bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking And Datasets For Ambient Clinical Documentation: A Scoping Review Of Existing Frameworks And Metrics For AI-Assisted Medical Note Generation
Authors: Gebauer Sarah 
Published: January 2025

AbstractBackgroundThe increasing adoption of ambient artificial intelligence (AI) scribes in healthcare has created an urgent need for robust evaluation frameworks to assess their performance and clinical utility. While these tools show promise in reducing documentation burden, there remains no standardized approach for measuring their effectiveness and safety.ObjectiveTo systematically review existing evaluation frameworks and metrics used to assess AI-assisted medical note generation from doctor-patient conversations, and provide recommendations for future evaluation approaches.MethodsA scoping review following PRISMA guidelines was conducted across PubMed, IEEE Explore, Scopus, Web of Science, and Embase to identify studies evaluating ambient scribe technology between 2020-2025. Studies were included if they were peer-reviewed, focused on clinical ambient scribe evaluation from speaking to note production, and described an evaluation approach. Extracted data included evaluation metrics, benchmarking approaches, dataset characteristics, and model performance.ResultsSeven studies met inclusion criteria. Evaluation approaches varied widely, from traditional natural language processing metrics like ROUGE and BERTScore to domain-specific measures such as clinical accuracy and bias. Critical gaps identified include: 1) wide diversity of evaluation metrics making cross-study comparison challenging, 2) limited integration of clinical relevance in automated metrics, 3) lack of standardized approaches for crucial metrics like hallucinations and errors, and 4) minimal diversity in clinical specialties evaluated. Only two datasets were publicly available for benchmarking.ConclusionsThis review reveals significant heterogeneity in how ambient scribes are evaluated, highlighting the need for standardized evaluation frameworks. We propose recommendations for developing comprehensive evaluation approaches that combine automated metrics with clinical quality measures. Future work should focus on creating public benchmarks across diverse clinical settings and establishing consensus on critical safety and quality metrics.
Federated Prediction Models and External Validation for Radiotherapy Outcomes in Oropharyngeal Cancer using F.A.I.R. Clinical and Radiomics Data
Authors: Gouthamchand Varsha , Gottardelli Benedetta , Kulkarni Gauri , Sherkhane Umesh B , Hogenboom Joshi , Subramanian Rajamenakshi , Jha Ashish Kumar , Mithun Sneha , Purandare Nilendu C , Agarwal Jai Prakash , Sekar Krithikaa , Lohith G. , Laskar Sarbani G , Sinha Shwetabh , Hoebers Frank JP , Rangarajan Venkatesh , Sunder Gaur , Dekker Andre , Soest Johan van , Wee Leonard 
Published: January 2025

AbstractDevelopment and validation of outcome prediction models in multi-centric cancer datasets are essential to ensure their applicability and accuracy across diverse populations. This study addresses the challenges of model generalizability in Head and Neck cancer research by utilizing combined clinical and radiomics data from centers in India and the Netherlands, following Findable-Accessible-Interoperable-Reusable (F.A.I.R.) data principles. We use Vantage6, a federated learning software infrastructure that implements the Personal Health Train (PHT) paradigm to ensure data privacy and security during collaborative research. Correlation-based Feature Selection (CFS) and LASSO regularized Cox regression were used to identify key features in training Cox proportional hazards models to predict Overall Survival (OS), Distant Metastasis (DM), and Locoregional Recurrence (LRR) in six datasets totaling 1131 oropharyngeal cancer patients. Our results highlight the efficacy of federated learning in providing a secure environment for multi-centric cancer research, enabling the development and validation of predictive models while upholding patient data confidentiality.
Reevaluating the Role of Education in Cognitive Decline and Brain Aging: Insights from Large-Scale Longitudinal Cohorts across 33 Countries
Authors: Fjell Anders M. , Røgeberg Ole , Sørensen Øystein , Amlien Inge K. , Bartrés-Faz David , Brandmaier Andreas M. , Cattaneo Gabriele , Düzel Sandra , Grydeland Håkon , Henson Richard N. , Kühn Simone , Lindenberger Ulman , Lyngstad Torkild Hovde , Mowinckel Athanasia M , Nyberg Lars , Pascual-Leone Alvaro , Solé-Padullés Cristina , Sneve Markus H. , Solana Javier , Strømstad Marie , Watne Leiv Otto ,   the Alzheimer’s Disease Neuroimaging Initiative,   the Vietnam Era Twin Study of Aging, Walhovd Kristine B. , Vidal-Piñeiro Didac 
Published: January 2025

