julilili42/papers huggingface dataset:
Endovascular therapy versus best medical treatment for symptomatic intracranial atherosclerotic stenosis: A systematic review and meta-analysis
2025-03-13

Introduction: Evidence on endovascular therapy (EVT) for symptomatic intracranial stenosis (sICAS) from randomized-controlled clinical trials (RCTs) is conflicting. While prior RCTs on percutaneous transluminal angioplasty and stenting (PTAS) demonstrated harm or no benefit over best medical treatment (BMT), recent data suggest that submaximal balloon angioplasty with BMT may be superior to BMT alone. Patients and methods: A systematic review and meta-analysis of RCTs was conducted to evaluate the safety and efficacy of elective EVT plus BMT compared to BMT alone for sICAS. Results: Six RCTs (5 on PTAS and 1 on balloon-angioplasty) comprising 1606 patients were included. EVT increased the risk of any stroke or death (RR = 2.68; 95% CI: 1.72–4.19; I 2 = 0%), ischemic stroke within the territory of the qualifying artery (RR = 2.51; 95% CI: 1.36–4.61; I 2 = 0%), any ischemic stroke (RR = 1.99; 95% CI: 1.17–3.38; I 2 = 0%), intracranial hemorrhage (RR = 6.23; 95% CI: 1.92–20.2; I 2 = 0%), and mortality (RR = 3.52; 95% CI: 1.04–11.88; I 2 = 0%) within 30 days. No significant benefit from EVT was detected regarding the risk of any stroke or death (RR = 0.29, 95% CI: 0.06–1.38; I 2 = 68%), ischemic stroke in the territory of the qualifying artery (RR = 0.44, 95% CI: 0.14–1.33; I 2 = 59%) and mortality (RR = 0.49, 95% CI: 0.16–1.55; I 2 = 0%) beyond 30 days through 1 year. Discussion and conclusion: EVT is associated with adverse early outcomes, without reducing the risk of long-term stroke recurrence or mortality compared to BMT. Further research is warranted to identify high-risk subgroups who may benefit from EVT for sICAS and refine interventions to minimize periprocedural risks.
Subliminal risk influences subjective value in the ventromedial prefrontal cortex
2025-03-13

Abstract The relationship between conscious awareness and decisions has been heavily debated. Here we investigated whether subliminal probabilities are integrated with conscious rewards to form subjective value (SV) representations in the anterior ventral striatum (aVS) and ventromedial prefrontal cortex (vmPFC). Participants played an incentivized competitive game with risky choice to accumulate points across trials in a behavioral and fMRI experiment. The game was a modified attentional-blink paradigm that rendered a probability cue unseen (indicating a 100% or 0% chance to win a risky reward). Following the probability cue, participants chose between a safe (1 point with certainty) or risky option (&gt;1 or 0 points depending on probability cue). The risky reward was either 2 or 5 points, varying across trials. In some trials the probability cue was absent (replaced by a random distractor) and the probability to win the risky reward was 50%. When probability cues were unseen, they did not influence choice, as value-maximizing choice (d’) was not greater than chance, but they did influence reaction time in both experiments. Consistent with SV integration, the BOLD signal in aVS and vmPFC was higher for both conscious rewards (high &gt; low) and subliminal probabilities (high &gt; low) and could not be explained by subliminal salience (cue present &gt; absent). Moreover, multivariate pattern similarity between conscious rewards and subliminal probabilities in vmPFC suggest integration into an abstract value representation. Additionally, we found brain-wide subliminal probability and salience effects. Taken together, these results suggest that conscious awareness is not necessary for probability to be integrated with conscious rewards to form an abstract “common currency” SV representation in vmPFC. Additionally, brain-wide subliminal probability and salience effects suggests information can have “global access” without conscious awareness.
Functional Outcome in Patients With Carotid Artery Dissection Undergoing Thrombectomy or Standard Medical Treatment
2025-03-14

This study provides Class III evidence that for patients with LVO due to CAD and admission NIHSS ≥6 points, thrombectomy compared with BMT significantly increases the probability of favorable outcome.
Fast and reliable probabilistic reflectometry inversion with prior-amortized neural posterior estimation
2025-03-14

Reconstructing the structure of thin films and multilayers from measurements of scattered x-rays or neutrons is key to progress in physics, chemistry, and biology. However, finding all structures compatible with reflectometry data is computationally prohibitive for standard algorithms, which typically results in unreliable analysis with only a single potential solution identified. We address this lack of reliability with a probabilistic deep learning method that identifies all realistic structures in seconds, redefining standards in reflectometry. Our method, prior-amortized neural posterior estimation (PANPE), combines simulation-based inference with adaptive priors that inform the inference network about known structural properties and controllable experimental conditions. PANPE networks support key scenarios such as high-throughput sample characterization, real-time monitoring of evolving structures, or the corefinement of several experimental datasets and can be adapted to provide fast, reliable, and flexible inference across many other inverse problems.
Clinical characteristics and treatment patterns of patients with gastroenteropancreatic neuroendocrine neoplasia in Germany receiving peptide receptor radionuclide therapy: A real-world data registry-based study
2025-03-14

Gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) are rare malignancies deriving from the endocrine system in the gastrointestinal tract including the pancreas. Prognosis is greatly heterogenous due to its dependency on various factors, most importantly stage and differentiation. Several studies report an alarming rise in incidence in the past decade. Despite there being some therapeutical options, best therapy sequence still needs to be defined, particularly for unresectable and/or intermediate and high-grade NENs. Peptide receptor radionuclide therapy (PRRT) was approved in Europe and USA in 2017 and 2018, respectively. Studies with real-world systematic data on characteristics and treatment patterns of PRRT-receiving patients was non-existent at the time of this writing. In this retrospective study, we identified within the German NET-Registry 203 patients diagnosed with GEP-NEN having received PRRT from 1995 to 2023. We assessed general clinical patient characteristics, disease-specific characteristics, treatments and outcomes. To obtain a more up-to-date picture of treatment modalities and outcomes, a subgroup of the study population was allocated to the “therapy cohort,” defined by patients with date of first diagnosis between 2010 and 2023 (open cohort). Mean age of the study population was 58 years (SD 12 years) with 51.7% being men. Most patients had a WHO performance score of 0 to 1 (41.4% and 50.5%, respectively). Most NEN cases were of small intestine/pancreatic origin (46.3% and 45.3%, respectively) and displayed well/moderate differentiation (55.3%). Ki-67 was generally within the 3% to 20% range (57.92%). Most patients presented with metastasis at diagnosis (73.9%). Somatostatin analogs (SSAs), chemotherapy and surgery were the most common non-PRRT therapy options (65.3%, 60.2%, and 50.0%, respectively). PRRT was most often applied as third- or second-line therapy (42.3% and 36.6%, respectively), usually after surgery and/or SSA treatment. As PRRT had been administered using different regimens, tumor response evaluation showed mixed responses. Given the low sample size and considerable amount of missing response data, no correlation analysis between PRRT sequencing and tumor response could be performed. Overall, the clinical characteristics and treatment patterns tend to follow trends observed in other studies or medical guidelines. Finally, this study presents real-world data that more accurately describes GEP-NEN disease in Germany and treatment modalities after PRRT’s approval.
Machine Learning Reveals Biocontrol Agents Shaping Disease Protection in Natural Arabidopsis Populations and Synthetic Communities
2025-03-14

<title>Abstract</title> Plants recruit beneficial microbes to defend against phytopathogens, and some are developed as biocontrol agents. However, identifying biocontrol agents depends on empirical screenings to assess microbial activity against pathogens of interest. In this study, we explored the association between infection status and phyllosphere microbiome dynamics over six generations from natural Arabidopsis populations and compared plants infected by the oomycete pathogen Albugo laibachii with uninfected controls. We found that infected plants exhibited reduced microbial diversity, a pattern driven primarily by site-dependent environmental factors rather than host genotypes. Microbial interaction networks of infected plants were less connected and highly modular, indicating a disruption in microbial community resilience. Using machine learning, we predicted the disease-associated and health-associated microbial signatures with 86–91% accuracy and identified key taxa correlated with disease outcomes. We selected bacteria, fungi, and cercozoa from these key taxa to test their biocontrol activeity against A. laibachii infection. We found all selected microbes exhibit various levels of plant protection, and disease-associated microbes offered less protection than health-associated microbes. We further validated the biocontrol capacity of the best candidate agent, Cystofilobasidium, by testing it within a synthetic community derived from the Arabidopsis core microbiome. This study reveals how microbial dynamics and functional connectivity support plant protection, providing a roadmap for using machine learning to devise robust biocontrol strategies that enhance crop resilience.
Disease stage-specific atrophy markers in Alzheimer’s disease
2025-03-14

Abstract INTRODUCTION Structural MRI often lacks diagnostic, prognostic, and monitoring value in Alzheimer’s disease (AD), particularly in early disease stages. To improve its utility, we aimed to identify optimal MRI readouts for different use cases. METHODS We included 363 older adults; healthy controls (HC) who were negative or positive for amyloid-beta (Aβ) and Aβ-positive patients with subjective cognitive decline (SCD), mild cognitive impairment, or dementia of the Alzheimer type. MRI and neuropsychological assessments were administered annually for up to three years. RESULTS Accelerated atrophy of distinct MTL subregions was evident already during preclinical AD. Symptomatic disease stages most notably differed in their hippocampal and parietal atrophy signatures. Associations of atrophy markers and cognitive inventories varied by intended use and disease stage. DISCUSSION With the appropriate readout, MRI can detect abnormal atrophy already during preclinical AD. To optimize performance, MRI readouts should be tailored to the targeted disease stage and intended use.
Investigating I/Ca ratio in planktic foraminifera: an integrated approach in the Mediterranean Sea and beyond
2025-03-14

