julilili42/papers huggingface dataset:
A universal language for finding mass spectrometry data patterns
2025-05-12

Abstract Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.
An inherently interpretable AI model improves screening speed and accuracy for early diabetic retinopathy
2025-05-12

Diabetic retinopathy (DR) is a frequent complication of diabetes, affecting millions worldwide. Screening for this disease based on fundus images has been one of the first successful use cases for modern artificial intelligence in medicine. However, current state-of-the-art systems typically use black-box models to make referral decisions, requiring post-hoc methods for AI-human interaction and clinical decision support. We developed and evaluated an inherently interpretable deep learning model, which explicitly models the local evidence of DR as part of its network architecture, for clinical decision support in early DR screening. We trained the network on 34,350 high-quality fundus images from a publicly available dataset and validated its performance on a large range of ten external datasets. The inherently interpretable model was compared to post-hoc explainability techniques applied to a standard DNN architecture. For comparison, we obtained detailed lesion annotations from ophthalmologists on 65 images to study if the class evidence maps highlight clinically relevant information. We tested the clinical usefulness of our model in a retrospective reader study, where we compared screening for DR without AI support to screening with AI support with and without AI explanations. The inherently interpretable deep learning model obtained an accuracy of .906 [.900–.913] (95%-confidence interval) and an AUC of .904 [.894–.913] on the internal test set and similar performance on external datasets, comparable to the standard DNN. High evidence regions directly extracted from the model contained clinically relevant lesions such as microaneurysms or hemorrhages with a high precision of .960 [.941–.976], surpassing post-hoc techniques applied to a standard DNN. Decision support by the model highlighting high-evidence regions in the image improved screening accuracy for difficult decisions and improved screening speed. This shows that inherently interpretable deep learning models can provide clinical decision support while obtaining state-of-the-art performance improving human-AI collaboration.
1,6-Diazapyrene: A Novel, Well-Defined, Small-Size Prototype System for Nitrogen-Containing PAHs
2025-05-12

The quest for nitrogen-doped (N-doped) polycyclic aromatic hydrocarbons (PAHs) requires well-defined prototype systems to understand the relationship between the structure and the resulting photophysical and photochemical properties. To this end, a novel, simple, and small compound, 1,6-diazapyrene, was synthesized. In-depth analysis, employing optical spectroscopy and (time-dependent) density functional theory, (TD-)DFT, elucidates the optical excitations on the basis of MO symmetry, energy, and topology considerations; the study further unveils the photophysical and photochemical deactivation kinetics after photoexcitation, revealing extreme changes against pyrene as well as against the well-known 2,7-diazapyrene isomer. The high sensitivity of the aza-substitution position to generate such changes is considered as highly relevant for the targeted design of N-doped PAHs in general.
Bloodstream infections in a rural hospital in Sierra Leone: a retrospective database study
2025-05-12

Background. The health system in Sierra Leone has limited infrastructure to provide data on the epidemiology of infectious diseases and to inform clinical decision-making. The diagnostic and research laboratory capacity at Masanga Teaching Hospital was systematically expanded with microbiology infrastructure-building as one of the centrepieces. Objective. This study aims to report the spectrum of bacterial pathogens from bloodstream infections (BSIs) in a rural hospital in Sierra Leone during the first year after the implementation of a blood culture infrastructure and characterize the detected antimicrobial resistances. Patients and methods. Patients treated at Masanga Hospital (Sierra Leone, March 2023–March 2024) were included in this database analysis if they were tested for BSI (BD BACTEC). Demographic and medical data were recorded for each patient. Antimicrobial susceptibility testing was done following EUCAST clinical guidelines. Results. Of the 340 blood cultures, 34 (10%) were positive for obligate pathogens. The three most frequent pathogens were Escherichia coli ( n =8), followed by Burkholderia cepacia complex ( n =7) and Salmonella enterica ( n =5). Almost all Klebsiella pneumoniae ( n =3/3) and E. coli ( n =7/8) were resistant to third-generation cephalosporins. All four Staphylococcus aureus isolates were methicillin susceptible ( mecA negative). Carbapenem resistance was detected in Acinetobacter baumannii complex ( bla NDM ) Conclusion. The proportion of positive blood cultures with obligate pathogens (10%) was within the suggested benchmark (5–15%). Gram-negative bacteria dominated the pathogen spectrum of BSI with high resistance rates to third-generation cephalosporins.
The impact of stress and self-awareness on food intake in children and adolescents with and without loss of control eating – an experimental test of the escape from self-awareness model
2025-05-12

