bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the heterogeneous performance of variant effect predictors across human protein-coding genes
Authors: Fawzy Mohamed , Marsh Joseph A. 
Published: October 2024

AbstractVariant effect predictors (VEPs) are computational tools developed to assess the impacts of genetic mutations, often in terms of likely pathogenicity, employing diverse algorithms and training data. Here, we investigate the performance of 35 VEPs in the discrimination between pathogenic and putatively benign missense variants across 963 human protein-coding genes. We observe considerable gene-level heterogeneity as measured by the widely used area under the receiver operating characteristic curve (AUROC) metric. To investigate the origins of this heterogeneity and the extent to which gene-level VEP performance is predictable, for each VEP, we train random forest models to predict the gene-level AUROC. We find that performance as measured by AUROC is related to factors such as gene function, protein structure, and evolutionary conservation. Notably, intrinsic disorder in proteins emerged as a significant factor influencing apparent VEP performance, often leading to inflated AUROC values due to their enrichment in weakly conserved putatively benign variants. Our results suggest that gene-level features may be useful for identifying genes where VEP predictions are likely to be more or less reliable. However, our work also shows that AUROC, despite being independent of class balance, still has crucial limitations when used for comparing VEP performance across different genes.
The effect of nitrogen management on seed yield and quality in traditional and canola-quality white mustard
Authors: Jankowski Krzysztof Józef , Szatkowski Artur , Załuski Dariusz 
Published: October 2024

AbstractThe article presents the results of a three-year field study that was conducted in Poland to evaluate the yield and quality of seeds and oil from traditional (SAM) and canola-quality white mustard (SAC) in response to different N fertilizer rates (0, 40, 80, 120, and 160 kg ha–1). Seed yields were 25% higher in SAM than SAC. The seeds of SAC contained more crude fat (by 3%) and crude fiber (by 6%) than the seeds of SAM. In turn, the seeds of SAM were a richer source of total protein (by 7%). The content of glucosinolates (GSLs) was 8–10 times lower in the seeds of SAC than SAM. The seeds of both mustard cultivars were most abundant in γ-tocopherol (γ-T) (90–94%). The seeds of SAC were characterized by a higher content of γ-T and a lower α-T/γ-T ratio than SAM seeds. White mustard oil contained mostly MUFAs (69–75%). However, C22:1 accounted for more than 50% of MUFAs in the oil SAM. In the oil SAC, the proportion of C22:1 did not exceed 6%, whereas C18:1 accounted for nearly 85% of total MUFAs. Nitrogen fertilization induced a significant increase in seed yields (by 33%), a decrease in crude fat content (by 3–4%), and an increase in total protein content (by 4%), and crude fiber content (by 7%). Nitrogen decreased GSL levels by 31% in SAM seeds. In SAC, N fertilization induced differences in the qualitative composition of GSLs, but did not affect the total GSL content of seeds. Higher N rates increased the content of α-T and γ-T, the α-T/γ-T ratio, and total T content. Nitrogen fertilization decreased the content of C18:3 in the seeds of the SAM. In SAC, the application of N decreased the content of C18, C18:1, and C18:3, and increased the biosynthesis of C18:2, C20:1, and C22:1.
Real-time imaging of cGMP signaling shows pronounced differences between glomerular endothelial cells and podocytes
Authors: Rutkowski Nelli , Görlitz Frederik , Wiesner Eva , Binz-Lotter Julia , Feil Susanne , Feil Robert , Benzing Thomas , Hackl Matthias J. 
Published: October 2024

