Network inference in matrix-variate Gaussian models with non-independent noise

Inferring a graphical model or network from observational data from a large number of variables is a well studied problem in machine learning and computational statistics. In this paper we consider a version of this problem that is relevant to the analysis of multiple phenotypes collected in genetic studies. In such datasets we expect correlations between phenotypes and between individuals. We model observations as a sum of two matrix normal variates such that the joint covariance function is a sum of Kronecker products. This model, which generalizes the Graphical Lasso, assumes observations are correlated due to known genetic relationships and corrupted with non-independent noise. We have developed a computationally efficient EM algorithm to fit this model. On simulated datasets we illustrate substantially improved performance in network reconstruction by allowing for a general noise distribution

Embodying Love in the Inner City : Undoing Injustice through Intentional Neighboring

In many American cities, middle-class, faith-motivated individuals and families are moving into poor, inner-city neighborhoods to live out their vision of social justice in the city by becoming “intentional neighbors.” Drawing from the commandment to “love thy neighbor,” these faith-motivated actors develop relationships with their neighbors and share their resources in order to work towards the transformation of these places. In this paper we use the case study of participants in Mission Year, a Christian community-development organization, to examine the spatial and embodied practices that are integral to “doing justice” and demonstrating love in the inner city.Dans de nombreuses villes américaines, des individus et des familles issus de la classe moyenne, motivés par leur foi, emménagent dans les quartiers pauvres du centre-ville pour mettre en pratique leur idéal de justice sociale en devenant des « voisins volontaires ». Inspirés par le commandement « tu aimeras ton prochain comme toi-même », ces citoyens motivés par la foi développent des relations avec leurs voisins et partagent leurs ressources afin d’œuvrer à la transformation de ces lieux de vie. Cet article est une étude de cas des membres de Mission Year, une organisation chrétienne de développement communautaire. Cette étude nous permet d’examiner les pratiques spatiales et concrètes qui font partie intégrante du « faire justice » dans les centres-villes

A model and test for coordinated polygenic epistasis in complex traits

Interactions between genetic variants—epistasis—is pervasive in model systems and can profoundly impact evolutionary adaption, population disease dynamics, genetic mapping, and precision medicine efforts. In this work, we develop a model for structured polygenic epistasis, called coordinated epistasis (CE), and prove that several recent theories of genetic architecture fall under the formal umbrella of CE. Unlike standard epistasis models that assume epistasis and main effects are independent, CE captures systematic correlations between epistasis and main effects that result from pathway-level epistasis, on balance skewing the penetrance of genetic effects. To test for the existence of CE, we propose the even-odd (EO) test and prove it is calibrated in a range of realistic biological models. Applying the EO test in the UK Biobank, we find evidence of CE in 18 of 26 traits spanning disease, anthropometric, and blood categories. Finally, we extend the EO test to tissue-specific enrichment and identify several plausible tissue–trait pairs. Overall, CE is a dimension of genetic architecture that can capture structured, systemic forms of epistasis in complex human traits

Keck Interferometer autoaligner: algorithms and techniques

The Keck Interferometer includes an autoalignment system consisting of pop-up targets located at strategic locations along the beam trains of each arm of the instrument along with a sensor and control system. We briefly describe the hardware of the system and then proceed to a description of the two operational modes of the system. These are: 1) to provide an initial alignment of the coude paths in each arm, and 2) to recover coude alignments between changes of the static delay sled positions. For the initial alignment mode, we review the system performance requirements along with the software used for image acquisition and centroiding. For coudé alignment recovery, we describe beam-train surveys through the static delay (Long Delay Line) and criteria for a successful recovery of a coudé alignment. Finally, we describe the results of testing of the autoalignment system

Visibility science operations with the Keck Interferometer

The visibility science mode of the Keck Interferometer fully transitioned into operations with the successful completion of its operational readiness review in April 2004. The goal of this paper is to describe this science mode and the operations structure that supports it

Keck Interferometer autoaligner: algorithms and techniques

The Keck Interferometer includes an autoalignment system consisting of pop-up targets located at strategic locations along the beam trains of each arm of the instrument along with a sensor and control system. We briefly describe the hardware of the system and then proceed to a description of the two operational modes of the system. These are: 1) to provide an initial alignment of the coude paths in each arm, and 2) to recover coude alignments between changes of the static delay sled positions. For the initial alignment mode, we review the system performance requirements along with the software used for image acquisition and centroiding. For coudé alignment recovery, we describe beam-train surveys through the static delay (Long Delay Line) and criteria for a successful recovery of a coudé alignment. Finally, we describe the results of testing of the autoalignment system

Greenland and Canadian Arctic ice temperature profiles database

Here, we present a compilation of 95 ice temperature profiles from 85 boreholes from the Greenland ice sheet and peripheral ice caps, as well as local ice caps in the Canadian Arctic. Profiles from only 31 boreholes (36 %) were previously available in open-access data repositories. The remaining 54 borehole profiles (64 %) are being made digitally available here for the first time. These newly available profiles, which are associated with pre-2010 boreholes, have been submitted by community members or digitized from published graphics and/or data tables. All 95 profiles are now made available in both absolute (meters) and normalized (0 to 1 ice thickness) depth scales and are accompanied by extensive metadata. These metadata include a transparent description of data provenance. The ice temperature profiles span 70 years, with the earliest profile being from 1950 at Camp VI, West Greenland. To highlight the value of this database in evaluating ice flow simulations, we compare the ice temperature profiles from the Greenland ice sheet with an ice flow simulation by the Parallel Ice Sheet Model (PISM). We find a cold bias in modeled near-surface ice temperatures within the ablation area, a warm bias in modeled basal ice temperatures at inland cold-bedded sites, and an apparent underestimation of deformational heating in high-strain settings. These biases provide process level insight on simulated ice temperatures

Visibility science operations with the Keck Interferometer

The visibility science mode of the Keck Interferometer fully transitioned into operations with the successful completion of its operational readiness review in April 2004. The goal of this paper is to describe this science mode and the operations structure that supports it