Dimension Reduction on Measures of Impulsivity

The main focus of this study was twofold: the first purpose being the assessment of convergent validity on six different measures of impulsivity, and the second being a comparison of dimension reduction techniques for quantitative data. Results from a Principal Components Analysis (PCA) were compared with results from a novel dimension technique known as Local Linear Embedding (LLE). LLE is an analysis of dimension reduction for nonlinear, high dimensional data. By computing neighborhood preserving embeddings, LLE aims to map newly constructed coordinates into a global coordinate structure of a lower dimension. Past research using LLE has solely been conducted on visual and auditory-oriented data. Thus, this is a novel approach, applying LLE to cognitive measures rather than visual or auditory data. This paper acts as a secondary analysis of data collected by a prior Masters student (Robles, 2016). The measures of impulsivity included in this study were: The Barratt Impulsiveness Scale (BIS), the Iowa Gambling Task (IGT), the UPPS-P Impulsive Behavior Scale, the Cued Go/No-Go Task, the Stroop Color-Word Interference Test, and the Delay and Probability Discounting Task (DPDT) – all tests performed in a Latin-square determined order by each of 151 students. Findings not only indicate that convergent validity was absent for certain measures of impulsivity, but that with future programming, LLE may be a suitable method of dimension reduction for quantitative data

Real-time Geoinformation Systems to Improve the Quality, Scalability, and Cost of Internet of Things for Agri-environment Research

With the increasing emphasis on machine learning and artificial intelligence to drive knowledge discovery in the agricultural sciences, spatial internet of things (IoT) technologies have become increasingly important for collecting real-time, high resolution data for these models. However, managing large fleets of devices while maintaining high data quality remains an ongoing challenge as scientists iterate from prototype to mature end-to-end applications. Here, we provide a set of case studies using the framework of technology readiness levels for an open source spatial IoT system. The spatial IoT systems underwent 3 major and 14 minor system versions, had over 2,727 devices manufactured both in academic and commercial contexts, and are either in active or planned deployment across four continents. Our results show the evolution of a generalizable, open source spatial IoT system designed for agricultural scientists, and provide a model for academic researchers to overcome the challenges that exist in going from one-off prototypes to thousands of internet-connected devices.Comment: 20 pages, 5 figures, 1 tabl

Improved annotation with <i>de novo</i> transcriptome assembly in four social amoeba species

Background: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species. Results: An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum. Conclusions: In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects

Assessing land use and flood management impacts on ecosystem services in a river landscape (Upper Danube, Germany)

Rivers and floodplains provide many regulating, provisioning and cultural ecosystem services (ES) such as flood risk regulation, crop production or recreation. Intensive use of resources such as hydropower production, construction of detention basins and intensive agriculture substantially change ecosystems and may affect their capacity to provide ES. Legal frameworks such as the European Water Framework Directive, Bird and Habitats Directive and Floods Directive already address various uses and interests. However, management is still sectoral and often potential synergies or trade‐offs between sectors are not considered. The ES concept could support a joint and holistic evaluation of impacts and proactively suggest advantageous options. The river ecosystem service index (RESI) method evaluates the capacity of floodplains to provide ES by using a standardized five‐point scale for 1 km‐floodplain segments based on available spatial data. This scaling allows consistent scoring of all ES and their integration into a single index. The aim of this article is to assess ES impacts of different flood prevention scenarios on a 75 km section of the Danube river corridor in Germany. The RESI method was applied to evaluate scenario effects on 13 ES with the standardized five‐point scale. Synergies and trade‐offs were identified as well as ES bundles and dependencies on land use and connectivity. The ratio of actual and former floodplain has the strongest influence on the total ES provision: the higher the percentage and area of an active floodplain, the higher the sum of ES. The RESI method proved useful to support decision‐making in regional planning.BMBF, 033W024A, ReWaM - Verbundprojekt RESI: River Ecosystem Service Index, Teilprojekt