AbstractWhy education is linked to higher cognitive function in aging is fiercely debated. Leading theories propose that education reduces brain decline in aging, enhances tolerance to brain pathology, or that it does not affect cognitive decline but rather reflects higher early-life cognitive function. To test these theories, we analyzed 407.356 episodic memory scores from 170.795 participants >50 years, alongside 15.157 brain MRIs from 6.472 participants across 33 Western countries. More education was associated with better memory, larger intracranial volume and slightly larger volume of memory-sensitive brain regions. However, education did not protect against age-related decline or weakened effects of brain decline on cognition. The most parsimonious explanation for the results is that the associations reflect factors present early in life, including propensity of individuals with certain traits to pursue more education. While education has numerous benefits, the notion that it provides protection against cognitive or brain decline is not supported.
Protein sequence editing defines distinct and overlapping functions of SKN-1A/Nrf1 and SKN-1C/Nrf2
Authors: Jochim Briar E. , Topalidou Irini , Lehrbach Nicolas J 
Published: January 2025

ABSTRACTThe Nrf/NFE2L family of transcription factors regulates redox balance, xenobiotic detoxification, metabolism, proteostasis, and aging. Nrf1/NFE2L1 is primarily responsible for stress-responsive upregulation of proteasome subunit genes and is essential for adaptation to proteotoxic stress. Nrf2/NFE2L2 is mainly involved in activating oxidative stress responses and promoting xenobiotic detoxification. Nrf1 and Nrf2 contain very similar DNA binding domains and can drive similar transcriptional responses. InC. elegans, a single gene,skn-1, encodes distinct protein isoforms, SKN-1A and SKN-1C, that function analogously to mammalian Nrf1 and Nrf2, respectively, and share an identical DNA binding domain. Thus, the extent to which SKN-1A/Nrf1 and SKN-1C/Nrf2 functions are distinct or overlapping has been unclear. Regulation of the proteasome by SKN-1A/Nrf1 requires post-translational conversion of N-glycosylated asparagine residues to aspartate by the PNG-1/NGLY1 peptide:N-glycanase, a process we term ‘sequence editing’. Here, we reveal the consequences of sequence editing for the transcriptomic output of activated SKN-1A. We confirm that activation of proteasome subunit genes is strictly dependent on sequence editing. In addition, we find that sequence edited SKN-1A can also activate genes linked to redox homeostasis and xenobiotic detoxification that are also regulated by SKN-1C, but the extent of these genes’ activation is antagonized by sequence editing. Using mutant alleles that selectively inactivate either SKN-1A or SKN-1C, we show that both isoforms promote optimal oxidative stress resistance, acting as effectors for distinct signaling pathways. These findings suggest that sequence editing governs SKN-1/Nrf functions by tuning the SKN-1A/Nrf1 regulated transcriptome.
Obligate cross-feeding of metabolites is common in soil microbial communities
Authors: Yousif Ghada , Zorrilla Francisco , Dash Swagatika , Oña Leonardo , Shekhar Aditi , Giri Samir , Guan Rui , Harshe Sharvari , Itermann Michael , Welter Daphne , Benes Vladimir , Patil Kiran R. , Kost Christian 
Published: January 2025

