bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sanger validation of WGS variants
Authors: Kopernik Arina , Sayganova Mariia , Zobkova Gaukhar , Doroschuk Natalia , Smirnova Anna , Molodtsova-Zolotukhina Daria , Sagaydak Olesya , Ryzhkova Oxana , Kutsev Sergey , Groznova Olga , Melikyan Lyusya , Bondarchuk Elizaveta , Woroncow Mary , Albert Eugene , Bogdanov Viktor , Volchkov Pavel 
Published: January 2025

Abstract
With the development of next-generation sequencing (NGS) technologies it became possible to simultaneously analyze millions of variants. Despite the quality improvement, it is generally still required to confirm the variants before reporting. However, in recent years the dominant idea is that one could define the quality thresholds for “high quality” variants which do not require orthogonal validation. Despite that, no works to date report the concordance between variants from whole genome sequencing and their gold-standard Sanger validation. In this study we analyzed the concordance for 1756 WGS variants in order to establish the appropriate thresholds for high-quality variants filtering. Resulting thresholds allowed us to drastically reduce the number of variants which require validation, to 4.8% and 1.2% of the initial set for caller-agnostic (DP, AF) and caller-dependent (QUAL) thresholds, respectively.
Resistance-breaking strains of tomato spotted wilt virus hamper photosynthesis and protein synthesis pathways in a virus accumulation-dependent manner in Sw5-carrying tomatoes
Authors: Prigigallo Maria Isabella , Picciotti Ugo , Bubici Giovanni 
Published: January 2025

Abstract
Tomato spotted wilt virus (TSWV; Orthotospovirus tomatomaculae) is one of the major horticultural threats due to its worldwide distribution and broad host range. In Italy, TSWV is widely spread in tomato (Solanum lycopersicum) crops and causes severe yield losses. In the last decades, several tomato varieties carrying the Sw-5b gene for resistance to TSWV have been released. We investigated the interaction between Sw-5b-carrying tomatoes and Sw5-Resistance-Breaking (SRB) TSWV to elucidate the molecular mechanisms underlying resistance breakage. Transcriptome sequencing (RNA-Seq) was used to analyze 18 tomato leaf samples collected from a field crop naturally infected by SRB TSWV in Italy. An increase in virus accumulation level in leaf tissues (titer) resulted in a higher number of differentially expressed genes (DEGs), ranging from 33 to 44% of the whole transcriptome, when the samples with the lowest and the highest virus titer were compared to the asymptomatic sample, respectively. Photosynthesis and protein biosynthesis were the main down-regulated biological processes, while enzyme families such as oxidoreductases and transferases, genes related to the response to biotic stimuli, solute transport, and vesicle trafficking were overall up-regulated. Remarkably, the expression of around 45% of genes (ca. 14000) of the whole transcriptome was significantly (P < 0.05) correlated (positively or negatively) to the virus titer, and in 6% of cases (about 2000 genes) the correlation was high (i.e., absolute value of R2 > 0.85). This phenomenon was also verified on 15 genes by a quantitative reverse transcription PCR assay on a greenhouse experiment with a different Sw-5b-tomato variety artificially inoculated with another SRB TSWV strain. In conclusion, the tomato transcriptome was considerably rearranged upon TSWV infection, with deregulation of photosynthesis, protein biosynthesis, and induction of defense pathways. Finally, this research demonstrated that the magnitude of transcriptional changes was proportional to the virus accumulation level in the leaves.
Identification of novel 7-hydroxycoumarin derivatives as ELOC binders with potential to modulate CRL2 complex formation
Authors: Kim Yonghyeok , Baek Seon Jeong , Yoon Eun-Kyung , Choi Minhee , Kim Jung-Hoon , Kim Kyungtae , Park Chi Hoon , Lee Byung Il 
Published: January 2025

