bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL33-induced neutrophil extracellular traps (NETs) mediate a positive feedback loop for synovial inflammation and NET amplification in rheumatoid arthritis
Authors: Tang Jifeng , Xia Jinfang , Gao Huali , Jiang Renquan , Xiao Lianbo , Sheng Huiming , Lin Jinpiao 
Published: December 2024

AbstractThis study investigated the mechanisms driving the induction and sustained presence of neutrophil extracellular traps (NETs) in the synovial microenvironment of rheumatoid arthritis (RA). Synovial tissue and fluid samples were collected from patients with RA and osteoarthritis (OA), and NET levels and cytokine concentrations were measured using a cytometric bead array and enzyme-linked immunosorbent assay (ELISA). The ability of interleukin-33 (IL-33) to induce NET formation was evaluated using quantitative assays, immunofluorescence staining, live-cell imaging, and electron microscopy. Coincubation experiments of NETs with fibroblast-like synovial cells (FLSs) were conducted, and a modified Transwell migration assay was designed to assess neutrophil migration. The role of IL-33 and NETs in RA progression was further investigated using a collagen antibody-induced arthritis (CAIA) mouse model. The results revealed an increase in NETs and IL-33 levels in the synovial fluid of RA patients, with a significant positive correlation between them. NET formation assays confirmed that IL-33 activates neutrophils to produce NETs and that neutrophils from RA patients exhibit increased responsiveness to IL-33 stimulation. Both in vitro and in vivo evidence has demonstrated that NETs stimulate FLSs to secrete IL-33 and the chemokine CXCL8 via Toll-like receptor 9, promoting further neutrophil recruitment and increasing NET production within the RA synovium. This study reveals a novel positive feedback loop involving NETs and FLSs that is mediated by IL-33 that increases NET accumulation in RA. Targeting IL-33 or NET formation and amplification may offer new therapeutic strategies for managing RA.
Distribution and impact of p16INK4A+ senescent cells in elderly tissues: a focus on senescent immune cell and epithelial dysfunction
Authors: Park Soon Sang , Lee Young-Kyoung , Kim Young Hwa , Park So Hyun , Kang Hee Young , Kim Jin Cheol , Kim Dong Jun , Lim Su Bin , Yoon Gyesoon , Kim Jang-Hee , Choi Yong Won , Park Tae Jun 
Published: December 2024

AbstractCellular senescence, recognized as a key hallmark of aging, leads to the accumulation of senescent cells in various tissues over time. While the detrimental effects of these cells on age-related pathological conditions are well-documented, there is still limited information about how senescent cells are distributed in normal tissues of both young and aged organs. Our research indicates that fully senescent p16INK4A+ cells are rarely identified in the parenchyma of organic tissues and in the stromal cells crucial for structural maintenance, such as fibroblasts and smooth muscle cells. Instead, p16INK4A+ cells are more commonly found in immune cells, whether they reside in the organ or are infiltrating. Notably, p16INK4A+ senescent T cells have been observed to induce apoptosis and inflammation in colonic epithelial cells through Granzyme A-PARs signaling, compromising the integrity of the epithelial lining. This study showed that the senescence of immune cells could affect the phenotypical change of the parenchymal cells in the elderly and suggests that targeting immunosenescence might be a strategy to control functional decline in this population.
EPRS1-mediated fibroblast activation and mitochondrial dysfunction promote kidney fibrosis
Authors: Son Seung Seob , Jeong Hee Seul , Lee Seong-Woo , Lee Eun Soo , Lee Jeong Geon , Lee Ji-Hye , Yi Jawoon , Park Mi Ju , Choi Min Sun , Lee Donghyeong , Choi Sin Young , Ha Jiheon , Kang Jeong Suk , Cho Nam-Jun , Park Samel , Gil Hyo-Wook , Chung Choon Hee , Park Joon Seok , Kim Myung Hee , Park Jihwan , Lee Eun Young 
Published: December 2024

