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https://www.readbyqxmd.com/read/28325916/automatic-time-shift-alignment-method-for-chromatographic-data-analysis
#1
Qing-Xia Zheng, Hai-Yan Fu, He-Dong Li, Bing Wang, Cui-Hua Peng, Sheng Wang, Jun-Lan Cai, Shao-Feng Liu, Xiao-Bing Zhang, Yong-Jie Yu
Time shift among samples remains a significant challenge in data analysis, such as quality control of natural plant extracts and metabolic profiling analysis, because this phenomenon may lead to invalid conclusions. In this work, we propose a new time shift alignment method, namely, automatic time-shift alignment (ATSA), for complicated chromatographic data analysis. This technique comprised the following alignment stages: (1) automatic baseline correction and peak detection stage for providing useful chromatographic information; (2) preliminary alignment stage through adaptive segment partition to correct alignment for the entire chromatogram; and (3) precise alignment stage based on test chromatographic peak information to accurately align time shift...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28269048/an-algorithm-for-rotor-tracking-in-atrial-fibrillation-using-graph-search-based-periodic-peak-detection
#2
Rupin Dalvi, Adrian Suszko, Vijay S Chauhan
Rotors are rotating electrical waves that may sustain atrial fibrillation (AF); thereby providing therapeutic targets for catheter ablation. We propose a method for identifying rotors from circular catheter recordings of bipolar intracardiac electrograms (EGM) during AF. We use dominant frequency-based periodicity detection along with a graph search algorithm to identify the most dominant periodic activations or peaks of interest in each bipolar EGM recorded by a multipolar circular catheter. We then track the activations across catheter bipoles to determine whether they conform to the rotational pattern of a rotor...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28268871/automatic-annotation-of-peaks-in-seismocardiogram-for-systolic-time-intervals
#3
Ghufran Shafiq, Sivanagaraja Tatinati, Kalyana C Veluvolu
Siemocardiography is a non-invasive technique for cardiomechanical assessment by analyzing the local vibrations on chest surface which can be readily acquired from cost-effective accelerometers. The peaks in siesmocardiogram (SCG) signal correspond to underlying mechanical events in heart cycle and have numerious potential clinical and health-awareness applications. However, utilization of SCG signal requires annotation of these peaks that is challenging due to variations in inter-subject morphology and noise prone characteristics of SCG signal...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227263/an-algorithm-for-rotor-tracking-in-atrial-fibrillation-using-graph-search-based-periodic-peak-detection
#4
Rupin Dalvi, Adrian Suszko, Vijay S Chauhan, Rupin Dalvi, Adrian Suszko, Vijay S Chauhan, Rupin Dalvi, Adrian Suszko, Vijay S Chauhan
Rotors are rotating electrical waves that may sustain atrial fibrillation (AF); thereby providing therapeutic targets for catheter ablation. We propose a method for identifying rotors from circular catheter recordings of bipolar intracardiac electrograms (EGM) during AF. We use dominant frequency-based periodicity detection along with a graph search algorithm to identify the most dominant periodic activations or peaks of interest in each bipolar EGM recorded by a multipolar circular catheter. We then track the activations across catheter bipoles to determine whether they conform to the rotational pattern of a rotor...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227069/automatic-annotation-of-peaks-in-seismocardiogram-for-systolic-time-intervals
#5
Ghufran Shafiq, Sivanagaraja Tatinati, Kalyana C Veluvolu, Ghufran Shafiq, Sivanagaraja Tatinati, Kalyana C Veluvolu, Kalyana C Veluvolu, Sivanagaraja Tatinati, Ghufran Shafiq
Siemocardiography is a non-invasive technique for cardiomechanical assessment by analyzing the local vibrations on chest surface which can be readily acquired from cost-effective accelerometers. The peaks in siesmocardiogram (SCG) signal correspond to underlying mechanical events in heart cycle and have numerious potential clinical and health-awareness applications. However, utilization of SCG signal requires annotation of these peaks that is challenging due to variations in inter-subject morphology and noise prone characteristics of SCG signal...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225594/mass-spectral-feature-list-optimizer-ms-flo-a-tool-to-minimize-false-positive-peak-reports-in-untargeted-liquid-chromatography-mass-spectroscopy-lc-ms-data-processing
#6
Brian C DeFelice, Sajjan Singh Mehta, Stephanie Samra, Tomáš Čajka, Benjamin Wancewicz, Johannes F Fahrmann, Oliver Fiehn
Untargeted metabolomics by liquid chromatography-mass spectrometry generates data-rich chromatograms in the form of m/z-retention time features. Managing such datasets is a bottleneck. Many popular data processing tools, including XCMS-online and MZmine2, yield numerous false-positive peak detections. Flagging and removing such false peaks manually is a time-consuming task and prone to human error. We present a web application, Mass Spectral Feature List Optimizer (MS-FLO), to improve the quality of feature lists after initial processing to expedite the process of data curation...
