Why GPS makes distances bigger than they are

Global Navigation Satellite Systems (GNSS), such as the Global Positioning System (GPS), are among the most important sensors for movement analysis. GPS is widely used to record the trajectories of vehicles, animals and human beings. However, all GPS movement data are affected by both measurement and interpolation error. In this article we show that measurement error causes a systematic bias in distances recorded with a GPS: the distance between two points recorded with a GPS is -- on average -- bigger than the true distance between these points. This systematic `overestimation of distance' becomes relevant if the influence of interpolation error can be neglected, which is the case for movement sampled at high frequencies. We provide a mathematical explanation of this phenomenon and we illustrate that it functionally depends on the autocorrelation of GPS measurement error ($C$). We argue that $C$ can be interpreted as a quality measure for movement data recorded with a GPS. If there is strong autocorrelation any two consecutive position estimates have very similar error. This error cancels out when average speed, distance or direction are calculated along the trajectory. Based on our theoretical findings we introduce a novel approach to determine $C$ in real-world GPS movement data sampled at high frequencies. We apply our approach to a set of pedestrian and a set of car trajectories. We find that the measurement error in the data is strongly spatially and temporally autocorrelated and give a quality estimate of the data. Finally, we want to emphasize that all our findings are not limited to GPS alone. The systematic bias and all its implications are bound to occur in any movement data collected with absolute positioning if interpolation error can be neglected.Comment: 17 pages, 8 figures, submitted to IJGI

Cloning and characterization of excision repair genes

For all living organisms, it is of vital importance to maintain intact the genetic information stored in the nucleotide sequence of DNA. Numerous environmental and genotoxic agents can affect the DNA and lead to, for example, mutagenesis or carcinogenesis. Study of the mechanism of UV-carcinogenesis has become even more pressing given recent concerns about atmospheric ozone depletion (Mimms, 1994; Watson, 1995), because such atmospheric alterations would result in increased UVB at the earth's surface. Carcinogenesis appears to be a multistep process through which normal cells progress from benign, through transitional stages to the fully malignant forms of cancer by the gradual accumulation of genetic errors (Bishop, 1995). Therefore, normal cells have an intricate quality control mechanism that recognizes and mends damage to the DNA helix

Neuro fuzzy control of the FES assisted freely swinging leg of paraplegic subjects

The authors designed a neuro fuzzy control strategy for control of cyclical leg movements of paraplegic subjects. The cyclical leg movements were specified by three `swing phase objectives', characteristic of natural human gait. The neuro fuzzy controller is a combination of a fuzzy logic controller and a neural network, which makes the controller self tuning and adaptive. Two experiments have been performed, in which the performance of the neuro fuzzy control strategy has been compared with conventional PID control strateg

A model-based approach to stabilizing crutch supported paraplegic standing by artifical hip joint stiffness

The prerequisites for stable crutch supported standing were analyzed in this paper. For this purpose, a biomechanical model of crutch supported paraplegic stance was developed assuming the patient was standing with extended knees. When using crutches during stance, the crutches will put a position constraint on the shoulder, thus reducing the number of degrees of freedom. Additional hip-joint stiffness was applied to stabilize the hip joint and, therefore, to stabilize stance. The required hip-joint stiffness for changing crutch placement and hip-joint offset angle was studied under static and dynamic conditions. Modeling results indicate that, by using additional hip-joint stiffness, stable crutch supported paraplegic standing can be achieved, both under static as well as dynamic situations. The static equilibrium postures and the stability under perturbations were calculated to be dependent on crutch placement and stiffness applied. However, postures in which the hip joint was in extension (C postures) appeared to the most stable postures. Applying at least 60 N /spl middot/ m/rad hip-joint stiffness gave stable equilibrium postures in all cases. Choosing appropriate hip-joint offset angles, the static equilibrium postures changed to more erect postures, without causing instability or excessive arm forces to occur

Gene expression and functional annotation of the human and mouse choroid plexus epithelium

