Reconstruction Error and Principal Component Based Anomaly Detection in Hyperspectral imagery

The rapid expansion of remote sensing and information collection capabilities demands methods to highlight interesting or anomalous patterns within an overabundance of data. This research addresses this issue for hyperspectral imagery (HSI). Two new reconstruction based HSI anomaly detectors are outlined: one using principal component analysis (PCA), and the other a form of non-linear PCA called logistic principal component analysis. Two very effective, yet relatively simple, modifications to the autonomous global anomaly detector are also presented, improving algorithm performance and enabling receiver operating characteristic analysis. A novel technique for HSI anomaly detection dubbed multiple PCA is introduced and found to perform as well or better than existing detectors on HYDICE data while using only linear deterministic methods. Finally, a response surface based optimization is performed on algorithm parameters such as to affect consistent desired algorithm performance

One place doesn't fit all: improving the effectiveness of sustainability standards by accounting for place

Includes bibliographical references (pages 8-10).The growing interest in incentivizing sustainable agricultural practices is supported by a large network of voluntary production standards, which aim to offer farmers and ranchers increased value for their product in support of reduced environmental impact. To be effective with producers and consumers alike, these standards must be both credible and broadly recognizable, and thus are typically highly generalizable. However, the environmental impact of agriculture is strongly place-based and varies considerably due to complex biophysical, socio-cultural, and management-based factors, even within a given sector in a particular region. We suggest that this contradiction between the placeless generality of standards and the placed-ness of agriculture renders many sustainability standards ineffective. In this policy and practice review, we examine this contradiction through the lens of beef production, with a focus on an ongoing regional food purchasing effort in Denver, Colorado, USA. We review the idea of place in the context of agricultural sustainability, drawing on life cycle analysis and diverse literature to find that recognition of place-specific circumstances is essential to understanding environmental impact and improving outcomes. We then examine the case of the Good Food Purchasing Program (GFPP), a broad set of food-purchasing standards currently being implemented for institutional purchasing in Denver. The GFPP was created through a lengthy stakeholder-inclusive process for use in Los Angeles, California, USA, and has since been applied to many cities across the country. The difference between Los Angeles' process and that of applying the result of Los Angeles' process to Denver is instructive, and emblematic of the flaws of generalizable sustainability standards themselves. We then describe the essential elements of a place-based approach to agricultural sustainability standards, pointing toward a democratic, process-based, and outcome-oriented strategy that results in standards that enable rather than hinder the creativity of both producers and consumers. Though prescription is anathema to our approach, we close by offering a starting point for the development of standards for beef production in Colorado that respect the work of people in place

X-ray Orbital Modulations in Intermediate Polars

We present an analysis of 30 archival ASCA and RXTE X-ray observations of 16 intermediate polars to investigate the nature of their orbital modulation. We show that X-ray orbital modulation is widespread amongst these systems, but not ubiquitous as indicated by previous studies that included fewer objects. Only seven of the sixteen systems show a clearly statistically significant modulation depth whose amplitude decreases with increasing X-ray energy. Interpreting this as due to photoelectric absorption in material at the edge of an accretion disc would imply that such modulations are visible for all system inclination angles in excess of 60 degrees. However, it is also apparent that the presence of an X-ray orbital modulation can appear and disappear on a timescale of ~years or months in an individual system. This may be evidence for the presence of a precessing, tilted accretion disc, as inferred in some low mass X-ray binaries.Comment: Accepted for publication in Astronomy & Astrophysics. 9 pages of text, plus 5 pages of tables, plus 33 pages of figure

Body size and shape changes and the risk of diabetes in the Diabetes Prevention Program

