julilili42/papers huggingface dataset:
GaVS: 3D-Grounded Video Stabilization via Temporally-Consistent Local Reconstruction and Rendering
2025-07-23

Video stabilization is pivotal for video processing, as it removes unwanted shakiness while preserving the original user motion intent. Existing approaches, depending on the domain they operate, suffer from several issues (e.g. geometric distortions, excessive cropping, poor generalization) that degrade the user experience. To address these issues, we introduce \\textbf{GaVS}, a novel 3D-grounded approach that reformulates video stabilization as a temporally-consistent `local reconstruction and rendering' paradigm. Given 3D camera poses, we augment a reconstruction model to predict Gaussian Splatting primitives, and finetune it at test-time, with multi-view dynamics-aware photometric supervision and cross-frame regularization, to produce temporally-consistent local reconstructions. The model are then used to render each stabilized frame. We utilize a scene extrapolation module to avoid frame cropping. Our method is evaluated on a repurposed dataset, instilled with 3D-grounded information, covering samples with diverse camera motions and scene dynamics. Quantitatively, our method is competitive with or superior to state-of-the-art 2D and 2.5D approaches in terms of conventional task metrics and new geometry consistency. Qualitatively, our method produces noticeably better results compared to alternatives, validated by the user study.
Neolactotetraosylceramide enables urinary detection of bladder cancer
2025-07-23

Glycosphingolipids (GSLs) are promising cancer biomarkers. Using multiplexed capillary gel-electrophoresis with laser-induced fluorescence detection (xCGE-LIF), we profile GSLs in bladder cancer (BC) tissues and find a significant increase in neolactotetraosylceramide (nLc4) compared to matched normal tissue (n = 30). Immunofluorescence confirms tumor-specific nLc4 expression in both non-muscle-invasive BC (NMIBC) and muscle-invasive BC (MIBC), colocalizing with luminal and basal urothelial markers. Analysis of paired tissue/urine samples, along with BC cell lines, reveals secretion of nLc4 associated with extracellular vesicles in MIBC. Urine profiling shows elevated nLc4 levels in BC patients (n = 16) versus controls (n = 50; area under the curve [AUC] 0.75; accuracy 82%). To support clinical translation, we apply an anti-nLc4 ELISA in a discovery cohort (n = 18) and a multi-center validation cohort (n = 123). In the validation set, urinary nLc4 levels are significantly elevated in MIBC (AUC 0.78; accuracy 64%) and increase with disease severity. These findings support the potential of urinary nLc4 as a non-invasive biomarker for BC detection.
Recreating pathophysiology of CLN2 disease and demonstrating reversion by TPP1 gene therapy in hiPSC-derived retinal organoids and retina-on-chip
2025-07-23

Mutations in the tripeptidyl peptidase 1 (TPP1) gene lead to neuronal ceroid lipofuscinosis type 2 (CLN2), characterized by lysosomal accumulation of lipofuscins predominantly in the brain and retina. The ocular phenotype is characterized by outer retinal degeneration that leads to vision loss. Leveraging human induced pluripotent stem cell (hiPSC)-derived retinal organoids (ROs), retinal pigmented epithelial cells, and the retina-on-chip system, we establish an in vitro CLN2 model that recreates the principal histological hallmarks, namely the accumulation of subunit C of mitochondrial ATP synthase (SCMAS) and lipids mainly in the outer retina. Furthermore, single-cell RNA sequencing reveals a dysregulation of translational and mitochondrial function in CLN2 cones. Finally, adeno-associated virus (AAV)-mediated TPP1 gene therapy can restore TPP1 expression and decrease and even prevent SCMAS accumulations. Our study uses an innovative human-relevant microphysiological retinal disease models, uncovers previously uncharacterized mechanisms of CLN2 pathophysiology, and demonstrates the potential of AAV9.hCLN2 gene therapy for CLN2 disease, potentially treating patient blindness.
Benthic biofilm structure and function under abrupt flow changes
2025-07-23