AbstractMany microorganisms are refractory to laboratory cultivation. One possible explanation, known as the great plate count anomaly, is metabolic dependencies among community members. However, systematic studies of these interactions in communities like soil are missing, hindering advances in understanding these ecologically important ecosystems. Here, we address this issue by systematically analysing 6,931 bacterial isolates of 27 soil microbial communities. We find that the growth of up to 50% of all community members depended essentially on supplementation with amino acids, vitamins, or nucleotides. In 73% of cases, supplementation with multiple amino acids was necessary. Genomic analysis of 62 strains revealed that accumulation of insertion sequences and specific gene loss was associated with the observed auxotrophies. Finally, genome-scale metabolic models, computational analyses, and cocultivation experiments demonstrated that other co-occurring genotypes complemented the metabolic needs of auxotrophs, thus facilitating their growth. Our results demonstrate that soil bacteria exist within integrated metabolic networks, which hampers their cultivation.
DMB labelling for detection and analysis of capsular polysaccharides
Authors: Rutschmann Christoph , Vershynina Kateryna , Mathew Corina , Piëch Lucas , Sulewska Małgorzata , Schilling Philipp E , Wenner Nicolas , Larsson Louise , Bertola Anouk , Barazzone Elisa Cappio , Domocos Ioana , Mores Carine Roese , Ndem-Galbert Jackie Raisse , Turgay Yagmur , Schumann Raffael , de Viragh Shirin , Lavender Hayley , Tang Chris , Diard Médéric , Sunagawa Shinichi , Wetter Michael , Fiebig Timm , Slack Emma , Keys Timothy G 
Published: January 2025

AbstractBacterial capsules are major virulence factors enabling systemic infection by undermining innate and adaptive immunity. Capsular polysaccharides are also the antigen in some of the most successful antibacterial vaccines – including the pneumococcal, neisserial and Hib conjugate vaccines. However, it remains exceptionally challenging to study capsules, primarily due to their high chemical diversity and the limited methods available for their detection and analysis. We describe a robust biochemical method for detection and analysis of ABC transporter-dependent capsular polysaccharides, a major class of capsules that are associated with extraintestinal pathogenicEscherichia coli(ExPEC). The method involves release and fluorescent tagging of polysaccharides from the cell surface. Anion exchange chromatography of labelled samples reveals the presence, relative abundance, and length-distribution of these diverse polysaccharide antigens. The method provides a modern approach to detecting the capsule phenotype, bridging a critical gap left by the decline of serotyping assays. It will enhance our understanding of fundamental capsule biology and advance the development of capsule-targeting vaccines.
A cell type-specific mechanism driving the rapid antidepressant effects of transcranial magnetic stimulation
Authors: Gongwer Michael W. , Qi Alex , Enos Alexander S. , Rueda Mora Sophia A. , Klune Cassandra B. , Shari Meelan , Kashay Adrienne Q. , Williams Owen H. , Hacking Aliza , Riley Jack P. , Wilke Gary A. , Yang Yihong , Lu Hanbing , Leuchter Andrew F. , DeNardo Laura A. , Wilke Scott A. 
Published: January 2025

AbstractRepetitive transcranial magnetic stimulation (rTMS) is an emerging treatment for brain disorders, but its therapeutic mechanism is unknown. We developed a novel mouse model of rTMS with superior clinical face validity and investigated the neural mechanism by which accelerated intermittent theta burst stimulation (aiTBS) – the first rapid-acting rTMS antidepressant protocol – reversed chronic stress-induced behavioral deficits. Using fiber photometry, we showed that aiTBS drives distinct patterns of neural activity in intratelencephalic (IT) and pyramidal tract (PT) projecting neurons in dorsomedial prefrontal cortex (dmPFC). However, only IT neurons exhibited persistently increased activity during both aiTBS and subsequent depression-related behaviors. Similarly, aiTBS reversed stress-related loss of dendritic spines on IT, but not PT neurons, further demonstrating cell type-specific effects of stimulation. Finally, chemogenetic inhibition of dmPFC IT neurons during rTMS blocked the antidepressant-like behavioral effects of aiTBS. Thus, we demonstrate a prefrontal mechanism linking rapid aiTBS-driven therapeutic effects to cell type-specific circuit plasticity.
Identification of Scaffold Specific Energy Transfer Networks in the Enthalpic Activation of Orotidine 5’-Monophosphate Decarboxylase
Authors: Dubey Pankaj , Somani Anish , Lin Jessica , Iavarone Anthony T. , Klinman Judith P. 
Published: January 2025

