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https://www.readbyqxmd.com/read/28108962/determination-of-equine-cytochrome-c-backbone-amide-hydrogen-deuterium-exchange-rates-by-mass-spectrometry-using-a-wider-time-window-and-isotope-envelope
#1
Yoshitomo Hamuro
A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism...
January 20, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28108871/quantitative-spm-analysis-involving-an-adaptive-template-may-be-easily-applied-to-18-f-fdg-pet-images-of-the-rat-brain
#2
Sylvain Poussier, Fatiha Maskali, Gaelle Vexiau, Antoine Verger, Henri Boutley, Gilles Karcher, Emmanuel Raffo, Pierre-Yves Marie
PURPOSE: The Statistical Parametric Mapping (SPM) software is frequently used for the quantitative analysis of patients' brain images obtained from 2-deoxy-2-[(18)F]fluoro-D-glucose positron emission tomography ([(18)F]FDG PET). However, its adaptation to small animals is difficult, particularly for the initial step of spatial normalization which requires a specific brain anatomical template. This study was aimed at determining whether SPM analysis can be applied to rat, and more specifically to the lithium-pilocarpine model of epilepsy, by using an adaptive template...
January 20, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/28108869/molecular-identification-of-malassezia-species-in-patients-with-malassezia-folliculitis-in-sfax-tunisia
#3
F Cheikhrouhou, R Guidara, A Masmoudi, H Trabelsi, S Neji, H Sellami, F Makni, A Ayadi
AIM: Malassezia folliculitis is caused by the invasion of hair follicles by large numbers of Malassezia cells. Several Malassezia researches still use cultures, morphology and biochemical techniques. The aim of this study was to identify Malassezia species isolated from patients diagnosed with folliculitis, at the Parasitology and Mycology Laboratory of Sfax University Hospital, and to explore the genetic diversity of Malassezia by using PCR-RFLP and PCR-sequencing targeting the rDNA region of the Malassezia genome...
January 20, 2017: Mycopathologia
https://www.readbyqxmd.com/read/28108656/functionally-interdependent-shape-switching-nanoparticles-with-controllable-properties
#4
Justin R Halman, Emily Satterwhite, Brandon Roark, Morgan Chandler, Mathias Viard, Anna Ivanina, Eckart Bindewald, Wojciech K Kasprzak, Martin Panigaj, My N Bui, Jacob S Lu, Johann Miller, Emil F Khisamutdinov, Bruce A Shapiro, Marina A Dobrovolskaia, Kirill A Afonin
We introduce a new concept that utilizes cognate nucleic acid nanoparticles which are fully complementary and functionally-interdependent to each other. In the described approach, the physical interaction between sets of designed nanoparticles initiates a rapid isothermal shape change which triggers the activation of multiple functionalities and biological pathways including transcription, energy transfer, functional aptamers and RNA interference. The individual nanoparticles are not active and have controllable kinetics of re-association and fine-tunable chemical and thermodynamic stabilities...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108641/spinal-cord-stimulation-scs-with-anatomically-guided-3d-neural-targeting-shows-superior-chronic-axial-low-back-pain-relief-compared-to-traditional-scs-lumina-study
#5
Elias Veizi, Salim M Hayek, James North, T Brent Chafin, Thomas L Yearwood, Louis Raso, Robert Frey, Kevin Cairns, Anthony Berg, John Brendel, Nameer Haider, Matthew McCarty, Henry Vucetic, Alden Sherman, Lilly Chen, Nitzan Mekel-Bobrov
: BACKGROUND : The aim of this study was to determine whether spinal cord stimulation (SCS) using 3D neural targeting provided sustained overall and low back pain relief in a broad routine clinical practice population. STUDY DESIGN AND METHODS:  This was a multicenter, open-label observational study with an observational arm and retrospective analysis of a matched cohort. After IPG implantation, programming was done using a patient-specific, model-based algorithm to adjust for lead position (3D neural targeting) or previous generation software (traditional)...
January 20, 2017: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
https://www.readbyqxmd.com/read/28108449/quantification-of-fibrous-spatial-point-patterns-from-single-molecule-localization-microscopy-smlm-data
#6
Ruby Peters, Marta Benthem Muñiz, Juliette Griffié, David J Williamson, George W Ashdown, Christian D Lorenz, Dylan M Owen
MOTIVATION: Unlike conventional microscopy which produces pixelated images, SMLM produces data in the form of a list of localization coordinates - a spatial point pattern (SPP). Often, such SPPs are analyzed using cluster analysis algorithms to quantify molecular clustering within, for example, the plasma membrane. While SMLM cluster analysis is now well developed, techniques for analyzing fibrous structures remain poorly explored. RESULTS: Here, we demonstrate statistical methodology, based on Ripley's K-function to quantitatively assess fibrous structures in 2D SMLM data sets...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108445/multi-rate-poisson-tree-processes-for-single-locus-species-delimitation-under-maximum-likelihood-and-markov-chain-monte-carlo
#7
P Kapli, S Lutteropp, J Zhang, K Kobert, P Pavlidis, A Stamatakis, T Flouri
MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108378/the-pressure-induced-deformation-response-of-the-human-lamina-cribrosa-analysis-of-regional-variations
#8
Dan E Midgett, Mary E Pease, Joan L Jefferys, Mohak Patel, Christian Franck, Harry A Quigley, Thao D Nguyen
: The objective of this study was to measure the pressure-induced deformation response of the human lamina cribrosa (LC) and analyze for variations with age and anatomical region. The posterior scleral cup of 8 eyes from 6 human donors was mounted onto a custom inflation chamber. A laser-scanning microscope was used for second harmonic generation (SHG), imaging the collagen structure in the posterior volume of the LC at pressures from 5 mmHg to 45 mmHg. The SHG volumes were analyzed by the Fast-Fourier Iterative Digital Volume Correlation (DVC) algorithm for the three dimensional (3D) displacement field...
