Mobile FTP Client: An Android Application

This project sets out to design and implement a mobile FTP client application for Android OS that accompanies a home media server using the Nas4Free operating system. The application utilizes Apache Commons’ .net Java library to perform three functions: connect remotely to an FTP server, browse through directory listings, and download single files or entire directories to the Android device. This senior project encompasses multiple concepts including the configuration of a network to allow external access to a server behind a firewall, understanding of SSL/TLS security including private key encryption and self-signed certificates, the FTP protocol and its associated commands, and centers on Android development and the creation of an Android application. This application is for personal use only, and will not be released on the Google Play Store

Fast Genome-Wide QTL Analysis Using Mendel

Pedigree GWAS (Option 29) in the current version of the Mendel software is an optimized subroutine for performing large scale genome-wide QTL analysis. This analysis (a) works for random sample data, pedigree data, or a mix of both, (b) is highly efficient in both run time and memory requirement, (c) accommodates both univariate and multivariate traits, (d) works for autosomal and x-linked loci, (e) correctly deals with missing data in traits, covariates, and genotypes, (f) allows for covariate adjustment and constraints among parameters, (g) uses either theoretical or SNP-based empirical kinship matrix for additive polygenic effects, (h) allows extra variance components such as dominant polygenic effects and household effects, (i) detects and reports outlier individuals and pedigrees, and (j) allows for robust estimation via the $t$-distribution. The current paper assesses these capabilities on the genetics analysis workshop 19 (GAW19) sequencing data. We analyzed simulated and real phenotypes for both family and random sample data sets. For instance, when jointly testing the 8 longitudinally measured systolic blood pressure (SBP) and diastolic blood pressure (DBP) traits, it takes Mendel 78 minutes on a standard laptop computer to read, quality check, and analyze a data set with 849 individuals and 8.3 million SNPs. Genome-wide eQTL analysis of 20,643 expression traits on 641 individuals with 8.3 million SNPs takes 30 hours using 20 parallel runs on a cluster. Mendel is freely available at \url{http://www.genetics.ucla.edu/software}

Moisture Modes and the Eastward Propagation of the MJO

The authors discuss modifications to a simple linear model of intraseasonal moisture modes. Wind–evaporation feedbacks were shown in an earlier study to induce westward propagation in an eastward mean low-level flow in this model. Here additional processes, which provide effective sources of moist static energy to the disturbances and which also depend on the low-level wind, are considered. Several processes can act as positive sources in perturbation easterlies: zonal advection (if the mean zonal moisture gradient is eastward), modulation of synoptic eddy drying by the MJO-scale wind perturbations, and frictional convergence. If the sum of these is stronger than the wind–evaporation feedback—as observations suggest may be the case, though with considerable uncertainty—the model produces unstable modes that propagate weakly eastward relative to the mean flow. With a small amount of horizontal diffusion or other scale-selective damping, the growth rate is greatest at the largest horizontal scales and decreases monotonically with wavenumber

Some Run Problems in Hypercubes (Tic-tac-toe)

1 online resource (PDF, 13 pages

Fast Genome-Wide QTL Association Mapping on Pedigree and Population Data

Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and pedigree data. Even data sets thought to consist of only unrelated individuals may include cryptic relationships that can lead to false positives if not discovered and controlled for. In addition, family designs possess compelling advantages. They are better equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Pedigrees selected for extreme trait values often segregate a single gene with strong effect. Finally, many pedigrees are available as an important legacy from the era of linkage analysis. Unfortunately, pedigree likelihoods are notoriously hard to compute. In this paper we re-examine the computational bottlenecks and implement ultra-fast pedigree-based GWAS analysis. Kinship coefficients can either be based on explicitly provided pedigrees or automatically estimated from dense markers. Our strategy (a) works for random sample data, pedigree data, or a mix of both; (b) entails no loss of power; (c) allows for any number of covariate adjustments, including correction for population stratification; (d) allows for testing SNPs under additive, dominant, and recessive models; and (e) accommodates both univariate and multivariate quantitative traits. On a typical personal computer (6 CPU cores at 2.67 GHz), analyzing a univariate HDL (high-density lipoprotein) trait from the San Antonio Family Heart Study (935,392 SNPs on 1357 individuals in 124 pedigrees) takes less than 2 minutes and 1.5 GB of memory. Complete multivariate QTL analysis of the three time-points of the longitudinal HDL multivariate trait takes less than 5 minutes and 1.5 GB of memory

The Quantitative-MFG Test: A linear mixed effect model to detect maternal-offspring gene interactions

