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Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression

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BIOINFORMATICS 2014年第2期30卷 266-273页

作者： Yuan, Lei Pan, Cheng Ji, Shuiwang McCutchan, Michael Zhou, Zhi-Hua Newfeld, Stuart J. Kumar, Sudhir Ye, Jieping Arizona State Univ Sch Comp Informat & Decis Syst Engn Tempe AZ 85287 USA Arizona State Univ Ctr Evolutionary Med & Informat Biodesign Inst Tempe AZ 85287 USA Nanjing Univ Natl Key Lab Novel Software Technol Nanjing 210023 Jiangsu Peoples R China Arizona State Univ Sch Life Sci Tempe AZ 85287 USA King Abdulaziz Univ Ctr Excellence Genom Med Res Jeddah 21413 Saudi Arabia

Motivation: Drosophila melanogaster is a major model organism for investigating the function and interconnection of animal genes in the earliest stages of embryogenesis. Today, images capturing Drosophila gene expression patterns are being produced at a higher throughput than ever before. The analysis of spatial patterns of gene expression is most biologically meaningful when images from a similar time point during development are compared. Thus, the critical first step is to determine the developmental stage of an embryo. This information is also needed to observe and analyze expression changes over developmental time. Currently, developmental stages (time) of embryos in images capturing spatial expression pattern are annotated manually, which is time-and labor-intensive. Embryos are often designated into stage ranges, making the information on developmental time course. This makes downstream analyses inefficient and biological interpretations of similarities and differences in spatial expression patterns challenging, particularly when using automated tools for analyzing expression patterns of large number of images. Results: Here, we present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In an analysis of 3724 images, the new approach shows high accuracy in predicting the developmental stage correctly (79%). In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores for all images containing expression patterns of the same gene enable a direct way to view expression changes over developmental time for any gene. We show that the genomewide-expression-maps generated using images from embryos in refined stages illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results whe

关键词： Algorithms Animals Computational Biology Drosophila melanogaster/embryology Drosophila melanogaster/genetics Drosophila Proteins/genetics Drosophila Proteins/genetics Embryo, Nonmammalian/cytology Embryo, Nonmammalian/metabolism Embryonic Development/genetics Gene Expression Profiling Gene Expression Regulation, Developmental image processing, computer-assisted Pattern Recognition, Automated

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Localized diffusion magnetic resonance micro-imaging of the live mouse brain

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NEUROimage 2014年 91卷 12-20页

作者： Wu, Dan Reisinger, Dominik Xu, Jiadi Fatemi, S. Ali van Zijl, Peter C. M. Mori, Susumu Zhang, Jiangyang Johns Hopkins Univ Sch Med Dept Radiol Baltimore MD 21205 USA Johns Hopkins Univ Sch Med Dept Biomed Engn Baltimore MD 21205 USA Johns Hopkins Univ Sch Med Dept Neurol Baltimore MD 21205 USA Kennedy Krieger Inst FM Kirby Res Ctr Funct Brain Imaging Baltimore MD USA Kennedy Krieger Inst Div Neurol & Dev Med Baltimore MD USA

High-resolution diffusion MRI (dMRI) is useful for resolving complex microstructures in the mouse brain, but technically challenging for in vivo studies due to the long scan time. In this study, selective excitation and a three-dimensional fast imaging sequence were used to achieve in vivo high-resolution dMRI of the mouse brain at 11.7 Tesla. By reducing the field of view using spatially selective radio frequency pulses, we were able to focus on targeted brain structures and acquire high angular resolution diffusion imaging (HARDI) data at an isotropic resolution of 0.1 mm and 30 diffusion encoding directions in approximately 1 h. We investigated the complex tissue microstructures of the mouse hippocampus, cerebellum, and several cortical areas using this localized dMRI approach, and compared the results with histological sections stained with several axonal and dendritic markers. In the mouse visual cortex, the results showed predominately radially arranged structures in an outer layer and tangentially arranged structures in an inner layer, similar to observations from postmortem human brain specimens. (C) 2014 Elsevier Inc. All rights reserved.

