julilili42/papers huggingface dataset:
Deep Learning Model for Breast Shear Wave Elastography to Improve Breast Cancer Diagnosis (INSPiRED 006): An International, Multicenter Analysis
2025-08-20

PURPOSE Shear wave elastography (SWE) has been investigated as a complement to B-mode ultrasound for breast cancer diagnosis. Although multicenter trials suggest benefits for patients with Breast Imaging Reporting and Data System (BI-RADS) 4(a) breast masses, widespread adoption remains limited because of the absence of validated velocity thresholds. This study aims to develop and validate a deep learning (DL) model using SWE images (artificial intelligence [AI]-SWE) for BI-RADS 3 and 4 breast masses and compare its performance with human experts using B-mode ultrasound. METHODS We used data from an international, multicenter trial (ClinicalTrials.gov identifier: NCT02638935 ) evaluating SWE in women with BI-RADS 3 or 4 breast masses across 12 institutions in seven countries. Images from 11 sites were used to develop an EfficientNetB1-based DL model. An external validation was conducted using data from the 12th site. Another validation was performed using the latest SWE software from a separate institutional cohort. Performance metrics included sensitivity, specificity, false-positive reduction, and area under the receiver operator curve (AUROC). RESULTS The development set included 924 patients (4,026 images); the external validation sets included 194 patients (562 images) and 176 patients (188 images, latest SWE software). AI-SWE achieved an AUROC of 0.94 (95% CI, 0.91 to 0.96) and 0.93 (95% CI, 0.88 to 0.98) in the two external validation sets. Compared with B-mode ultrasound, AI-SWE significantly reduced false-positive rates by 62.1% (20.4% [30/147] v 53.8% [431/801]; P &lt; .001) and 38.1% (33.3% [14/42] v 53.8% [431/801]; P &lt; .001), with comparable sensitivity (97.9% [46/47] and 97.8% [131/134] v 98.1% [311/317]; P = .912 and P = .810). CONCLUSION AI-SWE demonstrated accuracy comparable with human experts in malignancy detection while significantly reducing false-positive imaging findings (ie, unnecessary biopsies). Future studies should explore its integration into multimodal breast cancer diagnostics.
Physical and mental effects of different radical prostatectomy techniques on urologic surgeons
2025-08-20

Objective In this web-based international survey study, we aimed to show an association between physical exhaustion and patient, relatives, and employer-related mental stress for surgeons performing open radical prostatectomy (ORP), laparoscopic radical prostatectomy (LRP), and robot-assisted laparoscopic prostatectomy (RALP). Additionally, we also aimed to compare the outcomes of three approaches. Methods We sent a ten-question survey to the urologists performing ORP, LRP, and RALP via e-mail and social media. Only fully completed surveys were included in the study analysis. We asked questions about age, the preferred surgical approach for radical prostatectomy, frequency of weekly exercise, and their possible associations with physical exhaustion and musculoskeletal complaints. Results A total of 160 urologists completed the survey. The RALP group showed a lower physical exhaustion rate and increased eye strain ( p &lt; 0.001) and p = 0.002, respectively). Although walking was the most preferred sports activity, no correlation was found between regular sport or exercise and musculoskeletal complaints ( p &gt; 0.05). Conclusion Compared to ORP and LRP, physical exhaustion was lower in the RALP technique. Although the number of participants was limited, regular exercise weakly improved physical exhaustion and musculoskeletal complaints. We believe that regular sports activities by urologists dealing with LRP and RALP will help relieve physical discomfort.
Spastic Ataxia Composite (SPAXCOM): A Scale to Evaluate the Progression of Subjects with Spasticity and Ataxia
2025-08-20

