The application of KAZE features to the classification echocardiogram videos

In the computer vision field, both approaches of SIFT and SURF are prevalent in the extraction of scale-invariant points and have demonstrated a number of advantages. However, when they are applied to medical images with relevant low contrast between target structures and surrounding regions, these approaches lack the ability to distinguish salient features. Therefore, this research proposes a different approach by extracting feature points using the emerging method of KAZE. As such, to categorise a collection of video images of echocardiograms, KAZE feature points, coupled with three popular representation methods, are addressed in this paper, which includes the bag of words (BOW), sparse coding, and Fisher vector (FV). In comparison with the SIFT features represented using Sparse coding approach that gives 72% overall performance on the classification of eight viewpoints, KAZE feature integrated with either BOW, sparse coding or FV improves the performance significantly with the accuracy being 81.09%, 78.85% and 80.8% respectively. When it comes to distinguish only three primary view locations, 97.44% accuracy can be achieved when employing the approach of KAZE whereas 90% accuracy is realised while applying SIFT features

The Scenario Model Intercomparison Project (ScenarioMIP) for CMIP6

Model experiment description paperProjections of future climate change play a fundamental role in improving understanding of the climate system as well as characterizing societal risks and response options. The Scenario Model Intercomparison Project (ScenarioMIP) is the primary activity within Phase 6 of the Coupled Model Intercomparison Project (CMIP6) that will provide multi-model climate projections based on alternative scenarios of future emissions and land use changes produced with integrated assessment models. In this paper, we describe ScenarioMIP's objectives, experimental design, and its relation to other activities within CMIP6. The ScenarioMIP design is one component of a larger scenario process that aims to facilitate a wide range of integrated studies across the climate science, integrated assessment modeling, and impacts, adaptation, and vulnerability communities, and will form an important part of the evidence base in the forthcoming Intergovernmental Panel on Climate Change (IPCC) assessments. At the same time, it will provide the basis for investigating a number of targeted science and policy questions that are especially relevant to scenario-based analysis, including the role of specific forcings such as land use and aerosols, the effect of a peak and decline in forcing, the consequences of scenarios that limit warming to below 2 °C, the relative contributions to uncertainty from scenarios, climate models, and internal variability, and long-term climate system outcomes beyond the 21st century. To serve this wide range of scientific communities and address these questions, a design has been identified consisting of eight alternative 21st century scenarios plus one large initial condition ensemble and a set of long-term extensions, divided into two tiers defined by relative priority. Some of these scenarios will also provide a basis for variants planned to be run in other CMIP6-Endorsed MIPs to investigate questions related to specific forcings. Harmonized, spatially explicit emissions and land use scenarios generated with integrated assessment models will be provided to participating climate modeling groups by late 2016, with the climate model simulations run within the 2017-2018 time frame, and output from the climate model projections made available and analyses performed over the 2018-2020 period.CRESCENDO project members (V. Eyring, P. Friedlingstein, E. Kriegler, R. Knutti, J. Lowe, K. Riahi, D. van Vuuren) acknowledge funding received from the Horizon 2020 European Union’s Framework Programme for Research and Innovation under grant agreement no. 641816. C. Tebaldi, G. A. Meehl and B. M. Sanderson acknowledge the support of the Regional and Global Climate Modeling Program (RGCM) of the U.S. Department of Energy’s, Office of Science (BER), Cooperative Agreement DE-FC02-97ER6240

A gene-centric analysis of activated partial thromboplastin time and activated protein C resistance using the HumanCVD focused genotyping array.

Activated partial thromboplastin time (aPTT) is an important routine measure of intrinsic blood coagulation. Addition of activated protein C (APC) to the aPTT test to produce a ratio, provides one measure of APC resistance. The associations of some genetic mutations (eg, factor V Leiden) with these measures are established, but associations of other genetic variations remain to be established. The objective of this work was to test for association between genetic variants and blood coagulation using a high-density genotyping array. Genetic association with aPTT and APC resistance was analysed using a focused genotyping array that tests approximately 50 000 single-nucleotide polymorphisms (SNPs) in nearly 2000 cardiovascular candidate genes, including coagulation pathway genes. Analyses were conducted on 2544 European origin women from the British Women's Heart and Health Study. We confirm associations with aPTT at the coagulation factor XII (F12)/G protein-coupled receptor kinase 6 (GRK6) and kininogen 1 (KNG1)/histidine-rich glycoprotein (HRG) loci, and identify novel SNPs at the ABO locus and novel locus kallikrein B (KLKB1)/F11. In addition, we confirm association between APC resistance and factor V Leiden mutation, and identify novel SNP associations with APC resistance in the HRG and F5/solute carrier family 19 member 2 (SLC19A2) regions. In conclusion, variation at several genetic loci influences intrinsic blood coagulation as measured by both aPTT and APC resistance

