检索结果-内蒙古大学图书馆

arXiv 2023年

作者： Longo, Luca Brcic, Mario Cabitza, Federico Choi, Jaesik Confalonieri, Roberto Ser, Javier Del Guidotti, Riccardo Hayashi, Yoichi Herrera, Francisco Holzinger, Andreas Jiang, Richard Khosravi, Hassan Lecue, Freddy Malgieri, Gianclaudio Páez, Andrés Samek, Wojciech Schneider, Johannes Speith, Timo Stumpf, Simone The Artificial Intelligence and Cognitive Load Research Lab Technological University Dublin Ireland University of Zagreb Faculty of Electrical Engineering and Computing Croatia University of Milano-Bicocca Milan Italy IRCCS Ospedale Galeazzi Sant’Ambrogio Milan Italy Kim Jaechul Graduate School of AI Korea Advanced Institute of Science & Technology Korea Republic of INEEJI Corporation Korea Republic of Department of Mathematics University of Padua Italy Derio Spain Bilbao Spain University of Pisa Pisa Italy Department of Computer Science Meiji University Tokyo Japan Department of Computer Science and Artificial Intelligence DaSCI Andalusian Institute in Data Science & Computational Intelligence University of Granada Granada Spain Human-Centered AI Lab University of Natural Resources and Life Sciences Vienna Austria School of Computing and Communications Lancaster University United Kingdom The University of Queensland Brisbane Australia Sophia Antipolis France eLaw Center for Law and Digital Technologies Leiden University Netherlands Department of Philosophy Universidad de los Andes Bogotá Colombia Center for Research & Formation in Artificial Intelligence Universidad de los Andes Bogotá Colombia Technical University of Berlin Berlin Germany Fraunhofer Heinrich Hertz Institute Berlin Germany Berlin Germany Department of Information Systems and Computer Science University of Liechtenstein Liechtenstein Liechtenstein Department of Philosophy University of Bayreuth Bayreuth Germany Center for Perspicuous Computing Saarland University Saarbrücken Germany School of Computing Science University of Glasgow United Kingdom

As systems based on opaque Artificial Intelligence (AI) continue to flourish in diverse real-world applications, understanding these black box models has become paramount. In response, Explainable AI (XAI) has emerged as a field of research with practical and ethical benefits across various domains. This paper not only highlights the advancements in XAI and its application in real-world scenarios but also addresses the ongoing challenges within XAI, emphasizing the need for broader perspectives and collaborative efforts. We bring together experts from diverse fields to identify open problems, striving to synchronize research agendas and accelerate XAI in practical applications. By fostering collaborative discussion and interdisciplinary cooperation, we aim to propel XAI forward, contributing to its continued success. Our goal is to put forward a comprehensive proposal for advancing XAI. To achieve this goal, we present a manifesto of 27 open problems categorized into nine categories. These challenges encapsulate the complexities and nuances of XAI and offer a road map for future research. For each problem, we provide promising research directions in the hope of harnessing the collective intelligence of interested stakeholders. © 2023, CC BY-SA.

关键词： Ethical technology

来源：评论

学校读者我要写书评

暂无评论

Time- and memory-efficient representation of complex mesoscale potentials

引用

JOURNAL OF computational PHYSICS 2017年 343卷 110-114页

作者： Drozdov, Grigory Ostanin, Igor Oseledets, Ivan Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow Russia

We apply the modern technique of approximation of multivariate functions - tensor train cross approximation - to the problem of the description of physical interactions between complex-shaped bodies in a context of computational nanomechanics. In this note we showcase one particular example - van der Waals interactions between two cylindrical bodies - relevant to modeling of carbon nanotube systems. The potential is viewed as a tensor ( multidimensional table) which is represented in compact form with the help of tensor train decomposition. The described approach offers a universal solution for the description of van der Waals interactions between complex-shaped nanostructures and can be used within the framework of such systems of mesoscale modeling as recently emerged mesoscopic distinct element method (MDEM). (C) 2017 Elsevier Inc. All rights reserved.