关键词： Algorithms Animals Axons/physiology Brain/anatomy & histology Dendrites/physiology Diffusion Magnetic Resonance Imaging/instrumentation Diffusion Magnetic Resonance Imaging/methods Female image processing, computer-assisted Imaging, Three-Dimensional Immunohistochemistry Immunohistochemistry Mice Mice, Inbred C57BL Neuroimaging/instrumentation Neuroimaging/methods Software Visual Cortex/anatomy & histology Visual Cortex/physiology

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Knowledge-based automated reconstruction of human brain white matter tracts using a path-finding approach with dynamic programming

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NEUROimage 2014年 88卷 271-281页

作者： Li, Muwei Ratnanather, J. Tilak Miller, Michael I. Mori, Susumu Johns Hopkins Univ Sch Med Russell H Morgan Dept Radiol & Radiol Sci Baltimore MD 21218 USA Sichuan Univ Coll Elect & Informat Engn Chengdu 610064 Sichuan Peoples R China Johns Hopkins Univ Ctr Imaging Sci Baltimore MD USA Johns Hopkins Univ Inst Computat Med Baltimore MD USA Johns Hopkins Univ Dept Biomed Engn Baltimore MD USA Kennedy Krieger Inst FM Kirby Res Ctr Funct Brain Imaging Baltimore MD USA

It has been shown that the anatomy of major white matter tracts can be delineated using diffusion tensor imaging (DTI) data. Tract reconstruction, however, often suffers from a large number of false-negative results when a simple line propagation algorithm is used. This limits the application of this technique to only the core of prominent white matter tracts. By employing probabilistic path-generation algorithms, connectivity between a larger number of anatomical regions can be studied, but an increase in the number of false-positive results is inevitable. One of the causes of the inaccuracy is the complex axonal anatomy within a voxel;however, highangular resolution (HAR) methods have been proposed to ameliorate this limitation. However, HAR data are relatively rare due to the long scan times required and the low signal-to-noise ratio. In this study, we tested a probabilistic path-finding method in which two anatomical regions with known connectivity were pre-defined and a path that maximized agreement with the DTI data was searched. To increase the accuracy of the trajectories, knowledge-based anatomical constraints were applied. The reconstruction protocols were tested using DTI data from 19 normal subjects to examine test-retest reproducibility and cross-subject variability. Fifty-two tracts were found to be reliably reconstructed using this approach, which can be viewed on our website. (C) 2013 Elsevier Inc. All rights reserved.

关键词： Adult Algorithms Brain/anatomy & histology Diffusion Tensor Imaging Diffusion Tensor Imaging Female Humans image processing, computer-assisted Male Middle Aged Nerve Fibers, Myelinated Software Young Adult

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Diagnosing malaria infected cells at the single cell level using focal plane array Fourier transform infrared imaging spectroscopy

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ANALYST 2014年第19期139卷 4769-4774页

作者： Wood, Bayden R. Bambery, Keith. R. Dixon, Matthew W. A. Tilley, Leann Nasse, Michael J. Mattson, Eric Hirschmugl, Carol J. Monash Univ Sch Chem Ctr Biospectroscopy Clayton Vic 3800 Australia Australian Synchrotron Clayton Vic 3168 Australia Univ Melbourne Dept Biochem & Mol Biol Inst Bio21 Melbourne Vic 3010 Australia Univ Melbourne ARC Ctr Excellence Coherent Xray Sci Melbourne Vic 3010 Australia Karlsruhe Inst Technol Lab Applicat Synchrotron Radiat D-76049 Karlsruhe Germany Univ Wisconsin Dept Phys Milwaukee WI 53211 USA

New methods are needed to rapidly identify malaria parasites in blood smears. The coupling of a Focal Plane Array (FPA) infrared microscope system to a synchrotron light source at IRENI enables rapid molecular imaging at high spatial resolution. The technique, in combination with hyper-spectral processing, enables imaging and diagnosis of early stage malaria parasites at the single cell level in a blood smear. The method relies on the detection of distinct lipid signatures associated with the different stages of the malaria parasite and utilises resonant Mie extended multiplicative scatter correction to pre-process the spectra followed by full bandwidth image deconvolution to resolve the single cells. This work demonstrates the potential of focal plane technology to diagnose single cells in a blood smear. Brighter laboratory based infrared sources, optical refinements and higher sensitive detectors will soon see the emergence of focal plane array imaging in the clinical environment.

