bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumor-associated macrophages/C-X-C motif chemokine ligand 1 promotes breast cancer autophagy-mediated chemoresistance via IGF1R/STAT3/HMGB1 signaling
Authors: Yang Bowen , Li Guanzhi , Wang Shengqi , Zheng Yifeng , Zhang Juping , Pan Bo , Wang Neng , Wang Zhiyu 
Published: October 2024

AbstractAutophagy-mediated chemoresistance is the core mechanism for therapeutic failure and poor prognosis in breast cancer. Breast cancer chemotherapy resistance is believed to be influenced by tumor-associated macrophages (TAMs), by which C-X-C motif chemokine ligand 1 (CXCL1) is the most abundant cytokine secreted. Yet, its role in mediating autophagy-related chemoresistance is still unknown. This study aimed to explore the molecular mechanisms by which TAMs/CXCL1 induced autophagy-mediated chemoresistance in breast cancer. It was found that TAMs/CXCL1 promoted chemoresistance of breast cancer cells through autophagy activation in vitro, and CXCL1 silence could enhance the chemosensitivity of paclitaxel-resistant breast cancer cells via autophagy inhibition. A high-throughput quantitative PCR chip and subsequent target validation showed that CXCL1 induced autophagy-mediated chemoresistance by inhibiting VHL-mediated IGF1R ubiquitination. The elevated IGF1R then promoted STAT3/HMGB1 signaling to facilitate autophagy. Additionally, TAMs/CXCL1 silence improved paclitaxel chemosensitivity by suppressing autophagy in breast cancer mice xenografts, and clinical studies further linked CXCL1 to IGF1R/HMGB1 signaling, as well as shorter free survival of recurrence. Taken together, these results not only uncover the crucial role of TAMs/CXCL1 signaling in mediating breast cancer chemoresistance through enhancing autophagy, but also shed novel light on the molecular mechanism of IGF1R/STAT3/HMGB1 pathway in regulating autophagy and its impact on cancer prognosis.
Pressure-controlled luminescence in fast-response barium fluoride crystals
Authors: Cadatal-Raduban Marilou , Mui Luong Viet , Yamashita Masahiro , Shibazaki Yuki , Shimizu Toshihiko , Sarukura Nobuhiko , Yamanoi Kohei 
Published: October 2024

Abstract
Cross-luminescence (CL) in a barium fluoride (BaF2) scintillator arising from the recombination of a valence band electron and a core band hole results in a fast picosecond decay time. However, the CL emission wavelength in the vacuum ultraviolet region is difficult to detect, and intrinsically intense and slow nanosecond self-trapped exciton (STE) luminescence occurs. Herein, we report a redshift in the CL emission wavelength with high-pressure application. The wavelength of the CL emission shifted from 221 nm to 240 nm when 5.0 GPa was applied via a sapphire anvil cell. Increasing the pressure decreases the core-valence bandgap due to the downward expansion of the valence band, resulting in a decrease in the valence band minimum. The onset of a phase transition from a cubic crystal structure to an orthorhombic crystal structure at 3.7 GPa inhibited the recombination of conduction band electrons and self-trapped holes, leading to the disappearance of the STE emission. Manipulating the band structure of BaF2 by high-pressure application enables control of its luminescence emission, providing a pathway toward solving the problems inherent in this leading fast-response scintillator.
Pathogenic cryptic variants detectable through exome data reanalysis significantly increase the diagnostic yield in Joubert syndrome
Authors: D’Abrusco Fulvio , Serpieri Valentina , Taccagni Cecilia Maria , Garau Jessica , Cattaneo Luca , Boggioni Monica , Gana Simone , Battini Roberta , Bertini Enrico , Zanni Ginevra , Boltshauser Eugen , Borgatti Renato , Romaniello Romina , Signorini Sabrina , Leuzzi Vincenzo , Caputi Caterina , Manti Filippo , D’Arrigo Stefano , De Laurentiis Arianna , Graziano Claudio , Lemke Johannes R. , Morelli Federica , Petković Ramadža Danijela , Sirchia Fabio , Giorgio Elisa , Valente Enza Maria 
Published: October 2024

