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https://www.readbyqxmd.com/read/29036359/profia-a-data-preprocessing-workflow-for-flow-injection-analysis-coupled-to-high-resolution-mass-spectrometry
#1
Alexis Delabrière, Ulli M Hohenester, Benoit Colsch, Christophe Junot, François Fenaille, Etienne A Thévenot
Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Results: We thus developed the proFIA package, which implements a suite of innovative algorithms to preprocess FIA-HRMS raw files, and generates the table of peak intensities...
July 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29030275/metabolite-damage-and-repair-in-metabolic-engineering-design
#2
REVIEW
Jiayi Sun, James G Jeffryes, Christopher S Henry, Steven D Bruner, Andrew D Hanson
The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it...
October 10, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29018635/a-new-wavelet-based-ecg-delineator-for-the-evaluation-of-the-ventricular-innervation
#3
Matteo Cesari, Jesper Mehlsen, Anne-Birgitte Mehlsen, Helge Bjarup Dissing Sorensen
T-wave amplitude (TWA) has been proposed as a marker of the innervation of the myocardium. Until now, TWA has been calculated manually or with poor algorithms, thus making its use not efficient in a clinical environment. We introduce a new wavelet-based algorithm for the delineation QRS complexes and T-waves, and the automatic calculation of TWA. When validated in the MIT/BIH Arrhythmia database, the QRS detector achieved sensitivity and positive predictive value of 99.84% and 99.87%, respectively. The algorithm was validated also on the QT database and it achieved sensitivity of 99...
2017: IEEE Journal of Translational Engineering in Health and Medicine
https://www.readbyqxmd.com/read/28956859/an-efficient-hardware-circuit-for-spike-sorting-based-on-competitive-learning-networks
#4
Huan-Yuan Chen, Chih-Chang Chen, Wen-Jyi Hwang
This study aims to present an effective VLSI circuit for multi-channel spike sorting. The circuit supports the spike detection, feature extraction and classification operations. The detection circuit is implemented in accordance with the nonlinear energy operator algorithm. Both the peak detection and area computation operations are adopted for the realization of the hardware architecture for feature extraction. The resulting feature vectors are classified by a circuit for competitive learning (CL) neural networks...
September 28, 2017: Sensors
https://www.readbyqxmd.com/read/28952947/miniaturized-impedance-flow-cytometer-design-rules-and-integrated-readout
#5
Marco Carminati, Giorgio Ferrari, Michael D Vahey, Joel Voldman, Marco Sampietro
A dual-channel credit-card-sized impedance cell counter featuring a throughput of 2000 cell/s and detection of single yeast cells (5 μm) with a signal-to-noise ratio of 20 dB is presented. Its compactness is achieved by a CMOS ASIC combining a lock-in impedance demodulator with an oversampling 20-bit ΣΔ ADC and real-time peak detection embedded in field-programmable gate array. The module is coupled to a dielectrophoretic cell-sorting microfluidic device, offering compact and label-free electrical readout that replaces the need for a fluorescence microscope and, thus, is suitable for point-of-care diagnostics...
September 22, 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/28942951/the-algorithmic-performance-of-j-tpeak-for-drug-safety-clinical-trial
#6
Simon C Chien, Richard E Gregg
INTRODUCTION: The interval from J-point to T-wave peak (JTp) in ECG is a new biomarker able to identify drugs that prolong the QT interval but have different ion channel effects. If JTp is not prolonged, the prolonged QT may be associated with multi ion channel block that may have low torsade de pointes risk. From the automatic ECG measurement perspective, accurate and repeatable measurement of JTp involves different challenges than QT. We evaluated algorithm performance and JTp challenges using the Philips DXL diagnostic 12/16/18-lead algorithm...
August 15, 2017: Journal of Electrocardiology
https://www.readbyqxmd.com/read/28926828/are-all-amplitude-integrated-electroencephalogram-systems-equal
#7
Tobias Werther, Monika Olischar, Gunnar Naulaers, Philipp Deindl, Katrin Klebermass-Schrehof, Nathan Stevenson
BACKGROUND: Filter and peak detection algorithms implemented in amplitude-integrated electroencephalogram (aEEG) systems are not standardized. New aEEG systems are continuously enriching the market and clinicians are faced with different aEEG devices whose tracings may vary. OBJECTIVES: The aim of this work was to determine the role of different aEEG systems on quantitative measurements of the aEEG. METHODS: In this observational study, a single-channel aEEG recording (Olympic CFM 6000) with corresponding EEG signal was obtained from 32 infants at a gestational age of 36-44 weeks...
