Autonomous Repeat Image Feature Tracking (autoRIFT) and Its Application for Tracking Ice Displacement

In this paper, we build on past efforts with regard to the implementation of an efficient feature tracking algorithm for the mass processing of satellite images. This generic open-source feature tracking routine can be applied to any type of imagery to measure sub-pixel displacements between images. The routine consists of a feature tracking module (autoRIFT) that enhances computational efficiency and a geocoding module (Geogrid) that mitigates problems found in existing geocoding algorithms. When applied to satellite imagery, autoRIFT can run on a grid in the native image coordinates (such as radar or map) and, when used in conjunction with the Geogrid module, on a user-defined grid in geographic Cartesian coordinates such as Universal Transverse Mercator or Polar Stereographic. To validate the efficiency and accuracy of this approach, we demonstrate its use for tracking ice motion by using ESA’s Sentinel-1A/B radar data (seven pairs) and NASA’s Landsat-8 optical data (seven pairs) collected over Greenland’s Jakobshavn Isbræ glacier in 2017. Feature-tracked velocity errors are characterized over stable surfaces, where the best Sentinel-1A/B pair with a 6 day separation has errors in X/Y of 12 m/year or 39 m/year, compared to 22 m/year or 31 m/year for Landsat-8 with a 16-day separation. Different error sources for radar and optical image pairs are investigated, where the seasonal variation and the error dependence on the temporal baseline are analyzed. Estimated velocities were compared with reference velocities derived from DLR’s TanDEM-X SAR/InSAR data over the fast-moving glacier outlet, where Sentinel-1 results agree within 4% compared to 3–7% for Landsat-8. A comprehensive apples-to-apples comparison is made with regard to runtime and accuracy between multiple implementations of the proposed routine and the widely-used “dense ampcor" program from NASA/JPL’s ISCE software. autoRIFT is shown to provide two orders of magnitude of runtime improvement with a 20% improvement in accuracy

SnoPatrol: how many snoRNA genes are there?

Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found

Improved retrieval of land ice topography from CryoSat-2 data and its impact for volume-change estimation of the Greenland Ice Sheet

A new methodology for retrieval of glacier and ice sheet elevations and elevation changes from CryoSat-2 data is presented. Surface elevations and elevation changes determined using this approach show significant improvements over ESA's publicly available CryoSat-2 elevation product (L2 Baseline-B). The results are compared to near-coincident airborne laser altimetry from NASA's Operation IceBridge and seasonal height amplitudes from the Ice, Cloud, and Elevation Satellite (ICESat). Applying this methodology to CryoSat-2 data collected in interferometric synthetic aperture mode (SIN) over the high-relief regions of the Greenland Ice Sheet we find an improvement in the root-mean-square error (RMSE) of 27 and 40 % compared to ESA's L2 product in the derived elevation and elevation changes, respectively. In the interior part of the ice sheet, where CryoSat-2 operates in low-resolution mode (LRM), we find an improvement in the RMSE of 68 and 55 % in the derived elevation and elevation changes, respectively. There is also an 86 % improvement in the magnitude of the seasonal amplitudes when compared to amplitudes derived from ICESat data. These results indicate that the new methodology provides improved tracking of the snow/ice surface with lower sensitivity to changes in near-surface dielectric properties. To demonstrate the utility of the new processing methodology we produce elevations, elevation changes, and total volume changes from CryoSat-2 data for the Greenland Ice Sheet during the period January 2011 to January 2015. We find that the Greenland Ice Sheet decreased in volume at a rate of 289 ± 20 km3a−1, with high interannual variability and spatial heterogeneity in rates of loss. This rate is 65 km3a−1 more negative than rates determined from ESA's L2 product, highlighting the importance of CryoSat-2 processing methodologies.</p

Rehearsal: A Configuration Verification Tool for Puppet

Large-scale data centers and cloud computing have turned system configuration into a challenging problem. Several widely-publicized outages have been blamed not on software bugs, but on configuration bugs. To cope, thousands of organizations use system configuration languages to manage their computing infrastructure. Of these, Puppet is the most widely used with thousands of paying customers and many more open-source users. The heart of Puppet is a domain-specific language that describes the state of a system. Puppet already performs some basic static checks, but they only prevent a narrow range of errors. Furthermore, testing is ineffective because many errors are only triggered under specific machine states that are difficult to predict and reproduce. With several examples, we show that a key problem with Puppet is that configurations can be non-deterministic. This paper presents Rehearsal, a verification tool for Puppet configurations. Rehearsal implements a sound, complete, and scalable determinacy analysis for Puppet. To develop it, we (1) present a formal semantics for Puppet, (2) use several analyses to shrink our models to a tractable size, and (3) frame determinism-checking as decidable formulas for an SMT solver. Rehearsal then leverages the determinacy analysis to check other important properties, such as idempotency. Finally, we apply Rehearsal to several real-world Puppet configurations.Comment: In proceedings of ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI) 201

Influence of the dual ABCB1 and ABCG2 inhibitor tariquidar on the disposition of oral imatinib in mice