Maternal-offspring gene interactions, aka maternal-fetal genotype (MFG) incompatibilities, are neglected in complex diseases and quantitative trait studies. They are implicated in birth to adult onset diseases but there are limited ways to investigate their influence on quantitative traits. We present the Quantitative-MFG (QMFG) test, a linear mixed model where maternal and offspring genotypes are fixed effects and residual correlations between family members are random effects. The QMFG handles families of any size, common or general scenarios of MFG incompatibility, and additional covariates. We develop likelihood ratio tests (LRTs) and rapid score tests and show they provide correct inference. In addition, the LRT’s alternative model provides unbiased parameter estimates. We show that testing the association of SNPs by fitting a standard model, which only considers the offspring genotypes, has very low power or can lead to incorrect conclusions. We also show that offspring genetic effects are missed if the MFG modeling assumptions are too restrictive. With GWAS data from the San Antonio Family Heart Study, we demonstrate that the QMFG score test is an effective and rapid screening tool. The QMFG test therefore has important potential to identify pathways of complex diseases for which the genetic etiology remains to be discovered

Tropical Intraseasonal Variability in Version 3 of the GFDL Atmosphere Model

Tropical intraseasonal variability is examined in version 3 of the Geophysical Fluid Dynamics Laboratory Atmosphere Model (AM3). In contrast to its predecessor AM2, AM3 uses a new treatment of deep and shallow cumulus convection and mesoscale clouds. The AM3 cumulus parameterization is a mass-flux-based scheme but also, unlike that in AM2, incorporates subgrid-scale vertical velocities; these play a key role in cumulus microphysical processes. The AM3 convection scheme allows multiphase water substance produced in deep cumuli to be transported directly into mesoscale clouds, which strongly influence large-scale moisture and radiation fields. The authors examine four AM3 simulations using a control model and three versions with different modifications to the deep convection scheme. In the control AM3, using a convective closure based on CAPE relaxation, both MJO and Kelvin waves are weak relative to those in observations. By modifying the convective closure and trigger assumptions to inhibit deep cumuli, AM3 produces reasonable intraseasonal variability but a degraded mean state. MJO-like disturbances in the modified AM3 propagate eastward at roughly the observed speed in the Indian Ocean but up to 2 times the observed speed in the west Pacific Ocean. Distinct differences in intraseasonal convective organization and propagation exist among the modified AM3 versions. Differences in vertical diabatic heating profiles associated with the MJO are also found. The two AM3 versions with the strongest intraseasonal signals have a more prominent “bottom heavy” heating profile leading the disturbance center and “top heavy” heating profile following the disturbance. The more realistic heating structures are associated with an improved depiction of moisture convergence and intraseasonal convective organization in AM3

Nutrition and Exercise Education Initiatives in a Community Setting

Introduction: Maintaining a nutritious diet and physical activity is a challenge for many people,but especially for those with limited financial and social resources. Barriers to adequate exercise and healthy food include prohibitive costs of gym membership and high quality foods, lack of time during the day in which to exercise or prepare meals, and lack of access or transportation to exercise facilities or grocery stores. We assessed whether adoption of healthy exercise and eating habits could be established and sustained by educating participants on healthy diet guidelines and on non-traditional exercise forms. We encouraged family-centered activities such as walking, gardening, cleaning, dancing, and playing with children. We quantified changes in participants’ pre- and post-educational diets and exercise habits with 3-day dietary recall logs and pedometer-measured daily steps.https://scholarworks.uvm.edu/comphp_gallery/1037/thumbnail.jp

Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis

<p>Abstract</p> <p>Background</p> <p>Correctly merged data sets that have been independently genotyped can increase statistical power in linkage and association studies. However, alleles from microsatellite data sets genotyped with different experimental protocols or platforms cannot be accurately matched using base-pair size information alone. In a previous publication we introduced a statistical model for merging microsatellite data by matching allele frequencies between data sets. These methods are implemented in our software MicroMerge version 1 (v1). While MicroMerge v1 output can be analyzed by some genetic analysis programs, many programs can not analyze alignments that do not match alleles one-to-one between data sets. A consequence of such alignments is that codominant genotypes must often be analyzed as phenotypes. In this paper we describe several extensions that are implemented in MicroMerge version 2 (v2).</p> <p>Results</p> <p>Notably, MicroMerge v2 includes a new one-to-one alignment option that creates merged pedigree and locus files that can be handled by most genetic analysis software. Other features in MicroMerge v2 enhance the following aspects of control: 1) optimizing the algorithm for different merging scenarios, such as data sets with very different sample sizes or multiple data sets, 2) merging small data sets when a reliable set of allele frequencies are available, and 3) improving the quantity and 4) quality of merged data. We present results from simulated and real microsatellite genotype data sets, and conclude with an association analysis of three familial dyslipidemia (FD) study samples genotyped at different laboratories. Independent analysis of each FD data set did not yield consistent results, but analysis of the merged data sets identified strong association at locus D11S2002.</p> <p>Conclusion</p> <p>The MicroMerge v2 features will enable merging for a variety of genotype data sets, which in turn will facilitate meta-analyses for powering association analysis.</p