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Author Correction: Predicting the efficiency of prime editing guide RNAs in human cells

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Nature biotechnology 2024年第3期42卷 529页

作者： Hui Kwon Kim Goosang Yu Jinman Park Seonwoo Min Sungtae Lee Sungroh Yoon Hyongbum Henry Kim Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Graduate School of Data Science Seoul National University Seoul Republic of Korea. Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac. Severance Biomedical Science Institute Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of NanoScience and Technology Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac.

Analysis of Negative Capacitance MOSFETs Characteristic with Spacer

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Analysis of Negative Capacitance MOSFETs Characteristic with...

International Symposium on VLSI Technology, Systems and Applications

作者： Yu-Chun Lee Sekhar Reddy Kola Chieh-Yang Chen Min-Hui Chuang Yiming Li Parallel and Scientific Computing Laboratory Institute of Biomedical Engineering EECS International Graduate Program Institute of Communications Engineering Department of Electrical and Computer Engineering National Chiao Tung University Hsinchu Taiwan Center for mmWave Smart Radar System and Technologies National Chiao Tung University 1001 Ta-Hsueh Rd Hsinchu Taiwan

ISBN: (数字)9781728142326

ISBN: (纸本)9781728142333

In this work, our study comprises of design and investigation on negative capacitance (NC), metal-oxide-semiconductor (MOS) field effects transistors (MOSFETs) with spacer and source/drain (S/D) overlap engineering. The scope of the work is to boost the performance and high-energy efficiency of the studied NC-MOSFETs by using the ferro electric material (FE). The NC-MOSFETs with the spacer technology can achieve the admirable I on /I off ratio and subthreshold swing (SS), compared with planar MOSFETs. It makes device scaling possible by eliminating the short channel effect (SCE). We further estimated the effect of FE thickness and spacer, which are another critical parameter of obtaining better electrical characteristics and reducing SS.

关键词： Capacitance Iron Semiconductor device modeling MOSFET Integrated circuit modeling Mathematical model Ferroelectric materials

The ACROBAT 2022 Challenge: Automatic Registration Of Breast Cancer Tissue

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arXiv 2023年

作者： Weitz, Philippe Valkonen, Masi Solorzano, Leslie Carr, Circe Kartasalo, Kimmo Boissin, Constance Koivukoski, Sonja Kuusela, Aino Rasic, Dusan Feng, Yanbo Pouplier, Sandra Sinius Sharma, Abhinav Eriksson, Kajsa Ledesma Robertson, Stephanie Marzahl, Christian Gatenbee, Chandler D. Anderson, Alexander R.A. Wodzinski, Marek Jurgas, Artur Marini, Niccolò Atzori, Manfredo Müller, Henning Budelmann, Daniel Weiss, Nick Heldmann, Stefan Lotz, Johannes Wolterink, Jelmer M. De Santi, Bruno Patil, Abhijeet Sethi, Amit Kondo, Satoshi Kasai, Satoshi Hirasawa, Kousuke Farrokh, Mahtab Kumar, Neeraj Greiner, Russell Latonen, Leena Laenkholm, Anne-Vibeke Hartman, Johan Ruusuvuori, Pekka Rantalainen, Mattias Department of Medical Epidemiology and Biostatistics Karolinska Insitutet Stockholm Sweden Institute of Biomedicine University of Turku Turku Finland Institute of Biomedicine University of Eastern Finland Kuopio Finland Department of Surgical Pathology Zealand University Hospital Roskilde Denmark Department of Oncology and Pathology Karolinska Institutet Stockholm Sweden Gestalt Diagnostics Spokane United States Department of Integrated Mathematical Oncology Moffitt Cancer Center Tampa United States Informatics Institute University of Applied Sciences Western Switzerland Switzerland Department of Measurement and Electronics Agh University of Kraków Poland Department of Computer Science University of Geneva Geneva Switzerland Department of Neuroscience University of Padova Italy Medical Faculty University of Geneva Switzerland Fraunhofer Institute for Digital Medicine Mevis Lübeck Germany Department of Applied Mathematics Technical Medical Centre University of Twente Enschede Netherlands Multimodality Medical Imaging Technical Medical Centre University of Twente Enschede Netherlands Department of Electrical Engineering Indian Institute of Technology Bombay India Graduate School of Engineering Muroran Institute of Technology Hokkaido Japan Faculty of Medical Technology Niigata University of Health and Welfare Niigata Japan Forxai Business Operations Konica Minolta Inc. Osaka Japan Department of Computing Science University of Alberta EdmontonAB Canada Alberta Machine Intelligence Institute Edmonton Canada MedTechLabs BioClinicum Karolinska University Hospital Stockholm Sweden Faculty of Medicine and Health Technology Tampere University Tampere Finland

