检索结果-内蒙古大学图书馆

Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila

BIOINFORMATICS 2009年第3期25卷 346-352页

作者： Myasnikova, Ekaterina Surkova, Svetlana Panok, Lena Samsonova, Maria Reinitz, John St Petersburg State Polytech Univ St Petersburg 195251 Russia SUNY Stony Brook Stony Brook NY 11794 USA

Motivation: Currently the confocal scanning microscopy of fluorescently tagged molecules is extensively employed to acquire quantitative data on gene expression at cellular resolution. Following this approach, we generated a large dataset on the expression of segmentation genes in the Drosophila blastoderm, that is widely used in systems biology studies. As data accuracy is of critical importance for the success of studies in this field, we took a shot to evaluate possible errors introduced in the data by acquisition and processing methods. This article deals with errors introduced by confocal microscope. Results: In confocal imaging, the inevitable photon noise is commonly reduced by the averaging of multiple frames. The averaging may introduce errors into the data, if single frames are clipped by microscope hardware. A method based on censoring technique is used to estimate and correct this type of errors. Additional source of errors is the quanti. cation of blurred images. To estimate and correct these errors, the Richardson-Lucy deconvolution method was modified to provide the higher accuracy of data read off from blurred images of the Drosophila blastoderm. We have found that the sizes of errors introduced by confocal imaging make up similar to 5-7% of the mean intensity values and do not disguise the dynamic behavior and characteristic features of gene expression patterns. We also defined a range of microscope parameters for the acquisition of sufficiently accurate data.

关键词： Animals Blastoderm/metabolism Drosophila/genetics Drosophila/metabolism Gene Expression Gene Expression Profiling/methods Genes, Insect image processing, computer-assisted/methods Microscopy, Confocal/methods Regression Analysis

来源：评论

学校读者我要写书评

暂无评论

Systematic random sampling of the comet assay

引用

MUTAGENESIS 2009年第4期24卷 373-378页

作者： McArt, Darragh G. Wasson, Gillian R. McKerr, George Saetzler, Kurt Reed, Matt Howard, C. Vyvyan Univ Ulster Biomed Sci Res Inst Coleraine BT52 1SA Londonderry North Ireland

The comet assay is a technique used to quantify DNA damage and repair at a cellular level. In the assay, cells are embedded in agarose and the cellular content is stripped away leaving only the DNA trapped in an agarose cavity which can then be electrophoresed. The damaged DNA can enter the agarose and migrate while the undamaged DNA cannot and is retained. DNA damage is measured as the proportion of the migratory 'tail' DNA compared to the total DNA in the cell. The fundamental basis of these arbitrary values is obtained in the comet acquisition phase using fluorescence microscopy with a stoichiometric stain in tandem with image analysis software. Current methods deployed in such an acquisition are expected to be both objectively and randomly obtained. In this paper we examine the 'randomness' of the acquisition phase and suggest an alternative method that offers both objective and unbiased comet selection. In order to achieve this, we have adopted a survey sampling approach widely used in stereology, which offers a method of systematic random sampling (SRS). This is desirable as it offers an impartial and reproducible method of comet analysis that can be used both manually or automated. By making use of an unbiased sampling frame and using microscope verniers, we are able to increase the precision of estimates of DNA damage. Results obtained from a multiple-user pooled variation experiment showed that the SRS technique attained a lower variability than that of the traditional approach. The analysis of a single user with repetition experiment showed greater individual variances while not being detrimental to overall averages. This would suggest that the SRS method offers a better reflection of DNA damage for a given slide and also offers better user reproducibility.

关键词： Comet Assay/methods Comet Assay/standards DNA/drug effects DNA Damage DNA Repair Hela Cells Humans image processing, computer-assisted/methods Microscopy, Fluorescence/methods Models, Statistical Reproducibility of Results Software

来源：评论

学校读者我要写书评

暂无评论

The Brain under Self-Control: Modulation of Inhibitory and Monitoring Cortical Networks during Hypnotic Paralysis

引用

NEURON 2009年第6期62卷 862-875页

作者： Cojan, Yann Waber, Lakshmi Schwartz, Sophie Rossier, Laurent Forster, Alain Vuilleumier, Patrik Univ Geneva Dept Neurosci Univ Med Sch Geneva Switzerland Univ Geneva Ctr Neurosci Geneva Switzerland Univ Hosp Geneva Dept Addict Geneva Switzerland Univ Hosp Geneva Dept Anesthesiol Geneva Switzerland Univ Fribourg Dept Psychol CH-1700 Fribourg Switzerland

Brain mechanisms of hypnosis are poorly known. Cognitive accounts proposed that executive attentional systems may cause selective inhibition or disconnection of some mental operations. To assess motor and inhibitory brain circuits during hypnotic paralysis, we designed a go-nogo task while volunteers underwent functional magnetic resonance imaging (fMRI) in three conditions: normal state, hypnotic left-hand paralysis, and feigned paralysis. Preparatory activation arose in right motor cortex despite left hypnotic paralysis, indicating preserved motor intentions, but with concomitant increases in precuneus regions that normally mediate imagery and self-awareness. Precuneus also showed enhanced functional connectivity with right motor cortex. Right frontal areas subserving inhibition were activated by nogo trials in normal state and by feigned paralysis, but irrespective of motor blockade or execution during hypnosis. These results suggest that hypnosis may enhance self-monitoring processes to allow internal representations generated by the suggestion to guide behavior but does not act through direct motor inhibition.