January 17, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28108314/mirna-638-promotes-autophagy-and-malignant-phenotypes-of-cancer-cells-via-directly-suppressing-dact3
#9
Yanli Ren, Yujie Chen, Xue Liang, Yan Lu, Wenting Pan, Ming Yang
Dyregulation of autophagy is implicated in human cancers and the mechanism details remains largely unclear. Herein we report the regulatory role of miR-638 in autophagy of esophageal squamous cell carcinoma (ESCC) and breast cancer cells. We found that miR-638 overexpression promotes starvation- and rapamycin-induced autophagy. In ESCC and breast cancer cells, miR-638 acts as an oncogene and promote cell proliferation, migration, as well as invasion in vitro and in vivo. In accordance with this, we observed significantly higher miR-638 expression in ESCC and breast cancer tissues compared to normal tissues...
January 17, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28108305/efficient-dynamic-programming-algorithm-with-prior-knowledge-for-protein-%C3%AE-strand-alignment
#10
Mostafa Sabzekar, Mahmoud Naghibzadeh, Javad Sadri
One of the main tasks towards the prediction of protein β-sheet structure is to predict the native alignment of β-strands. The alignment of two β-strands defines similar regions that may reflect functional, structural, or evolutionary relationships between them. Therefore, any improvement in β-strands alignment not only reduces the computational search space but also improves β-sheet structure prediction accuracy. To define the alignment scores, previous studies utilized predicted residue-residue contacts (contact maps)...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28108294/the-dimensional-reduction-method-for-identification-of-parameters-that-trade-off-due-to-similar-model-roles
#11
Shaun M Davidson, Paul D Docherty, Rua Murray
Parameter identification is an important and widely used process across the field of biomedical engineering. However, it is susceptible to a number of potential difficulties, such as parameter trade-off, causing premature convergence at non-optimal parameter values. The proposed Dimensional Reduction Method (DRM) addresses this issue by iteratively reducing the dimension of hyperplanes where trade off occurs, and running subsequent identification processes within these hyperplanes. The DRM was validated using clinical data to optimize 4 parameters of the widely used Bergman Minimal Model of glucose and insulin kinetics, as well as in-silico data to optimize 5 parameters of the Pulmonary Recruitment (PR) Model...
January 17, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28108205/modifying-the-phenotypic-frailty-model-in-predicting-risk-of-major-osteoporotic-fracture-in-the-elderly
#12
Guowei Li, Alexandra Papaioannou, Lehana Thabane, Mitchell A H Levine, George Ioannidis, Andy K O Wong, Arthur Lau, Jonathan D Adachi
INTRODUCTION: The phenotypic frailty (PF) model (including slow walking, low physical activity, exhaustion, weakness, and unintentional weight loss) has been widely used to quantify the degree of frailty and predict risks of adverse health outcomes for the elderly. However, evidence has shown that not all the components included in the PF model contribute equally, and low predictive accuracy of the PF model has been reported in predicting risks of outcomes. We aimed to improve predictive accuracy of the PF model in risk of major osteoporotic fracture (MOF) in the elderly by modifying its weighting of individual components...
January 17, 2017: Journal of the American Medical Directors Association
https://www.readbyqxmd.com/read/28108198/ted-a-tolerant-edit-distance-for-segmentation-evaluation
#13
Jan Funke, Jonas Klein, Francesc Moreno-Noguer, Albert Cardona, Matthew Cook
In this paper, we present a novel error measure to compare a computer-generated segmentation of images or volumes against ground truth. This measure, which we call Tolerant Edit Distance (TED), is motivated by two observations that we usually encounter in biomedical image processing: (1) Some errors, like small boundary shifts, are tolerable in practice. Which errors are tolerable is application dependent and should be explicitly expressible in the measure. (2) Non-tolerable errors have to be corrected manually...
January 17, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28108101/development-of-a-high-resolution-voxelised-head-phantom-for-medical-physics-applications
#14
REVIEW
V Giacometti, S Guatelli, M Bazalova-Carter, A B Rosenfeld, R W Schulte
Computational anthropomorphic phantoms have become an important investigation tool for medical imaging and dosimetry for radiotherapy and radiation protection. The development of computational phantoms with realistic anatomical features contribute significantly to the development of novel methods in medical physics. For many applications, it is desirable that such computational phantoms have a real-world physical counterpart in order to verify the obtained results. In this work, we report the development of a voxelised phantom, the HIGH_RES_HEAD, modelling a paediatric head based on the commercial phantom 715-HN (CIRS)...
