bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging the Garlock Fault Zone With a Fiber: A Limited Damage Zone and Hidden Bimaterial Contrast
Authors: Atterholt James , Zhan Zhongwen , Yang Yan , Zhu Weiqiang 
Published: July 2024

AbstractThe structure of fault zones and the ruptures they host are inextricably linked. Fault zones are narrow, which has made imaging their structure at seismogenic depths a persistent problem. Fiber‐optic seismology allows for low‐maintenance, long‐term deployments of dense seismic arrays, which present new opportunities to address this problem. We use a fiber array that crosses the Garlock Fault to explore its structure. With a multifaceted imaging approach, we peel back the shallow structure around the fault to see how the fault changes with depth in the crust. We first generate a shallow velocity model across the fault with a joint inversion of active source and ambient noise data. Subsequently, we investigate the fault at deeper depths using travel‐time observations from local earthquakes. By comparing the shallow velocity model and the earthquake travel‐time observations, we find that the fault's low‐velocity zone below the top few hundred meters is at most unexpectedly narrow, potentially indicating fault zone healing. Using differential travel‐time measurements from earthquake pairs, we resolve a sharp bimaterial contrast at depth that suggests preferred westward rupture directivity.
Nonlinear encoding in diffractive information processing using linear optical materials
Authors: Li Yuhang , Li Jingxi , Ozcan Aydogan 
Published: July 2024

AbstractNonlinear encoding of optical information can be achieved using various forms of data representation. Here, we analyze the performances of different nonlinear information encoding strategies that can be employed in diffractive optical processors based on linear materials and shed light on their utility and performance gaps compared to the state-of-the-art digital deep neural networks. For a comprehensive evaluation, we used different datasets to compare the statistical inference performance of simpler-to-implement nonlinear encoding strategies that involve, e.g., phase encoding, against data repetition-based nonlinear encoding strategies. We show that data repetition within a diffractive volume (e.g., through an optical cavity or cascaded introduction of the input data) causes the loss of the universal linear transformation capability of a diffractive optical processor. Therefore, data repetition-based diffractive blocks cannot provide optical analogs to fully connected or convolutional layers commonly employed in digital neural networks. However, they can still be effectively trained for specific inference tasks and achieve enhanced accuracy, benefiting from the nonlinear encoding of the input information. Our results also reveal that phase encoding of input information without data repetition provides a simpler nonlinear encoding strategy with comparable statistical inference accuracy to data repetition-based diffractive processors. Our analyses and conclusions would be of broad interest to explore the push-pull relationship between linear material-based diffractive optical systems and nonlinear encoding strategies in visual information processors.
The recruitment of CD8+ T cells through YBX1 stabilization abrogates tumor intrinsic oncogenic role of MIR155HG in lung adenocarcinoma
Authors: Li Rutao , Zhang Yijian , Wang Anpeng , Feng Yipeng , Zhang Te , Wang Hui , Chen Yuzhong , Yu Xinnian , Song Xuming , Ding HanLin , Xu Lin , Dong Gaochao , Jiang Feng 
Published: July 2024

AbstractPrevious studies revealed that MIR155HG possessed an oncogenic role in many types of tumors including lung adenocarcinoma (LUAD), along with higher expression in tumors. However, in our study, we observed a positive correlation between MIR155HG expression and overall survival across different cohorts. The transferred PBMC on the NCG mouse model abrogated the tumor intrinsic oncogenic role of MIR155HG in LUAD. Upregulation of MIR155HG positively correlated with CD8+ T cell infiltration both in vitro and in vivo, as well as LUAD tissues. Mechanistically, we revealed that MIR155HG increased the cytokine CCL5 expression at the transcriptional level, which depended on the interaction between MIR155HG and YBX1 protein, a novel transcription factor of CCL5, resulting in the more protein stability of YBX1 through dampening ubiquitination. Additionally, we also observed that MIR155 could increase PD-L1 expression to hamper the activity of recruited CD8+ T cells, which could be rescued through PD-L1 mAb addition. Finally, we uncovered that patients with high MIR155HG expression had a higher response rate to immunotherapy, and the combination of MIR155HG overexpression and PD-L1 mAb increased the efficacy of PD-L1 mAb. Together, our study provides a novel biomarker and potential combination treatment strategy for patients who received immunotherapy.
Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations
Authors: Diaz Daniel J. , Gong Chengyue , Ouyang-Zhang Jeffrey , Loy James M. , Wells Jordan , Yang David , Ellington Andrew D. , Dimakis Alexandros G. , Klivans Adam R. 
Published: July 2024

AbstractEngineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph-transformer framework that achieves SOTA performance on accurately identifying thermodynamically stabilizing mutations. Our framework introduces several innovations to overcome well-known challenges in data scarcity and bias, generalization, and computation time, such as: Thermodynamic Permutations for data augmentation, structural amino acid embeddings to model a mutation with a single structure, a protein structure-specific attention-bias mechanism that makes transformers a viable alternative to graph neural networks. We provide training/test splits that mitigate data leakage and ensure proper model evaluation. Furthermore, to examine our data engineering contributions, we fine-tune ESM2 representations (Prostata-IFML) and achieve SOTA for sequence-based models. Notably, Stability Oracle outperforms Prostata-IFML even though it was pretrained on 2000X less proteins and has 548X less parameters. Our framework establishes a path for fine-tuning structure-based transformers to virtually any phenotype, a necessary task for accelerating the development of protein-based biotechnologies.
Mutant mice with rod-specific VPS35 deletion exhibit retinal α-synuclein pathology-associated degeneration
Authors: Fu Cheng , Yang Nan , Chuang Jen-Zen , Nakajima Nobuyuki , Iraha Satoshi , Roy Neeta , Wu Zhenquan , Jiang Zhichun , Otsu Wataru , Radu Roxana A. , Yang Howard Hua , Lee Maxwell Ping , Worgall Tilla S. , Xiong Wen-Cheng , Sung Ching-Hwa 
Published: July 2024

AbstractVacuolar protein sorting 35 (VPS35), the core component of the retromer complex which regulates endosomal trafficking, is genetically linked with Parkinson’s disease (PD). Impaired vision is a common non-motor manifestation of PD. Here, we show mouse retinas with VPS35-deficient rods exhibit synapse loss and visual deficit, followed by progressive degeneration concomitant with the emergence of Lewy body-like inclusions and phospho-α-synuclein (P-αSyn) aggregation. Ultrastructural analyses reveal VPS35-deficient rods accumulate aggregates in late endosomes, deposited as lipofuscins bound to P-αSyn. Mechanistically, we uncover a protein network of VPS35 and its interaction with HSC70. VPS35 deficiency promotes sequestration of HSC70 and P-αSyn aggregation in late endosomes. Microglia which engulf lipofuscins and P-αSyn aggregates are activated, displaying autofluorescence, observed as bright dots in fundus imaging of live animals, coinciding with pathology onset and progression. The Rod∆Vps35 mouse line is a valuable tool for further mechanistic investigation of αSyn lesions and retinal degenerative diseases.
Determinants of transthyretin levels and their association with adverse clinical outcomes among UK Biobank participants
Authors: Shetty Naman S. , Gaonkar Mokshad , Patel Nirav , Pampana Akhil , Vekariya Nehal , Li Peng , Arora Garima , Arora Pankaj 
Published: July 2024

AbstractTransthyretin is a transport protein whose misfolding has been implicated in the development of cardiac amyloidosis. Here, we examine the clinical correlates of transthyretin levels, the differences in transthyretin levels according to the pathogenic V142I TTR variant carrier status, and the association of transthyretin levels with outcomes among 35,206 UK Biobank participants who underwent plasma profiling and were free from prevalent cardiovascular disease and chronic renal disease. Transthyretin levels are lower in females, decrease with increasing C-reactive protein levels, and increase with body mass index, systolic blood pressure, diastolic blood pressure, total cholesterol, albumin levels, triglyceride levels, and creatinine levels. V142I non-carriers [n = 35,167, mean: −0.1 (0.3)] have higher adjusted transthyretin levels compared with the carriers [n = 39, mean: −0.5 (0.3)] (p:<0.001). A standard deviation decrease in transthyretin levels increases the risk of heart failure [HRadj: 1.17 (95% Confidence Interval = 1.08–1.26)] and all-cause mortality [HRadj: 1.18 (95% Confidence Interval = 1.14–1.24)]. This study shows that individuals with low transthyretin levels, such as those carrying the V142I variant, are at a higher risk of heart failure and mortality.
CAR T-cells targeting FGFR4 and CD276 simultaneously show potent antitumor effect against childhood rhabdomyosarcoma
Authors: Tian Meijie , Wei Jun S. , Cheuk Adam Tai-Chi , Milewski David , Zhang Zhongmei , Kim Yong Yean , Chou Hsien-Chao , Liu Can , Badr Sherif , Pope Eleanor G. , Rahmy Abdelrahman , Wu Jerry T. , Kelly Michael C. , Wen Xinyu , Khan Javed 
Published: July 2024