关键词： Erythrocytes/cytology Erythrocytes/parasitology Humans image processing, computer-assisted Malaria/diagnosis Malaria/parasitology Photomicrography Plasmodium falciparum/immunology Plasmodium falciparum/isolation & purification Principal Component Analysis Single-Cell Analysis Spectroscopy, Fourier Transform Infrared Tissue Array Analysis

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Applications of multivariate modeling to neuroimaging group analysis: A comprehensive alternative to univariate general linear model

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NEUROimage 2014年 99卷 571-588页

作者： Chen, Gang Adleman, Nancy E. Saad, Ziad S. Leibenluft, Ellen Cox, Robert W. NIMH Sci & Stat Comp Core NIH Dept Hlth & Human Serv Bethesda MD 20892 USA Catholic Univ Amer Dept Psychol Washington DC 20064 USA NIMH Sect Bipolar Spectrum Disorders Emot & Dev Branch NIHDept Hlth & Human Serv Bethesda MD USA

All neuroimaging packages can handle group analysis with t-tests or general linear modeling (GLM). However, they are quite hamstrung when there are multiple within-subject factors or when quantitative covariates are involved in the presence of a within-subject factor. In addition, sphericity is typically assumed for the variance-co-variance structure when there are more than two levels in a within-subject factor. To overcome such limitations in the traditional AN(C)OVA and GLM, we adopt a multivariate modeling (MVM) approach to analyzing neuroimaging data at the group level with the following advantages: a) there is no limit on the number of factors as long as sample sizes are deemed appropriate;b) quantitative covariates can be analyzed together with within-subject factors;c) when a within-subject factor is involved, three testing methodologies are provided: traditional univariate testing (UVT) with sphericity assumption (UVT-UC) and with correction when the assumption is violated (UVT-SC), and within-subject multivariate testing (MVT-WS);d) to correct for sphericity violation at the voxel level, we propose a hybrid testing (FIT) approach that achieves equal or higher power via combining traditional sphericity correction methods (Greenhouse-Geisser and Huynh-Feldt) with MVT-WS. To validate the MVM methodology, we performed simulations to assess the controllability for false positives and power achievement. A real FMRI dataset was analyzed to demonstrate the capability of the MVM approach. The methodology has been implemented into an open source program 3dMVM in AFNI, and all the statistical tests can be performed through symbolic coding with variable names instead of the tedious process of dummy coding. Our data indicates that the severity of sphericity violation varies substantially across brain regions. The differences among various modeling methodologies were addressed through direct comparisons between the MVM approach and some of the GLM implementations in the

关键词： Adolescent Child False Positive Reactions Female Humans image processing, computer-assisted Linear Models Magnetic Resonance Imaging Male Models, Neurological Multivariate Analysis Neuroimaging/methods Reaction Time/physiology Reading Reproducibility of Results Sample Size

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Investigating intrinsic connectivity networks using simultaneous BOLD and CBF measurements

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NEUROimage 2014年 99卷 111-121页

作者： Mayhew, S. D. Mullinger, K. J. Bagshaw, A. P. Bowtell, R. Francis, S. T. Univ Birmingham Sch Psychol BUIC Birmingham B15 2TT W Midlands England Univ Nottingham Sch Phys & Astron Sir Peter Mansfield Magnet Resonance Ctr Nottingham NG7 2RD England