Abstract Background Current clinical scales that track disease progression are more tailored to spasticity or ataxia, with limited sensitivity to change. Objectives The aim was to develop a sensitive and valid scale specifically geared towards optimized sensitivity to change and adapted to patients presenting with both spasticity and ataxia. Methods Longitudinal data from 127 spastic paraplegia type 7 (SPG7) and 112 autosomal recessive spastic ataxia Charlevoix‐Saguenay (ARSACS) patients were collected within the multicenter PROSPAX study. Sensitivity to change over 2 years of 30 items from the Scale for the Rating and Assessment of Ataxias (SARA), Spastic Paraplegia Rating Scale (SPRS), and the Activities of Daily Living subscale of the Friedreich's Ataxia Rating Scale (FARS‐ADL) was evaluated. Items that demonstrated the highest sensitivity to change were used to build the Spastic Ataxia Composite scale (SPAXCOM). Results With seven items, the SPAXCOM showed an effect size of 0.71, higher than reference scales (SARA: 0.43, SPRS: 0.42, FARS‐ADL: 0.27). The SPAXCOM had a similar sensitivity to change for both genotypes and was more sensitive in participants with a SARA lower than 10 and within the intermediate disease stage (FARS‐Disease Staging: 2–3.5). The SPAXCOM showed a high correlation with disease duration ( r = 0.67 [0.60; 0.72]) and disease stage ( r = 0.86 [0.83; 0.89]). Perception of improvement, stagnation, and worsening were associated with a mean yearly SPAXCOM change of 0.44 (−0.14; 1.01), 0.61 (0.19; 1.03), and 1.22 (0.96; 1.49), respectively. Conclusion The SPAXCOM is more sensitive to change and homogeneous across genotypes than the reference scales, allowing a reduction of the required sample size in future clinical trials. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Support vector machines predict postoperative memory outcomes in temporal lobe epilepsies
2025-08-20

Abstract Objective We aimed to predict the side of epilepsy as well as the pre‐ and postoperative verbal and nonverbal memory performance in a cohort of left and right temporal lobe epilepsy (TLE) patients based on hippocampal activations during three different memory fMRI tasks (verbal, nonverbal and combined verbal and nonverbal) using support vector machines (SVM). Methods Thirty‐five patients with unilateral TLE (20 left) were investigated before mesial temporal resection using a verbal, a nonverbal, and a face‐name (combined verbal and nonverbal) memory fMRI paradigm. SVM was used to test whether voxel‐by‐voxel activation patterns within the bilateral hippocampus during each of the three paradigms can be used to classify TLE patients according to their side of epilepsy, preoperative and postoperative verbal and nonverbal memory outcome. Results Classification accuracy regarding the side of epilepsy was best for the face‐name paradigm closely followed by the verbal paradigm. Classification accuracy of the preoperative verbal memory performance was formally statistically significant for all three paradigms, but specificities were low. Regarding the preoperative nonverbal memory performance, activations during the nonverbal and the verbal paradigm provided high prediction accuracies. The results regarding the postoperative memory outcome revealed that activations during the verbal paradigm can be used to predict postoperative verbal memory outcome, whereas activations during the nonverbal paradigm can be used for the prediction of the nonverbal memory outcome. Preoperative activations during the face‐name paradigm were able to predict both the verbal and the nonverbal postoperative memory outcome. Significance It is possible to classify TLE patients according to their side of epilepsy as well as their postoperative memory performance using SVM based on hippocampal activations during task‐based memory fMRI. The highest classification accuracies were obtained for the face‐name paradigm, suggesting this combined verbal and nonverbal paradigm to be most suitable to address these clinical questions. However, further validation in a larger cohort would be necessary. Plain Language Summary This study aims to investigate whether it is possible to predict the side of epilepsy as well as the preoperative and postoperative verbal and nonverbal memory performance in left and right temporal lobe epilepsy patients using support vector machines (a machine learning technique) based on hippocampal activations during three different memory fMRI tasks. Results showed that classification of patients according to their side of epilepsy and their postoperative memory performance is possible, with the highest classification accuracies being obtained using a face‐name association task.
Neural contrast sensitivity is not affected by myopic blur
2025-08-20

Abstract The prevalence of myopia is increasing worldwide, accompanied by an increase of potentially under-corrected myopes. Because neural pathways are prone to adaptation in relation to the sensory input, we wondered to what extent neural contrast sensitivity (NCS) is altered in the presence of image blur arising from under-correction. No significant differences in NCS were observed between the three groups but were significantly equivalent between emmetropes, well-corrected, and under-corrected myopes (all p &lt; 0.001). Across all healthy participants, NCS variability increased with increasing spatial frequency which could not be explained by variations in foveolar cone density. For an albinism patient, a large difference between the cut-off frequency and central cone density derived Nyquist sampling limit was observed. In conclusion, NCS is unaffected by myopia and remains stable for under-correction of up to 1.5 D. Furthermore, NCS testing can relate visual deficits to an underlying neurological disorder.
Impact of bleeding and thrombosis on outcome of 945 COVID-19 VV-ECMO cases from a German registry
2025-08-20