关键词： Mesoscale modeling Tensor train cross approximation

来源：评论

学校读者我要写书评

暂无评论

The HuaBiao project:whole-exome sequencing of 5000 Han Chinese individuals

引用

Journal of Genetics and Genomics 2021年第11期48卷 1032-1035页

作者： Meng Hao Weilin Pu Yi Li Shaoqing Wen Chang Sun Yanyun Ma Hongxiang Zheng Xingdong Chen Jingze Tan Guoqing Zhang Menghan Zhang Shuhua Xu Yi Wang Hui Li Jiucun Wang Li Jin State Key Laboratory of Genetic Engineering Collaborative Innovation Center for Genetics and DevelopmentHuman Phenome InstituteFudan UniversityShanghai 200433China State Key Laboratory of Genetic Engineering Collaborative Innovation Center for Genetics and DevelopmentHuman Phenome InstituteInstitute for Six-sector EconomyFudan UniversityShanghai 200433China Ministry of Education Key Laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesInstitute of Archaeological ScienceFudan UniversityShanghai 200433China Ministry of Education Key Laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesFudan UniversityShanghai 200433China Ministry of Education Key Laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesInstitute for Six-sector EconomyFudan UniversityShanghai 200433China Taizhou Institute of Health and Sciences Fudan UniversityTaizhouJiangsu 225300China Key Laboratory of Computational Biology Bio-Med Big Data CenterShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Ministry of Education Key Laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesHuman Phenome InstituteFudan UniversityShanghai 200433China

Next-generation sequencing technologies have significantly accelerated the identification of disease-causing mutations and facilitated the emergence of personalized medicine(Genomes Project Consortium et al.,2015;Goodwin et al.,2016;Sirugo et al.,2019).In comparison with whole-genome sequencing,whole-exome sequencing(WES),which covers the coding regions of the genome,offers a cost-efficacy *** provides deeper sequencing depth(>100)and allows the more accurate detection of rare variants that are tailored for clinical applications(Lek et al.,2016).

关键词： exo cost rare

来源：评论

学校读者我要写书评

暂无评论

JARVIS-Leaderboard: A Large Scale Benchmark of Materials Design Methods

arXiv

引用

arXiv 2023年

作者： Choudhary, Kamal Wines, Daniel Garrity, Kevin F. Williams, Maureen Tavazza, Francesca Li, Kangming Hattrick-Simpers, Jason Gupta, Vishu Romero, Aldo H. Krogel, Jaron T. Saritas, Kayahan Fuhr, Addis Ganesh, Panchapakesan Kent, Paul R.C. Yan, Keqiang Lin, Yuchao Ji, Shuiwang Blaiszik, Ben Reiser, Patrick Friederich, Pascal Agrawal, Ankit Tiwary, Pratyush Beyerle, Eric Minch, Peter Rhone, Trevor David Takeuchi, Ichiro Wexler, Robert B. Mannodi-Kanakkithodi, Arun Ertekin, Elif Mishra, Avanish Mathew, Nithin Wood, Mitchell Rohskopf, Andrew Dale Wang, Shih-Han Achenie, Luke E.K. Xin, Hongliang Biacchi, Adam J. Material Measurement Laboratory National Institute of Standards and Technology MD20899 United States Department of Materials Science and Engineering University of Toronto 27 King’s College Cir TorontoON Canada Department of Electrical and Computer Engineering Northwestern University EvanstonIL60208 United States Lewis-Sigler Institute for Integrative Genomics Princeton University PrincetonNJ08544 United States Ludwig Institute for Cancer Research Princeton University PrincetonNJ08544 United States Department of Physics and Astronomy West Virginia University MorgantownWV26506 United States Materials Science and Technology Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Center for Nanophase Materials Science Oak Ridge National Laboratory Oak RidgeTN37831 United States Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Department of Computer Science and Engineering Texas A&M University College StationTX77843 United States Globus University of Chicago IL60637 United States Data Science Learning Division National Lab ArgonneIL60439 United States Institute of Nanotechnology Karlsruhe Institute of Technology Kaiserstraße 12 Karlsruhe76131 Germany Institute of Theoretical Informatics Karlsruhe Institute of Technology Kaiserstraße 12 Karlsruhe76131 Germany Department of Chemistry and Biochemistry Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States Department of Physics Applied Physics and Astronomy Rensselaer Polytechnic Institute TroyNY12180 United States Department of Materials Science and Engineering University of Maryland College ParkMD20742 United States Department of Chemistry Institute of Materials Science and Engineering Washington University in St. Louis St. LouisMO63130 United States School of Materials Engineering Purdue University West LafayetteIN47907 United States Department of Mechan

Lack of rigorous reproducibility and validation are significant hurdles for scientific development across many fields. Materials science, in particular, encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data-points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://***/jarvis_leaderboard/ © 2023, CC BY.