When the sensory cortex is stimulated and directly receiving afferent input, modulations can also be observed in the activity of other brain regions comprising spatially distributed, yet intrinsically connected networks, suggesting that these networks support brain function during task performance. Such networks can exhibit subtle or unpredictable task responses which can pass undetected by conventional general linear modelling (GLM). Additionally, the metabolic demand of these networks in response to stimulation remains incompletely understood. Here, we recorded concurrent BOLD and CBF measurements during median nerve stimulation (MNS) and compared GLM analysis with independent component analysis (ICA) for identifying the spatial, temporal and metabolic properties of responses in the primary sensorimotor cortex (S1/M1), and in the default mode (DMN) and fronto-parietal (FPN) networks. Excellent spatial and temporal agreement was observed between the positive BOLD and CBF responses to MNS detected by GLM and ICA in contralateral S1/M1. Values of the change in cerebral metabolic rate of oxygen consumption (Delta%CMRO2) and the Delta%CMRO2/Delta%CBF coupling ratio were highly comparable when using either GLM analysis or ICA to extract the contralateral S1/M1 responses, validating the use of ICA for estimating changes in CMRO2. ICA identified DMN and FPN network activity that was not detected by GLM analysis. Using ICA, spatially coincident increases/decreases in both BOLD and CBF signals to MNS were found in the FPN/DMN respectively. Calculation of CMRO2 changes in these networks during MNS showed that the Delta%CMRO2/Delta%CBF ratio is comparable between the FPN and S1/M1 but is larger in the DMN than in the FPN, assuming an equal value of the parameter M in the DMN, FPN and S1/M1. This work suggests that metabolism-flow coupling may differ between these two fundamental brain networks, which could originate from differences between task-positive and task-negative fMR

关键词： Adult Brain/anatomy & histology Cerebrospinal Fluid/physiology Electric Stimulation Female Frontal Lobe/anatomy & histology Humans image processing, computer-assisted Magnetic Resonance Imaging Male Median Nerve/physiology Nerve Net/anatomy & histology Oxygen/blood Parietal Lobe/anatomy & histology

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The Principal Role of Ku in Telomere Length Maintenance Is Promotion of Est1 Association with Telomeres

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GENETICS 2014年第4期197卷 1123-U112页

作者： Williams, Jaime M. Ouenzar, Faissal Lemon, Laramie D. Chartrand, Pascal Bertuch, Alison A. Baylor Coll Med Dept Mol & Human Genet Houston TX 77030 USA Baylor Coll Med Integrat Mol & Biomed Sci Grad Program Houston TX 77030 USA Baylor Coll Med Dept Pediat Houston TX 77030 USA Univ Montreal Dept Biochem Montreal PQ H3C 3J7 Canada

Telomere length is tightly regulated in cells that express telomerase. The Saccharomyces cerevisiae Ku heterodimer, a DNA end-binding complex, positively regulates telomere length in a telomerase-dependent manner. Ku associates with the telomerase RNA subunit TLC1, and this association is required for TLC1 nuclear retention. Ku-TLC1 interaction also impacts the cell-cycle-regulated association of the telomerase catalytic subunit Est2 to telomeres. The promotion of TLC1 nuclear localization and Est2 recruitment have been proposed to be the principal role of Ku in telomere length maintenance, but neither model has been directly tested. Here we study the impact of forced recruitment of Est2 to telomeres on telomere length in the absence of Ku's ability to bind TLC1 or DNA ends. We show that tethering Est2 to telomeres does not promote efficient telomere elongation in the absence of Ku TLC1 interaction or DNA end binding. Moreover, restoration of TLC1 nuclear localization, even when combined with Est2 recruitment, does not bypass the role of Ku. In contrast, forced recruitment of Est1, which has roles in telomerase recruitment and activation, to telomeres promotes efficient and progressive telomere elongation in the absence of Ku-TLC1 interaction, Ku DNA end binding, or Ku altogether. Ku associates with Est1 and Est2 in a TLC1-dependent manner and enhances Est1 recruitment to telomeres independently of Est2. Together, our results unexpectedly demonstrate that the principal role of Ku in telomere length maintenance is to promote the association of Est1 with telomeres, which may in turn allow for efficient recruitment and activation of the telomerase holoenzyme.

