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Research Square 2021年

作者： Xu, Sheng Lei, Yusheng Li, Yuheng Lu, Chengchangfeng Yan, Qizhang Gong, Huaxin Zhang, Song Zhou, Jiayun Zhang, Ruiqi Chen, Yimu Tsai, Hsinhan Gu, Yue Hu, Hongjie Lo, Yu-Hwa Nie, Wanyi Lee, Taeyoon Luo, Jian Yang, Kesong Jang, Kyung-In Department of Nanoengineering University of California San Diego La Jolla CA92093-0448 United States Department of Chemical Engineering Stanford University StanfordCA94305 United States Department of Electrical and Computer Engineering University of California San Diego La Jolla CA92093 United States Material Science and Engineering Program University of California San Diego La Jolla CA92093-0418 United States Los Alamos National Laboratory Los AlamosNM87545 United States School of Electrical and Electronic Engineering Yonsei University Seoul03722 Korea Republic of Department of Bio and Brain Engineering Korea Institute of Science and Technology Korea Republic of Department of Robotics Engineering Daegu Gyeongbuk Institute of Science and Technology Daegu42988 Korea Republic of Department of Bioengineering University of California San Diego La Jolla CA92093-0412 United States

Compared with their three-dimensional counterparts, low-dimensional metal halide perovskites with periodic inorganic/organic structures have shown promising stability and hysteresis-free electrical performance, which paves the way for next-generation optoelectronic devices. However, when integrated in devices, they have relatively limited efficiencies because devices usually require carrier transport through the film thickness direction. In conventionally grown single crystals, the carrier transport in the thickness direction is hindered by the insulating organic spacers. In addition, the strong quantum confinement from the organic spacers limits the generation and transport of free carriers. The carrier dynamics is further compromised by the presence of grain boundaries in polycrystals. Here, we report a low-dimensional metal halide perovskite superlattice with efficient carrier transport in three dimensions by epitaxial growth. Epitaxy on a slightly lattice-mismatched substrate compresses the organic spacers in the superlattice, which weakens the quantum confinement and further improves carrier dynamics. The performance of a low-dimensional perovskite superlattice solar cell has been certified under the quasi-steady state for the first time. Moreover, the device shows an unusually high open-circuit voltage, due to a unique intra-band exciton relaxation mechanism. © 2021, CC BY.

关键词： Grain boundaries

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Attenuation coefficient estimation for PET/MRI with Bayesian deep learning pseudo-CT and maximum likelihood estimation of activity and attenuation

arXiv

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arXiv 2020年

作者： Leynes, Andrew Palmera Ahn, Sangtae P. Wangerin, Kristen A. Kaushik, Sandeep S. Wiesinger, Florian Hope, Thomas A. Larson, Peder E.Z. The Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA94158 United States The UC Berkeley Joint Graduate Program in Bioengineering BerkeleyCA United States UC San Francisco Joint Graduate Program in Bioengineering San FranciscoCA United States GE Research NiskayunaNY United States GE Healthcare WaukeshaWI United States GE Healthcare Munich Germany The Department of Computer Science Technical University of Munich Munich Germany The Department of Radiology San Francisco VA Medical Center San FranciscoCA United States

A major remaining challenge for magnetic resonance-based attenuation correction methods (MRAC) is their susceptibility to sources of MRI artifacts (e.g. implants, motion) and uncertainties due to the limitations of MRI contrast (e.g. accurate bone delineation and density, and separation of air/bone). We propose using a Bayesian deep convolutional neural network that, in addition to generating an initial pseudo-CT from MR data, also produces uncertainty estimates of the pseudo-CT to quantify the limitations of the MR data. These outputs are combined with MLAA reconstruction that uses the PET emission data to improve the attenuation maps. With the proposed approach (UpCT-MLAA), we demonstrate accurate estimation of PET uptake in pelvic lesions and show recovery of metal implants. In patients without implants, UpCT-MLAA had acceptable but slightly higher RMSE than Zero-echo-time and Dixon Deep pseudo-CT when compared to CTAC. In patients with metal implants, MLAA recovered the metal implant;however, anatomy outside the implant region was obscured by noise and crosstalk artifacts. Attenuation coefficients from the pseudo-CT from Dixon MRI were accurate in normal anatomy;however, the metal implant region was estimated to have attenuation coefficients of air. UpCT-MLAA estimated attenuation coefficients of metal implants alongside accurate anatomic depiction outside of implant regions. © 2020, CC BY.

