bluuebunny/crossref_metadata_2025_split huggingface dataset:
A generalised computer vision model for improved glaucoma screening using fundus images
Authors: Chaurasia Abadh K. , Liu Guei-Sheung , Greatbatch Connor J. , Gharahkhani Puya , Craig Jamie E. , Mackey David A. , MacGregor Stuart , Hewitt Alex W. 
Published: November 2024

Abstract

Importance
Worldwide, glaucoma is a leading cause of irreversible blindness. Timely detection is paramount yet challenging, particularly in resource-limited settings. A novel, computer vision-based model for glaucoma screening using fundus images could enhance early and accurate disease detection.

Objective
To develop and validate a generalised deep-learning-based algorithm for screening glaucoma using fundus image.

Design, setting and participants
The glaucomatous fundus data were collected from 20 publicly accessible databases worldwide, resulting in 18,468 images from multiple clinical settings, of which 10,900 were classified as healthy and 7568 as glaucoma. All the data were evaluated and downsized to fit the model’s input requirements. The potential model was selected from 20 pre-trained models and trained on the whole dataset except Drishti-GS. The best-performing model was further trained to classify healthy and glaucomatous fundus images using Fastai and PyTorch libraries.

Main outcomes and measures
The model’s performance was compared against the actual class using the area under the receiver operating characteristic (AUROC), sensitivity, specificity, accuracy, precision and the F1-score.

Results
The high discriminative ability of the best-performing model was evaluated on a dataset comprising 1364 glaucomatous discs and 2047 healthy discs. The model reflected robust performance metrics, with an AUROC of 0.9920 (95% CI: 0.9920–0.9921) for both the glaucoma and healthy classes. The sensitivity, specificity, accuracy, precision, recall and F1-scores were consistently higher than 0.9530 for both classes. The model performed well on an external validation set of the Drishti-GS dataset, with an AUROC of 0.8751 and an accuracy of 0.8713.

Conclusions and relevance
This study demonstrated the high efficacy of our classification model in distinguishing between glaucomatous and healthy discs. However, the model’s accuracy slightly dropped when evaluated on unseen data, indicating potential inconsistencies among the datasets—the model needs to be refined and validated on larger, more diverse datasets to ensure reliability and generalisability. Despite this, our model can be utilised for screening glaucoma at the population level.
Opportunities for retrieval and tool augmented large language models in scientific facilities
Authors: Prince Michael H. , Chan Henry , Vriza Aikaterini , Zhou Tao , Sastry Varuni K. , Luo Yanqi , Dearing Matthew T. , Harder Ross J. , Vasudevan Rama K. , Cherukara Mathew J. 
Published: November 2024

AbstractUpgrades to advanced scientific user facilities such as next-generation x-ray light sources, nanoscience centers, and neutron facilities are revolutionizing our understanding of materials across the spectrum of the physical sciences, from life sciences to microelectronics. However, these facility and instrument upgrades come with a significant increase in complexity. Driven by more exacting scientific needs, instruments and experiments become more intricate each year. This increased operational complexity makes it ever more challenging for domain scientists to design experiments that effectively leverage the capabilities of and operate on these advanced instruments. Large language models (LLMs) can perform complex information retrieval, assist in knowledge-intensive tasks across applications, and provide guidance on tool usage. Using x-ray light sources, leadership computing, and nanoscience centers as representative examples, we describe preliminary experiments with a Context-Aware Language Model for Science (CALMS) to assist scientists with instrument operations and complex experimentation. With the ability to retrieve relevant information from facility documentation, CALMS can answer simple questions on scientific capabilities and other operational procedures. With the ability to interface with software tools and experimental hardware, CALMS can conversationally operate scientific instruments. By making information more accessible and acting on user needs, LLMs could expand and diversify scientific facilities’ users and accelerate scientific output.
Microstructure and radiation shielding capabilities of Al-Cu and Al-Mn alloys
Authors: El-Samrah Moamen G. , Nabil Islam M. , Shamekh Mohamed E. , Elmasry M. , Osman M. 
Published: November 2024