Sediment accumulation reduces the capacity of dammed systems worldwide, therefore understanding sediment stability and transport within a reservoir is fundamental for sustainable management. Fluctuating hydrodynamics can alter the physical disturbance exerted on the sediment bed and can lead to substantial resuspension of bottom sediments and benthic biofilms. Removal of the biofilm can drastically alter the biochemical environment in the bed, and its ability to stabilize underlying sediments as microphytobenthic and bacteria communities are removed. In this experiment, an 8-week long hydraulic flume experiment was conducted to examine the response, adaptation and functionality of biofilms exposed to abrupt increases in flow typical of flow managed systems. Water and resuspended sediment from an oligotrophic reservoir in Germany, were used to develop biofilms on inserted flume cartridges. Developed biofilms were haphazardly distributed across two flow treatments: high bed shear stress (0.7 Pa) or low bead shear stress (0.1 Pa) for 28 days. Biochemical changes and biostabilization potential (adhesiveness) were examined over this period. Microphytobenthic biomass and composition, bacterial community diversity and extracellular polymeric carbohydrates/proteins were all initially altered by the abrupt increase in flow as the biofilm was stripped away. Biochemical properties largely recovered by the end of the experimental period (28-days) with recovery time and the degree of re-establishment dependent on the initial biofilm condition. However, sediment beds exposed to higher flows remained less stable, suggesting this functional role of the biofilm may take longer to reestablish itself after periods of higher flow. Findings suggest flow management has the potential to alter biofilm development and highlight the importance of protein content and microphytobenthic biomass in the recovery of biostabilization, Microphytobenthic diversity and carbohydrate content had less influence in the recovery of biostabilization. The findings may be useful to reservoir managers to manipulate flow to allow stable benthic biofilms to improve water quality and/or reduce infilling.
Kayaca, a new vertebrate locality from the Upper Miocene of Türkiye and its importance for the Turolian biogeography of the eastern peri-Mediterranean region
2025-07-23

Abstract We present here a new Upper Miocene vertebrate locality, Kayaca, from the Beyağaç Basin in southwestern Türkiye that was discovered after surface survey and was subsequently systematically excavated. The locality yielded a diverse and rich vertebrate fauna notably including several complete cranial specimens. In this article we provide the first results on the taxonomy of the large mammal assemblage, and we discuss the biochronological implications. The Kayaca large mammal assemblage is dominated by hipparionine horses ( Hipparion dietrichi morphotype, Cremohipparion sp.) and bovids ( Gazella cf. ancyrensis , Sporadotragus parvidens , Tragoportax sp., Palaeoryx pallasi and the rare Gangraia ), but includes also rhinocerotids ( Miodiceros neumayri , Diceros sp.), suids ( Hippopotamodon major ), giraffids ( Palaeotragus rouenii , Samotherium major ), hystricids ( Hystrix sp.), orycteropodids ( Amphiorycteropus gaudryi ), proboscideans ( Deinotherium sp., Elephantimorpha indet.) and carnivorans. The latter are identified by some well-preserved specimens belonging to ictitheres ( Protictitherium sp.), hyaenids ( Adcrocuta eximia ), felids ( Pontosmilus sp. and a medium-sized felid) but also to the rare mustelid Parataxidea maraghana . The preliminary comparison with already known and well-studied faunal assemblages of Türkiye and the wider region, particularly the neighboring localities of Samos in Greece, suggest an age of ca. 7.4, close to the transition of early/middle Turolian (MN 11/12). Located at the western corner of Asia, Kayaca comprises a key location linking the vertebrate faunas of Asia and Europe and offers valuable insights into the Late Miocene terrestrial ecosystems of the eastern peri-Mediterranean region.
Validation of the CFAbd-Score.kidⒸ, a Novel gastrointestinal patient reported outcome measure, specific for children with cystic fibrosis
2025-07-23

The novel CFAbd-Score.kid©, well accepted among children, allows recording of AS in cwCF. The total CFAbd-Score.kid© and three of its five domains reveal a significantly and markedly elevated burden of AS in cwCF, compared to HC.
Members of the MYB68 subclade orchestrate cork differentiation by regulating stem cell proliferation and suberin deposition
2025-07-23

