bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual heterozygosities prompt examining hybridogenesis that could mediate insular occurrence of a narrow endemic spiny frog
Authors: Zheng Yuchi , Wang Bin , Cao Yue , Zeng Xiaomao , Xia Yun 
Published: November 2024

Abstract

Hybridogenesis is a rare reproductive mode where interspecific hybrids produce gametes each carrying one of the parental genomes, with the other one discarded but renewed by backcross. It may in theory mediate species range expansion, since such hybrids can also have pure-species offspring for establishing new populations and are often widespread probably due to hybrid vigor. Being inspired by a magnitude difference between estimates of individual heterozygosity, we collected genome-wide data and examined hybridogenesis between the wide-range Asian spiny frog Quasipaa boulengeri and a narrow endemic, Q. robertingeri, distinguished it from other atypical modes of reproduction, and provided the first evidence supporting that hybridogenesis mediated the occurrence of individuals far from the species range (~ 500 km). Despite contributing to early evidence of the only inferred hybridogenetic complex in ten years, individual heterozygosity has likely been an often overlooked variable. Furthermore, the spiny frog system occurs in a generally less well-studied region from a natural history perspective, shows co-occurrence of female and male F1 types, harbors structurally abnormal non-sex-specific chromosomes, and exhibits significant parental mitochondrial divergence comparable to those of known hybridogenetic systems. It may be helpful to include a consideration of these factors for future detection of hybridogenesis. The findings in spiny frogs make a case that genome-wide data provide crucial evidence for updating our knowledge on the life-history evolution of taxa.
WITHDRAWN: A Study Protocol for “Comparative Evaluation of Effectiveness of Demineralized Freeze-Dried Bone Allografts (DFDBA) with Titanium Platelet Rich Fibrin (T-PRF) and Autologous Dentin Graft (ADG) with T-PRF in Alveolar Socket Preservation: A Randomized Controlled Clinical Trial”
Authors: Thakre Shivani , Bajaj Pavan 
Published: November 2024

Abstract

The full text of this preprint has been withdrawn, as it was submitted in error. Therefore, the authors do not wish this work to be cited as a reference. Questions should be directed to the corresponding author.
WITHDRAWN: Underwater Image Compression and Reconstruction Based on VQ-VAE-2
Authors: Yang Qiuling , Fei Hansheng , Zhang ZhiPeng , Chen Jianan , Zhang Yunuo 
Published: November 2024

Abstract

The full text of this preprint has been withdrawn, as it was submitted in error. Therefore, the authors do not wish this work to be cited as a reference. Questions should be directed to the corresponding author.
Denosumab attenuates knee osteoarthritis progression by inhibiting synovial inflammation via the RANK/TRAF6/FSTL1 signalling pathway
Authors: Tong Wei , Hu Yuxiang , Chen Wei , Lan Shenghui , Ming Chaochang , Xu Dongdong , Li Haitao , Xu Hao , Shi Deyao , Liu Weijian , Dai Zhipeng , Wang Jian , He Zhili , Xu Weihua , Shao Zengwu , Liu Yong , Tian Hongtao 
Published: November 2024