AbstractOrotidine 5’-monophosphate decarboxylase (OMPDC) is one of the most efficient enzyme systems studied, enhancing the decarboxylation of OMP to uridine 5’-monophosphate (UMP) by ca. 17 orders of magnitude, primarily by reducing the enthalpy of activation by ca. 28 kcal/mol. Despite a substantial reduction in activation enthalpy, OMPDC requires 15 kcal/mol of activation energy post- ES complex formation. This study investigates the physical basis of how thermal energy from solvent collisions is directed into the active site of enzyme to enable efficient thermal activation of the reaction. Comparative study of temperature-dependent hydrogen-deuterium exchange mass spectrometry (TDHDX) for WT and mutant forms of enzymes has recently been shown to uncover site specific protein networks for thermal energy transfer from solvent to enzyme active sites. In this study, we interrogate region-specific changes in the enthalpic barrier for local protein flexibility using a native OMPDC fromMethanothermobacter thermautotrophicus(Mt-OMPDC) and a single site variant (Leu123Ala) that alters the activation enthalpy for catalytic turnover. The data obtained implicate four spatially resolved, thermally sensitive networks that originate at different protein/solvent interfaces and terminate at sites surrounding the substrate near the substrate phosphate-binding region (R203), the substrate- ribose binding region (K42), and a reaction enhancing loop5 (S127). These are proposed to act synergistically, transiently optimizing the position and electrostatics of the reactive carboxylate of the substrate to facilitate activated complex formation. The uncovered complexity of thermal activation networks in Mt-OMPDC distinguishes this enzyme from other members of the TIM barrel family previously investigated by TDHDX. The new findings extend the essential role of protein scaffold dynamics in orchestrating enzyme activity, with broad implications for the design of highly efficient biocatalysts.
Dopamine signaling drives skin invasion by human-infective nematodes
Authors: Patel Ruhi , Romero Aracely Garcia , Bryant Astra S. , Agak George W. , Hallem Elissa A. 
Published: January 2025

ABSTRACTSkin-penetrating nematodes are one of the most prevalent causes of disease worldwide – nearly 15% of the global population is infected with at least one species of skin-penetrating nematode1,2. The World Health Organization has targeted these parasites for elimination by 20303, but the lack of preventative measures is a major obstacle to this goal. The infective larvae of skin-penetrating nematodes enter hosts through skin4, and blocking skin penetration is an as-yet unexplored approach for preventing infection. However, in order to prevent worm ingress via the skin, an understanding of the behavioral and neural mechanisms that drive skin penetration is required. Here, we describe the skin-penetration behaviors of the human-infective threadwormStrongyloides stercoralis. Using fluorescently labeled worms to enable visualization on the skin coupled with time-lapse microscopy, we show thatS. stercoralisengages in repeated cycles of pushing, puncturing, and crawling on the skin surface before penetrating the skin. Pharmacological inhibition of dopamine signaling inhibits these behaviors inS. stercoralisand the human hookwormAncylostoma ceylanicum,suggesting a critical role for dopamine signaling in driving skin penetration across distantly related nematodes. CRISPR-mediated disruption of dopamine biosynthesis and chemogenetic silencing of dopaminergic neurons also inhibit skin penetration. Finally, inactivation of the TRPN channel TRP-4, which is expressed in the dopaminergic neurons, blocks skin penetration on both rat and human skin. Our results suggest that drugs targeting TRP-4 and other nematode-specific components of the dopaminergic pathway could be developed into topical prophylactics that block skin penetration, thereby preventing infections.
Visual Influence Networks in Walking Crowds
Authors: Yoshida Kei , di Bernardo Mario , Warren William H. 
Published: January 2025

AbstractCollective motion in human crowds has been understood as a self-organizing phenomenon that is generated from local visual interactions between neighboring pedestrians. To analyze these interactions, we introduce an approach that estimates local influences in observational data on moving human crowds and represents them as spatially-embedded dynamic networks (visual influence networks). We analyzed data from a human “swarm” experiment (N= 10, 16, 20) in which participants were instructed to walk about the tracking area while staying together as a group. We reconstructed the network every 0.5 seconds using Time-Dependent Delayed Correlation (TDDC). Using novel network measures of local and global leadership (direct influenceandbranching influence), we find that both measures strongly depend on an individual’s spatial position within the group, yielding similar but distinctive leadership gradients from the front to the back. There was also a strong linear relationship between individual influence and front-back position in the crowd. The results reveal that influence is concentrated in specific positions in a crowd, a fact that could be exploited by individuals seeking to lead collective crowd motion.
Ultrastructure analysis of mitochondria, lipid droplet and sarcoplasmic reticulum apposition in human heart failure
Authors: Latchman Nadina R. , Stevens Tyler L. , Bedi Kenneth C. , Prosser Benjamin L. , Margulies Kenneth B. , Elrod John W. 
Published: January 2025