Plants have developed specialized barriers to isolate the inner tissues from the environment. The periderm is a dynamic barrier comprising a stem-cell niche, the cork cambium, which produces the cork. Cork cells have a unique cell wall impregnated with hydrophobic polymers such as suberin and lignin, which are essential for the barrier function. Despite its importance, the cork differentiation network remains largely unknown. Here, we identify MYB68 subclade transcription factors as activators of suberin biosynthesis and polymerization, as well as repressors of cork cambium proliferation. We further show that suberin deposition in the cork is also regulated by MYBs from other subclades. However, only MYB68 subclade members suppress cell proliferation, revealing both shared and distinct roles of MYB transcription factors. These findings have broad applicability, as tissue-specific manipulation of MYB activity has the potential to improve the traits of biotechnological interest, such as thicker periderms and more suberized cork layers.
Staphylococcus aureus : a model for bacterial cell biology and pathogenesis
2025-07-24

ABSTRACT Staphylococcus aureus has emerged as an important model organism in bacterial cell biology and pathogenesis due to its clinical relevance, genetic versatility, and adaptability. This review explores how S. aureus has contributed to advances in the fields of bacterial cell wall synthesis and cell division, particularly due to its minimal cell wall synthesis machinery and simple spherical shape. S. aureus has also been fundamental in antimicrobial resistance studies, particularly due to the increasing threat of antibiotic-resistant S. aureus strains. Furthermore, S. aureus ’ dual lifestyle as both a commensal and a pathogen has provided key insights into host–microbe interactions, biofilm formation, and immune evasion strategies. This review underscores the importance of continued research on S. aureus as a basis for the development of novel antimicrobial strategies and vaccine approaches.
Myonuclear domain-associated and central nucleation-dependent spatial restriction of dystrophin protein expression in a novel DMD mouse model
2025-07-24

Abstract The restoration of uniformly-distributed dystrophin protein expression is an important consideration for the development of advanced therapeutics for Duchenne muscular dystrophy (DMD). To explore this concept, we generated a novel genetic mouse model ( mdx52-Xist Δhs ) that expresses variable, and non-uniformly distributed, dystrophin protein from birth as a consequence of skewed X-chromosome inactivation. mdx52-Xist Δhs myofibers are heterokaryons containing a mixture of myonuclei expressing either wild-type or mutant dystrophin alleles in a mutually exclusive manner, resulting in dystrophin protein being spatially restricted to corresponding dystrophin-expressing myonuclear domains. This phenotype models the situation in female DMD carriers, and dystrophic muscle in which dystrophin has been incompletely restored by partially-effective experimental therapeutics. Total dystrophin expression increased in aged (60-week-old) mdx52-Xist Δhs mice relative to 6-week-old adults, suggestive of an accumulation of dystrophin-expressing myonuclei through positive selection, although this was insufficient to resolve sarcolemmal dystrophin patchiness. Nevertheless, compared to mice expressing no dystrophin, non-uniformly-distributed dystrophin was protective against pathology-related muscle turnover in an expression-level-dependent manner in both adult and aged mdx52-Xist Δhs mice. Systematic classification of isolated mdx52-Xist Δhs myofibers revealed profound differences associated with central nucleation, with dystrophin found to be translationally repressed in centrally-nucleated myofibers and myofiber segments. These findings have important implications for the development of dystrophin restoration therapies.
Minimizing social bias with sequential collaboration: the role of contributor features in dependent judgments
2025-07-24