Abstract

Synovitis plays a critical role in osteoarthritis (OA), and inhibiting synovitis can significantly alleviate OA symptoms. Denosumab, a monoclonal antibody targeting RANKL, inhibits the RANK/NF-κB pathway in monocyte–macrophage lineage cells, crucial in inflammation. Here, we report a novel role of denosumab in fibroblast-like synoviocytes (FLSs) where it attenuates synovitis and OA progression. We first demonstrated that RANKL and RANK were highly expressed in synovium of OA mice and patients. Denosumab, administered systemically via injection, was primarily enriched in the synovium and effectively reduced synovitis, thereby delaying OA progression in post-traumatic, inflammatory, and aged OA mouse models. Mechanistically, single-cell RNA sequencing (scRNA-seq) showed that FLSs were the most significantly altered cell cluster in joint cells, and cell–cell interaction analysis indicated enhanced FLS–chondrocyte crosstalk in OA, which was markedly reduced following denosumab treatment, suggesting FLSs as the primary responsive cells to denosumab in OA joints. Furthermore, immunoprecipitation assay revealed that RANKL promoted RANK–TRAF6 binding, activating the NF-κB signalling pathway, leading to the upregulation of various pro-inflammatory and chondrocyte catabolic cytokines in FLSs. Further sequencing analysis and western blotting identified follistatin-like protein 1 (FSTL1) as the most upregulated cytokine in FLSs, inducing inflammatory reactions and chondrocyte catabolism, effects that were significantly inhibited by denosumab. Consistent with the mouse model, we observed reduced synovitis and OA progression in a beagle dog model of OA. Finally, a single-arm clinical trial demonstrated that denosumab alleviated synovitis and pain, improved joint function in knee OA patients, associated with reduced expression of pro-inflammatory and chondrocyte catabolic cytokines in FLSs induced by FSTL1. These findings provide a translational basis for using denosumab to treat knee OA patients.
Time to Save: How Time Perspective Nudges Cut Food Waste
Authors: Lin Meizhen , Li Yaoqi , Zhang Ye , Jiang Qiumin , Wang Jingqiang 
Published: November 2024

Abstract

Predominant endeavors to mitigate food waste involve utilizing regulations and marketing campaigns. However, this kind of explicit advocacy frequently encounters resistance stemming from consumer autonomy, necessitating highly effective implicit interventions. This study explored the potential of time-perspective nudging as a supplementary technique for curbing food waste. Through 2,109 individual observations from a natural field experiment in a restaurant, this study assessed the effectiveness of time-perspective priming in reducing food waste. Additionally, we evaluated the broader applicability of this approach across countries by analyzing secondary data on time perspective and food waste from 56 countries. These findings demonstrate a close cross-country relationship between cyclical time perspective and food waste reduction, as well as the dominant effectiveness of cyclical time perspective nudging in reducing food waste. This implicit nudge throws insights into future food waste reduction initiatives, promoting pro-sustainability dining behaviors ethically and effectively.
Generative AI Enables Medical Image Segmentation in Ultra Low-Data Regimes
Authors: Xie Pengtao , Zhang Li , Jindal Basu , Alaa Ahmed , Weinreb Robert , Wilson David , Segal Eran , Zou James 
Published: November 2024

Abstract

Semantic segmentation of medical images is pivotal in applications like disease diagnosis and treatment planning. While deep learning has excelled in automating this task, a major hurdle is the need for numerous annotated segmentation masks, which are resource-intensive to produce due to the required expertise and time. This scenario often leads to ultra low-data regimes, where annotated images are extremely limited, posing significant challenges for the generalization of conventional deep learning methods on test images. To address this, we introduce a generative deep learning framework, which uniquely generates high-quality paired segmentation masks and medical images, serving as auxiliary data for training robust models in data-scarce environments. Unlike traditional generative models that treat data generation and segmentation model training as separate processes, our method employs multi-level optimization for end-to-end data generation. This approach allows segmentation performance to directly influence the data generation process, ensuring that the generated data is specifically tailored to enhance the performance of the segmentation model. Our method demonstrated strong generalization performance across 9 diverse medical image segmentation tasks and on 16 datasets, in ultra-low data regimes, spanning various diseases, organs, and imaging modalities. When applied to various segmentation models, it achieved performance improvements of 10-20% (absolute), in both same-domain and out-of-domain scenarios. Notably, it requires 8 to 20 times less training data than existing methods to achieve comparable results. This advancement significantly improves the feasibility and cost-effectiveness of applying deep learning in medical imaging, particularly in scenarios with limited data availability.
Grid-scale Corrosion-free Zn/Br Flow Batteries Enabled by Multi-electron Transfer Reaction
Authors: Li Xianfeng , Xu Yue , Li Tianyu , Peng Zhangquan , Xie Congxin 
Published: November 2024

