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MorPhiC Consortium: towards functional characterization of all human genes

Nature 2025年第8050期638卷 351-359页

作者： Adli, Mazhar Przybyla, Laralynne Burdett, Tony Burridge, Paul W. Cacheiro, Pilar Chang, Howard Y. Engreitz, Jesse M. Gilbert, Luke A. Greenleaf, William J. Hsu, Li Huangfu, Danwei Hung, Ling-Hong Kundaje, Anshul Li, Shuzhao Parkinson, Helen Qiu, Xiaojie Robson, Paul Schürer, Stephan C. Shojaie, Ali Skarnes, William C. Smedley, Damian Studer, Lorenz Sun, Wei Vidović, Dušica Vierbuchen, Thomas White, Brian S. Yeung, Ka Yee Yue, Feng Zhou, Ting Žurauskienė, Justina Zhong, Aaron Zheng, Shujian Zhao, Hengqiang Zhang, Nan Zhang, Zhehao Zhang, Stephen Zeng, Tony Yu, Bo Yordanova, Galabina N. Yang, Dapeng Xing, De Wang, Xianming Wang, Ping Torre, Denis Tang, Wenzhuo Shivalikanjli, Anu Sengupta, Kaustav Seker, Fidan Ventura, Enrique Sapena Ross, Nicolette C. Rivera-Diaz, Jamilex Rana, Arushi Pongpamorn, Praeploy Poirion, Olivier B. Pillai, Ajay Pilarczyk, Marcin Parker, Devon Ning, Gang Neyisci, Ozlem Nasam, Niharika Mittal, Varun Mitchell, Joshua M. Metzl-Raz, Eyal Meng, Chen Melo-Carrillo, Adrian McDonough, Justin A. Marengo, Gabriel Mao, Yuzhen Leite, Davi Lyra Luo, Renhe Liu, Nianping Liu, Dingyu Liu, Zukai Liu, Si Li, Zhaoheng Kraft, Katerina Koci, Orges A. Kirsammer, Gina Kendra, Angelina Hutter, Carolyn Huebner, Aaron J. Huang, Yung-Hsin Hu, Nan Gupta, Dipayan Gupta, Revant Guo, Tingfeng Griffiths, Alexandra M. Goyal, Juhee Glenn, Rachel A. Garofalo, Jessica L. Fukuda, Bryce Nobutoshi Fu, Yihao Flynn, William F. Flores, Jesse Fletcher, Colin F. Fleming, Patrick J. Felsenfeld, Adam L. Eraslan, Basak Doty, Anthony Dahlstrom, Thomas J. Chung, Caty E. Choudhary, Anshul Cho, Hyein S. Chen, Xintong Chen, Sijie Chan, Chia Baroch, Jacob J. Baker, Dylan S. Bai, Tao Avireddy, Rohan N. V. S. R. K. Amiri, Anahita Diniz, Juliana Alcoforado Abbaszadeh, Neda Robert H. Lurie Comprehensive Cancer Center Department of Obstetrics and Gynecology Northwestern University Feinberg School of Medicine Chicago IL United States Department of Biochemistry and Biophysics University of California San Francisco CA United States Omics Section European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Hinxton United Kingdom Department of Pharmacology Center for Pharmacogenomics Northwestern University Feinberg School of Medicine Evanston IL United States William Harvey Research Institute Clinical Pharmacology and Precision Medicine Queen Mary University of London London United Kingdom Department of Dermatology Stanford University Stanford CA United States Department of Genetics Stanford University Stanford CA United States Basic Science and Engineering (BASE) Initiative Stanford University Stanford CA United States Department of Urology University of California San Francisco CA United States Department of Biostatistics Public Health Sciences Fred Hutchinson Cancer Center Seattle WA United States Developmental Biology Program Sloan Kettering Institute New York NY USA School of Engineering and Technology University of Washington Tacoma Tacoma WA United States Departments of Genetics and Computer Science Stanford University Stanford CA United States Jackson Laboratory for Genomic Medicine Farmington CT United States Knowledge Management Section European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Hinxton United Kingdom Molecular and Cellular Pharmacology Sylvester Comprehensive Cancer Center University of Miami Coral Gables FL USA Department of Biostatistics University of Washington Seattle WA United States Department of Biochemistry and Molecular Genetics Robert H. Lurie Comprehensive Cancer Center Northwestern University Feinberg School of Medicine Chicago IL United States

