High-Angular Resolution Electron Backscatter Diffraction as a New Tool for Mapping Lattice Distortion in Geological Minerals

Analysis of distortions of the crystal lattice within individual mineral grains is central to the investigation of microscale processes that control and record tectonic events. These distortions are generally combinations of lattice rotations and elastic strains, but a lack of suitable observational techniques has prevented these components being mapped simultaneously and routinely in earth science laboratories. However, the technique of high-angular resolution electron backscatter diffraction (HR-EBSD) provides the opportunity to simultaneously map lattice rotation and elastic strain gradients with exceptional precision, on the order of 0.01° for rotations and 10−4 in strain, using a scanning electron microscope. Importantly, these rotations and lattice strains relate to densities of geometrically necessary dislocations and residual stresses. Recent works have begun to apply and adapt HR-EBSD to geological minerals, highlighting the potential of the technique to provide new insights into the microphysics of rock deformation. Therefore, the purpose of this review is to provide a summary of the technique, to identify caveats and targets for further development, and to suggest areas where it offers potential for major advances. In particular, HR-EBSD is well suited to characterizing the roles of different dislocation types during crystal plastic deformation and to mapping heterogeneous internal stress fields associated with specific deformation mechanisms/microstructures or changes in temperature, confining pressure, or macroscopic deviatoric stress. These capabilities make HR-EBSD a particularly powerful new technique for analyzing the microstructures of deformed geological materials.D. Wallis, L. N. Hansen, and A. J. Wilkinson acknowledge support from the Natural Environment Research Council grant NE/M0009661. T. B. Britton acknowledges support for his research fellowship from the Royal Academy of Engineering

Update to the study protocol, including statistical analysis plan for a randomized clinical trial comparing comprehensive cardiac rehabilitation after heart valve surgery with control: the CopenHeartVR trial

Comparative StudyRandomized Controlled TrialThis is the final version of the article. Available from BioMed Central via the DOI in this record.BACKGROUND: Heart valve diseases are common with an estimated prevalence of 2.5% in the Western world. The number is rising because of an ageing population. Once symptomatic, heart valve diseases are potentially lethal, and heavily influence daily living and quality of life. Surgical treatment, either valve replacement or repair, remains the treatment of choice. However, post-surgery, the transition to daily living may become a physical, mental and social challenge. We hypothesize that a comprehensive cardiac rehabilitation program can improve physical capacity and self-assessed mental health and reduce hospitalization and healthcare costs after heart valve surgery. METHODS: This randomized clinical trial, CopenHeartVR, aims to investigate whether cardiac rehabilitation in addition to usual care is superior to treatment as usual after heart valve surgery. The trial will randomly allocate 210 patients 1:1 to an intervention or a control group, using central randomization, and blinded outcome assessment and statistical analyses. The intervention consists of 12 weeks of physical exercise and a psycho-educational intervention comprising five consultations. The primary outcome is peak oxygen uptake (VO2 peak) measured by cardiopulmonary exercise testing with ventilatory gas analysis. The secondary outcome is self-assessed mental health measured by the standardized questionnaire Short Form-36. Long-term healthcare utilization and mortality as well as biochemistry, echocardiography and cost-benefit will be assessed. A mixed-method design will be used to evaluate qualitative and quantitative findings, encompassing a survey-based study before the trial and a qualitative pre- and post-intervention study. CONCLUSION: This randomized clinical trial will contribute with evidence of whether cardiac rehabilitation should be provided after heart valve surgery. The study is approved by the local regional Research Ethics Committee (H-1-2011-157), and the Danish Data Protection Agency (j.nr. 2007-58-0015). TRIAL REGISTRATION: Trial registered 16 March 2012; ClinicalTrials.gov ( NCT01558765 ).This work is supported by the Strategic Research Council, The Heart Centre Research Foundation Rigshospitalet, Familien Hede Nielsens Fond, The Regional Research Council of Region Sealand (Denmark), The National Institute of Public Health, and the University of Southern Denmark

Tutorial: Crystal orientations and EBSD - Or which way is up?

