantly up- or down-regulated in E. coli after sublethal treatment with aPDT. Expression of 1018 genes was up-regulated and of 648 genes was down-regulated after sublethal treatment with aPDT as compared to irradiated controls. Analysis of differentially expressed genes and significantly de-regulated pathways showed regulation of genes involved in oxidative stress response and bacterial membrane damage. In conclusion, the results show a transcriptomic stress response in E. coli upon exposure to aPDT using SAPYR and give an insight into potential molecular mechanisms that may result in development of adaptation. Graphical abstract
Skew-product attractors of non-autonomous Caputo fractional differential equations
2024-08-01

A non-autonomous Caputo fractional differential equation (FDE) of order α∈(0,1) in Rd with a driving system on a compact base space P is shown to generate a skew-product semi-flow on Cα×P, where Cα is the space of continuous functions f:R+→Rd with a weighted norm giving uniform convergence on compact time subsets. This skew-product semi-flow is then shown to have a bounded and closed attractor when the vector field of the Caputo FDE satisfies a uniform dissipativity condition. It attracts bounded sets of constant initial functions f in here Cα. The properties and structure of this attractor in Cα×P are also discussed.
CatReNet: interactive analysis of (auto-) catalytic reaction networks
2024-08-01

Abstract Summary Catalytic reaction networks serve as fundamental models for understanding biochemical systems. CatReNet is a novel software designed to facilitate interactive analysis of such networks. It offers fast and exact algorithms for computing various types of self-sustaining autocatalytic subnetworks, including so-called CAFs (constructively autocatalytic food-generated networks), RAFs (reflexively autocatalytic food-generated networks), and pseudo-RAFs. It provides dynamic visualizations to aid exploration and understanding. Availability and implementation This open-source Java application runs on Linux, MacOS, and Windows. It is available at https://github.com/husonlab/catrenet under a GPL3 license.
Die Differenz im Einssein Notizen zur arendtschen „Banalität des Bösen“
2024-08-01

Abstract This paper takes up the controversial arendtian term “banality of evil” and shows how plurality rooted in non-indifference is necessary for preventing us from acting bad. Distinct from “radical Evil” the “Banality of Evil” is not in itself banal. Evil deeds sneak into everyday life if being-one with oneself by consulting with oneself on the actions to be taken is missing. Hence, being-one presupposes plurality for the inner dialogue. As a matter of fact, plurality is rooted in the natality of human beings, in being born as being separated and differentiated from others. Nevertheless, conscious plurality as active non-indifference in thought and judgment is yet necessary.
Retrieval Augmented Zero-Shot Text Classification
2024-08-02

Zero-shot text learning enables text classifiers to handle unseen classes efficiently, alleviating the need for task-specific training data. A simple approach often relies on comparing embeddings of query (text) to those of potential classes. However, the embeddings of a simple query sometimes lack rich contextual information, which hinders the classification performance. Traditionally, this has been addressed by improving the embedding model with expensive training. We introduce QZero, a novel training-free knowledge augmentation approach that reformulates queries by retrieving supporting categories from Wikipedia to improve zero-shot text classification performance. Our experiments across six diverse datasets demonstrate that QZero enhances performance for state-of-the-art static and contextual embedding models without the need for retraining. Notably, in News and medical topic classification tasks, QZero improves the performance of even the largest OpenAI embedding model by at least 5% and 3%, respectively. Acting as a knowledge amplifier, QZero enables small word embedding models to achieve performance levels comparable to those of larger contextual models, offering the potential for significant computational savings. Additionally, QZero offers meaningful insights that illuminate query context and verify topic relevance, aiding in understanding model predictions. Overall, QZero improves embedding-based zero-shot classifiers while maintaining their simplicity. This makes it particularly valuable for resource-constrained environments and domains with constantly evolving information.
Turbinal bones are still one of the last frontiers of the tetrapod skull: hypotheses, challenges and perspectives
2024-08-02

ABSTRACT Turbinals are bony or cartilaginous structures that are present in the nasal cavity of most tetrapods. They are involved in key functions such as olfaction, heat, and moisture conservation, as well as protection of the respiratory tract. Despite recent studies that challenged long‐standing hypotheses about their physiological and genomic correlation, turbinals remain largely unexplored, particularly for non‐mammalian species. Herein, we review and synthesise the current knowledge of turbinals using an integrative approach that includes comparative anatomy, physiology, histology and genomics. In addition, we provide synonyms and correspondences of tetrapod turbinals from about 80 publications. This work represents a first step towards drawing hypotheses of homology for the whole clade, and provides a strong basis to develop new research avenues.
Immune signature of patients with cardiovascular disease predicts increased risk for a severe course of COVID‐19
2024-08-02

