julilili42/papers huggingface dataset:
Linking Microbial Gene‐Expression and Denitrification Rates in Aquifers: Insights From an Intermediate‐Scale In Situ Injection‐Extraction Experiment and Reaction Model
2025-11-01

Abstract Microorganisms catalyze the turnover of reactants in the subsurface, determining the fate of major groundwater constituents and contaminants. Yet our quantitative understanding of microbial dynamics lags behind its importance. Functional molecular‐biological methods offer a powerful tool (box) to quantify microbial dynamics in the environment. Their quantitative potential has only recently been probed via the integration of DNA‐synthesis and RNA‐transcription processes into reaction models. Here, we present the results of an experiment where we actively stimulated the microbial community via nitrate injection into an anaerobic aquifer and monitored concentrations in an extraction well 1.6 m apart. We installed microbial trapping devices (MTDs) to monitor the sediment‐associated microbial community (16S rRNA gene sequencing and qPCR) over time. A nitrate‐driven exponential increase in napA and narG gene copies and a shift in the relative abundances of the microbial community toward known denitrifying taxa in the trapping devices highlight the fast response of the microbial community throughout the 17‐day experiment. We developed a gene‐explicit reaction model that simulates the concentration dynamics measured at the extraction well and considers an additional electron‐donor limitation that explains the observed drop in gene abundances despite nitrate availability. Our model also yielded a relationship between measured denitrification genes and computed rates, confirming previous predictions that the gene‐rate relationship is non‐linear and hysteretic. While the MTDs provided easy access to microbial biomass, our model shows that the kinetics therein differed from those in the aquifer. Thus, MTDs may not be truly representative of the conditions experienced by microbes in the aquifer itself.
Muscle–tendon mechanics resolve the trade-off between energy-efficient and robust locomotion
2025-11-01

Animals utilize elastic tendons in their limbs to store and release energy, reducing muscle effort and overall energy expenditure. At the same time, they navigate rough terrain dynamically without falling, despite significant neural delays. This ability allows them to achieve both robust and energy-efficient locomotion simultaneously—two properties often considered trade-offs in robotics. Through computational simulations, this study demonstrates how muscle–tendon mechanics can facilitate both energy-efficient and robust locomotion during perturbed vertical hopping across different muscle–tendon length configurations. Integrating muscle–tendon-like viscoelastic materials into legged robots may offer a solution to the previously perceived trade-off.
Radar Polarimetry in Glaciology: Theory, Measurement Techniques, and Scientific Applications for Investigating the Anisotropy of Ice Masses
2025-11-02

Abstract Dielectric anisotropy in ice alters the propagation of polarized radio waves, so polarimetric radar sounding can be used to survey anisotropic properties of ice masses. Ice anisotropy is either intrinsic, associated with ice‐crystal orientation fabric (COF), or extrinsic, associated with material heterogeneity, such as bubbles, fractures, and directional roughness at the glacier bed. Anisotropy develops through a history of snow deposition and ice flow, and the consequent mechanical properties of anisotropy then feed back to influence ice flow. Constraints on anisotropy are therefore important for understanding ice dynamics, ice‐sheet history, and future projections of ice flow and associated sea‐level change. Radar techniques, applied using ground‐based, airborne, or spaceborne instruments, can be deployed more quickly and over a larger area than either direct sampling, via ice‐core drilling, or analogous seismic techniques. Here, we review the physical nature of dielectric anisotropy in glacier ice, the general theory for radio‐wave propagation through anisotropic media, polarimetric radar instruments and survey strategies, and the extent of applications in glacier settings. We close by discussing future directions, such as polarimetric interpretations outside COF, planetary and astrophysical applications, innovative survey geometries, and polarimetric profiling. We argue that the recent proliferation in polarimetric subsurface sounding radar marks a critical inflection, since there are now several approaches for data collection and processing. This review aims to guide the expanding polarimetric user base to appropriate techniques so they can address new and existing challenges in glaciology, such as constraining ice viscosity, a critical control on ice flow and future sea‐level change.
Simulating the impact of an educational and digital approach using patient journey modelling to overcome practical challenges in the management of chronic spontaneous urticaria in Germany
2025-11-02