关键词： DNA, Fungal/genetics DNA-Binding Proteins/genetics DNA-Binding Proteins/metabolism image processing, computer-assisted In Situ Hybridization, Fluorescence In Situ Hybridization, Fluorescence Promoter Regions, Genetic Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins/genetics Saccharomyces cerevisiae Proteins/metabolism Telomerase/genetics Telomerase/metabolism Telomere/metabolism Telomere Homeostasis/genetics

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Estimating time-varying brain connectivity networks from functional MRI time series

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NEUROimage 2014年 103卷 427-443页

作者： Monti, Ricardo Pio Hellyer, Peter Sharp, David Leech, Robert Anagnostopoulos, Christoforos Montana, Giovanni Univ London Imperial Coll Sci Technol & Med Dept Math London SW7 2AZ England Univ London Imperial Coll Sci Technol & Med Hammersmith Hosp Computat Cognit & Clin Neuroimaging Lab London W12 0NN England Kings Coll London Dept Biomed Engn St Thomas Hosp London SE1 7EH England

At the forefront of neuroimaging is the understanding of the functional architecture of the human brain. Inmost applications functional networks are assumed to be stationary, resulting in a single network estimated for the entire time course. However recent results suggest that the connectivity between brain regions is highly non-stationary even at rest. As a result, there is a need for new brain imaging methodologies that comprehensively account for the dynamic nature of functional networks. In this work we propose the Smooth Incremental Graphical Lasso Estimation ( SINGLE) algorithm which estimates dynamic brain networks from fMRI data. We apply the proposed algorithm to functional MRI data from 24 healthy patients performing a Choice Reaction Task to demonstrate the dynamic changes in network structure that accompany a simple but attentionally demanding cognitive task. Using graph theoretic measures we show that the properties of the Right Inferior Frontal Gyrus and the Right Inferior Parietal lobe dynamically change with the task. These regions are frequently reported as playing an important role in cognitive control. Our results suggest that both these regions play a key role in the attention and executive function during cognitively demanding tasks and may be fundamental in regulating the balance between other brain regions. (C) 2014 Published by Elsevier Inc.

关键词： Algorithms Brain/physiology Brain Mapping/methods Brain Mapping/methods Humans image processing, computer-assisted Magnetic Resonance Imaging/methods Neural Pathways/physiology

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Electrophysiology of Arcuate Neurokinin B Neurons in Female Tac2-EGFP Transgenic Mice

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ENDOCRINOLOGY 2014年第7期155卷 2555-2565页

作者： Cholanian, Marina Krajewski-Hall, Sally J. Levine, Richard B. McMullen, Nathaniel T. Rance, Naomi E. Univ Arizona Coll Med Dept Pathol Tucson AZ 85724 USA Univ Arizona Dept Neurosci Tucson AZ 85724 USA Univ Arizona Coll Med Dept Cellular & Mol Med Tucson AZ 85724 USA Univ Arizona Coll Med Dept Neurol Tucson AZ 85724 USA Univ Arizona Coll Med Evelyn F McKnight Brain Inst Tucson AZ 85724 USA

Neurons in the arcuate nucleus that coexpress kisspeptin, neurokinin B (NKB), and dynorphin (KNDy neurons) play an important role in the modulation of reproduction by estrogens. Here, we study the anatomical and electrophysiological properties of arcuate NKB neurons in heterozygous female transgenic mice with enhanced green fluorescent protein (EGFP) under the control of the Tac2 (NKB) promoter (Tac2-EGFP mice). The onset of puberty, estrous cyclicity, and serum LH were comparable between Tac2-EGFP and wild-type mice. The location of EGFP-immunoreactive neurons was consistent with previous descriptions of Tac2 mRNA-expressing neurons in the rodent. In the arcuate nucleus, nearly 80% of EGFP neurons expressed pro-NKB-immunoreactivity. Moreover, EGFP fluorescent intensity in arcuate neurons was increased by ovariectomy and reduced by 17 beta-estradiol (E-2) treatment. Electrophysiology of single cells in tissue slices was used to examine the effects of chronic E-2 treatment on Tac2-EGFP neurons in the arcuate nucleus of ovariectomized mice. Whole-cell recordings revealed arcuate NKB neurons to be either spontaneously active or silent in both groups. E-2 had no significant effect on the basic electrophysiological properties or spontaneous firing frequencies. Arcuate NKB neurons exhibited either tonic or phasic firing patterns in response to a series of square-pulse current injections. Notably, E-2 reduced the number of action potentials evoked by depolarizing current injections. This study demonstrates the utility of the Tac2-EGFP mouse for electrophysiological and morphological studies of KNDy neurons in tissue slices. In parallel to E-2 negative feedback on LH secretion, E-2 decreased the intensity of the EGFP signal and reduced the excitability of NKB neurons in the arcuate nucleus of ovariectomized Tac2-EGFP mice.

