julilili42/papers huggingface dataset:
Open-Source and FAIR Research Software for Proteomics
2025-04-23

Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.
Recurrent stroke in patients with history of stroke/transient ischemic attack and device-detected atrial fibrillation: A systematic review and meta-analysis
2025-04-23

Introduction: Prolonged cardiac monitoring after stroke increases the detection of device-detected atrial fibrillation (DDAF), leading to a clinical dilemma regarding anticoagulation for secondary stroke prevention. While anticoagulation reduces thromboembolic risk in clinical AF, its benefit-risk profile in DDAF remains uncertain. Methods: In this systematic review and meta-analysis, randomized-controlled clinical trials (RCTs) evaluating anticoagulation among patients with DDAF post stroke or transient ischemic attack (TIA) were pooled. The primary efficacy outcome was any stroke recurrence, while stroke or systemic embolism, ischemic stroke recurrence, myocardial infarction, and cardiovascular mortality were assessed as secondary efficacy outcomes. The primary safety outcome was major bleeding, while hemorrhagic stroke and all-cause mortality were assessed as secondary safety outcomes. Results: Two RCTs with 599 patients (294 anticoagulation, 305 no-anticoagulation) were included. Anticoagulation significantly reduced any stroke recurrence (RR: 0.47; 95% CI: 0.23–0.94; p = 0.034; number-needed-to-treat = 34). Anticoagulation lowered the risk of the composite outcome of stroke recurrence and systemic embolism (RR: 0.45; 95% CI: 0.22–0.90; p = 0.023). However, anticoagulation was associated with an increased risk of major bleeding (RR: 2.30; 95% CI: 1.06–4.98; p = 0.035; number-needed-to-harm = 37). There were no differences in ischemic stroke recurrence (RR: 0.53; 95% CI: 0.26–1.09; p = 0.084), myocardial infarction (RR: 0.58; 95% CI: 0.17–1.96; p = 0.379), cardiovascular mortality (RR: 0.68; 95% CI: 0.35–1.34; p = 0.265), hemorrhagic stroke (RR: 0.25; 95% CI: 0.03–2.24; p = 0.217) or all-cause mortality (RR: 0.97; 95% CI: 0.66–1.41; p = 0.857). Discussion: Anticoagulation in DDAF patients with prior stroke/TIA reduces any stroke recurrence but increases major bleeding risk without raising hemorrhagic stroke incidence. This trade-off underscores the need for individualized risk stratification. Conclusions: Anticoagulation lowers any stroke recurrence in DDAF patients post-stroke/TIA but raises major bleeding risk.
ExplainitAI: When do we trust artificial intelligence? The influence of content and explainability in a cross-cultural comparison
2025-04-23

This study investigates cross-cultural differences in the perception of AI-driven chatbots between Germany and South Korea, focusing on topic dependency and explainability. Using a custom AI chat interface, ExplainitAI, we systematically examined these factors with quota-based samples from both countries (N = 297). Our findings revealed significant cultural distinctions: Korean participants exhibited higher trust, more positive user experience ratings, and more favorable perception of AI compared to German participants. Additionally, topic dependency was a key factor, with participants reporting lower trust in AI when addressing societally debated topics (e.g., migration) versus health or entertainment topics. These perceptions were further influenced by interactions among cultural context, content domains, and explainability conditions. The result highlights the importance of integrating cultural and contextual nuances into the design of AI systems, offering actionable insights for the development of culturally adaptive and explainable AI tailored to diverse user needs and expectations across domains.
Chimeric antigen receptor NK-92 cell function is modulated by HLA class I expression of target cells
2025-04-23

Chimeric antigen receptors - natural killer (CAR-NK) cells are a promising new cancer treatment approach. They possess distinct benefits over CAR-T cells, including an intrinsic ability to differentiate between malignant and non-malignant cells, and a lower risk of graft-versus-host disease. Here, we evaluated two CAR-NK-92 cell lines, targeting either CD276 or HER2, and their potential on-target/off-tumor effects <i>in vitro</i>. CD276-directed CAR-NK-92 cells showed little dependence on target antigen density, while HER2-directed CAR-NK-92 displayed a pronounced dependence on target antigen density, mostly sparing target cells with low amounts of HER2. The activity of both cell lines was modulated by the expression of HLA-I on target cells, ultimately reducing their activity against non-malignant cells. Lower modulation of activity of HER2-directed CAR-NK-92 can be explained by the lower surface expression of inhibitory NK receptors, such as NKG2A and ILT-2. These results underscore the importance of thoroughly testing new cell products to fine-tune anti-cancer activity, while limiting potential on-target/off-tumor toxicity.
Angiotensin II-induced cardiac fibrosis and dysfunction are exacerbated by deletion of cGKI in periostin+ myofibroblasts
2025-04-23