AbstractIn this study, the microstructure and elemental analysis of aluminum-copper alloy type-2024, Al-2024, and aluminum-manganese alloy type-3003, Al-3003, have been investigated by using a scanning electron microscope (SEM) equipped with Energy dispersive spectroscopy (EDS) detector. Experimental and theoretical radiation shielding studies were performed to assess the radiation shielding capabilities of the studied alloys. Considering the radiation shielding theoretical assessment, some reliable software tools were used, such as Phy-X/PSD, MCNP5, NXCom, and MRCsC. The microstructural observations and results have shown the presence of second phases rich with the main alloying elements in both alloys. Considering Al-2024 alloy, coarse second-phase particles, having a size range of 8–15 μm, were found aligning in lines parallel to the rolling direction, whereas smaller ones, having a size range of 2–8 μm, were found decorated the grain boundaries. Also, dark holes represent the pull-out large particles separated during preparation indicated poor adhesion with the main matrix that could be a result of losing particle coherency with the matrix where the misorientation in-between the atomic planes increase. However, better adhesion of the second-phase particles with the matrix, which were found possessing smaller particle size, have been observed in the Al-3003 alloy indicating good coherency and better manufacturing process for the non-heat-treatable alloy. The second-phase particles in case of Al-2024 alloy were found containing significant content of high-Z elements like Cu with greater volume fraction equals 7.5%. On the other side, Al-3003 alloy has possessed second-phase particles which lack of high-Z elements with only volume fraction equals 3.5%. All the former besides the higher density and content of high-Z elements like copper in Al-2024 alloy in compare to Al-3003 alloy and pure aluminum, led to relatively better radiation shielding capabilities against energetic photons, the highest in the low energy band and decreases with the increase of the photon energy, and slight superiority in the case of fast neutrons with only 3%inc. over pure aluminum. For instance, the radiation protection efficiency (RPE) values dropped from about; 23.2, 21.6, and 20.8% at 0.100 MeV to only 5.7, 5.9, and 5.6% at Eγ = 2 MeV, for; Al-2024, Al-3003, and Al-Pure, respectively."Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary.""confirmed"
Therapeutic potential of hyaluronic acid hydrogel combined with bone marrow stem cells-conditioned medium on arthritic rats’ TMJs
Authors: Assi Mai M. , Grawish Mohammed E. , Elsabaa Heba Mahmoud , Helal Mohamad E. , Ezzat Samah K. 
Published: November 2024

AbstractConditioned media (CM) is derived from mesenchymal stem cells (MSC) culture and contains biologically active components. CM is easy to handle and reduces inflammation while repairing injured joints. Combination therapy of the CM with cross-linked hyaluronic acid (HA) could ameliorate the beneficial effect of HA in treating degenerative changes of articulating surfaces associated with arthritic rats’ temporomandibular joints (TMJs). This study aimed to evaluate the therapeutic potential of HA hydrogel combined with bone marrow stem cells-conditioned medium (BMSCs-CM) on the articulating surfaces of TMJs associated with complete Freund’s adjuvant (CFA)-induced arthritis. Fifty female Sprague-Dawley rats were divided randomly into five equal groups. Rats of group I served as the negative controls and received intra-articular (IA) injections of 50 µl saline solution, whereas rats of group II were subjected to twice IA injections of 50 µg CFA in 50 µl; on day 1 of the experiment to induce persistent inflammation and on day 14 to induce arthritis. Rats of group III and IV were handled as group II and instead, they received an IA injection of 50 µl HA hydrogel and 50 µl of BMSCs-CM, respectively. Rats of group V were given combined IA injections of 50 µl HA hydrogel and BMSCs-CM. All rats were euthanized after the 4th week of inducing arthritis. The joints were processed for sectioning and histological staining using hematoxylin and eosin, Masson’s trichrome and toluidine blue special staining, and immunohistochemical staining for nuclear factor-kappa B (NF-κB). SPSS software was used to analyze the data and one-way analysis of variance followed by post-hoc Tukey statistical tests were used to test the statistical significance at 0.05 for alpha and 0.2 for beta. In the pooled BMSC-CM, 197.14 pg/ml of platelet-derived growth factor and 112.22 pg/ml of interleukin-10 were detected. Compared to TMJs of groups III and IV, TMJs of group V showed significant improvements (P = 0.001) in all parameters tested as the disc thickness was decreased (331.79 ± 0.73), the fibrocartilaginous layer was broadened (0.96 ± 0.04), and the amount of the trabecular bone was distinctive (19.35 ± 1.07). The mean values for the collagen amount were increased (12.29 ± 1.38) whereas the mean values for the NF-κB expression were decreased (0.62 ± 0.15). Combination therapy of HA hydrogel and BMSCs-CM is better than using HA hydrogel or BMSCs-CM, separately to repair degenerative changes in rats’ TMJs associated with CFA-induced arthritis.
Regulation of neutrophil associated RNASET2 expression in rheumatoid arthritis
Authors: Passari Mauro , Scutera Sara , Schioppa Tiziana , Tiberio Laura , Piantoni Silvia , Tamassia Nicola , Bugatti Mattia , Vermi William , Angeli Fabrizio , Caproli Alessia , Salvi Valentina , Sozio Francesca , Gismondi Angela , Stabile Helena , Franceschini Franco , Bosisio Daniela , Acquati Francesco , Vermeren Sonja , Sozzani Silvano , Andreoli Laura , Del Prete Annalisa , Musso Tiziana 
Published: November 2024