AbstractKidney fibrosis causes irreversible structural damage in chronic kidney disease and is characterized by aberrant extracellular matrix (ECM) accumulation. Although glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is a crucial enzyme involved in proline-rich protein synthesis, its role in kidney fibrosis remains unclear. The present study revealed that EPRS1 expression levels were increased in the fibrotic kidneys of patients and mice, especially in fibroblasts and proximal tubular epithelial cells, on the basis of single-cell analysis and immunostaining of fibrotic kidneys. Moreover, C57BL/6 EPRS1tm1b heterozygous knockout (Eprs1+/−) and pharmacological EPRS1 inhibition with the first-in-class EPRS1 inhibitor DWN12088 protected against kidney fibrosis and dysfunction by preventing fibroblast activation and proximal tubular injury. Interestingly, in vitro assays demonstrated that EPRS1-mediated nontranslational pathways in addition to translational pathways under transforming growth factor β-treated conditions by phosphorylating SMAD family member 3 in fibroblasts and signal transducers and activators of transcription 3 in injured proximal tubules. EPRS1 knockdown and catalytic inhibition suppressed these pathways, preventing fibroblast activation, proliferation, and subsequent collagen production. Additionally, we revealed that EPRS1 caused mitochondrial damage in proximal tubules but that this damage was attenuated by EPRS1 inhibition. Our findings suggest that the EPRS1-mediated ECM accumulation induces kidney fibrosis via fibroblast activation and mitochondrial dysfunction. Therefore, targeting EPRS1 could be a potential therapeutic target for alleviating fibrotic injury in chronic kidney disease.
Preliminary insights: exploring irrigation practices during endodontic treatment among general dental practitioners in Malaysia
Authors: Chiew Kai Qi , Lim Xin Ni , Bhatia Shekhar , Chhabra Naveen 
Published: December 2024

AbstractObjective(s) This questionnaire study aimed to analyse the irrigation knowledge and current trends in irrigation practice during endodontic treatment among general dental practitioners (GDPs) in Malaysia.Materials and methods A three-part, self-administered questionnaire with multiple-choice questions was distributed to dentists in Malaysia. The survey comprised three sections: demographic data; irrigant selection and protocol; and other irrigation practices. Knowledge questions were marked based on a recommended answer by endodontists and the scores were analysed among various groups having different years of experience using the Kruskal-Wallis test.Results Out of 172 responses, the mean knowledge score of all respondents was 12.92 (standard deviation = 2.774) out of a possible total score of 18. For the scores of groups of practitioners with different years of experience, the Kruskal-Wallis test showed p = 0.069. Sodium hypochlorite appeared as the most used irrigant. Most respondents routinely practised smear layer removal using ethylenediaminetetraacetic acid (EDTA). Antibacterial capability and tissue dissolution were the main factors in irrigant selection. In total, 65.6% of the GDPs claimed to change their irrigation protocol to suit different pulpal and periapical diagnoses. There was considerable variation regarding the type of irrigants used, irrigation protocol, concentration, volume, time spent for irrigation, irrigation needle usage and additional adjunct methods used.Conclusion(s) Respondents of the survey were following the recommended irrigation practices in terms of irrigant selection but there is scope for improvement in other aspects of irrigation practice. Further investigation with a larger sample size is needed for more robust conclusions.
Genetically-stable engineered optogenetic gene switches modulate spatial cell morphogenesis in two- and three-dimensional tissue cultures
Authors: Beyer Hannes M. , Kumar Sant , Nieke Marius , Diehl Carroll M. C. , Tang Kun , Shumka Sara , Koh Cha San , Fleck Christian , Davies Jamie A. , Khammash Mustafa , Zurbriggen Matias D. 
Published: December 2024