Loss of control eating (LOC-E) is the most common form of disordered eating in childhood and adolescence. Negative emotions and stress play a crucial role in its development and maintenance. The purpose of this study is to experimentally test the escape from self-awareness model, which proposes that LOC-E occurs because individuals attempt to reduce their emotional distress by shifting their focus from an aversive self-perception to the immediate environment, such as food. We investigated the effect of stress (false negative or positive performance feedback) and self-awareness (opened or closed full-body mirrors) inductions on desire to eat (DTE) and food intake in adolescents with and without LOC-E. While there were no effects of stress on DTE irrespective of group membership, participants with and without LOC-E ate less (rather than more, as hypothesized) in the high stress condition. Neither of these effects interacted with the self-awareness condition. Because the stress induction had the unintended effect of increasing participants' self-awareness, we found evidence that participants decreased their food intake when experiencing stress and high self-awareness concurrently. The results of this study contribute to a further understanding of the role of stress and self-awareness on DTE and food intake in children and adolescents with and without LOC-E.
Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor
2025-05-12

Epithelial-mesenchymal transition (EMT) plays an essential role in embryonic development, wound healing, and tumor progression. Partial EMT states have been linked to metastatic dissemination and drug resistance. Several interconnected feedback loops at the RNA and protein levels control the transition between different cellular states. Using a combination of mathematical modeling and experimental analyses in the TGFβ-responsive breast epithelial MCF10A cell model, we identify a central role for the tumor suppressor protein Deleted in Liver Cancer 1 (DLC1) during EMT. By extending a previous model of EMT comprising key transcription factors and microRNAs, our work shows that DLC1 acts as a positive regulator of TGFβ-driven EMT, mainly by promoting SNAIL1 expression. Our model predictions indicate that DLC1 loss impairs EMT progression. Experimental analyses confirm this prediction and reveal the acquisition of a partial EMT phenotype in DLC1-depleted cells. Furthermore, our model results indicate a possible EMT reversion to partial or epithelial states upon DLC1 loss in MCF10A cells induced toward mesenchymal phenotypes. The increased EMT plasticity of cells lacking DLC1 may explain its importance as a tumor suppressor.
Addressing organizational learning to increase readiness for physical activity promotion in seven German nursing homes
2025-05-12

Promoting physical activity among nursing home residents is essential for enhancing physical and mental well-being. However, organizational structures often prioritize basic care and indirectly hinder physical activity promotion. This study investigates organizational and individual learning processes to increase readiness for physical activity promotion in seven German nursing homes between 2020 and 2023. We selected a heterogeneous mix of nursing homes from the applications representing different forms of organizations regarding environmental contexts, capacity, care providers, and resident population composition. We used a mixed-methods approach for data collection, including interviews, documents, surveys, photologs, and fieldnotes. Data was treated confidentially and recorded pseudonymously. Applying qualitative content analysis, we revealed that physical activity promotion was initially insufficiently incorporated into organizational structures. Through a comprehensive assessment tool, we analyzed post-intervention changes in organizational readiness. Using a public management organizational learning model, we identified key processes that drove these changes. To maintain reflexivity, two authors analyzed data and discussed the results. Combining different data collection forms reduced the risk of researcher bias. Collaborating with external stakeholders helped validate the findings. Our findings highlight the significance of individual and organizational learning, which led to notable shifts: Individual learning improved staff awareness for the relevance of and competencies in physical activity promotion, as well as resident participation levels in actions offered. Organizational learning led to an adaptation of weekly activity schedules, modification of existing actions to promote PA in close alignment with home-specific needs, and the creation of PA-friendly infrastructures. Health-promoting leadership and shared values emerged as crucial factors in fostering a culture of physical activity promotion. Our study demonstrates the feasibility of promoting physical activity in nursing homes by integrating it into organizational structures and fostering a culture of readiness. This approach can enhance resident well-being and quality of life.
Effects of corticothalamic feedback depend on visual responsiveness and stimulus type
2025-05-12

In the dorsolateral geniculate nucleus (dLGN) of the thalamus, stimulus-driven signals combine with modulatory inputs such as corticothalamic (CT) feedback and behavioral state, but their impact in shaping dLGN activity is debated. We recorded extracellular responses in the dLGN of mice viewing a movie stimulus, while photosuppressing CT feedback and tracking locomotion and pupil size. Using generalized linear models fit to single neuron responses, we found that including CT feedback and behavioral state improved model predictions, especially for a subpopulation of neurons poorly responsive to the movie. Intriguingly, the impact of CT feedback was stronger without a patterned visual stimulus. Finally, for neurons sensitive to CT feedback, visual stimuli could be more easily discriminated when CT feedback was suppressed. Together, these results show that the effects of modulatory inputs in dLGN depend on visual responsiveness and stimulus type, with CT feedback affecting sensitivity and reliability, potentially to tune the thalamic relay.
Axisymmetric stability of neutron stars as extreme rotators in massive scalar-tensor theory
2025-05-12