AbstractNeutrophils (PMNs) are key players of innate immune responses through the release of cytoplasmic granule content and the formation of neutrophil extracellular traps (NETs). RNASET2 is an acidic ribonuclease, recently proposed as an alarmin signal associated with inflammatory responses. Here we show that, along the neutrophil maturation cascade, RNASET2 is expressed in segmented and mature PMNs. In human PMNs, RNASET2 colocalized with primary and tertiary granules and was found to be associated with NETs following PMA or Nigericin stimulation. Similarly, activation of PMNs by soluble immune complexes, a hallmark of several autoimmune diseases, also induced RNASET2-associated NETs. Genome-wide association studies recently identified RNASET2 among a cluster of genes associated with increased susceptibility to develop autoimmune diseases, including rheumatoid arthritis (RA). RNASET2 was found expressed by PMNs and macrophages infiltrating inflamed joints in a murine model of RA (K/BxN Serum-Transfer-Induced Arthritis, STIA), by immunostaining. Similar results were found in synovial biopsies of RA patients with active disease. In addition, we demonstrate that RNASET2 circulating levels correlated with the onset and the severity of disease in two mouse models of inflammatory arthritis, STIA and CIA (Collagen-Induced Arthritis) and in serum of RA patients. These results show that PMNs are an important source of RNASET2 and that its circulating levels are associated with RA development suggesting a role for RNASET2 in the pathogenesis of immune-mediated diseases.
Prevalence and aggravation of cervical spine instabilities in rheumatoid arthritis during over 10 years: a prospective multicenter cohort study
Authors: Kanda Yutaro , Yurube Takashi , Hirata Hiroaki , Sumi Masatoshi 
Published: November 2024

AbstractWe designed a prospective multicenter cohort study to clarify a long-term, > 10-year prevalence and aggravation of cervical spine instabilities in rheumatoid arthritis (RA). In 2001–2002, 634 outpatients were enrolled, and 233 (36.8%) were followed for > 10 years. Cervical spine instability was defined as atlantoaxial subluxation (AAS, > 3-mm atlantodental interval), vertical subluxation (VS, < 13-mm Ranawat value), and subaxial subluxation (SAS, ≥ 2-mm irreducible vertebral translation). The aggravation was determined as ≥ 2 mm decrease of the Ranawat value in VS, ≥ 2-mm increase of slippage in SAS, and these new developments. The prevalence of VS and SAS increased during both the initial and last > 5 years (all, p ≤ 0.049). While VS aggravation was associated with pre-existing AAS (p = 0.007) and VS (p = 0.002), SAS aggravation correlated with pre-existing VS (p = 0.002). Multivariable analysis found hand mutilating changes (odds ratio [OR] = 4.048, p = 0.008), RA duration ≥ 5 years (OR = 3.711, p = 0.013), C-reactive protein (CRP) level ≥ 3.8 mg/dL (OR = 2.187, p = 0.044), and previous joint surgery (OR = 2.147, p = 0.021) as predictors for VS aggravation. Pre-existing VS (OR = 2.252, p = 0.024) and CRP ≥ 1.0 mg/dL (OR = 2.139, p = 0.013) were disclosed as predictors for SAS aggravation. Low disease activity and clinical remission before the development of VS and advanced peripheral joint destruction are essential to prevent progressive cervical spine instability in RA.
CCDC28A deficiency causes head-tail coupling defects and immotility in murine spermatozoa
Authors: Stojanovic Nena , Hernández Rosario Ortiz , Ramírez Nayeli Torres , Martínez Olga Margarita Echeverría , Hernández Abrahan Hernández , Shibuya Hiroki 
Published: November 2024