March 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28210934/adarri-a-novel-method-to-detect-spurious-r-peaks-in-the-electrocardiogram-for-heart-rate-variability-analysis-in-the-intensive-care-unit
#7
Dennis J Rebergen, Sunil B Nagaraj, Eric S Rosenthal, Matt T Bianchi, Michel J A M van Putten, M Brandon Westover
We developed a simple and fully automated method for detecting artifacts in the R-R interval (RRI) time series of the ECG that is tailored to the intensive care unit (ICU) setting. From ECG recordings of 50 adult ICU-subjects we selected 60 epochs with valid R-peak detections and 60 epochs containing artifacts leading to missed or false positive R-peak detections. Next, we calculated the absolute value of the difference between two adjacent RRIs (adRRI), and obtained the empirical probability distributions of adRRI values for valid R-peaks and artifacts...
February 16, 2017: Journal of Clinical Monitoring and Computing
https://www.readbyqxmd.com/read/28143631/automatic-biological-cell-counting-using-a-modified-gradient-hough-transform
#8
Emmanuel Denimal, Ambroise Marin, Stéphane Guyot, Ludovic Journaux, Paul Molin
We present a computational method for pseudo-circular object detection and quantitative characterization in digital images, using the gradient accumulation matrix as a basic tool. This Gradient Accumulation Transform (GAT) was first introduced in 1992 by Kierkegaard and recently used by Kaytanli & Valentine. In the present article, we modify the approach by using the phase coding studied by Cicconet, and by adding a "local contributor list" (LCL) as well as a "used contributor matrix" (UCM), which allow for accurate peak detection and exploitation...
February 1, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28108660/from-benchmarking-hits-clip-peak-detection-programs-to-a-new-method-for-identification-of-mirna-binding-sites-from-ago2-clip-data
#9
Silvia Bottini, Nedra Hamouda-Tekaya, Bogdan Tanasa, Laure-Emmanuelle Zaragosi, Valerie Grandjean, Emanuela Repetto, Michele Trabucchi
Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28097210/preclinical-positron-emission-tomography-scanner-based-on-a-monolithic-annulus-of-scintillator-initial-design-study
#10
Alexander V Stolin, Peter F Martone, Gangadhar Jaliparthi, Raymond R Raylman
Positron emission tomography (PET) scanners designed for imaging of small animals have transformed translational research by reducing the necessity to invasively monitor physiology and disease progression. Virtually all of these scanners are based on the use of pixelated detector modules arranged in rings. This design, while generally successful, has some limitations. Specifically, use of discrete detector modules to construct PET scanners reduces detection sensitivity and can introduce artifacts in reconstructed images, requiring the use of correction methods...