Electron backscatter diffraction (EBSD) is an automated technique that can measure the orientation of crystals in a sample very rapidly. There are many sophisticated software packages that present measured data. Unfortunately, due to crystal symmetry and differences in the set-up of microscope and EBSD software, there may be accuracy issues when linking the crystal orientation to a particular microstructural feature. In this paper we outline a series of conventions used to describe crystal orientations and coordinate systems. These conventions have been used to successfully demonstrate that a consistent frame of reference is used in the sample, unit cell, pole figure and diffraction pattern frames of reference. We establish a coordinate system rooted in measurement of the diffraction pattern and subsequently link this to all other coordinate systems. A fundamental outcome of this analysis is to note that the beamshift coordinate system needs to be precisely defined for consistent 3D microstructure analysis. This is supported through a series of case studies examining particular features of the microscope settings and/or unambiguous crystallographic features. These case studies can be generated easily in most laboratories and represent an opportunity to demonstrate confidence in use of recorded orientation data. Finally, we include a simple software tool, written in both MATLAB® and Python, which the reader can use to compare consistency with their own microscope set-up and which may act as a springboard for further offline analysis.The authors would like to thank a range of funders that underpin this collaborative work: T.B. Britton has a fellowship from the Royal Academy of Engineering. J. Jiang is funded by AVIC BIAM. T.B. Britton and A.J. Wilkinson have project funding from EPSRC through the HexMat programme grant (www.imperial.ac.uk/hexmat EP/K034332/1). DW, A.J. Wilkinson and L. Hanson have project funding from NERC through NE/M000966/1. A.J. Wilkinson and A. Vilalta-Clemente have project funding from EPSRC through EP/J016098/1

High-angular resolution electron backscatter diffraction as a new tool for mapping lattice distortion in geological minerals

Analysis of distortions of the crystal lattice within individual mineral grains is central to the investigation of microscale processes that control and record tectonic events. These distortions are generally combinations of lattice rotations and elastic strains, but a lack of suitable observational techniques has prevented these components being mapped simultaneously and routinely in earth science laboratories. However, the technique of high‐angular resolution electron backscatter diffraction (HR‐EBSD) provides the opportunity to simultaneously map lattice rotation and elastic strain gradients with exceptional precision, on the order of 0.01° for rotations and 10−4 in strain, using a scanning electron microscope. Importantly, these rotations and lattice strains relate to densities of geometrically necessary dislocations and residual stresses. Recent works have begun to apply and adapt HR‐EBSD to geological minerals, highlighting the potential of the technique to provide new insights into the microphysics of rock deformation. Therefore, the purpose of this review is to provide a summary of the technique, to identify caveats and targets for further development, and to suggest areas where it offers potential for major advances. In particular, HR‐EBSD is well suited to characterizing the roles of different dislocation types during crystal plastic deformation and to mapping heterogeneous internal stress fields associated with specific deformation mechanisms/microstructures or changes in temperature, confining pressure, or macroscopic deviatoric stress. These capabilities make HR‐EBSD a particularly powerful new technique for analyzing the microstructures of deformed geological materials

Neonatal jaundice and its management: knowledge, attitude and practice of community health workers in Nigeria

BACKGROUND: Neonatal jaundice (NNJ) is still a leading cause of preventable brain damage, physical and mental handicap, and early death among infants in many communities. Greater awareness is needed among all health workers. The objective of the study was to assess the knowledge of primary health care workers about the description, causes, effective treatment, and sequelae of NNJ. METHODS: The setting was a local government area i.e. an administrative district within the south-western part of Nigeria. Community health workers in this area were interviewed by means of a self-administered questionnaire which focused on awareness and knowledge of neonatal jaundice and its causes, treatment and complications. RESULTS: Sixty-six community health workers participated in the survey and male-to-female ratio was 1:5. Their work experience averaged 13.5 (SD 12.7) years. Only 51.5% of the respondents gave a correct definition of NNJ. 75.8 % knew how to examine for this condition while 84.9 % knew at least two of its major causes in our environment. Also, only 54.5 % had adequate knowledge of effective treatment namely, phototherapy and exchange blood transfusion. Rather than referring affected babies to hospitals for proper management, 13.4 %, 10.4 % and 3 % of the participants would treat with ineffective drugs, natural phototherapy and herbal remedies respectively. None of the participants knew any effective means of prevention. CONCLUSION: Primary health care workers may have inadequate knowledge and misconceptions on NNJ which must be addressed concertedly before the impact of the condition on child health and well-being can be significantly reduced. We recommend regular training workshops and seminars for this purpose

How do Zimbabweans value health states?