关键词： Magnetic resonance

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The neuroconnectionist research programme

arXiv

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arXiv 2022年

作者： Doerig, A. Sommers, R. Seeliger, K. Richards, B. Ismael, J. Lindsay, G. Kording, K. Konkle, T. van Gerven, M.A.J. Kriegeskorte, N. Kietzmann, T.C. Donders Institute for Brain Cognition & Behaviour Nijmegen Netherlands Institute of Cognitive Science University of Osnabrück Germany Max Planck Institute for Psycholinguistics Department of Neurobiology of Language Nijmegen Netherlands Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany Dept. of Neurology and Neurosurgery McGill University MontréalQC Canada School of Computer Science McGill University MontréalQC Canada Mila MontréalQC Canada Montréal Neurological Institute MontréalQC Canada Learning in Machines and Brains Program CIFAR TorontoON Canada Columbia University New York United States New York University New York United States Bioengineering Neuroscience University of Pennsylvania Pennsylvania PA United States Harvard University CambridgeMA United States Zuckerman Institute Columbia University New York United States

Artificial Neural Networks (ANNs) inspired by biology are beginning to be widely used to model behavioral and neural data, an approach we call neuroconnectionism. ANNs have been lauded as the current best models of information processing in the brain, but also criticized for failing to account for basic cognitive functions. We propose that arguing about the successes and failures of a restricted set of current ANNs is the wrong approach to assess the promise of neuroconnectionism. Instead, we take inspiration from the philosophy of science, and in particular from Lakatos, who showed that the core of scientific research programmes is often not directly falsifiable, but should be assessed by its capacity to generate novel insights. Following this view, we present neuroconnectionism as a cohesive large-scale research programme centered around ANNs as a computational language for expressing falsifiable theories about brain computation. We describe the core of the programme, the underlying computational framework and its tools for testing specific neuroscientific hypotheses. Taking a longitudinal view, we review past and present neuroconnectionist projects and their responses to challenges, and argue that the research programme is highly progressive, generating new and otherwise unreachable insights into the workings of the brain. © 2022, CC BY.

关键词： Neural networks

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Plasmonic bacteria on a nanoporous mirror via hydrodynamic trapping for rapid identification of waterborne pathogens

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Light(science & Applications) 2018年第1期7卷 359-367页

作者： Keumrai Whang Jong-Hwan Lee Yonghee Shin Wooju Lee Young Wan Kim Dongchoul Kim Luke P.Lee Taewook Kang Department of Chemical and Biomolecular Engineering Sogang UniversitySeoul 04107Korea Berkeley Sensor and Actuator Center Departments of BioengineeringElectrical Engineering and Computer ScienceBiophysics Graduate ProgramUniversity of CaliforniaBerkeleyBerkeleyCA 94720USA Department of Mechanical Engineering Sogang UniversitySeoul 04107Korea

A rapid,precise method for identifying waterborne pathogens is critically needed for effective disinfection and better ***,conventional methods,such as culture-based counting,generally suffer from slow detection times and low ***,we developed a rapid detection method for tracing waterborne pathogens by an innovative optofluidic platform,a plasmonic bacteria on a nanoporous mirror,that allows effective hydrodynamic cell trapping,enrichment of pathogens,and optical signal *** designed and simulated the integrated optofluidic platform to maximize the enrichment of the bacteria and to align bacteria on the nanopores and plasmonic mirror via hydrodynamic cell *** nanoparticles are self-assembled to form antenna arrays on the surface of bacteria,such as Escherichia coli and Pseudomonas aeruginosa,by replacing citrate with hydroxylamine hydrochloride in order to amplify the signal of the plasmonic optical *** to the synergistic contributions of focused light via the nanopore geometry,self-assembled nanoplasmonic optical antennas on the surface of bacteria,and plasmonic mirror,we obtain a sensitivity of detecting *** as low as 102 cells/ml via surface-enhanced Raman *** believe that our label-free strategy via an integrated optofluidic platform will pave the way for the rapid,precise identification of various pathogens.