关键词： Analysis of Variance Attention Brain Mapping Brain Mapping Decision Making/physiology Functional Laterality/physiology Humans Hypnosis/methods image processing, computer-assisted/methods Inhibition (Psychology) Magnetic Resonance Imaging/methods Motor Cortex/blood supply Motor Cortex/physiopathology Movement/physiology Neural Pathways/physiopathology Neuropsychological Tests Oxygen/blood Paralysis/etiology Paralysis/pathology Psychomotor Performance/physiology Reaction Time/physiology Self Concept

来源：评论

学校读者我要写书评

暂无评论

Automated image analysis of cytokinesis-blocked micronuclei: an adapted protocol and a validated scoring procedure for biomonitoring

引用

MUTAGENESIS 2009年第1期24卷 85-93页

作者： Decordier, Ilse Papine, Alexander Plas, Gina Roesems, Sam Vande Loock, Kim Moreno-Palomo, Jennifer Cemeli, Eduardo Anderson, Diana Fucic, Aleksandra Marcos, Ricardo Soussaline, Francoise Kirsch-Volders, Micheline Vrije Univ Brussel Lab Cellulaire Genet B-1050 Brussels Belgium IMSTAR F-75006 Paris France Univ Autonoma Barcelona Dept Genet & Microbiol Grp Mutagenesi Bellaterra Spain Univ Bradford Dept Biomed Sci Bradford BD7 1DP W Yorkshire England Inst Med Res & Occupat Hlth Zagreb 10000 Croatia

Micronuclei (MN) frequencies in peripheral blood lymphocytes have been used worldwide as a biomarker of chromosomal damage for genotoxicity testing and biomonitoring studies. Automation of MN analysis would provide faster and more reliable results with minimizing subjective MN identification. We developed an automated facility for the scoring of the in vitro MN cytokinesis-block assay for biomonitoring on Giemsa-stained slides, fulfilling the following criteria: applicable to the cytokinesis-block micronucleus methodology, discriminating between mono-, bi- and polynucleated cells, MN scoring according to HUMN scoring criteria, false-negative MN rate < 10% and false-positive (FP) MN rate < 1%. We first adapted the slide preparation protocol to obtain an optimal cell density and dispersion, which is important for image analysis. We developed specific algorithms starting from the cell as a detection unit. The whole detection and scoring process was separated into two distinct steps: in the first step, the cells and nuclei are detected;then, in the second step, the MN are searched for in the detected cells. Since the rate of FP MN obtained by the automatic analysis was in the range of 0.5-1.5%, an interactive visual validation step was introduced, which is not time consuming and allows quality control. Validation of the automated scoring procedure was undertaken by comparing the results of visual and automated scoring of micronucleated mono- and binucleated cells in human lymphocytes induced by two clastogens (ionizing radiation and methyl methane-sulphonate), two aneugens (nocodazole and carbendazim) and one apoptogen (staurosporine). Although the absolute MN frequencies obtained with automated scoring were lower as compared to those detected by visual scoring, a clear dose response for MNBN frequencies was observed with the automated scoring system, indicating that it is able to produce biologically relevant and reliable results. These observations, together with its

关键词： Adult Biological Markers Cytokinesis DNA Damage Environmental Monitoring/methods Humans image processing, computer-assisted/methods Lymphocytes/chemistry Lymphocytes/ultrastructure Micronuclei, Chromosome-Defective Micronucleus Tests Reproducibility of Results

来源：评论

学校读者我要写书评

暂无评论

Training Improves Multitasking Performance by Increasing the Speed of Information processing in Human Prefrontal Cortex

引用

NEURON 2009年第1期63卷 127-138页

作者： Dux, Paul E. Tombu, Michael N. Harrison, Stephenie Rogers, Baxter P. Tong, Frank Marois, Rene Vanderbilt Univ Dept Psychol Vanderbilt Vis Res Ctr Ctr Integrat & Cognit Neurosci Nashville TN 37240 USA Vanderbilt Univ Inst Imaging Sci Nashville TN 37240 USA Vanderbilt Univ Dept Radiol & Radiol Sci Nashville TN 37240 USA Univ Queensland Sch Psychol Brisbane Qld 4072 Australia