<p>Abstract</p> <p>Background</p> <p>Imatinib, a tyrosine kinase inhibitor currently approved for treatment of several malignancies, has been shown to be a substrate for multiple efflux-transporter proteins, including ABCB1 (P-glycoprotein) and ABCG2 (BCRP). The effect of inhibiting these transporters on tissue exposure to imatinib remains unclear.</p> <p>Objective</p> <p>To assess the role of these transporters on drug disposition, 50 mg/kg imatinib was administered to Balb/C mice, 30 minutes after receiving tariquidar (10 mg/kg), an inhibitor of both ABCB1 and ABCG2, or vehicle, via oral gavage.</p> <p>Methods</p> <p>Quantitative determination of imatinib in mouse plasma, liver and brain was performed using a newly-developed and validated liquid-chromatography-mass spectrometric method. Results: Exposure to imatinib was 2.2-fold higher in plasma, liver and brain in mice that received tariquidar, as compared to those that received the vehicle (P = 0.001). The peak plasma concentration did not increase substantially, suggesting that tariquidar is affecting the distribution, metabolism and/or excretion of imatinib, rather than absorption. Though tariquidar increased the absolute exposure of imatinib, the brain-to-plasma ratio of imatinib was unaffected.</p> <p>Conclusion</p> <p>This study suggests that intentional inhibition of ABCB1 and ABCG2 function at the blood-brain barrier is unlikely to significantly improve clinical outcome of imatinib with currently used dosing regimens.</p

An Assessment of Regional ICESat-2 Sea-Level Trends

Sea-level rise is an important indicator of ongoing climate change and well observed by satellite altimetry. However, observations from conventional altimetry degrade at the coast where regional sea-level changes can deviate from the open-ocean and impact local communities. With the 2018 launch of the laser altimeter onboard ICESat-2, new high-resolution observations of ice, land, and ocean elevations are available. Here we assess the potential benefits of sea level measured by ICESat-2 by comparing to data from Jason-3 and tide gauges. We find good agreement in the linear rates computed from the independent observations, with an absolute average residual of 3.60 ± 0.03 cm yr−1 between global ICESat-2 and Jason-3 observations at a 1° posting. The recent La Niña is clearly evident in ICESat-2 observations, as well as small-scale features. By demonstrating the quality of the ICESat-2-measured sea level, we provide support for integrating it into the existing suite of sea-level observations

A haptic-robotic platform for upper-limb reaching stroke therapy: Preliminary design and evaluation results

<p>Abstract</p> <p>Background</p> <p>It has been shown that intense training can significantly improve post-stroke upper-limb functionality. However, opportunities for stroke survivors to practice rehabilitation exercises can be limited because of the finite availability of therapists and equipment. This paper presents a haptic-enabled exercise platform intended to assist therapists and moderate-level stroke survivors perform upper-limb reaching motion therapy. This work extends on existing knowledge by presenting: 1) an anthropometrically-inspired design that maximizes elbow and shoulder range of motions during exercise; 2) an unobtrusive upper body postural sensing system; and 3) a vibratory elbow stimulation device to encourage muscle movement.</p> <p>Methods</p> <p>A multi-disciplinary team of professionals were involved in identifying the rehabilitation needs of stroke survivors incorporating these into a prototype device. The prototype system consisted of an exercise device, postural sensors, and a elbow stimulation to encourage the reaching movement. Eight experienced physical and occupational therapists participated in a pilot study exploring the usability of the prototype. Each therapist attended two sessions of one hour each to test and evaluate the proposed system. Feedback about the device was obtained through an administered questionnaire and combined with quantitative data.</p> <p>Results</p> <p>Seven of the nine questions regarding the haptic exercise device scored higher than 3.0 (somewhat good) out of 4.0 (good). The postural sensors detected 93 of 96 (97%) therapist-simulated abnormal postures and correctly ignored 90 of 96 (94%) of normal postures. The elbow stimulation device had a score lower than 2.5 (neutral) for all aspects that were surveyed, however the therapists felt the rehabilitation system was sufficient for use without the elbow stimulation device.</p> <p>Conclusion</p> <p>All eight therapists felt the exercise platform could be a good tool to use in upper-limb rehabilitation as the prototype was considered to be generally well designed and capable of delivering reaching task therapy. The next stage of this project is to proceed to clinical trials with stroke patients.</p

Freedom in the Expansion and Obstacles to Integrability in Multiple-Soliton Solutions of the Perturbed KdV Equation

The construction of a solution of the perturbed KdV equation encounters obstacles to asymptotic integrability beyond the first order, when the zero-order approximation is a multiple-soliton wave. In the standard analysis, the obstacles lead to the loss of integrability of the Normal Form, resulting in a zero-order term, which does not have the simple structure of the solution of the unperturbed equation. Exploiting the freedom in the perturbative expansion, we propose an algorithm that shifts the effect of the obstacles from the Normal Form to the higher-order terms. The Normal Form then remains integrable, and the zero-order approximation retains the multiple-soliton structure of the unperturbed solution. The obstacles are expressed in terms of symmetries of the unperturbed equation, and decay exponentially away from the soliton-interaction region. As a result, they generate a bounded correction term, which decays exponentially away from the origin in the x-t plane. The computation is performed through second order.Comment: 22 pages, including 3 figure