Differentiation of cardiac fibroblasts (CFs) into myofibroblasts (CMFs) is considered a critical event in response to the maladaptive cardiac remodeling triggered by angiotensin II (Ang II). Active CMFs are proliferative and contribute to the production of extracellular matrix and matricellular proteins such as periostin, to myocardial fibrosis, and thus to muscle stiffness. Although previous studies provided substantial evidence for the antifibrotic signaling elicited by NO/NP-cGMP-cGKI, the role of this axis in modulating CMF function(s) in vivo remains unclear. To address this, Ang II was delivered through osmotic minipumps into tamoxifen-induced CMF-specific cGKI knockout (cmfKO) and littermate control (CTR) male mice. CMF-restricted Cre activity in periostin+ cells resulted in an effective depletion of the cGKI protein observed in myocardial sections and in primary CF/CMF protein lysates obtained from Ang II- and tamoxifen-treated cmfKO. Although both genotypes responded identically to Ang II in terms of blood pressure (BP) and cardiac enlargement, cmfKO hearts showed significantly increased cardiomyocyte cross-sectional areas and developed a marked increase in myocardial fibrosis. Moreover, non-invasive echocardiography revealed a structure-related distortion of global systolic function and longitudinal deformation capacity in cmfKO versus CTR. Consistent with the results obtained in vivo, we observed a higher proliferation rate of CF/CMF derived from Ang II-treated cmfKO hearts compared with respective CTR cells, as well as an increase in cardiomyocyte apoptosis in the absence of cGKI in periostin+ CMF. Our data confirm that endogenous cGKI function in periostin+ CMFs counteracts the Ang II-induced morphologic and structural changes that impair cardiomyocyte survival ultimately causing loss of heart function in mice.
Task-specific regional circuit adaptations in distinct mouse retinal ganglion cells
2025-04-23

In the mouse retina, sustained ON alpha (sONα) retinal ganglion cells (RGCs) have different dendritic and receptive field sizes along the nasotemporal axis, with temporal sONα RGCs likely playing a role in visually guided hunting. Thus, we hypothesized that this cell type also exhibits regional adaptations in dendritic signal processing and that these adaptations are advantageous for prey capture. Here, we measured dendritic signals from individual sONα RGCs at different retinal locations. We measured both postsynaptic Ca 2+ signals at dendrites and presynaptic glutamate signals from bipolar cells (BCs). We found that temporal sONα RGCs exhibit, in addition to sustained-ON signals with only weak surrounds, signals with strong surround suppression, which were not present in nasal sONα RGCs. This difference was also present in the presynaptic inputs from BCs. Last, using population models in an encoder-decoder paradigm, we showed that these adaptations might be beneficial for detecting crickets in hunting behavior.
Online Training to Increase Genetic and Risk Literacy in Physicians Counseling Breast and Ovarian Cancer Patients for Genetic Testing
2025-04-23

&lt;p&gt;Introduction: The increasing use of germline genetic testing for the clinical management of patients with a family history of breast and ovarian cancer requires an improvement in the genetic and risk literacy of physicians and healthcare professionals. In order to offer high-quality care throughout Germany, from genetic counseling to risk-adapted prevention, the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) and the German Cancer Society (DKG) have established a nation-wide cooperation partner network with certified gynecological and breast cancer centers. As a core element of this cooperation, an online-based training program has been developed in which the “state-of-the-art knowledge” on the topic is conveyed. Methods: The training is aimed at physicians and healthcare professionals working in the specialized centers of the GC-HBOC/certified centers for familial breast and ovarian cancer (FBREK centers) or the cooperating certified gynecological and breast cancer centers. It consists of an online-based part (15 lectures) covering interdisciplinary basics and competencies on political frameworks, genetic and nongenetic risk factors including individual risk calculation, and nondirective communication on risk-adapted prevention options. Patient involvement with voting rights during the development and implementation of the training increased its accuracy of fit for patient needs. After a successful online knowledge test, employees of certified gynecological and breast cancer centers participate in a 1-day, on-site internship at an FBREK center with which a cooperation is planned. Results: From November 2021 to July 2024, 1,860 participants registered for the online training, of which 1,329 have started to work on the content. So far, 898 participants have passed the online knowledge test. More than 560 participants took part in the accompanying evaluation in which the majority stated that the course helped to increase their professional knowledge, it was relevant to their practical medical work, and it contributed to a more confident approach to patients with a family history of cancer. Most participants stated that it was worthwhile participating in the training in terms of time and organization and that the content, didactics, visual presentations, and comprehensibility were appropriate. Conclusion: The online-based training serves to impart and expand interdisciplinary knowledge and skills in genetics and risk counseling. It is well received, has been positively evaluated and the format proves to be suitable for strengthening the networked care of patients across sectoral boundaries and promoting the rapid translation of new research findings into clinical practice within the framework of knowledge-generating care. &lt;/p&gt;
Pre-clinical medical students' perception of surgical professions – too demanding and difficult to balance with private life?
2025-04-23

