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https://www.readbyqxmd.com/read/28527623/automated-gold-particle-quantification-of-immunogold-labeled-micrographs
#1
Rune Enger
BACKGROUND: Immunogold cytochemistry is the method of choice for precise localization of antigens on a subcellular scale. The process of immunogold quantification in electron micrographs is laborious, especially for proteins with a dense distribution pattern. NEW METHODS: Here I present a MATLAB based toolbox that is optimized for a typical immunogold analysis workflow. It combines automatic detection of gold particles through a multi-threshold algorithm with manual segmentation of cell membranes and regions of interests...
May 17, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28523339/medial-meniscal-extrusion-a-validation-study-comparing-different-methods-of-assessment
#2
Luke D Jones, Stephen J Mellon, Neil Kruger, Andrew P Monk, Andrew J Price, David J Beard
PURPOSE: Longitudinal cohort studies of knee OA aetiology use MRI to assess meniscal extrusion within the same knee at sequential time points. A validated method of assessment is required to ensure that extrusion is measured at the same location within the knee at each time point. Absolute perpendicular extrusion from the tibial edge can be assessed using the reference standard of segmentation of the tibia and medial meniscus. This is labour intensive and unsuitable for large cohorts...
April 21, 2017: Knee Surgery, Sports Traumatology, Arthroscopy: Official Journal of the ESSKA
https://www.readbyqxmd.com/read/28520900/accelerating-high-dimensional-clustering-with-lossless-data-reduction
#3
Bahjat F Qaqish, Jonathon J O'Brien, Jonathan C Hibbard, Katie J Clowers
Motivation: For cluster analysis, high dimensional data is associated with instability, decreased classification accuracy and high computational burden. The latter challenge can be eliminated as a serious concern. For applications where dimension reduction techniques are not implemented, we propose a temporary transformation which accelerates computations with no loss of information. The algorithm can be applied for any statistical procedure depending only on Euclidean distances and can be implemented sequentially to enable analyses of data that would otherwise exceed memory limitations...
May 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28520848/pattern-fusion-analysis-by-adaptive-alignment-of-multiple-heterogeneous-omics-data
#4
Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen
Motivation: Integrating different omics profiles is a challenging task, which provides a comprehensive way to understand complex diseases in a multi-view manner. One key for such an integration is to extract intrinsic patterns in concordance with data structures, so as to discover consistent information across various data types even with noise pollution. Thus, we proposed a novel framework called "pattern fusion analysis" (PFA), which performs automated information alignment and bias correction, to fuse local sample-patterns (e...
May 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28513707/systematic-study-of-interdependent-relationship-on-gold-nanorod-synthesis-assisted-by-electron-microscopy-image-analysis
#5
Seokyoung Yoon, Byoungsang Lee, Jaesub Yun, Jeon Geon Han, Jong-Seok Lee, Jung Heon Lee
Here, we systematically investigated the independent, multiple, and synergic effects of three major components, namely, ascorbic acid (AA), seed, and silver ions (Ag(+)), on the characteristics of gold nanorods (GNRs), i.e., longitudinal localized surface plasmon resonance (LSPR) peak position, shape, size, and monodispersity. To quantitatively assess the shape and dimensions of GNRs, we used an automated transmission electron microscopy image analysis method using a MATLAB-based code developed in-house and the concept of solidity, which is the ratio between the area of a GNR and the area of its convex hull...
May 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/28506280/optimouse-a-comprehensive-open-source-program-for-reliable-detection-and-analysis-of-mouse-body-and-nose-positions
#6
Yoram Ben-Shaul
BACKGROUND: Accurate determination of mouse positions from video data is crucial for various types of behavioral analyses. While detection of body positions is straightforward, the correct identification of nose positions, usually more informative, is far more challenging. The difficulty is largely due to variability in mouse postures across frames. RESULTS: Here, we present OptiMouse, an extensively documented open-source MATLAB program providing comprehensive semiautomatic analysis of mouse position data...
May 15, 2017: BMC Biology
https://www.readbyqxmd.com/read/28499896/decreased-prefrontal-brain-activation-during-verbal-fluency-task-in-patients-with-somatoform-pain-disorder-an-exploratory-multi-channel-near-infrared-spectroscopy-study
#7
Xiajin Ren, Jinlong Lu, Xiaomin Liu, Chenyu Shen, Xiaoqian Zhang, Xiangyun Ma, Jingjing Sun, Gaoxiang Sun, Kun Feng, Bo Xu, Pozi Liu
BACKGROUND: Pain is a common phenomenon. Patients with somatoform pain disorder (SPD) suffer from lasting chronic pain which may cause cognitive impairment. The dysfunction of prefrontal cortex (PFC) may be involved in pain-induced cognition impairment, which is the most important part in regulating of cognitive function. Multi-channel near-infrared spectroscopy (NIRS) is a noninvasive and low-cost functional neuroimaging technique being used to detect the prefrontal cortex activation during cognitive tasks to demonstrate the relationship between PFC dysfunction and cognition impairment in SPD patients...