Summary Background and Objective Despite the availability of guidelines and effective escalation therapies, chronic spontaneous urticaria (CSU) is often inadequately treated in Germany. Implementation science can help to transfer evidence‐based care into practice. The aim of this work is to analyze practical challenges, develop intervention strategies and simulate their potential impact on patient outcomes. Methodology A multi‐stage approach with literature research, market research, expert interviews and focus groups with healthcare professionals enabled a comprehensive context analysis. Based on this, intervention strategies were developed and simulated using a patient journey model. The focus was on an educational program and telemedicine monitoring. Results CSU management is hampered by delayed diagnosis and underutilization of available therapies. Barriers include lack of knowledge of diagnostic tools, lack of referral standards and structural barriers to the use of patient‐reported outcomes. Two strategies were proposed: a training program to improve diagnostics and therapy and telemedicine to optimize monitoring. Simulations show that educational measures could increase diagnosis and treatment rates and digital approaches could reduce waiting times. Conclusion The study systematically identifies barriers in CSU care and uses a patient journey approach to show the potential effects of targeted implementation strategies. Educational measures in particular could significantly improve care.
Simulation-based inference for subject-specific tuning of middle ear finite-element models towards personalized objective diagnosis
2025-11-03

Abstract Computational models, particularly finite-element (FE) models, are essential for interpreting experimental data and predicting system behavior, especially when direct measurements are limited. Tuning these models is particularly challenging when a large number of parameters are involved. Traditional methods, such as sensitivity analyses, are time-consuming and often provide only a single set of parameter values, focusing on reproducing averaged trends rather than capturing experimental variability. New approaches are needed to make computational models more adaptable to patient-specific clinical applications. We applied simulation-based inference (SBI) using neural posterior estimation (NPE) to tune an FE model of the human middle ear against subject-specific data. The training dataset consisted of 10,000 FE simulations of stapes velocity, ear-canal input impedance, and absorbance, paired with seven FE parameter values sampled within plausible ranges. By using simulated data, we generated a diverse training dataset, enabling efficient learning by the neural network (NN). The NN learned the association between parameters and simulation outcomes, providing a probability distribution of parameter values, which could be used to produce subject-specific computational inferences. By accounting for noise and test–retest variability, the method provided a probability distribution of parameters, rather than a single set, fitting three experimental datasets simultaneously. Importantly, examining the inferred parameter distributions alongside prior knowledge of normal ranges enables individualized differential inference used for diagnosis. SBI offers an objective alternative to sensitivity analyses, uncovering parameter interactions, supporting personalized diagnosis and treatment, and compensating for limited clinical training data. This method is applicable to any computational model, enhancing its potential for improved patient outcomes.
Threshold-Based Overlap of Breast Cancer High-Risk Classification Using Family History, Polygenic Risk Scores, and Traditional Risk Models in 180,398 Women
2025-11-03