Abstract Severe acute respiratory syndrome coronavirus type 2 (SARS‐CoV‐2) infection can lead to life‐threatening clinical manifestations. Patients with cardiovascular disease (CVD) are at higher risk for severe courses of COVID‐19. So far, however, there are hardly any strategies for predicting the course of SARS‐CoV‐2 infection in CVD patients at hospital admission. Thus, we investigated whether this prediction is achievable by prospectively analysing the blood immunophenotype of 94 nonvaccinated participants, including uninfected and acutely SARS‐CoV‐2‐infected CVD patients and healthy donors, using a 36‐colour spectral flow cytometry panel. Unsupervised data analysis revealed little differences between healthy donors and CVD patients, whereas the distribution of the cell populations changed dramatically in SARS‐CoV‐2‐infected CVD patients. The latter had more mature NK cells, activated monocyte subsets, central memory CD4 + T cells, and plasmablasts but fewer dendritic cells, CD16 + monocytes, innate lymphoid cells, and CD8 + T‐cell subsets. Moreover, we identified an immune signature characterised by CD161 + T cells, intermediate effector CD8 + T cells, and natural killer T (NKT) cells that is predictive for CVD patients with a severe course of COVID‐19. Thus, intensified immunophenotype analyses can help identify patients at risk of severe COVID‐19 at hospital admission, improving clinical outcomes through specific treatment.
In silico and biological analyses of missense variants of the human biliary efflux transporter ABCC2: effects of novel rare missense variants
2024-08-02

Abstract Background and Purpose The ATP‐dependent biliary efflux transporter ABCC2, also known as multidrug resistance protein 2 (MRP2), is essential for the cellular disposition and detoxification of various xenobiotics including drugs as well as endogenous metabolites. Common functionally relevant ABCC2 genetic variants significantly alter drug responses and contribute to side effects. The aim of this study was to determine functional consequences of rare variants identified in subjects with European ancestry using in silico tools and in vitro analyses. Experimental Approach Targeted next‐generation sequencing of the ABCC2 gene was used to identify novel variants in European subjects (n = 143). Twenty‐six in silico tools were used to predict functional consequences. For biological validation, transport assays were carried out with membrane vesicles prepared from cell lines overexpressing the newly identified ABCC2 variants and estradiol β‐glucuronide and carboxydichlorofluorescein as the substrates. Key Results Three novel rare ABCC2 missense variants were identified (W227R, K402T, V489F). Twenty‐five in silico tools predicted W227R as damaging and one as potentially damaging. Prediction of functional consequences was not possible for K402T and V489F and for the common linked variants V1188E/C1515Y. Characterisation in vitro showed increased function of W227R, V489F and V1188E/C1515Y for both substrates, whereas K402T function was only increased for carboxydichlorofluorescein. Conclusion and Implications In silico tools were unable to accurately predict the substrate‐dependent increase in function of ABCC2 missense variants. In vitro biological studies are required to accurately determine functional activity to avoid misleading consequences for drug therapy.
Volume Regulation and Nonosmotic Volume of Individual Human Platelets Quantified by High-Speed Scanning Ion Conductance Microscopy
2024-08-02

Abstract Platelets are anucleate cells that play an important role in wound closure following vessel injury. Maintaining a constant platelet volume is critical for platelet function. For example, water-induced swelling can promote procoagulant activity and initiate thrombosis. However, techniques for measuring changes in platelet volume such as light transmittance or impedance techniques have inherent limitations as they only allow qualitative measurements or do not work on the single-cell level. Here, we introduce high-speed scanning ion conductance microscopy (HS-SICM) as a new platform for studying volume regulation mechanisms of individual platelets. We optimized HS-SICM to quantitatively image the morphology of adherent platelets as a function of time at scanning speeds up to 7 seconds per frame and with 0.1 fL precision. We demonstrate that HS-SICM can quantitatively measure the rapid swelling of individual platelets after a hypotonic shock and the following regulatory volume decrease (RVD). We found that the RVD of thrombin-, ADP-, and collagen-activated platelets was significantly reduced compared with nonactivated platelets. Applying the Boyle–van't Hoff relationship allowed us to extract the nonosmotic volume and volume fraction on a single-platelet level. Activation by thrombin or ADP, but not by collagen, resulted in a decrease of the nonosmotic volume, likely due to a release reaction, leaving the total volume unaffected. This work shows that HS-SICM is a versatile tool for resolving rapid morphological changes and volume dynamics of adherent living platelets.
Antiphospholipid Antibody Testing in a Maximum Care Hospital: Method-Dependent Differences
2024-08-02

