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https://www.readbyqxmd.com/read/28079878/a-complete-workflow-for-high-resolution-spectral-stitching-nanoelectrospray-direct-infusion-mass-spectrometry-based-metabolomics-and-lipidomics
#1
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...
February 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
#2
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
#3
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...
December 3, 2016: 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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/27798545/hospital-based-surveillance-for-rotavirus-gastroenteritis-among-young-children-in-bangladesh-defining-the-potential-impact-of-a-rotavirus-vaccine-program
#11
Syed Satter, Paul Gastanaduy, Khaleda Islam, Mahmudur Rahman, Mustafizur Rahman, Stephen Luby, James Heffelfinger, Umesh Parashar, Emily Gurley
BACKGROUND: In anticipation of introduction of a rotavirus vaccine into the national immunization program of Bangladesh, active hospital-based surveillance was initiated to provide pre-vaccine baseline data on rotavirus disease. METHODS: Children 5 years of age and younger admitted with acute gastroenteritis (AGE) (≥3 watery or looser-than-normal stools or ≥1 episode of forceful vomiting) at 7 hospitals throughout Bangladesh were identified. Clinical information and stool specimens were collected from every 4th patient...
October 25, 2016: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/27797775/optimizing-chip-seq-peak-detectors-using-visual-labels-and-supervised-machine-learning
#12
Toby Dylan Hocking, Patricia Goerner-Potvin, Andreanne Morin, Xiaojian Shao, Tomi Pastinen, Guillaume Bourque
MOTIVATION: Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily labeled by visual inspection of aligned read counts in a genome browser. We propose a supervised machine learning approach for ChIP-seq data analysis, using labels that encode qualitative judgments about which genomic regions contain or do not contain peaks...
October 24, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27757822/monitoring-conformational-landscape-of-ovine-prion-protein-monomer-using-ion-mobility-coupled-to-mass-spectrometry
#13
Guillaume Van der Rest, Human Rezaei, Frédéric Halgand
Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry...
October 18, 2016: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/27751349/metastatic-tissue-proteomic-profiling-predicts-5-year-outcomes-in-patients-with-colorectal-liver-metastases
#14
Santiago Marfà, Josep Marti, Adalgiza Reyes, Gregori Casals, Guillermo Fernández-Varo, Silvia Carvajal, J C García-Valdecasas, Josep Fuster, Wladimiro Jiménez
Colorectal cancer (CRC) is one of the most common cancers in the developed countries, and nearly 70% of patients with CRC develop colorectal liver metastases (CRLMs). During the last decades, several scores have been proposed to predict recurrence after CRLM resection. However, these risk scoring systems do not accurately reflect the prognosis of these patients. Therefore, this investigation was designed to identify a proteomic profile in human hepatic tumor samples to classify patients with CRLM as "mild" or "severe" based on the 5-year survival...
October 2016: Translational Oncology
https://www.readbyqxmd.com/read/27743370/automated-integration-of-a-uplc-glycomic-profile
#15
Anna Agakova, Frano Vučković, Lucija Klarić, Gordan Lauc, Felix Agakov
Ultra-performance liquid chromatography (UPLC) is the established technology for accurate analysis of IgG Fc N-glycosylation due to its superior sensitivity, resolution, speed, and its capability to provide branch-specific information of glycan species. Correct and cost-efficient preprocessing of chromatographic data is the major prerequisite for subsequent analyses ranging from inference of structural isomers to biomarker discovery and prediction of humoral immune response from characterized changes in glycosylation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27734807/robust-qrs-peak-detection-by-multimodal-information-fusion-of-ecg-and-blood-pressure-signals
#16
Quan Ding, Yong Bai, Yusuf Bugra Erol, Rebeca Salas-Boni, Xiaorong Zhang, Xiao Hu
QRS peak detection is a challenging problem when ECG signal is corrupted. However, additional physiological signals may also provide information about the QRS position. In this study, we focus on a unique benchmark provided by PhysioNet/Computing in Cardiology Challenge 2014 and Physiological Measurement focus issue: robust detection of heart beats in multimodal data, which aimed to explore robust methods for QRS detection in multimodal physiological signals. A dataset of 200 training and 210 testing records are used, where the testing records are hidden for evaluating the performance only...
October 13, 2016: Physiological Measurement
https://www.readbyqxmd.com/read/27714402/optimization-of-lc-orbitrap-hrms-acquisition-and-mzmine-2-data-processing-for-nontarget-screening-of-environmental-samples-using-design-of-experiments
#17
Meng Hu, Martin Krauss, Werner Brack, Tobias Schulze
Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a well-established technique for nontarget screening of contaminants in complex environmental samples. Automatic peak detection is essential, but its performance has only rarely been assessed and optimized so far. With the aim to fill this gap, we used pristine water extracts spiked with 78 contaminants as a test case to evaluate and optimize chromatogram and spectral data processing. To assess whether data acquisition strategies have a significant impact on peak detection, three values of MS cycle time (CT) of an LTQ Orbitrap instrument were tested...
November 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27686713/cardiac-arrhythmia-beat-classification-using-dost-and-pso-tuned-svm
#18
Sandeep Raj, Kailash Chandra Ray, Om Shankar
BACKGROUND AND OBJECTIVE: The increase in the number of deaths due to cardiovascular diseases (CVDs) has gained significant attention from the study of electrocardiogram (ECG) signals. These ECG signals are studied by the experienced cardiologist for accurate and proper diagnosis, but it becomes difficult and time-consuming for long-term recordings. Various signal processing techniques are studied to analyze the ECG signal, but they bear limitations due to the non-stationary behavior of ECG signals...
November 2016: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/27673369/web-server-for-peak-detection-baseline-correction-and-alignment-in-two-dimensional-gas-chromatography-mass-spectrometry-based-metabolomics-data
#19
Tze-Feng Tian, San-Yuan Wang, Tien-Chueh Kuo, Cheng-En Tan, Guan-Yuan Chen, Ching-Hua Kuo, Chi-Hsin Sally Chen, Chang-Chuan Chan, Olivia A Lin, Y Jane Tseng
Two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) is superior for chromatographic separation and provides great sensitivity for complex biological fluid analysis in metabolomics. However, GC×GC/TOF-MS data processing is currently limited to vendor software and typically requires several preprocessing steps. In this work, we implement a web-based platform, which we call GC(2)MS, to facilitate the application of recent advances in GC×GC/TOF-MS, especially for metabolomics studies...
October 13, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27667882/normal-gamma-bernoulli-peak-detection-for-analysis-of-comprehensive-two-dimensional-gas-chromatography-mass-spectrometry-data
#20
Seongho Kim, Hyejeong Jang, Imhoi Koo, Joohyoung Lee, Xiang Zhang
Compared to other analytical platforms, comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC×GC-MS) has much increased separation power for analysis of complex samples and thus is increasingly used in metabolomics for biomarker discovery. However, accurate peak detection remains a bottleneck for wide applications of GC×GC-MS. Therefore, the normal-exponential-Bernoulli (NEB) model is generalized by gamma distribution and a new peak detection algorithm using the normal-gamma-Bernoulli (NGB) model is developed...
January 2017: Computational Statistics & Data Analysis
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