An Algebraic Framework for the Real-Time Solution of Inverse Problems on Embedded Systems

This article presents a new approach to the real-time solution of inverse problems on embedded systems. The class of problems addressed corresponds to ordinary differential equations (ODEs) with generalized linear constraints, whereby the data from an array of sensors forms the forcing function. The solution of the equation is formulated as a least squares (LS) problem with linear constraints. The LS approach makes the method suitable for the explicit solution of inverse problems where the forcing function is perturbed by noise. The algebraic computation is partitioned into a initial preparatory step, which precomputes the matrices required for the run-time computation; and the cyclic run-time computation, which is repeated with each acquisition of sensor data. The cyclic computation consists of a single matrix-vector multiplication, in this manner computation complexity is known a-priori, fulfilling the definition of a real-time computation. Numerical testing of the new method is presented on perturbed as well as unperturbed problems; the results are compared with known analytic solutions and solutions acquired from state-of-the-art implicit solvers. The solution is implemented with model based design and uses only fundamental linear algebra; consequently, this approach supports automatic code generation for deployment on embedded systems. The targeting concept was tested via software- and processor-in-the-loop verification on two systems with different processor architectures. Finally, the method was tested on a laboratory prototype with real measurement data for the monitoring of flexible structures. The problem solved is: the real-time overconstrained reconstruction of a curve from measured gradients. Such systems are commonly encountered in the monitoring of structures and/or ground subsidence.Comment: 24 pages, journal articl

A new reference genome assembly for the microcrustacean Daphnia pulex

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with similar to 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome

DADOS-Prospective: an open source application for Web-based prospective data collection

BACKGROUND: Randomized, prospective trials involving multi-institutional collaboration have become a central part of clinical and translational research. However, data management and coordination of multi-center studies is a complex process that involves developing systems for data collection and quality control, tracking data queries and resolutions, as well as developing communication procedures. We describe DADOS-Prospective, an open-source Web-based application for collecting and managing prospective data on human subjects for clinical and translational trials. DADOS-Prospective not only permits users to create new clinical research forms (CRF) and supports electronic signatures, but also offers the advantage of containing, in a single environment, raw research data in downloadable spreadsheet format, source documentation and regulatory files stored in PDF format, and audit trails. RESULTS: Feedback from formal and field usability tests was used to guide the design and development of DADOS-Prospective. To date, DADOS-Prospective has been implemented in five prospective clinical studies at our institution. Four of these studies are still in the CRF creation phase and one study has been entirely launched. CONCLUSION: DADOS-Prospective has significant advantages over existing Web-based data collecting programs. At our institution, it has been demonstrated to be an efficient tool for prospective clinical studies

Hubble Space Telescope Observations of Comet 9P/Tempel 1 during the Deep Impact Encounter

We report on the Hubble Space Telescope program to observe periodic comet 9P/Tempel 1 in conjunction with NASA's Deep Impact mission. Our objectives were to study the generation and evolution of the coma resulting from the impact and to obtain wide-band images of the visual outburst generated by the impact. Two observing campaigns utilizing a total of 17 HST orbits were carried out: the first occurred on 2005 June 13-14 and fortuitously recorded the appearance of a new, short-lived fan in the sunward direction on June 14. The principal campaign began two days before impact and was followed by contiguous orbits through impact plus several hours and then snapshots one, seven, and twelve days later. All of the observations were made using the Advanced Camera for Surveys (ACS). For imaging, the ACS High Resolution Channel (HRC) provides a spatial resolution of 36 km (16 km/pixel) at the comet at the time of impact. Baseline images of the comet, made prior to impact, photometrically resolved the comet's nucleus. The derived diameter, 6.1 km, is in excellent agreement with the 6.0 +/- 0.2 km diameter derived from the spacecraft imagers. Following the impact, the HRC images illustrate the temporal and spatial evolution of the ejecta cloud and allow for a determination of its expansion velocity distribution. One day after impact the ejecta cloud had passed out of the field-of-view of the HRC.Comment: 15 pages, 14 postscript figures. Accepted for publication in Icarus special issue on Deep Impac

Using meta-research methods to examine the inclusion of women, pregnant women, and women-specific health outcomes in studies that contributed to the dietary reference intakes for one-carbon metabolism micronutrients

Purpose: Maternal micronutrient deficiencies occurring during periconceptional, pregnancy, and postpartum periods are a leading cause of adverse pregnancy outcomes globally. The Dietary Reference Intakes (DRIs) are a set of reference values used to assess and guide nutrient intakes of healthy individuals. However, the current DRIs for pregnancy and lactation may be limited in their methods and included populations. The present study analyzed the current DRIs for their inclusion of pregnant women and geographic representativeness. Methods: Meta-research methods were applied to the DRI report for vitamins B6, B12, folate, and choline in four steps: search, screening, full-text data extraction, and data analysis. For each target micronutrient, sections that contributed data to setting the average requirement were focused on, “Selection of Indicators for Estimating the Requirement,” “Findings by Life Stage and Gender Group,” and “Tolerable Upper Intake Limit” for adults, pregnancy, and lactation sub-sections. Screening involved reviewing the reference list to determine whether a reference directly contributed to setting the DRI. Full-text data extraction of primary data was conducted in areas of: 1) administrative information; 2) study methods; 3) human population characteristics; and 4) non-human subjects. Descriptive analyses were performed to describe the inclusion of women, pregnant women, geographic patterns, and demographic diversity. Results: For Vitamin B12, 100% of indicator studies and 71% of life stages studies included women, with a total of 3,246 women participants. However, none of the indicator studies and 15% of life stages studies included pregnant women, with a total of 556 pregnant women participants. None of the indicator studies and 8% of life stages studies reported health measurements specific to women, pregnancy, or lactation. Geographically, 54% of studies were conducted in the United States, and 18% took place in low-and middle-income countries. Data analysis is ongoing for the remaining micronutrients. Conclusions: Preliminary findings indicate that the body of evidence informing the current DRIs are limited in their inclusion of women and pregnant women. Numerous adverse pregnancy and birth outcomes are preventable through optimal maternal nutrition. Therefore, it is critical to ensure that the DRIs are suitable for their intended population. Despite their original intent for use in North America, the DRIs are widely adopted globally. Thus, geographic representation of the studies underlying the DRIs have implications for generalizability

Animal microsurgery using microfluidics

Small multicellular genetic organisms form a central part of modern biological research. Using these small organisms provides significant advantages in genetic tractability, manipulation, lifespan and cost. Although the small size is generally advantageous, it can make procedures such as surgeries both time consuming and labor intensive. Over the past few years there have been dramatic improvements in microfluidic technologies that enable significant improvements in microsurgery and interrogation of small multicellular model organisms