bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold Diffusion Model for Seismic Denoising
Authors: Trappolini Daniele , Laurenti Laura , Poggiali Giulio , Tinti Elisa , Galasso Fabio , Michelini Alberto , Marone Chris 
Published: June 2024

AbstractSeismic waves contain information about the earthquake source, the geologic structure they traverse, and many forms of noise. Separating the noise from the earthquake is a difficult task because optimal parameters for filtering noise typically vary with time and, if chosen inappropriately, may strongly alter the original seismic waveform. Diffusion models based on Deep Learning have demonstrated remarkable capabilities in restoring images and audio signals. However, those models assume a Gaussian distribution of noise, which is not the case for typical seismic noise. Motivated by the effectiveness of “cold” diffusion models in speech enhancement, medical anomaly detection, and image restoration, we present a cold variant for seismic data restoration. We describe the first Cold Diffusion Model for Seismic Denoising (CDiffSD), including key design aspects, model architecture, and noise handling. Using metrics to quantify the performance of CDiffSD models compared to previous works, we demonstrate that it provides a new standard in performance. CDiffSD significantly improved the Signal to Noise Ratio by about 18% compared to previous models. It also enhanced Cross‐correlation by 6%, showing a better match between denoised and original signals. Moreover, testing revealed a 50% increase in the recall of P‐wave picks for seismic picking. Our work show that CDiffSD outperforms existing benchmarks, further underscoring its effectiveness in seismic data denoising and analysis. Additionally, the versatility of this model suggests its potential applicability across a range of tasks and domains, such as GNSS, Lab Acoustic Emission, and Distributed Acoustic Sensing data, offering promising avenues for further utilization.
The identification of effective tumor-suppressing neoantigens using a tumor-reactive TIL TCR-pMHC ternary complex
Authors: Kim Sang Hoon , Lee Bo Ryeong , Kim Sung-Min , Kim Sungsik , Kim Min-seok , Kim Jaehyun , Lee Inkyu , Kim Hee-Soo , Nam Gi-Hoon , Kim In-San , Song Kyuyoung , Choi Yoonjoo , Lee Dong-Sup , Park Woong-Yang 
Published: June 2024

AbstractNeoantigens are ideal targets for cancer immunotherapy because they are expressed de novo in tumor tissue but not in healthy tissue and are therefore recognized as foreign by the immune system. Advances in next-generation sequencing and bioinformatics technologies have enabled the quick identification and prediction of tumor-specific neoantigens; however, only a small fraction of predicted neoantigens are immunogenic. To improve the predictability of immunogenic neoantigens, we developed the in silico neoantigen prediction workflows VACINUSpMHC and VACINUSTCR: VACINUSpMHC incorporates physical binding between peptides and MHCs (pMHCs), and VACINUSTCR integrates T cell reactivity to the pMHC complex through deep learning-based pairing with T cell receptors (TCRs) of putative tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs). We then validated our neoantigen prediction workflows both in vitro and in vivo in patients with hepatocellular carcinoma (HCC) and in a B16F10 mouse melanoma model. The predictive abilities of VACINUSpMHC and VACINUSTCR were confirmed in a validation cohort of 8 patients with HCC. Of a total of 118 neoantigen candidates predicted by VACINUSpMHC, 48 peptides were ultimately selected using VACINUSTCR. In vitro validation revealed that among the 48 predicted neoantigen candidates, 13 peptides were immunogenic. Assessment of the antitumor efficacy of the candidate neoepitopes using a VACINUSTCR in vivo mouse model suggested that vaccination with the predicted neoepitopes induced neoantigen-specific T cell responses and enabled the trafficking of neoantigen-specific CD8 + T cell clones into the tumor tissue, leading to tumor suppression. This study showed that the prediction of immunogenic neoantigens can be improved by integrating a tumor-reactive TIL TCR-pMHC ternary complex.
Conditional knockout of Shank3 in the ventral CA1 by quantitative in vivo genome-editing impairs social memory in mice
Authors: Chung Myung , Imanaka Katsutoshi , Huang Ziyan , Watarai Akiyuki , Wang Mu-Yun , Tao Kentaro , Ejima Hirotaka , Aida Tomomi , Feng Guoping , Okuyama Teruhiro 
Published: June 2024