AbstractRecent clinical trials of drugs enhancing cyclic guanosine monophosphate (cGMP) signaling for cardiovascular diseases have renewed interest in cGMP biology within the kidney. However, the role of cGMP signaling in glomerular endothelial cells (GECs) and podocytes remains largely unexplored. Using acute kidney slices from mice expressing the FRET-based cGMP biosensor cGi500 in endothelial cells or podocytes enabled real-time visualization of cGMP. Stimulation with atrial natriuretic peptide (ANP) or SNAP (NO donor) and various phosphodiesterase (PDE) inhibitors elevated intracellular cGMP in both cell types. GECs showed a transient cGMP response upon particulate or soluble guanylyl cyclase activation, while the cGMP response in podocytes reached a plateau following ANP administration. Co-stimulation (ANP + SNAP) led to an additive response in GECs. The administration of PDE inhibitors revealed a broader basal PDE activity in GECs dominated by PDE2a. In podocytes, basal PDE activity was mainly restricted to PDE3 and PDE5 activity. Our data demonstrate the existence of both guanylyl cyclase pathways in GECs and podocytes with cell-specific differences in cGMP synthesis and degradation, potentially suggesting new therapeutic options for kidney diseases.
Psychometric properties of the Persian version of the workplace fun scale among nurses: a cross-sectional study
Authors: Hashemian Moghadam Azam , Imashi Reza , Yaghoobi Saghezchi Roghayeh , Mirzaei Alireza 
Published: October 2024

AbstractPrevious research has highlighted the importance of workplace fun in enhancing employee satisfaction and performance, particularly in high-stress professions like nursing. However, a notable gap exists in understanding how workplace fun is perceived and measured among nurses in Persian-speaking countries. This study addresses this gap by translating the Workplace Fun Scale and assessing its psychometric properties among nurses. The findings will provide insights into the scale’s applicability in these contexts and pave the way for healthcare organizations to significantly explore ways to enhance nurses’ enjoyment of work in Persian-speaking countries. This survey, which involved 321 nurses from medical education centers in Ardabil, was conducted with a meticulous and rigorous methodology. Standard questionnaires collected the data, including a demographic form and the translated Workplace Fun Scale. The study examined the three aspects of workplace fun: fun activities, coworker socializing, and manager support for fun. Confirmatory factor analysis was used to validate the structure, and reliability was assessed through retest coefficients, Cronbach’s alpha coefficients, and composite reliability coefficients. The data were analyzed using SPSS version 14 and LISREL version 8.8, ensuring the highest research standards. The validity of both form and content was confirmed through translation and reverse translation. The Workplace Fun Scale showed high internal consistency and reliability, with significant Cronbach’s alpha coefficients, composite reliability, and two-week retest coefficients of 0.859, 0.885, and 0.459, respectively (all at the p < 0.01 level). Fit indices, including GFI (0.97), AGFI (0.94), CFI (0.99), NFI (0.98), TLI (0.97), and SRMR (0.04), indicated a good fit of the measurement model, confirming the validity of the scale in assessing workplace fun. The confirmatory factor analysis results indicated that the translated version of the workplace fun scale, adapted from Tews, exhibited a robust factor structure and internal homogeneity within the Iranian sample. Furthermore, the scale demonstrated positive internal validity and reliability in Persian translation. These findings suggest that the scale possesses acceptable psychometric properties, making it a valuable tool for assessing workplace fun among nurses in Persian-speaking countries.
NOTE: non-parametric oversampling technique for explainable credit scoring
Authors: Han Seongil , Jung Haemin , Yoo Paul D. , Provetti Alessandro , Cali Andrea 
Published: October 2024

AbstractCredit scoring models are critical for financial institutions to assess borrower risk and maintain profitability. Although machine learning models have improved credit scoring accuracy, imbalanced class distributions remain a major challenge. The widely used Synthetic Minority Oversampling TEchnique (SMOTE) struggles with high-dimensional, non-linear data and may introduce noise through class overlap. Generative Adversarial Networks (GANs) have emerged as an alternative, offering the ability to model complex data distributions. Conditional Wasserstein GANs (cWGANs) have shown promise in handling both numerical and categorical features in credit scoring datasets. However, research on extracting latent features from non-linear data and improving model explainability remains limited. To address these challenges, this paper introduces the Non-parametric Oversampling Technique for Explainable credit scoring (NOTE). The NOTE offers a unified approach that integrates a Non-parametric Stacked Autoencoder (NSA) for capturing non-linear latent features, cWGAN for oversampling the minority class, and a classification process designed to enhance explainability. The experimental results demonstrate that NOTE surpasses state-of-the-art oversampling techniques by improving classification accuracy and model stability, particularly in non-linear and imbalanced credit scoring datasets, while also enhancing the explainability of the results.
Optical control of multiple resistance levels in graphene for memristic applications
Authors: Mann Harsimran Kaur , Mondal Mainak , Sah Vivek , Watanabe Kenji , Taniguchi Takashi , Singh Akshay , Bid Aveek 
Published: October 2024