Abstract
The VHL-containing cullin-RING E3 ubiquitin ligase (CRL2VHL) complex is an E3 ligase commonly used in targeted protein degradation (TPD). Hydroxyproline-based ligands that mimic VHL substrates have been developed as anchor molecules for proteolysis-targeting chimeras (PROTACs) in TPD. To expand the chemical space for VHL ligands, we conducted fragment screening using VHL–ELOB–ELOC (VBC) proteins. We found that certain 7-hydroxycoumarin derivatives (7HCs), rather than VHL, would bind to the ELOC component of the VBC complex. The 7HC binding site overlapped with the CUL2 binding interface on ELOC but did not overlap with the CUL5 binding interface, suggesting that 7HCs may influence the formation of CRL2 but not CRL5. Although the binding affinities of these 7HCs to the VBC complex were relatively low, they represent novel and promising foundational agents for the development of chemical probes or inhibitors that target ELOC-containing CRLs.
SLC25A1 and ACLY maintain cytosolic acetyl-CoA and regulate ferroptosis susceptibility via FSP1 acetylation
Authors: Li Wei , Han Jing , Huang Bin , Xu Tengteng , Wan Yihong , Luo Dan , Kong Weiyao , Yu Ying , Zhang Lei , Nian Yong , Chu Bo , Yin Chengqian 
Published: January 2025

Abstract
Ferroptosis, an iron-dependent form of programmed cell death characterized by excessive lipid hydroperoxides accumulation, emerges as a promising target in cancer therapy. Among the solute carrier (SLC) superfamily, the cystine/glutamate transporter system antiporter components SLC3A2 and SLC7A11 are known to regulate ferroptosis by facilitating cystine import for ferroptosis inhibition. However, the contribution of additional SLC superfamily members to ferroptosis remains poorly understood. Here, we use a targeted CRISPR-Cas9 screen of the SLC superfamily to identify SLC25A1 as a critical ferroptosis regulator in human cancer cells. SLC25A1 drives citrate export from the mitochondria to the cytosol, where it fuels acetyl-CoA synthesis by ATP citrate lyase (ACLY). This acetyl-CoA supply sustains FSP1 acetylation and prevents its degradation by the proteasome via K29-linked ubiquitin chains. K168 is the primary site of FSP1 acetylation and deacetylation by KAT2B and HDAC3, respectively. Pharmacological inhibition of SLC25A1 and ACLY significantly enhances cancer cell susceptibility to ferroptosis both in vitro and in vivo. Targeting the SLC25A1-ACLY axis is therefore a potential therapeutic strategy for ferroptosis-targeted cancer intervention.
Poly(butylene succinate) filaments for fused deposition modelling (FDM) 3D-printing
Authors: Chen Yong , Xu Jielin , Chen Ye , Wang Chaosheng , Wang Huaping , Wu Jing 
Published: January 2025

We adopted an in situ branch modification strategy to improve the melt processing of PBS. The filament that meets the needs of FDM 3D printing has been successfully prepared, and a single PBS material was used to achieve a 3D printing product.
Medical data analysis and transaction type prediction using machine learning and blockchain technology
Authors: Maheshwari Shruti , Jain Pramod Kumar , Al‐Sharify Noor T. , Ghosh Swagata , Dubey Dhanraj , Kaur Gagandeep 
Published: January 2025

AbstractIn the world of healthcare, joining machine learning with block chain tech offers a smart path for future predictions. The study aims on guessing what kinds of transactions happen in healthcare data stored on a block chain. Machine learning is used to sort these transactions right. This helps make healthcare tasks work on their own and do better. Health data is taken from block chains, looked at it closely, and ran various algorithms on it. Using features such as operation, date, and symbolic indicators, logistic regression, decision tree, random forest, and support vector machine are applied to classify transaction types. The decision tree algorithm achieved the highest accuracy at 89.29%, followed by random forest at 67.86%, logistic regression at 33.93%, and support vector machine at 39.29%. The findings demonstrate the effectiveness of machine learning in improving transaction classification within secure, decentralized medical data environments.
Topology‐aware tensor decomposition for meta‐graph learning
Authors: Yang Hansi , Yao Quanming 
Published: January 2025