Abstract Collaborative online projects rely on sequential collaboration; a process in which entries are adjusted consecutively by contributors. Sequential collaboration has recently been examined for numerical judgment aggregation for which it produces highly accurate information. However, the impact of additional information about previous contributors on subsequent judgments remains unclear. Thus, Experiments 1A (N = 85), 1B (N = 186), and 1C (N = 302) examined the effect of presented expertise, gender, and group membership of the previous participant, respectively, on participants’ behavior in sequential collaboration. We did not find a significant effect of any of the presented features on change probability or change magnitude. In Experiments 2 (N = 538) and 3 (N = 878), we focused on previous participants’ expertise as a highly relevant presented feature. We did not find an effect of previous participants’ expertise in Experiment 2. Experiment 3 revealed significant but small effects below the smallest effect size of interest. Overall, these findings suggest that sequential collaboration shows some robustness against simple social influences highlighting its potential as a method for judgment aggregation. This study adds to the understanding of how collaborative processes can be optimized for accuracy and reliability. For collaborative projects these results further emphasize that sequential collaboration is a successful and bias-preventing way of collaboration.
Impact of Naturally Composed and Size-Excluded Hymenoptera Venom Preparations on the Safety and Efficacy of Venom Immunotherapy: A Monocentric Experience
2025-07-24

Introduction: The first-line treatment for patients with Hymenoptera venom allergy, a potentially life-threatening condition, is venom immunotherapy (VIT). However, for reasons still unclear, honeybee VIT (HBV-IT) is less effective than yellow jacket VIT (YJV-IT). Methods: This retrospective monocentric study aimed to investigate the safety and efficacy of naturally composed Hymenoptera venom (NC-HV) in a rush protocol involving a high total venom dose and to compare the results with those previously obtained using size-excluded Hymenoptera venom (SE-HV). Data regarding the number of build-up cycles and maintenance of VIT with NC-HV were retrieved from institutional records. The VIT protection rate was determined by the results of the sting challenge test (SCT). Results: We evaluated 648 individuals treated with NC-HV and compared their results with data from 1,258 individuals treated with SE-HV. The frequency of systemic reactions (SRs) with NC-HV in HBV-IT was 25.6%, and that with YJV-IT was 10.1%. Compared with previous experience with SE-HV, the use of NC-HV was associated with an increased frequency of SRs (SR rates of HBV-IT 10.4 and YJV-IT 6.3%). The protection rate in HBV-IT, as determined by SCT, was 100% with NC-HV, which is notably higher than the 95.4% previously reported with SE-HV. The efficacy of YJV-IT was equivalent to 99.0% for NC-HV and 99.6% for SE-HV. Conclusion: Nearly complete protection was achieved with the NC-HV. The efficacy gap between HBV-IT and YJV-IT, which has limited VIT for decades, can be overcome with NC-HV in combination with a high total venom dose rush protocol.
The mammalian protein MTCH1 can function as an insertase
2025-07-24

ABSTRACT The outer mitochondrial membrane (OMM) hosts a variety of proteins such as import machineries, enzymes, fission and fusion factors, and pore proteins. In Saccharomyces cerevisiae, the MIM complex, consisting of Mim1 and Mim2, mediates the insertion of α-helical proteins into the OMM. Until recently, it was unclear which proteins served this function in higher eukaryotes. Recent studies have identified MTCH2 as the insertase responsible for inserting α-helical proteins into the OMM in mammals. MTCH1 is a paralogue of MTCH2 but its general function and contribution to the biogenesis process are not clear. To better characterize MTCH1, we explored whether MTCH1 or MTCH2 could functionally replace Mim1 and/or Mim2 in yeast. Expression of MTCH1 and MTCH2 in yeast cells lacking Mim1, Mim2 or both revealed that MTCH1, but not MTCH2, could compensate for the growth defects upon deleting the MIM complex. Furthermore, MTCH1 could restore the biogenesis of MIM substrates, translocase of the outer membrane (TOM) complex stability and morphology of mitochondria. These findings indicate that MTCH1, by itself, has insertase activity and is a functional equivalent for the MIM complex, despite the absence of any evolutionary relation between the mammalian and yeast insertases.
Risk Stratification of Dengue Cases Requiring Hospitalization
2025-07-24