AbstractMale infertility presents a substantial challenge in reproductive medicine, often attributed to impaired sperm motility. The present study investigates the role of CCDC28A, a protein expressed specifically in male germ cells, whose paralog CCDC28B has been implicated in ciliogenesis. We identify unique expression patterns for CCDC28A and CCDC28B within the mouse testes, where CCDC28A is expressed in germ cells, whereas CCDC28B is expressed in supporting somatic cells. Through knockout mouse models and histological analyses, we reveal that CCDC28A deficiency results in diminished sperm motility and structural aberrations in sperm tails, notably affecting the head-tail coupling apparatus (HTCA), thereby causing male infertility. Fine structural analyses by transmission electron microscopy reveal disruptions at the capitulum-basal plate junction of the HTCA in the CCDC28A mutants. This results in the bending of the head within the neck region, often accompanied by thickening of the tail midpiece. Our discovery demonstrates that CCDC28A plays an essential role in male fertility and sperm tail morphogenesis through the formation of HTCA.
Bridging organ transcriptomics for advancing multiple organ toxicity assessment with a generative AI approach
Authors: Li Ting , Chen Xi , Tong Weida 
Published: November 2024

AbstractTranslational research in toxicology has significantly benefited from transcriptomic profiling, particularly in drug safety. However, its application has predominantly focused on limited organs, notably the liver, due to resource constraints. This paper presents TransTox, an innovative AI model using a generative adversarial network (GAN) method to facilitate the bidirectional translation of transcriptomic profiles between the liver and kidney under drug treatment. TransTox demonstrates robust performance, validated across independent datasets and laboratories. First, the concordance between real experimental data and synthetic data generated by TransTox was demonstrated in characterizing toxicity mechanisms compared to real experimental settings. Second, TransTox proved valuable in gene expression predictive models, where synthetic data could be used to develop gene expression predictive models or serve as “digital twins” for diagnostic applications. The TransTox approach holds the potential for multi-organ toxicity assessment with AI and advancing the field of precision toxicology.
An engineered aldolase enables the biocatalytic synthesis of 2′-functionalized nucleoside analogues
Authors: Willmott Matthew , Finnigan William , Birmingham William R. , Derrington Sasha R. , Heath Rachel S. , Schnepel Christian , Hayes Martin A. , Smith Peter D. , Falcioni Francesco , Turner Nicholas J. 
Published: November 2024

Abstract
Nucleosides functionalized at the 2′-position play a crucial role in therapeutics, serving as both small-molecule drugs and modifications in therapeutic oligonucleotides. However, the synthesis of these molecules often presents substantial synthetic challenges. Here we present an approach to the synthesis of 2′-functionalized nucleosides based on enzymes from the purine nucleoside salvage pathway. Initially, active-site variants of deoxyribose-5-phosphate aldolase were generated for the highly stereoselective synthesis of d-ribose-5-phosphate analogues with a broad range of functional groups at the 2-position. Thereafter, these 2-modified pentose phosphates were converted into 2′-modified purine analogues by construction of one-pot multienzyme cascade reactions, leading to the synthesis of guanosine (2′-OH) and adenosine (2′-OH, 2′-Me, 2′-F) analogues. This cascade allows for the control of the 2′-functional group alongside 2-stereochemistry. Our findings demonstrate the capability of these biocatalytic cascades to efficiently generate 2′-functionalized nucleosides, starting from simple starting materials.
One-pot facile synthesis of rod-like Bi2S3 particles in deep eutectic solvent and their ppb-level selective H2S gas detection
Authors: Furukawa Reiko , Hasegawa Takuya , Okawa Ayahisa , Yin Shu 
Published: November 2024

Rod-like Bi2S3 particles were synthesized by one-pot reactions with choline chloride-based DESs, and showed sub-ppm level selective H2S gas detection. Acetamide-based DES yielded uniform particles with excellent gas sensitivity.
zk‐STARKs based scheme for sealed auctions in chains
Authors: Wei Li , Peili Liang , Fei Li 
Published: November 2024