September 20, 2017: Neonatology
https://www.readbyqxmd.com/read/28920895/matched-filtering-for-heart-rate-estimation-on-compressive-sensing-ecg-measurements
#8
Giulia Da Poian, Christopher J Rozell, Riccardo Bernardini, Roberto Rinaldo, Gari D Clifford
OBJECTIVE: Compressive Sensing (CS) has recently been applied as a low complexity compression framework for long-term monitoring of electrocardiogram signals using Wireless Body Sensor Networks. Long-term recording of ECG signals can be useful for diagnostic purposes and to monitor the evolution of several widespread diseases. In particular, beat to beat intervals provide important clinical information, and these can be derived from the ECG signal by computing the distance between QRS complexes (R-peaks)...
September 14, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28910313/a-detailed-comparison-of-analysis-processes-for-mcc-ims-data-in-disease-classification-automated-methods-can-replace-manual-peak-annotations
#9
COMPARATIVE STUDY
Salome Horsch, Dominik Kopczynski, Elias Kuthe, Jörg Ingo Baumbach, Sven Rahmann, Jörg Rahnenführer
MOTIVATION: Disease classification from molecular measurements typically requires an analysis pipeline from raw noisy measurements to final classification results. Multi capillary column-ion mobility spectrometry (MCC-IMS) is a promising technology for the detection of volatile organic compounds in the air of exhaled breath. From raw measurements, the peak regions representing the compounds have to be identified, quantified, and clustered across different experiments. Currently, several steps of this analysis process require manual intervention of human experts...
2017: PloS One
https://www.readbyqxmd.com/read/28887765/heartbeat-detection-in-multimodal-physiological-signals-using-signal-quality-assessment-based-on-sample-entropy
#10
Omkar Singh, Ramesh Kumar Sunkaria
This paper presents a novel technique to identify heartbeats in multimodal data using electrocardiogram (ECG) and arterial blood pressure (ABP) signals. Multiple physiological signals such as ECG, ABP, and Respiration are often recorded in parallel from the activity of heart. These signals generally possess related information as they are generated by the same physical system. The ECG and ABP correspond to the same phenomenon of contraction and relaxation activity of heart. Multiple signals acquired from various sensors are generally processed independently, thus discarding the information from other measurements...
September 8, 2017: Australasian Physical & Engineering Sciences in Medicine
https://www.readbyqxmd.com/read/28877205/identification-of-shiga-toxigenic-escherichia-coli-outbreak-isolates-by-a-novel-data-analysis-tool-after-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry
#11
Martin Christner, Dirk Dressler, Mark Andrian, Claudia Reule, Orlando Petrini
The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e...
2017: PloS One
https://www.readbyqxmd.com/read/28868973/key-compounds-contributing-to-the-fruity-aroma-characterization-in-japanese-raw-soy-sauce
#12
Qi Meng, Miho Imamura, Hiroshi Katayama, Akio Obata, Etsuko Sugawara
In order to clarify the aroma characteristics of raw soy sauce (RS), the application of gas chromatography-olfactometry analysis to the aroma concentrate from a RS revealed 76 aroma peaks, of which 25 peaks showed fruit-like aromas. Furthermore, the head space aromatic compounds of RS were analyzed with 32 peaks detected. Ethyl 2-methylpropanoate, ethyl butanoate, ethyl 2-methylbutanoate, ethyl 3-methylbutanoate, and ethyl 4-methylpentanoate were detected with higher flavor dilution factor (FD factor) than other aroma compounds by aroma extract dilution analysis...
October 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28829309/microbubble-axial-localization-errors-in-ultrasound-super-resolution-imaging
#13
Kirsten Christensen-Jeffries, Sevan Harput, Jemma Brown, Peter N T Wells, Paul Aljabar, Chris Dunsby, Meng-Xing Tang, Robert J Eckersley
Acoustic super-resolution imaging has allowed visualization of microvascular structure and flow beyond the diffraction limit using standard clinical ultrasound systems through the localization of many spatially isolated microbubble signals. The determination of each microbubble position is typically performed by calculating the centroid, finding a local maximum, or finding the peak of a 2-D Gaussian function fit to the signal. However, the backscattered signal from a microbubble depends not only on diffraction characteristics of the waveform, but also on the microbubble behavior in the acoustic field...