关键词： mirror trapping precise

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

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Genome biology 2025年第1期26卷 31页

作者： Jacob Matthew Schreiber Carles A Boix Jin Wook Lee Hongyang Li Yuanfang Guan Chun-Chieh Chang Jen-Chien Chang Alex Hawkins-Hooker Bernhard Schölkopf Gabriele Schweikert Mateo Rojas Carulla Arif Canakoglu Francesco Guzzo Luca Nanni Marco Masseroli Mark James Carman Pietro Pinoli Chenyang Hong Kevin Y Yip Jefrey P Spence Sanjit Singh Batra Yun S Song Shaun Mahony Zheng Zhang Wuwei Tan Yang Shen Yuanfei Sun Minyi Shi Jessika Adrian Richard S Sandstrom Nina P Farrell Jessica M Halow Kristen Lee Lixia Jiang Xinqiong Yang Charles B Epstein J Seth Strattan Bradley E Bernstein Michael P Snyder Manolis Kellis William S Noble Anshul Bharat Kundaje Department of Genetics Stanford University Stanford CA USA. jmschreiber91@***. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA. Department of Genetics Stanford University Stanford CA USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. Department of Research and Development DeepSeq.AI San Francisco CA USA. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Department of Empirical Inference Max Planck Institute for Intelligent Systems Stuttgart Germany. School of Life Sciences University of Dundee Dundee UK. Department of Electronics Information and Bioengineering Politecnico Di Milano Milan Italy. Department of Computational Biology University of Lausanne Lausanne Switzerland. Department of Computer Science and Engineering The Chinese University of Hong Kong Sha Tin Hong Kong. Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA. Department of Electrical Engineering and Computer Sciences University of California Berkeley Berkeley CA USA. Department of Statistics University of California Berkeley Berkeley CA USA. Department of Biochemistry & Molecular Biology Center for Eukaryotic Gene Regulation Pennsylvania State University University Park PA USA. Department of Statistics Pennsylvania State University University Park PA USA. Department of Electrical and Computer Engineering Texas A&M University College Station TX USA. Altius Institute Seattle WA USA. Epigenomics Program The Broad Institute of MIT and Harvard Cambridge MA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Computer Science Stanford University Stanford CA USA.

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Author Correction: Generation of accurate, expandable phylogenomic trees with uDance

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Nature biotechnology 2024年第5期42卷 814页

作者： Metin Balaban Yueyu Jiang Qiyun Zhu Daniel McDonald Rob Knight Siavash Mirarab Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. Biodesign Center for Fundamental and Applied Microbiomics Arizona State University Tempe AZ USA. School of Life Sciences Arizona State University Tempe AZ USA. Department of Pediatrics University of California San Diego La Jolla CA USA. Department of Computer Science and Engineering Jacobs School of Engineering University of California San Diego La Jolla CA USA. Department of Bioengineering University of California San Diego La Jolla CA USA. Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu. Department of Computer Science and Engineering Jacobs School of Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu. Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu.

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Deep learning improves contrast in low-fluence photoacoustic imaging

arXiv

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arXiv 2020年

作者： Hariri, Ali Alipour, Kamran Mantri, Yash Schulze, Jurgen P. Jokerst, Jesse V. Department of NanoEngineering University of California San Diego San DiegoCA92093 United States Department of Computer Science University of California San Diego San DiegoCA92093 United States Department of BioEngineering University of California San Diego San DiegoCA92093 United States Qualcomm Institute University of California San Diego San DiegoCA92093 United States Department of Radiology University of California San Diego San DiegoCA92093 United States Material Science Program University of California San Diego San DiegoCA92093 United States

Low fluence illumination sources can facilitate clinical transition of photoacoustic imaging because they are rugged, portable, affordable, and safe. However, these sources also decrease image quality due to their low fluence. Here, we propose a denoising method using a multi-level wavelet-convolutional neural network to map low fluence illumination source images to its corresponding high fluence excitation map. Quantitative and qualitative results show a significant potential to remove the background noise and preserve the structures of target. Substantial improvements up to 2.20, 2.25, and 4.3-fold for PSNR, SSIM, and CNR metrics were observed, respectively. We also observed enhanced contrast (up to 1.76-fold) in an in vivo application using our proposed methods. We suggest that this tool can improve the value of such sources in photoacoustic imaging. Copyright © 2020, The Authors. All rights reserved.