关键词： Electronic structure

来源：评论

学校读者我要写书评

暂无评论

Prediction of oral food challenge outcomes via ensemble learning

引用

Informatics in Medicine Unlocked 2023年 36卷

作者： Zhang, Justin Lee, Deborah Jungles, Kylie Shaltis, Diane Najarian, Kayvan Ravikumar, Rajan Sanders, Georgiana Gryak, Jonathan Department of Electrical and Computer Engineering University of Michigan Ann Arbor MI United States Department of Internal Medicine University of Michigan Ann Arbor MI United States Department of Pediatrics University of Michigan Ann Arbor MI United States Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI United States Michigan Institute for Data Science University of Michigan Ann Arbor MI United States Department of Emergency Medicine University of Michigan Ann Arbor MI United States Department of Computer Science and Engineering University of Michigan Ann Arbor MI United States Max Harry Weil Institute for Critical Care Research and Innovation University of Michigan Ann Arbor MI United States Mary H. Weiser Food Allergy Center University of Michigan Ann Arbor MI United States Department of Computer Science Queens College City University of New York New York NY United States

Oral Food Challenges (OFCs) are essential to accurately diagnosing food allergy due to the limitations of existing clinical testing. However, some patients are hesitant to undergo OFCs, while those willing suffer from limited access to allergists in rural/community healthcare settings. Despite its success in predicting patient outcomes in other clinical settings, few applications of machine learning to food allergy have been developed. Thus, in this study, we seek to leverage machine learning methodologies for OFC outcome prediction. Retrospective data was gathered from 1,112 patients who collectively underwent a total of 1,284 OFCs, and consisted of clinical factors including serum-specific Immunoglobulin E (IgE), total IgE, skin prick tests (SPTs), comorbidities, sex, and age. Using these features, multiple machine learning models were constructed to predict OFC outcomes for three common allergens: peanut, egg, and milk. The best performing model for each allergen was an ensemble of random forest (egg) or Learning Using Concave and Convex Kernels (LUCCK) (peanut, milk) models, which achieved an Area under the Curve (AUC) of 0.91, 0.96, and 0.94, in predicting OFC outcomes for peanut, egg, and milk, respectively. Moreover, all such models had sensitivity and specificity values ≥89%. Model interpretation via SHapley Additive exPlanations (SHAP) indicates that specific IgE, along with wheal and flare values from SPTs, are highly predictive of OFC outcomes. The results of this analysis suggest that ensemble learning has the potential to predict OFC outcomes and reveal relevant clinical factors for further study. © 2022 The Author(s)

关键词： Ensemble learning Learning Using Concave and Convex Kernels Machine learning Oral food challenges SHAP

来源：评论

学校读者我要写书评

暂无评论

Generating Synthetic Computed Tomography for Radiotherapy: SynthRAD2023 Challenge Report