May 9, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28499817/use-of-cellnetanalyzer-in-biotechnology-and-metabolic-engineering
#8
Axel von Kamp, Sven Thiele, Oliver Hädicke, Steffen Klamt
Mathematical models of the cellular metabolism have become an essential tool for the optimization of biotechnological processes. They help to obtain a systemic understanding of the metabolic processes in the used microorganisms and to find suitable genetic modifications maximizing the production performance. In particular, methods of stoichiometric and constraint-based modeling are frequently used in the context of metabolic and bioprocess engineering. Since metabolic networks can be complex and comprise hundreds or even thousands of metabolites and reactions, dedicated software tools are required for an efficient analysis...
May 9, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28499413/ranking-metrics-in-gene-set-enrichment-analysis-do-they-matter
#9
Joanna Zyla, Michal Marczyk, January Weiner, Joanna Polanska
BACKGROUND: There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment Analysis seems to be one of the most commonly used (over 10,000 citations). An important parameter, which could affect the final result, is the choice of a metric for the ranking of genes. Applying a default ranking metric may lead to poor results. METHODS AND RESULTS: In this work 28 benchmark data sets were used to evaluate the sensitivity and false positive rate of gene set analysis for 16 different ranking metrics including new proposals...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28497476/optimization-of-a-novel-large-field-of-view-distortion-phantom-for-mr-only-treatment-planning
#10
Ryan G Price, Robert A Knight, Ken-Pin Hwang, Ersin Bayram, Siamak P Nejad-Davarani, Carri K Glide-Hurst
PURPOSE: MR-only treatment planning requires images of high geometric fidelity, particularly for large fields of view (FOV). However, the availability of large FOV distortion phantoms with analysis software is currently limited. This work sought to optimize a modular distortion phantom to accommodate multiple bore configurations and implement distortion characterization in a widely implementable solution. METHOD AND MATERIALS: To determine candidate materials, 1...
May 12, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28497058/impact-of-an-intensive-perinatal-handwashing-promotion-intervention-on-maternal-handwashing-behavior-in-the-neonatal-period-findings-from-a-randomized-controlled-trial-in-rural-bangladesh
#11
Pavani Kalluri Ram, Sharifa Nasreen, Kelly Kamm, Jelena Allen, Swapna Kumar, Mohammad Anisur Rahman, K Zaman, Shams El Arifeen, Stephen P Luby
One-quarter of neonatal deaths are attributed to infections. Maternal handwashing with soap may prevent neonatal sepsis. We examined impact of intensive handwashing promotion on handwashing behavior of mothers of neonates. In Matlab, Bangladesh, we randomly allocated pregnant women at 28-32 weeks' gestation to intensive handwashing promotion or control. Behavior change communicators used a participatory approach to motivate maternal handwashing with soap and provided soap and handwashing stations. In the neonatal period, we observed soap and water at handwashing places and, at the end of the neonatal period, we estimated impact on maternal handwashing by structured observation...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28494801/spectral-imaging-toolbox-segmentation-hyperstack-reconstruction-and-batch-processing-of-spectral-images-for-the-determination-of-cell-and-model-membrane-lipid-order
#12
Miles Aron, Richard Browning, Dario Carugo, Erdinc Sezgin, Jorge Bernardino de la Serna, Christian Eggeling, Eleanor Stride
BACKGROUND: Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually characterized by the generalized polarization (GP) parameter. With the development of commercial microscopes equipped with spectral detectors, spectral imaging has become a convenient and powerful technique for measuring GP and other membrane properties. The existing tools for spectral image processing, however, are insufficient for processing the large data sets afforded by this technological advancement, and are unsuitable for processing images acquired with rapidly internalized fluorescent probes...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28494118/objective-automated-quantification-of-fluorescence-signal-in-histological-sections-of-rat-lens
#13
Nooshin Talebizadeh, Nanna Zhou Hagström, Zhaohua Yu, Martin Kronschläger, Per Söderberg, Carolina Wählby
Visual quantification and classification of fluorescent signals is the gold standard in microscopy. The purpose of this study was to develop an automated method to delineate cells and to quantify expression of fluorescent signal of biomarkers in each nucleus and cytoplasm of lens epithelial cells in a histological section. A region of interest representing the lens epithelium was manually demarcated in each input image. Thereafter, individual cell nuclei within the region of interest were automatically delineated based on watershed segmentation and thresholding with an algorithm developed in Matlab™...
