FIJICLIM description and users guide

The FIJICLIM prototype is based on PACCLIM which was developed by the International Global Change Institute (IGCI) as part of the Pacific Islands Climate Change Assistance Programme (PICCAP) executed by the South Pacific Regional Environment Programme (SPREP). Both FIJICLIM and PACCLIM build directly on a comparable model development for New Zealand, known as the CLIMPACTS system (Kenny et al., 1995, 1999; Warrick et al., 1996, 1999). The development of CLIMPACTS has been funded by the Foundation for Research Science and Technology since 1993. Its core components, which include a graphic user interface (GUI), a customised geographic information system (GIS), and data compression routines, have provided the basis for the development of FIJICLIM. The development of FIJICLIM is complementary to similar developments that have evolved from CLIMPACTS, for Bangladesh (BDCLIM), Australia (OZCLIM), and for training in climate change V&A assessment (VANDACLIM)

Bayesian detection of embryonic gene expression onset in C. elegans

To study how a zygote develops into an embryo with different tissues, large-scale 4D confocal movies of C. elegans embryos have been produced recently by experimental biologists. However, the lack of principled statistical methods for the highly noisy data has hindered the comprehensive analysis of these data sets. We introduced a probabilistic change point model on the cell lineage tree to estimate the embryonic gene expression onset time. A Bayesian approach is used to fit the 4D confocal movies data to the model. Subsequent classification methods are used to decide a model selection threshold and further refine the expression onset time from the branch level to the specific cell time level. Extensive simulations have shown the high accuracy of our method. Its application on real data yields both previously known results and new findings.Comment: Published at http://dx.doi.org/10.1214/15-AOAS820 in the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A Bayesian approach for applying Haseman-Elston methods

The main goal of this paper is to couple the Haseman-Elston method with a simple yet effective Bayesian factor-screening approach. This approach selects markers by considering a set of multigenic models that include epistasis effects. The markers are ranked based on their marginal posterior probability. A significant improvement over our previously proposed Bayesian variable selection methodology is a simple Metropolis-Hasting algorithm that requires minimum tuning on the prior settings. The algorithm, however, is also flexible enough for us to easily incorporate our hypotheses and avoid computational pitfalls. We apply our approach to the microsatellite data of Collaborative Studies on Genetics of Alcoholism using the coded values for the ALDX1 variable as our response

Locating disease genes using Bayesian variable selection with the Haseman-Elston method

BACKGROUND: We applied stochastic search variable selection (SSVS), a Bayesian model selection method, to the simulated data of Genetic Analysis Workshop 13. We used SSVS with the revisited Haseman-Elston method to find the markers linked to the loci determining change in cholesterol over time. To study gene-gene interaction (epistasis) and gene-environment interaction, we adopted prior structures, which incorporate the relationship among the predictors. This allows SSVS to search in the model space more efficiently and avoid the less likely models. RESULTS: In applying SSVS, instead of looking at the posterior distribution of each of the candidate models, which is sensitive to the setting of the prior, we ranked the candidate variables (markers) according to their marginal posterior probability, which was shown to be more robust to the prior. Compared with traditional methods that consider one marker at a time, our method considers all markers simultaneously and obtains more favorable results. CONCLUSIONS: We showed that SSVS is a powerful method for identifying linked markers using the Haseman-Elston method, even for weak effects. SSVS is very effective because it does a smart search over the entire model space

Improving VIP viewer Gaze Estimation and Engagement Using Adaptive Dynamic Anamorphosis

Anamorphosis for 2D displays can provide viewer centric perspective viewing, enabling 3D appearance, eye contact and engagement, by adapting dynamically in real time to a single moving viewer’s viewpoint, but at the cost of distorted viewing for other viewers. We present a method for constructing non-linear projections as a combination of anamorphic rendering of selective objects whilst reverting to normal perspective rendering of the rest of the scene. Our study defines a scene consisting of five characters, with one of these characters selectively rendered in anamorphic perspective. We conducted an evaluation experiment and demonstrate that the tracked viewer-centric imagery for the selected character results in an improved gaze and engagement estimation. Critically, this is performed without sacrificing the other viewers’ viewing experience. In addition, we present findings on the perception of gaze direction for regularly viewed characters located off-center to the origin, where perceived gaze shifts from being aligned to misalignment increasingly as the distance between viewer and character increases. Finally, we discuss different viewpoints and the spatial relationship between objects