January 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28079878/a-complete-workflow-for-high-resolution-spectral-stitching-nanoelectrospray-direct-infusion-mass-spectrometry-based-metabolomics-and-lipidomics
#11
Andrew D Southam, Ralf J M Weber, Jasper Engel, Martin R Jones, Mark R Viant
Metabolomic and lipidomic studies measure and discover metabolic and lipid profiles in biological samples, enabling a better understanding of the metabolism of specific biological phenotypes. Accurate biological interpretations require high analytical reproducibility and sensitivity, and standardized and transparent data processing. Here we describe a complete workflow for nanoelectrospray ionization (nESI) direct-infusion mass spectrometry (DIMS) metabolomics and lipidomics. After metabolite and lipid extraction from tissues and biofluids, samples are directly infused into a high-resolution mass spectrometer (e...
2016: Nature Protocols
https://www.readbyqxmd.com/read/28048754/su-f-j-204-carbon-digitally-reconstructed-radiography-cdrr-a-gpu-based-tool-for-fast-and-versatile-carbonimaging-simulation
#12
M F Dias, J Seco, G Baroni, M Riboldi
PURPOSE: Research in carbon imaging has been growing over the past years, as a way to increase treatment accuracy and patient positioning in carbon therapy. The purpose of this tool is to allow a fast and flexible way to generate CDRR data without the need to use Monte Carlo (MC) simulations. It can also be used to predict future clinically measured data. METHODS: A python interface has been developed, which uses information from CT or 4DCT and thetreatment calibration curve to compute the Water Equivalent Path Length (WEPL) of carbon ions...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28042994/assessing-neuromuscular-junction-stability-from-stimulated-emg-in-children
#13
Matthew C Pitt, John C Mchugh, Jacquie Deeb, Ralph A Smith
OBJECTIVE: We present our 9-year experience of stimulated EMG potential analysis using concentric electrodes (SPACE) to evaluate neuromuscular junction (NMJ) disorders in awake children. The technique uses high frequency filtration of stimulated motor unit potentials and applies peak detection software to estimate mean consecutive difference (MCD). METHODS: SPACE was carried out in orbicularis oculi of 878 children (377 girls; median age 47months) between 2007 and 2015, stimulating the facial nerve with a monopolar cathode...
February 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/27995864/detection-of-mycobacteria-by-voc-analysis-of-in-vitro-cultures-using-differential-ion-mobility-spectrometry-dms
#14
Roman Purkhart, Gunther Becher, Petra Reinhold, Heike U Köhler
Differential ion mobility spectrometry (DMS) is an analytical technique to detect volatile organic compounds (VOCs) in gaseous samples at very low concentration ranges from ppb to ppt. The aim of this study was to investigate whether VOC analysis by DMS is capable of detecting Mycobacterium avium subspecies paratuberculosis (MAP). Headspaces of in vitro cultures of two different MAP strains at 1, 2, 3, 4 and 6 weeks after inoculation (each at two dilutions) were analyzed with DMS in comparison to control samples without viable bacteria ([i] blank medium, [ii] medium inoculated with heat-inactivated MAP, and [iii] sterile-filtered MAP culture broth)...
December 19, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27983972/early-detection-of-trichinella-spiralis-dna-in-the-feces-of-experimentally-infected-mice-by-using-pcr
#15
Xiao Lin Liu, Hua Nan Ren, Ya Li Shi, Chen Xi Hu, Yan Yan Song, Jiang Yang Duan, Hui Ping Zhang, Xin Rui Du, Ruo Dan Liu, Peng Jiang, Zhong Quan Wang, Jing Cui
The aim of this study was to detect Trichinella spiralis DNA in mouse feces during the early stages of infection using PCR. The target gene fragment, a 1.6kb repetitive sequence of T. spiralis genome, was amplified by PCR from feces of mice infected with 100 or 300 larvae at 3-24h post infection (hpi) and 2-28dpi. The sensitivity of PCR was 0.016 larvae in feces. The primers used were highly specific for T. spiralis. No cross-reactivity was observed with the DNA of other intestinal helminths. T. spiralis DNA was detected in 100% (12/12) of feces of mice infected with 100 or 300 larvae as early as 3hpi, with the peak detection lasting to 12-24hpi, and then fluctuating before declining gradually...
