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Thermoacoustic imaging:From single-element scanning to portable and array-based imaging

Journal of Electronic Science and Technology 2023年第3期21卷 1-20页

作者： Yi-Jie Huang Qi-Kai-Yu Feng Lin Huang School of Electronic Science and Engineering University of Electronic Science and Technology of ChinaChengdu610054China Zhangjiang Laboratory Shanghai201204China

The microwave-induced thermoacoustic imaging(TAI)technology has both the advantages of high contrast of microwave imaging and high resolution of ultrasound imaging(UI),so it has carried out exploratory application research in various areas,such as the early detection of breast tumors and cerebrovascular ***,the microwave generator used in the traditional TAI technology is huge and expensive,and the temporal resolution is also too low due to the single-element scanning ***,it is difficult to meet the needs of clinical *** this paper,the iterative process and the analysis of related application scenarios from single-element scanning to portable and array-based TAI,such as the miniaturized microwave generator,handheld antenna,multi-channel data acquisition,and UI/TAI􀀁dual-modality imaging,are reviewed,and the future trends of this technology are *** review helps researchers in the field of TAI learn the technological development process and future *** also deepens clinicians’understanding of TAI so as to put forward more application requirements.

关键词： array-based Portable Single-element scanning Thermoacoustic imaging(TAI)

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EXPERIMENTAL AND NUMERICAL INVESTIGATION OF THERMAL PERFORMANCE OF CHANNELS WITH STAGGERED array-based DIMPLES

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THERMAL SCIENCE 2015年第Sup1期19卷 S213-S219页

作者： Xie, Yong-Hui Shen, Zhong-Yang Liu, Tian-Yuan Xie, Gong-Nan Xi An Jiao Tong Univ Sch Energy & Power Engn Xian 710049 Peoples R China Northwestern Polytech Univ Sch Mech Engn Engn Simulat & Aerosp Comp Xian 710072 Peoples R China

Numerical simulation coupled with experimental method was carried out to study the flow and heat transfer characteristics in rectangular channel with staggered array-based dimples. The effect of different dimple depths and Reynolds number were investigated using the shear stress transport turbulent model coupled with gamma-theta transition model. The results indicated that heat transfer and flow resistance of the dimpled surface increases with the increase of dimple depth. Moreover, the thermal performance is sensitive to the flow transition. Heat transfer in each single dimple region increases monotonously in the streamwise direction with Reynolds number increasing. Heat transfer characteristics almost remain the same when the flow is under fully laminar or turbulent but increases greatly when the flow is transited from laminar condition to turbulent condition. Besides, the variations of friction coefficients and thermal performance coefficients are quite similar to those of heat transfer enhancement coefficients, which firstly increases then decreases with the increase of Reynolds number. By comparing the experimental and numerical results, it is found that staggered array-based dimples with delta/D = 0.2 was the most effective structure from the aspect of thermal performance.

关键词： dimple array-based flow characteristics thermal performance heat transfer characteristics

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Experimental and Computational Challenges from array-based to Sequence-based ChIP Techniques

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CURRENT BIOINFORMATICS 2012年第4期7卷 447-453页

作者： Lan, Xun Jin, Victor X. Ohio State Univ Dept Biomed Informat Columbus OH 43210 USA

Transcriptional regulation is a key step to control the level of mRNA formed. Recent view of transcriptional regulation has evolved from a one-dimensional mode, i.e. RNA Polymerase II assembles with general transcription factors, and cis-regulatory elements (CREs) interact with transcription factors, to a much complex multiple-dimensional mode, involving combinatorial interactions between transcription factors and regulatory sequences, chromatin structure, histone modifications, DNA methylation. High throughput experimental technologies, such as array-based ChIP-chip and sequencing-based ChIP-seq, have been developed to survey in vivo transcription factor binding sites and histone modifications. Despite many efforts have been made to analyze and interpret the data, challenges remain in many aspects of both experimental protocols and computational analyses. For example, how to determine the optimized number of PCR cycles? How to normalize multiple datasets from multiple experiments? How to utilize the large number of unmapped and multiple mapped tags in ChIP-seq experiment? This review focuses on issues emerged in high throughput data processing and discusses advantages and disadvantages of various strategies.