AbstractIndividuals with autism spectrum disorder (ASD) have a higher prevalence of social memory impairment. A series of our previous studies revealed that hippocampal ventral CA1 (vCA1) neurons possess social memory engram and that the neurophysiological representation of social memory in the vCA1 neurons is disrupted in ASD-associated Shank3 knockout mice. However, whether the dysfunction of Shank3 in vCA1 causes the social memory impairment observed in ASD remains unclear. In this study, we found that vCA1-specific Shank3 conditional knockout (cKO) by the adeno-associated virus (AAV)- or specialized extracellular vesicle (EV)- mediated in vivo gene editing was sufficient to recapitulate the social memory impairment in male mice. Furthermore, the utilization of EV-mediated Shank3-cKO allowed us to quantitatively examine the role of Shank3 in social memory. Our results suggested that there is a certain threshold for the proportion of Shank3-cKO neurons required for social memory disruption. Thus, our study provides insight into the population coding of social memory in vCA1, as well as the pathological mechanisms underlying social memory impairment in ASD.
Low-energy electronic structure in the unconventional charge-ordered state of ScV6Sn6
Authors: Kundu Asish K. , Huang Xiong , Seewald Eric , Ritz Ethan , Pakhira Santanu , Zhang Shuai , Sun Dihao , Turkel Simon , Shabani Sara , Yilmaz Turgut , Vescovo Elio , Dean Cory R. , Johnston David C. , Valla Tonica , Birol Turan , Basov Dmitri N. , Fernandes Rafael M. , Pasupathy Abhay N. 
Published: June 2024

AbstractKagome vanadates AV3Sb5 display unusual low-temperature electronic properties including charge density waves (CDW), whose microscopic origin remains unsettled. Recently, CDW order has been discovered in a new material ScV6Sn6, providing an opportunity to explore whether the onset of CDW leads to unusual electronic properties. Here, we study this question using angle-resolved photoemission spectroscopy (ARPES) and scanning tunneling microscopy (STM). The ARPES measurements show minimal changes to the electronic structure after the onset of CDW. However, STM quasiparticle interference (QPI) measurements show strong dispersing features related to the CDW ordering vectors. A plausible explanation is the presence of a strong momentum-dependent scattering potential peaked at the CDW wavevector, associated with the existence of competing CDW instabilities. Our STM results further indicate that the bands most affected by the CDW are near vHS, analogous to the case of AV3Sb5 despite very different CDW wavevectors.
Three-dimensional hidden phase probed by in-plane magnetotransport in kagome metal CsV3Sb5 thin flakes
Authors: Wei Xinjian , Tian Congkuan , Cui Hang , Zhai Yuxin , Li Yongkai , Liu Shaobo , Song Yuanjun , Feng Ya , Huang Miaoling , Wang Zhiwei , Liu Yi , Xiong Qihua , Yao Yugui , Xie X. C. , Chen Jian-Hao 
Published: June 2024

AbstractTransition metal compounds with kagome structure have been found to exhibit a variety of exotic structural, electronic, and magnetic orders. These orders are competing with energies very close to each other, resulting in complex phase transitions. Some of the phases are easily observable, such as the charge density wave (CDW) and the superconducting phase, while others are more challenging to identify and characterize. Here we present magneto-transport evidence of a new phase below ~ 35 K in the kagome topological metal CsV3Sb5 (CVS) thin flakes between the CDW and the superconducting transition temperatures. This phase is characterized by six-fold rotational symmetry in the in-plane magnetoresistance (MR) and is connected to the orbital current order in CVS. Furthermore, the phase is characterized by a large in-plane negative magnetoresistance, which suggests the existence of a three-dimensional, magnetic field-tunable orbital current ordered phase. Our results highlight the potential of magneto-transport to reveal the interactions between exotic quantum states of matter and to uncover the symmetry of such hidden phases.
CoHIT: a one-pot ultrasensitive ERA-CRISPR system for detecting multiple same-site indels
Authors: Liu Yin , Liu Xinyi , Wei Dongyi , Dang Lu , Xu Xiaoran , Huang Shisheng , Li Liwen , Wu Sanyun , Wu Jinxian , Liu Xiaoyan , Sun Wenjun , Tao Wanyu , Wei Yongchang , Huang Xingxu , Li Kui , Wang Xinjie , Zhou Fuling 
Published: June 2024