关键词： Photoacoustic effect

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Benchmark problems for transcranial ultrasound simulation: Intercomparison of compressional wave models

arXiv

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arXiv 2022年

作者： Aubry, Jean-Francois Bates, Oscar Boehm, Christian Pauly, Kim Butts Christensen, Douglas Cueto, Carlos Gélat, Pierre Guasch, Lluis Jaros, Jiri Jing, Yun Jones, Rebecca Li, Ningrui Marty, Patrick Montanaro, Hazael Neufeld, Esra Pichardo, Samuel Pinton, Gianmarco Pulkkinen, Aki Stanziola, Antonio Thielscher, Axel Treeby, Bradley Van't Wout, Elwin Physics for Medicine Paris INSERM U1273 ESPCI Paris PSL University CNRS UMR 8063 France Department of Bioengineering Imperial College London Exhibition Road LondonSW7 2AZ United Kingdom Institute of Geophysics ETH Zürich Sonneggstrasse 5 Zürich8092 Switzerland Department of Radiology Stanford University StanfordCA United States Department of Biomedical Engineering Department of Electrical and Computer Engineering University of Utah United States Department of Surgical Biotechnology Division of Surgery and Interventional Science University College London LondonNW3 2PF United Kingdom Earth Science and Engineering Department Imperial College London London United Kingdom Centre of Excellence IT4Innovations Faculty of Information Technology Brno University of Technology Bozetechova 2 Brno612 00 Czech Republic Graduate Program in Acoustics The Pennsylvania State University University Park PA16802 United States Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill North Carolina State University NC United States Department of Electrical Engineering Stanford University StanfordCA United States Zurich Switzerland Laboratory for Acoustics / Noise control Empa Swiss Federal Laboratories for Materials Science and Technology Dubendorf Switzerland Zurich Switzerland Radiology and Clinical Neurosciences Departments Cumming School of Medicine University of Calgary Canada Department of Applied Physics University of Eastern Finland Kuopio70211 Finland Department of Medical Physics and Biomedical Engineering University College London Gower Street LondonWC1E 6BT United Kingdom Technical University of Denmark Denmark Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre Denmark Institute for Mathematical and Computational Engineering School of Engineering and Faculty of Mathematics Pontificia Universidad Catolica de Chile Santiago Chile

Computational models of acoustic wave propagation are frequently used in transcranial ultrasound therapy, for example, to calculate the intracranial pressure field or to calculate phase delays to correct for skull distortions. To allow intercomparison between the different modeling tools and techniques used by the community, an international working group was convened to formulate a set of numerical benchmarks. Here, these benchmarks are presented, along with intercomparison results. Nine different benchmarks of increasing geometric complexity are defined. These include a single-layer planar bone immersed in water, a multi-layer bone, and a whole skull. Two transducer configurations are considered (a focused bowl and a plane piston), giving a total of 18 permutations of the benchmarks. Eleven different modeling tools are used to compute the benchmark results. The models span a wide range of numerical techniques, including the finite-difference time-domain method, angular-spectrum method, pseudospectral method, boundary-element method, and spectral-element method. Good agreement is found between the models, particularly for the position, size, and magnitude of the acoustic focus within the skull. When comparing results for each model with every other model in a cross comparison, the median values for each benchmark for the difference in focal pressure and position are less than 10% and 1 mm, respectively. The benchmark definitions, model results, and intercomparison codes are freely available to facilitate further comparisons. Copyright © 2022, The Authors. All rights reserved.

关键词： Bone

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Some Remarks on Robust Gene Regulation in a Biomolecular Integral Controller

Some Remarks on Robust Gene Regulation in a Biomolecular Int...