关键词： array-based ChiP ChiP-seq cis-regulatory elements (CREs) omics sequence-based

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Genome-wide profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization

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LARYNGOSCOPE 2006年第5期116卷 735-741页

作者： Sparano, A Quesnelle, KM Kumar, MS Wang, Y Sylvester, AJ Feldman, M Sewell, DA Weinstein, GS Brose, MS Univ Penn Dept Otorhinolaryngol Head & Neck Surg Philadelphia PA 19104 USA Univ Penn Dept Med Philadelphia PA 19104 USA Univ Penn Dept Pathol Philadelphia PA 19104 USA

Objectives. array-based comparative genomic hybridization (aCGH) was used to develop a genome-wide molecular profile of oral squamous cell carcinoma (OSCC). Copy number alterations (CNAs) were identified by chromosomal region, mapped to specific genes, and compared with several previously documented CNAs associated with head and neck squamous cell carcinoma (HNSCC). The status of 512 commonly altered cancer genes was assessed and evaluated as potential correlates of tumor behavior. Methods: Tumor tissue DNA was isolated for aCGH from 21 prospectively collected fresh-frozen OSCC specimens. aCGH was performed at 0.9-Mb resolution to identify distinct regions of genomic alteration and their associated genes. Cancer genes commonly altered were then correlated with clinicopathologic tumor data. Results: Genomic regions most frequently amplified (>35%) were located on 3q, 5p, 8q, 9q, and 20q, although regions most frequently deleted (>40%) involved chromosomes 3p, 8p, 13q, and 18q. Minimal regions of CNA identified, by aCGH narrowed larger, previously documented CNAs associated with HNSCC to significantly smaller regions, yielding shorter lists of candidate genes. Cancer-related genes altered in greater than 25% OSCC samples were identified (22 amplified, 17 deleted). Several genes associated with the Fanconi anemia DNA-damage response pathway were frequently altered, including BRCA1, BRCA2, FANCD2, and FANCG. Other cancer-related genes linked to hereditary cancer syndromes include VHL, MLH1, XPC, and RB1. Conclusions: Genome-wide aCGH can be used to detect and map CNAs in OSCC tissue specimens with high resolution. These data implicate several candidate genes and gene pathways in the tumorigenesis of sporadic OSCC.

关键词： head and neck neoplasm aCGH array-based comparative genomic hybridization copy number alterations oral squamous cell carcinoma OSCC Fanconi anemia cancer genes

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A spatiotemporal indexing approach for efficient processing of big array-based climate data with MapReduce

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INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE 2017年第1期31卷 17-35页

作者： Li, Zhenlong Hu, Fei Schnase, John L. Duffy, Daniel Q. Lee, Tsengdar Bowen, Michael K. Yang, Chaowei George Mason Univ NSF Spatiotemporal Innovat Ctr Fairfax VA 22030 USA Univ South Carolina Dept Geog Columbia SC 29208 USA NASA Goddard Space Flight Ctr Off Computat & Informat Sci & Technol Greenbelt MD USA NASA Goddard Space Flight Ctr Ctr Climate Simulat Greenbelt MD USA NASA Earth Sci Div Washington DC 20546 USA

Climate observations and model simulations are producing vast amounts of array-based spatiotemporal data. Efficient processing of these data is essential for assessing global challenges such as climate change, natural disasters, and diseases. This is challenging not only because of the large data volume, but also because of the intrinsic high-dimensional nature of geoscience data. To tackle this challenge, we propose a spatiotemporal indexing approach to efficiently manage and process big climate data with MapReduce in a highly scalable environment. Using this approach, big climate data are directly stored in a Hadoop Distributed File System in its original, native file format. A spatiotemporal index is built to bridge the logical array-based data model and the physical data layout, which enables fast data retrieval when performing spatiotemporal queries. based on the index, a data-partitioning algorithm is applied to enable MapReduce to achieve high data locality, as well as balancing the workload. The proposed indexing approach is evaluated using the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. The experimental results show that the index can significantly accelerate querying and processing (similar to 10x speedup compared to the baseline test using the same computing cluster), while keeping the index-to-data ratio small (0.0328%). The applicability of the indexing approach is demonstrated by a climate anomaly detection deployed on a NASA Hadoop cluster. This approach is also able to support efficient processing of general array-based spatiotemporal data in various geoscience domains without special configuration on a Hadoop cluster.

关键词： Spatiotemporal index big climate data array-based Hadoop MapReduce HDFS NASA MERRA climate change

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Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates

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NUCLEIC ACIDS RESEARCH 1998年第21期26卷 4975-4982页

作者： Hacia, JG Woski, SA Fidanza, J Edgemon, K Hunt, N McGall, G Fodor, SPA Collins, FS Natl Human Genome Res Inst NIH Bethesda MD 20892 USA Univ Alabama Dept Chem Tuscaloosa AL 35487 USA Affymetrix Santa Clara CA 95051 USA

Pairs of high density oligonucleotide arrays (DNA chips) consisting of >96 000 oligonucleotides were designed to screen the entire 5.53 kb coding region of the hereditary breast and ovarian cancer BRCA1 gene for all possible sequence changes in the homozygous and heterozygous states. Single-stranded RNA targets were generated by PCR amplification of individual BRCA1 exons using primers containing T3 and T7 RNA polymerase promoter tails followed by in vitro transcription and partial fragmentation reactions. Fluorescent hybridization signals from targets containing the four natural bases to >5592 different fully complementary 25mer oligonucleotide probes an the chip varied over two orders of magnitude. To examine the thermodynamic contribution of *** and *** *** base pairs to this variability, modified uridine [5-methyluridine and 5-(1-propynyl)-uridine)] and modified adenosine (2,6-diaminopurine riboside) 5'-triphosphates were incorporated into BRCA1 targets. Hybridization specificity was assessed based upon hybridization signals from >33 200 probes containing centrally localized single base pair mismatches relative to target sequence. Targets containing 5-methyluridine displayed promising localized enhancements in hybridization signal, especially in pyrimidine-rich target tracts, while maintaining single nucleotide mismatch hybridization specificities comparable with those of unmodified targets.

