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Functionally specific optogenetic modulation in primate visual cortex

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2018年第41期115卷 10505-10510页

作者： Chernov, Mykyta M. Friedman, Robert M. Chen, Gang Stoner, Gene R. Roe, Anna Wang Oregon Hlth & Sci Univ Oregon Natl Primate Res Ctr Div Neurosci Beaverton OR 97006 USA Zhejiang Univ Qiushi Acad Adv Studies Interdisciplinary Inst Neurosci & Technol Hangzhou 310029 Zhejiang Peoples R China Zhejiang Univ Coll Biomed Engn & Instrument Sci Key Lab Biomed Engn Minist Educ Hangzhou 310027 Zhejiang Peoples R China Zhejiang Univ Sch Med Hangzhou 310058 Zhejiang Peoples R China Zhejiang Univ Coll Biomed Engn & Instrument Sci Zhejiang Prov Key Lab Cardiocerebral Vasc Detect Hangzhou 310027 Zhejiang Peoples R China Salk Inst Biol Studies Vis Ctr Lab 10010 N Torrey Pines Rd La Jolla CA 92037 USA

In primates, visual perception is mediated by brain circuits composed of submillimeter nodes linked together in specific networks that process different types of information, such as eye specificity and contour orientation. We hypothesized that optogenetic stimulation targeted to cortical nodes could selectively activate such cortical networks. We used viral transfection methods to confer light sensitivity to neurons in monkey primary visual cortex. Using intrinsic signal optical imaging and single-unit electrophysiology to assess effects of targeted optogenetic stimulation, we found that (i) optogenetic stimulation of single ocular dominance columns (eye-specific nodes) revealed preferential activation of nearby same-eye columns but not opposite-eye columns, and (ii) optogenetic stimulation of single orientation domains increased visual response of matching orientation domains and relatively suppressed nonmatching orientation selectivity. These findings demonstrate that optical stimulation of single nodes leads to modulation of functionally specific cortical networks related to underlying neural architecture.

关键词： primary visual cortex functional connectivity nonhuman primates optogenetics cortical columns

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A simple method based on Sanger sequencing and MS Word wildcard searching to identify Cas9-induced frameshift mutations

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LABORATORY INVESTIGATION 2017年第12期97卷 1500-1507页

作者： Jie, Hui Li, Zhuoling Wang, Ping Zhao, Linjie Zhang, Qian Yao, Xiaomin Song, Xiangrong Zhao, Yinglan Yao, Shaohua Sichuan Univ West China Hosp State Key Lab Biotherapy Canc Ctr 17 3rd Sect South Renmin Rd Chengdu 610041 Sichuan Peoples R China

Recent advances in targeted genome editing have enabled sequence-specific modifications in eukaryotic genomes. As it can be easily reprogrammed, the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 nuclease system has been studied extensively and is now a widely used genome editing tool. Generally, Cas9 nucleases are designed to target the coding regions in exons of protein-coding genes, which are expected to cause frameshift indel mutations and interrupt protein expression. In such cases, it is often necessary to separate single clones that harbor double frameshift mutant alleles from clones that harbor the wild-type allele or an in-frame mutant allele. We developed a simple and efficient method to identify frameshift mutations in diploid genomes based on Sanger sequencing and MS Word wildcard searching (SWS). As indel mutations induced by Cas9 are varied, Sanger sequencing of PCR products from a single mutant genome will generate double peaks that begin at the indel sites. By positioning the putative sequences deduced from the double peak regions in the sequencing graph onto the wild-type sequence by MS Word wildcard searching, it is possible to predict exactly how many nucleotides were deleted or inserted in each allele of the genome. The SWS strategy greatly facilitates the process of identifying single clones with biallelic frameshift mutations from pooled cells or model organisms.

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Fast first-photon ghost imaging

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SCIENTIFIC REPORTS 2018年第1期8卷 5012-5012页

作者： Liu, Xialin Shi, Jianhong Wu, Xiaoyan Zeng, Guihua Shanghai Jiao Tong Univ State Key Lab Adv Opt Commun Syst & Networks Shanghai 200240 Peoples R China Shanghai Jiao Tong Univ Ctr Quantum Sensing & Informat Proc QSIP Shanghai 200240 Peoples R China

Conventional imaging at low light levels requires hundreds of detected photons per pixel to suppress the Poisson noise for accurate reflectivity inference. We propose a high-efficiency photon-limited imaging technique, called fast first-photon ghost imaging, which recovers the image by conditional averaging of the reference patterns selected by the first-photon detection signal. Our technique merges the physics of low-flux measurements with the framework of computational ghost imaging. Experimental results demonstrate that it can reconstruct an image from less than 0.1 detected photon per pixel, which is three orders of magnitude less than conventional imaging techniques. A signalto-noise ratio model of the system is established for noise analysis. With less data manipulation and shorter time requirements, our technique has potential applications in many fields, ranging from biological microscopy to remote sensing.