ABSTRACTBackgroundCardiomyocyte structural remodeling is reported as a causal contributor to heart failure (HF) development and progression. Growing evidence highlights the role of organelle apposition in cardiomyocyte function and homeostasis. Disruptions in organelle crosstalk, such as that between the sarcoplasmic reticulum (SR) and mitochondria, are thought to impact numerous cellular processes such as calcium handling and cellular bioenergetics; two processes that are disrupted and implicated in cardiac pathophysiology. While the physical distance between organelles is thought to be essential for homeostatic cardiomyocyte function, whether the interactions and coupling of organelles are altered in human heart failure remains unclear.MethodsHere, we utilized transmission electron microscopy and careful quantification of ultrastructure to characterize the changes in organelle apposition in cardiomyocytes isolated from the hearts of patients diagnosed with various types of HF. Subsequently we employed molecular approaches to examine the expression of proposed organelle tethers.ResultsWe demonstrate that cardiomyocytes isolated from dilated cardiomyopathy, hypertrophic cardiomyopathy and ischemic cardiomyopathy hearts display smaller, more rounded mitochondria, as compared to nonfailing controls. Failing cardiomyocytes also exhibited disrupted SR-mitochondria juxtaposition and changes in the expression of proposed molecular tethers. Further analysis revealed alterations in lipid droplet dynamics including decreased lipid droplet content and less lipid droplets in association with mitochondria in failing cardiomyocytes.ConclusionHere we observed changes in organelle dynamics in cardiomyocytes isolated from heart failure patients diagnosed with differing etiologies. Our results suggest that organelle structure and apposition may be a ubiquitous contributor to human HF progression.RESEARCH PERSPECTIVEWhat is New?We provide a detailed analysis of organelle apposition in human heart failure, which has been understudied, and report that that failing human cardiomyocytes display an increase in distance between mitochondria and both the sarcoplasmic reticulum and lipid droplets.Structural changes in organelles are correlated with the expression of proposed organelle tethers.Resource of ultrastructural changes in organelle apposition in human heart failure resulting from various etiologies.What Questions Should be Addressed next?The results from this study provide rationale for causal experimentation to elucidate the contribution of organelle apposition to the progression of heart failure. Future studies examining mechanisms of mitochondrial tethering to the SR or lipid droplet will evaluate specific targets for therapeutic application.
Is the finite temperature effective potential effective for dynamics?
Authors: Herring Nathan , Cao Shuyang , Boyanovsky Daniel 
Published: January 2025

We study the applicability of the finite temperature effective potential in the equation of motion of a homogeneous “misaligned” scalar condensate φ and find important caveats that severely restrict its domain of validity: (i) the of local thermodynamic equilibrium is in general not warranted, (ii) we show a direct relation between the effective potential and the thermodynamic entropy density S=−∂Veff(T,φ)/∂T, which entails that for a dynamical φ(t) the entropy becomes a nonmonotonic function of time, (iii) parametric instabilities in both cases with and without spontaneous symmetry breaking lead to profuse particle production with nonthermal distribution functions, (iv) in the case of spontaneous symmetry breaking spinodal instabilities yield a complex effective potential, internal energy and , an untenable situation in thermodynamics. All these caveats associated with using the effective potential in the of the condensate cannot be overcome by finite temperature equilibrium resummation schemes. We argue that the dynamics of the condensate leads to decoupling and freeze-out from local thermodynamic equilibrium, and propose a quantum system approach based on unitary time evolution. It yields the correct equations of motion without the caveats of the effective potential, and provides a fully renormalized and thermodynamically consistent framework to study the dynamics of the “misaligned” condensate, with real and conserved energy and entropy amenable to numerical study. The evolution of the condensate leads to profuse with nonthermal distribution functions. Possible emergent asymptotic nonthermal states and eventual rethermalization are conjectured.

Published by the American Physical Society
2025