January 17, 2017: Physica Medica: PM
https://www.readbyqxmd.com/read/28108033/the-utility-of-repeat-sestamibi-scans-in-patients-with-primary-hyperparathyroidism-after-an-initial-negative-scan
#15
Vikram D Krishnamurthy, Sara Sound, Alexis K Okoh, Pinar Yazici, Hakan Yigitbas, Donald Neumann, Krupa Doshi, Eren Berber
BACKGROUND: We analyzed the utility of repeated sestambi scans in patients with primary hyperparathyroidism and its effects on operative referral. METHODS: We carried out a retrospective review of patients with primary hyperparathyroidism who underwent repeated sestambi scans exclusively within our health system between 1996-2015. Patient demographic, presentation, laboratory, imaging, operative, and pathologic data were reviewed. Univariate analysis with JMP Pro v12 was used to identify factors associated with conversion from an initial negative to a subsequent positive scan...
January 17, 2017: Surgery
https://www.readbyqxmd.com/read/28108004/nonlinear-svm-dtc-for-induction-motor-drive-using-input-output-feedback-linearization-and-high-order-sliding-mode-control
#16
Abdelkarim Ammar, Amor Bourek, Abdelhamid Benakcha
This paper presents a nonlinear Direct Torque Control (DTC) strategy with Space Vector Modulation (SVM) for an induction motor. A nonlinear input-output feedback linearization (IOFL) is implemented to achieve a decoupled torque and flux control and the SVM is employed to reduce high torque and flux ripples. Furthermore, the control scheme performance is improved by inserting a super twisting speed controller in the outer loop and a load torque observer to enhance the speed regulation. The combining of dual nonlinear strategies ensures a good dynamic and robustness against parameters variation and disturbance...
January 17, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28108003/active-disturbance-rejection-control-based-human-gait-tracking-for-lower-extremity-rehabilitation-exoskeleton
#17
Yi Long, Zhijiang Du, Lin Cong, Weidong Wang, Zhiming Zhang, Wei Dong
This paper presents an active disturbance rejection control (ADRC) based strategy, which is applied to track the human gait trajectory for a lower limb rehabilitation exoskeleton. The desired human gait trajectory is derived from the Clinical Gait Analysis (CGA). In ADRC, the total external disturbance can be estimated by the extended state observer (ESO) and canceled by the designed control law. The observer bandwidth and the controller bandwidth are determined by the practical principles. We simulated the proposed methodology in MATLAB...
January 17, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28108002/reduced-order-model-based-active-disturbance-rejection-control-of-hydraulic-servo-system-with-singular-value-perturbation-theory
#18
Chengwen Wang, Long Quan, Shijie Zhang, Hongjun Meng, Yuan Lan
Hydraulic servomechanism is the typical mechanical/hydraulic double-dynamics coupling system with the high stiffness control and mismatched uncertainties input problems, which hinder direct applications of many advanced control approaches in the hydraulic servo fields. In this paper, by introducing the singular value perturbation theory, the original double-dynamics coupling model of the hydraulic servomechanism was reduced to a integral chain system. So that, the popular ADRC (active disturbance rejection control) technology could be directly applied to the reduced system...
January 17, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28107913/quantitative-structure-retention-relationship-model-for-the-determination-of-naratriptan-hydrochloride-and-its-impurities-based-on-artificial-neural-networks-coupled-with-genetic-algorithm
#19
Mikołaj Mizera, Anna Krause, Przemysław Zalewski, Robert Skibiński, Judyta Cielecka-Piontek
Mathematical modeling of Quantitative Structure - Property Relationships met great interest in fields of in silico drug design and more recently, pharmaceutical analysis. In our approach we proposed automated method of creation Quantitative Structure-Retention Relationship (QSRR) for analysis of triptans, selective serotonin 5-HT1 receptor agonists used for the treatment of acute headache. The method was created using hybrid machine learning approach, namely Genetic algorithm (GA) coupled with artificial neutral networks (ANN)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107881/a-census-to-determine-the-prevalence-and-risk-factors-for-caprine-arthritis-encephalitis-virus-and-visna-maedi-virus-in-the-swiss-goat-population
#20
B Thomann, L C Falzon, G Bertoni, H R Vogt, G Schüpbach-Regula, I Magouras
In Switzerland, viruses belonging to two different phylogenetic groups of small ruminant lentiviruses (SRLV) are currently circulating: the caprine arthritis-encephalitis virus (CAEV) and visna/maedi virus (VMV). In the past two decades, a mandatory national control program has led to a very low prevalence of seropositivity, while completely eliminating CAE as a clinical manifestation. However, in order to reduce the high costs and effort associated with this program, adjustments based on the most recent epidemiological knowledge are needed...
February 1, 2017: Preventive Veterinary Medicine
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