Differentially rotating scalarized neutron stars can possess an enormous amount of angular momentum larger than what could possibly be sustained in a neutron star in general relativity by about one order of magnitude. A natural question to ask is whether these solutions are stable and thus can be realized in a binary coalescence. With this motivation in mind, we examine the criterion of dynamical stability against axisymmetric perturbations for these ultra-rotators by numerically tracking their nonlinear evolution in an axisymmetric setup. We demonstrate that the turning-point criterion still serves as a sufficient condition for axisymmetric stability within the accuracy of the performed simulations. Our findings open an interesting question of whether the merger of two scalarized neutron stars can produce (possibly short-lived) ultra-highly rotating merger remnants.
COVID-19 knowledge, attitude, and practice in combating TB and COVID-19 in Cameroon
2025-05-12

Background: COVID-19 and tuberculosis (TB) were the top two leading causes of death from a single infectious agent in 2022. Aim: This study aimed at assessing COVID-19 knowledge, attitude, and practices (KAP) and their associated factors among pulmonary TB patients and healthy individuals in Yaoundé, Cameroon. Setting: The study was conducted at the Jamot Hospital in Yaoundé, a main referral hospital for TB management in Cameroon. Methods: A cross-sectional design was used to recruit a consecutive sample of TB patients and healthy participants at Jamot Hospital and communities in Yaoundé, Cameroon, from April 2022 to March 2023. Data on socio-demographic characteristics and COVID-19 KAP were collected and analysed using logistic regression with significance considered at p &lt; 0.05. Results: Out of 409 participants, 67.5% had good knowledge, 54% had a favourable attitude, and 22.5% had good practices towards COVID-19. Multivariate analysis identified TB status, age, sex, and marital status as significant factors influencing KAP scores. Good knowledge and good practices were associated with being healthy, young, and single (p &lt; 0.05). In addition, the female gender, good knowledge, and favourable attitudes were associated with good practices (p &lt; 0.05). Conclusion: Gaps in COVID-19 KAP among TB patients highlight the need for targeted public health interventions, with a focus on TB patients, males, the elderly, and married individuals for better control. Contribution: Tuberculosis patients are not adopting positive prevention practices as required, thus increasing their risk of getting COVID-19 and transmitting TB, necessitating urgent action.
LGDE: Local Graph-based Dictionary Expansion
2025-05-12

Abstract We present Local Graph-based Dictionary Expansion (LGDE), a method for data-driven discovery of the semantic neighbourhood of words using tools from manifold learning and network science. At the heart of LGDE lies the creation of a word similarity graph from the geometry of word embeddings followed by local community detection based on graph diffusion. The diffusion in the local graph manifold allows the exploration of the complex nonlinear geometry of word embeddings to capture word similarities based on paths of semantic association, over and above direct pairwise similarities. Exploiting such semantic neighbourhoods enables the expansion of dictionaries of pre-selected keywords, an important step for tasks in information retrieval, such as database queries and online data collection. We validate LGDE on two user-generated English-language corpora and show that LGDE enriches the list of keywords with improved performance relative to methods based on direct word similarities or co-occurrences. We further demonstrate our method through a real-world use case from communication science, where LGDE is evaluated quantitatively on the expansion of a conspiracy-related dictionary from online data collected and analysed by domain experts. Our empirical results and expert user assessment indicate that LGDE expands the seed dictionary with more useful keywords due to the manifold-learning-based similarity network.
AutoMLST2: a web server for phylogeny and microbial taxonomy
2025-05-13

Abstract Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 (https://automlst2.ziemertlab.com) is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes. It builds on the foundation of AutoMLST, which remains widely used due to its user-friendly interface compared to similar tools. Given its continued popularity and utility, we have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more customizable processing modes, containerization to prevent queue accumulations, and parallel computing for large-scale studies. By incorporating up-to-date databases and workflows, AutoMLST2 continues to provide an accessible and efficient platform for researchers in microbiology, evolutionary ecology, and natural product discovery.
A comparative analysis of technical data: At-home vs. in-clinic application of transcranial direct current stimulation in depression
2025-05-13