Abstract

Aqueous flow batteries are one of the most competitive technologies for storing electricity from intermittent renewable energy sources, which are intrinsically safe and scalable. Zinc/bromine flow batteries (Zn/Br FB) are popular due to the high theoretical energy densities (>500 Wh L-1) and inexpensive (600 cycles vs. <30 cycles) at 40 mA cm-2. Using this new bromine reaction, we built a large-scale battery system (5kW/6.6 kWh, EE 78%).
Fast High-resolution Lifetime Image Reconstruction for Positron Lifetime Tomography
Authors: Qi Jinyi , Huang Bangyan , Wang Zipai , Zeng Xinjie , Goldan Amir 
Published: November 2024

Abstract

The life history of a positron before annihilation has long been overlooked by current positron emission tomography (PET) techniques. Due to the ortho-positronium formed prior to the annihilation, the lifetime of a positron is sensitive to the tissue microenvironment and can potentially provide valuable information for monitoring disease progression and treatment response. In this paper, we develop a positron lifetime image reconstruction method called SIMPLE (Statistical IMage reconstruction of Positron Lifetime via time-wEighting) and perform a real scan to demonstrate, for the first time, high-resolution positron lifetime imaging of an extended heterogeneous tissue on a time-of-flight (TOF) PET scanner. The SIMPLE method involves minimum modification to the standard list-mode maximum-likelihood expectation-maximization (MLEM) algorithm with a computation cost equivalent to the reconstruction of two PET activity images and a spatial resolution comparable to that of PET activity images. The proposed experimental design utilizes a 22Na point source to realize lifetime imaging in an extended area. The reconstructed positron lifetime image shows a clear separation between the muscle and fat tissues. The proposed method paves the way for high-resolution positronium lifetime imaging in humans.
Induction of p53-mediated apoptosis by azacitidine in patient-derived xenograft follicular helper T-cell lymphoma model
Authors: Lemonnier François , TARI Gamze , ARI-YUKA Selcen , Fischer Anja , Chour Mohamed , SAKO Nouhoum , Robe Cyrielle , NAUDET Julie , GONON Alexis , MBOUMBA Diana Laure , DELFAU-LARUE Marie-Hélène , ORTONNE Nicolas , Alcazer Vincent , Siebert Reiner , Gaulard Philippe 
Published: November 2024

Abstract

Follicular helper T-cell lymphoma (TFHL) is the most common non-cutaneous T-cell lymphoma in the Western world and is associated with a poor prognosis. Neoplastic cells rely heavily on the tumor microenvironment, demonstrated by the absence of TFHL-derived cell lines, which hinders therapeutic progress.
To overcome this limitation, we developed and characterized patient-derived xenograft TFHL (TFHL-PDXs). Fifteen TFHLs were implanted into immunodeficient mice, generating nine PDXs. The tumor microenvironment was detected in the first passage but progressively disappeared in subsequent passages. TET2 mutations persisted in all cases and TFHL-specific mutations were observed in most. The models were treated with azacitidine and patient sensitivity was fully recapitulated. To elucidate the mechanism of action of azacitidine, we analyzed the differences in DNA methylation and gene expression in four TFHL-PDX models. Global DNA hypomethylation occurred in azacitidine-treated cells in drug-sensitive models but not in the resistant one. DNA hypomethylation was associated with global upregulation of gene expression, including that of various cancer-related pathways, suggestive of p53-pathway-mediated cytotoxicity.
Overall, the PDXs recapitulated TFHL features and exhibited sensitivity to azacitidine. They also made it possible to decipher the mechanism responsible for the effect of azacitidine, revealing the activation of p53-mediated apoptosis associated with DNA hypomethylation.
Host range expansion of asexual parasite can be explained by loss of adaptions in Muller’s Ratchet
Authors: Jex Aaron , Tichkule Swapnil , Oosterhout Cock van , Cacciò Simone , Weisz Filip , Balan Balu , Nohynkova Eva , Naung Myo , Ansell Brendan R. E. , Emery-Corbin Samantha , Baker Louise , Lalle Marco , Svard Staffan , Gasser Robin B. 
Published: November 2024