Background: Antiphospholipid antibody (aPL) testing is critical for the classification of antiphospholipid syndrome. The 2023 ACR/EULAR classification criteria recommend the use of enzyme-linked immunosorbent assays (ELISAs) and specific thresholds for aPL positivity. Since non-ELISA methods are increasingly used, we compared and evaluated ELISA and non-ELISA aPL assays in a real-world maximum care hospital setting. Methods: Between January 2021 and June 2024, anticardiolipin (aCL; IgG and IgM) and anti-beta2 glycoprotein I (aß2GPI; IgG and IgM) antibodies were measured using ELISA (n = 5115) and a chemiluminescence-based automated immunoassay (CLIA) (n = 3820). Results of parallel testing were compared, and associations with clinical and laboratory characteristics were evaluated. Results: A total of 946 samples were tested using ELISA and CLIA in parallel. A total of 136 (14%) specimens were positive for at least one aPL, and 55 (6%) specimens were from patients diagnosed with APS. Among the latter, 47 (85%) and 41 (75%) patients were positive when ELISA- or CLIA-based aPL assays were used, respectively. After applying the &gt;40 units threshold of the new classification criteria, the number of aPL-positive specimens was significantly lower. In the entire cohort, the agreement between ELISA and CLIA aPL assays was acceptable only for aß2GPI IgG; the results from the two methods did not agree for aCL IgG/IgM and aß2GPI IgM. In APS patients, the agreement between ELISA and CLIA aPL assays was acceptable for aß2GPI IgG and IgM but poor for aCL IgG and IgM. Antibody levels in APS patients were significantly higher using CLIA compared to ELISA. Conclusions: The method-dependent discrepancies between ELISA- and CLIA-based aPL assays regarding the quantitative and qualitative results are substantial. Both methods are suitable for APS classification, but the choice of aPL assay may influence the classification, and therefore, aPL results should be interpreted carefully in the clinical context.
Noun-adjective collocations in L2 Portuguese: Exploring the effects of proficiency and native language in a large-scale learner corpus
2024-08-02

Abstract We examined learners’ use and development of multiword expressions in Portuguese, an understudied L2. We analyzed essays from a large pool of learners across five proficiency levels (i.e., beginner, elementary, intermediate, upper intermediate, advanced), representing a variety of typologically diverse L1s (N = 679). Specifically, we investigated learners’ use of multiword expressions in terms of five different measures of collocability: phrase frequency, mutual information, log dice and two measures of Delta P, as functions of two key learner-related variables: proficiency levels, and the word-order typology of learners’ L1s. We also examined the accuracy in learners’ use of multiword expressions. The results of our mixed-effects models revealed a complex picture. While highly proficient learners use multiword expressions more accurately, they do not always produce more frequent and idiomatic outputs. Typological similarity between learners’ L1s and Portuguese do not consistently result in more idiomatic multiword expression use. Keywords: Multiword expressions; learner corpora; collocations; association measures; Portuguese, usage-based approaches
Weakening of meltwater plume reduces basal melting in summer at Ekström Ice Shelf, Antarctica
2024-08-02

Abstract. Basal melting of ice shelves significantly contributes to the mass loss of the Antarctic Ice Sheet. However, little is known about the ocean-driven melting of the numerous ice shelves of Dronning Maud Land in East Antarctica. We present a multi-year record of basal melt rates at the Ekström Ice Shelf, obtained using an autonomous phase-sensitive radar system. Our data reveal a low mean annual melt rate of 0.45 m a-1, with seasonal patterns showing reduced melt in summer and peaks in winter and spring. Sea-ice growth just in front of Ekström Ice Shelf correlates with the melt rate time series. A simple ice shelf water plume simulation suggests that melting is reduced in summer in the presence of Antarctic Surface Water, which reduces the velocity of the ice shelf water plume due to the lower density contrast. In winter, when dense water from the sea ice formation erodes the stratification below the ice shelf, more vigorous plumes cause an increase in melt rates. Thus, meltwater plume velocity primarily drives the basal melt rate at the Ekström Ice Shelf, with ambient water temperature being a secondary factor. Upscaling these observations to other ice shelves in this Antarctic sector will improve the overall assessment of the ice-shelf mass balance and improve future projections.
Exploring the nexus between sleep, chronotype, and non-cognitive predictors in university students: Implications for academic success
2024-08-02

While the association between sleep-related variables and academic achievement is widely acknowledged, limited attention has been directed towards exploring non-cognitive predictors of academic achievement such as conscientiousness and self-regulation. In this study, we investigated the relationships between various sleep-related factors (circadian preference, chronotype, sleep duration, quality, and irregularity) and non-cognitive predictors (conscientiousness, self-regulation, self-efficacy, and achievement motivation) in 637 university students. Bivariate analyses revealed moderate to strong correlations among several sleep-related measures. Notably, distinctness, representing the subjective perception of daily changes, and daytime sleepiness exhibited negative associations with self-regulation, while high sleep quality was positively linked to robust self-regulation. These findings emphasize the importance of exploring various measures, particularly distinctness within circadian typology. Furthermore, we discuss the potential integration of sleep intervention programs with strategies aimed at enhancing self-regulation.
Directional long-distance electron transfer from reduced to oxidized zones in the subsurface
2024-08-03

Electron transfer (ET) is the fundamental redox process of life and element cycling. The ET distance is normally as short as nanometers or micrometers in the subsurface. However, the redox gradient in the subsurface is as long as centimeters or even meters. This gap triggers an intriguing question whether directional long-distance ET from reduced to oxidized zones exists along the redox gradient. By using electron-donating capacity variation as a proxy of ET, we show that ET can last over 10 cm along the redox gradient in sediment columns, through a directional long-distance ET chain from reduced to oxidized zones constituted by a series of short-distance electron hopping reactions. Microbial and chemical processes synergistically mediate the long-distance ET chain, with an estimated flux of 6.73 μmol e<sup>-</sup>/cm<sup>2</sup> per day. This directional long-distance ET represents an overlooked but important "remote" source of electrons for local biogeochemical and environmental processes.