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Félix Proulx-Giraldeau, Thomas J Rademaker, Paul François
Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. Here, we propose a simple procedure (called ϕ¯) to reduce biological models to functional submodules, using statistical mechanics of complex systems combined with a fitness-based approach inspired by in silico evolution. The ϕ¯ algorithm works by putting parameters or combination of parameters to some asymptotic limit, while keeping (or slightly improving) the model performance, and requires parameter symmetry breaking for more complex models...
October 17, 2017: Biophysical Journal
Delphine Vallot, Olivier Caselles, Leonor Chaltiel, Anthony Fernandez, Erwan Gabiache, Lawrence Dierickx, Slimane Zerdoud, Mathilde Bauriaud, Frédéric Courbon
PURPOSE: The aim of this study was to evaluate the impact of using the Bayesian penalized likelihood (BPL) algorithm on a bismuth germanium oxide positron emission tomography (PET)/computed tomography (CT) system for F-FDG PET/CT exams in case of low injected activity and scan duration. MATERIALS AND METHODS: F-FDG respiratory gated PET/CT performed on 102 cancer patients, injected with ∼2 MBq/kg of F-FDG, were reconstructed using two algorithms: ordered subset expectation maximization (OSEM) and BPL...
November 2017: Nuclear Medicine Communications
Gyu Rie Lee, Lim Heo, Chaok Seok
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted residue contacts. Given semi-reliable or incomplete structural information, structure quality of a protein model has to be improved by ab initio methods such as energy-based simulation. In this study, we describe a new automatic refinement server method designed to improve locally inaccurate regions and overall structure simultaneously...
October 16, 2017: Proteins
David Godefroy, Chloé Dominici, Hélène Hardin-Pouzet, Youssef Anouar, Stéphane Melik-Parsadaniantz, William Rostene, Annabelle Reaux-Le Goazigo
Over the years, advances in immunohistochemistry techniques have been a critical step in detecting and mapping neuromodulatory substances in the central nervous system. The better quality and specificity of primary antibodies, new staining procedures and the spectacular development of imaging technologies have allowed such progress. Very recently, new methods permitting tissue transparency have been successfully used on brain tissues. In this work, we combined whole-mount immunostaining for tyrosine hydroxylase (TH), oxytocin (OXT) and arginine vasopressin (AVP), with iDISCO+ clearing method, light-sheet microscopy and semi automated counting of 3D-labelled neurons to obtain a 3D distribution of these neuronal populations in a 5-day postnatal (P5) mouse brain...
October 16, 2017: Journal of Neuroendocrinology
Luciano A Abriata, Lisa N Kinch, Giorgio E Tamò, Bohdan Monastyrskyy, Andriy Kryshtafovych, Matteo Dal Peraro
For assessment purposes, CASP targets are split into evaluation units. We herein present the official definition of CASP12 evaluation units (EUs) and their classification into difficulty categories. Each target can be evaluated as one EU (the whole target) or/and several EUs (separate structural domains or groups of structural domains). The specific scenario for a target split is determined by the domain organization of available templates, the difference in server performance on separate domains versus combination of the domains, and visual inspection...
October 16, 2017: Proteins
Iyas Hamdan, Julien Bert, Catherine Cheze Le Rest, Jean Pierre Tasu, Nicolas Boussion, Antoine Valeri, Guillaume Dardenne, Dimitris Visvikis
PURPOSE: In prostate radiotherapy, dose distribution may be calculated on CT images, while the MRI can be used to enhance soft tissue visualization. Therefore, a registration between MR and CT images could improve the overall treatment planning process, by improving visualization with a demonstrated inter-observer delineation variability when segmenting the prostate, which in turn can lead to a more precise planning. This registration must compensate for prostate deformations caused by changes in size and form between the acquisitions of both modalities...
October 17, 2017: Medical Physics
Dev Kumar DAS, Asok Kumar Maiti, Chandan Chakraborty
In this paper, we have presented a new computer-aided technique for automatic detection of nucleated red blood cells (NRBCs) or normoblast cell from peripheral blood smear image. The proposed methodology initiates with the localization of the nucleated cells by adopting multilevel thresholding approach in smear images. A novel colour space transformation technique has been introduced to differentiate nucleated blood cells [white blood cells (WBCs) and NRBC] from red blood cells (RBCs) by enhancing the contrast between them...