Abstract

Sexual recombination is a hallmark of eukaryotic evolution. Without recombination, asexual eukaryotes should succumb to deleterious mutations and more rapidly evolving pathogens. Giardia duodenalis, a parasitic protist, sits within one of the earliest-branching eukaryotic lineages and has no known sexual stage. Whether Giardia are ‘ancient asexuals’ is long explored but unresolved. Here, we find clear evidence of sex in Giardia but also discover an asexual sublineage that has a broader host range than its sexual ancestor. This asexual lineage is not ancient, and is accumulating deleterious mutations. Unlike its sexual counterparts, its genetic variation lacks the signatures of selection and Red Queen coevolution. We propose a new hypothesis that explains how a mutational meltdown during Muller’s Ratchet might enable asexual pathogens to expand their host ranges transiently. Fittingly, Giardia is not the last exception to but further proof of the essentiality of eukaryotic sex.
Improvement of Generalization Performance of Diagnostic System for Drill Bit Abnormality in Rotary Percussion Drilling with Grad-CAM
Authors: Nakazawa Yuna , Okada Natsuo , Sasaki Jo , Senjoba Lesego , Ohtomo Yoko , Kawamura Youhei 
Published: November 2024

Abstract

Rotary percussion drills, specifically top hammer types, are essential in resource extraction and exploration. These drills frequently suffer damage at the drill button, necessitating effective decision-making to address issues. Traditionally, on-site operators relied on intuition, but recent advancements promote automated systems to enhance safety and failure detection in challenging mining environments. This study employs Convolutional Neural Networks (CNN) to develop an automated system for detecting drill bit abnormalities. In a prior investigation, a CNN model was established to discern normal functioning and four distinct abnormalities. To enhance generalization performance, researchers endeavored to create a filter using Gradient-weighted Class Activation Mapping (Grad-CAM), an inverse analysis technique. However, challenges arose as the frequency bands contributing significantly to judgments varied among the five identified states. In response, this study adopts a refined approach, constructing a model that categorizes drill performance into two states: normal and abnormal. Leveraging Grad-CAM, the research identifies the frequency band with a high contribution rate to judgment and applies a filter tailored to this specific band. Notably, by training the CNN model to recognize differences in rock types, the resulting model exhibits adaptability to changes in drill bit types, achieving an accuracy rate of 83.3%.
Interaction studies unveil potential binding sites on bovine serum albumin for gut metabolite trimethylamine n-oxide (TMAO)
Authors: Verma Awadhesh Kumar , Gulati Payal , Lakshmi GBVS , Mohan Anand , Sharma Neeta Raj , Solanki Pratima R , Kumar Anil 
Published: November 2024

Abstract

Trimethylamine-N-oxide (TMAO) is the most studied gut microbiota-derived metabolite and its binding to serum albumin has huge significance to understand the underlying mechanisms in human health and diseases. The interaction between BSA and TMAO has not been well studied; the binding mechanism, preferred binding locations, and subsequent conformation of BSA are still unclear. In the present work, spectroscopic, photoluminescence, Fourier transform infrared contact angle, circular dichroism, density functional theory, molecular docking, and molecular dynamics simulation approaches were used to probe TMAO-BSA interaction and identifying putative binding sites for TMAO on BSA. Non-covalent interaction of TMAO with bovine serum albumin forming stable docking complex with binding score of -3.6 kcal/mol was revealed through docking and simulation study. The docking complex of TMAO-BSA was found stable through hydrogen bond and electrostatic, Vander waals interaction, and water bridges via amino acid residues. Hydrophilicity/Hydrophobicity of the TMAO-BSA was studied using contact angle (Ɵ) measurement. Present study may be helpful for making strategies for Chronic Kidney Disease and other disease treatments wherein interaction of TMAO with serum albumin matters. Also, pharmacodynamics and pharmacokinetics of TMAO, as well as its mechanism of binding to BSA, may be better understood with the help of this study's findings.
Genomic characteristics of Vibrio vulnificus isolated from clinical and environmental sources
Authors: Lee Jinkyeong , Shin Jeong-Ih , Cho Woo Young , Park Kun Take , Chung Yeun-Jun , Jung Seung-Hyun 
Published: November 2024