AbstractChimeric antigen receptor (CAR) T-cells targeting Fibroblast Growth Factor Receptor 4 (FGFR4), a highly expressed surface tyrosine receptor in rhabdomyosarcoma (RMS), are already in the clinical phase of development, but tumour heterogeneity and suboptimal activation might hamper their potency. Here we report an optimization strategy of the co-stimulatory and targeting properties of a FGFR4 CAR. We replace the CD8 hinge and transmembrane domain and the 4-1BB co-stimulatory domain with those of CD28. The resulting CARs display enhanced anti-tumor activity in several RMS xenograft models except for an aggressive tumour cell line, RMS559. By searching for a direct target of the RMS core-regulatory transcription factor MYOD1, we identify another surface protein, CD276, as a potential target. Bicistronic CARs (BiCisCAR) targeting both FGFR4 and CD276, containing two distinct co-stimulatory domains, have superior prolonged persistent and invigorated anti-tumor activities compared to the optimized FGFR4-specific CAR and the other BiCisCAR with the same 4-1BB co-stimulatory domain. Our study thus lays down the proof-of-principle for a CAR T-cell therapy targeting both FGFR4 and CD276 in RMS.
Large oscillatory thermal hall effect in kagome metals
Authors: Zhang Dechen , Chen Kuan-Wen , Zheng Guoxin , Yu Fanghang , Shi Mengzhu , Zhu Yuan , Chan Aaron , Jenkins Kaila , Ying Jianjun , Xiang Ziji , Chen Xianhui , Li Lu 
Published: July 2024

AbstractThe thermal Hall effect recently provided intriguing probes to the ground state of exotic quantum matters. These observations of transverse thermal Hall signals lead to the debate on the fermionic versus bosonic origins of these phenomena. The recent report of quantum oscillations (QOs) in Kitaev spin liquid points to a possible resolution. The Landau level quantization would most likely capture only the fermionic thermal transport effect. However, the QOs in the thermal Hall effect are generally hard to detect. In this work, we report the observation of a large oscillatory thermal Hall effect of correlated Kagome metals. We detect a 180-degree phase change of the oscillation and demonstrate the phase flip as an essential feature for QOs in the thermal transport properties. More importantly, the QOs in the thermal Hall channel are more profound than those in the electrical Hall channel, which strongly violates the Wiedemann–Franz (WF) law for QOs. This result presents the oscillatory thermal Hall effect as a powerful probe to the correlated quantum materials.
A multi-classifier system integrated by clinico-histology-genomic analysis for predicting recurrence of papillary renal cell carcinoma
Authors: Huang Kang-Bo , Gui Cheng-Peng , Xu Yun-Ze , Li Xue-Song , Zhao Hong-Wei , Cao Jia-Zheng , Chen Yu-Hang , Pan Yi-Hui , Liao Bing , Cao Yun , Zhang Xin-Ke , Han Hui , Zhou Fang-Jian , Liu Ran-Yi , Chen Wen-Fang , Jiang Ze-Ying , Feng Zi-Hao , Jiang Fu-Neng , Yu Yan-Fei , Xiong Sheng-Wei , Han Guan-Peng , Tang Qi , Ouyang Kui , Qu Gui-Mei , Wu Ji-Tao , Cao Ming , Dong Bai-Jun , Huang Yi-Ran , Zhang Jin , Li Cai-Xia , Li Pei-Xing , Chen Wei , Zhong Wei-De , Guo Jian-Ping , Liu Zhi-Ping , Hsieh Jer-Tsong , Xie Dan , Cai Mu-Yan , Xue Wei , Wei Jin-Huan , Luo Jun-Hang 
Published: July 2024

AbstractIntegrating genomics and histology for cancer prognosis demonstrates promise. Here, we develop a multi-classifier system integrating a lncRNA-based classifier, a deep learning whole-slide-image-based classifier, and a clinicopathological classifier to accurately predict post-surgery localized (stage I–III) papillary renal cell carcinoma (pRCC) recurrence. The multi-classifier system demonstrates significantly higher predictive accuracy for recurrence-free survival (RFS) compared to the three single classifiers alone in the training set and in both validation sets (C-index 0.831-0.858 vs. 0.642-0.777, p < 0.05). The RFS in our multi-classifier-defined high-risk stage I/II and grade 1/2 groups is significantly worse than in the low-risk stage III and grade 3/4 groups (p < 0.05). Our multi-classifier system is a practical and reliable predictor for recurrence of localized pRCC after surgery that can be used with the current staging system to more accurately predict disease course and inform strategies for individualized adjuvant therapy.
Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet
Authors: Choi Sanghyeon , Lee Youngjin , Park Shinhye , Jang Song Yee , Park Jongbin , Oh Do Won , Kim Su-Man , Kim Tae-Hwan , Lee Ga Seul , Cho Changyi , Kim Byoung Sik , Lee Donghan , Kim Eun-Hee , Cheong Hae-Kap , Moon Jeong Hee , Song Ji-Joon , Hwang Jungwon , Kim Myung Hee 
Published: July 2024