<title>Abstract</title> <bold>Background:</bold> Surgical professions in Western Europe deal with serious challenges to inspire students to pursue a surgical career and counteract demographic change. Students’ interest in sub-specialization is influenced by socio-economic factors including work-life balance, flexible working hours and appreciation. However, robust data about the current perception of surgical professions in the early stage of medical education is lacking so far. <bold>Methods:</bold> We performed a voluntary online survey amongstudents who participated in an elective neurosurgical course during their preclinical stage of medical studies. The survey addressed perception of surgical professions, including personal requirements, profession impact on health and lifestyle and the topic of gender disparities and family planning. We also assessed viewpoints on support programs facilitating compatibility of surgical training and family life. <bold>Results: </bold>A total of 109 students participated in the voluntary survey (66.1% female; 33.0% male, 0.9% unknown). 55.5% of respondents had prior experiences with surgical professions and 33.9% planned to pursue a surgical career. Most respondents rated surgical professions as more demanding for the physical health and more harmful for the health of physicians than other specialties. However, mental implications were higher rated in other professions. Interestingly, female participants agreed to higher career chances for male residents as well as to difficulties to combine family planning and performing the surgical profession, whereas male participants remained more neutral to both statements. Overall, 89.0% of participants expressed interest in support programs increasing compatibility of professional and personal life. Furthermore, 65.1% of participants would be willing to accept an extension of their surgical resident time by a year. <bold>Conclusions: </bold>In summary, pre-clinical medical students rate surgical disciplines as highly demanding, competitive and difficult to balance with private life. Early awareness of structured support programs may positively influence may improve sustainable resident application numbers in surgical sub-specialties.
Clinical manifestations of dual-gene variants involving ABCA4 in retinal dystrophies
2025-04-23

Abstract Background This study investigates the clinical manifestations of inherited retinal diseases (IRD) associated with dual-gene variant constellations involving biallelic ABCA4 variants. Methods We assess four cases for their unique phenotypic outcomes due to biallelic ABCA4 variants and additional genotypes in CACNA1F , IMPG1 , HK1 and MYO7A , respectively. Results This study investigates the phenotypic impact of dual-gene variants, including biallelic ABCA4 variants and additional retinal gene variants in CACNA1F , IMPG1 , HK1 and MYO7A . In MST465-II:1, the ABCA4 - CACNA1F constellation led to progressive macular atrophy and night blindness, with nystagmus linked to CACNA1F . In MST448-II:1, ABCA4 variants primarily contributed to a macular dystrophy, while the IMPG1 variant had no obvious impact, suggesting it may be a benign polymorphism. In SRP1400-II:1, a de novo HK1 variant caused retinitis pigmentosa (RP)-like retinal degeneration and intellectual disability and in USHI105-II:1, MYO7A variants primarily resulted in an Usher syndrome 1 phenotype. In both latter cases, ABCA4 variants play a more subtle role. These findings illustrate the importance of critical phenotype and genotype assessment and how complex interactions between ABCA4 and other genetic variants can configure the phenotype, making it challenging to distinguish the contributions of each gene. Conclusions This study underscores the importance of advanced diagnostic tools and careful genotype evaluation to accurately identify and understand potential complex genetic interactions in IRDs. The observed phenotypes enhance our understanding of how these genes contribute to human retinal function and dysfunction. Furthermore, these insights can impact clinical decision-making, as patients with dual-gene variant constellations might experience questionable benefit from potential future gene therapies. Thus, careful patient selection and complete genotype and phenotype assessment before treatment is essential to manage potential risks and costs effectively.
Did Avicenna Write a Risāla fī l-Wujūd?
2025-04-23