May 11, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28493938/sleep-spindle-detection-based-on-non-experts-a-validation-study
#14
Rui Zhao, Jinbo Sun, Xinxin Zhang, Huanju Wu, Peng Liu, Xuejuan Yang, Wei Qin
Accurate and efficient detection of sleep spindles is a methodological challenge. The present study describes a method of using non-experts for manual detection of sleep spindles. We recruited five experts and 168 non-experts to manually identify spindles in stage N2 and stage N3 sleep data using a MATLAB interface. Scorers classified each spindle into definite and indefinite spindle (with weights of 1 and 0.5, respectively). First, a method of optimizing the thresholds of the expert/non-expert group consensus according to the results of experts and non-experts themselves is described...
2017: PloS One
https://www.readbyqxmd.com/read/28493880/identifying-stochastic-oscillations-in-single-cell-live-imaging-time-series-using-gaussian-processes
#15
Nick E Phillips, Cerys Manning, Nancy Papalopulu, Magnus Rattray
Multiple biological processes are driven by oscillatory gene expression at different time scales. Pulsatile dynamics are thought to be widespread, and single-cell live imaging of gene expression has lead to a surge of dynamic, possibly oscillatory, data for different gene networks. However, the regulation of gene expression at the level of an individual cell involves reactions between finite numbers of molecules, and this can result in inherent randomness in expression dynamics, which blurs the boundaries between aperiodic fluctuations and noisy oscillators...
May 11, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28490352/a-diagnostic-biomarker-profile-for-fibromyalgia-syndrome-based-on-an-nmr-metabolomics-study-of-selected-patients-and-controls
#16
Bontle G Malatji, Helgard Meyer, Shayne Mason, Udo F H Engelke, Ron A Wevers, Mari van Reenen, Carolus J Reinecke
BACKGROUND: Fibromyalgia syndrome (FMS) is a chronic pain syndrome. A plausible pathogenesis of the disease is uncertain and the pursuit of measurable biomarkers for objective identification of affected individuals is a continuing endeavour in FMS research. Our objective was to perform an explorative metabolomics study (1) to elucidate the global urinary metabolite profile of patients suffering from FMS, and (2) to explore the potential of this metabolite information to augment existing medical practice in diagnosing the disease...
May 11, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28488257/a-comparison-of-four-software-programs-for-implementing-decision-analytic-cost-effectiveness-models
#17
REVIEW
Chase Hollman, Mike Paulden, Petros Pechlivanoglou, Christopher McCabe
The volume and technical complexity of both academic and commercial research using decision analytic modelling has increased rapidly over the last two decades. The range of software programs used for their implementation has also increased, but it remains true that a small number of programs account for the vast majority of cost-effectiveness modelling work. We report a comparison of four software programs: TreeAge Pro, Microsoft Excel, R and MATLAB. Our focus is on software commonly used for building Markov models and decision trees to conduct cohort simulations, given their predominance in the published literature around cost-effectiveness modelling...
May 9, 2017: PharmacoEconomics
https://www.readbyqxmd.com/read/28488217/electrical-stimulation-increases-random-migration-of-human-dermal-fibroblasts
#18
Sarah Snyder, Carlisle DeJulius, Rebecca Kuntz Willits
Exogenous electrical stimulation (ES) has been investigated as a therapy for chronic wounds, as the skin produces currents and electrical fields (EFs) during wound healing. ES therapies operate by applying small EFs to the skin to mimic the transepithelial potentials that occur during the granulation phase of wound healing. Here, we investigated the effect of short duration (10 min) ES on the migration of HDFs using various magnitudes of physiologically relevant EFs. We modeled cutaneous injury by culturing HDFs in custom chambers that allowed the application of ES and then performed timelapse microscopy on a standard wound model...
May 9, 2017: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/28487831/a-new-parallel-approach-for-accelerating-the-gpu-based-execution-of-edge-detection-algorithms
#19
Zahra Emrani, Soroosh Bateni, Hossein Rabbani
Real-time image processing is used in a wide variety of applications like those in medical care and industrial processes. This technique in medical care has the ability to display important patient information graphi graphically, which can supplement and help the treatment process. Medical decisions made based on real-time images are more accurate and reliable. According to the recent researches, graphic processing unit (GPU) programming is a useful method for improving the speed and quality of medical image processing and is one of the ways of real-time image processing...
January 2017: Journal of Medical Signals and Sensors
https://www.readbyqxmd.com/read/28485748/genespider-gene-regulatory-network-inference-benchmarking-with-controlled-network-and-data-properties
#20
Andreas Tjärnberg, Daniel C Morgan, Matthew Studham, Torbjörn E M Nordling, Erik L L Sonnhammer
A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method. We present GeneSPIDER - a Matlab package for tuning, running, and evaluating inference algorithms that allows independent control of network and data properties to enable data-driven benchmarking. GeneSPIDER is uniquely suited to address this question by first extracting salient properties from the experimental data and then generating simulated networks and data that closely match these properties...
May 9, 2017: Molecular BioSystems
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