Bleeding and thromboembolic events (BTE) increase the mortality of COVID-19 acute respiratory distress syndrome (ARDS) treated with extracorporeal membrane oxygenation (ECMO). The current analysis aimed to assess frequency and determinants of BTE according to their location and severity in a retrospective analysis of the German ECMO COVID-19 registry. Logistic regression was applied to identify factors influencing ICU survival as well as variables associated with risks of BTE. In total, 708 of 945 patients (75%) suffered from BTE. Overall, 1,348 events were registered, including 406 (30%) major bleeding and 258 (19%) major thromboembolic events. Most common major bleeding locations were intracranial ( n = 133, 10%) and pulmonary bleeding ( n = 116, 9%). In-ICU survival was 35, 46% without BTE and 22% with major bleeding ( p &amp;lt; 0.05). In summary, major bleeding was a core outcome-determinant of COVID-19 ECMO mortality with intracranial major bleeding as the most devastating complication (OR: 5.3; CI: 2.9–9.9; p &amp;lt; 0.001). Neither major thromboembolism nor minor BTE impacted ICU-mortality. Potentially modifiable factors associated with major bleeding included prolonged duration of ECMO &amp;gt;14 days (OR: 2.9; CI 1.8–4.7; p &amp;lt; 0.001) and platelet counts &amp;lt;100.000/μL ≥ 72 h (OR: 2.0; CI 1.1–3.6; p = 0.018). Hence, prevention, early recognition and treatment of major bleedings are key to increase the survival of COVID-19 ECMO. In this regard, our data indicate that the implementation of early weaning strategies to minimize duration of ECMO therapy and prevention of prolonged thrombocytopenia with platelet counts &amp;lt;100.000/μl ≥ 72 h could decrease the risk of devastating bleeds and could ameliorate survival. Clinical trial registration Registered in the German Clinical Trials Register (study ID: DRKS00022964), retrospectively registered, September 7th 2020, https://drks.de/DRKS00022964 .
The tail domain of the plant kinesin-12 POK2 is a versatile interaction hub
2025-08-21

ABSTRACT Tissue development and function rely on correct cell patterning. In plants, patterns are determined by the new cell wall formed during mitosis. During preprophase in embryophytes, ring-like positional cues already mark the future division plane on the plasma membrane. These cues include the kinesin-12 motors PHRAGMOPLAST ORIENTING KINESIN 2 (POK2, also known as KIN12D) and its paralogue POK1 (KIN12C). They are essential for correctly aligning the phragmoplast – a microtubule scaffold for cell wall formation. Although we have a basic understanding of how these motors align the phragmoplast, we currently lack information on how they are targeted to and maintained at the plasma membrane. Here, we reconstituted recombinant POK2 tail fragments on microtubules and vesicles in vitro. We found that the POK2 tail interacted with microtubules, the microtubule-associated protein MAP65-3, as well as with certain anionic lipids. We identified a short element in the POK2 tail responsible for all three interactions. Our data suggest a sequential and cooperative mechanism that targets POK2 specifically to the future division site. There, it is robustly maintained through interactions with the plasma membrane to establish the cell division plane.
Enhancing Wastewater Treatment Sustainability Through Integrated Anaerobic Digestion and Hydrothermal Carbonization: A Life-Cycle Perspective
2025-08-21