AbstractJoubert syndrome (JS) is a genetically heterogeneous neurodevelopmental ciliopathy. Despite exome sequencing (ES), several patients remain undiagnosed. This study aims to increase the diagnostic yield by uncovering cryptic variants through targeted ES reanalysis. We first focused on 26 patients in whom ES only disclosed heterozygous pathogenic coding variants in a JS gene. We reanalyzed raw ES data searching for copy number variants (CNVs) and intronic variants affecting splicing. We validated CNVs through real-time PCR or chromosomal microarray, and splicing variants through RT-PCR or minigenes. Cryptic variants were then searched in additional 44 ES-negative JS individuals. We identified cryptic “second hits” in 14 of 26 children (54%) and biallelic cryptic variants in 3 of 44 (7%), reaching a definite diagnosis in 17 of 70 (overall diagnostic gain 24%). We show that CNVs and intronic splicing variants are a common mutational mechanism in JS; more importantly, we demonstrate that a significant proportion of such variants can be disclosed simply through a focused reanalysis of available ES data, with a significantly increase of the diagnostic yield especially among patients previously found to carry heterozygous coding variants in the KIAA0586, CC2D2A and CPLANE1 genes.
Advanced glycation end-product crosslinking activates a type VI secretion system phospholipase effector protein
Authors: Jensen Steven J. , Cuthbert Bonnie J. , Garza-Sánchez Fernando , Helou Colette C. , de Miranda Rodger , Goulding Celia W. , Hayes Christopher S. 
Published: October 2024

AbstractAdvanced glycation end-products (AGE) are a pervasive form of protein damage implicated in the pathogenesis of neurodegenerative disease, atherosclerosis and diabetes mellitus. Glycation is typically mediated by reactive dicarbonyl compounds that accumulate in all cells as toxic byproducts of glucose metabolism. Here, we show that AGE crosslinking is harnessed to activate an antibacterial phospholipase effector protein deployed by the type VI secretion system of Enterobacter cloacae. Endogenous methylglyoxal reacts with a specific arginine-lysine pair to tether the N- and C-terminal α-helices of the phospholipase domain. Substitutions at these positions abrogate both crosslinking and toxic phospholipase activity, but in vitro enzyme function can be restored with an engineered disulfide that covalently links the N- and C-termini. Thus, AGE crosslinking serves as a bona fide post-translation modification to stabilize phospholipase structure. Given the ubiquity of methylglyoxal in prokaryotic and eukaryotic cells, these findings suggest that glycation may be exploited more generally to stabilize other proteins. This alternative strategy to fortify tertiary structure could be particularly advantageous in the cytoplasm, where redox potentials preclude disulfide bond formation.
Energy transfer-mediated multiphoton synergistic excitation for selective C(sp3)–H functionalization with coordination polymer
Authors: Wang Zhonghe , Tang Yang , Liu Songtao , Zhao Liang , Li Huaqing , He Cheng , Duan Chunying 
Published: October 2024

AbstractActivation and selective oxidation of inert C(sp3)–H bonds remain one of the most challenging tasks in current synthetic chemistry due to the inherent inertness of C(sp3)–H bonds. In this study, inspired by natural monooxygenases, we developed a coordination polymer with naphthalenediimide (NDI)-based ligands and binuclear iron nodes. The mixed-valence FeIIIFeII species and chlorine radicals (Cl•) are generated via ligand-to-metal charge transfer (LMCT) between FeIII and chlorine ions. These Cl• radicals abstract a hydrogen atom from the inert C(sp3)–H bond of alkanes via hydrogen atom transfer (HAT). In addition, NDI converts oxygen to 1O2 via energy transfer (EnT), which then coordinates to FeII, forming an FeIV = O intermediate for the selective oxidation of C(sp3)–H bonds. This synthetic platform, which combines photoinduced EnT, LMCT and HAT, provides a EnT-mediated parallel multiphoton excitation strategy with kinetic synergy effect for selective C(sp3)–H oxidation under mild conditions and a blueprint for designing coordination polymer-based photocatalysts for C(sp3)–H bond oxidation.
The microstructure-corrosion relationships in laser-welded dissimilar steel-to-aluminium joints
Authors: Ahuir-Torres J. I. , Jabar S. , Franciosa P. , Ceglarek D. , Kotadia H. R. 
Published: October 2024