The alignment of tissue between histopathological whole-slide-images (WSI) is crucial for research and clinical applications. Advances in computing, deep learning, and availability of large WSI datasets have revolutionised WSI analysis. Therefore, the current state-of-the-art in WSI registration is unclear. To address this, we conducted the ACROBAT challenge, based on the largest WSI registration dataset to date, including 4,212 WSIs from 1,152 breast cancer patients. The challenge objective was to align WSIs of tissue that was stained with routine diagnostic immunohistochemistry to its H&E-stained counterpart. We compare the performance of eight WSI registration algorithms, including an investigation of the impact of different WSI properties and clinical covariates. We find that conceptually distinct WSI registration methods can lead to highly accurate registration performances and identify covariates that impact performances across methods. These results establish the current state-of-the-art in WSI registration and guide researchers in selecting and developing methods. Copyright © 2023, The Authors. All rights reserved.

关键词： Tissue

Characterisation of state-preparation uncertainty in quantum key distribution

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arXiv 2022年

作者： Huang, Anqi Mizutani, Akihiro Lo, Hoi-Kwong Makarov, Vadim Tamaki, Kiyoshi Institute for Quantum Information State Key Laboratory of High Performance Computing College of Computer Science and Technology National University of Defense Technology Changsha410073 China Graduate School of Engineering Science Osaka University Toyonaka Osaka560-8531 Japan Department of Electrical & Computer Engineering Department of Physics University of Toronto TorontoONM5S 3G4 Canada Department of Physics University of Hong Kong Pokfulam Hong Kong Quantum Bridge Technologies Inc. 100 College Street TorontoONM5G 1L5 Canada Russian Quantum Center Skolkovo Moscow121205 Russia Shanghai Branch National Laboratory for Physical Sciences at Microscale and CAS Center for Excellence in Quantum Information University of Science and Technology of China Shanghai201315 China NTI Center for Quantum Communications National University of Science and Technology MISiS Moscow119049 Russia Faculty of Engineering University of Toyama Gofuku 3190 Toyama930-8555 Japan

To achieve secure quantum key distribution, all imperfections in the source unit must be incorporated in a security proof and measured in the lab. Here we perform a proof-of-principle demonstration of the experimental techniques for characterising the source phase and intensity fluctuation in commercial quantum key distribution systems. When we apply the measured phase fluctuation intervals to the security proof that takes into account fluctuations in the state preparation, it predicts a key distribution distance of over 100 km of fiber. The measured intensity fluctuation intervals are however so large that the proof predicts zero key, indicating a source improvement may be needed. Our characterisation methods pave the way for a future certification standard. Copyright © 2022, The Authors. All rights reserved.

关键词： Quantum cryptography

Molecular mechanics-driven graph neural network with multiplex graph for molecular structures

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arXiv 2020年

作者： Zhang, Shuo Liu, Yang Xie, Lei Ph.D. Program in Computer Science Graduate Center City University of New York United States Department of Computer Science Hunter College City University of New York United States Helen & Robert Appel Alzheimer’s Disease Research Institute Feil Family Brain & Mind Research Institute Weill Cornell Medicine Cornell University United States

The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge. These models improve their expressive power by incorporating auxiliary information in molecules while inevitably increase their computational complexity. In this work, we aim to design a GNN which is both powerful and efficient for molecule structures. To achieve such goal, we propose a molecular mechanics-driven approach by first representing each molecule as a two-layer multiplex graph, where one layer contains only local connections that mainly capture the covalent interactions and another layer contains global connections that can simulate non-covalent interactions. Then for each layer, a corresponding message passing module is proposed to balance the trade-off of expression power and computational complexity. Based on these two modules, we build Multiplex Molecular Graph Neural Network (MXMNet). When validated by the QM9 dataset for small molecules and PDBBind dataset for large protein-ligand complexes, MXMNet achieves superior results to the existing state-of-the-art models under restricted resources. Copyright © 2020, The Authors. All rights reserved.