AbstractMultiple bacterial genera take advantage of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin to invade host cells. Secretion of the MARTX toxin by Vibrio vulnificus, a deadly opportunistic pathogen that causes primary septicemia, the precursor of sepsis, is a major driver of infection; however, the molecular mechanism via which the toxin contributes to septicemia remains unclear. Here, we report the crystal and cryo-electron microscopy (EM) structures of a toxin effector duet comprising the domain of unknown function in the first position (DUF1)/Rho inactivation domain (RID) complexed with human targets. These structures reveal how the duet is used by bacteria as a potent weapon. The data show that DUF1 acts as a RID-dependent transforming NADase domain (RDTND) that disrupts NAD+ homeostasis by hijacking calmodulin. The cryo-EM structure of the RDTND-RID duet complexed with calmodulin and Rac1, together with immunological analyses in vitro and in mice, provide mechanistic insight into how V. vulnificus uses the duet to suppress ROS generation by depleting NAD(P)+ and modifying Rac1 in a mutually-reinforcing manner that ultimately paralyzes first line immune responses, promotes dissemination of invaders, and induces sepsis. These data may allow development of tools or strategies to combat MARTX toxin-related human diseases.
Fundamental causal bounds of quantum random access memories
Authors: Wang Yunfei , Alexeev Yuri , Jiang Liang , Chong Frederic T. , Liu Junyu 
Published: July 2024

AbstractOur study evaluates the limitations and potentials of Quantum Random Access Memory (QRAM) within the principles of quantum physics and relativity. QRAM is crucial for advancing quantum algorithms in fields like linear algebra and machine learning, purported to efficiently manage large data sets with $${{{\mathcal{O}}}}(\log N)$$

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circuit depth. However, its scalability is questioned when considering the relativistic constraints on qubits interacting locally. Utilizing relativistic quantum field theory and Lieb–Robinson bounds, we delve into the causality-based limits of QRAM. Our investigation introduces a feasible QRAM model in hybrid quantum acoustic systems, capable of supporting a significant number of logical qubits across different dimensions-up to ~107 in 1D, ~1015 to ~1020 in 2D, and ~1024 in 3D, within practical operation parameters. This analysis suggests that relativistic causality principles could universally influence quantum computing hardware, underscoring the need for innovative quantum memory solutions to navigate these foundational barriers, thereby enhancing future quantum computing endeavors in data science.
Expanding access to water quality monitoring with the open-source WaterScope testing platform
Authors: Dabrowska Alicja , Lewis George R. , Atlabachew Minaleshewa , Salter Susannah J. , Henderson Cassi , Ji Chang , Ehlers Annike , Stirling Julian , Mower Sophie , Allen Lara , Lay Elizabeth , Stuart Kara , Appavou Lisa , Bowman Richard , Zhao Tianheng , Patel Nalin , Patto Alexander , Holmes Mark A. , Baumberg Jeremy J. , Mahdi Sammy 
Published: July 2024

AbstractIncreasing access to water quality tests in low-income communities is a crucial strategy toward achieving global water equality. Recent studies in the Water Sanitation and Hygiene (WASH) sector underscore the importance of addressing practical concerns in water testing, such as robustness and results communication. In response, we present the WaterScope testing kit; an open-source, validated platform for drinking water quality assessment. It modernises the testing process with the inclusion of a unique cartridge/slider mechanism, machine-learning-enhanced classification and full digitalisation of results. WaterScope’s equivalency to conventional methods for quantifying E. coli is established through extensive validation experiments in both laboratory and field environments. This versatile platform provides potential to expand its applications to test other bacteria, perform colorimetric assays, and analyse clinical samples such as blood/urine samples. We anticipate that the system’s ease-of-use, portability, affordability, robustness, and digital nature will accelerate progress toward global water equality.
Retinal Image Dataset of Infants and Retinopathy of Prematurity
Authors: Timkovič Juraj , Nowaková Jana , Kubíček Jan , Hasal Martin , Varyšová Alice , Kolarčík Lukáš , Maršolková Kristýna , Augustynek Martin , Snášel Václav 
Published: July 2024