Global ocean oxygen depletion is a growing concern, with direct observations showing widespread decline that is not fully captured by existing models. The dynamics of oxygenation are critical to marine ecosystem health and are influenced by physical and biogeochemical factors. To reconstruct past variation of dissolved oxygen content, foraminiferal iodine to calcium (I/Ca) ratio has been developed. This proxy is based on the fact that iodine speciation is dependent on oxygen content and that only iodate ions (IO3-) can be incorporated into the calcite lattice by substitution for carbonate ions. However, our knowledge of foraminiferal I/Ca behavior needs improvement because the relationship between planktonic foraminiferal I/Ca and oxygen content in the upper 500m water column appears to be empirical and the influence of physical and biogeochemical parameters has not been fully addressed yet, and thus prohibits the development of a fully quantitative proxy.In this study, we present the first planktic foraminiferal I/Ca data from core-top material (late Holocene) in the Mediterranean Sea and a compilation of previously published core-top and plankton tow I/Ca data from the global ocean. We use this database to examine the influence of the maximum and minimum oxygen concentration, temperature, salinity, nutrients, pH, alkalinity, chlorophyll, water velocities and mixed layer depth on the I/Ca proxy. Additionally, we assess the effects of water depth and sample age to monitor possible iodine accumulation during the foraminiferal test settling and early diagenetic effects. We also investigate the potential for differential behaviour between foraminiferal species by categorising by the presence/absence of symbionts.We find unexpectedly low I/Ca as low as 1 &amp;#181;mol/mol in samples from the western basin of the Mediterranean Sea, providing the first low I/Ca from fossil foraminiferal which lived in waters thought to be highly oxygenated. Principal Component Analysis (PCA) confirms the dominance of oxygen content on foraminiferal I/Ca, however, analysis of the foraminiferal I/Ca residuals after subtraction of oxygen dependence suggest a potential role of temperature. No clear trend is not observed between the residuals and sample age, suggesting a negligible influence of burial diagenesis. Iodine accumulation during the settling of foraminiferal tests has been proposed to explain the high I/Ca of fossil samples when compared to plankton tows, but no trends are visible between our residuals and water depth, implying that there is no systematic effect from post-mortem settling. The cause of low foraminiferal I/Ca in oxygenated waters remains unclear and may involve poorly constrained local oxygen variability, the chemical dynamics of iodine, iodine incorporation mechanisms, or other unknown parameters.
&#160;Deglaciation and abrupt events in a coupled comprehensive atmosphere--ocean--ice sheet--solid earth model
2025-03-14

During the last 20,000 years, the climate of the Earth evolved from a state much colder than today with large ice sheets covering North America and Northwest Eurasia to its present state. The fully-interactive simulation of this transition represented a hitherto unsolved challenge for state-of-the-art climate models. We use a novel coupled comprehensive atmosphere-ocean-vegetation-ice sheet-solid earth model to simulate this transient climate evolution, referred to as the last deglaciation. The model considers dynamical changes of ice sheets (shape and extent) as well as changes in the land-sea mask and river routing. The model also contains a dynamical iceberg component. An ensemble of eight transient model simulations realistically captures the key features of the last deglaciation, as depicted by proxy estimates.In addition, our model simulates a series of abrupt climate changes, which can be attributed to different drivers. Sudden weakenings of the Atlantic meridional overturning circulation during the glacial state and the first half of the deglaciation are caused by Heinrich-event like ice-sheet surges, which are part of the model&amp;#8217;s internal variability. We show that the timing of these surges depends on the initial state and the model parameters, illustrating the stochastic nature of the events. Abrupt events during the second half of the deglaciation are caused by a long-term shift in the sign of the Arctic freshwater budget, by changes in the opening of ocean passages and/or by abrupt changes in the river routing. In contrast to the Heinrich-event like ice-sheet surges, the abrupt events of the second half of the deglaciation are deterministic, as they occur as inherent features of the deglaciation.
New insights into Hydrology and Lake Dynamics Upstream of Thwaites Glacier
2025-03-14

