Using visualization for visualization : an ecological interface design approach to inputting data

Visualization is experiencing growing use by a diverse community, with continuing improvements in the availability and usability of systems. In spite of these developments the problem of how first to get the data in has received scant attention: the established approach of pre-defined readers and programming aids has changed little in the last two decades. This paper proposes a novel way of inputting data for scientific visualization that employs rapid interaction and visual feedback in order to understand how the data is stored. The approach draws on ideas from the discipline of ecological interface design to extract and control important parameters describing the data, at the same time harnessing our innate human ability to recognize patterns. Crucially, the emphasis is on file format discovery rather than file format description, so the method can therefore still work when nothing is known initially of how the file was originally written, as is often the case with legacy binary data. © 2013 Elsevier Ltd

Interpretative modelling of a geological cross section from boreholes: sources of uncertainty and their quantification

We conducted a designed experiment to quantify sources of uncertainty in geologists' interpretations of a geological cross section. A group of 28 geologists participated in the experiment. Each interpreted borehole record included up to three Palaeogene bedrock units, including the target unit for the experiment: the London Clay. The set of boreholes was divided into batches from which validation boreholes had been withheld; as a result, we obtained 129 point comparisons between the interpreted elevation of the base of the London Clay and its observed elevation in a borehole not used for that particular interpretation. Analysis of the results showed good general agreement between the observed and interpreted elevations, with no evidence of systematic bias. Between-site variation of the interpretation error was spatially correlated, and the variance appeared to be stationary. The between-geologist component of variance was smaller overall, and depended on the distance to the nearest borehole. There was also evidence that the between-geologist variance depends on the degree of experience of the individual. We used the statistical model of interpretation error to compute confidence intervals for any one interpretation of the base of the London Clay on the cross section, and to provide uncertainty measures for decision support in a hypothetical route-planning process. The statistical model could also be used to quantify error propagation in a full 3-D geological model produced from interpreted cross sections

Embryonic Markers Of Cone Differentiation

Purpose: Photoreceptor cells are born in two distinct phases of vertebrate retinogenesis. In the mouse retina, cones are born primarily during embryogenesis, while rod formation occurs later in embryogenesis and early postnatal ages. Despite this dichotomy in photoreceptor birthdates, the visual pigments and phototransduction machinery are not reactive to visual stimulus in either type of photoreceptor cell until the second postnatal week. Several markers of early cone formation have been identified, including Otx2, Crx, Blimp1, NeuroD, Trβ2, Rorβ, and Rxrγ, and all are thought to be involved in cellular determination. However, little is known about the expression of proteins involved in cone visual transduction during early retinogenesis. Therefore, we sought to characterize visual transduction proteins that are expressed specifically in photoreceptors during mouse embryogenesis. Methods: Eye tissue was collected from control and phosducin-null mice at embryonic and early postnatal ages. Immunohistochemistry and quantitative reverse transcriptase-PCR (qPCR) were used to measure the spatial and temporal expression patterns of phosducin (Pdc) and cone transducin γ (Gngt2) proteins and transcripts in the embryonic and early postnatal mouse retina. Results: We identified the embryonic expression of phosducin (Pdc) and cone transducin γ (Gngt2) that coincides temporally and spatially with the earliest stages of cone histogenesis. Using immunohistochemistry, the phosducin protein was first detected in the retina at embryonic day (E)12.5, and cone transducin γ was observed at E13.5. The phosducin and cone transducin γ proteins were seen only in the outer neuroblastic layer, consistent with their expression in photoreceptors. At the embryonic ages, phosducin was coexpressed with Rxrγ, a known cone marker, and with Otx2, a marker of photoreceptors. Pdc and Gngt2 mRNAs were detected as early as E10.5 with qPCR, although at low levels. Conclusions: Visual transduction proteins are expressed at the earliest stages in developing cones, well before the onset of opsin gene expression. Given the delay in opsin expression in rods and cones, we speculate on the embryonic function of these G-protein signaling components beyond their roles in the visual transduction cascade

The London Basin superficial and bedrock LithoFrame 50 Model

This report describes the methodology and datasets used in the construction of the 1:50 000 resolution superficial and bedrock geological model of the London Basin. The London Basin study area was divided into twelve 20 x 20 km tiles, with construction of the first tiles beginning in 2006 and completion of the combined model in 2014. This time period coincided with the ongoing development of GSI3D software which was used to construct much of the model. The GSI3D software was used to calculate a rockhead (base Quaternary and Anthropocene) surface that was then used as a capping surface for the modelling of the bedrock geology in the GOCAD® software. The model complements the corresponding DiGMapGB-50 tiles of the area and consists of about 80 modelled geological units, comprising mass movement (landslip), artificial, superficial, and bedrock. This report supersedes an earlier report detailing the construction of the superficial part of this model (Burke et al. 2013). A glossary of technical terms used is included at the end of this report