The study demonstrates that monitoring the technical parameters of at-home tDCS used in this study is essential. However, it may be not sufficient for ensuring safety and promptly detecting or preventing adverse events. Quality control protocols including digital training and monitoring techniques should be systematically developed and tested for a reliable and safe application of at-home tDCS therapies.
How childhood adversities shape minds and lives: An analysis across the affective-to-psychotic spectrum
2025-05-13

Adverse childhood experiences (ACE) contribute significantly to mental disorders. While existing research has primarily focused on specific diagnostic categories, a comprehensive understanding of how childhood trauma interacts with biological factors, symptom severity and functioning requires a broader perspective. Therefore, this study adopted a cross-diagnostic approach to examine the impact of ACE on quality of life (QoL), psychosocial functioning, and symptom burden by analyzing data from the PsyCourse Study, a longitudinal, multicenter research project conducted in Germany and Austria. We used multivariate linear regression models and cluster analysis to evaluate data from 725 participants with affective and psychotic disorders and healthy controls who completed the self-assessed Childhood Trauma Screener (CTS) during the course of the study. The results showed that across diagnoses, QoL was significantly impacted by ACE, particularly emotional neglect. An ablation study revealed that 2.3 % to 6.2 % of the variability in QoL domains could be attributed to ACE. Across diagnoses, symptoms of depression were significantly associated with ACE, especially emotional abuse, but psychotic and manic symptoms were not. Polygenic risk scores (PRS) did not emerge as significant predictors for any examined outcomes. Cluster analysis revealed distinct symptom profiles: Averaged over time, patients with less trauma exposure were rather in the subclinical than in the clinically ill clusters. We conclude that the pervasive influence of ACE on disease severity should be considered when evaluating and treating patients with affective and psychotic disorders.
Structure-activity relationships of inactive-conformation binding EGFR inhibitors: Linking the ATP and allosteric pockets
2025-05-13

Epidermal growth factor receptor (EGFR) tyrosine kinase is an important therapeutic target in non-small cell lung cancer (NSCLC). However, the continual emergence of resistance mutations in the treatment of EGFR mutation-positive NSCLC with currently approved tyrosine kinase inhibitors warrants the development of next generation inhibitors. Since research for ATP-competitive EGFR TKIs that extend into the back pocket has been neglected in the recent past, we survey the extent to which such binding functional groups can be incorporated into an ATP-site imidazole scaffold. We find that meta-substituted amide linkers derivatized with fluorine in 2,6-positions and/or a hydroxy group in 3-position of the back pocket phenyl exhibit the highest potency. Structural insights into how the back pocket groups are bound through points of connection provide new directions for the discovery and optimization of inactive conformation targeting agents in EGFR and other kinases.
Compability of family and clinical-scientific career for German gynecologists in different workplaces: a sub- analysis of the systematic trinational FARBEN Survey
2025-05-13

<title>Abstract</title> Introduction The trinational survey project conducted by the Young Forums of the German, Austrian, and Swiss Societies for Gynecology and Obstetrics aims to assess the preferences of prospective and practicing gynecologists regarding various work-time models, educations systems, career and work-family-live balance. Materials and Methods Between October 2023 and May 2024, a total of 1,364 participants took part in the FARBEN survey. The questionnaire consisted of 62 questions covering topics such as the workplace in general, work-time models, training priorities, team compositions, and professional goals. Participation was voluntary and anonymous. This is a national subanalysis evaluating individual preferences according to current workplace (university vs. non-university departments vs. outpatient care) of German participants. Results Of 1,008 participants from Germany, 26.3% were employed in university departments, 55.4% in non-university departments and 10.8% in outpatient care. Respondents employed in university departments were more likely to pursue a scientific-academic career (68.0% held a doctorate, 7.5% a habilitation [highest academic achievement in German-speaking countries] or a professorship; 38.5% aspiring to a habilitation vs. 6.6% in non-university departments). Women at university departments became mothers later than at non-university departments and returned earlier from parental leave. Childcare provided by the workplace was reported as better and more flexible at university departments (20.4% vs. 9.6% at non-university departments and 8.4% in outpatient care). 34.1% of participants from university departments reported their head of department was female, compared to 19.2% at non-university departments (p &lt; 0.001). Conclusions The compatibility of family and career and a good work-life balance are important for the majority of gynecologists in specialty training, regardless of their place of work. Participants working in university settings were more likely to pursue academic career and reported higher flexibility and better childcare support. In times of a deficite of upcoming medical physicians, employment policy should focus on these points. Guidelines such as “Safe surgery during pregnancy” can help to ensure that family planning does not hinder clinical training.