Wastewater treatment plants (WWTPs) are critical infrastructure that lessen the environmental impacts of human activity by stabilizing wastewaters laden with organics, chemicals, and nutrients. WWTPs face an increasing global population, greater wastewater volumes, stricter environmental regulations, and additional societal pressures to implement more sustainable and energy-efficient waste management strategies. WWTPs are energy-intensive facilities that generate significant GHG emissions and involve high operational costs. Therefore, improving the process efficiency can lead to widespread environmental and economic benefits. One promising approach is to integrate anaerobic digestion (AD) with hydrothermal carbonization (HTC) to enhance sludge treatment, optimize energy recovery, create valuable bio-based materials, and minimize sludge disposal. This study employs an LCA to evaluate the environmental impact of coupling HTC with AD compared to conventional AD treatment. HTC degrades wastewater sludge in an aqueous medium, producing carbon-dense hydrochar while reducing sludge volumes. HTC also generates an aqueous byproduct containing &gt;30% of the original carbon as simple organics. In this system model, the aqueous byproduct is returned to AD to generate additional biogas, which then provides heat and power for the WWTP and HTC process. The results indicate that the integrated AD + HTC system significantly reduces environmental emissions and sludge volumes, increases net energy recovery, and improves wastewater sludge valorization compared to conventional AD. This research highlights the potential of AD + HTC as a key circular bioeconomy strategy, offering an innovative and efficient solution for advancing the sustainability of WWTPs.
Fructose-1,6-bisphosphatase (FBPase) is involved in heterotrophic growth and glycogen metabolism in cyanobacteria
2025-08-21

Abstract Cyanobacteria switch between photoautotrophic and heterotrophic carbon metabolism during diurnal cycles. A classical control point is characterized by two glycolytic phosphofructokinases (PFKs) and a bifunctional fructose-1,6-biphosphatase/sedoheptulose-1,7-biphosphatase (F/SBPase; slr2094), which catalyzes two reactions in the Calvin-Benson-Bassham (CBB) cycle. In addition, Synechocystis possesses a fructose-1,6-bisphosphatase (FBPase; slr0952) with yet unknown physiological function and biochemical properties. Our aim was to elucidate the physiological role of FBPase, in combination with the above-mentioned enzymes. We discovered that FBPase is specific for fructose 1,6-bisphosphate (FBP), showing no SBPase activity, and unlike F/SBPase does not exhibit any biochemical regulatory properties. In contrast to F/SBPase, FBPase is not involved in the CBB cycle, but instead affects growth and glycogen metabolism under heterotrophic conditions. We hypothesize that FBPase may influence glycogen turnover by controlling cellular levels of its substrate FBP, since FBP is involved in the formation of glucose 1,6-bisphosphate (GBP), which is a regulatory metabolite for the control point between glycogen and central carbon metabolism at the level of phosphoglucomutases. Our data indicate that PFK and FBPase act as an antagonistic enzyme couple in darkness. Furthermore, we found redox-insensitive FBPases from plant chloroplasts to be closely related to Synechocystis FBPase, indicating that they might serve a similar function.
MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis
2025-08-21

Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core “scaffold”, which is subsequently modified by tailoring enzymes to define the molecule’s final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS chemical pattern language. Both human- and machine-readable, MITE can be used as a knowledgebase, for in silico biosynthesis, or to train machine learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.
Nonlinear Optical Response in Layer‐Stacked Gallenene with Ferroelectric Polarization
2025-08-21

Abstract Polar metals are very rare and challenging to realize due to the incompatibility of ferroelectricity and metallicity. Mobile electrons in polar metals effectively screen the static electric field and dipoles. Recent studies show that 2D van der Waals metals without an inversion center can have polar order due to specific layer stacking. However, room temperature reversible ferroelectricity and nonlinear second harmonic generation in non‐centrosymmetric polar metals remain unrealized. Here, the experimental realization of AB‐stacked gallenene (a100) nanocrystals with a room temperature ferroelectric polarization in a liquid gallium environment is reported. Using first‐principles calculations, the origin of spontaneous polarization (Ps) due to a broken symmetry in multilayer gallenene structures, resulting in P1 (space group) and C1 (point group) symmetry is explained. The reversible polarization switching is characterized using piezoresponse force microscopy. This results demonstrate the reversible nonlinear optical response of the AB‐stacked gallenene crystal through second harmonic generation (SHG) microscopy. The intensities of SHG signals are controlled via angular rotations and thermal heating, which indicate a phase transition at high temperatures. Furthermore, electrical perturbation enables the tunability of SHG intensity. Bipolar resistive switching is demonstrated in a two‐terminal device. These findings open avenues for advancements in 2D ferroelectricity, piezoelectricity, and topological superconductivity.
Uncovering the Structural Space of Marine Dissolved Organic Matter
2025-08-21