Sugar-sweetened beverage intake associations with fasting glucose and insulin concentrations are not modified by selected genetic variants in a ChREBP-FGF21 pathway : a meta-analysis

Aims/hypothesis Sugar-sweetened beverages (SSBs) are a major dietary contributor to fructose intake. A molecular pathway involving the carbohydrate responsive element-binding protein (ChREBP) and the metabolic hormone fibroblast growth factor 21 (FGF21) may influence sugar metabolism and, thereby, contribute to fructose-induced metabolic disease. We hypothesise that common variants in 11 genes involved in fructose metabolism and the ChREBP-FGF21 pathway may interact with SSB intake to exacerbate positive associations between higher SSB intake and glycaemic traits. Methods Data from 11 cohorts (six discovery and five replication) in the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium provided association and interaction results from 34,748 adults of European descent. SSB intake (soft drinks, fruit punches, lemonades or other fruit drinks) was derived from food-frequency questionnaires and food diaries. In fixed-effects meta-analyses, we quantified: (1) the associations between SSBs and glycaemic traits (fasting glucose and fasting insulin); and (2) the interactions between SSBs and 18 independent SNPs related to the ChREBP-FGF21 pathway. Results In our combined meta-analyses of discovery and replication cohorts, after adjustment for age, sex, energy intake, BMI and other dietary covariates, each additional serving of SSB intake was associated with higher fasting glucose (beta +/- SE 0.014 +/- 0.004 [mmol/l], p = 1.5 x 10(-3)) and higher fasting insulin (0.030 +/- 0.005 [log(e) pmol/l], p = 2.0 x 10(-10)). No significant interactions on glycaemic traits were observed between SSB intake and selected SNPs. While a suggestive interaction was observed in the discovery cohorts with a SNP (rs1542423) in the beta-Klotho (KLB) locus on fasting insulin (0.030 +/- 0.011 log(e) pmol/l, uncorrected p = 0.006), results in the replication cohorts and combined meta-analyses were non-significant. Conclusions/interpretation In this large meta-analysis, we observed that SSB intake was associated with higher fasting glucose and insulin. Although a suggestive interaction with a genetic variant in the ChREBP-FGF21 pathway was observed in the discovery cohorts, this observation was not confirmed in the replication analysis.Peer reviewe

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes

dentification of sequence variants robustly associated with predisposition to diabetic kidney disease (DKD) has the potential to provide insights into the pathophysiological mechanisms responsible. We conducted a genome-wide association study (GWAS) of DKD in type 2 diabetes (T2D) using eight complementary dichotomous and quantitative DKD phenotypes: the principal dichotomous analysis involved 5,717 T2D subjects, 3,345 with DKD. Promising association signals were evaluated in up to 26,827 subjects with T2D (12,710 with DKD). A combined T1D+T2D GWAS was performed using complementary data available for subjects with T1D, which, with replication samples, involved up to 40,340 subjects with diabetes (18,582 with DKD). Analysis of specific DKD phenotypes identified a novel signal near GABRR1 (rs9942471, P = 4.5 x 10(-8)) associated with microalbuminuria in European T2D case subjects. However, no replication of this signal was observed in Asian subjects with T2D or in the equivalent T1D analysis. There was only limited support, in this substantially enlarged analysis, for association at previously reported DKD signals, except for those at UMOD and PRKAG2, both associated with estimated glomerular filtration rate. We conclude that, despite challenges in addressing phenotypic heterogeneity, access to increased sample sizes will continue to provide more robust inference regarding risk variant discovery for DKD.Peer reviewe

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.National Institute of Allergy and Infectious Diseases (U.S.)National Institutes of Health. Department of Health and Human Services (contract HHSN266200400001C)National Institutes of Health. Department of Health and Human Services(contract HHSN2722009000018C)Brazil. National Council for Scientific and Technological Developmen