Infrastructure-based Multi-Camera Calibration using Radial Projections

Multi-camera systems are an important sensor platform for intelligent systems such as self-driving cars. Pattern-based calibration techniques can be used to calibrate the intrinsics of the cameras individually. However, extrinsic calibration of systems with little to no visual overlap between the cameras is a challenge. Given the camera intrinsics, infrastucture-based calibration techniques are able to estimate the extrinsics using 3D maps pre-built via SLAM or Structure-from-Motion. In this paper, we propose to fully calibrate a multi-camera system from scratch using an infrastructure-based approach. Assuming that the distortion is mainly radial, we introduce a two-stage approach. We first estimate the camera-rig extrinsics up to a single unknown translation component per camera. Next, we solve for both the intrinsic parameters and the missing translation components. Extensive experiments on multiple indoor and outdoor scenes with multiple multi-camera systems show that our calibration method achieves high accuracy and robustness. In particular, our approach is more robust than the naive approach of first estimating intrinsic parameters and pose per camera before refining the extrinsic parameters of the system. The implementation is available at https://github.com/youkely/InfrasCal.Comment: ECCV 202

Efficient screening for ‘genetic pollution’ in an anthropogenic crested newt hybrid zone

Genetic admixture between endangered native and non-native invasive species poses a complex conservation problem. Decision makers often need to quickly screen large numbers of individuals and distinguish natives from morphologically similar invading species and their genetically admixed offspring. We describe a protocol using the fast and economical Kompetitive Allele Specific PCR (KASP) technology for genotyping on a large scale. We apply this protocol to a case study of hybridization between a native and an invasive crested newt species. Using previously published data, we designed a panel of ten nuclear and one mitochondrial diagnostic SNP markers. We observed only minor differences between KASP and next-generation sequencing data previously produced with the Ion Torrent platform. We briefly discuss practical considerations for tackling the insidious conservation problem of genetic admixture between native and invasive species. The KASP genotyping protocol facilitates policy decision making for the crested newt case and is generally applicable to invasive hybridization with endangered taxa

The geography of recent genetic ancestry across Europe

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.Comment: Full size figures available from http://www.eve.ucdavis.edu/~plralph/research.html; or html version at http://ralphlab.usc.edu/ibd/ibd-paper/ibd-writeup.xhtm

The association of academic tracking to depressive symptoms among adolescents in three Caribbean countries

<p>Abstract</p> <p>Background</p> <p>Students who are tracked into low performing schools or classrooms that limit their life chances may report increased depressive symptoms. Limited research has been conducted on academic tracking and its association with depressive symptoms among high school students in the Caribbean. This project examines levels of depressive symptoms among tenth grade students tracked within and between high schools in Jamaica, St. Vincent and St. Kitts and Nevis.</p> <p>Methods</p> <p>Students enrolled in grade ten of the 2006/2007 academic year in Jamaica, St. Kitts and Nevis and St. Vincent were administered the Beck Depression Inventory II (BDI-II). In Jamaica and St. Vincent, academic tracking was operationalized using data provided by the local Ministries of Education. These Ministries ranked ordered schools according to students' performance on Caribbean school leaving examinations. In St. Kitts and Nevis tracking was operationalized by classroom assignments within schools whereby students were grouped into classrooms according to their levels of academic achievement. Multiple regression analyses were conducted to examine the relationships between academic tracking and BDI-II depression scores.</p> <p>Results</p> <p>A wide cross-section of 4^thform students in each nation was sampled (n = 1738; 278 from Jamaica, 737 St. Kitts and Nevis, 716 from St. Vincent; 52% females, 46.2% males and 1.8% no gender reported; age 12 to 19 years, mean = 15.4 yrs, sd = .9 yr). Roughly half (53%) of the students reported some symptoms of depression with 19.2% reporting moderate and 10.7% reporting severe symptoms of depression. Students in Jamaica reported significantly higher depression scores than those in either St. Kitts and Nevis or St. Vincent (p < .01). Students assigned to a higher academic track reported significantly lower BDI-II scores than students who were assigned to the lower academic track (p < .01).</p> <p>Conclusions</p> <p>There appears to be an association between academic tracking and depressive symptoms that is differentially manifested across the islands of Jamaica, St. Kitts and Nevis and St. Vincent.</p

Evaluation of the Re-entry Vulnerability Index to Predict Ventricular Tachycardia Circuits Using High Density Contact Mapping

