Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes

Causal inference approaches in systems genetics exploit quantitative trait loci (QTL) genotypes to infer causal relationships among phenotypes. The genetic architecture of each phenotype may be complex, and poorly estimated genetic architectures may compromise the inference of causal relationships among phenotypes. Existing methods assume QTLs are known or inferred without regard to the phenotype network structure. In this paper we develop a QTL-driven phenotype network method (QTLnet) to jointly infer a causal phenotype network and associated genetic architecture for sets of correlated phenotypes. Randomization of alleles during meiosis and the unidirectional influence of genotype on phenotype allow the inference of QTLs causal to phenotypes. Causal relationships among phenotypes can be inferred using these QTL nodes, enabling us to distinguish among phenotype networks that would otherwise be distribution equivalent. We jointly model phenotypes and QTLs using homogeneous conditional Gaussian regression models, and we derive a graphical criterion for distribution equivalence. We validate the QTLnet approach in a simulation study. Finally, we illustrate with simulated data and a real example how QTLnet can be used to infer both direct and indirect effects of QTLs and phenotypes that co-map to a genomic region.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS288 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

An Abstract Framework for Deadlock Prevention in BIP

Part 6: Session 5: Model CheckingInternational audienceWe present a sound but incomplete criterion for checking deadlock freedom of finite state systems expressed in BIP: a component-based framework for the construction of complex distributed systems. Since deciding deadlock-freedom for finite-state concurrent systems is PSPACE-complete, our criterion gives up completeness in return for tractability of evaluation. Our criterion can be evaluated by model-checking subsystems of the overall large system. The size of these subsystems depends only on the local topology of direct interaction between components, and not on the number of components in the overall system. We present two experiments, in which our method compares favorably with existing approaches. For example, in verifying deadlock freedom of dining philosphers, our method shows linear increase in computation time with the number of philosophers, whereas other methods (even those that use abstraction) show super-linear increase, due to state-explosion

Correspondence - Attie Bostick Feb. 23, 1934 - Wade Bostick

A correspondence from Attie T. Bostick. Includes handwritten note to Mrs. H.L. Packard and a partial letter from Wade Bostick.https://digitalcommons.gardner-webb.edu/baptist-historical-collections-bostick-family-missions/1019/thumbnail.jp

Evidence of photospheric vortex flows at supergranular junctions observed by FG/SOT (Hinode)

Twisting motions of different nature are observed in several layers of the solar atmosphere. Chromospheric sunspot whorls and rotation of sunspots or even higher up in the lower corona sigmoids are examples of the large scale twisted topology of many solar features. Nevertheless, their occurrence at large scale in the quiet photosphere has not been investigated. The present study reveals the existence of vortex flows located at the supergranular junctions of the quiet Sun. We use a 1-hour and a 5-hour time series of the granulation in Blue continuum and G-band images from FG/SOT to derive the photospheric flows. A feature tracking technique called Balltracking is performed to track the granules and reveal the underlying flow fields. In both time series we identify long-lasting vortex flow located at supergranular junctions. The first vortex flow lasts at least 1 hour and is ~20-arcsec-wide (~15.5 Mm). The second vortex flow lasts more than 2 hours and is ~27-arcsec-wide (~21 Mm).Comment: 4 pages, 10 figure

The INTEGRAL/SPI response and the Crab observations

The Crab region was observed several times by INTEGRAL for calibration purposes. This paper aims at underlining the systematic interactions between (i) observations of this reference source, (ii) in-flight calibration of the instrumental response and (iii) the development and validation of the analysis tools of the SPI spectrometer. It first describes the way the response is produced and how studies of the Crab spectrum lead to improvements and corrections in the initial response. Then, we present the tools which were developed to extract spectra from the SPI observation data and finally a Crab spectrum obtained with one of these methods, to show the agreement with previous experiments. We conclude with the work still ahead to understand residual uncertainties in the response.Comment: 4 pages, 4 figures, Proc. of the 5th INTEGRAL Workshop (Feb. 16-20 2004), to be published by ES

A linear CO chemistry parameterization in a chemistry-transport model: evaluation and application to data assimilation

This paper presents an evaluation of a new linear parameterization valid for the troposphere and the stratosphere, based on a first order approximation of the carbon monoxide (CO) continuity equation. This linear scheme (hereinafter noted LINCO) has been implemented in the 3-D Chemical Transport Model (CTM) MOCAGE (MOdèle de Chimie Atmospherique Grande Echelle). First, a one and a half years of LINCO simulation has been compared to output obtained from a detailed chemical scheme output. The mean differences between both schemes are about ±25 ppbv (part per billion by volume) or 15% in the troposphere and ±10 ppbv or 100% in the stratosphere. Second, LINCO has been compared to diverse observations from satellite instruments covering the troposphere (Measurements Of Pollution In The Troposphere: MOPITT) and the stratosphere (Microwave Limb Sounder: MLS) and also from aircraft (Measurements of ozone and water vapour by Airbus in-service aircraft: MOZAIC programme) mostly flying in the upper troposphere and lower stratosphere (UTLS). In the troposphere, the LINCO seasonal variations as well as the vertical and horizontal distributions are quite close to MOPITT CO observations. However, a bias of ~−40 ppbv is observed at 700 Pa between LINCO and MOPITT. In the stratosphere, MLS and LINCO present similar large-scale patterns, except over the poles where the CO concentration is underestimated by the model. In the UTLS, LINCO presents small biases less than 2% compared to independent MOZAIC profiles. Third, we assimilated MOPITT CO using a variational 3D-FGAT (First Guess at Appropriate Time) method in conjunction with MOCAGE for a long run of one and a half years. The data assimilation greatly improves the vertical CO distribution in the troposphere from 700 to 350 hPa compared to independent MOZAIC profiles. At 146 hPa, the assimilated CO distribution is also improved compared to MLS observations by reducing the bias up to a factor of 2 in the tropics. This study confirms that the linear scheme is able to simulate reasonably well the CO distribution in the troposphere and in the lower stratosphere. Therefore, the low computing cost of the linear scheme opens new perspectives to make free runs and CO data assimilation runs at high resolution and over periods of several years