Understanding Antarctic subglacial hydrology is crucial for assessing ice sheet dynamics and their contributions to global sea-level rise. Subglacial water modulates basal friction, influencing ice flow and glacier stability, as shown in studies of Thwaites Glacier and other West Antarctic systems. Here, we present new insights into subglacial hydrology derived from geophysical observations. By integrating radar-derived bed reflectivity with subglacial topography analysis, and the geometry of englacial layers we identify potential subglacial flow pathways. Our study focuses on a 350 km&amp;#178; region located 124 km upstream of the Thwaites Glacier grounding line, where an active subglacial lake has been inferred from satellite altimetry, reflecting periodic ice surface uplift and depression. We investigate the ice-bed interface reflectivity to identify areas of potential water accumulation or saturated sediments beneath the glacier. Additionally, we analyse the geometry of englacial layers to further explore subglacial water distribution and drainage patterns. To account for the influence of basal topography, we remove the topographic signal to derive layers relative to a "flattened" base. Residual englacial layers above regions of high bed reflectivity were examined for drawdowns and uplifts linked to subglacial hydrological processes. We also simulate the hydropotential in this region to delineate the most likely drainage pathways around the active subglacial lake's fringe. Our findings reveal high bed reflectivity areas coinciding with englacial layer drawdowns, along with regions of apparent uplift in the englacial stratigraphy. These results suggest a potential flow routing for Subglacial Lake Thw 124 and indicate that its previously defined boundary may be overestimated, implying episodic lake growth.
Modeling the Ammonium Removal Processes in Household Sand Filters
2025-03-14

Elevated ammonium (NH4+) concentrations in groundwater (GW) pose significant challenges to existing GW treatment systems, particularly in simplified systems such as household sand filters (HSFs), which are widely used in developing countries. We previously conducted a series of column experiments (sand filter materials collected in Hanoi, Vietnam) mimicking HSFs. These experiments revealed limited and fluctuating NH4+ removal, highlighting the need for a comprehensive process-based model to elucidate the complex interplay of physical and biochemical processes that influence NH4+ concentration dynamics in these systems. Here, we established a one-dimensional advective-dispersive-reactive model conditioned on data from column experiments under laboratory (artificial GW inflow with sand materials from local HSFs) and field conditions (natural GW inflow with sand materials from local supplier), accounting for temporal variations in reaction kinetics, transport processes, and a previously unconsidered inter-phase transfer process for nitrate (NO3-). The modeled breakthrough curves capture the complex dynamics of NH4+, nitrite (NO2-), and NO3- concentrations under both laboratory and field conditions. The reaction rates of the nitrogen species show strong hysteresis in response to substrate (NH4+ and NO2-) concentrations, suggesting that potential lags in the biochemical reactions caused by inhibitions and low retention time lead to the incomplete NH4+ removal. Our scenario analysis indicates that, without inhibition effects, the current bio-reactive environment could reduce NH4+ concentrations to the legal target level (within up to eight hours retention time under field conditions). This study represents one of the few process-based modeling efforts mimicking HSFs. Future modeling research should parameterize various inhibition effects into the existing reactive transport models in order to gain quantitative insight into enhancement methods for HSFs.
Multilabel Classification for Entry-Dependent Expert Selection in Distributed Gaussian Processes
2025-03-14

By distributing the training process, local approximation reduces the cost of the standard Gaussian process. An ensemble method aggregates predictions from local Gaussian experts, each trained on different data partitions, under the assumption of perfect diversity among them. While this assumption ensures tractable aggregation, it is frequently violated in practice. Although ensemble methods provide consistent results by modeling dependencies among experts, they incur a high computational cost, scaling cubically with the number of experts. Implementing an expert-selection strategy reduces the number of experts involved in the final aggregation step, thereby improving efficiency. However, selection approaches that assign a fixed set of experts to each data point cannot account for the unique properties of individual data points. This paper introduces a flexible expert-selection approach tailored to the characteristics of individual data points. To achieve this, we frame the selection task as a multi-label classification problem in which experts define the labels, and each data point is associated with specific experts. We discuss in detail the prediction quality, efficiency, and asymptotic properties of the proposed solution. We demonstrate the efficiency of the proposed method through extensive numerical experiments on synthetic and real-world datasets. This strategy is easily extendable to distributed learning scenarios and multi-agent models, regardless of Gaussian assumptions regarding the experts.
The situated multimodality of integrating ethics: orientation work for co-laborative reflexivity and empowerment
2025-03-14

My paper is meant as orientation work for those who shall give orientation in innovation processes and struggle for orientation themselves in their work of integrating ethics. Drawing upon my work in/about integrating ethics and in actualizing some of the long-discussed issues in the field, I argue that integrating ethics is not only about taking an informed decision for a certain method. It rather is a situated, evolving, epistemic and social activity. It draws upon a repertoire of different modes of research that alternate over the course of a project. That are (1) joint problem solving, (2) joint processes of labor, (3) ethical impulses, (4) ethical services, (5) research on/in the field of innovation, and (6) ethical research. For each mode, I sketch out its characteristics and inner tensions as well as the tensions between the modes. I conclude that instead of expecting integration ethicists should be prepared for co-laboration.