bluuebunny/crossref_metadata_2025_split huggingface dataset:
CaXML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features
Authors: Zhang Pengzhi , Nde Jules , Eliaz Yossi , Jennings Nathaniel , Cieplak Piotr , Cheung Margaret S. 
Published: January 2025

AbstractProteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium‐binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium‐binding protein variants. Here, we developed a chemistry‐informed, machine‐learning algorithm that implements a game theoretic approach to explain the output of a machine‐learning model without the prerequisite of an excessively large database for high‐performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium‐binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of CaXML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium‐binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.
Conformational dynamics in specialized C2H2 zinc finger domains enable zinc‐responsive gene repression in S. pombe
Authors: Wadhwa Vibhuti , Jamshidi Cameron , Stachowski Kye , Bird Amanda J. , Foster Mark P. 
Published: January 2025

AbstractLoz1 is a zinc‐responsive transcription factor in fission yeast that maintains cellular zinc homeostasis by repressing the expression of genes required for zinc uptake in high zinc conditions. Previous deletion analysis of Loz1 found a region containing two tandem C2H2 zinc‐fingers and an upstream “accessory domain” rich in histidine, lysine, and arginine residues to be sufficient for zinc‐dependent DNA binding and gene repression. Here we report unexpected biophysical properties of this pair of seemingly classical C2H2 zinc fingers. Isothermal titration calorimetry and NMR spectroscopy reveal two distinct zinc binding events localized to the zinc fingers. NMR spectra reveal complex dynamic behavior in this zinc‐responsive region spanning time scales from fast 10−12–10−10 to slow >100 s. Slow exchange due to cis‐trans isomerization of the TGERP linker results in the doubling of many signals in the protein. Conformational exchange on the 10−3 s timescale throughout the first zinc finger distinguishes it from the second and is linked to a weaker affinity for zinc. These findings reveal a mechanism of zinc sensing by Loz1 and illuminate how the protein's rough free‐energy landscape enables zinc sensing, DNA binding and regulated gene expression.
NumSimEX: A method using EXX hydrogen exchange mass spectrometry to map the energetics of protein folding landscapes
Authors: Flint Jasper A. G. , Witten Jacob , Han Isabella , Strahan John , Damjanovic Jovan , Song Nevon , Poterba Tim , Cartagena Alexis Jaramillo , Hirsch Angelika , Ni Tony , Sohl Julie L. , Wagaman Amy S. , Jaswal Sheila S. 
Published: January 2025

AbstractHydrogen exchange mass spectrometry (HXMS) is a powerful tool to understand protein folding pathways and energetics. However, HXMS experiments to date have used exchange conditions termed EX1 or EX2 which limit the information that can be gained compared to the more general EXX exchange regime. If EXX behavior could be understood and analyzed, a single HXMS timecourse on an intact protein could fully map its folding landscape without requiring denaturation. To address this challenge, we developed a numerical simulation method called NumSimEX that models EXX exchange for arbitrarily complex folding pathways. NumSimEx fits protein folding dynamics to experimental HXMS data by iteratively comparing the simulated and experimental timecourses, allowing for determination of both kinetic and thermodynamic protein folding parameters. After analytically verifying NumSimEX's accuracy, we demonstrated its power on HXMS data from beta‐2 microglobulin (β2M), a protein involved in dialysis‐related amyloidosis. In particular, using NumSimEX, we identified three‐state kinetics that near‐perfectly matched experimental observation. This proof‐of‐principle application of NumSimEX sets the stage for harnessing HXMS to expand our understanding of proteins currently excluded from traditional protein folding methods. NumSimEX is freely available at https://github.com/JaswalLab/NumSimEX_Public.
Deployment and transcriptional evaluation of nitisinone, an FDA‐approved drug, to control bed bugs
Authors: Sterkel Marcos , Tompkin Joshua , Schal Coby , Guerra Luiza R. M. , Pessoa Grasielle C. D. , Oliveira Pedro L. , Benoit Joshua B. 
Published: January 2025