AbstractHeterogeneous graphs generally refer to graphs with different types of nodes and edges. A common approach for extracting useful information from heterogeneous graphs is to use meta‐graphs, which can be seen as a special kind of directed acyclic graph with same node and edge types as the heterogeneous graph. However, how to design proper meta‐graphs is challenging. Recently, there have been many works on learning suitable meta‐graphs from a heterogeneous graph. Existing methods generally introduce continuous weights for edges that are independent of each other, which ignores the topological structures of meta‐graphs and can be ineffective. To address this issue, the authors propose a new viewpoint from tensor on learning meta‐graphs. Such a viewpoint not only helps interpret the limitation of existing works by CANDECOMP/PARAFAC (CP) decomposition, but also inspires us to propose a topology‐aware tensor decomposition, called TENSUS, that reflects the structure of DAGs. The proposed topology‐aware tensor decomposition is easy to use and simple to implement, and it can be taken as a plug‐in part to upgrade many existing works, including node classification and recommendation on heterogeneous graphs. Experimental results on different tasks demonstrate that the proposed method can significantly improve the state‐of‐the‐arts for all these tasks.
Adaptive dynamic programming for trajectory tracking control of a tractor‐trailer wheeled mobile robot
Authors: Ghasemzadeh Aliakbar , Amjadifard Roya , Keymasi‐Khalaji Ali 
Published: January 2025

AbstractTractor‐trailer wheeled mobile robots (TTWMRs) possess complex nonlinear dynamics that make their precise trajectory tracking control challenging. This paper explores an adaptive dynamic programming (ADP) approach that utilizes critic neural networks to improve tracking control for continuous‐time TTWMRs. To achieve this, the decoupled kinematic and dynamic loops of the TTWMR are considered, and ADP controllers are proposed aimed at integrated trajectory and velocity tracking. Tis study defines two tracking error systems related to the kinematic and dynamic control loops, which reduces the computational load compared to previous research. The two critic neural networks approximate the optimal cost functions and enable the adaptive tuning of the control policies. Theoretical analysis demonstrates both closed‐loop stability and convergence. Simulation results indicate that the proposed method offers superior tracking performance compared to earlier techniques, exhibiting lower errors and reduced control efforts. This underscores the advantages of using ADP to optimize the control of TTWMRs, even in the presence of partially unknown dynamics.
Enhanced post‐fault recovery in MTDC networks using active damping approach
Authors: Sharma Monika , Torres José L. Rueda 
Published: January 2025

AbstractThe increasing deployment of offshore wind farms necessitates robust and stable high‐voltage direct current networks. Achieving optimal stability, especially in damping oscillations on the DC side, remains a significant challenge. This study focuses on mitigating post‐fault converter de‐blocking oscillations, a critical issue exacerbated by complex interactions between AC and DC systems, converter dynamics, and system faults. These behavior are governed by nonlinear system dynamics, making traditional control methods less effective in ensuring stability. A comprehensive analysis of DC side oscillations and their interaction with converter dynamics is developed to understand the key factors influencing system stability. The research investigates a DC voltage regulation damping approach, identified as the most effective solution in the literature. Comprehensive parametric sensitivity analysis evaluates system behavior under diverse operational conditions. Addressing current damping method limitations during converter de‐blocking, this work proposes an innovative control approach integrating fuzzy logic control and proportional–integral controllers. This approach enhances DC voltage regulation and incorporates a modified circulating current suppression control in the inner loop. The coordinated fuzzy logic control and proportional–integral controller dynamically adjusts to nonlinear system dynamics in real‐time, providing a robust framework for improved post‐fault recovery. It aims to achieve faster recovery times and reduced overshoot compared to conventional methods. The proposed controller's efficacy is validated through comparative analysis with existing approaches. Electromagnetic transient) simulations using the real‐time digital simulator platform demonstrate the controller's performance under realistic operating conditions.
System for assistance in ultrasound‐guided percutaneous hepatic interventions using augmented reality: First steps
Authors: Salazar Carrasco Lucía , Sánchez‐Varo Ignacio , Caballero Jorna Daniel , Iribar‐Zabala Amaia , Bertelsen‐Simonetti Álvaro , Sánchez‐Margallo Juan A. , Sánchez‐Margallo Francisco M. 
Published: January 2025