关键词： .nucleoside Sequence Analysis Pyrimidine Unmodified Triphosphates Diaminopurine array-based density oligonucleotide

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Rescue Karyotyping: a Case Series of array-based Comparative Genomic Hybridization Evaluation of Archival Conceptual Tissue

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2016年

作者： rashmi kudesia

Rescue Karyotyping: a Case Series of array-based Comparative Genomic Hybridization Evaluation of Archival Conceptual Tissue. by Kudesia, Rashmi; Li, Marilyn; Smith, Janice; Patel, Ankita; Williams, Zev; published by

关键词： archival array-based comparative conceptual evaluation

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NASA Technical Reports Server (Ntrs) 19870017106: Simulation of an array-based Neural Net Model

引用

2017年

NASA Technical Reports Server (Ntrs) 19870017106: Simulation of an array-based Neural Net Model by NASA Technical Reports Server (Ntrs); published by

关键词： (ntrs) 19870017106: array-based arrays barnden, john a. cognition computer systems performance computerized simulation data structures information processing (biology) massively parallel processors mathematical models mental performance model nasa technical reports server (ntrs) neural neural nets parallel processing (computers) pascal (programming language)

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Beamforming for large-area scan and improved SNR in array-based photoacoustic microscopy

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ULTRASONICS 2021年 111卷 106317-106317页

作者： Cebrecos, A. Garcia-Garrigos, J. J. Descals, A. Jimenez, N. Benlloch, J. M. Camarena, F. Univ Politecn Valencia UPV Consejo Super Invest Cient CSIC Inst Instrumentac Imagen Mol i3M Camino Vera S-N Valencia 46022 Spain

Beamforming enhances the performance of array-based photoacoustic microscopy (PAM) systems for large-area scan. In this study, we quantify the imaging performance of a large field-of-view optical-resolution photoacoustic-microscopy system using an phased-array detector. The system combines a low-cost pulsed-laser diode with a 128-element linear ultrasound probe. Signal-to-noise ratio (SNR) and generalized contrast-to-noise ratio (gCNR) are quantified using the phased-array detector and applying three beamforming strategies: a no-beamforming method equivalent to a single-element flat transducer, a fixed focus beamforming method that mimics a single-element focused transducer, and a dynamic focus beamforming using a delay-and-sum (DAS) algorithm. The imaging capabilities of the system are demonstrated generating high-resolution images of tissue-mimicking phantoms containing sub-millimetre ink tubes and an ex vivo rabbit's ear. The results show that dynamic focus DAS beamforming increases and homogenizes SNR along 1-cm(2) images, reaching values up to 15 dB compared to an unfocused detector and up to 30 dB compared to out-of-focus regions of the fixed focus configuration. Moreover, the obtained values of gCNR using the DAS beamformer indicate an excellent target visibility, both on phantoms and ex vivo. This strategy makes it possible to scan larger surfaces compared to standard configurations using single-element detectors, paving the way for advanced array-based PAM systems.

关键词： Photoacoustic imaging OR-PAM array-based DAS beamforming Large-area scan Pulsed laser diode

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A digital array based bit serial processor for arbitrary window size kernel convolution in vision sensors

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INTEGRATION-THE VLSI JOURNAL 2014年第4期47卷 417-430页

作者： Habibi, Mehdi Bafandeh, Alireza Montazerolghaem, Muhammad Ali Univ Isfahan Dept Elect Engn Esfahan Iran

The high speed and in-pixel processing of image data in smart vision sensors is an important solution for real time machine vision tasks. Diverse architectures have been presented for array based kernel convolution processing, many of which use analog processing elements to save space. In this paper a digital array based bit serial architecture is presented to perform certain image filtering tasks in the digital domain and hence gain higher accuracies than the analog methods. The presented method benefits from more diverse convolution options such as arbitrary size kernel windows, compared with the digital pulse based approaches. The proposed digital cell structure is compact enough to fit inside an image sensor pixel. When incorporated in a vision chip, resolutions of up to 12 bit accuracy can be obtained in kernel convolution functions with 35 x 28 mu m(2) layout area usage per pixel in a 90 nm technology. Still, higher accuracies can be obtained with larger pixels. The power consumption of the approach is approximately 10 nW/pixel at a frame rate of 1 kfps. (C) 2013 Elsevier B.V. All rights reserved.

关键词： array-based Bit serial Vision sensors Kernel convolution Digital processing

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