Our ability to multitask is severely limited: task performance deteriorates when we attempt to undertake two or more tasks simultaneously. Remarkably, extensive training can greatly reduce such multitasking costs. While it is not known how training alters the brain to solve the multitasking problem, it likely involves the prefrontal cortex given this brain region's purported role in limiting multitasking performance. Here, we show that the reduction of multitasking interference with training is not achieved by diverting the flow of information processing away from the prefrontal cortex or by segregating prefrontal cells into independent task-specific neuronal ensembles, but rather by increasing the speed of information processing in this brain region, thereby allowing multiple tasks to be processed in rapid succession. These results not only reveal how training leads to efficient multitasking, they also provide a mechanistic account of multitasking limitations, namely the poor speed of information processing in human prefrontal cortex.

关键词： Acoustic Stimulation Adult Brain Mapping Brain Mapping Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Male Mental Processes/physiology Oxygen/blood Photic Stimulation/methods Prefrontal Cortex/blood supply Prefrontal Cortex/physiology Psychomotor Performance/physiology Reaction Time/physiology Task Performance and Analysis Teaching/methods Young Adult

来源：评论

学校读者我要写书评

暂无评论

Graphical methods for quantifying macromolecules through bright field imaging

引用

BIOINFORMATICS 2009年第8期25卷 1070-1075页

作者： Chang, Hang DeFilippis, Rosa Anna Tlsty, Thea D. Parvin, Bahram Univ Calif Berkeley Lawrence Berkeley Lab Berkeley CA 94720 USA Chinese Acad Sci Inst Automat Beijing Peoples R China Univ Calif San Francisco Dept Pathol San Francisco CA USA Univ Calif Riverside Dept Elect Engn Riverside CA 92521 USA

Bright field imaging of biological samples stained with antibodies and/or special stains provides a rapid protocol for visualizing various macromolecules. However, this method of sample staining and imaging is rarely employed for direct quantitative analysis due to variations in sample fixations, ambiguities introduced by color composition and the limited dynamic range of imaging instruments. We demonstrate that, through the decomposition of color signals, staining can be scored on a cell-by-cell basis. We have applied our method to fibroblasts grown from histologically normal breast tissue biopsies obtained from two distinct populations. Initially, nuclear regions are segmented through conversion of color images into gray scale, and detection of dark elliptic features. Subsequently, the strength of staining is quantified by a color decomposition model that is optimized by a graph cut algorithm. In rare cases where nuclear signal is significantly altered as a result of sample preparation, nuclear segmentation can be validated and corrected. Finally, segmented stained patterns are associated with each nuclear region following region-based tessellation. Compared to classical non-negative matrix factorization, proposed method: (i) improves color decomposition, (ii) has a better noise immunity, (iii) is more invariant to initial conditions and (iv) has a superior computing performance.

关键词： Algorithms Animals Humans image Enhancement/methods image processing, computer-assisted/methods Pattern Recognition, Automated/methods

来源：评论

学校读者我要写书评

暂无评论

Separate Neural Mechanisms Underlie Choices and Strategic Preferences in Risky Decision Making

引用

NEURON 2009年第4期62卷 593-602页

作者： Venkatraman, Vinod Payne, John W. Bettman, James R. Luce, Mary Frances Huettel, Scott A. Duke Univ Med Ctr Brain Imaging & Anal Ctr Durham NC 27710 USA Duke Univ Ctr Neuroecon Studies Durham NC 27710 USA Duke Univ Fuqua Sch Business Durham NC 27708 USA

Adaptive decision making in real-world contexts often relies on strategic simplifications of decision problems. Yet, the neural mechanisms that shape these strategies and their implementation remain largely unknown. Using an economic decision-making task, we dissociate brain regions that predict specific choices from those predicting an individual's preferred strategy. Choices that maximized gains or minimized losses were predicted by functional magnetic resonance imaging activation in ventromedial prefrontal cortex or anterior insula, respectively. However, choices that followed a simplifying strategy (i.e., attending to overall probability of winning) were associated with activation in parietal and lateral prefrontal cortices. Dorsomedial prefrontal cortex, through differential functional connectivity with parietal and insular cortex, predicted individual variability in strategic preferences. Finally, we demonstrate that robust decision strategies follow from neural sensitivity to rewards. We conclude that decision making reflects more than compensatory interaction of choice-related regions;in addition, specific brain systems potentiate choices depending on strategies, traits, and context.