AbstractThis study aims to develop a system based on mixed reality imaging for assistance in percutaneous ultrasound‐guided liver interventions. A liver phantom, an ultrasound scanner with an abdominal probe, an electromagnetic tracking system for localization of the ultrasound probe, and the percutaneous needle were used to develop the system. A gelatin liver phantom was fabricated, including a set of lesions (with agarose, glycerol, and sephadex) and artificial blood vessels 3D printed with thermoplastic polyurethane (TPU) elastic fibres. Intraoperative ultrasound images from a BK5000 ultrasound scanner were acquired using a video capture system and transmitted to 3D Slicer. The NDI Aurora electromagnetic tracking system, coupled to the ultrasound probe and intracorporeal needle, was used for real‐time trajectory tracking, providing us with spatial localization information. These images are then sent to the augmented reality HoloLens device as the primary visualization system. This work lays the groundwork for the development of a more comprehensive system to assist ultrasound‐guided percutaneous liver interventions in order to improve the accuracy and safety of these procedures. The use of mixed reality imaging technology allows a better integration of image‐guided surgery systems, such as the one presented in this work, in real clinical environments, and closer to the patient.
A novel composite control approach to enhance stability in wind/PV/PEM fuel cell/hydrogen/BESS—based DC microgrids
Authors: Islam Md Saiful , Roy Tushar Kanti , Bushra Israt Jahan , Ghosh Subarto Kumar , Oo Amanullah Maung Than 
Published: January 2025

AbstractThis paper addresses the critical challenge of combating global warming by developing an advanced control strategy for DC microgrids powered by renewable energy sources. It proposes a novel composite controller based on an enhanced fast‐reaching law, integrating a recursive backstepping controller with an integral terminal sliding mode controller to ensure stable DC‐bus voltage and seamless power management. The proposed composite controller effectively coordinates multiple components, including proton exchange membrane fuel cells fuelled by green hydrogen, solar photovoltaic systems, wind turbines with permanent magnet synchronous generators, and battery energy storage systems. To maximize energy generation from photovoltaic and permanent magnet synchronous generator, a deep neural network‐based maximum power point tracking algorithm is employed. Moreover, a fuzzy logic control‐based energy management system regulates power flow, factoring in key parameters such as the battery energy storage system's state of charge, fuel cell capacity, and available renewable energy sources power. The robustness of the composite controller is rigorously validated using the control Lyapunov theory to ensure stability under varying operating conditions. Both MATLAB/Simulink simulations and processor‐in‐the‐loop testing demonstrate the composite controller's superior performance, showing a dramatic 85% to 100% improvement in settling time and overshoot compared to existing controllers.
Hydrogenation of acetaldehyde on interstellar ice analogs results in limited destruction
Authors: Molpeceres G. , Nguyen T. , Oba Y. , Watanabe N. 
Published: January 2025

Context. Acetaldehyde (CH3CHO) is one of the most abundant interstellar complex organic molecules and its hydrogenation has important implications in several fundamental processes of interstellar chemistry, such as deuterium fractionation, reactive desorption, or the relation between organic functional groups of detected molecules.
Aims. We seek to determine what the main hydrogenation paths of CH3CHO are. As a partially unsaturated molecule, CH3CHO can have links with more hydrogenated species, such as ethanol (C2H5OH), or with more unsaturated ones, such as ketene (H2CCO).
Methods. We used highly accurate quantum chemical calculations to determine the reaction rate constants for the CH3CHO + H/D reaction. We later studied, using more approximated methods, the fate of the majoritarian product of the reaction, the acetyl radical CH3CO after subsequent reaction with hydrogen or deuterium atoms. Our theoretical results were tested with our experiments on the hydrogenation and deuteration of CH3CHO ice.
Results. We find that acetaldehyde resists hydrogenation, with only a 10% of conversion to products different than CH3CHO. This is due to a predominance of H abstraction at the HCO moiety, with reaction rate constants up to four orders of magnitude higher than the next possible reaction channel, which is hydrogenation at the aldehydic carbon. The formed CH3CO radical experiences barrierless or nearly barrierless reactions in all possible reaction positions, reforming CH3CHO and creating a closed loop that protects the molecule against hydrogenation. We constrained the branching ratios for the second reaction from the experiments. Our experiments agree with the calculations and from the combination of both we can explain the presence of H2CCO, CO, CH4, C2H5OH, H2CO, or CH3OH as minor products at the end of the reaction. We provide recommendations for future modeling efforts.
Conclusions. Our results show limited destruction of acetaldehyde, reinforcing the vision of this molecule as an abundant and resilient COM. From the experiments, we are not able to observe the reactive desorption of this molecule. Our results align with other modeling works, showing that the link between CH3CHO and C2H5OH is not direct. Finally, our results can explain the excess of CH3CDO found in prestellar cores.
Tidal tails of nearby open clusters
Authors: Risbud Dhanraj , Jadhav Vikrant V. , Kroupa Pavel 
Published: January 2025