October 17, 2017: Journal of Microscopy
Mustafa Ugur Daloglu, Aydogan Ozcan
Not only essential for scientific research, but also in the analysis of male fertility and for animal husbandry, sperm tracking and characterization techniques have been greatly benefiting from computational imaging. Digital image sensors, in combination with optical microscopy tools and powerful computers, have enabled the use of advanced detection and tracking algorithms that automatically map sperm trajectories and calculate various motility parameters across large data sets. Computational techniques are driving the field even further, facilitating the development of unconventional sperm imaging and tracking methods that do not rely on standard optical microscopes and objective lenses, which limit the field of view and volume of the semen sample that can be imaged...
August 1, 2017: Biology of Reproduction
Ke Fan, Sheng Zhang, Ying Zhang, Jun Lu, Mike Holcombe, Xiao Zhang
During cellular reprogramming, the mesenchymal-to-epithelial transition is accompanied by changes in morphology, which occur prior to iPSC colony formation. The current approach for detecting morphological changes associated with reprogramming purely relies on human experiences, which involve intensive amounts of upfront training, human error with limited quality control and batch-to-batch variations. Here, we report a time-lapse-based bright-field imaging analysis system that allows us to implement a label-free, non-invasive approach to measure morphological dynamics...
October 18, 2017: Scientific Reports
Mark Fricker, Luke Heaton, Nick Jones, Boguslaw Obara, Stefanie J Müller, Andreas J Meyer
The plant endoplasmic reticulum forms a network of tubules connected by three-way junctions or sheet-like cisternae. Although the network is three-dimensional, in many plant cells, it is constrained to a thin volume sandwiched between the vacuole and plasma membrane, effectively restricting it to a 2-D planar network. The structure of the network, and the morphology of the tubules and cisternae can be automatically extracted following intensity-independent edge-enhancement and various segmentation techniques to give an initial pixel-based skeleton, which is then converted to a graph representation...
2018: Methods in Molecular Biology
Hui Zhang, Yi Jin, John S Y Chan, Feng-Chi Yang, Fang Cui
Chronic alcohol intoxication impairs multiple cognitive functions. According to the dual system model (DSM), the development of alcohol dependence (AD) involves the imbalance between the automatic-affective system and the reflective system. However, the cognitive functions of non-AD hazardous drinkers (HDs) remain unclear. The present study aimed to explore how the HDs process facial expressions differently from the healthy subjects. Sixteen HDs and seventeen control subjects (CSs) completed an emotional working memory (WM) task while the electroencephalogram (EEG) was recorded...
October 17, 2017: Scientific Reports
Ran Rubin, L F Abbott, Haim Sompolinsky
Neurons and networks in the cerebral cortex must operate reliably despite multiple sources of noise. To evaluate the impact of both input and output noise, we determine the robustness of single-neuron stimulus selective responses, as well as the robustness of attractor states of networks of neurons performing memory tasks. We find that robustness to output noise requires synaptic connections to be in a balanced regime in which excitation and inhibition are strong and largely cancel each other. We evaluate the conditions required for this regime to exist and determine the properties of networks operating within it...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
Seth D Scheetz, Enhua Shao, Yangzhong Zhou, Clinton L Cario, Qing Bai, Edward A Burton
BACKGROUND: Optokinetic reflex (OKR) responses provide a convenient means to evaluate oculomotor, integrative and afferent visual function in larval zebrafish models, which are commonly used to elucidate molecular mechanisms underlying development, disease and repair of the vertebrate nervous system. NEW METHOD: We developed an open-source MATLAB-based solution for automated quantitative analysis of OKR responses in larval zebrafish. The package includes applications to: (i) generate sinusoidally-transformed animated grating patterns suitable for projection onto a cylindrical screen to elicit the OKR; (ii) determine and record the angular orientations of the eyes in each frame of a video recording showing the OKR response; and (iii) analyze angular orientation data from the tracking program to yield a set of parameters that quantify essential elements of the OKR...
October 14, 2017: Journal of Neuroscience Methods
Silvia Marino, Rosa Morabito, S De Salvo, L Bonanno, A Bramanti, P Pollicino, R Giorgianni, Placido Bramanti
Gerstmann-Sträussler-Scheinker syndrome (GSS) is an inherited autosomal dominant prion disease, caused by a codon 102 proline to leucine substitution (P102L) in the prion protein gene (PRNP). We describe the case of a 40-year-old male, affected by a slowly progressive gait disturbance, leg weakness and cognitive impairment. Genomic DNA revealed a point mutation of PRNP at codon 102, resulting in P102L, and the diagnosis of GSS was confirmed. Somatosensory evoked potentials showed alterations of principal parameters, particularly in the right upper and lower limbs...