August 17, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28814850/increased-parasympathetic-cardiac-modulation-in-patients-with-acute-exacerbation-of-copd-how-should-we-interpret-it
#14
Erika Zavaglia Kabbach, Adriana Mazzuco, Audrey Borghi-Silva, Ramona Cabiddu, Aline Galvão Agnoleto, Jessica Fernanda Barbosa, Luiz Carlos Soares de Carvalho Junior, Renata Gonçalves Mendes
BACKGROUND: Cardiac autonomic modulation (CAM) is impaired in patients with stable COPD. Exacerbation aggravates the patients' health status and functional capacity. While the clinical and functional effects of exacerbation are known, no studies investigated CAM during exacerbation and whether there is a relationship between CAM and functional capacity and dyspnea. METHODS: Thirty-two patients with moderate to severe COPD were enrolled into two groups: stable COPD (GSta, n=16) and acute exacerbation of COPD (GAE, n=16)...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28808439/saxs4coll-an-integrated-software-tool-for-analysing-fibrous-collagen-based-tissues
#15
Ahmed Abass, James S Bell, Martin T Spang, Sally Hayes, Keith M Meek, Craig Boote
This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28771171/vehicle-speed-and-length-estimation-using-data-from-two-anisotropic-magneto-resistive-amr-sensors
#16
Vytautas Markevicius, Dangirutis Navikas, Adam Idzkowski, Algimantas Valinevicius, Mindaugas Zilys, Darius Andriukaitis
Methods for estimating a car's length are presented in this paper, as well as the results achieved by using a self-designed system equipped with two anisotropic magneto-resistive (AMR) sensors, which were placed on a road lane. The purpose of the research was to compare the lengths of mid-size cars, i.e., family cars (hatchbacks), saloons (sedans), station wagons and SUVs. Four methods were used in the research: a simple threshold based method, a threshold method based on moving average and standard deviation, a two-extreme-peak detection method and a method based on the amplitude and time normalization using linear extrapolation (or interpolation)...
August 3, 2017: Sensors
https://www.readbyqxmd.com/read/28752757/detailed-investigation-and-comparison-of-the-xcms-and-mzmine-2-chromatogram-construction-and-chromatographic-peak-detection-methods-for-preprocessing-mass-spectrometry-metabolomics-data
#17
Owen D Myers, Susan J Sumner, Shuzhao Li, Stephen Barnes, Xiuxia Du
XCMS and MZmine 2 are two widely used software packages for preprocessing untargeted LC/MS metabolomics data. Both construct extracted ion chromatograms (EICs) and detect peaks from the EICs, the first two steps in the data preprocessing workflow. While both packages have performed admirably in peak picking, they also detect a problematic number of false positive EIC peaks and can also fail to detect real EIC peaks. The former and latter translate downstream into spurious and missing compounds and present significant limitations with most existing software packages that preprocess untargeted mass spectrometry metabolomics data...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28752754/one-step-forward-for-reducing-false-positive-and-false-negative-compound-identifications-from-mass-spectrometry-metabolomics-data-new-algorithms-for-constructing-extracted-ion-chromatograms-and-detecting-chromatographic-peaks
#18
Owen D Myers, Susan J Sumner, Shuzhao Li, Stephen Barnes, Xiuxia Du
False positive and false negative peaks detected from extracted ion chromatograms (EIC) are an urgent problem with existing software packages that preprocess untargeted liquid or gas chromatography-mass spectrometry metabolomics data because they can translate downstream into spurious or missing compound identifications. We have developed new algorithms that carry out the sequential construction of EICs and detection of EIC peaks. We compare the new algorithms to two popular software packages XCMS and MZmine 2 and present evidence that these new algorithms detect significantly fewer false positives...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28731935/predictive-value-of-the-water-drinking-test-and-the-risk-glaucomatous-visual-field-progression
#19
Carlos G De Moraes, Remo Susanna, Lisandro M Sakata, Marcelo Hatanaka
PURPOSE: The purpose of this is to test the hypothesis the intraocular pressure (IOP) peaks during a stress test [the water drinking test (WDT)] can estimate the risk of future visual field progression in treated primary open-angle glaucoma (POAG) patients. PATIENTS AND METHODS: Design: Prospective, longitudinal study. SETTING: Clinical practice. STUDY POPULATION: Treated POAG patients whose IOP was ≤18 mm Hg and who had no IOP-lowering interventions between the date of the WDT and the last eligible visual field...
July 20, 2017: Journal of Glaucoma
https://www.readbyqxmd.com/read/28708586/whole-genome-and-transcriptome-analysis-reveal-maldi-tof-ms-and-sds-page-have-limited-performance-for-the-detection-of-the-key-outer-membrane-protein-in-carbapenem-resistant-klebsiella-pneumoniae-isolates
#20
Naina Adren Pinto, Roshan D'Souza, In Sik Hwang, Jongrak Choi, Yong Ha In, Hyung Soon Park, Choong-Min Ryu, Dongeun Yong, Kyungwon Lee
To detect the outer membrane protein (OMP), which plays a key role in carbapenem resistance, whole-genome and transcriptome analysis of the clinical carbapenem-resistant Klebsiella pneumoniae was carried out. The index strain lacked both OmpK35 and OmpK36, whereas the other strains lacked only OmpK35. After SDS-PAGE, the putative OMP bands were excised and identified as OmpA and OmpK36. MALDI-TOF MS showed peaks at ~36 and ~38 kDa that corresponded to OmpA and OmpK36, respectively. In all the strains except YMC2014/03/P345, the ~38 kDa peaks were present...
July 5, 2017: Oncotarget
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