关键词： Adolescent Adult Brain Mapping Brain Mapping Cerebral Cortex/anatomy & histology Cerebral Cortex/blood supply Cerebral Cortex/physiology Choice Behavior/physiology Female Gambling Humans image processing, computer-assisted/methods Individuality Logistic Models Magnetic Resonance Imaging/methods Male Nerve Net/anatomy & histology Nerve Net/blood supply Nerve Net/physiology Neuropsychological Tests Oxygen/blood Predictive Value of Tests Probability Reward Risk-Taking Young Adult

来源：评论

学校读者我要写书评

暂无评论

Automatic cortical sulcal parcellation based on surface principal direction flow field tracking

引用

NEUROimage 2009年第4期46卷 923-937页

作者： Li, Gang Guo, Lei Nie, Jingxin Liu, Tianming Univ Georgia Dept Comp Sci Athens GA 30602 USA Univ Georgia Bioimaging Res Ctr Athens GA 30602 USA Northwestern Polytech Univ Sch Automat Xian 710072 Peoples R China

The human cerebral cortex is a highly convoluted Structure composed of sulci and gyri, corresponding to the valleys and ridges of the cortical surface respectively. Automatic parcellation of the cortical surface into sulcal regions is of great importance in structural and functional mapping of the human brain. In this paper, a novel method is proposed for automatic Cortical sulcal parcellation based on the geometric characteristics of cortical surface including its principal curvatures and principal directions. This method is composed of two major steps: 1) employing the hidden Markov random field model (HMRF) and the expectation maximization (EM) algorithm on the maximum principal curvatures of the cortical surface for sulcal region segmentation, and 2) using a principal direction flow field tracking method on the cortical surface for sulcal basin segmentation. The flow field is obtained by diffusing the principal direction field on the cortical surface mesh. A unique feature of this method is that the automatic sulcal parcellation process is quite robust and efficient, and is independent of any external guidance Such as atlas-based warping. The method has been successfully applied to the inner cortical surfaces of twelve healthy human brain MR images. Both quantitative and qualitative evaluation results demonstrate the validity and efficiency of the proposed method. (C) 2009 Elsevier Inc. All rights reserved.

关键词： Algorithms Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/anatomy & histology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Reproducibility of Results

来源：评论

学校读者我要写书评

暂无评论

VANO: a volume-object image annotation system

引用

BIOINFORMATICS 2009年第5期25卷 695-697页

作者： Peng, Hanchuan Long, Fuhui Myers, Eugene W. Howard Hughes Med Inst Ashburn VA USA

Volume-object annotation system (VANO) is a cross-platform image annotation system that enables one to conveniently visualize and annotate 3D volume objects including nuclei and cells. An application of VANO typically starts with an initial collection of objects produced by a segmentation computation. The objects can then be labeled, categorized, deleted, added, split, merged and redefined. VANO has been used to build high-resolution digital atlases of the nuclei of Caenorhabditis elegans at the L1 stage and the nuclei of Drosophila melanogaster's ventral nerve cord at the late embryonic stage.

关键词： Animals Caenorhabditis elegans/metabolism Databases, Factual Drosophila/metabolism image processing, computer-assisted/methods Software User-computer Interface

来源：评论

学校读者我要写书评

暂无评论

Three-Dimensional Analysis of the Internal Structure of the Mandibular Condyle in Dentulous and Edentulous Jaws Using Micro-CT

引用

CRANIO-THE JOURNAL OF CRANIOMANDIBULAR & SLEEP PRACTICE 2009年第2期27卷 78-87页

作者： Sugisaki, Masanori Agematsu, Hiroko Matsunaga, Satoru Saka, Hideki Sakiyama, Koji Ide, Yoshinobu Tokyo Dent Coll Dept Anat Mihama Ku Chiba 2618502 Japan

This study clarifies the internal structure of the mandibular condyle in dentulous and edentulous jaws;three-dimensional observation and morphological measurements were performed using micro-CT. The materials used in this study were 14 mandibular condyles each removed from the dentulous and edentulous cadavers. Internal structures of the mandibular condyle were morphologically analyzed in three anatomical planes. Additionally, morphometrical observations of the trabecular bone structure at five regions of interest and cortical bone thickness were performed. The mandibular condyle of dentulous jaws consisted predominantly of regularly aligned plate-shaped trabeculae. Conversely, edentulous jaws were predominantly irregularly aligned narrow rod-shaped trabeculae. The results of morphometrical analysis showed that trabecular separation (***) in the central region of the mandibular condyle most closely reflected the difference between dentulous and edentulous jaws. These results suggest that, in edentulous jaws, reduced masticatory function due to tooth loss affects the internal structures of mandibular condyle.

关键词： Adult Aged Aged, 80 and over Bone Density/physiology Cadaver Dentition Female Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Jaw, Edentulous/pathology Jaw, Edentulous/radiography Male Mandible/pathology Mandible/radiography Mandibular Condyle/pathology Mandibular Condyle/radiography Middle Aged X-Ray Microtomography/methods

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：