AbstractOn‐chain sealed auctions represent a novel approach to electronic bidding auctions, wherein the introduction of zero‐knowledge proof technology has significantly enhanced the security of auctions. However, most mainstream on‐chain sealed auction schemes currently employ Bulletproofs to prove auction correctness, which leaves room for optimization in terms of verification time and inherent security. Addressing these issues, an on‐chain sealed auction scheme based on zero‐knowledge succinct non‐interactive argument of knowledge (zk‐STARK) is proposed. This scheme leverages the decentralization and immutability of blockchain and smart contracts to eliminate third‐party involvement while ensuring the security of the auction process. The Inter Planetary File System is utilized to provide a qualification review mechanism for the auctioneer, enabling the screening of unqualified bidders before the auction. Additionally, the scheme employs RSA encryption to conceal bidders' bids, Pedersen commitments to ensure the consistency of bidding information, and zk‐STARKs to verify the correctness of the winning bid. Security analysis and experimental results demonstrate that the proposed scheme meets the required security standards, with time consumption at various stages of the auction being within acceptable limits, and effectively reduces the time required for proof verification.
Optimal performance design of bat algorithm: An adaptive multi‐stage structure
Authors: Yu Helong , Song Jiuman , Chen Chengcheng , Heidari Ali Asghar , Ma Yuntao , Chen Huiling , Zhang Yudong 
Published: November 2024

AbstractThe bat algorithm (BA) is a metaheuristic algorithm for global optimisation that simulates the echolocation behaviour of bats with varying pulse rates of emission and loudness, which can be used to find the globally optimal solutions for various optimisation problems. Knowing the recent criticises of the originality of equations, the principle of BA is concise and easy to implement, and its mathematical structure can be seen as a hybrid particle swarm with simulated annealing. In this research, the authors focus on the performance optimisation of BA as a solver rather than discussing its originality issues. In terms of operation effect, BA has an acceptable convergence speed. However, due to the low proportion of time used to explore the search space, it is easy to converge prematurely and fall into the local optima. The authors propose an adaptive multi‐stage bat algorithm (AMSBA). By tuning the algorithm's focus at three different stages of the search process, AMSBA can achieve a better balance between exploration and exploitation and improve its exploration ability by enhancing its performance in escaping local optima as well as maintaining a certain convergence speed. Therefore, AMSBA can achieve solutions with better quality. A convergence analysis was conducted to demonstrate the global convergence of AMSBA. The authors also perform simulation experiments on 30 benchmark functions from IEEE CEC 2017 as the objective functions and compare AMSBA with some original and improved swarm‐based algorithms. The results verify the effectiveness and superiority of AMSBA. AMSBA is also compared with eight representative optimisation algorithms on 10 benchmark functions derived from IEEE CEC 2020, while this experiment is carried out on five different dimensions of the objective functions respectively. A balance and diversity analysis was performed on AMSBA to demonstrate its improvement over the original BA in terms of balance. AMSBA was also applied to the multi‐threshold image segmentation of Citrus Macular disease, which is a bacterial infection that causes lesions on citrus trees. The segmentation results were analysed by comparing each comparative algorithm's peak signal‐to‐noise ratio, structural similarity index and feature similarity index. The results show that the proposed BA‐based algorithm has apparent advantages, and it can effectively segment the disease spots from citrus leaves when the segmentation threshold is at a low level. Based on a comprehensive study, the authors think the proposed optimiser has mitigated the main drawbacks of the BA, and it can be utilised as an effective optimisation tool.
Observer‐based PID control for fuzzy dynamic systems with memory triggering protocol
Authors: Liao Xiao , Guan Qingshu , Cui Wei , Wang Ying , Zhong Xianjing , Cao Hui 
Published: November 2024

AbstractThis paper addresses the issue of observer‐based proportional–integral–derivative control for Takagi–Sugeno fuzzy dynamic systems using a memory triggering protocol. To tackle the challenges of managing nonlinear systems, the Takagi–Sugeno fuzzy approach is employed to approximate these systems with a series of local linear models. A novel memory event‐triggering mechanism is introduced, utilizing a computer's storage unit to store historical data and adjust the triggering threshold based on this data, thereby reducing unnecessary network resource usage. Given that the system state can be affected by external disturbances and become unpredictable, an observer‐based proportional–integral–derivative controller is designed to manage these uncertainties. Finally, a car‐damper‐spring model is presented to validate the proposed methodology.