Background Quality of life weights based on valuations of health states are often used in cost utility analysis and population health measures. This paper reports on an attempt to develop quality of life weights within the Zimbabwe context. Methods 2,384 residents in randomly selected small residential plots of land in a high-density suburb of Harare valued descriptors of 38 health states based on different combinations of the five domains of the EQ-5D (mobility, self-care, usual activities, pain or discomfort and anxiety or depression). The English version of the EQ-5D was used. The time trade-off method was used to determine the values, and 19,020 individual preferences for health states were analysed. A residual maximum likelihood linear mixed model was used to estimate a function for predicting the values of all possible combinations of levels on the five domains. The model was fit to a random subset of two-thirds of the observations, with the remaining observations reserved for analysis of predictive validity. The results were compared to a similar study undertaken in the United Kingdom. Results A credible model was developed to predict the values of states that were not valued directly. In the subset of observations reserved for validation, the mean absolute difference between predicted and observed values was 0.045. All domains of the EQ-5D were found to contribute significantly to the model, both at the moderate and severe levels. Severe pain was found to have the largest negative coefficient, followed by the inability to wash and dress oneself. Conclusion Despite a generally lower education level than their European counterparts, urban Zimbabweans appear to value health states in a consistent manner, and the determination of a global method of establishing quality of life weights may be feasible and valid. However, as the relative weightings of the different domains, although correlated, differed from the standard set of weights recommended by the EuroQol Group, the locally determined coefficients should be used within the Zimbabwean context

Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues

<p>Abstract</p> <p>Background</p> <p>We aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R) and its ligand the tuberoinfundibular peptide of 39 residues (TIP39) by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) are compared with the complex to examine their interactions.</p> <p>Findings</p> <p>In the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation.</p> <p>Conclusions</p> <p>A model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed.</p

Big-Data-Driven Materials Science and its FAIR Data Infrastructure

This chapter addresses the forth paradigm of materials research -- big-data driven materials science. Its concepts and state-of-the-art are described, and its challenges and chances are discussed. For furthering the field, Open Data and an all-embracing sharing, an efficient data infrastructure, and the rich ecosystem of computer codes used in the community are of critical importance. For shaping this forth paradigm and contributing to the development or discovery of improved and novel materials, data must be what is now called FAIR -- Findable, Accessible, Interoperable and Re-purposable/Re-usable. This sets the stage for advances of methods from artificial intelligence that operate on large data sets to find trends and patterns that cannot be obtained from individual calculations and not even directly from high-throughput studies. Recent progress is reviewed and demonstrated, and the chapter is concluded by a forward-looking perspective, addressing important not yet solved challenges.Comment: submitted to the Handbook of Materials Modeling (eds. S. Yip and W. Andreoni), Springer 2018/201

Immunoblot analysis of the seroreactivity to recombinant Borrelia burgdorferi sensu lato antigens, including VlsE, in the long-term course of treated patients with Erythema migrans

Objective: We evaluated whether immunoblotting is capable of substantiating the posttreatment clinical assessment of patients with erythema migrans ( EM), the hallmark of early Lyme borreliosis. Methods: In 50 patients, seroreactivity to different antigens of Borrelia burgdorferi sensu lato was analyzed by a recombinant immunoblot test (IB) in consecutive serum samples from a minimum follow-up period of 1 year. Antigens in the IgG test were decorin- binding protein A, internal fragment of p41 (p41i), outer surface protein C (OspC), p39, variable major protein-like sequence expressed (VlsE), p58 and p100; those in the IgM test were p41i, OspC and p39. Immune responses were correlated with clinical and treatment-related parameters. Results: Positive IB results were found in 50% before, in 57% directly after therapy and in 44% by the end of the follow-up for the IgG class, and in 36, 43 and 12% for the IgM class. In acute and convalescence phase sera, VlsE was most immunogenic on IgG testing 60 and 70%), and p41i (46 and 57%) and OspC (40 and 57%) for the IgM class. By the end of the follow-up, only the anti-p41i lgM response was significantly decreased to 24%. Conclusions: No correlation was found between IB results and treatment-related parameters. Thus, immunoblotting does not add to the clinical assessment of EM patients after treatment. Copyright (c) 2008 S. Karger AG, Basel