AbstractBACKGROUNDBed bugs are blood‐feeders that rapidly proliferate into large indoor infestations. Their bites can cause allergies, secondary infections and psychological stress, among other problems. Although several tactics for their management have been used, bed bugs continue to spread worldwide wherever humans reside. This is mainly due to human‐mediated transport and their high resistance to several classes of insecticides. New treatment options with novel modes of action are required for their control. In this study, we evaluated the use of nitisinone (NTBC), an FDA‐approved drug, for bed bug control in an insecticide‐susceptible (HH) and an insecticide‐resistant (CIN) population.RESULTSAlthough NTBC was lethal to both populations when administered orally or applied topically in very low doses, we observed a slight but significant resistance in the CIN population. Transcriptomic analysis in both populations indicated that NTBC treatment elicited a broad suppression of genes associated with RNA post‐transcriptional modifications, translation, endomembrane system, protein post‐translational modifications and protein folding. The CIN population exhibited higher adenosine triphosphate (ATP) production and xenobiotic detoxification. Feeding studies on a mouse model suggest that NTBC could be used as a control method of bed bugs by host treatment.CONCLUSIONThe results indicate that NTBC can be used as a new active ingredient for bed bug control by topical or oral treatment and shed light on the molecular mechanisms of suppressed tyrosine metabolism following NTBC treatment. © 2025 Society of Chemical Industry.
Foliar spray double‐stranded RNA targeting HvIAP1 induces high larval and adult mortality in Henosepilachna vigintioctopunctata
Authors: Ji Tianliang , Li Langcheng , Zhu Xin , Wang Guirong 
Published: January 2025

AbstractBACKGROUNDExogenous double‐stranded RNA (dsRNA) has the potential to serve as an effective alternative to conventional chemical pesticides for the control of insect pests, because it can specifically inhibit essential gene expression in these organisms. However, identifying suitable gene targets remains a crucial step in the development of RNA interference (RNAi)‐based pest control strategies.RESULTSIn this study, three apoptosis‐related genes were selected to evaluate their potential for RNAi‐induced lethality in Henosepilachna vigintioctopunctata via foliar spray dsRNAs. Our results revealed that silencing of HvIAP1 (inhibitor of apoptosis protein 1) had a significant lethal effect on larvae, whereas silencing of HvAIF1 and HvASPP1 did not, correlating with distinct expression patterns. Larvae ingested leaves sprayed with bacterially expressed dsHvIAP1 at a concentration of 100 ng/cm2 resulting in the impairment of cuticle tanning, cessation of feeding, and ultimately, 100% mortality within 7 days. In addition, the potential of dsHvIAP1 to mediate for adult control was also investigated and showed that administration of 200 ng/cm2 dsHvIAP1 resulted in 100% adult mortality within 9 days, accompanied by a significant reduction in leaf consumption and suppression of HvIAP1 expression compared with the dsGFP group.CONCLUSIONSOur findings demonstrate that HvIAP1 is a highly lethal molecular target with a notable difference in the concentration required for larval and adult mortality. These findings provide a foundation for the future development of RNAi pesticides for environmentally friendly control of H. vigintioctopunctata. © 2025 Society of Chemical Industry.
Nocturnin promotes NADH and ATP production for juvenile hormone biosynthesis in adult insects
Authors: Qiao Lintao , Zhuang Zitong , Wang Yage , Xie Kairui , Zhang Xinyan , Shen Yifan , Song Jiasheng , Zhou Shutang 
Published: January 2025