Marine dissolved organic matter (DOM) represents one of Earth's most complex exometabolomes, playing a central role in marine carbon cycling and long-term sequestration. Despite its biogeochemical importance, the molecular complexity of DOM has long challenged its analytical characterization. Here, we review recent advancements in structure-resolved analytical techniques for DOM. In addition to spectroscopic methods, we focus on liquid chromatography–tandem mass spectrometry and ion mobility spectrometry, as these technologies can provide unprecedented molecular-level insights into DOM composition. By integrating high-resolution analytical techniques with computational pipelines, researchers are now able to resolve previously obscured molecular structures, which has the potential to refine models of DOM cycling and its interactions with microbial communities. Continued innovation in structure-resolved methodologies will be essential for unraveling the molecular complexity of marine DOM and understanding its implications for global biogeochemical processes.
The ribosome-associated complex regulates cytosolic translation upon mitoprotein-induced stress
2025-08-21

Abstract The biogenesis of mitochondria relies on the import of newly synthesized precursor proteins from the cytosol. Tom70 is a mitochondrial surface receptor which recognizes precursors and serves as an interface between mitochondrial protein import and the cytosolic proteostasis network. Mitochondrial import defects trigger a complex stress response, in which compromised protein synthesis rates are a characteristic element. The molecular interplay that connects mitochondrial (dys)function to cytosolic translation rates in yeast cells is however poorly understood. Here, we show that the deletion of the two Tom70 paralogs of yeast ( TOM70 and TOM71 ) leads to defects in mitochondrial biogenesis and slow cell growth. Surprisingly, upon heat stress, the deletion of ZUO1 , a chaperone of the ribosome-associated complex (RAC), largely prevented the slow growth and the reduced translation rates in the tom70Δ/tom71Δ double deletion mutant. In contrast, the mitochondrial defects were not cured but even enhanced by ZUO1 deletion. Our study shows that Zuo1 is a critical component in the signaling pathway that mutes protein synthesis upon mitochondrial dysfunction. We propose a novel paradigm according to which RAC serves as a stress-controlled regulatory element of the cytosolic translation machinery.
Long range energy-energy correlator at the LHC
2025-08-21

We study the forward-backward azimuthal angular correlations of hadrons in association with multiparticle production in the central rapidity region in proton-proton collisions at the LHC. We apply the nucleon energy-energy correlator framework, where the spinning gluon distribution introduces a nontrivial <a:math xmlns:a="http://www.w3.org/1998/Math/MathML" display="inline"><a:mi>cos</a:mi><a:mo stretchy="false">(</a:mo><a:mn>2</a:mn><a:mi>φ</a:mi><a:mo stretchy="false">)</a:mo></a:math> asymmetries. We will demonstrate that the fundamental helicity structure of quantym chromodynamics (QCD) amplitudes predicts a unique power counting rule: <e:math xmlns:e="http://www.w3.org/1998/Math/MathML" display="inline"><e:mi>cos</e:mi><e:mo stretchy="false">(</e:mo><e:mn>2</e:mn><e:mi>φ</e:mi><e:mo stretchy="false">)</e:mo></e:math> asymmetry starts at <i:math xmlns:i="http://www.w3.org/1998/Math/MathML" display="inline"><i:mi mathvariant="script">O</i:mi><i:mo stretchy="false">(</i:mo><i:msubsup><i:mi>α</i:mi><i:mi>s</i:mi><i:mn>2</i:mn></i:msubsup><i:mo stretchy="false">)</i:mo></i:math> order for dijet, <n:math xmlns:n="http://www.w3.org/1998/Math/MathML" display="inline"><n:mi mathvariant="script">O</n:mi><n:mo stretchy="false">(</n:mo><n:msub><n:mi>α</n:mi><n:mi>s</n:mi></n:msub><n:mo stretchy="false">)</n:mo></n:math> for three jet and <s:math xmlns:s="http://www.w3.org/1998/Math/MathML" display="inline"><s:mi mathvariant="script">O</s:mi><s:mo stretchy="false">(</s:mo><s:mn>1</s:mn><s:mo stretchy="false">)</s:mo></s:math> for four (and more) jet productions. Our results will help us to understand the longstanding puzzle of nearside ridge behavior observed in high multiplicity events of <x:math xmlns:x="http://www.w3.org/1998/Math/MathML" display="inline"><x:mi>p</x:mi><x:mi>p</x:mi></x:math> collisions at the LHC.