关键词： Molecules

Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas

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arXiv 2021年

作者： Casamitjana Díaz, Adrià Lorenzi, Marco Ferraris, Sebastiano Peter, Loïc Modat, Marc Stevens, Allison Fischl, Bruce Vercauteren, Tom Iglesias, Juan Eugenio Center for Medical Image Computing University College London United Kingdom Université Côte dÁzur Inria Epione Team Sophia Antipolis06902 France School of Biomedical Engineering & Imaging Sciences King’s College London United Kingdom Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology United States Program in Health Sciences and Technology Massachusetts Institute of Technology United States

Joint registration of a stack of 2D histological sections to recover 3D structure ("3D histology reconstruction") finds application in areas such as atlas building and validation of in vivo imaging. Straightforward pairwise registration of neighbouring sections yields smooth reconstructions but has well-known problems such as "banana effect" (straightening of curved structures) and "z-shift" (drift). While these problems can be alleviated with an external, linearly aligned reference (e.g., Magnetic Resonance (MR) images), registration is often inaccurate due to contrast differences and the strong nonlinear distortion of the tissue, including artefacts such as folds and tears. In this paper, we present a probabilistic model of spatial deformation that yields reconstructions for multiple histological stains that that are jointly smooth, robust to outliers, and follow the reference shape. The model relies on a spanning tree of latent transforms connecting all the sections and slices of the reference volume, and assumes that the registration between any pair of images can be see as a noisy version of the composition of (possibly inverted) latent transforms connecting the two images. Bayesian inference is used to compute the most likely latent transforms given a set of pairwise registrations between image pairs within and across modalities. We consider two likelihood models: Gaussian (`2 norm, which can be minimised in closed form) and Laplacian (`1 norm, minimised with linear programming). Results on synthetic deformations on multiple MR modalities, show that our method can accurately and robustly register multiple contrasts even in the presence of outliers. The framework is used for accurate 3D reconstruction of two stains (Nissl and parvalbumin) from the Allen human brain atlas, showing its benefits on real data with severe distortions. Moreover, we also provide the registration of the reconstructed volume to MNI space, bridging the gaps between two of the most widely

关键词： Brain

THz Emission from Exchange-Coupled Fe/Ru/Ni Spintronic Emitters

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THz Emission from Exchange-Coupled Fe/Ru/Ni Spintronic Emitt...

International Conference on Infrared and Millimeter Waves

作者： R. Adam C. Greb D. E. Bürgler D. Cao S. Heidtfeld F. Wang J. Cheng D. Chakraborty I. Komissarov H. Hardtdegen M. Mikulics M. Büscher C. M. Schneider Roman Sobolewski Research Centre Jülich Peter Grünberg Institute (PGI-6) Jülich Germany Institut für Laser- und Plasmaphysik Heinrich Heine Universität Düsseldorf Düsseldorf Germany College of Physics Center for Marine Observation and Communications Qingdao University Qingdao China Materials Science Graduate Program University of Rochester Rochester New York USA Laboratory for Laser Energetics University of Rochester Rochester New York USA Department of Electrical and Computer Engineering University of Rochester Rochester New York USA Research Centre Jülich Ernst Ruska Centre for Microscopy and Spectroscopy with Electrons Jülich Germany Faculty of Physics University Duisburg-Essen Duisburg Germany Department of Physics University of California Davis Davis California USA

We explored THz emission from $\mathrm{Si}^{2} / \mathrm{SiO}_{2} / / \mathrm{Ta} / \mathrm{Fe} / \mathrm{Ru} /$ $\mathrm{Ni} / \mathrm{Al}_{2} \mathrm{O}_{3}$ spintronic emitters. We tuned magnetization alignment of Fe and Ni layers by varying the interlayer exchange coupling (IEC) strength using a range of Ru layer thickness t. Depending on IEC strength, magnetization hysteresis shows either ferromagnetic $(t=1.1 \mathrm{~nm}, 1.5 \mathrm{~nm})$, antiferromagnetic $(t=1.3 \mathrm{~nm})$ or canted $(t=1.7 \mathrm{~nm}, 1.9 \mathrm{~nm})$ relative alignment. Competition between IEC and an external magnetic field results in a dramatic difference in THz emission from the ferromagnetically (FM) and anti-ferromagnetically (AFM) coupled structures. The resulting THz emission from IEC structures is a result of an interference of THz transiens generated by the individual $\mathrm{Fe} / \mathrm{Ru}$ and $\mathrm{Ru} / \mathrm{Ni}$ emitters.