BACKGROUND: Identifying arrhythmogenic sites to improve ventricular tachycardia (VT) ablation outcomes remains unresolved. The re-entry vulnerability index (RVI) combines activation and repolarization timings to identify sites critical for re-entrant arrhythmia initiation without inducing VT. OBJECTIVE: To provide the first assessment of RVI's capability to identify VT sites of origin using high-density contact mapping and comparison with other activation-repolarization markers of functional substrate. METHODS: 18 VT ablation patients (16M, 72% ischemic) were studied. Unipolar electrograms were recorded during ventricular pacing and analysed off-line. Activation time (AT), activation-recovery interval (ARI), repolarization time (RT) were measured. Vulnerability to re-entry was mapped based on RVI and spatial distribution of AT, ARI and RT. The distance from sites identified as vulnerable to re-entry to the VT site of origin was measured, with distances 20 mm indicating accurate and inaccurate localization, respectively. RESULTS: The origin of 18 VTs was identified (n=6 entrainment, n=12 pace-mapping). RVI maps included 1012, 408-2098 (median, 1st-3rd quartiles) points/patient. RVI accurately localized 72.2% VT sites of origin, with median distance equal to 5.1, 3.2-10.1 mm. Inaccurate localization was significantly less frequent for RVI than AT (5.6% vs 33.3%, OR=0.12, P=0.035). Compared to RVI, distance to VT sites of origin was significantly larger for sites showing prolonged RT and ARI, and non-significantly larger for sites showing highest AT and ARI gradients. CONCLUSION: RVI identifies vulnerable regions closest to VT sites of origin. Activation-repolarization metrics may improve VT substrate delineation and inform novel ablation strategies

Systematically missing confounders in individual participant data meta-analysis of observational cohort studies.

One difficulty in performing meta-analyses of observational cohort studies is that the availability of confounders may vary between cohorts, so that some cohorts provide fully adjusted analyses while others only provide partially adjusted analyses. Commonly, analyses of the association between an exposure and disease either are restricted to cohorts with full confounder information, or use all cohorts but do not fully adjust for confounding. We propose using a bivariate random-effects meta-analysis model to use information from all available cohorts while still adjusting for all the potential confounders. Our method uses both the fully adjusted and the partially adjusted estimated effects in the cohorts with full confounder information, together with an estimate of their within-cohort correlation. The method is applied to estimate the association between fibrinogen level and coronary heart disease incidence using data from 154,012 participants in 31 cohort

Quantification of atopy, lung function and airway hypersensitivity in adults

<p>Abstract</p> <p>Background</p> <p>Studies in children have shown that concentration of specific serum IgE (sIgE) and size of skin tests to inhalant allergens better predict wheezing and reduced lung function than the information on presence or absence of atopy. However, very few studies in adults have investigated the relationship of quantitative atopy with lung function and airway hyperresponsiveness (AHR).</p> <p>Objective</p> <p>To determine the association between lung function and AHR and quantitative atopy in a large sample of adults from the UK.</p> <p>Methods</p> <p>FEV₁ and FVC (% predicted) were measured using spirometry and airway responsiveness by methacholine challenge (5-breath dosimeter protocol) in 983 subjects (random sample of 800 parents of children enrolled in a population-based birth cohort enriched with 183 patients with physician-diagnosed asthma). Atopic status was assessed by skin prick tests (SPT) and measurement of sIgE (common inhalant allergens). We also measured indoor allergen exposure in subjects' homes.</p> <p>Results</p> <p>Spirometry was completed by 792 subjects and 626 underwent methacholine challenge, with 100 (16.0%) having AHR (dose-response slope>25). Using sIgE as a continuous variable in a multiple linear regression analysis, we found that increasing levels of sIgE to mite, cat and dog were significantly associated with lower FEV₁ (mite p = 0.001, cat p = 0.0001, dog p = 2.95 × 10^-8). Similar findings were observed when using the size of wheal on skin testing as a continuous variable, with significantly poorer lung function with increasing skin test size (mite p = 8.23 × 10^-8, cat p = 3.93 × 10^-10, dog p = 3.03 × 10^-15, grass p = 2.95 × 10^-9). The association between quantitative atopy with lung function and AHR remained unchanged when we repeated the analyses amongst subjects defined as sensitised using standard definitions (sIgE>0.35 kUa/l, SPT-3 mm>negative control).</p> <p>Conclusions</p> <p>In the studied population, lung function decreased and AHR increased with increasing sIgE levels or SPT wheal diameter to inhalant allergens, suggesting that atopy may not be a dichotomous outcome influencing lung function and AHR.</p