Prezentowane badanie przeprowadzono w celu sprawdzenia hipotezy, zgodnie z którą ryzyko rozwoju cukrzycy typu 2 zmniejsza się wraz z redukcją masy ciała i otyłości brzusznej. Do badania Diabetes Prevention Program (DPP) włączono osoby, u których rozpoznawano upośledzoną tolerancję glukozy, i zakwalifikowano je do grup otrzymujących placebo lub metforminę albo wprowadzono tylko modyfikację stylu życia. U uczestników badania określono wzrost, masę ciała oraz zmierzono tkankę tłuszczową na poziomie L2-L3 i L4-L5 za pomocą tomografii komputerowej na początku badania oraz po roku. Zastosowano modele proporcjonalnego ryzyka Coxa w celu oceny, zależnie od płci, wpływu zmiany tych parametrów w ciągu roku na rozwój cukrzycy w okresie dalszej obserwacji, którą prowadzono u 758 osób. Modyfikacja stylu życia doprowadziła do redukcji trzewnej tkanki tłuszczowej na poziomie L2-L3 (mężczyźni: -24,3%; kobiety: -18,2%) oraz na poziomie L4-L5 (mężczyźni: -22,4%, kobiety: -17,8%), tkanki tłuszczowej podskórnej na poziomie L2-L3 (mężczyźni: -15,7%, kobiety: -11,4%) i L4-L5 (mężczyźni: -16,7%, kobiety: -11,9%), do zmniejszenia masy ciała (mężczyźni: -8,2%, kobiety: -7,8%), wskaźnika masy ciała (mężczyźni: -8,2%, kobiety: -7,8%) oraz obwodu talii (mężczyźni: -7,5%, kobiety -6,1%). W grupie otrzymującej metforminę zaobserwowano redukcję masy ciała (-2,9%) i obniżenie wskaźnika masy ciała (-2,9%) u mężczyzn oraz zmniejszenie ilości podskórnej tkanki tłuszczowej (-3,6% na poziomie L2-L3 i -4,7% na poziomie L4-L5), masy ciała (-3,3%), wskaźnika masy ciała (-3,3%) oraz obwodu talii (-2,8%) u kobiet. Zmniejszenie ryzyka rozwoju cukrzycy poprzez zmianę stylu życia wiązało się z redukcją masy ciała, wskaźnika masy ciała oraz rozkładu tkanki tłuszczowej po skorygowaniu względem wieku oraz pochodzenia etnicznego (ustalano je na podstawie informacji uzyskanej od uczestników). Zmniejszenie ryzyka rozwoju cukrzycy poprzez zmianę stylu życia może nastąpić zarówno poprzez wpływ na całą tkankę tłuszczową, jak i brzuszną tkankę tłuszczową; wpływ metforminy wydawał się niezależny od zmian tkanki tłuszczowej.The researchers conducted this study to test the hypothesis that risk of type 2 diabetes is less following reductions in body size and central adiposity. The Diabetes Prevention Program (DPP) recruited and randomized individuals with impaired glucose tolerance to treatment with placebo, metformin, or lifestyle modification. Height, weight, waist circumference, and subcutaneous and visceral fat at L2-L3 and L4-L5 by computed tomography were measured at baseline and at 1 year. Cox proportional hazards models assessed by sex the effect of change in these variables over the 1st year of intervention upon development of diabetes over subsequent follow- up in a subset of 758 participants. Lifestyle reduced visceral fat at L2-L3 (men -24.3%, women -18.2%) and at L4-L5 (men -22.4%, women -17.8%), subcutaneous fat at L2-L3 (men -15.7%, women -11.4%) and at L4-L5 (men -16.7%, women -11.9%), weight (men –8.2%, women –7.8%), BMI (men -8.2%, women -7.8%), and waist circumference (men -7.5%, women -6.1%). Metformin reduced weight (-2.9%) and BMI (-2.9%) in men and subcutaneous fat (-3.6% at L2-L3 and -4.7% at L4-L5), weight (-3.3%), BMI (-3.3%), and waist circumference (-2.8%) in women. Decreased diabetes risk by lifestyle intervention was associated with reductions of body weight, BMI, and central body fat distribution after adjustment for age and self-reported ethnicity. Reduced diabetes risk with lifestyle intervention may have been through effects upon both overall body fat and central body fat but with metformin appeared to be independent of body fat

CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity.

Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases

A Prospective Randomized Controlled Trial of the Effects of Vitamin D Supplementation on Cardiovascular Disease Risk

Vitamin D (VitD) supplementation has been advocated for cardiovascular risk reduction; however, supporting data are sparse. The objective of this study was to determine whether VitD supplementation reduces cardiovascular risk. Subjects in this prospective, randomized, double-blind, placebo-controlled trial of post-menopausal women with serum 25-hydroxyvitamin D concentrations >10 and <60 ng/mL were randomized to Vitamin D3 2500 IU or placebo, daily for 4 months. Primary endpoints were changes in brachial artery flow-mediated vasodilation (FMD), carotid-femoral pulse wave velocity (PWV), and aortic augmentation index (AIx). The 114 subjects were mean (standard deviation) 63.9 (3.0) years old with a 25-hydroxyvitamin D level of 31.3 (10.6) ng/mL. Low VitD (<30 ng/mL) was present in 47% and was associated with higher body-mass index, systolic blood pressure, glucose, CRP, and lower FMD (all p<0.05). After 4 months, 25-hydroxyvitamin D levels increased by 15.7 (9.3) ng/mL on vitamin D3 vs. −0.2 (6.1) ng/mL on placebo (p<0.001). There were no significant differences between groups in changes in FMD (0.3 [3.4] vs. 0.3 [2.6] %, p = 0.77), PWV (0.00 [1.06] vs. 0.05 [0.92] m/s, p = 0.65), AIx (2.7 [6.3] vs. 0.9 [5.6] %, p = 0.10), or CRP (0.3 [1.9] vs. 0.3 [4.2] mg/L, p = 0.97). Multivariable models showed no significant interactions between treatment group and low VitD status (<30 ng/mL) for changes in FMD (p = 0.65), PWV (p = 0.93), AIx (p = 0.97), or CRP (p = 0.26).In conclusion, VitD supplementation did not improve endothelial function, arterial stiffness, or inflammation. These observations do not support use of VitD supplementation to reduce cardiovascular disease risk