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The 2022 report of the Lancet Countdown on health and climate change: health at the mercy of fossil fuels (vol 400, pg 1619, 2022)

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LANCET 2022年第10365期400卷 1766-1766页

作者： Romanello, M. Di Napoli, C. Drummond, P. Institute for Global Health University College London London UK School of Agriculture Policy and Development University of Reading Reading UK Institute for Sustainable Resources University College London London UK Department of Global Health Centre for Health and the Global Environment University of Washington Seattle WA USA UCL Energy Institute University College London London UK Department of Health Sciences University of York York UK Department of Meteorology University of Reading Reading UK Institute for Risk and Disaster Reduction University College London London UK School of Earth and Environment University of Leeds Leeds UK Centre on Climate Change and Planetary Health London School of Hygiene & Tropical Medicine London UK School of Population Health University of Melbourne Melbourne VIC Australia Department of Earth System Science Tsinghua University Beijing China Mercator Research Institute on Global Commons and Climate Change Berlin Germany Department of Environment Climate Change and Health World Health Organization Geneva Switzerland Institute of Environmental Sciences University of Geneva Geneva Switzerland Cardiovascular Epidemiology Unit Department of Public Health & Primary Care University of Cambridge Cambridge UK School of Government University of Birmingham Birmingham UK Economic Analysis of Climate Impacts and Policy Division Centro Euro-Mediterraneo sui Cambiamenti Climatici Venice Italy Institute for Environmental Design and Engineering University College London London UK Natural Resources Institute University of Greenwich London UK Department of Environmental Health Sciences and Yale Center on Climate Change and Health Yale University New Haven CT USA Department of Civil and Environmental Engineering Northeastern University Boston MA USA Department of Fish and Wildlife Conservation Virginia Polytechnic Institute and State University Blacksburg VA USA Department of Geography University College London London UK NU

With advancements in the science of detection and attribution studies, the influence of climate change over many events has now been quantified. Because of the rapidly increasing temperatures, vulnerable populations (adults older than 65 years, and children younger than one year of age) were exposed to 3·7 billion more heatwave days in 2021 than annually in 1986–2005 (indicator 1.1.2), and heat-related deaths increased by 68% between 2000–04 and 2017–21 (indicator 1.1.5), a death toll that was significantly exacerbated by the confluence of the COVID-19 pandemic. Despite the local cooling and overall health benefits of urban greenspaces, only 277 (27%) of 1038 global urban centres were at least moderately green in 2021 (indicator 2.2.3), and the number of households with air conditioning increased by 66% from 2000 to 2020, a maladaptive response that worsens the energy crisis and further increases urban heat, air pollution, and greenhouse gas emissions. [...]millions of people do not have access to the energy needed to keep their homes at healthy temperatures, preserve food and medication, and meet the seventh Sustainable Development Goal (to ensure access to affordable, reliable, sustainable, and modern energy for all). Aggravating this situation even further, governments continue to incentivise fossil fuel production and consumption: 69 (80%) of 86 countries reviewed had net-negative carbon prices (ie, provided a net subsidy to fossil fuels) for a net total of US$400 billion

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SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining

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arXiv 2021年

作者： Billot, Benjamin Greve, Douglas N. Puonti, Oula Thielscher, Axel Van Leemput, Koen Fischl, Bruce Dalca, Adrian V. Iglesias, Juan Eugenio Centre for Medical Image Computing University College London United Kingdom Martinos Center for Biomedical Imaging Department of Radiology Massachusetts General Hospital Harvard Medical School United States Danish Research Centre for Magnetic Resonance Centre for Functional and Diagnostic Imaging and Research Copenhagen University Hospital Denmark Department of Health Technology Technical University of Denmark Denmark Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology United States Program in Health Sciences and Technology Massachusetts Institute of Technology United States

Despite advances in data augmentation and transfer learning, convolutional neural networks (CNNs) difficultly generalise to unseen domains. When segmenting brain scans, CNNs are highly sensitive to changes in resolution and contrast: even within the same MRI modality, performance can decrease across datasets. Here we introduce SynthSeg, the first segmentation CNN robust against changes in contrast and resolution. SynthSeg is trained with synthetic data sampled from a generative model conditioned on segmentations. Crucially, we adopt a domain randomisation strategy where we fully randomise the contrast and resolution of the synthetic training data. Consequently, SynthSeg can segment real scans from a wide range of target domains without retraining or fine-tuning, which enables straightforward analysis of huge amounts of heterogeneous clinical data. Because SynthSeg only requires segmentations to be trained (no images), it can learn from labels obtained by automated methods on diverse populations (e.g., ageing and diseased), thus achieving robustness to a wide range of morphological variability. We demonstrate SynthSeg on 5,000 scans of six modalities (including CT) and ten resolutions, where it exhibits unparalleled generalisation compared with supervised CNNs, state-of-the-art domain adaptation, and Bayesian segmentation. Finally, we demonstrate the generalisability of SynthSeg by applying it to cardiac MRI and CT scans. Copyright © 2021, The Authors. All rights reserved.

关键词： computerized tomography