AbstractThis study investigated the corrosion behaviour of dissimilar steel-to-aluminium laser-welded conduction, and keyhole mode (partial- and full-penetration) lap joints through electrochemical techniques and advanced microstructural characterisation. The corrosion resistance of the weld was found to be higher than the base materials, primarily due to the presence of cathodic FexAly (η-Fe2Al5, θ-Fe4Al13, β-FeAl) intermetallic compounds (IMCs) with high corrosion potential. The different micro and macro-galvanic corrosion mechanisms were found at various interfaces around the weld, resulting in localised pitting corrosion. The keyhole mode welding showed improved corrosion resistance, primarily attributed to the type, size, and distribution of IMCs.
A community effort to optimize sequence-based deep learning models of gene regulation
Authors: Rafi Abdul Muntakim , Nogina Daria , Penzar Dmitry , Lee Dohoon , Lee Danyeong , Kim Nayeon , Kim Sangyeup , Kim Dohyeon , Shin Yeojin , Kwak Il-Youp , Meshcheryakov Georgy , Lando Andrey , Zinkevich Arsenii , Kim Byeong-Chan , Lee Juhyun , Kang Taein , Vaishnav Eeshit Dhaval , Yadollahpour Payman ,   Random Promoter DREAM Challenge Consortium, Bornelöv Susanne , Svensson Fredrik , Trapotsi Maria-Anna , Tran Duc , Nguyen Tin , Tu Xinming , Zhang Wuwei , Qiu Wei , Ghotra Rohan , Yu Yiyang , Labelson Ethan , Prakash Aayush , Narayanan Ashwin , Koo Peter , Chen Xiaoting , Jones David T. , Tinti Michele , Guan Yuanfang , Ding Maolin , Chen Ken , Yang Yuedong , Ding Ke , Dixit Gunjan , Wen Jiayu , Zhou Zhihan , Dutta Pratik , Sathian Rekha , Surana Pallavi , Ji Yanrong , Liu Han , Davuluri Ramana V. , Hiratsuka Yu , Takatsu Mao , Chen Tsai-Min , Huang Chih-Han , Wang Hsuan-Kai , Shih Edward S. C. , Chen Sz-Hau , Wu Chih-Hsun , Chen Jhih-Yu , Huang Kuei-Lin , Alsaggaf Ibrahim , Greaves Patrick , Barton Carl , Wan Cen , Abad Nicholas , Körner Cindy , Feuerbach Lars , Brors Benedikt , Li Yichao , Röner Sebastian , Dash Pyaree Mohan , Schubach Max , Soylemez Onuralp , Møller Andreas , Kavaliauskaite Gabija , Madsen Jesper , Lu Zhixiu , Queen Owen , Babjac Ashley , Emrich Scott , Kardamiliotis Konstantinos , Kyriakidis Konstantinos , Malousi Andigoni , Palaniappan Ashok , Gupta Krishnakant , Kumar S Prasanna , Bradford Jake , Perrin Dimitri , Salomone Robert , Schmitz Carl , JiaXing Chen , JingZhe Wang , AiWei Yang , Kim Sun , Albrecht Jake , Regev Aviv , Gong Wuming , Kulakovskiy Ivan V. , Meyer Pablo , de Boer Carl G. 
Published: October 2024

AbstractA systematic evaluation of how model architectures and training strategies impact genomics model performance is needed. To address this gap, we held a DREAM Challenge where competitors trained models on a dataset of millions of random promoter DNA sequences and corresponding expression levels, experimentally determined in yeast. For a robust evaluation of the models, we designed a comprehensive suite of benchmarks encompassing various sequence types. All top-performing models used neural networks but diverged in architectures and training strategies. To dissect how architectural and training choices impact performance, we developed the Prix Fixe framework to divide models into modular building blocks. We tested all possible combinations for the top three models, further improving their performance. The DREAM Challenge models not only achieved state-of-the-art results on our comprehensive yeast dataset but also consistently surpassed existing benchmarks on Drosophila and human genomic datasets, demonstrating the progress that can be driven by gold-standard genomics datasets.
Rutin loaded bilosomes for enhancing the oral activity and nephroprotective effects of rutin in potassium dichromate induced acute nephrotoxicity in rats
Authors: Mohsen Amira Mohamed , Wagdi Marwa Anwar , Salama Abeer 
Published: October 2024