Recent advances in functional genomics and human cellular models have substantially enhanced our understanding of the structure and regulation of the human genome. However, our grasp of the molecular functions of human genes remains incomplete and biased towards specific gene classes. The Molecular Phenotypes of Null Alleles in Cells (MorPhiC) Consortium aims to address this gap by creating a comprehensive catalogue of the molecular and cellular phenotypes associated with null alleles of all human genes using in vitro multicellular systems. In this Perspective, we present the strategic vision of the MorPhiC Consortium and discuss various strategies for generating null alleles, as well as the challenges involved. We describe the cellular models and scalable phenotypic readouts that will be used in the consortium's initial phase, focusing on 1,000 protein-coding genes. The resulting molecular and cellular data will be compiled into a catalogue of null-allele phenotypes. The methodologies developed in this phase will establish best practices for extending these approaches to all human protein-coding genes. The resources generated-including engineered cell lines, plasmids, phenotypic data, genomic information and computational tools-will be made available to the broader research community to facilitate deeper insights into human gene functions. © 2025. Springer Nature Limited.

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ESG Investing: A Statistically Valid Approach to Data-Driven Decision Making and the Impact of ESG Factors on Stock Returns and Risk

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IEEE Access 2024年 12卷 69434-69444页

作者： Teja, Kamurthi Ravi Liu, Chuan-Ming National Taipei University of Technology International Program of Electrical Engineering and Computer Science Taipei10608 Taiwan National Taipei University of Technology Department of Computer Science and Information Engineering Taipei10608 Taiwan

This study examines the impact of environmental, social, and governance (ESG) factors on economic investment from a statistical perspective, aiming to develop a tested investment strategy that capitalizes on the connection between ESG factors and financial performance. ESG investing: A statistically valid approach to data-driven decision-making (ESGI-SVADDM) investment strategy is based on a rigorous, statistically valid approach that utilizes data, math, statistics, and data science libraries to drive investment decisions, eliminating the need for personal opinions and subjectivity. The process includes establishing an investment thesis, formulating testable hypotheses (HPS), retrieving and refining relevant data, calculating relevant measures, and testing and validating all hypotheses. The study uses S&P 500 stock data and ESG data from Sustainalytics to test the hypotheses. The empirical tests conducted revealed a negative correlation between ESG risk and expected returns, as well as a positive trend in the relationship between ESG risk and the overall risk of stocks. Moreover, the study found that higher ESG risk scores are associated with lower returns for investors, and that adopting a strategy of investing in stocks with low ESG risk and shorting stocks with high ESG risk yields superior returns compared to the market portfolio. © 2013 IEEE.

关键词： Investments

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Trade Ease with Machine Learning and AWS

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IEEE Access 2023年 11卷 25893-25905页

Global trading is undergoing significant changes, necessitating modifications to the trading strategies. This study presents a newly developed cloud-based trading strategy that uses Amazon Web Services (AWS), machine learning (ML), and data science to automate trading tasks. The study begins by creating a machine learning trading strategy using a customized deep neural network (DNN). The strategy was then tested using a trading station before deployment on a cloud machine. The execution of the strategy resulted in a total profit of 42.74526 USD, with a test accuracy score of 87.45% and a training accuracy score of 89.15% over 6047 epochs. The roadmap provides a step-by-step overview of the entire process from strategy development to execution. In addition, this study offers insights into related issues and solutions that can enhance the effectiveness of trading strategies. Overall, this study contributes significantly to the field of cloud-based trading strategies and opens avenues for future research. © 2013 IEEE.

关键词： Deep neural networks

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Stability in the temporal dynamics of word meanings 40

Stability in the temporal dynamics of word meanings

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40th Annual Meeting of the cognitive science Society: Changing Minds, CogSci 2018

作者： Luo, Yiwei Xu, Yang Department of Linguistics Stanford University United States Department of Computer Science Cognitive Science Program University College University of Toronto Canada

ISBN: (纸本)9780991196784

Words show complex dynamics of meaning change. In some cases, a word may acquire novel senses. In other cases, existing senses of a word may become obsolete. The rates at which words gain and lose senses may vary, but it is an open question which factors might account for this variation. Building on work in computational linguistics and cognitive science, we develop a computational approach that explores this question by leveraging word sense records from a large historical database of English. Our results suggest that polysemous words tend to gain and lose senses more than words with fewer senses, and that these effects are robust when word frequency and length are both controlled for. These results are consistent with recent findings on the mechanisms of emergent word meanings and they further suggest stability in the temporal dynamics of word meanings. © 2018 Proceedings of the 40th Annual Meeting of the cognitive science Society, CogSci 2018. All rights reserved.

