Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems.
BackgroundThe structure of a social network as well as peer behaviours are thought to affect personal substance use. Where substance use may create health risks, understanding the contribution of social networks to substance use may be valuable for the design and implementation of harm reduction or other interventions. We examined the social support network of people living in precarious housing in a socially marginalized neighborhood of Vancouver, and analysed associations between social network structure, personal substance use, and supporters’ substance use.MethodsAn ongoing, longitudinal study recruited 246 participants from four single room occupancy hotels, with 201 providing social network information aligned with a 6-month observation period. Use of tobacco, alcohol, cannabis, cocaine (crack and powder), methamphetamine, and heroin was recorded at monthly visits. Ego- and graph-level measures were calculated; the dispersion and prevalence of substances in the network was described. Logistic mixed effects models were used to estimate the association between ego substance use and peer substance use. Permutation analysis was done to test for randomness of substance use dispersion on the social network.ResultsThe network topology corresponded to residence (Hotel) with two clusters differing in demographic characteristics (Cluster 1 –Hotel A: 94% of members, Cluster 2 –Hotel B: 95% of members). Dispersion of substance use across the network demonstrated differences according to network topology and specific substance. Methamphetamine use (overall 12%) was almost entirely limited to Cluster 1, and absent from Cluster 2. Different patterns were observed for other substances. Overall, ego substance use did not differ over the six-month period of observation. Ego heroin, cannabis, or crack cocaine use was associated with alter use of the same substances. Ego methamphetamine, powder cocaine, or alcohol use was not associated with alter use, with the exception for methamphetamine in a densely using part of the network. For alters using multiple substances, cannabis use was associated with lower ego heroin use, and lower ego crack cocaine use. Permutation analysis also provided evidence that dispersion of substance use, and the association between ego and alter use was not random for all substances.ConclusionsIn a socially marginalized neighborhood, social network topology was strongly influenced by residence, and in turn was associated with type(s) of substance use. Associations between personal use and supporter’s use of a substance differed across substances. These complex associations may merit consideration in the design of interventions to reduce risk and harms associated with substance use in people living in precarious housing.
Industrial Design originally focused on product development. However, since a decade the attention has extended from design for products to design for users, design for experiences and design for emotions. Recently, several projects have been initiated to design products to be used in the application area of mental healthcare -ultimately aiming at an improvement of the patient's Quality of Life by improving their emotion regulation. All these projects involve specific game elements but the designed products are not necessarily digitally. The projects share a design strategy that involves input from clinical practitioners and patients. This paper presents an overview of three projects. The first project has the aftercare of cancer patients as its topic. After breast cancer treatment, a large population of patients suffers from severe fatigue obstructing them to pick up their old life. A product was developed using the game elements tangible interaction and challenge to increase their energy management. The second project has a clinical group of soft-drugs addicted youth as its target group. The developed product aimed to increase their therapy adherence using game elements social coherence and tangible interaction. The third project has burn-out patients as a target group. The prototype consists of an online-game that aims to improve the patient's self-esteem and behavior. The used game-element is virtuality and amount of control. Gradually the game transgresses from low-interaction abstract games to high-interactive realistic role-playing. All projects have been evaluated by the respective patient groups.
Differences in DNA methylation of white blood cell types at birth and in adulthood 1reflect postnatal immune maturation and influence accuracy of cell type 2 prediction 3 4 Abstract 36Background: DNA methylation profiling of peripheral blood leukocytes has many 37 research applications, and characterizing the changes in DNA methylation of specific 38 white blood cell types between newborn and adult could add insight into the maturation 39 of the immune system. As a consequence of developmental changes, DNA methylation 40 profiles derived from adult white blood cells are poor references for prediction of cord 41 blood cell types from DNA methylation data. We thus examined cell-type specific 42 differences in DNA methylation in leukocyte subsets between cord and adult blood, and 43 assessed the impact of these differences on prediction of cell types in cord blood. 44Results: Though all cell types showed differences between cord and adult blood, some 45 specific patterns stood out that reflected how the immune system changes after birth. In 46 cord blood, lymphoid cells showed less variability than in adult, potentially 47 demonstrating their naïve status. In fact, cord CD4 and CD8 T cells were so similar that 48 genetic effects on DNA methylation were greater than cell type effects in our analysis, 49and CD8 T cell frequencies remained difficult to predict, even after optimizing the library 50 used for cord blood composition estimation. Myeloid cells showed fewer changes 51 between cord and adult and also less variability, with monocytes showing the fewest 52 sites of DNA methylation change between cord and adult. Finally, including nucleated 53 red blood cells in the reference library was necessary for accurate cell type predictions 54in cord blood. 55Conclusion: Changes in DNA methylation with age were highly cell type specific, and 56those differences paralleled what is known about the maturation of the postnatal 57 immune system. 58 59Keywords: DNA methylation, immune system, development, cord blood, white blood 60 cells, 450k 61 62Background 63 One of the main established roles for DNA methylation (DNAm) is in development, 64where it contributes to the functional maturation, lineage commitment and fate of cells. 1 65This has two important implications; the first is that DNAm within a given cell type will 66 change over time as cells differentiate and function develops. 2 The second is that 67 different types of terminally differentiated cells will have very distinct DNAm profiles. 3,4 68As the age of individuals and cell type are two of the major determinants of DNAm 69 variability, analyses of DNAm data must carefully consider those variables. 5,6 Due to an 70 important role of DNAm in development, close assessment of developmental 71 processes, by identifying specific genes or genomic regions that change with age. 72 This is of particular interest in blood, where development of the immune system in early 73 life is linked to long term health outcomes, and so the analysis of the changes in DNAm 74 from birt...
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.