AbstractRutin, a flavone glycoside, has shown to have a significant beneficial kidney protection effect in drug-induced nephropathy. However, its poor solubility and low oral bioavailability have limited its pharmacological applications. This study aimed at formulating rutin-loaded bilosomes to enhance the renal protective effect of rutin for oral application. Rutin-loaded bilosomes were developed using thin-film hydration technique. The prepared formulations were characterized by entrapment efficiency percentage (EE%), vesicular size (VS) and zeta potential (ZP) measurement. The developed formula exhibited moderate EE%, ranging from 20.02 ± 2.85 to 48.57 ± 3.57%, suitable VS results that ranged from 502.1 ± 36 to 665.1 ± 45 nm and high ZP values (≤ -41.4 ± 7.27 mV). Transmission electron microscopy revealed the spherical shape of the developed bilosomes. The in-vitro release study revealed prolonged release of rutin from bilosomes, relative to free drug. F2, prepared using the molar ratio span 60: cholesterol: sodium cholate 1:1:0.5, was selected for further investigations as it showed the highest EE%, smallest VS, optimum ZP, and persistent release profile. In-vivo studies were performed on drug-induced nephropathy in rats. Acute renal failure was induced using a single dose of potassium dichromate (PDC; 15 mg/kg; i.p). The selected formulation, F2, alleviated kidney dysfunction, oxidative stress and inflammation via decreasing MDA, TNF-α and TGF-β and increasing GSH. In addition, F2 promoted Akt/PI3K activation against PDC-induced acute renal failure. Histopathology results came in accordance with in-vivo results. Thus, bilosomes could be considered a potential delivery system for enhancing the oral delivery and kidney protection activity of rutin.
A lightweight defect detection algorithm for escalator steps
Authors: Yu Hui , Chen Jiayan , Yu Ping , Feng Da 
Published: October 2024

AbstractIn this paper, we propose an efficient target detection algorithm, ASF-Sim-YOLO, to address issues encountered in escalator step defect detection, such as an excessive number of parameters in the detection network model, poor adaptability, and difficulties in real-time processing of video streams. Firstly, to address the characteristics of escalator step defects, we designed the ASF-Sim-P2 structure to improve the detection accuracy of small targets, such as step defects. Additionally, we incorporated the SimAM (Similarity-based Attention Mechanism) by combining SimAM with SPPF (Spatial Pyramid Pooling-Fast) to enhance the model’s ability to capture key information by assigning importance weights to each pixel. Furthermore, to address the challenge posed by the small size of step defects, we replaced the traditional CIoU (Complete-Intersection-over-Union) loss function with NWD (Normalized Wasserstein Distance), which alleviated the problem of defect missing. Finally, to meet the deployment requirements of mobile devices, we performed channel pruning on the model. The experimental results showed that the improved ASF-Sim-YOLO model achieved an average accuracy (mAP50) of 96.8% on the test data set, which was a 22.1% improvement in accuracy compared to the baseline model. Meanwhile, the computational complexity (in GFLOPS) of the model was reduced to a quarter of that of the baseline model, while the frame rate (FPS) was improved to 575.1. Compared with YOLOv3-tiny, YOLOv5s, YOLOv8s, Faster-RCNN, TOOD, RTMDET and other deep learning-based target recognition algorithms, ASF-Sim-YOLO has better detection accuracy and real-time processing capability. These results demonstrate that ASF-Sim-YOLO effectively balances lightweight design and performance improvement, making it highly suitable for real-time detection of step defects, which can meet the demands of escalator inspection operations.
The potential of federated learning for self-configuring medical object detection in heterogeneous data distributions
Authors: Rashidi Gabriel , Bounias Dimitrios , Bujotzek Markus , Mora Andrés Martínez , Neher Peter , Maier-Hein Klaus H. 
Published: October 2024

AbstractMedical Object Detection (MOD) is a clinically relevant image processing method that locates structures of interest in radiological image data at object-level using bounding boxes. High-performing MOD models necessitate large datasets accurately reflecting the feature distribution of the corresponding problem domain. However, strict privacy regulations protecting patient data often hinder data consolidation, negatively affecting the performance and generalization of MOD models. Federated Learning (FL) offers a solution by enabling model training while the data remain at its original source institution. While existing FL solutions for medical image classification and segmentation demonstrate promising performance, FL for MOD remains largely unexplored. Motivated by this lack of technical solutions, we present an open-source, self-configuring and task-agnostic federated MOD framework. It integrates the FL framework Flower with nnDetection, a state-of-the-art MOD framework and provides several FL aggregation strategies. Furthermore, we evaluate model performance by creating simulated Independent Identically Distributed (IID) and non-IID scenarios, utilizing the publicly available datasets. Additionally, a detailed analysis of the distributions and characteristics of these datasets offers insights into how they can impact performance. Our framework’s implementation demonstrates the feasibility of federated self-configuring MOD in non-IID scenarios and facilitates the development of MOD models trained on large distributed databases.
Intrinsic anomalous, spin and valley Hall effects in ’ex-so-tic’ van-der-Waals structures
Authors: Wojciechowska I. , Dyrdał A. 
Published: October 2024

AbstractWe consider the anomalous, spin, valley, and valley spin Hall effects in a pristine graphene-based van-der-Waals (vdW) heterostructure consisting of a bilayer graphene (BLG) sandwiched between a semiconducting van-der-Waals material with strong spin-orbit coupling (e.g., $$\hbox {WS}_2$$