关键词： Dynamics

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Measurement of peripheral nerve magnetostimulation thresholds of a head solenoid coil between 200 Hz and 88.1 kHz

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IEEE Journal of Translational engineering in Health and Medicine 2025年

作者： Barksdale, Alex C. Ferris, Natalie G. Mattingly, Eli Sliwiak, Monika Guerin, Bastien Wald, Lawrence L. Davids, Mathias Klein, Valerie MIT Department of Electrical Engineering and Computer Science Cambridge MA United States Martinos Center for Biomedical Imaging Charlestown MA United States Harvard University Harvard Graduate Program in Biophysics Cambridge MA United States Harvard-MIT Division of Health Sciences and Technology Boston MA United States Harvard Medical School Boston MA United States

Objective: Magnetic fields switching at kilohertz frequencies induce electric fields in the body, which can cause peripheral nerve stimulation (PNS). Although magnetostimulation has been extensively studied below 10 kHz, the behavior of PNS at higher frequencies remains poorly understood. This study aims to investigate PNS thresholds at frequencies up to 88.1 kHz and to explore deviations from the widely accepted hyperbolic strength-duration curve (SDC). Methods and procedures: PNS thresholds were measured in the head of 8 human volunteers using a solenoidal coil at 16 distinct frequencies, ranging from 200 Hz to 88.1 kHz. A hyperbolic SDC was used as a reference to compare the frequency-dependent behavior of PNS thresholds. Results: Contrary to the predictions of the hyperbolic SDC, PNS thresholds did not decrease monotonically with frequency. Instead, thresholds reached a minimum near 25 kHz, after which they increased by an average of 39% from 25 kHz to 88.1 kHz across subjects. This pattern indicates a significant deviation from previously observed behavior at lower frequencies. Conclusion: Our results suggest that PNS thresholds exhibit a non-monotonic frequency dependence at higher frequencies, diverging from the traditional hyperbolic SDC. These findings offer critical data for refining neurodynamic models and provide insights for setting PNS safety limits in applications like MRI gradient coils and magnetic particle imaging (MPI). Further investigation is needed to understand the biological mechanisms driving these deviations beyond 25 kHz. Clinical impact: These findings call for further basic research into biological mechanisms underlying high frequency PNS threshold trends, and supports refinement of safety guidelines for MRI and MPI systems for clinical implementation. © 2013 IEEE.

关键词： high frequency magnetostimulation magnetic particle imaging (MPI) magnetic resonance imaging (MRI) MRI gradient safety peripheral nerve stimulation

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Survey of Online Exam Proctoring Model to Detect Cheating Behavior based on Face Recognition 8

Survey of Online Exam Proctoring Model to Detect Cheating Be...

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8th International Conference on Systems and Informatics, ICSAI 2022

作者： Rabiha, Sucianna Ghadati Kartowisastro, Iman Herwidiana Setiawan, Reina Budiharto, Widodo Bina Nusantara University Binus Graduate Program - Computer Science. Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Faculty of Engineering Computer Science Department Binus Graduate Program - Computer Science Computer Engineering Department Jakarta11480 Indonesia Bina Nusantara University School of Computer Science Computer Science Department Binus Graduate Program - Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665474481

Exams are an important component of any educational program, including online education. In any test, there is a possibility of cheating, so its detection and prevention is important. This study aims to conduct an in-depth study of the online exam monitoring model approach based on facial recognition used to detect cheating. Based on the inclusion and exclusion criteria designed, 13 selected studies were obtained. From these studies, we conducted further analysis regarding the Face Detection Method, Face Recognition Method, Initial Feature, Behavior Analysis and Evaluation Metrics used in each study so as to provide answers to research questions. the most frequently used Face detection method was Viola-Jones with a presentation of 20%, then CNN and MTCNN with a total presentation of 21%. The most widely used face recognition method in selected studies is CNN and metrics Accuracy is one of the most frequently used evaluations with a percentage of 33%. While the features that are usually used to detect cheating during online exams include facial motion and head pose which occupies the first position. The second is eye movement, then multiple faces gaze estimation and facial expression is in third place. Other features that also play a role in analyzing cheating behavior are mouth detection, facial vector, landmark location, gesture and posture. © 2022 IEEE.

关键词： Face recognition

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Relationship of IQ with Causal Connections Between Brain Salient Network Regions 31

Relationship of IQ with Causal Connections Between Brain Sal...