Background: Breast cancer polygenic risk scores (PRS) and traditional risk models (e.g., the Gail model [Gail]) are known to contribute largely independent information, but it is unclear how the overlap varies by ancestry, age, disease type (invasive breast cancer, DCIS), and risk threshold. Methods: In a retrospective case–control study, we evaluated risk prediction performance in 180,398 women (161,849 of European ancestry; 18,549 of Asian ancestry). Odds ratios (ORs) from logistic regression models and the area under the receiver operating characteristic curve (AUC) were estimated. Results: PRS for invasive disease showed a stronger association in younger (&lt;50 years) women (OR = 2.51, AUC = 0.622) than in women ≥ 50 years (OR = 2.06, AUC = 0.653) of European ancestry. PRS performance in Asians was lower (OR range = 1.62–1.64, AUC = 0.551–0.600). Gail performance was modest across groups and poor in younger Asian women (OR = 0.94–0.99, AUC = 0.523–0.533). Age interactions were observed for both PRS (p &lt; 0.001) and Gail (p &lt; 0.001) in Europeans, whereas in Asians, age interaction was observed only for Gail (invasive: p &lt; 0.001; DCIS: p = 0.002). PRS identified more high-risk individuals than Gail in Asian populations, especially ≥50 years, while Gail identified more in Europeans. Overlap between PRS, Gail, and family history was limited at higher thresholds. Calibration analysis, comparing empirical and model-based ROC curves, showed divergence for both PRS and Gail (p &lt; 0.001), which indicates miscalibration. In Europeans, family history and prior biopsies drove Gail discrimination. In younger Asians, age at first live birth was influential. Conclusions: PRS adds value to risk stratification beyond traditional tools, especially in younger women and Asian ancestry populations.
Practice makes perfect: A behavioral challenge intervention to develop social, emotional, and behavioral skills
2025-11-03

The present research tested whether a behavioral challenge intervention could facilitate the volitional development of social, emotional, and behavioral (SEB) skills, and whether changes in perceived skills were linked with positive life outcomes. A total of 470 young adults participated in a 16-week intervention, in which they (a) identified the SEB skills that they would most like to change, (b) set weekly behavioral challenge goals designed to practice those skills, and (c) evaluated their success in pursuing each challenge goal. Results suggest that the intervention promoted development of four major skill domains: self-management, social engagement, emotional resilience, and innovation skills. Moreover, gains in perceived skills during the intervention were linked with positive changes in outcomes including social relationships, academic and civic engagement, health, and well-being. These findings provide initial support for a low-cost, highly scalable intervention for promoting skill development.
The overlooked role of manganese in biodegradation studies of higher aminopolyphosphonates
2025-11-04

Abstract Higher aminopolyphosphonates (APPs, with three or more C–P bonds) are common complexing agents, but their environmental fate and degradation/transformation pathways remain poorly understood. While abiotic degradation of higher APPs has been reported, recent studies have also proposed the potential for enzymatic breakdown based on laboratory model systems. However, herein, we show rapid transformation of two representative higher APPs – aminotris(methylenephosphonate) (ATMP, with three C–P bonds) and ethylenediaminetetramethylenephosphonate (EDTMP, with four C–P bonds) – in bacterial growth media both in the presence and the absence of Achromobacter insolitus strain Kg 19. The abiotic transformation was driven by trace levels of dissolved Mn(II) – typically present in mineral solutions used in growth media. Mn(II) catalyzed the abiotic oxidation of ATMP by molecular oxygen, yielding iminodimethylenephosphonate (IDMP) and orthophosphate ( o -PO4) as transformation products, via a known mechanism previously described in simpler matrices. The addition of ethylenediaminetetraacetic acid (EDTA) as metal complexing agent retarded but did not prevent the abiotic transformation. Bacterial growth under phosphorous (P)-limiting conditions in the presence of ATMP and EDTMP was thus supported by the formation of P-containing transformation products of the concurrent abiotic degradation rather than biotransformation of ATMP and EDTMP. These findings reveal a critical limitation in prior biodegradation studies of higher APPs, which likely overestimated biotransformation by overlooking Mn(II)–mediated abiotic degradation. Future research must redesign biodegradation approaches and disentangle biotic and abiotic mechanisms to accurately evaluate the actual biodegradability of higher APPs. Graphical Abstract
Is there computational creativity?
2025-11-04