arXiv

引用

arXiv 2024年

作者： Huijben, Evi M.C. Terpstra, Maarten L. Galapon, Arthur Pai, Suraj Thummerer, Adrian Koopmans, Peter Afonso, Manya van Eijnatten, Maureen Gurney-Champion, Oliver Chen, Zeli Zhang, Yiwen Zheng, Kaiyi Li, Chuanpu Pang, Haowen Ye, Chuyang Wang, Runqi Song, Tao Fan, Fuxin Qiu, Jingna Huang, Yixing Ha, Juhyung Park, Jong Sung Alain-Beaudoin, Alexandra Bériault, Silvain Yu, Pengxin Guo, Hongbin Huang, Zhanyao Li, Gengwan Zhang, Xueru Fan, Yubo Liu, Han Xin, Bowen Nicolson, Aaron Zhong, Lujia Deng, Zhiwei Müller-Franzes, Gustav Khader, Firas Li, Xia Zhang, Ye Hémon, Cédric Boussot, Valentin Zhang, Zhihao Wang, Long Bai, Lu Wang, Shaobin Mus, Derk Kooiman, Bram Sargeant, Chelsea A.H. Henderson, Edward G.A. Kondo, Satoshi Kasai, Satoshi Karimzadeh, Reza Ibragimov, Bulat Helfer, Thomas Dafflon, Jessica Chen, Zijie Wang, Enpei Perko, Zoltan Maspero, Matteo Department of Biomedical Engineering Eindhoven University of Technology Eindhoven Netherlands Radiotherapy Department University Medical Center Utrecht Utrecht Netherlands Computational Imaging Group for MR Diagnostics & Therapy University Medical Center Utrecht Utrecht Netherlands Department of Radiation Oncology University Medical Center Groningen University of Groningen Groningen Netherlands GROW School for Oncology Maastricht University Medical Centre Maastricht Netherlands Department of Radiation Oncology LMU University Hospital LMU Munich Munich Germany Department of Radiation Oncology Radboud University Medical Center Nijmegen Netherlands Wageningen University & Research Wageningen Plant Research Wageningen Netherlands Department of Radiology and Nuclear Medicine Amsterdam UMC Location University of Amsterdam Amsterdam Netherlands Cancer Center Amsterdam Imaging and Biomarkers Amsterdam Netherlands School of Biomedical Engineering Southern Medical University Guangzhou China School of Integrated Circuits and Electronics Beijing Institute of Technology Beijing China School of Biomedical Engineering ShanghaiTech University Shanghai China Fudan University Shanghai China Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Germany Indiana University Bloomington United States Advanced Development Engineering Elekta Ltd Montreal Canada Infervision Medical Technology Co. Ltd. Beijing China Department of Biomedical Engineering Shantou University China Independent researchers Department of Computer Science Vanderbilt University Nashville United States Australian e-Health Research Centre CSIRO HerstonQLD Australia Los AngelesCA United States University Hospital Aachen Aachen Germany Center for Proton Therapy Paul Scherrer Institut Villigen Switzerland Department of Computer Science ETH Zurich Zurich Switzerland University Rennes 1 CLCC Eugène Marquis INSERM LTSI Rennes France Subtle Medical Shanghai China MedMind Technology Co.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information, while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (≥ 0.87/0.90) and gamma pass rates for photon (≥ 98.1%/99.0%) and proton (≥ 97.3%/97.0%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy. It showcased the growing capacity of deep learning to produce high-quality sCT, reducing reliance on conventional CT for treatment planning. © 2024, CC

关键词： Radiotherapy

来源：评论

学校读者我要写书评

暂无评论

Genome assembly and transcriptome analysis provide insights into the antischistosome mechanism of Microtus fortis

引用

Journal of Genetics and Genomics 2020年第12期47卷 743-755页

作者： Hong Li Zhen Wang Shumei Chai Xiong Bai Guohui Ding Yuanyuan Li Junyi Li Qingyu Xiao Benpeng Miao Weili Lin Jie Feng Mingyue Huang Cheng Gao Bin Li Wei Hu Jiaojiao Lin Zhiqiang Fu Jianyun Xie Yixue Li Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Animal ParasitologyMinistry of AgricultureShanghai 200241China Shanghai Laboratory Animal Research Center Shanghai 201203China Institute for Digital Health International Human Phenome Institutes(Shanghai)Shanghai 200433China Shanghai Center for Bioinformation Technology Shanghai Academy of Science and TechnologyShanghai 201203China School of Computer Science and Technology Harbin Institute of Technology(Shenzhen)ShenzhenGuangdong 518055China Shanghai Institute of Immunology Department of Immunology and MicrobiologyShanghai JiaoTong University School of MedicineShanghai 200025China State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Contemporary AnthropologyCollaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200438China Hangzhou Institute for Advanced Study University of Chinese Academy of SciencesHangzhouZhejiang 330106China

Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum ***,the underlying molecular mechanisms of this resistance are not yet ***,we perform the first de novo genome assembly of ***,comprehensive gene annotation analysis,and evolution ***,we compare the recovery rate of schistosomes,pathological changes,and liver transcriptomes between *** and mice at different time points after *** observe that the time and type of immune response in *** are different from those in *** activates immune and inflammatory responses on the 10th day post infection,such as leukocyte extravasation,antibody activation,Fc-gamma receptor-mediated phagocytosis,and the interferon signaling cascade,which play important roles in preventing the development of *** contrast,an intense immune response occurrs in mice at the late stages of infection and could not eliminate *** mice suffer severe pathological injury and continuous decreases in cell cycle,lipid metabolism,and other *** findings offer new insights into the intrinsic resistance mechanism of *** against schistosome *** genome sequence also provides the basis for future studies of other important traits in ***.