July 2017: Functional Neurology
Ju-Fen Lu, Ching-Min Chen, Chien-Yeh Hsu
Objective This study aimed to evaluate the effectiveness of home telehealth care combined with case management by public health nurses, in improving blood pressure control in patients with hypertension. Methods This cohort study examined the data of patients with hypertension obtained from a telehealth service centre database, between July 2011- June 2012. Eligible patients were adults (≥40 years old) with both prehypertension and hypertension, living alone or in the remote suburbs of metropolitan areas. Demographic data were collected from 12 district public health centre in Taipei, Taiwan...
January 1, 2017: Journal of Telemedicine and Telecare
Yunlong Meng, Wei Lin, Chenglin Li, Shih-Chi Chen
We present a new two-snapshot structured light illumination (SLI) reconstruction algorithm for fast image acquisition. The new algorithm, which only requires two mutually π phase-shifted raw structured images, is implemented on a custom-built temporal focusing fluorescence microscope (TFFM) to enhance its axial resolution via a digital micromirror device (DMD). First, the orientation of the modulated sinusoidal fringe patterns is automatically identified via spatial frequency vector detection. Subsequently, the modulated in-focal-plane images are obtained via rotation and subtraction...
September 18, 2017: Optics Express
Chenxing Wang, Qian Kemao, Feipeng Da
Fringe-based optical measurement techniques require reliable fringe analysis methods, where empirical mode decomposition (EMD) is an outstanding one due to its ability of analyzing complex signals and the merit of being data-driven. However, two challenging issues hinder the application of EMD in practical measurement. One is the tricky mode mixing problem (MMP), making the decomposed intrinsic mode functions (IMFs) have equivocal physical meaning; the other is the automatic and accurate extraction of the sinusoidal fringe from the IMFs when unpredictable and unavoidable background and noise exist in real measurements...
October 2, 2017: Optics Express
Yan Chen, Zhongliang Li, Nan Nan, Yang Bu, Xuan Wang, Liuhua Pan, Xiangzhao Wang
Accurate wavelength assignment is important for Fourier domain polarization-sensitive optical coherence tomography. Incorrect wavelength mapping between the orthogonal horizontal (H) and vertical (V) polarization channels leads to broadening the axial point spread function and generating polarization artifacts. To solve the problem, we propose an automatic spectral calibration method by seeking the optimal calibration coefficient between wavenumber kH and kV. The method first performs a rough calibration to get the relationship between the wavelength λ and the pixel number x of the CCD for each channel...
October 2, 2017: Optics Express
Alexander D Hill, David Hervas, Joseph Nash, Martin Graham, Alexander Burgers, Uttam Paudel, Duncan Steel, Christian Schneider, Martin Kamp, Sven Höfling, Jin Wang, Jiahe Lin, Wanying Zhao, Paul G Kwiat
The collection efficiency of light from a point-like emitter may be extremely poor due to aberrations induced by collection optics and the emission distribution of the source. Analyzing the aberrant wavefront (e.g., with a Shack-Hartmann sensor) and correcting accordingly can be infeasible on the single-photon level. We present a technique that uses a genetic algorithm to control a deformable mirror for correcting wavefront aberrations in single-photon signals from point emitters. We apply our technique to both a simulated point source and a real InAs quantum dot, achieving coupling increases of up to 50% and automatic reduction of system drift...
August 7, 2017: Optics Express
Jinke Zhang, Bryan M Williams, Samuel Lawman, David Atkinson, Zijian Zhang, Yaochun Shen, Yalin Zheng
Automotive coating systems are designed to protect vehicle bodies from corrosion and enhance their aesthetic value. The number, size and orientation of small metallic flakes in the base coat of the paint has a significant effect on the appearance of automotive bodies. It is important for quality assurance (QA) to be able to measure the properties of these small flakes, which are approximately 10μm in radius, yet current QA techniques are limited to measuring layer thickness. We design and develop a time-domain (TD) full-field (FF) optical coherence tomography (OCT) system to scan automotive panels volumetrically, non-destructively and without contact...
August 7, 2017: Optics Express
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