AbstractNeuromorphic computing has emphasized the need for memristors with non-volatile, multiple conductance levels. This paper demonstrates the potential of hexagonal boron nitride (hBN)/graphene heterostructures to act as memristors with multiple resistance states that can be optically tuned using visible light. The number of resistance levels in graphene can be controlled by modulating doping levels, achieved by varying the electric field strength or adjusting the duration of optical illumination. Our measurements show that this photodoping of graphene results from the optical excitation of charge carriers from the nitrogen-vacancy levels of hBN to its conduction band, with these carriers then being transferred to graphene by the gate-induced electric field. We develop a qualitative model to describe our observations. Additionally, utilizing our device architecture, we propose a memristive crossbar array for vector-matrix multiplications.
Fractional quantum Hall phases in high-mobility n-type molybdenum disulfide transistors
Authors: Zhao Siwen , Huang Jinqiang , Crépel Valentin , Xiong Zhiren , Wu Xingguang , Zhang Tongyao , Wang Hanwen , Han Xiangyan , Li Zhengyu , Xi Chuanying , Pan Senyang , Wang Zhaosheng , Kuang Guangli , Luo Jun , Shen Qinxin , Yang Jie , Zhou Rui , Watanabe Kenji , Taniguchi Takashi , Sacépé Benjamin , Zhang Jing , Wang Ning , Lu Jianming , Regnault Nicolas , Han Zheng Vitto 
Published: October 2024

AbstractTransistors based on semiconducting transition metal dichalcogenides can, in theory, offer high carrier mobilities, strong spin–orbit coupling and inherently strong electronic interactions at the quantum ground states. This makes them well suited for use in nanoelectronics at low temperatures. However, creating robust ohmic contacts to transition metal dichalcogenide layers at cryogenic temperatures is difficult. As a result, it is not possible to reach the quantum limit at which the Fermi level is close to the band edge and thus probe electron correlations in the fractionally filled Landau-level regime. Here we show that ohmic contacts to n-type molybdenum disulfide can be created over a temperature range from millikelvins to 300 K using a window-contacted technique. We observe field-effect mobilities of over 100,000 cm2 V−1 s−1 and quantum mobilities of over 3,000 cm2 V−1 s−1 in the conduction band at low temperatures. We also report evidence for fractional quantum Hall states at filling fractions of 4/5 and 2/5 in the lowest Landau levels of bilayer molybdenum disulfide.
Biomolecular analysis of the Epigravettian human remains from Riparo Tagliente in northern Italy
Authors: Yavuz Orhan Efe , Oxilia Gregorio , Silvestrini Sara , Tassoni Laura , Reiter Ella , Drucker Dorothée G. , Talamo Sahra , Fontana Federica , Benazzi Stefano , Posth Cosimo 
Published: October 2024