Background: The choroid plexus epithelium (CPE) is a lobed neuro-epithelial structure that forms the outer blood-brain barrier. The CPE protrudes into the brain ventricles and produces the cerebrospinal fluid (CSF), which is crucial for brain homeostasis. Malfunction of the CPE is possibly implicated in disorders like Alzheimer disease, hydrocephalus or glaucoma. To study human genetic diseases and potential new therapies, mouse models are widely used. This requires a detailed knowledge of similarities and differences in gene expression and functional annotation between the species. The aim of this study is to analyze and compare gene expression and functional annotation of healthy human and mouse CPE. Methods: We performed 44k Agilent microarray hybridizations with RNA derived from laser dissected healthy human and mouse CPE cells. We functionally annotated and compared the gene expression data of human and mouse CPE using the knowledge database Ingenuity. We searched for common and species specific gene expression patterns and function between human and mouse CPE. We also made a comparison with previously published CPE human and mouse gene expression data. Results: Overall, the human and mouse CPE transcriptomes are very similar. Their major functionalities included epithelial junctions, transport, energy production, neuro-endocrine signaling, as well as immunological, neurological and hematological functions and disorders. The mouse CPE presented two additional functions not found in the human CPE: carbohydrate metabolism and a more extensive list of (neural) developmental functions. We found three genes specifically expressed in the mouse CPE compared to human CPE, being ACE, PON1 and TRIM3 and no human specifically expressed CPE genes compared to mouse CPE. Conclusion: Human and mouse CPE transcriptomes are very similar, and display many common functionalities. Nonetheless, we also identified a few genes and pathways which suggest that the CPE between mouse and man differ with respect to transport and metabolic functions

A distinct epigenetic signature at targets of a leukemia protein

BACKGROUND: Human myelogenous leukemia characterized by either the non random t(8; 21)(q22; q22) or t(16; 21)(q24; q22) chromosome translocations differ for both their biological and clinical features. Some of these features could be consequent to differential epigenetic transcriptional deregulation at AML1 targets imposed by AML1-MTG8 and AML1-MTG16, the fusion proteins deriving from the two translocations. Preliminary findings showing that these fusion proteins lead to transcriptional downregulation of AML1 targets, marked by repressive chromatin changes, would support this hypothesis. Here we show that combining conventional global gene expression arrays with the power of bioinformatic genomic survey of AML1-consensus sequences is an effective strategy to identify AML1 targets whose transcription is epigenetically downregulated by the leukemia-associated AML1-MTG16 protein. RESULTS: We interrogated mouse gene expression microarrays with probes generated either from 32D cells infected with a retroviral vector carrying AML1-MTG16 and unable of granulocyte differentiation and proliferation in response to the granulocyte colony stimulating factor (G-CSF), or from 32D cells infected with the cognate empty vector. From the analysis of differential gene expression alone (using as criteria a p value < 0.01 and an absolute fold change > 3), we were unable to conclude which of the 37 genes downregulated by AML1-MTG16 were, or not, direct AML1 targets. However, when we applied a bioinformatic approach to search for AML1-consensus sequences in the 10 Kb around the gene transcription start sites, we closed on 17 potential direct AML1 targets. By focusing on the most significantly downregulated genes, we found that both the AML1-consensus and the transcription start site chromatin regions were significantly marked by aberrant repressive histone tail changes. Further, the promoter of one of these genes, containing a CpG island, was aberrantly methylated. CONCLUSION: This study shows that a leukemia-associated fusion protein can impose a distinct epigenetic repressive signature at specific sites in the genome. These findings strengthen the conclusion that leukemia-specific oncoproteins can induce non-random epigenetic changes

IReport: A generalised Galaxy solution for integrated experimental reporting

Background: Galaxy offers a number of visualisation options with components, such as Trackster, Circster and Galaxy Charts, but currently lacks the ability to easily combine outputs from different tools into a single view or report. A number of tools produce HTML reports as output in order to combine the various output files from a single tool; however, this requires programming and knowledge of HTML, and the reports must be custom-made for each new tool.Findings: We have developed a generic and flexible reporting tool for Galaxy, iReport, that allows users to create interactive HTML reports directly from the Galaxy UI, with the ability to combine an arbitrary number of outputs from any number of different tools. Content can be organised into different tabs, and interactivity can be added to components. To demonstrate the capability of iReport we provide two publically available examples, the first is an iReport explaining about iReports, created for, and using content from the recent Galaxy Community Conference 2014. The second is a genetic report based on a trio analysis to determine candidate pathogenic variants which uses our previously developed Galaxy toolset for whole-genome NGS analysis, CGtag. These reports may be adapted for outputs from any sequencing platform and any results, such as omics data, non-high throughput results and clinical variables.Conclusions: iReport provides a secure, collaborative, and flexible web-based reporting system that is compatible with Galaxy (and non-Galaxy) generated content. We demonstrate its value with a real-life example of reporting genetic trio-analysis