February 2017: Acta Tropica
https://www.readbyqxmd.com/read/27957405/smart-helmet-wearable-multichannel-ecg-and-eeg
#16
Wilhelm Von Rosenberg, Theerasak Chanwimalueang, Valentin Goverdovsky, David Looney, David Sharp, Danilo P Mandic
Modern wearable technologies have enabled continuous recording of vital signs, however, for activities such as cycling, motor-racing, or military engagement, a helmet with embedded sensors would provide maximum convenience and the opportunity to monitor simultaneously both the vital signs and the electroencephalogram (EEG). To this end, we investigate the feasibility of recording the electrocardiogram (ECG), respiration, and EEG from face-lead locations, by embedding multiple electrodes within a standard helmet...
2016: IEEE Journal of Translational Engineering in Health and Medicine
https://www.readbyqxmd.com/read/27924495/autopiquer-a-robust-and-reliable-peak-detection-algorithm-for-mass-spectrometry
#17
David P A Kilgour, Sam Hughes, Samantha L Kilgour, C Logan Mackay, Magnus Palmblad, Bao Quoc Tran, Young Ah Goo, Robert K Ernst, David J Clarke, David R Goodlett
We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time-consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data, whilst keeping as much of the (isotopic) structure as possible...
December 6, 2016: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/27874050/automatic-identification-of-systolic-time-intervals-in-seismocardiogram
#18
Ghufran Shafiq, Sivanagaraja Tatinati, Wei Tech Ang, Kalyana C Veluvolu
Continuous and non-invasive monitoring of hemodynamic parameters through unobtrusive wearable sensors can potentially aid in early detection of cardiac abnormalities, and provides a viable solution for long-term follow-up of patients with chronic cardiovascular diseases without disrupting the daily life activities. Electrocardiogram (ECG) and siesmocardiogram (SCG) signals can be readily acquired from light-weight electrodes and accelerometers respectively, which can be employed to derive systolic time intervals (STI)...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27834656/automated-detection-of-atrial-fibrillation-based-on-time-frequency-analysis-of-seismocardiagrams
#19
Tero Hurnanen, Eero Lehtonen, Mojtaba Jafari Tadi, Tom Kuusela, Tuomas Kiviniemi, Antti Saraste, Tuija Vasankari, Juhani Airaksinen, Tero Koivisto, Mikko Pankaala
In this paper, a novel method to detect atrial fibrillation from a seismocardiogram (SCG) is presented. The proposed method is based on linear classification of the spectral entropy and a heart rate variability index computed from the SCG. The performance of the developed algorithm is demonstrated on data gathered from 13 patients in clinical setting. After motion artefact removal, in total 119 minutes of AFib data and 126 minutes of sinus rhythm data were considered for automated atrial fibrillation detection...
November 4, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/27832957/the-physio-toolbox-for-modeling-physiological-noise-in-fmri-data
#20
Lars Kasper, Steffen Bollmann, Andreea O Diaconescu, Chloe Hutton, Jakob Heinzle, Sandra Iglesias, Tobias U Hauser, Miriam Sebold, Zina-Mary Manjaly, Klaas P Pruessmann, Klaas E Stephan
BACKGROUND: Physiological noise is one of the major confounds for fMRI. A common class of correction methods model noise from peripheral measures, such as ECGs or pneumatic belts. However, physiological noise correction has not emerged as a standard preprocessing step for fMRI data yet due to: (1) the varying data quality of physiological recordings, (2) non-standardized peripheral data formats and (3) the lack of full automatization of processing and modeling physiology, required for large-cohort studies...
January 30, 2017: Journal of Neuroscience Methods
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