AbstractThe Epigravettian human remains from Riparo Tagliente in northern Italy represent some of the earliest evidence of human occupation in the southern Alpine slopes after the Last Glacial Maximum. Genomic analyses of the 17,000-year-old Tagliente 2 mandible revealed the oldest presence of a genetic profile with affinities to the Near East in the Italian peninsula, which later became the most widespread hunter-gatherer ancestry across Europe. However, a comparable biomolecular characterization of the Tagliente 1 burial remains unavailable, preventing us from defining its biological relationships with Tagliente 2. Here, we apply paleogenomic, isotopic, and radiocarbon dating analyses on a femur fragment of Tagliente 1 and compare the reconstructed data with previously reported results from Tagliente 2. Despite their different isotopic signatures and non-overlapping radiocarbon dates, we reveal that the two human remains belong to the same male individual. We determine that the distinct isotopic values can be explained by different dietary practices during lifetime, whereas the non-overlapping radiocarbon dates can be caused by minimal radiocarbon contamination, possibly deriving from chemical treatments for conservation purposes. These findings highlight the importance of interdisciplinary biomolecular studies in offering new perspectives on the Palaeolithic fossil record and addressing long-standing bioarchaeological questions.
Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis
Authors: Esplin Edward D. , Hanson Casey , Wu Si , Horning Aaron M. , Barapour Nasim , Nevins Stephanie A. , Jiang Lihua , Contrepois Kévin , Lee Hayan , Guha Tuhin K. , Hu Zheng , Laquindanum Rozelle , Mills Meredith A. , Chaib Hassan , Chiu Roxanne , Jian Ruiqi , Chan Joanne , Ellenberger Mathew , Becker Winston R. , Bahmani Bahareh , Khan Aziz , Michael Basil , Weimer Annika K. , Esplin D. Glen , Shen Jeanne , Lancaster Samuel , Monte Emma , Karathanos Thomas V. , Ladabaum Uri , Longacre Teri A. , Kundaje Anshul , Curtis Christina , Greenleaf William J. , Ford James M. , Snyder Michael P. 
Published: October 2024

AbstractFamilial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected persons and is an ideal model to study transitions of early precancer states to colorectal cancer (CRC). We performed deep multiomic profiling of 93 samples, including normal mucosa, benign polyps and dysplastic polyps, from six persons with FAP. Transcriptomic, proteomic, metabolomic and lipidomic analyses revealed a dynamic choreography of thousands of molecular and cellular events that occur during precancerous transitions toward cancer formation. These involve processes such as cell proliferation, immune response, metabolic alterations (including amino acids and lipids), hormones and extracellular matrix proteins. Interestingly, activation of the arachidonic acid pathway was found to occur early in hyperplasia; this pathway is targeted by aspirin and other nonsteroidal anti-inflammatory drugs, a preventative treatment under investigation in persons with FAP. Overall, our results reveal key genomic, cellular and molecular events during the earliest steps in CRC formation and potential mechanisms of pharmaceutical prophylaxis.
Untethered bistable origami crawler for confined applications
Authors: Cai Catherine Jiayi , Huang Hui , Ren Hongliang 
Published: October 2024

AbstractMagnetically actuated miniature origami crawlers are capable of robust locomotion in confined environments but are limited to passive functionalities. Here, we propose a bistable origami crawler that can shape-morph to access two separate regimes of folding degrees of freedom that are separated by an energy barrier. Using the modified bistable V-fold origami crease pattern as the fundamental unit of the crawler, we incorporated internal permanent magnets to enable untethered shape-morphing. By modulating the orientation of the external magnetic field, the crawler can reconfigure between an undeployed locomotion state and a deployed load-bearing state. In the undeployed state, the crawler can deform to enable out-of-plane crawling for robust bi-directional locomotion and navigation in confined environments based on friction anisotropy. In the deployed state, the crawler can execute microneedle insertion in confined environments. Through this work, we demonstrated the advantage of incorporating bistability into origami mechanisms to expand their capabilities in space-constraint applications.
A high robust control scheme of grid‐side converter for DFIG system
Authors: Shi Shuqi , Liu Zongze , Ren Long , Tang Hongwei , Song Dongran 
Published: October 2024

