amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R

Proteomics is the study of the abundance, function and dynamics of all proteins present in a living organism, and mass spectrometry (MS) has become its most important tool due to its unmatched sensitivity, resolution and potential for high-throughput experimentation. A frequently used variant of mass spectrometry is coupled with liquid chromatography (LC) and is denoted as "LC/MS". It produces two-dimensional raw data, where significant distortions along one of the dimensions can occur between different runs on the same instrument, and between instruments. A compensation of these distortions is required to allow for comparisons between and inference based on different experiments. This article introduces the amsrpm software package. It implements a variant of the Robust Point Matching (RPM) algorithm that is tailored for the alignment of LC and LC/MS experiments. Problem-specific enhancements include a specialized dissimilarity measure, and means to enforce smoothness and monotonicity of the estimated transformation function. The algorithm does not rely on pre-specified landmarks, it is insensitive towards outliers and capable of modeling nonlinear distortions. Its usefulness is demonstrated using both simulated and experimental data. The software is available as an open source package for the statistical programming language R.

EEG and EMG dataset for the detection of errors introduced by an active orthosis device

This paper presents a dataset containing recordings of the electroencephalogram (EEG) and the electromyogram (EMG) from eight subjects who were assisted in moving their right arm by an active orthosis device. The supported movements were elbow joint movements, i.e., flexion and extension of the right arm. While the orthosis was actively moving the subject's arm, some errors were deliberately introduced for a short duration of time. During this time, the orthosis moved in the opposite direction. In this paper, we explain the experimental setup and present some behavioral analyses across all subjects. Additionally, we present an average event-related potential analysis for one subject to offer insights into the data quality and the EEG activity caused by the error introduction. The dataset described herein is openly accessible. The aim of this study was to provide a dataset to the research community, particularly for the development of new methods in the asynchronous detection of erroneous events from the EEG. We are especially interested in the tactile and haptic-mediated recognition of errors, which has not yet been sufficiently investigated in the literature. We hope that the detailed description of the orthosis and the experiment will enable its reproduction and facilitate a systematic investigation of the influencing factors in the detection of erroneous behavior of assistive systems by a large community.Comment: Revised references to our datasets, general corrections to typos, and latex template format changes, Overall Content unchange

Continuous ErrP detections during multimodal human-robot interaction

Human-in-the-loop approaches are of great importance for robot applications. In the presented study, we implemented a multimodal human-robot interaction (HRI) scenario, in which a simulated robot communicates with its human partner through speech and gestures. The robot announces its intention verbally and selects the appropriate action using pointing gestures. The human partner, in turn, evaluates whether the robot's verbal announcement (intention) matches the action (pointing gesture) chosen by the robot. For cases where the verbal announcement of the robot does not match the corresponding action choice of the robot, we expect error-related potentials (ErrPs) in the human electroencephalogram (EEG). These intrinsic evaluations of robot actions by humans, evident in the EEG, were recorded in real time, continuously segmented online and classified asynchronously. For feature selection, we propose an approach that allows the combinations of forward and backward sliding windows to train a classifier. We achieved an average classification performance of 91% across 9 subjects. As expected, we also observed a relatively high variability between the subjects. In the future, the proposed feature selection approach will be extended to allow for customization of feature selection. To this end, the best combinations of forward and backward sliding windows will be automatically selected to account for inter-subject variability in classification performance. In addition, we plan to use the intrinsic human error evaluation evident in the error case by the ErrP in interactive reinforcement learning to improve multimodal human-robot interaction

NITPICK: peak identification for mass spectrometry data

<p>Abstract</p> <p>Background</p> <p>The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments.</p> <p>Results</p> <p>This contribution proposes a sparse template regression approach to peak picking called NITPICK. NITPICK is a Non-greedy, Iterative Template-based peak PICKer that deconvolves complex overlapping isotope distributions in multicomponent mass spectra. NITPICK is based on <it>fractional averagine</it>, a novel extension to Senko's well-known averagine model, and on a modified version of sparse, non-negative least angle regression, for which a suitable, statistically motivated early stopping criterion has been derived. The strength of NITPICK is the deconvolution of overlapping mixture mass spectra.</p> <p>Conclusion</p> <p>Extensive comparative evaluation has been carried out and results are provided for simulated and real-world data sets. NITPICK outperforms pepex, to date the only alternate, publicly available, non-greedy feature extraction routine. NITPICK is available as software package for the R programming language and can be downloaded from <url>http://hci.iwr.uni-heidelberg.de/mip/proteomics/</url>.</p

amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R

Proteomics is the study of the abundance, function and dynamics of all proteins present in a living organism, and mass spectrometry (MS) has become its most important tool due to its unmatched sensitivity, resolution and potential for high-throughput experimentation. A frequently used variant of mass spectrometry is coupled with liquid chromatography (LC) and is denoted as "LC/MS". It produces two-dimensional raw data, where significant distortions along one of the dimensions can occur between different runs on the same instrument, and between instruments. A compensation of these distortions is required to allow for comparisons between and inference based on different experiments. This article introduces the amsrpm software package. It implements a variant of the Robust Point Matching (RPM) algorithm that is tailored for the alignment of LC and LC/MS experiments. Problem-specific enhancements include a specialized dissimilarity measure, and means to enforce smoothness and monotonicity of the estimated transformation function. The algorithm does not rely on pre-specified landmarks, it is insensitive towards outliers and capable of modeling nonlinear distortions. Its usefulness is demonstrated using both simulated and experimental data. The software is available as an open source package for the statistical programming language R

Turbulence effect on gas transport in three contrasting forest soils

peer reviewe