AbstractGenetic testing is crucial for precision cancer medicine. However, detecting multiple same-site insertions or deletions (indels) is challenging. Here, we introduce CoHIT (Cas12a-based One-for-all High-speed Isothermal Test), a one-pot CRISPR-based assay for indel detection. Leveraging an engineered AsCas12a protein variant with high mismatch tolerance and broad PAM scope, CoHIT can use a single crRNA to detect multiple NPM1 gene c.863_864 4-bp insertions in acute myeloid leukemia (AML). After optimizing multiple parameters, CoHIT achieves a detection limit of 0.01% and rapid results within 30 minutes, without wild-type cross-reactivity. It successfully identifies NPM1 mutations in 30 out of 108 AML patients and demonstrates potential in monitoring minimal residual disease (MRD) through continuous sample analysis from three patients. The CoHIT method is also competent for detecting indels of KIT, BRAF, and EGFR genes. Integration with lateral flow test strips and microfluidic chips highlights CoHIT’s adaptability and multiplexing capability, promising significant advancements in clinical cancer diagnostics.
M6A reduction relieves FUS-associated ALS granules
Authors: Di Timoteo Gaia , Giuliani Andrea , Setti Adriano , Biagi Martina C. , Lisi Michela , Santini Tiziana , Grandioso Alessia , Mariani Davide , Castagnetti Francesco , Perego Eleonora , Zappone Sabrina , Lattante Serena , Sabatelli Mario , Rotili Dante , Vicidomini Giuseppe , Bozzoni Irene 
Published: June 2024

AbstractAmyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease due to gradual motoneurons (MN) degeneration. Among the processes associated to ALS pathogenesis, there is the formation of cytoplasmic inclusions produced by aggregation of mutant proteins, among which the RNA binding protein FUS. Here we show that, in neuronal cells and in iPSC-derived MN expressing mutant FUS, such inclusions are significantly reduced in number and dissolve faster when the RNA m6A content is diminished. Interestingly, stress granules formed in ALS conditions showed a distinctive transcriptome with respect to control cells, which reverted to similar to control after m6A downregulation. Notably, cells expressing mutant FUS were characterized by higher m6A levels suggesting a possible link between m6A homeostasis and pathological aggregates. Finally, we show that FUS inclusions are reduced also in patient-derived fibroblasts treated with STM-2457, an inhibitor of METTL3 activity, paving the way for its possible use for counteracting aggregate formation in ALS.
UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168
Authors: Yalçin Zeliha , Lam Shiu Yeung , Peuscher Marieke H. , van der Torre Jaco , Zhu Sha , Iyengar Prasanna V. , Salas-Lloret Daniel , de Krijger Inge , Moatti Nathalie , van der Lugt Ruben , Falcone Mattia , Cerutti Aurora , Bleijerveld Onno B. , Hoekman Liesbeth , González-Prieto Román , Jacobs Jacqueline J. L. 
Published: June 2024

AbstractMaintenance of genome integrity requires tight control of DNA damage response (DDR) signalling and repair, with phosphorylation and ubiquitination representing key elements. How these events are coordinated to achieve productive DNA repair remains elusive. Here we identify the ubiquitin-conjugating enzyme UBE2D3 as a regulator of ATM kinase-induced DDR that promotes non-homologous end-joining (NHEJ) at telomeres. UBE2D3 contributes to DDR-induced chromatin ubiquitination and recruitment of the NHEJ-promoting factor 53BP1, both mediated by RNF168 upon ATM activation. Additionally, UBE2D3 promotes NHEJ by limiting RNF168 accumulation and facilitating ATM-mediated phosphorylation of KAP1-S824. Mechanistically, defective KAP1-S824 phosphorylation and telomeric NHEJ upon UBE2D3-deficiency are linked to RNF168 hyperaccumulation and aberrant PP2A phosphatase activity. Together, our results identify UBE2D3 as a multi-level regulator of NHEJ that orchestrates ATM and RNF168 activities. Moreover, they reveal a negative regulatory circuit in the DDR that is constrained by UBE2D3 and consists of RNF168- and phosphatase-mediated restriction of KAP1 phosphorylation.
Simulating multiple variability in spatially resolved transcriptomics with scCube
Authors: Qian Jingyang , Bao Hudong , Shao Xin , Fang Yin , Liao Jie , Chen Zhuo , Li Chengyu , Guo Wenbo , Hu Yining , Li Anyao , Yao Yue , Fan Xiaohui , Cheng Yiyu 
Published: June 2024

AbstractA pressing challenge in spatially resolved transcriptomics (SRT) is to benchmark the computational methods. A widely-used approach involves utilizing simulated data. However, biases exist in terms of the currently available simulated SRT data, which seriously affects the accuracy of method evaluation and validation. Herein, we present scCube (https://github.com/ZJUFanLab/scCube), a Python package for independent, reproducible, and technology-diverse simulation of SRT data. scCube not only enables the preservation of spatial expression patterns of genes in reference-based simulations, but also generates simulated data with different spatial variability (covering the spatial pattern type, the resolution, the spot arrangement, the targeted gene type, and the tissue slice dimension, etc.) in reference-free simulations. We comprehensively benchmark scCube with existing single-cell or SRT simulators, and demonstrate the utility of scCube in benchmarking spot deconvolution, gene imputation, and resolution enhancement methods in detail through three applications.
Electrical noise spectroscopy of magnons in a quantum Hall ferromagnet
Authors: Kumar Ravi , Srivastav Saurabh Kumar , Roy Ujjal , Park Jinhong , Spånslätt Christian , Watanabe K. , Taniguchi T. , Gefen Yuval , Mirlin Alexander D. , Das Anindya 
Published: June 2024