ABSTRACT Dengue pathogenesis involves immune‐driven inflammation that contributes to severe disease progression. This study assessed a machine learning model to identify a minimal, yet highly predictive biomarker set, aiming to support clinical decision‐making and patient triage. A total of 48 inflammatory mediators were quantified from plasma samples collected at admission from confirmed dengue patients, classified as either dengue without warning signs (DF) or dengue with warning signs/severe dengue (DWS/SD). A random forest approach was applied to identify the most predictive biomarkers associated with disease severity requiring hospitalization, based on admission‐time variables. Among the 48 immune mediators, 43 were differentially expressed in dengue patients versus healthy controls, and 26 showed significant differences between DF and DWS/SD cases. Lymphocyte counts negatively correlated with IL‐1RA, while liver enzymes showed positive correlations with HGF and SCGF‐beta; platelet counts also negatively correlated with these markers. Key severity‐associated markers included HGF, TNF‐beta, MIP‐1‐beta, and SCGF‐beta. A model incorporating these markers and fever duration achieved nearly 80% accuracy in distinguishing DWS/SD from DF cases, independent of clinical examination. The findings suggest that targeted cytokine profiling may guide early hospitalization decisions and ease healthcare burdens in dengue‐endemic regions.
Detection of small water bodies for vector control using deep learning on multispectral imagery from unmanned aerial vehicles
2025-07-24

Abstract Vector-borne diseases pose a persistent public health challenge in tropical regions such as Vietnam, where traditional ground-based surveillance methods struggle with scale and accuracy. This study presents a framework that integrates Unmanned Aerial Vehicle (UAV) multispectral imagery with deep learning techniques to detect small-to-medium-sized water bodies, important habitats for arbovirus vectors. High-resolution multispectral images were captured with the DJI Phantom 4 (P4M) Multispectral UAV in rural and peri-urban areas of Binh Duong province in Vietnam. A curated dataset of 982 annotated images was created, comprising RGB, near-infrared (NIR), and normalized difference water index (NDWI) bands. Six state-of-the-art object detection and segmentation models were evaluated, including YOLOv7, YOLOv7x, DocF, U-Net, MSNet, and RTFNet. Among them, segmentation models (U-Net and MSNet) using RGB + Green + NIR + NDWI achieved the best performance with dice scores above 0.92. The results show that the combination of UAV multispectral imagery with deep learning significantly improves the detection accuracy of water bodies in complex tropical conditions. This approach provides a scalable, cost-effective solution for mapping small water bodies and contributes to targeted vector control and disease prevention measures in arbovirus-prone regions.
Validation of the EVendo score for assessing high-risk varices in Western European patients with cirrhosis
2025-07-24

Background : Gastroesophageal varices (GEV) and associated bleeding are serious complications of cirrhosis, leading to considerable morbidity and mortality. While esophagogastroduodenoscopy (EGD) remains the gold standard for detecting GEV, it is an invasive procedure. The EVendo score, a non-invasive predictive tool, has demonstrated promise in identifying GEV and varices needing treatment (VNT). However, its effectiveness has not been extensively studied in Western European populations. This study aims to evaluate the utility of the EVendo score in predicting GEV and VNT among patients with cirrhosis. Methods : This retrospective study, conducted at Klinikum Stuttgart in Germany, screened over 700 patients with cirrhosis who underwent EGD from 2014 to 2021. After applying strict inclusion and exclusion criteria, 86 patients were included. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were assessed for EVendo score cutoffs of ≤ 3.9, ≤ 4.5, and a cohort-optimized cutoff of ≤ 4.3. Results : GEV was present in 94.2% of patients, with 41.9% requiring treatment (VNT). At ≤ 3.9, the EVendo score showed high sensitivity for GEV (79.8%) and VNT (87.2%), but specificity remained 0% for GEV and 24% for VNT. Increasing the cutoff to ≤ 4.5 slightly reduced the sensitivity to 77% for GEV and 85% for VNT, with specificity improving to 26% for VNT. This cutoff avoided 22.1% of EGDs, missing three VNT cases. The cohort-specific cutoff of ≤ 4.3 provided the highest area under the receiver operating characteristic curve (0.57), avoiding 22.1% of EGDs and missing two VNT cases. Conclusion : The EVendo score shows promise for reducing unnecessary EGDs, with high sensitivity across different cutoffs. However, its limited specificity for GEV suggests the need for further refinement, particularly in advanced liver disease stages, to optimize clinical utility. Further validation in diverse, larger cohorts is recommended.