AbstractBACKGROUNDJuvenile hormone (JH) is a key endocrine governing insect development, metamorphosis and reproduction. JH analogs have offered great potential for insect pest control. In adulthood, JH titer rapidly increases in the previtellogenic period and reaches a peak in the vitellogenic phase. However, the regulatory mechanisms of JH biosynthesis in corpora allata (CA) of adult insects remain largely unknown.RESULTSWe observed that the mitochondrial abundance, as well as the levels of NADH (nicotinamide adenine dinucleotide, reduced form) and adenosine triphosphate (ATP), increased in the CA of previtellogenic adults, peaking during the vitellogenic stage. The transcripts of Nocturnin (Noct), which converts nicotinamide adenine dinucleotide phosphate (NADPH) to NADH for ATP production, were more abundant in the CA compared to those of other enzymes involved in conventional NADH‐producing metabolic pathways. The developmental expression pattern of Noct was like that of ATP and NADH level. RNA interference‐mediated knockdown of Noct caused a significant decrease of NADH and ATP contents, along with markedly reduced expression levels of 12 genes involved in JH biosynthesis pathway. Loss of Noct function resulted in remarkably reduced expression of vitellogenin, accompanied by arrested ovarian growth and oocyte maturation.CONCLUSIONOur results demonstrated that Noct plays a crucial role in high levels of JH biosynthesis in adult insects via regulating NADH and ATP production. The findings reveal a previously unknown aspect of mitochondrial metabolism in JH biosynthesis and provide valuable information for developing pest control strategies targeting hormone pathways. © 2025 Society of Chemical Industry.
Noise‐Augmented ℓ0 Regularization of Tensor Regression With Tucker Decomposition
Authors: Yan Tian , Li Yinan , Liu Fang 
Published: January 2025

ABSTRACTTensor data are multi‐dimensional arrays. Low‐rank decomposition‐based regression methods with tensor predictors exploit the structural information in tensor predictors while significantly reducing the number of parameters in tensor regression. We propose a method named (Noise Augmentation for regularization on Core Tensor in Tucker decomposition) to regularize the parameters in tensor regression (TR), coupled with Tucker decomposition. We establish theoretically that achieves exact regularization on the core tensor from the Tucker decomposition in linear TR and generalized linear TR. To our knowledge, is the first Tucker decomposition‐based regularization method in TR to achieve regularization in core tensors. is implemented through an iterative procedure and involves two straightforward steps in each iteration—generating noisy data based on the core tensor from the Tucker decomposition of the updated parameter estimate and running a regular GLM on noise‐augmented data on vectorized predictors. We demonstrate the implementation of and its regularization effect in both simulation studies and real data applications. The results suggest that can improve predictions compared with other decomposition‐based TR approaches, with or without regularization and it identifies important predictors though not designed for that purpose.
Transition‐ and Lanthanide‐Metal‐Based Coordination Polymers Offer Efficient Methylene Blue Adsorption
Authors: Moodley Cresten , Mallick Kaushik , Muller Alfred , Williams D. Bradley G. 
Published: January 2025

AbstractThis study presents a novel approach toward wastewater remediation via the synthesis of a series of coordination polymers that combine benzene‐1,4‐dicarboxylic acid, benzene‐1,4‐dihydroxamic acid, and 5‐nitroisophthalic acid linkers with Cu, Cr, Ce, and La metal salts to target efficient methylene blue removal. Through a detailed characterization process using techniques like ¹H NMR, PXRD, FTIR, TGA, SEM‐EDX, ICP‐OES, and BET, the structural and surface properties of these CPs were optimized for stability and enhanced adsorption performance. Notably, the CPs exhibited rapid MB adsorption within 10 min and followed pseudo‐second‐order kinetics, indicating a chemisorption‐driven process. This work advances the field by demonstrating that increased pH significantly improves adsorption capacity and that the Sips model best describes the heterogeneous adsorptive behavior, highlighting a mixed Langmuir–Freundlich mechanism. Furthermore, stability and reusability studies revealed minimal metal leaching in the best‐performing CPs, addressing critical environmental concerns around long‐term CP use. This integrated approach not only fills vital knowledge gaps in CP‐based dye adsorption kinetics but also underscores the potential of these materials as sustainable, scalable, and effective solutions for real‐world water treatment applications.
Composite Fe3O4/Si/Poly(N‐Isopropyl Acrylamide)/Au Catalyst for Heck, Suzuki, and Sonogashira Cross‐Coupling Reactions
Authors: Kafshboran Hadieh Rahbar , Ghasemi Soheila 
Published: January 2025