关键词： Action Potentials/drug effects Action Potentials/physiology Animals Arcuate Nucleus of Hypothalamus/cytology Arcuate Nucleus of Hypothalamus/metabolism Estradiol/blood Estradiol/pharmacology Estrogens/blood Estrogens/pharmacology Female Green Fluorescent Proteins/genetics Green Fluorescent Proteins/metabolism image processing, computer-assisted Immunohistochemistry Immunohistochemistry Luteinizing Hormone/blood Membrane Potentials/drug effects Membrane Potentials/physiology Mice Mice, Transgenic Mice, Transgenic Microscopy, Fluorescence Neurokinin B/genetics Neurokinin B/metabolism Neurons/metabolism Neurons/physiology Ovariectomy Patch-Clamp Techniques Patch-Clamp Techniques Promoter Regions, Genetic/genetics Protein Precursors/genetics Protein Precursors/metabolism

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Webcam-based flow cytometer using wide-field imaging for low cell number detection at high throughput

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ANALYST 2014年第17期139卷 4322-4329页

作者： Balsam, Joshua Bruck, Hugh Alan Rasooly, Avraham US FDA Div Biol Off Sci & Engn Silver Spring MD 20993 USA Univ Maryland College Pk MD 20742 USA Natl Canc Inst Div Canc Biol NIH NCI Rockville MD 20850 USA

Here we describe a novel low-cost flow cytometer based on a webcam capable of tow cell number detection in a large volume which may overcome the limitations of current flow cytometry. Several key elements have been combined to yield both high throughput and high sensitivity. The first element is a commercially available webcam capable of 187 frames per second video capture at a resolution of 320 x 240 pixels. The second element in this design is a 1 W 450 nm laser module for area-excitation, which combined with the webcam allows for rapid interrogation of a flow field. The final element is a 2D flow-cell which overcomes the flow limitation of hydrodynamic focusing and allows for higher sample throughput in a wider flow field. This cell allows for the linear velocity of target cells to be lower than in a conventional "1D" hydrodynamic focusing flow-cells typically used in cytometry at similar volumetric flow rates. It also allows cells to be imaged at the full frame rate of the webcam. Using this webcam-based flow cytometer with wide-field imaging, it was confirmed that the detection of fluorescently tagged 5 gm polystyrene beads in "1D" hydrodynamic focusing flow-cells was not practical for low cell number detection due to streaking from the motion of the beads, which did not occur with the 2D flow-cell design. The sensitivity and throughput of this webcam-based flow cytometer was then investigated using THP-1 human monocytes stained with SYTO-9 florescent dye in the 2D flow-cell The flow cytometer was found to be capable of detecting fluorescently tagged cells at concentrations as low as 1 cell per mL at flow rates of 500 mu L min(-1) in buffer and in blood. The effectiveness of detection was concentration dependent: at 100 cells per mL 84% of the cells were detected compared to microscopy, 10 cells per mL 79% detected and 1 cell per mL 59% of the cells were detected. With the blood samples spiked to 100 cells per mL, the average concentration for all samples was 9

关键词： Cell Count Cell Count Cell Line Equipment Design Flow Cytometry/instrumentation Flow Cytometry/instrumentation Fluorescent Dyes/analysis High-Throughput Screening Assays/instrumentation Humans Hydrodynamics image processing, computer-assisted Microfluidic Analytical Techniques Monocytes/cytology Organic Chemicals/analysis

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