Splash!: a prospective birth cohort study of the impact of environmental, social and family-level influences on child oral health and obesity related risk factors and outcomes

Background: Dental caries (decay) is the most prevalent disease of childhood. It is often left untreated and can impact negatively on general health, and physical, developmental, social and learning outcomes. Similar to other health issues, the greatest burden of dental caries is seen in those of low socio-economic position. In addition, a number of diet-related risk factors for dental caries are shared risk factors for the development of childhood obesity. These include high and frequent consumption of refined carbohydrates (predominately sugars), and soft drinks and other sweetened beverages, and low intake of (fluoridated) water. The prevalence of childhood obesity is also at a concerning level in most countries and there is an opportunity to determine interventions for addressing both of these largely preventable conditions through sustainable and equitable solutions. This study aims to prospectively examine the impact of drink choices on child obesity risk and oral health status.Methods/Design: This is a two-stage study using a mixed methods research approach. The first stage involves qualitative interviews of a sub-sample of recruited parents to develop an understanding of the processes involved in drink choice, and inform the development of the Discrete Choice Experiment analysis and the measurement instruments to be used in the second stage. The second stage involves the establishment of a prospective birth cohort of 500 children from disadvantaged communities in rural and regional Victoria, Australia (with and without water fluoridation). This longitudinal design allows measurement of changes in the child&rsquo;s diet over time, exposure to fluoride sources including water, dental caries progression, and the risk of childhood obesity.Discussion: This research will provide a unique contribution to integrated health, education and social policy and program directions, by providing clearer policy relevant evidence on strategies to counter social and environmental factors which predispose infants and children to poor health, wellbeing and social outcomes; and evidence-based strategies to promote health and prevent disease through the adoption of healthier lifestyles and diet. Further, given the absence of evidence on the processes and effectiveness of contemporary policy implementation, such as community water fluoridation in rural and regional communities it&rsquo;s approach and findings will be extremelyinformative.<br /

A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

Background: Rare variants have gathered increasing attention as a possible alternative source of missing heritability. Since next generation sequencing technology is not yet cost-effective for large-scale genomic studies, a widely used alternative approach is imputation. However, the imputation approach may be limited by the low accuracy of the imputed rare variants. To improve imputation accuracy of rare variants, various approaches have been suggested, including increasing the sample size of the reference panel, using sequencing data from study-specific samples (i.e., specific populations), and using local reference panels by genotyping or sequencing a subset of study samples. While these approaches mainly utilize reference panels, imputation accuracy of rare variants can also be increased by using exome chips containing rare variants. The exome chip contains 250 K rare variants selected from the discovered variants of about 12,000 sequenced samples. If exome chip data are available for previously genotyped samples, the combined approach using a genotype panel of merged data, including exome chips and SNP chips, should increase the imputation accuracy of rare variants. Results: In this study, we describe a combined imputation which uses both exome chip and SNP chip data simultaneously as a genotype panel. The effectiveness and performance of the combined approach was demonstrated using a reference panel of 848 samples constructed using exome sequencing data from the T2D-GENES consortium and 5,349 sample genotype panels consisting of an exome chip and SNP chip. As a result, the combined approach increased imputation quality up to 11 %, and genomic coverage for rare variants up to 117.7 % (MAF < 1 %), compared to imputation using the SNP chip alone. Also, we investigated the systematic effect of reference panels on imputation quality using five reference panels and three genotype panels. The best performing approach was the combination of the study specific reference panel and the genotype panel of combined data. Conclusions: Our study demonstrates that combined datasets, including SNP chips and exome chips, enhances both the imputation quality and genomic coverage of rare variants

Association of vitamin D status with arterial blood pressure and hypertension risk : a mendelian randomisation study

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