Abstract The paper claims that Avicenna authored a thus far unknown treatise on existence, following a hint in Fakhr al-Dīn al-Rāzī’s Jawābāt al-masāʾil al-bukhāriyya . Al-Rāzī informs us about the doctrinal content of the treatise–Avicenna held that existence does not have a second-order existence–as well as about its textual history–a portion of the treatise was preserved in Bahmanyār’s Taḥṣīl . Al-Rāzī’s report is confirmed by several manuscript witnesses of the Taḥṣīl , which contain an anomalous layer of text corresponding to his description. Additional evidence comes from comparing the doctrines defended in the text to other Avicennian works, as well as to al-Khayyām’s own treatise on existence. This leads to the additional conclusion that Avicenna’s treatise (or the portion preserved by Bahmanyār) is among the sources of al-Khayyām’s. Finally, the paper outlines the content of the available portion of the treatise, highlighting its connections to other Avicennian and early post-Avicennian works.
Ecomorphology in Kenya's Koobi Fora Formation: Reconstructing Early Pleistocene hominin paleoenvironments with 3D geometric morphometric analyses of bovid metapodials
2025-04-23

This research presents a new method of ecological morphology (ecomorphology) analysis using three-dimensional geometric morphometrics to quantify shape variation in extant bovid metapodials with known habitat preferences. Extant data were used to create a model for classifying bones into distinct habitat categories and to test functional hypotheses related to locomotor behavior in different habitats. The model was then applied to fossils from the Koobi Fora Formation, Kenya, to assess the environmental context during important events in hominin evolution. The use of three-dimensional geometric morphometrics demonstrates significant improvement over traditional methods using caliper measurements. Discriminant function analysis successfully classified 94% of metacarpals and 93% of metatarsals into their correct habitat categories for modern specimens. The protocol was reduced to a subset of landmarks focused on the distal epiphyses. This model produced greater overlap, but classification success rates remained high, with 82% and 83% correct classification for modern metacarpals and metatarsals, respectively. We applied the reduced model to metapodials from Upper Burgi (1.98-1.87 Ma), KBS (1.87-1.56 Ma), and Okote (1.56-1.38 Ma) members in the Koobi Fora Formation. This location is important to understanding human evolution, fossil diversity, and paleoecology. Moreover, previous studies on faunal abundance, paleosol carbonates, and carbon isotopes provide a robust framework to compare the findings of this study. Our analyses classified the majority of fossil specimens as open-habitat dwellers, with a few specimens grouped as closed-adapted, the highest number of these falling within the Okote Member sample. This suggests that open and likely xeric environments dominated the East Turkana region during the Early Pleistocene. These findings are consistent with many previous reconstructions, though with a more open signal for the Okote Member than expected based on bovid abundance research.
Rocks and clay: Potters’ technological choices within the cultural dynamics of Bronze Age Kazakhstan
2025-04-23

Through regular interactions with their neighbors, diverse groups inhabiting areas along the Inner Asian Mountain Corridor during the Bronze Age formed dynamic interregional networks that saw the proliferation and persistence of shared material cultures over vast geographic areas. In this paper we advocate for ceramics analyses that combine both macro- and micro-scale technological studies alongside those of style, in order not to lose sight of the actual people who drove defining transformations in the Bronze Age. We present a petrographic study of pottery from the Zhetysu region, southeastern Kazakhstan, to examine diachronic technological traditions with a special focus on routines of selection and raw material processing. Our results demonstrate site-specific potting technologies as well as traits that transcend both time and space across episodes of high genetic turnover in the human population.
Conventional and organic farms with more intensive management have lower soil functionality
2025-04-24

Organic farming is often considered to be more sustainable than conventional farming. However, both farming systems comprise highly variable management practices. In this study, we show that in organic and conventional arable fields, the multifunctionality of soils decreases with increasing agricultural management intensity. Soil organic carbon content and bacterial biomass, respectively, were the strongest abiotic and biotic predictors of soil multifunctionality. Greater soil multifunctionality was associated with less-frequent inversion tillage and higher frequency of grass-legume cover cropping, and organic farming did not outperform conventional farming. Our results suggest that reducing management intensity will enhance soil multifunctionality in both conventional and organic farming. This implies that, in contexts where high-yielding, high-intensity agriculture prevails, the paradigm of sustainable intensification should be replaced by “productive deintensification.”
An overview of progress in human metapneumovirus (hMPV) research: Structure, function, and therapeutic opportunities
2025-04-24

The human metapneumovirus (hMPV), a member of the Pneumoviridae family, is a significant respiratory pathogen that causes severe infections in infants, children, the elderly, adults with chronic illnesses, and individuals with immunocompromised conditions. Globally, hMPV is recognized as the second leading cause of bronchiolitis and pneumonia among children under five. The absence of targeted antiviral treatments or vaccines for hMPV significantly strains the global health-care system. This review summarizes recent advances and scientific findings on hMPV by reviewing the current literature on its life cycle, structure, function, prevention, and treatment options.