Subtree power analysis finds optimal species for comparative genomics

Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. In a study of vertebrate species, we show that the optimal species subset is not in general the most evolutionarily diverged subset. Our results suggest that marsupials are prime sequencing candidates.Comment: 16 pages, 3 figures, 3 table

Comment on "Support Vector Machines with Applications"

Comment on "Support Vector Machines with Applications" [math.ST/0612817]Comment: Published at http://dx.doi.org/10.1214/088342306000000475 in the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Approximate Inference for Constructing Astronomical Catalogs from Images

We present a new, fully generative model for constructing astronomical catalogs from optical telescope image sets. Each pixel intensity is treated as a random variable with parameters that depend on the latent properties of stars and galaxies. These latent properties are themselves modeled as random. We compare two procedures for posterior inference. One procedure is based on Markov chain Monte Carlo (MCMC) while the other is based on variational inference (VI). The MCMC procedure excels at quantifying uncertainty, while the VI procedure is 1000 times faster. On a supercomputer, the VI procedure efficiently uses 665,000 CPU cores to construct an astronomical catalog from 50 terabytes of images in 14.6 minutes, demonstrating the scaling characteristics necessary to construct catalogs for upcoming astronomical surveys.Comment: accepted to the Annals of Applied Statistic

Ethics in the interface between multidisciplinary teams: a narrative in stages for inter-professional education

An ethically problematic clinical case is used to illustrate the potential importance of understanding clinical ethics in an interdisciplinary context. Whilst much has been written on ethics education for multidisciplinary and interdisciplinary teams, we argue that it is important that both healthcare professions and healthcare teams are able to look outside their own disciplinary ethos and sometimes outside their formal teams when considering the ramifications of an ethical issue. A complex (fictional but based on the authors’ pooled experiences) case involving the delivery of a new-born from a mother with HIV is used to illustrate this, because multiple clinical teams will be involved at different times and in parallel with one another

Materials discovery using in situ reduction and X-ray diffraction

Materials discovery is important for pushing new and existing technologies forward. In this thesis, a systematic approach to materials discovery is presented that highlights the combined use of in situ reduction reactions and X-ray diffraction to quickly explore compositional space. Reduction reactions provide a synthesis route that has been shown to gently traverse a compositional space. Traditional synthesis at high temperatures tends to only favor the formation of thermodynamically stable compounds, however, with a more controlled synthesis route, kinetically stable and metastable compounds may be easier to discover. By coupling reduction reactions with in situ X-ray diffraction, intermediate and metastable phases can be observed. Once a phase is observed using in situ X-ray diffraction, attempts can be made to stabilize the phase ex situ in order to solve the structure and understand the material's properties. In this thesis, an in situ cell is described that can be used to perform these in situ reduction reactions using a laboratory X-ray diffractometer. Since the technique can now be performed on a laboratory scale, rapid phase exploration can be performed. This combined approach will be discussed with regard to two different materials systems, K-Sn-O and Fe-S. In the K-Sn-O system, in situ and ex situ studies are performed in order to search for new p-type transparent conducting oxides. In the Fe-S system, in situ reduction is used to solve a highly debated question of whether or not pyrite FeS2 is a non-stoichiometric compound and to quantify the possible extent of non-stoichiometry

The ontogeny of children's social emotions in response to (un)fairness

Humans have a deeply rooted sense of fairness, but its emotional foundation in early ontogeny remains poorly understood. Here, we asked if and when 4- to 10-year-old children show negative social emotions, such as shame or guilt, in response to advantageous unfairness expressed through a lowered body posture (measured using a Kinect depth sensor imaging camera). We found that older, but not younger children, showed more negative emotions, i.e. a reduced upper body posture, after unintentionally disadvantaging a peer on (4,1) trials than in response to fair (1,1) outcomes between themselves and others. Younger children, in contrast, expressed more negative emotions in response to the fair (1,1) split than in response to advantageous inequity. No systematic pattern of children's emotional responses was found in a non-social context, in which children divided resources between themselves and a non-social container. Supporting individual difference analyses showed that older children in the social context expressed negative emotions in response to advantageous inequity without directly acting on this negative emotional response by rejecting an advantageously unfair offer proposed by an experimenter at the end of the study. These findings shed new light on the emotional foundation of the human sense of fairness and suggest that children's negative emotional response to advantageous unfairness developmentally precedes their rejection of advantageously unfair resource distributions

A Spatially Varying Two-Sample Recombinant Coalescent, With Applications to HIV Escape Response

Statistical evolutionary models provide an important mechanism for describing and understanding the escape response of a viral population under a particular therapy. We present a new hierarchical model that incorporates spatially varying mutation and recombination rates at the nucleotide level. It also maintains sep- arate parameters for treatment and control groups, which allows us to estimate treatment effects explicitly. We use the model to investigate the sequence evolu- tion of HIV populations exposed to a recently developed antisense gene therapy, as well as a more conventional drug therapy. The detection of biologically rele- vant and plausible signals in both therapy studies demonstrates the effectiveness of the method