AbstractCollective spin-wave excitations, magnons, are promising quasi-particles for next-generation spintronics devices, including platforms for information transfer. In a quantum Hall ferromagnets, detection of these charge-neutral excitations relies on the conversion of magnons into electrical signals in the form of excess electrons and holes, but if the excess electron and holes are equal, detecting an electrical signal is challenging. In this work, we overcome this shortcoming by measuring the electrical noise generated by magnons. We use the symmetry-broken quantum Hall ferromagnet of the zeroth Landau level in graphene to launch magnons. Absorption of these magnons creates excess noise above the Zeeman energy and remains finite even when the average electrical signal is zero. Moreover, we formulate a theoretical model in which the noise is produced by equilibration between edge channels and propagating magnons. Our model also allows us to pinpoint the regime of ballistic magnon transport in our device.
Programmable melanoma-targeted radio-immunotherapy via fusogenic liposomes functionalized with multivariate-gated aptamer assemblies
Authors: Ren Xijiao , Xue Rui , Luo Yan , Wang Shuang , Ge Xinyue , Yao Xuemei , Li Liqi , Min Junxia , Li Menghuan , Luo Zhong , Wang Fudi 
Published: June 2024

AbstractRadio-immunotherapy exploits the immunostimulatory features of ionizing radiation (IR) to enhance antitumor effects and offers emerging opportunities for treating invasive tumor indications such as melanoma. However, insufficient dose deposition and immunosuppressive microenvironment (TME) of solid tumors limit its efficacy. Here we report a programmable sequential therapeutic strategy based on multifunctional fusogenic liposomes (Lip@AUR-ACP-aptPD-L1) to overcome the intrinsic radio-immunotherapeutic resistance of solid tumors. Specifically, fusogenic liposomes are loaded with gold-containing Auranofin (AUR) and inserted with multivariate-gated aptamer assemblies (ACP) and PD-L1 aptamers in the lipid membrane, potentiating melanoma-targeted AUR delivery while transferring ACP onto cell surface through selective membrane fusion. AUR amplifies IR-induced immunogenic death of melanoma cells to release antigens and damage-associated molecular patterns such as adenosine triphosphate (ATP) for triggering adaptive antitumor immunity. AUR-sensitized radiotherapy also upregulates matrix metalloproteinase-2 (MMP-2) expression that combined with released ATP to activate ACP through an “and” logic operation-like process (AND-gate), thus triggering the in-situ release of engineered cytosine-phosphate-guanine aptamer-based immunoadjuvants (eCpG) for stimulating dendritic cell-mediated T cell priming. Furthermore, AUR inhibits tumor-intrinsic vascular endothelial growth factor signaling to suppress infiltration of immunosuppressive cells for fostering an anti-tumorigenic TME. This study offers an approach for solid tumor treatment in the clinics.
PRDX6 augments selenium utilization to limit iron toxicity and ferroptosis
Authors: Fujita Hiroaki , Tanaka Yu-ki , Ogata Seiryo , Suzuki Noriyuki , Kuno Sota , Barayeu Uladzimir , Akaike Takaaki , Ogra Yasumitsu , Iwai Kazuhiro 
Published: June 2024

AbstractFerroptosis is a form of regulated cell death induced by iron-dependent accumulation of lipid hydroperoxides. Selenoprotein glutathione peroxidase 4 (GPX4) suppresses ferroptosis by detoxifying lipid hydroperoxides via a catalytic selenocysteine (Sec) residue. Sec, the genetically encoded 21st amino acid, is biosynthesized from a reactive selenium donor on its cognate tRNA[Ser]Sec. It is thought that intracellular selenium must be delivered ‘safely’ and ‘efficiently’ by a carrier protein owing to its high reactivity and very low concentrations. Here, we identified peroxiredoxin 6 (PRDX6) as a novel selenoprotein synthesis factor. Loss of PRDX6 decreases the expression of selenoproteins and induces ferroptosis via a reduction in GPX4. Mechanistically, PRDX6 increases the efficiency of intracellular selenium utilization by transferring selenium between proteins within the selenocysteyl-tRNA[Ser]Sec synthesis machinery, leading to efficient synthesis of selenocysteyl-tRNA[Ser]Sec. These findings highlight previously unidentified selenium metabolic systems and provide new insights into ferroptosis.
Alteration of circulating ACE2-network related microRNAs in patients with COVID-19
Authors: Wicik Zofia , Eyileten Ceren , Nowak Anna , Keshwani Disha , Simões Sérgio N. , Martins David C. , Klos Krzysztof , Wlodarczyk Wojciech , Assinger Alice , Soldacki Dariusz , Chcialowski Andrzej , Siller-Matula Jolanta M. , Postula Marek 
Published: June 2024