AbstractRecent advances in tissue engineering have been remarkable, yet the precise control of cellular behavior in 2D and 3D cultures remains challenging. One approach to address this limitation is to genomically engineer optogenetic control of cellular processes into tissues using gene switches that can operate with only a few genomic copies. Here, we implement blue and red light-responsive gene switches to engineer genomically stable two- and three-dimensional mammalian tissue models. Notably, we achieve precise control of cell death and morphogen-directed patterning in 2D and 3D tissues by optogenetically regulating cell necroptosis and synthetic WNT3A signaling at high spatiotemporal resolution. This is accomplished using custom-built patterned LED systems, including digital mirrors and photomasks, as well as laser techniques. These advancements demonstrate the capability of precise spatiotemporal modulation in tissue engineering and open up new avenues for developing programmable 3D tissue and organ models, with significant implications for biomedical research and therapeutic applications.
Regulation and function of a polarly localized lignin barrier in the exodermis
Authors: Manzano Concepcion , Morimoto Kevin W. , Shaar-Moshe Lidor , Mason G. Alex , Cantó-Pastor Alex , Gouran Mona , De Bellis Damien , Ursache Robertas , Kajala Kaisa , Sinha Neelima , Bailey-Serres Julia , Geldner Niko , del Pozo J. Carlos , Brady Siobhan M. 
Published: December 2024

Abstract
Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root’s response to abiotic and biotic stimuli.
A quantum leaky integrate-and-fire spiking neuron and network
Authors: Brand Dean , Petruccione Francesco 
Published: December 2024

AbstractQuantum machine learning is in a period of rapid development and discovery, however it still lacks the resources and diversity of computational models of its classical complement. With the growing difficulties of classical models requiring extreme hardware and power solutions, and quantum models being limited by noisy intermediate-scale quantum (NISQ) hardware, there is an emerging opportunity to solve both problems together. Here we introduce a new software model for quantum neuromorphic computing — a quantum leaky integrate-and-fire (QLIF) neuron, implemented as a compact high-fidelity quantum circuit, requiring only 2 rotation gates and no CNOT gates. We use these neurons as building blocks in the construction of a quantum spiking neural network (QSNN), and a quantum spiking convolutional neural network (QSCNN), as the first of their kind. We apply these models to the MNIST, Fashion-MNIST, and KMNIST datasets for a full comparison with other classical and quantum models. We find that the proposed models perform competitively, with comparative accuracy, with efficient scaling and fast computation in classical simulation as well as on quantum devices.
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma
Authors: Sarkar Suryadipto , Möller Anna , Hartebrodt Anne , Erdmann Michael , Ostalecki Christian , Baur Andreas , Blumenthal David B. 
Published: December 2024

AbstractCutaneous T-cell lymphomas (CTCLs) are non-Hodgkin lymphomas caused by malignant T cells which migrate to the skin and lead to rash-like lesions which can be difficult to distinguish from inflammatory skin conditions like atopic dermatitis (AD) and psoriasis (PSO). To characterize CTCL in comparison to these differential diagnoses, we carried out multi-antigen imaging on 69 skin tissue samples (21 CTCL, 23 AD, 25 PSO). The resulting protein abundance maps were then analyzed via scoring functions to quantify the heterogeneity of the individual cells’ neighborhoods within spatial graphs inferred from the cells’ positions in the tissue samples. Our analyses reveal characteristic patterns of skin tissue organization in CTCL as compared to AD and PSO, including a combination of increased local entropy and egophily in T-cell neighborhoods. These results could not only pave the way for high-precision diagnosis of CTCL, but may also facilitate further insights into cellular disease mechanisms.
Enhanced lion swarm optimization and elliptic curve cryptography scheme for secure cluster head selection and malware detection in IoT-WSN
Authors: D Udaya Suriya Rajkumar , R Sathiyaraj , A Bharathi , D Mohan , Pellakuri Vidyullatha 
Published: December 2024