Context. Tidal tails of open clusters are the result of stellar evaporation from the cluster through the Galactic potential and internal dynamics. With the recent availability of high-precision data, tidal tails are being detected for most of the nearby open clusters.
Aims. We identify the tidal tail members for all open clusters within a distance of 400 pc that are older than 100 Myr and have >100 members. To do this, we use model-independent methods.
Methods. We used the convergent-point (CP) method to identify the co-moving stars near the open clusters using Gaia DR3 data. A new method called the self-compact convergent-point method was proposed and applied to some of the clusters. It performed better overall in tracing the tails. We also analysed the colour-magnitude diagrams and orbital energy to diagnose possible contamination.
Results. Nineteen out of 21 clusters have tidal tails. Five of them were discovered for the first time through this work. The typical span of the tidal tails is 20–200 pc, and 30–700 member stars lie in the region inside the tidal radius and the tidal tails. Four out of 19 tidal tails are tilted away from direction of the Galactic centre. This contradicts the known theory of the tidal-tail formation. The luminosity functions of the tails and clusters are consistent with each other and with the canonical stellar interstellar mass function, but systematically higher radial velocities for the trailing tail than for the leading tail were observed for the first time.
Conclusions. The CP method is useful for detecting tidal tails on a scale of ≈100 pc for clusters closer than 400 pc. A further analysis of theoretical N-body models is required to understand the incompleteness and biases in the current sample of tidal tails.
The Impact of Changing Physicians on Compliance with Management of Myopia Progression
Authors: Schibli Fabian , Palmowski-Wolfe Anja 
Published: January 2025

Abstract
Background The global incidence of high myopia is increasing, with projections indicating a rise from 3 to 10% of the global population by 2050. Effective treatment options exist to reduce myopia progression, but their success is contingent on patient adherence. This study assesses the impact of changes in treating physicians on adherence to therapy to control myopia progression.
Patients and Methods This retrospective observational study analyzed data from the Myopia Clinic at the University Eye Hospital of Basel from 2020 to 2023. Adherence rates were compared between consultations with and without a change in the treating physician, as well as between resident and senior physicians. Statistical analysis was performed using unpaired t-tests and chi-squared tests.
Results A total of 73 patients, with a mean age of 10.76 years, who had at least three axial length measurements were included. Overall, 84.79% of consultations adhered to the recommended treatment. A significantly higher nonadherence rate of 21.43% was observed in consultations following a change in physician, compared to 6.42% with physician stability (p = 0.0037). Nonadherence was also higher with resident physicians (18.31%) compared to senior physicians (8.70%; p = 0.0310). No significant difference in adherence was found between optical and medical treatment options (p = 0.6293). Age and gender did not significantly influence adherence.
Discussion The study reveals a significant negative impact of physician changes on patient adherence in therapy to control myopia progression control. The findings emphasize the importance of consistent physician care, particularly in avoiding frequent rotations among resident physicians, in order to enhance treatment adherence. While the studyʼs limitations include a small sample size and single-center data, the results suggest that strategies to minimize changes in treating physicians could improve adherence outcomes.
Bi- und multimodale Endoskopie der Harnblase in Diagnostik und Therapie
Authors: Nientiedt Malin , Waldbillig Frank 
Published: January 2025

ZusammenfassungDie Weißlichtzystoskopie ist ein präzises Instrument zur Detektion und Therapie von papillären Blasentumoren. Verschiedene zusätzliche makroskopische Detektionstechniken sind etabliert. Bei einigen dieser, allen voran der PDD oder NBI konnte ein zusätzlicher Nutzen auf die Blasentumorrezidivraten nachgewiesen werden, sodass die Anwendung im Rahmen der Diagnostik und Therapie nach Verfügbarkeit erfolgen sollte. Weitere mikroskopische Klassifizierungstechniken oder multimodale Verfahren sind in der Entwicklung. Die breitflächige Anwendung der Techniken ist bislang ausstehend. Neuere Modalitäten wie beispielsweise multiparametrische Bildgebung oder KI-gestützte Endoskopie versprechen in Zukunft einen bedeutenden Innovationssprung und könnten dafür sorgen, dass die urologische Echtzeit-Endoskopie entscheidend weiterentwickelt wird.