MethControl

Computed tomographic colonography (CTC) combined with a computer aided detection system has the potential for improving colonic polyp detection and increasing the use of CTC for colon cancer screening. In the clinical use of CTC, a true colonic polyp will be confirmed with high confidence if a radiologist can find it on both the supine and prone scans. To assist radiologists in CTC reading, we propose a new method for matching polyp findings on the supine and prone scans. The method performs a colon registration using four automatically identified anatomical salient points and correlation o...

Mass spectrometry imaging (MSI) is a technique that provides comprehensive molecular information with high spatial resolution from tissue. Today, there is a strong push toward sharing data sets through public repositories in many research fields where MSI is commonly applied; yet, there is no standardized protocol for analyzing these data sets in a reproducible manner. Shifts in the mass-to-charge ratio (m/z) of molecular peaks present a major obstacle that can make it impossible to distinguish one compound from another. Here, we present a label-free m/z alignment approach that is compatibl...

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Two different algorithms for time‐alignment as a preprocessing step in linear factor models are studied. Correlation optimized warping and dynamic time warping are both presented in the literature as methods that can eliminate shift‐related artifacts from measurements by correcting a sample vector towards a reference. In this study both the theoretical properties and the practical implications of using signal warping as preprocessing for chromatographic data are investigated. The connection between the two algorithms is also discussed. The findings are illustrated by means of a case study o...

Replicating Market Indices using Quantitative methods

Purpose: In computed tomographic colonography (CTC), a patient will be scanned twice—Once supine and once prone—to improve the sensitivity for polyp detection. To assist radiologists in CTC reading, in this paper we propose an automated ...

Introduction to RGCxGC package

Retrieval and comparative editing/modeling of motion data require temporal alignment. In other words, for such processes to perform accurately, critical features of motion sequences need to occur simultaneously. In this paper, we propose correlation-optimized time warping (CoTW) for aligning motion data. CoTW utilizes a correlation-based objective function for characterizing alignment. The method solves an optimization problem to determine the optimum warping degree for different segments of the sequence. Using segment-wise interpolated warping, smooth motion trajectories are achieved that ...

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Abstract. Summary: Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as h

Analysis of exhaled breath samples reveals the presence of many volatile organic compounds (VOCs). The VOC composition of the breath, the so-called breath profile, contains a variety of information...

Abstract. The application of dynamic time warping (DTW) to the correction of retention time shift in chromatographic fingerprints of Radix Puerariae thomsonii (

A new method for chemical fingerprinting of petroleum biomakers is described. The method consists of GC-MS analysis, preprocessing of GC-MS chromatograms, and principal component analysis (PCA) of selected regions. The preprocessing consists of baseline removal by derivatization, normalization, and alignment using correlation optimized warping. The method was applied to chromatograms of m/z 217 (tricyclic and tetracyclic steranes) of oil spill samples and source oils. Oil spill samples collected from the coastal environment in the weeks after the Baltic Carrier oil spill were clustered in p...

The multivariate calibration methods—principal component regression (PCR) and partial least squares (PLSs)—were employed for the prediction of total phenol contents of four Prunella species. High performance liquid chromatography (HPLC) and spectrophotometric approaches were used to determine the total phenol content of the Prunella samples. Several preprocessing techniques such as smoothing, normalization, and column centering were employed to extract the chemically relevant information from the data after alignment with correlation optimized warping (COW). The importance of the preprocess...

The U.S. Department of Energy's Office of Scientific and Technical Information

Bifidobacteria are a major microbial component of infant gut microbiota, which is believed to promote health benefits for the host and stimulate maturation of the immune system. Despite their perceived importance, very little is known about the natural development of and possible correlations between bifidobacteria in human populations. To address this knowledge gap, we analyzed stool samples from a randomly selected healthy cohort of 87 infants and their mothers with >90% of vaginal delivery and nearly 100% breast-feeding at 4 months. Fecal material was sampled during pregnancy, at 3 and 1...

Dynamic Time Warping (DTW) is a widely used technique for univariate time series comparison. This paper proposes a new algorithm for the comparison of multivariate time series which generalize DTW for the needs of correlated multivariate time series.

Background In proteomics studies, liquid chromatography coupled to mass spectrometry (LC-MS) has proven to be a powerful technology to investigate differential expression of proteins/peptides that are characterized by their peak intensities, mass-to-charge ratio (m/z), and retention time (RT). The variable complexity of peptide mixtures and occasional drifts lead to substantial variations in m/z and RT dimensions. Thus, label-free differential protein expression studies by LC-MS technology require alignment with respect to both RT and m/z to ensure that same proteins/peptides are compared f...

Yvan Heyden studies Electromagnetic Fields and Microwave Techniques, Biomaterials and Tissue Engineering, and Biosensors.

The last two decades have seen tremendous progress in the application of two-dimensional correlation spectroscopy (2D-COS) as a versatile analysis method for da...