Abstract Computational creativity has gained in the recent years momentum as an established interdisciplinary field, whose aim is to investigate, design and foster artificial intelligence. This article analyses whether artificial outputs can appear to as being creative and assesses thus computational creativity from the standpoint of the receiver. While taking Boden’s distinction between several forms of creativity as a starting point, I argue that creativity implies besides surprise and value an additional essential feature, namely the creative intention, not only from the standpoint of the creator but also of the receiver. Following the notion that I propose, creative intention cannot be identified to the mere absence of randomness, but implies the possibility of interpreting the intention, as well as volition and the expression of personal lived experiences. Subsequently I reflect on the possibility of attributing creativity to computer programs while being aware of their lack of creative intention. I argue that the best solution for this purpose is considering computer programs as co-creative partners, which can be credited as contributors to the creative process. In my conclusive remarks, I assess the implications of this possibility for the notion of creative subject. More precisely, I raise the question whether the latter should necessarily be linked to the notion of creativity, and hence, whether co-creative artificial programs should necessarily be considered as creative subjects.
Cognitive performance in patients with ischemic stroke and additional myocardial injury – results from the multicenter prospective observational PRAISE study
2025-11-04

Abstract Background In the general population, cognitive impairment and dementia are more common in individuals with prior myocardial injury, defined as elevated levels of high-sensitive cardiac troponin (hs-cTn). In stroke patients, data on the link between myocardial injury and cognitive outcome are scarce. We aimed to analyze the association between the severity of myocardial injury (degree of hs-cTn elevation), presence of acute myocardial injury (dynamic change in elevated hs-cTn values &gt; 20% in serial measurements) and cognitive performance over time after acute ischemic stroke. Methods This is a prespecified analysis of the prospective multicenter observational PRediction of Acute coronary syndrome in acute Ischemic StrokE (PRAISE) study. PRAISE included 254 patients with an acute ischemic stroke or transient ischemic attack (TIA) and myocardial injury in 26 centers in Germany. Patients underwent cognitive assessment at baseline and before hospital discharge using the Montreal Cognitive Assessment (MoCA) and at three and twelve months after the index event using the Telephone Interview for Cognitive Status (TICS). We used linear regression to analyze the associations between cognitive performance and (1) severity of myocardial injury and (2) presence of acute myocardial injury. The association between hs-cTn and TICS scores over time was examined using inverse probability weighted generalized linear models. Results Severity of myocardial Injury was associated with lower MoCA scores (adjusted beta − 2.6, 95% CI -4.0 - -1.2, p &lt; 0.001) and higher proportion of cognitive impairment (i.e. MoCA score &lt; 26 points) (adjusted OR 2.9, 95%CI 1.3–6.7, p = 0.012). Acute myocardial injury was associated with better cognitive performance (adjusted beta 1.8, 95% CI 0.4–3.1, p = 0.011). We found no association between hs-cTn and cognitive decline over twelve months. Conclusions In patients with ischemic stroke, the severity of myocardial injury in general but not the presence of acute myocardial injury at time of stroke is associated with cognitive impairment. Trial registration Clinicaltrials.gov NCT03609385 https://clinicaltrials.gov/study/NCT03609385?term=NCT03609385&amp;rank=1 Date of registration 6th July 2018.
The Elusive B Cell Antigen in Multiple Sclerosis: Time to Rethink CNS B Cell Functions
2025-11-05

Although the pivotal role of B cells in the pathogenesis of multiple sclerosis (MS) is well established, their precise functions in disease mechanisms remain incompletely understood. For decades, MS-related B cell research has focused on identifying B cell antigens that could induce pathogenic antibodies contributing to the initiation and maintenance of CNS lesion formation and inflammation. In this review, we conducted a systematic literature search to compile and critically assess proposed antigens with respect to their specificity for MS and the plausibility of findings across different publications. We identified 26 antigens in total. Among these, 15 antigens did not demonstrate high specificity for MS, 9 antigens yielded controversial or contradictory results, and 2 antigens may still be regarded as provisional at the time of our analysis. Based on these findings, a primarily antibody-mediated mechanism driving initial lesion formation is not supported by current evidence, although it cannot be excluded entirely. Instead, a secondary immune response to CNS tissue damage—characterized by local antibody production and alternative B cell functions such as antigen presentation, cytokine secretion and cell-to-cell communication—appears more plausible. Taken together, our review highlights the necessity of expanding B cell–oriented MS research beyond antibody production to include a broader spectrum of B cell functions.