AbstractIn this study, a high robust control—second‐order sliding‐mode control (SOSMC) scheme is proposed to improve the DC‐link voltage dynamic performance of the grid‐side converter (GSC) for the doubly‐fed induction generator (DFIG) system under the wind turbine power disturbance and DC‐link capacitance parameter disturbance. In general, the wind speed is change with the environment and further has an effect on the power generation of the DFIG system. Besides, the capacitance of DC‐link capacitor may change with the working condition. To address this issue, a SOSMC scheme is proposed to replace the conventional proportional integral (PI) control for the DC‐link voltage controller of the GSC for the DFIG system in this study. By using the non‐linear SOSMC controller, the DFIG system is robust to the disturbance of the wind speed and the parameter of DC‐link capacitance. Compared with the conventional PI control scheme, the DFIG system with the proposed SOSMC scheme is much more robust, which has been verified in the MATLAB/Simulink platform.
Robust network topology for unbalanced active distribution networks with uncertain injections
Authors: Paul Sanat Kumar , Mohapatra Abheejeet , Chandra Das Dulal 
Published: October 2024

AbstractThis research paper introduces a comprehensive formulation for robust dynamic network reconfiguration (NR) of unbalanced active electric distribution networks (DNs). Network reconfiguration is a potent strategy to minimise active power loss in DN as it involves altering network topology through sectionalising (normally closed) and tie‐line switches (normally open). However, NR is usually a mixed integer NP‐hard non‐linear optimisation problem due to the discrete nature of the switches. Hence, including variable injection uncertainties (from generation or load) for an unbalanced active DN with all its attributes further poses a significant challenge in solving NR. The proposed formulation addresses these challenges in a robust optimisation (RO) framework to get a robust topology and power and voltage set points for dispatchable Distributed Generators (DGs). Also, Chance‐Constrained robust formulations are proposed to regulate the conservatism of RO. Numerical analyses demonstrate the impact of conservative robust NR on DG set points compared to the non‐robust NR method. Tests on a modified unbalanced IEEE 34‐bus system and comparison with previous formulations verify the efficacy of the proposed approach, showcasing its effectiveness.
Hyperparameter free sparse estimation for wideband multiple‐input‐multiple‐output radar direction finding without secondary data
Authors: Xiao Jiong , Tang Bo 
Published: October 2024

AbstractThe estimation of target directions of arrival (DOA) for wideband multiple‐input‐multiple‐output (MIMO) radar is investigated in this article. First, the authors establish a signal model for wideband MIMO radar systems. Then, an algorithm is proposed to estimate the target angles without secondary data (i.e. the training data from slow‐time is not required).The proposed algorithm unitises the spatial sparsity of target signals and it is derived under the Bayesian framework. It can estimate the spatial pseudo‐spectra of the targets through cyclic optimisation. Additionally, it is hyperparameter‐free and guarantees convergence. To analyse the performance of the proposed algorithm, the Cramér‐Rao bound (CRB) is derived for DOA estimation with wideband MIMO radar. Numerical examples demonstrate that even without secondary data, the proposed algorithm can accurately estimate the DOA of the targets.
Application of simultaneous evaluation of criteria and alternatives for prioritization of photovoltaic power plant location
Authors: Lak Khashayar , Kashani Arash Haghparast , Azizi Amir , Karimi Naser , Hosseinpour Morteza 
Published: October 2024

AbstractThis research contributes to the ongoing efforts to transition towards clean and renewable energy sources by providing a practical framework for decision‐making in energy resource planning. Hence, a recently developed multi‐criteria decision making technique tool is proposed for simultaneous evaluation of criteria and alternatives (SECA) to find an optimal site for establishing photovoltaic power stations in Iran. The proposed SECA method provides a systematic and comprehensive approach to evaluating renewable energy resources, taking into account technical, economic, environmental, and social factors. The data required for this research has also been collected from the Global Solar Atlas as well as the Iran Meteoritical Organization. The results show that despite the main influence of the solar radiation factor, it should be noted that among all the climatic and environmental indicators, “cloudiness factor” by weight of 0.2339 and “annual temperature” by weight of 0.2320 have been selected as the most important criteria. It was also found that among the ten candidate cities, Zahedan (w = 0.8939), Shahrekord (w = 0.8341) and Kerman (w = 0.8112) have the highest potential for building a solar power plant. The results of the study highlight the potential for solar energy resources to meet Iran's electricity needs in a sustainable manner.