AbstractIn this research, a magnetic catalyst with immobilized gold nanoparticles (Au NPs) for C─C cross‐coupling reactions has been introduced. The catalyst consists of Au NPs immobilized on functionalized poly(N‐isopropyl acrylamide) (PNIPAM) grafted to Fe3O4 magnetic nanoparticles (MNPs) modified with silica. For the catalyst synthesis, firstly, the Fe3O4 MNP core is prepared, modified with silica, coated with PNIPAM, and subsequently functionalized with amino functional group and EDTA. Finally, it is decorated with Au NPs to create the desired catalyst (Fe3O4/Si/modified PNIPAM‐Au). TEM images of the catalyst confirmed the presence of spherical gold NPs with an approximate size of 13 nm on the catalyst matrix. Also, XPS analysis well proves the presence of zero metallic gold. The catalytic performance of the Au catalyst was evaluated through the C─C coupling transformations, for example, Suzuki–Miyaura, Mizoroki–Heck, and Sonogashira–Hagihara reactions. The results demonstrated significant catalytic activity of the as‐synthesized Au catalyst. Using a magnet, the catalyst could be isolated from the reaction mixture and employed again in eight consecutive coupling reactions. During these reactions, some reduction in catalytic efficiency and gold leaching is observed. Overall, this catalyst shows excellent potential for efficient catalytic reactions, offering the advantages of easy separation, recyclability, and high catalytic activity.
Impact of Chitosan as a Binder in Graphene Gas Sensor for Volatile Organic Compound Detection
Authors: Chachuli Siti Amaniah Mohd , Muhammad ‘Azmi Noor Athirah , Shamsudin N. H. , Coban Omer , Aziz Siti Asma Che 
Published: January 2025

AbstractExposure to high amounts of volatile organic compounds (VOC) in the short term can cause headaches, dizziness, worsening asthma symptoms, vomiting, and eye, nose, and throat irritation. Thus, a gas sensor is needed to detect VOC gases. Chitosan as a nonconducting polymer was used as an alternative binder for thick film gas sensors in this study. Chitosan was dissolved in an acetic acid to produce a polymer solution and mixed with graphene nanoflakes to make a graphene gas sensor. Two chitosan binder recipes were used in this study to investigate their performance in gas sensors for the VOCs acetone and ethanol. A single layer and a double layer of graphene were deposited to study their effects on VOC sensing. Single and double layers of graphene gas sensors had little effect on the sensing response to acetone and ethanol vapor. Results revealed that the gas sensors were prepared by binder B responded better than binder A in sensing response to acetone and ethanol with a response value achieved by T2‐2‐S1(3) and, T2‐2‐S1(1) with a response value of 1.0579 and, 1.0532, respectively. In addition, chitosan in graphene gas sensors had outstanding performances, in terms of linearity and repeatability characteristics.
Green Extraction of Peppermint as an Antibacterial Agent in Thermosensitive Hydrogel for Diabetic Wound Healing
Authors: Rahmi Nindy Samira , Maharani Misyelia Putri , Irianto Khairunnisa , Rizky Intan Adella , Fadillah Aulya Pramuditha , Firdaus Maulidan 
Published: January 2025