Abstract

Vibrio vulnificus is a gram-negative pathogenic bacterium that is transmitted through undercooked seafood or contaminated seawater, causing septicemia and wound infections. In this study, 15 clinical isolates and 11 environmental isolates were analyzed, revealing a total of 20 sequence types (STs), 8 of which were newly identified. Antibiotic resistance gene analysis revealed that the CRP gene was frequently present in both clinical and environmental isolates. Interestingly, the clinical and environmental isolates showed notable not-susceptible to third-generation cephalosporins, such as ceftazidime and cefotaxime, which may complicate treatment strategies for V. vulnificus infections. The Multiple Antibiotic Resistance (MAR) index ranged from 0.1 to 0.5, with clinical isolates having a higher mean MAR index compared to environmental isolates, indicating a broader spectrum of resistance in clinical strains. No quantitative (124.3 versus 126.5) and qualitative (adherence, antiphagocytosis, and chemotaxis/motility) differences in virulence factors were observed between environmental and clinical strains. The molecular characteristics identified in this study may provide a basis for understanding the virulence of Vibrio vulnificus strains in South Korea and highlight the need for continuous surveillance of antibiotic resistance in emerging V. vulnificus strains.
Autonomous Design of Ordered Gas Diffusion Layers for High-performing Fuel Cells via Bayesian Machine Learning
Authors: Zhao Tianshou , Sun Jing , Lin Pengzhu , Zeng Lin , Guo Zixiao , Jiang Yuting , Xiao Cailin , Jian Qinping , Ren Jiayou , Pan Lyuming , Xu Xiaosa , Li Zheng , Wei Lei 
Published: November 2024

Abstract

Rational design of gas diffusion layers (GDL) is an example of a long-standing pursuit to increase the power density and reduce the cost of proton exchange membrane fuel cells (PEMFC). However, current state-of-the-art GDLs are designed by trial and error, which is a time-consuming endeavor. Here, we propose an autonomous Bayesian machine learning approach to optimize the design of GDL structures. With the artificial neural network accelerating the calculation of anisotropic transport properties of reconstructed 7621 fibrous GDLs, Bayesian optimization algorithm identifies optimal structures in only 40 steps, maximizing the PEMFC’s limiting current density. Results suggest that the optimal GDL structure consists of highly orientated fibers with moderate diameters (~10 µm), which is successfully fabricated with a controlled electrospinning technique. Impressively, the PEMFC demonstrates a record high power density of 2.17 W cm-2 and a limiting current density of ~7200 mA cm-2, far exceeding that with commercial GDL which only achieves 1.33 W cm-2 and ~2700 mA cm-2. The approach reported here represents how the advanced algorithms can aid the innovative material design to address the critical water flooding issues in PEMFCs, leading to significant performance improvements, which paves the way for further application across various scientific fields.
Mathematical Modeling of Tangential Filtration Processes for Winery Wastewater Treatment
Authors: BIRON DIONISIO DA SILVA , Santos Venina dos , Ongaratto Ricardo Schmitz , Cantão Renato Fernandes , Venezuela Antonio Luís 
Published: November 2024

Abstract

In membrane separation processes, permeate flux decay throughout microfiltration is one of the predicted phenomena and arises due to fouling. This decay is one of the main contributors defining permeate flux characteristics, and its inclusion in mathematical modeling has been a challenge for researchers in this area. Therefore, this study performed the mathematical modeling of tangential filtration processes applied to wastewater treatment from a winery. The mathematical modeling started from the modified resistance in series model and used the GITT (Generalized Integral Transform Technique) hybrid method. Experimental data were obtained from microfiltration of a winery’s effluent, evaluating transmembrane pressures between 50 and 600 kPa, fluid flow rates on the input between 0.06 and 0.15 m s− 1 and effluent concentrations between 1/1 and 1/40 (dilutions ratio effluent:distilated water), using 0.4 µm alumina ceramic membrane. The results showed a significant convergence between the modeled and experimental data, with 80% of the data showing relative differences less than 10%. Thus, the model with the proposed modifications can be used to determine the behavior of permeate flux throughout the laminar flow process. Moreover, from the proposed methodology it is possible to determine the limiting flux in order to identify when the process is losing energy unnecessarily.