关键词： Genome assembly Microtus fortis Schistosome Immune Transcriptome

来源：评论

学校读者我要写书评

暂无评论

Translation dysregulation in cancer as a source for targetable antigens

引用

Cancer Cell 2025年第5期43卷 823-840.e18,20页

作者： Weller, Chen Bartok, Osnat McGinnis, Christopher S. Palashati, Heyilimu Chang, Tian-Gen Malko, Dmitry Shmueli, Merav D. Nagao, Asuteka Hayoun, Deborah Murayama, Ayaka Sakaguchi, Yuriko Poulis, Panagiotis Khatib, Aseel Erlanger Avigdor, Bracha Gordon, Sagi Cohen Shvefel, Sapir Zemanek, Marie J. Nielsen, Morten M. Boura-Halfon, Sigalit Sagie, Shira Gumpert, Nofar Yang, Weiwen Alexeev, Dmitry Kyriakidou, Pelgia Yao, Winnie Zerbib, Mirie Greenberg, Polina Benedek, Gil Litchfield, Kevin Petrovich-Kopitman, Ekaterina Nagler, Adi Oren, Roni Ben-Dor, Shifra Levin, Yishai Pilpel, Yitzhak Rodnina, Marina Cox, Jürgen Merbl, Yifat Satpathy, Ansuman T. Carmi, Yaron Erhard, Florian Suzuki, Tsutomu Buskirk, Allen R. Olweus, Johanna Ruppin, Eytan Schlosser, Andreas Samuels, Yardena Department of Molecular Cell Biology Weizmann Institute of Science Rehovot 7610001 Israel Department of Pathology Stanford University Stanford 94305 CA United States Parker Institute for Cancer Immunotherapy San Francisco 94129 CA United States Department of Cancer Immunology Institute for Cancer Research Oslo University Hospital Oslo 0379 Norway Precision Immunotherapy Alliance University of Oslo Oslo Norway Cancer Data Science Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda 20892 MD United States Department of Systems Immunology Weizmann Institute of Science Rehovot 7610001 Israel Department of Chemistry and Biotechnology of Engineering The University of Tokyo Tokyo 113-8656 Japan Department of Physical Biochemistry Max Planck Institute for Multidisciplinary Sciences Göttingen 37077 Germany Department of Pathology Sackler School of Medicine Tel Aviv University Tel Aviv 69978 Israel Department of Immunology and Regenerative Biology Weizmann Institute of Science Rehovot 7610001 Israel Computational Systems Biochemistry Research Group Max-Planck Institute of Biochemistry Martinsried 82152 Germany Department of Veterinary Resources Weizmann Institute of Science Rehovot 7610001 Israel Tissue Typing and Immunogenetics Unit Hadassah Hebrew University Hospital Jerusalem 9112102 Israel CRUK Lung Cancer Centre of Excellence University College London Cancer Institute London WC1E 6DD United Kingdom Tumour Immunogenomics and Immunosurveillance Laboratory University College London Cancer Institute London WC1E 6DD United Kingdom Department of Life Science Core Facilities Weizmann Institute of Science Rehovot 7610001 Israel Bioinformatics Unit Department of Life Sciences Core Facilities Weizmann Institute of Science Rehovot 7610001 Israel de Botton Institute for Protein Profiling the Nancy and Stephen Grand Israel National Center for Personalized Medicine Weizmann Institute of Science Rehovot

Aberrant peptides presented by major histocompatibility complex (MHC) molecules are targets for tumor eradication, as these peptides can be recognized as foreign by T cells. Protein synthesis in malignant cells is dysregulated, which may result in the generation and presentation of aberrant peptides that can be exploited for T cell-based therapies. To investigate the role of translational dysregulation in immunological tumor control, we disrupt translation fidelity by deleting tRNA wybutosine (yW)-synthesizing protein 2 (TYW2) in tumor cells and characterize the downstream impact on translation fidelity and immunogenicity using immunopeptidomics, genomics, and functional assays. These analyses reveal that TYW2 knockout (KO) cells generate immunogenic out-of-frame peptides. Furthermore, Tyw2 loss increases tumor immunogenicity and leads to anti-programmed cell death 1 (PD-1) checkpoint blockade sensitivity in vivo. Importantly, reduced TYW2 expression is associated with increased response to checkpoint blockade in patients. Together, we demonstrate that defects in translation fidelity drive tumor immunogenicity and may be leveraged for cancer immunotherapy. © 2025 The Author(s)