AbstractDiabetic wounds are notoriously problematic to heal, often leading to an increased risk of infection with conventional wound dressings. To address this problem, thermosensitive hydrogels (hydrogel TM) loaded with peppermint extracts as antibacterial agents were developed. The objective of this study was to synthesize and optimize the hydrogel TM formulation and to evaluate its efficacy in accelerating diabetic wound healing through integrative in silico, in vitro, and in vivo approaches. The optimal hydrogel TM formulation was determined using response surface methodology (RSM) and peppermint green extraction via ultrasonic‐assisted extraction (UAE). Characterization of hydrogel TM was performed using FTIR, TGA‐DSC, and SEM, while the peppermint extract was examined by GC/MS. The synthesized hydrogel TM, with optimal formulations of 3.320 %w/v methyl cellulose and 3.671 %w/v trisodium citrate, displayed a gelation temperature of 37 °C. The loading of peppermint extract was proven through a smoother porous structure based on SEM analysis. In silico and in vitro tests demonstrated significant antibacterial activity, and in vivo studies showed complete wound closure within 9 days, proving the efficacy of the hydrogel TM@PM in accelerating diabetic wound healing.
Dissecting Code Features: An Evolutionary Analysis of Kernel Versus Nonkernel Code in Operating Systems
Authors: Zhao Yangyang , Li Chenglin , Chen Zhifei , Ding Zuohua 
Published: January 2025

ABSTRACTUnderstanding the evolution of software systems is crucial for advancing software engineering practices. Many studies have been devoted to exploring software evolution. However, they primarily treat software as an entire entity and overlook the inherent differences between subsystems, which may lead to biased conclusions. In this study, we attempt to explore variations between subsystems by investigating the code feature differences between kernel and nonkernel components from an evolutionary perspective. Based on three operating systems as case studies, we examine multiple dimensions, including the code churn characteristics and code inherent characteristics. The main findings are as follows: (1) The proportion of kernel code remains relatively small, and exhibits consistent stability across the majority of versions as systems evolve. (2) Kernel code exhibits higher stability in contrast to nonkernel code, characterized by a lower modification rate and finer modification granularity. The patterns of modification activities are similar in both kernel and nonkernel code, with a preference of changing code and a tendency to avoid the combination of adding and deleting code. (3) The cumulative code size and complexity of kernel files show an upward trajectory as the system evolves. (4) Kernel files exhibit a significantly higher code density and complexity than nonkernel files, featuring a greater number of code line, comments, and statements, along with a larger program length, vocabulary, and volume. Conversely, kernel functions prioritize modularity and maintainability, with a significantly smaller size and lower complexity than nonkernel functions. These insights contribute to a deeper understanding of the dynamics within operating system codebases and highlight the necessity of targeted maintenance strategies for different subsystems.
Considerations for Implementation of Model‐Based Systems Engineering in Different Sectors and System Types Based on Academic Literature
Authors: Teper Thomas , Campo Kelly X. , Eaton Casey E. , Bhatia Garima , Mesmer Bryan 
Published: January 2025

ABSTRACTThe emergence and adoption of Model‐Based Systems Engineering (MBSE) is driven in part by claimed benefits over traditional Document‐Based Systems Engineering. Despite high enthusiasm for MBSE, few studies have evaluated the value of MBSE implementation or the needs in MBSE implementation across various system types and industry sectors, which may require differing drivers of implementation and analyses of added value. This study investigates the perceptions of MBSE across sectors including Commercial, Contractor, and Government, as well as across system types including Astronautical, Aeronautical, and Infrastructure, to determine the perceived drivers and considerations of MBSE implementation across different industries. From 60 academic sources, this study collected and coded over 2900 claims about MBSE using 68 MBSE attributes. Our study's findings determine that the considerations for MBSE implementation likely vary by both sector and by system. Perceptions of MBSE, regardless of application grouping, were largely positive—negative attributes often captured unfavorable perceptions of implementation and tooling immaturity. The findings of this study suggest that practitioners may need to tailor the implementation of MBSE partly to their organizational priorities and needs, and to be cautious of relying only on broadly reported benefits of MBSE.