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Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

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COMPUTER PHYSICS COMMUNICATIONS 2017年 211卷 73-78页

作者： Hu Changjun Bai He He Xinfu Zhang Boyao Nie Ningming Wang Xianmeng Ren Yingwen Univ Sci & Technol Beijing Beijing 100083 Peoples R China China Inst Atom Energy Beijing Peoples R China Chinese Acad Sci Supercomp Ctr Comp Network Informat Ctr Beijing Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster. (C) 2016 Elsevier B.V. All rights reserved.

关键词： Irradiation environment Molecular dynamics Data structure high-performance computing

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Magneto-optical double resonance driven by fictitious fields

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OPTICS EXPRESS 2017年第7期25卷 7668-7676页

作者： Lin, Zaisheng Peng, Xiang Li, Wenhao Wang, Haidong Guo, Hong Peking Univ State Key Lab Adv Opt Commun Syst & Networks Sch Elect Engn & Comp Sci Beijing 100871 Peoples R China Peking Univ Ctr Quantum Informat Technol Beijing 100871 Peoples R China

Light-shift caused by the interaction between atoms and detuned light can be equivalent to the phenomena that atoms are coupled to an external magnetic or electric field. A fictitious magnetic or electric field is used to describe the effect of light-shift. Whether fictitious magnetic or electric field should be used depends on the polarization state of the detuned light. The fictitious fields can shift Zeeman sublevels and excite transitions between different sublevels. We study the magneto-optical double resonance of optically polarized He-4 atoms driven by the detuned light with either circular or linear polarization states, model the light-shift with effective Hamiltonian, and the polarized He-4 metastable state with density matrix calculations. Our proposed theoretical explanations based on the fictitious fields show good agreement with experimental results, especially for amplitude and frequency shifts of the signals at Larmor frequency and double Larmor frequency driven by the fictitious electric field. (C) 2017 Optical Society of America

关键词： Atomic spectroscopy Beam expanders Fiber lasers Light intensity Light wavelength Stark effect

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The preparation of oleylamine modified micro-size sphere silver particles and its application in crystalline silicon solar cells

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RSC ADVANCES 2018年第30期8卷 16866-16872页

作者： Lan, Feng Bai, Jintao Wang, Hui Northwest Univ Xian Coll Chem & Mat Sci Minist Educ Key Lab Synthet & Nat Funct Mol Chem Xian 710069 Shaanxi Peoples R China Northwest Univ Xian Natl Key Lab Photoelect Technol & Funct Mat Cultu Natl Photoelectr Technol & Funct Mat & Applicat I Inst Photon & Photon Technol Xian 710069 Shaanxi Peoples R China

In this paper, micro-sized silver particles were prepared using a simple chemical approach without adjusting the pH of the solution, and oleylamine as a capping agent was described to promote the dispersion of the silver particles. The effects of temperature, feeding time and stirring speed on the morphology and size distribution of silver particles were discussed. The optimal reaction parameters (35 degrees C, 45 min, 300 rpm) for large scale industrial production were selected to obtained optimal silver particles for preparation of the silver paste for poly-crystalline silicon solar cells. The photoelectric conversion efficiency of the solar cells made with silver paste by using the silver particles can reach 18.623%, which is similar to the industrial production of solar cell made with commercial silver paste. This work contributes to the development of the synthesis of highly disperse silver particles used in solar cells in large scale industrial productions.

关键词： Silver

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Rock fragmentation under different installation polar angles of TBM disc cutters

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Journal of Central South University 2017年第10期24卷 2306-2313页

作者： CHENG Yong-liang ZHONG Jue MEI Yong-bing XIA Yi-min State Key Laboratory of High Performance Complex Manufacturing Central South University China Railway Construction Heavy Industry Co. Ltd.

The disc cutters of tunnel boring machine(TBM) are installed with different polar angles. This causes the cutting depth difference between adjacent disc cutters on the tunnel face. A rock-cutting model was established to study the rock fragmentation law between adjacent disc cutters with different polar angles based on particle flow code(PFC). The influence of polar angle of adjacent disc cutters on rock cracks and stresses under different cutter spacing and penetration was studied. research shows that polar angle difference leads to the discontinuity of rock-fragmentation process by adjacent cutters. The effect of rock-fragmentation is influenced by the cutting depth difference between adjacent cutters. The effect of rock-fragmentation performed best, meanwhile large rock blocks were flaked when the difference of cutting depth is half of the penetration. Too large or small difference of the cutting depth will cause high specific energy consumption of rock fragmentation. The specific energy consumption is relatively small when the difference of cutting depth is half of the penetration.