WS
2

) and a ferromagnetic insulating vdW material (e.g. $$\hbox {Cr}_2$$

Cr
2

$$\hbox {Ge}_2$$

Ge
2

$$\hbox {Te}_6$$

Te
6

). Due to the exchange proximity effect from one side and spin-orbit proximity effect from the other side of graphene, such a structure is referred to as graphene based ’ex-so-tic’ structure. First, we derive an effective Hamiltonian describing the low-energy states of the structure. Then, using the Green’s function formalism, we obtain analytical results for the Hall conductivities as a function of the Fermi energy and gate voltage. For specific values of these parameters, we find a quantized valley Hall conductivity.
Assessing vitamin E acetate as a proxy for E-cigarette additives in a realistic pulmonary surfactant model
Authors: Korolainen Hanna , Olżyńska Agnieszka , Pajerski Wojciech , Chytrosz-Wrobel Paulina , Vattulainen Ilpo , Kulig Waldemar , Cwiklik Lukasz 
Published: October 2024

AbstractAdditives in vaping products, such as flavors, preservatives, or thickening agents, are commonly used to enhance user experience. Among these, Vitamin E acetate (VEA) was initially thought to be harmless but has been implicated as the primary cause of e-cigarette or vaping product use-associated lung injury, a serious lung disease. In our study, VEA serves as a proxy for other e-cigarette additives. To explore its harmful effects, we developed an exposure system to subject a pulmonary surfactant (PSurf) model to VEA-rich vapor. Through detailed analysis and atomic-level simulations, we found that VEA tends to cluster into aggregates on the PSurf surface, inducing deformations and weakening its essential elastic properties, critical for respiratory cycle function. Apart from VEA, our experiments also indicate that propylene glycol and vegetable glycerin, widely used in e-liquid mixtures, or their thermal decomposition products, alter surfactant properties. This research provides molecular-level insights into the detrimental impacts of vaping product additives on lung health.
Type-H endothelial cell protein Clec14a orchestrates osteoblast activity during trabecular bone formation and patterning
Authors: Neag Georgiana , Lewis Jonathan , Turner Jason D. , Manning Julia E. , Dean Isaac , Finlay Melissa , Poologasundarampillai Gowsihan , Woods Jonathan , Sahu Muhammad Arham , Khan Kabir A. , Begum Jenefa , McGettrick Helen M. , Bellantuono Ilaria , Heath Victoria , Jones Simon W. , Buckley Christopher D. , Bicknell Roy , Naylor Amy J. 
Published: October 2024

AbstractType-H capillary endothelial cells control bone formation during embryogenesis and postnatal growth but few signalling mechanisms underpinning this influence have been characterised. Here, we identify a highly expressed type-H endothelial cell protein, Clec14a, and explore its role in coordinating osteoblast activity. Expression of Clec14a and its ligand, Mmrn2 are high in murine type-H endothelial cells but absent from osteoblasts. Clec14a−/− mice have premature condensation of the type-H vasculature and expanded distribution of osteoblasts and bone matrix, increased long-bone length and bone density indicative of accelerated skeletal development, and enhanced osteoblast maturation. Antibody-mediated blockade of the Clec14a-Mmrn2 interaction recapitulates the Clec14a−/− phenotype. Endothelial cell expression of Clec14a regulates osteoblast maturation and mineralisation activity during postnatal bone development in mice. This finding underscores the importance of type-H capillary control of osteoblast activity in bone formation and identifies a novel mechanism that mediates this vital cellular crosstalk.
Advanced photovoltaic technology can reduce land requirements and climate impact on energy generation
Authors: Saxena Ankita , Brown Calum , Arneth Almut , Rounsevell Mark 
Published: October 2024

AbstractFuture changes in solar radiation and rising temperatures will likely reduce global solar photovoltaic potential, but advancing photovoltaic technologies could counteract these effects. We investigate the potential of photovoltaic to satisfy energy demands given climate change and technological development. We find that conventional photovoltaic will require 0.5 to 1.2% of global land area to meet projected energy demands by 2085 without accounting for climate change effects. When considering climate impacts, this requirement increases to 0.7–1.5% of the global land area. However, utilising advanced photovoltaic technologies can reduce this area to 0.3–1.2%, effectively mitigating climate impacts. Regional climate change impacts vary substantially, resulting in photovoltaic potential decreases of up to 3% in Latin America and the Caribbean, and by up to 8% in South Asia. Our results suggest that technology-driven increases in future global photovoltaic energy production can more than compensate for the climate related reductions.