Empowerment and embodiment for collaborative mixed reality systems: Empowerment and Embodiment

We present several mixed‐reality‐based remote collaboration settings by using consumer head‐mounted displays. We investigated how two people are able to work together in these settings. We found that the person in the AR system will be regarded as the “leader” (i.e., they provide a greater contribution to the collaboration), whereas no similar “leader” emerges in augmented reality (AR)‐to‐AR and AR‐to‐VRBody settings. We also found that these special patterns of leadership only emerged for 3D interactions and not for 2D interactions. Results about the participants' experience of leadership, collaboration, embodiment, presence, and copresence shed further light on these findings

A gene-model-free method for linkage analysis of a disease-related-trait based on analysis of proband/sibling pairs

In this paper we investigate the power of finding linkage to a disease locus through analysis of the disease-related traits. We propose two family-based gene-model-free linkage statistics. Both involve considering the distribution of the number of alleles identical by descent with the proband and comparing siblings with the disease-related trait to those without the disease-related-trait. The objective is to find linkages to disease-related traits that are pleiotropic for both the disease and the disease-related-traits. The power of these statistics is investigated for Kofendrerd Personality Disorder-related traits a (Joining/founding cults) and trait b (Fear/discomfort with strangers) of the simulated data. The answers were known prior to the execution of the reported analyses. We find that both tests have very high power when applied to the samples created by combining the data of the three cities for which we have nuclear family data

Estimating Allele Frequency from Next-Generation Sequencing of Pooled Mitochondrial DNA Samples

Background: Both common and rare mitochondrial DNA (mtDNA) variants may contribute to genetic susceptibility to some complex human diseases. Understanding of the role of mtDNA variants will provide valuable insights into the etiology of these diseases. However, to date, there have not been any large-scale, genome-wide association studies of complete mtDNA variants and disease risk. One reason for this might be the substantial cost of sequencing the large number of samples required for genetic epidemiology studies. Next-generation sequencing of pooled mtDNA samples will dramatically reduce the cost of such studies and may represent an appealing approach for large-scale genetic epidemiology studies. However, the performance of the different designs of sequencing pooled mtDNA has not been evaluated. Methods: We examined the approach of sequencing pooled mtDNA of multiple individuals for estimating allele frequency using the Illumina genome analyzer (GA) II sequencing system. In this study the pool included mtDNA samples of 20 subjects that had been sequenced previously using Sanger sequencing. Each pool was replicated once to assess variation of the sequencing error between pools. To reduce such variation, barcoding was used for sequencing different pools in the same lane of the flow cell. To evaluate the effect of different pooling strategies pooling was done at both the pre- and post-PCR amplification step. Results: The sequencing error rate was close to that expected based on the Phred score. When only reads with Phred ≥ 20 were considered, the average error rate was about 0.3%. However, there was significant variation of the base-calling errors for different types of bases or at different loci. Using the results of the Sanger sequencing as the standard, the sensitivity of single nucleotide polymorphism detection with post-PCR pooling (about 99%) was higher than that of the pre-PCR pooling (about 82%), while the two approaches had similar specificity (about 99%). Among a total of 298 variants in the sample, the allele frequencies of 293 variants (98%) were correctly estimated with post-PCR pooling, the correlation between the estimated and the true allele frequencies being >0.99, while only 206 allele frequencies (69%) were correctly estimated in the pre-PCR pooling, the correlation being 0.89. Conclusion: Sequencing of mtDNA pooled after PCR amplification is a viable tool for screening mitochondrial variants potentially related to human diseases