AbstractRetinopathy of prematurity (ROP) represents a vasoproliferative disease, especially in newborns and infants, which can potentially affect and damage the vision. Despite recent advances in neonatal care and medical guidelines, ROP still remains one of the leading causes of worldwide childhood blindness. The paper presents a unique dataset of 6,004 retinal images of 188 newborns, most of whom are premature infants. The dataset is accompanied by the anonymized patients’ information from the ROP screening acquired at the University Hospital Ostrava, Czech Republic. Three digital retinal imaging camera systems are used in the study: Clarity RetCam 3, Natus RetCam Envision, and Phoenix ICON. The study is enriched by the software tool ReLeSeT which is aimed at automatic retinal lesion segmentation and extraction from retinal images. Consequently, this tool enables computing geometric and intensity features of retinal lesions. Also, we publish a set of pre-processing tools for feature boosting of retinal lesions and retinal blood vessels for building classification and segmentation models in ROP analysis.
3D meshes dataset of sagittal otoliths from red mullet in the Mediterranean Sea
Authors: Andrialovanirina Nicolas , Poloni Lauriane , Laffont Rémi , Poisson Caillault Émilie , Couette Sébastien , Mahé Kélig 
Published: July 2024

AbstractThis paper presents a dataset of 3D sagittal left otolith meshes from 339 individual red mullet (Mullus barbatus). These immature specimens were collected from 17 geographical areas covering the entire Mediterranean Sea. Measured biological parameters were: fish total length (TL ± 1 mm, range from 125 to 238 mm), total weight (W ± 0.1 g, range from 14.9 to 168.0 g), sex (S), sexual maturity staging (Mat). The 3D otolith dataset comprises high-resolution meshes of otoliths obtained using microtomography (29.2 μm voxel size). The data offer valuable insights into the morphological variability and population structure of red mullet populations in the Mediterranean Sea. Potential applications of the dataset include age determination, stock identification, and population connectivity analysis. These applications aim to enhance the understanding of red mullet populations and contribute to the sustainable management of marine resources in the Mediterranean Sea.
Molecular detection and characterization of Anaplasma marginale and Babesia canis vogeli infecting dogs in Luxor, Egypt
Authors: Mahmoud Hassan Y. A. H. , Shahat Moshera S. , Fereig Ragab M. , Ali Alsagher O. , Emeish Walaa F. A. , Soliman Ahmed M. , Khalifa Fatma A. , Tanaka Tetsuya 
Published: July 2024

AbstractTick-borne diseases in animals are increasing rapidly worldwide, but there is insufficient information about tick-borne diseases infecting dogs in southern Egypt. Thus, in the current study, we detected the presence of Anaplasma marginale (A. marginale) and Babesia canis vogeli (B. canis vogeli) in the blood of dogs. The results revealed that 4/100 (4%) were positive, and a higher infection rate was found in males (75%), than females (25%). The phylogenetic analysis for the major surface protein 4 (msp4) gene in this study was compared with amplicons separate from other reported isolates with alignment by identity 100% with cattle and camels from Egypt, and the phylogenetic analysis for the B. canis vogeli small subunit ribosomal RNA (SSU rRNA) gene in this study identified identity by 99.89% with dogs from Egypt. This report is considered the first report in southern Egypt about A. marginale in dogs based on the sequence analysis of the msp4 gene, providing new data for the classification and identification of A. marginale in dogs compared to A. marginale isolated from other animals in southern Egypt.
A novel methodology utilizing microchip implants to monitor individual activity and body temperature for assessing knee pain in group-housed rats
Authors: Hasegawa Shoichi , Yamashita Riko , Nakagawa Yusuke , Miyatake Kazumasa , Katagiri Hiroki , Nakamura Tomomasa , Koga Hideyuki , Sekiya Ichiro , Yoshii Toshitaka , Rosen Vicki , Tsuji Kunikazu 
Published: July 2024

AbstractThe pain assessment in animals is challenging as they cannot verbally express the site and severity of pain. In this study, we tried a small implantable actimeter, “Nanotag”, to monitor spontaneous locomotor activity and body temperature in animals suffering from a chemical-induced rat knee arthritis as compared to naïve and steroid-treated rats. Nanotag could detect the decrease in locomotor activity quickly after the arthritis induction and anti-inflammation analgesic treatment by intra-articular injection of steroid significantly improved locomotor activity. These changes were in the same line with those of a conventional knee pain evaluation method (incapacitance test). Nanotag can be utilized as the non-interventional, continuous, and completely objective monitoring the amount of pain in rat knee arthritis model. This traditional yet innovative method may be universally applicable to various pain models and species, making it a worthwhile device for research across diverse fields.