关键词： cancer immunopeptidome immune checkpoint blockade neoantigens non-canonical peptides translation fidelity

来源：评论

学校读者我要写书评

暂无评论

Integrating spatially-resolved transcriptomics data across tissues and individuals: challenges and opportunities

arXiv

引用

arXiv 2024年

作者： Guo, Boyi Ling, Wodan Kwon, Sang Ho Panwar, Pratibha Ghazanfar, Shila Martinowich, Keri Hicks, Stephanie C. Department of Biostatistics Johns Hopkins Bloomberg School of Public Health BaltimoreMD United States Division of Biostatistics Department of Population Health Sciences Weill Cornell Medicine NY United States Lieber Institute for Brain Development Johns Hopkins Medical Campus BaltimoreMD United States Solomon H. Snyder Department of Neuroscience Johns Hopkins School of Medicine BaltimoreMD United States Biochemistry Cellular and Molecular Biology Graduate Program Johns Hopkins School of Medicine BaltimoreMD United States School of Mathematics and Statistics The University of Sydney NSW2006 Australia Sydney Precision Data Science Centre University of Sydney NSW2006 Australia Charles Perkins Centre The University of Sydney NSW2006 Australia Department of Psychiatry and Behavioral Sciences Johns Hopkins School of Medicine BaltimoreMD United States Johns Hopkins Kavli Neuroscience Discovery Institute BaltimoreMD United States Department of Biomedical Engineering Johns Hopkins University BaltimoreMD United States Center for Computational Biology Johns Hopkins University BaltimoreMD United States Malone Center for Engineering in Healthcare Johns Hopkins University BaltimoreMD United States

Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide an exciting opportunity to create large-scale atlases that integrate SRT data across multiple tissues, individuals, species, or phenotypes to perform population-level analyses. Here, we describe unique challenges of varying spatial resolutions in SRT data, as well as highlight the opportunities for standardized preprocessing methods along with computational algorithms amenable to atlas-scale datasets leading to improved sensitivity and reproducibility in the future. © 2024, CC BY-NC-ND.

关键词： Biotic

来源：评论

学校读者我要写书评

暂无评论

Correlation analysis of strongly fluctuating atomic volumes, charges, and stresses in body-centered cubic refractory high-entropy alloys

引用

Physical Review Materials 2020年第2期4卷 023608-023608页

作者： Shoji Ishibashi Yuji Ikeda Fritz Körmann Blazej Grabowski Jörg Neugebauer Computational Materials Design Max-Planck-Institut für Eisenforschung GmbH D-40237 Düsseldorf Germany Research Center for Computational Design of Advanced Functional Materials (CD-FMat) National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki 305-8568 Japan Center for Materials Research by Information Integration (CMI2) Research and Services Division of Materials Data and Integrated System (MaDIS) National Institute for Materials Science (NIMS) Tsukuba Ibaraki 305-0047 Japan Institute of Materials Science University of Stuttgart Pfaffenwaldring 55 D-70569 Stuttgart Germany Materials Science and Engineering Delft University of Technology 2628 CD Delft The Netherlands

Local lattice distortions in a series of body-centered cubic alloys, including refractory high-entropy alloys, are investigated by means of atomic volumes, atomic charges, and atomic stresses defined by the Bader charge analysis based on first-principles calculations. Analyzing the extensive data sets, we find large distributions of these atomic properties for each element in each alloy, indicating a large impact of the varying local chemical environments. We show that these local-environment effects can be well understood and captured already by the first and the second nearest neighbor shells. Based on this insight, we employ linear regression models up to the second nearest neighbor shell to accurately predict these atomic properties. Finally, we find that the elementwise-averaged values of the atomic properties correlate linearly with the averaged valence-electron concentration of the considered alloys.

关键词： Body-centered cubic Disordered alloys Density functional theory First-principles calculations

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：