A Systematic Review of Dental Disease in Patients Undergoing Cancer Therapy

Introduction: The purpose of this systematic review was to evaluate the literature and update our current understanding of the impact of present cancer therapies on the dental apparatus (teeth and periodontium) since the 1989 NIH Development Consensus Conference on the Oral Compli­cations of Cancer Therapies. Review Method: A systematic literature search was con­ducted with assistance from a research librarian in the databases MEDLINE/PubMed and EMBASE for articles published between 1 January 1990 and 31 December 2008. Each study was independently assessed by two reviewers. Taking into account predetermined quality measures, a weighted prevalence was calculated for the prevalence of dental caries, severe gingival disease, and dental infection. Data on DMFT/dmft, DMFS/dmfs, plaque, and gingival indexes were also gathered. The level of evidence, recommendation, and guideline (if possible) were given for published preventive and management strategies. Results: Sixty-four published papers between 1990 and 2008 were reviewed. The weighted overall prevalence of dental caries was 28.1%. The overall DMFT for patients who were post-antineoplastic therapy was 9.19 (SD, 7.98; n=457). The overall plaque index for patients who were post­antineoplastic therapy was 1.38 (SD, 0.25; n=189). The GI for patients who were post-chemotherapy was 1.02 (SD, 0.15; n=162). The weighted prevalence of dental infections/ abscess during chemotherapy was reported in three studies and was 5.8%. Conclusions: Patients who were post-radiotherapy had the highest DMFT. The use of fluoride products and chlorhex­idine rinses are beneficial in patients who are post-radiotherapy. There continues to be lack of clinical studies on the extent and severity of dental disease that are associated with infectious complications during cancer therapy

Regulation of development by Rx genes

The paired-like homeobox-containing gene Rx has a critical role in the eye development of several vertebrate species including Xenopus, mouse, chicken, medaka, zebrafish and human. Rx is initially expressed in the anterior neural region of developing embryos, and later in the retina and ventral hypothalamus. Abnormal regulation or function of Rx results in severe abnormalities of eye formation. Overexpression of Rx in Xenopus and zebrafish embryos leads to overproliteration of retinal cells. A targeted elimination of Rx in mice results in a lack of eye formation. Mutations in Rx genes are the cause of the mouse mutation eyeless (ey1), the medaka temperature sensitive mutation eyeless (el) and the zebrafish mutation chokh. In humans, mutations in Rx lead to anophthalmia. All of these studies indicate that Rx genes are key factors in vertebrate eye formation. Because these results cannot be easily reconciled with the most popular dogmas of the field, we offer our interpretation of eye development and evolution

Patients' experiences of deep brain stimulation for Parkinson's disease: a qualitative systematic review and synthesis.

Published onlineJournal ArticleThis is the final version of the article. Available from BMJ Publishing Group via the DOI in this record.OBJECTIVE: To review and synthesise qualitative research studies that have explored patients' experience of deep brain stimulation (DBS) in advanced Parkinson's disease (PD). DESIGN: Systematic review and meta-synthesis of 7 original papers, using metaethnography. SETTING: Studies conducted in Denmark, France and Sweden. PARTICIPANTS: 116 patients who had undergone DBS and 9 spouses of patients. RESULTS: Prior to surgery, the experience of advancing PD is one of considerable loss and a feeling of loss of control. There are significant hopes for what DBS can bring. Following surgery, a sense of euphoria is described by many, although this does not persist and there is a need for significant transitions following this. We suggest that normality as a concept is core to the experience of DBS and that a sense of control may be a key condition for normality. Experience of DBS for patients and spouses, and of the transitions that they must undertake, is influenced by their hopes of what surgery will enable them to achieve, or regain (ie, a new normality). CONCLUSIONS: There is a need for further qualitative research to understand the nature of these transitions to inform how best patients and their spouses can be supported by healthcare professionals before, during and after DBS. In assessing the outcomes of DBS and other treatments in advanced PD, we should consider how to capture holistic concepts such as normality and control. Studies that examine the outcomes of DBS require longer term follow-up.This work was part funded by the Medical Research Council Midland Hub for Trials Methodology Research (Grant Number: G0800808). RG is partially supported by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care (CLAHRC) for the South West Peninsula (PenCLAHRC)

Determining the fate of selenium in wheat biofortification: an isotopically labelled field trial study

Aims The principal aim of this research was to quantify retention of a single, realistic Se biofortification application (10 g ha-1) in contrasting soils over two growing seasons utilizing an enriched stable Se isotope (77Se) to discriminate between applied Se and native soil Se. Methods Isotopically enriched 77Se (Na2SeO4) was applied (10 g ha-1) to four replicate plots (2 m x 2 m) of winter wheat, on three contrasting soils on the University of Nottingham farm (UK), at early stem extension in May 2012. Labelled 77Se was assayed in soil and crop fractions by ICP-MS. Results Topsoil retained a proportion of applied Se at harvest (c. 15 – 31 %) with only minor retention in subsoil (2-4 %), although losses were 37 – 43 %. Further analysis of topsoil 77Se, the following spring, and at second harvest, suggested that labelled Se retained in soil was25 fixed and uptake by a following crop was negligible. Conclusions Prolonged biofortification leads to accumulation of Se in soil but the retained Se has very low bioavailability and mobility. The time required to double the soil Se content would be about 500 years. However, reincorporation of cereal straw could provide a residual source of Se for a following crop, depending on timing and management