AbstractWireless Sensor Networks present a significant issue for data routing because of the potential use of obtaining data from far locations with greater energy efficiency. Networks have become essential to modern concepts of the Internet of Things. The primary foundation for supporting diverse service-centric applications has continued to be the sensor node activity of both sensing phenomena in their local environs and relaying their results to centralized Base Stations. Malware detection and inadequate Cluster Heads node selection are issues with the current technology, resulting in a drastic decrease in the total Internet of Things-based performance of sensor networks. The paper proposes an Enhanced Lion Swarm Optimization (ELSO) and Elliptic Curve Cryptography (ECC) scheme for secure cluster head selection and malware detection in IoT-based Wireless Sensor Networks (WSNs). The paper includes network models, choice of Cluster Head (CH) and attack detection procedures. The proposed method chooses the Cluster Head with the best fitness function values, increasing data transmission speeds and energy efficiencies. Minimum Hop Detection has been implemented to provide the best routing paths against attack nodes. Security level for quick data transmissions via the Internet of Things using Wireless Sensor Networks strengthen sinkhole attacks and black hole nodes, which are successfully removed using this method. The proposed method integrates the use of Lion Swarm Optimization and Elliptic Curve Cryptography (ECC) enhances network security by ensuring secure data transmission and preventing unauthorized access, which is particularly important in IoT-WSN environments. The proposed method achieves less End delay, increased throughput of 93%, lower energy utilization of 4%, increased network lifetime of up to 96%, Packet Delivery Ratio of up to 98% and 97% of malicious node detection efficiently compared to existing methods.
Progress towards sustainable agriculture hampered by siloed scientific discourses
Authors: Fischer Klara , Vico Giulia , Röcklinsberg Helena , Liljenström Hans , Bommarco Riccardo 
Published: December 2024

Abstract
There is no consensus in society on how to achieve sustainability. Scientists’ limited experience in reflecting on their guiding assumptions, combined with a tendency to inflate their own research findings, hinders interdisciplinary dialogue and limits the usefulness of science. Through bibliometrics and discourse analysis, we analysed highly cited articles on agroecology and sustainable intensification. In broad terms, agroecology prioritizes diversity while sidelining productivity and adheres to relational epistemology, while sustainable intensification emphasizes boosting crop production while reducing environmental impact within a reductionist epistemology. Both discourses claim to have the solution to agricultural sustainability but are largely inexplicit about their guiding assumptions and their own limitations, and rarely engage with research in the other discourse. Interdisciplinary dialogue based on transparent and self-critical reflection on the assumptions and limitations of research could increase the relevance of science in societal dialogues about alternative pathways towards sustainable agriculture.
Efficient data-driven joint-level calibration of cable-driven surgical robots
Authors: Peng Haonan , Lewis Andrew , Su Yun-Hsuan , Lin Shan , Chiang Dun-Tin , Jiang Wenfan , Lai Helen , Hannaford Blake 
Published: December 2024

AbstractAccurate joint position estimation is crucial for the control of cable-driven laparoscopic surgical robots like the RAVEN-II. However, any slack and stretch in the cable can lead to errors in kinematic estimation, complicating precise control. This work proposes an efficient data-driven calibration method, requiring no additional sensors post-training. The calibration takes 8–21 min and maintains high accuracy during a 6-hour heavily loaded operating. The Deep Neural Network (DNN) model reduces errors by 76%, achieving accuracy of 0.104∘, 0.120∘, and 0.118 mm for joints 1, 2, and 3, respectively. Compared to end-to-end models, the DNN achieves better accuracy and faster convergence by correcting original inaccurate joint positions. Additionally, a linear regression model offers 160 times faster inference speed than the DNN, suitable for RAVEN’s 1000 Hz control loop, with slight compromises in accuracy. This approach should significantly enhance the accuracy of similar cable-driven robots.
Flagellar rotation facilitates the transfer of a bacterial conjugative plasmid
Authors: Bhattacharya Saurabh , Bejerano-Sagie Michal , Ravins Miriam , Zeroni Liat , Kaur Prabhjot , Gopu Venkadesaperumal , Rosenshine Ilan , Ben-Yehuda Sigal 
Published: December 2024

Abstract
Conjugation-mediated DNA delivery is the primary mode for antibiotic resistance spread in bacteria; yet, molecular mechanisms regulating the conjugation process remain largely unexplored. While conjugative plasmids typically require bacterial attachment to solid surfaces for facilitation of donor-to-recipient proximity, the pLS20 conjugative plasmid, prevalent among Gram-positive Bacillus spp., uniquely requires fluid environments to enhance its transfer. Here, we show that pLS20, carried by Bacillus subtilis, induces multicellular clustering, which can accommodate various species, hence offering a stable platform for DNA delivery in a liquid milieu. We further discovered that induction of pLS20 promoters, governing crucial conjugative genes, is dependent on the presence of donor cell flagella, the major bacterial motility organelle. Moreover, the pLS20 regulatory circuit is controlled by a mechanosensing signal transduction pathway responsive to flagella rotation, thus activating conjugation gene expression exclusively during the host motile phase. This flagella-conjugation coupling strategy may allow the dissemination of the plasmid to remote destinations, allowing infiltration into new niches.
A cooperative control strategy for balancing SoC and power sharing in multiple energy storage unit within DC microgrids
Authors: Li Jianlin , You Honghao 
Published: December 2024

