Finding faint HI structure in and around galaxies: scraping the barrel

Soon to be operational HI survey instruments such as APERTIF and ASKAP will produce large datasets. These surveys will provide information about the HI in and around hundreds of galaxies with a typical signal-to-noise ratio of $\sim$ 10 in the inner regions and $\sim$ 1 in the outer regions. In addition, such surveys will make it possible to probe faint HI structures, typically located in the vicinity of galaxies, such as extra-planar-gas, tails and filaments. These structures are crucial for understanding galaxy evolution, particularly when they are studied in relation to the local environment. Our aim is to find optimized kernels for the discovery of faint and morphologically complex HI structures. Therefore, using HI data from a variety of galaxies, we explore state-of-the-art filtering algorithms. We show that the intensity-driven gradient filter, due to its adaptive characteristics, is the optimal choice. In fact, this filter requires only minimal tuning of the input parameters to enhance the signal-to-noise ratio of faint components. In addition, it does not degrade the resolution of the high signal-to-noise component of a source. The filtering process must be fast and be embedded in an interactive visualization tool in order to support fast inspection of a large number of sources. To achieve such interactive exploration, we implemented a multi-core CPU (OpenMP) and a GPU (OpenGL) version of this filter in a 3D visualization environment ($\tt{SlicerAstro}$).Comment: 17 pages, 9 figures, 4 tables. Astronomy and Computing, accepte

3-D interactive visualisation tools for HI spectral line imaging

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present $\tt{SlicerAstro}$, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling

SlicerAstro: a 3-D interactive visual analytics tool for HI data

SKA precursors are capable of detecting hundreds of galaxies in HI in a single 12 hours pointing. In deeper surveys one will probe more easily faint HI structures, typically located in the vicinity of galaxies, such as tails, filaments, and extraplanar gas. The importance of interactive visualization has proven to be fundamental for the exploration of such data as it helps users to receive immediate feedback when manipulating the data. We have developed SlicerAstro, a 3-D interactive viewer with new analysis capabilities, based on traditional 2-D input/output hardware. These capabilities enhance the data inspection, allowing faster analysis of complex sources than with traditional tools. SlicerAstro is an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing. We demonstrate the capabilities of the current stable binary release of SlicerAstro, which offers the following features: i) handling of FITS files and astronomical coordinate systems; ii) coupled 2-D/3-D visualization; iii) interactive filtering; iv) interactive 3-D masking; v) and interactive 3-D modeling. In addition, SlicerAstro has been designed with a strong, stable and modular C++ core, and its classes are also accessible via Python scripting, allowing great flexibility for user-customized visualization and analysis tasks.Comment: 18 pages, 11 figures, Accepted by Astronomy and Computing. SlicerAstro link: https://github.com/Punzo/SlicerAstro/wiki#get-slicerastr

Understanding inconsistent step-length asymmetries across hemiplegic stroke patients: Impairments and compensatory gait

Background. In hemiplegic gait, step length typically differs in magnitude between paretic and nonparetic sides. However, the direction of step-length asymmetry varies across stroke patients. Objective. The study sought to understand directional variations in step-length asymmetry in terms of asymmetries in forward foot placement relative to the trunk and trunk progression. Methods. A total of 10 hemiplegic stroke patients and 9 healthy elderly controls walked at a self-selected comfortable speed while pelvic and heel marker positions were recorded. Step length, forward foot placement relative to the trunk, and trunk progression of paretic and nonparetic steps were quantified, as well as the asymmetries therein. Results. The 3 asymmetry indices in question varied within individual patients and occasionally fell within control reference ranges, whereas directional variations across stroke patients were observed for asymmetries in step length and forward foot placement only. Despite heterogeneity in asymmetry across patients, step-length asymmetry was determined by the sum of asymmetries in forward foot placement and trunk progression. Asymmetries in trunk progression and forward foot placement were negatively correlated. No significant association was observed between step-length asymmetry and any other asymmetry index. Conclusions. Step-length asymmetry was accounted for by asymmetries in forward foot placement and trunk progression, whereas their relative contribution accounted for directional variations in step-length asymmetry. Partitioning of step-length asymmetry further helped to identify individual impairments and compensatory gait strategies. An encompassing hemiplegic gait evaluation should therefore include an assessment of foot positioning relative to the trunk

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

A morphological algorithm for improving radio-frequency interference detection

A technique is described that is used to improve the detection of radio-frequency interference in astronomical radio observatories. It is applied on a two-dimensional interference mask after regular detection in the time-frequency domain with existing techniques. The scale-invariant rank (SIR) operator is defined, which is a one-dimensional mathematical morphology technique that can be used to find adjacent intervals in the time or frequency domain that are likely to be affected by RFI. The technique might also be applicable in other areas in which morphological scale-invariant behaviour is desired, such as source detection. A new algorithm is described, that is shown to perform quite well, has linear time complexity and is fast enough to be applied in modern high resolution observatories. It is used in the default pipeline of the LOFAR observatory.Comment: Accepted for publication in A&

Informational and Neuromuscular Contributions to Anchoring in Rhythmic Wrist Cycling

Continuous rhythmic movements are often geared toward particular points in the movement cycle, as evidenced by a local reduction in trajectory variability. These so-called anchor points provide a window into motor control, since changes in the degree of anchoring may reveal how informational and/or neuromuscular properties are exploited in the organization of rhythmic movements. The present experiment examined the relative contributions of informational timing (metronome beeps) and neuromuscular (wrist postures) constraints on anchoring by systematically varying both factors at movement reversal points. To this end, participants cycled their right wrist in a flexed, neutral, or extended posture, either self-paced or synchronized to a metronome pacing peak flexion, peak extension, or both peak flexion and extension. The effects of these manipulations were assessed in terms of kinematics, auditory-motor coordination, and muscle activity. The degree of anchoring seen at the reversal points depended on the degree of compatibility of the prevailing configuration of neuromuscular and informational timing constraints, which had largely independent effects. We further observed systematic changes in muscular activity, which revealed distinct contributions of posture- and muscle-dependent neuromuscular properties to motor control. These findings indicate that the anchor-based discretization of the control of continuous rhythmic wrist movements is determined by both informational timing and neuromuscular constraints in a task-specific manner with subtle interactions between the two, and exemplify how movement variability may be exploited to gain such insights

Attentional costs of walking are not affected by variations in lateral balance demands in young and older adults

Increased attentional costs of walking in older adults have been attributed to age-related changes in visuomotor and/or balance control of walking. The present experiment was conducted to examine the hypothesis that attentional costs of walking vary with lateral balance demands during walking in young and older adults. Twenty young and twenty older adults walked on a treadmill at their preferred walking speed under five conditions: unconstrained normal walking, walking on projected visual lines corresponding to either the participant’s preferred step width or 50% thereof (i.e. increased balance demand), and walking within low- and high-stiffness lateral stabilization frames (i.e. lower balance demands). Attentional costs were assessed using a probe reaction-time task during these five walking conditions, normalized to baseline performance as obtained during sitting. Both imposed step-width conditions were more attentionally demanding than the three other conditions, in the absence of any other significant differences between conditions. These effects were similar in the two groups. The results indicate that the attentional costs of walking were, in contrast to what has been postulated previously, not influenced by lateral balance demands. The observed difference in attentional costs between normal walking and both visual lines conditions suggests that visuomotor control processes, rather than balance control, strongly affect the attentional costs of walking. A tentative explanation of these results may be that visuomotor control processes are mainly governed by attention-demandingcortical processes, whereas balance is regulated predominantly subcortically