关键词： tunnel boring machine disc cutter polar angle particle flow code rock fragmentation

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Discriminative latent semantic feature learning for pedestrian detection

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NEUROCOMPUTING 2017年 238卷 126-138页

作者： Zhu, Chao Peng, Yuxin Univ Sci & Technol Beijing Sch Comp & Commun Engn Beijing 100083 Peoples R China Peking Univ Inst Comp Sci & Technol Beijing 100871 Peoples R China

Features act as a key factor in pedestrian detection task. Most widely-used ones like HOG are manually designed and hard to be adaptive, thus now more attention has been paid to the features automatically learned on data. In this paper, a novel approach of learning discriminative features is proposed, addressing two main limitations of the methods in the literature. On one hand, unlike those methods of learning features on low-level pixels, we propose to learn features via a particular sparse coding algorithm enhanced on mid-level image representation, in order to obtain higher-level latent semantics and robustness;On the other hand, those methods usually utilize label information in model training such as deformable part model (DPM) with high computation cost. Instead, we propose to extend the learning process via a maximum margin criterion, in order to better encode discriminative information directly in features by optimizing them to be close to each other if from the same class and far from each other if from different classes. Furthermore, a boosted detection framework rather than the complex DPM is adopted to achieve both high accuracy and efficiency. The proposed approach achieves promising results on several standard pedestrian detection benchmarks. (C) 2017 Elsevier B.V. All rights reserved.

关键词： Pedestrian detection Feature learning Latent semantics Discriminative power

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A 12-bit 4928 x 3264 pixel CMOS image signal processor for digital still cameras

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INTEGRATION-THE VLSI JOURNAL 2017年 59卷 206-217页

作者： Jin, Wei He, Guanghui He, Weifeng Mao, Zhigang Shanghai Jiao Tong Univ Circuits & Syst Shanghai Peoples R China Shanghai Jiao Tong Univ Shanghai Peoples R China Shanghai Jiao Tong Univ Dept Micronano Elect Shanghai Peoples R China

In this paper a 4928 x 3264 pixel CMOS image signal processor (ISP) is proposed for digital still cameras with low complexity and high performance. To reduce hardware cost and keep high performance, novel algorithms are proposed to process image signals. Firstly, a joint demosaic and denoise algorithm is presented for both color interpolation and Gaussian noise removal. This novel joint algorithm achieves high performance and saves line buffers. Furthermore, image edge enhancement is performed jointly with this algorithm to save memory cost. Secondly, a low complexity auto white balance hardware architecture is presented based on histogram equalization algorithm. This algorithm can handle some extremely bad scenes. To reduce hardware cost, the contrast enhancement is realized jointly with auto white balance. Thirdly, to remove pulse noise, a high performance and low complexity hardware implementation is proposed based on median filter using only nine comparators. Based on these algorithms and hardware, the VLSI architecture of the ISP is proposed and implemented in a SMIC 65 nm CMOS technology. The gate count of the ISP is 158k and core area is 1.5 mm(2). Only 8 line buffers with total 462 Kb SRAM are used in the ISP. The throughput of the ISP is 12 Gb/s with a frequency of 333 MHz and power consumption of 77 mW.

关键词： Bayer image format Digital still camera (DSC) Image signal processor (ISP) VLSI implementation

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Focal infrared neural stimulation with high-field functional MRI: A rapid way to map mesoscale brain connectomes

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SCIENCE ADVANCES 2019年第4期5卷 eaau7046页

作者： Xu, Augix Guohua Qian, Meizhen Tian, Feiyan Xu, Bin Friedman, Robert M. Wang, Jianbao Song, Xuemei Sun, Yi Chernov, Mykyta M. Cayce, Jonathan M. Jansen, E. Duco Mahadevan-Jansen, Anita Zhang, Xiaotong Chen, Gang Roe, Anna Wang Zhejiang Univ Interdisciplinary Inst Neurosci & Technol Qiushi Acad Adv Studies Affiliated Hosp 2Sch Med Hangzhou 310029 Peoples R China Zhejiang Univ Minist Educ Key Lab Biomed Engn Hangzhou 310029 Peoples R China Vanderbilt Univ Dept Psychol Nashville TN 37203 USA Oregon Hlth & Sci Univ Oregon Natl Primate Res Ctr Div Neurosci Beaverton OR 97239 USA Siemens Healthcare MR Collaborat Northeast Asia Shanghai 200001 Peoples R China Vanderbilt Univ Dept Biomed Engn Nashville TN 37203 USA Vanderbilt Univ Biophoton Ctr Nashville TN 37232 USA Vanderbilt Univ Med Ctr Nashville TN 37232 USA

We have developed a way to map brain-wide networks using focal pulsed infrared neural stimulation in ultrahigh-field magnetic resonance imaging (MRI). The patterns of connections revealed are similar to those of connections previously mapped with anatomical tract tracing methods. These include connections between cortex and subcortical locations and long-range cortico-cortical connections. Studies of local cortical connections reveal columnar-sized laminar activation, consistent with feed-forward and feedback projection signatures. This method is broadly applicable and can be applied to multiple areas of the brain in different species and across different MRI platforms. Systematic point-by-point application of this method may lead to fundamental advances in our understanding of brain connectomes.

关键词： Magnetic resonance imaging

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