AbstractThis paper proposes a distributed cooperative control scheme for multiple energy storage unit (ESU) in DC microgrids to achieve the control objectives of SoC balancing, power sharing, and bus voltage recovery. In the primary control part, the proposed scheme constructs a control function between the SoC values of each ESU and the droop coefficients to dynamically adjust the droop coefficients. Through a communication network, information is exchanged with neighbouring ESUs to achieve SoC convergence. In the secondary control part, by exchanging power information with neighbouring ESUs, precise power distribution is achieved. Additionally, the proposed scheme maintains bus voltage stability. Finally, a DC microgrid simulation model and experimental platform were developed, demonstrating the feasibility and plug‐and‐play capability of the proposed control strategy through both simulation and experimental case tests.
Torque ripple reduction using adaptive gain model predictive control for induction motor drives
Authors: Banihashemy Seyed Morteza , Bromi Yousef Alinejad 
Published: December 2024

AbstractThis article introduces a new method for induction motor speed control based on predictive control. The presented method is a modified type of model predictive control (MPC) to improve the performance and reduce the torque ripple of the induction motor. Its basis is to consider magnitude changes in the voltage vector to be applied to the motor in each sector. To validate the effectiveness of the proposed scheme, an experimental setup has been established on a prototype induction motor (IM) drive built on a Texas Instrument TMS320F28335 floating point Digital Signal Processor (DSP) board. The results of the proposed MPC demonstrates even more than 30% better performance on the IM compared to the conventional MPC in most cases.
Morphologies of galaxies within voids
Authors: Argudo-Fernández M. , Gómez Hernández C. , Verley S. , Zurita A. , Duarte Puertas S. , Blázquez Calero G. , Domínguez-Gómez J. , Espada D. , Florido E. , Pérez I. , Sánchez-Menguiano L. 
Published: December 2024

Context. Among the largest structures in which matter is distributed in the Universe, we find cosmic voids, which are large, under-dense regions almost devoid of galaxies. The study of these structures and the galaxies that inhabit them, the void galaxies, provides key information for understanding galaxy evolution.
Aims. In this work we investigate the effects of the environment on the evolution of void galaxies. In particular, we study their morphology and explore its dependence on the location within the void where the galaxies reside, as well as on the properties of the void, such as its size and the galaxy number density.
Methods. The sample of void galaxies that we use in this study is based on the catalogue of cosmic voids and void galaxies in the Sloan Digital Sky Survey Data Release 7 (SDSS-DR7). As we are interested in studying the morphology of void galaxies, we select galaxies in the redshift range of 0.005 ≤ z ≤ 0.080, and use the public galaxy morphologies of the SDSS sample together with deep learning algorithms to divide the sample into early- and late-type void galaxies. We analyse the fractions of galaxies of each morphological type as a function of the void-centric distance, the size of the voids, and the density of galaxies in each void.
Results. There is a higher abundance of late-type galaxies with respect to early-type galaxies within voids, which remains nearly constant from the inner to the outer part of the voids. We do not find any dependence of the fraction of early- and late-type galaxies on void size or on the number-density of galaxies in the voids.
Conclusions. Galaxies in voids follow the morphology–density relation, in the sense that the majority of the galaxies in voids (the most under-dense large-scale environments) are late-type galaxies. However, we find no difference between voids with lower or higher volume number-density of galaxies: the fractions of early- and late-type galaxies do not depend on the density of the voids. The physical processes responsible for the evolution from late towards earlier types (such as external environmental quenching) are not sufficiently effective in voids or are so slow (internal secular quenching) that their contributions do not appear in the morphology–density relation.