引用

IEEE Annual Conference on Decision and Control

作者： Deepak K. Agrawal Ryan Marshall M. Ali Al-Radhawi Vincent Noireaux Eduardo D Sontag Department of Bioengineering and Department of Electrical and Computer Engineering Northeastern University Boston MA USA School of Physics and Astronomy University of Minnesota Minneapolis MN USA Laboratory of Systems Pharmacology Program in Therapeutic Science Harvard Medical School Boston MA USA

ISBN: (数字)9781728113982

ISBN: (纸本)9781728113999

Integral feedback can help achieve robust tracking independently of external disturbances. Motivated by this knowledge, biological engineers have proposed various designs of biomolecular integral feedback controllers to regulate biological processes. In this paper, we theoretically analyze the operation of a particular synthetic biomolecular integral controller, which we have recently proposed and implemented experimentally. Using a combination of methods, ranging from linearized analysis to sum-of-squares (SOS) Lyapunov functions, we demonstrate that, when the controller is operated in closed-loop, it is capable of providing integral corrections to the concentration of an output species in such a manner that the output tracks a reference signal linearly over a large dynamic range. We investigate the output dependency on the reaction parameters through sensitivity analysis, and quantify performance using control theory metrics to characterize response properties, thus providing clear selection guidelines for practical applications. We then demonstrate the stable operation of the closed-loop control system by constructing quartic Lyapunov functions using SOS optimization techniques, and establish global stability for a unique equilibrium. Our analysis suggests that by incorporating effective molecular sequestration, a biomolecular closed-loop integral controller that is capable of robustly regulating gene expression is feasible.

关键词： Steady-state Robustness Mathematical model Proteins Gene expression Kinetic theory Production

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Bioelectrical Interfaces Beyond Cellular Excitability: Cancer, Aging, and Gene Expression Reprogramming

arXiv

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arXiv 2025年

作者： Cadinu, Paolo Burgess, Matthew Jones, Catarina Franco Luciani, Titouan Iarossi, Marzia Schröter, Manuel Nakatsuka, Nako Djamgoz, Mustafa B.A. Gonçalves, Gil Sanjuán-Alberte, Paola Mendes, Paula M. Rawson, Frankie J. Nair, Malavika Levin, Michael Moreddu, Rosalia Program in Cellular and Molecular Medicine Boston Children’s Hospital BostonMA02115 United States Department of Microbiology Blavatnik Institute Harvard Medical School BostonMA02115 United States Institute of Biomedical Engineering Department of Engineering Science University of Oxford Oxford United Kingdom Department of Bioengineering Institute for Bioengineering and Biosciences Instituto Superior Técnico University of Lisbon Lisbon Portugal Associate Laboratory i4HB Institute for Health and Bioeconomy Instituto Superior Técnico Universidade de Lisboa Lisbon Portugal Department of Neuroscience Institut Pasteur Paris75015 France Department of Biomedical Engineering Technion Israel Institute of Technology Haifa Israel ETH Zurich Department of Biosystems Science and Engineering Basel Switzerland Laboratory of Chemical Nanotechnology Neuro-X Institute EPFL Genève1202 Switzerland Department of Life Sciences Imperial College London United Kingdom Department of Mechanical Engineering University of Aveiro Aveiro3810-193 Portugal Guimarães4800-058 Portugal School of Chemical Engineering University of Birmingham Birmingham United Kingdom Bioelectronics Laboratory Division of Regenerative Medicine and Cellular Therapies School of Pharmacy Biodiscovery Institute University of Nottingham Nottingham United Kingdom Allen Discovery Centre Tufts University Tufts University MedfordMA United States Wyss Institute for Bioinspired Engineering Harvard University BostonMA United States School of Electronics and Computer Science University of Southampton Southampton United Kingdom Institute for Life Sciences University of Southampton Southampton United Kingdom

Bioelectrical interfaces represent a significant evolution in the intersection of nanotechnology and biophysics, oRering new strategies for probing and influencing cellular processes. These systems capitalize on the subtle but powerful electric fields within living matter, potentially enabling applications beyond cellular excitability, ranging from targeted cancer therapies to interventions in genetic mechanisms and aging. This perspective article envisions the translation, development and application of next-generation solid-state bioelectrical interfaces and their transformative impact across several critical areas of medical research. © 2025, CC BY.

关键词： Medical nanotechnology

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