AbstractAngiotensin converting enzyme 2 (ACE2) serves as the primary receptor for the SARS-CoV-2 virus and has implications for the functioning of the cardiovascular system. Based on our previously published bioinformatic analysis, in this study we aimed to analyze the diagnostic and predictive utility of miRNAs (miR-10b-5p, miR-124-3p, miR-200b-3p, miR-26b-5p, miR-302c-5p) identified as top regulators of ACE2 network with potential to affect cardiomyocytes and cardiovascular system in patients with COVID-19. The expression of miRNAs was determined through qRT-PCR in a cohort of 79 hospitalized COVID-19 patients as well as 32 healthy volunteers. Blood samples and clinical data of COVID-19 patients were collected at admission, 7-days and 21-days after admission. We also performed SHAP analysis of clinical data and miRNAs target predictions and advanced enrichment analyses. Low expression of miR-200b-3p at the seventh day of admission is indicative of predictive value in determining the length of hospital stay and/or the likelihood of mortality, as shown in ROC curve analysis with an AUC of 0.730 and a p-value of 0.002. MiR-26b-5p expression levels in COVID-19 patients were lower at the baseline, 7 and 21-days of admission compared to the healthy controls (P < 0.0001). Similarly, miR-10b-5p expression levels were lower at the baseline and 21-days post admission (P = 0.001). The opposite situation was observed in miR-124-3p and miR-302c-5p. Enrichment analysis showed influence of analyzed miRNAs on IL-2 signaling pathway and multiple cardiovascular diseases through COVID-19-related targets. Moreover, the COVID-19-related genes regulated by miR-200b-3p were linked to T cell protein tyrosine phosphatase and the HIF-1 transcriptional activity in hypoxia. Analysis focused on COVID-19 associated genes showed that all analyzed miRNAs are strongly affecting disease pathways related to CVDs which could be explained by their strong interaction with the ACE2 network.
Adaptive control for memristive system via compensatory controller and Chebyshev neural network
Authors: Wang Shaofu 
Published: June 2024

AbstractIn this paper, based on linear matrix inequality technique, a simple controller and a compensatory controller are designed. It can track arbitrary fixed points and any periodic orbits. In addition, a synchronization control method via Chebyshev neural network with external disturbances is proposed. An adaptive controller is given. The Chebyshev neural network is used to approximate the uncertain nonlinear function and the adaptive law is used to adjust the corresponding parameters in the system. Taking a 4D memristive chaotic system as examples, the results are in consistent with the simulations. From a framework and control theoretical point of view, the proposed synchronization approach via compensation controller and Chebyshev neural network is firstly presented. From an application point of view, the proposed scheme can simplify the complexity of controller design. It is promising in many applications for mem-systems as secure communications and neural networks.
HCSRL: hyperledger composer system for reducing logistics losses in the pharmaceutical product supply chain using a blockchain-based approach
Authors: Dash Satyabrata , Ghugar Umashankar , Godavarthi Deepthi , Mohanty Sachi Nandan 
Published: June 2024

AbstractBlockchain technology uses a secure and decentralised framework for transaction management and data sharing within supply chains. This is particularly crucial in the pharmaceutical industry, where product authenticity and traceability are paramount. Blockchain plays a pivotal role in preventing product loss and counterfeiting, while simultaneously enhancing transparency and efficiency throughout the supply chain. The research introduces a step-by-step approach to implementing a proof-of-concept (PoC) for Supply Chain Risk Management (SCRM) through blockchain technology. This PoC involves simulating a supply chain process to assess feasibility and measure key performance indicators. Engaging stakeholders and gathering feedback is integral to refining the blockchain-based SCRM system. The study rigorously evaluates the performance of the SCRM blockchain across various test scenarios, featuring differing numbers of organizations and clients. Multiple fabric networks are employed to assess the system’s scalability and performance under diverse conditions. The results of these comprehensive tests inform practical deployment decisions and highlight areas for potential optimization and further development. So this research provides valuable insights into the application of blockchain in pharmaceutical supply chains, offering a roadmap for implementation and improving supply chain security, efficiency, and transparency.