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31st National and 9th International Iranian Conference on Biomedical engineering, ICBME 2024

作者： Ghoorchian, Mina Soltanian-Zadeh, Hamid Pedram, Mir Mohsen Sadeghi, Mohsen Mir Mohammad Institute for Cognitive Science Studies Department of Cognitive Science Tehran Iran University of Tehran School of Electrical and Computer Engineering Tehran Iran Kharazmi University Department of Electrical and Computer Engineering Faculty of Engineering Tehran Iran

ISBN: (纸本)9798331529710

IQ is one of the indicators that has always been of interest to psychiatrists, doctors and cognitive science researchers. Since this index plays a key role in people's lives and also in the occurrence of brain abnormalities, many studies have been conducted on it. In this paper, we used the resting state magnetic resonance imaging data available in the HCP database to classify people into three groups with low, medium, and high IQ and applied machine learning methods on the matrix of causal connections between related network regions. We applied brain highlights. We calculated the matrix of causal relationships in this network by the spDCM algorithm and then obtained the differences of the three groups using the ANOVA statistical test and 6 edges out of 169 edges with p-value © 2024 IEEE.

关键词： Support vector regression

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Unobtrusive workstation farming without inconveniencing owners: Learning Backgammon with a genetic algorithm 1

Unobtrusive workstation farming without inconveniencing owne...

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1st IEEE computer Society International Workshop on Cluster Computing, IWCC 1999

作者： Darwen, P.J. Cognitive Science Research Group Department of Computer Science and Electrical Engineering University of Queensland Brisbane4072 Australia

ISBN: (纸本)0769503438

Most efforts at low-cost parallel computing assume a monopoly on the hardware being used. That all-or-nothing attitude ignores many machines dedicated to other activities, but which sit idle for 16 hours a day. However naive attempts to utilize idle machines can interfere with their primary purpose. This paper describes the successful effort to unobtrusively farm idle machines, for an artificial intelligence system using a genetic algorithm to learn the game Backgammon. It maintains owners' full access to their machines, without causing any detectable interference. © 1999 IEEE.

关键词： Genetic algorithms

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Advancements in AI-Assisted Plant Disease Diagnosis 4

Advancements in AI-Assisted Plant Disease Diagnosis

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4th IEEE International Conference on Computing, Communication, and Intelligent Systems, ICCCIS 2023

作者： Chhabra, Anmol Saroch, Tarun Gupta, Ruchika Shukla, Aditya Raghav Chandigarh University Centre of Excellence-Data Science and Cognitive Computing Computer Science & Engineering Department Mohali India

ISBN: (纸本)9798350306118

Plant disease detection is a crucial task in agriculture to ensure healthy crop production. It is vital to identify plant diseases early in order to avert economic and environmental damages. A Machine learning-based approach including Deep Learning techniques for identifying plant disease was developed using Grape leaf images in this work. Inception v3, Squeezenet, VGG-16, and VGG-19 are some embedders that are used in the suggested method to convert raw image data into a fixed-length vector representation, also known as a 'embedding' or 'feature vector.' Our research concludes that CNN stands out with exceptional accuracy above 99.70% compared to classifiers like Naive Bayes, Logistic Regression, and SVM. Additionally, Inception V3 proved to be an efficient feature extractor, enhancing feature representation and reducing processing time. © 2023 IEEE.

关键词： Embeddings

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Recent advances in tip-enhanced Raman spectroscopy probe designs

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Nano Research 2023年第4期16卷 5555-5571页

作者： Da Xu Boqun Liang Yaodong Xu Ming Liu Department of Electrical and Computer Engineering University of California-RiversideRiversideCalifornia 92521USA Materials Science and Engineering program University of California-RiversideRiversideCalifornia 92521USA

Tip-enhanced Raman spectroscopy(TERS)imaging is a super-resolution imaging technique that features the merits of both surface-enhanced Raman spectroscopy(SERS)and scanning probe microscopy(SPM),such as the high chemical sensitivity from the former and the nanoscale spatial resolution from the *** advantages make TERS an essential nanospectroscopic characterization technique for chemical analysis,materials science,bio-sensing,*** probes,the most critical factor determining the TERS imaging quality,are expected to provide a highly confined electromagnetic hotspot with a minimized scattering background for the generation of Raman signals with high spatial *** two decades of development,numerous probe design concepts have been proposed and *** review provides a comprehensive overview of the state-of-the-art TERS probe designs,from the working mechanism to the practical *** start with reviewing the recent development of TERS configurations and the corresponding working mechanisms,including the SPM platforms,optical excitation/collection techniques,and probe preparation *** then review the emerging novel TERS probe designs,including the remote-excitation probes,the waveguide-based nanofocusing probes,the metal-coated nanofocusing probes,the nanowire-assisted selective-coupling probes,and the tapered metal-insulator-metal *** discussion focuses on a few critical aspects,including the surface-plasmon-polariton(SPP)hotspot excitation technique,conversion efficiency,working frequency,and *** the end,we review the latest TERS applications and give a perspective on the future of TERS.

关键词： tip-enhanced Raman spectroscopy plasmonics scanning probe microscopy nanoscale imaging nanophotonics nanofocusing

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