Partial DNA Assembly: A Rate-Distortion Perspective

Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the assembly graph, each of which correspond to a candidate assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an assembly graph and analyze its performance on real genomes.Comment: To be published at ISIT-2016. 11 pages, 10 figure

Training Novices to Evaluate the Quality of Physical Activity Promotion Material: Results of a Pilot Study

The credibility and usability of lay physical activity promotion material are a persistent problem (Thomas & Cardinal, 2020, TJACM). These quality issues deter the material in promoting health literacy, a major predictor of prevention-oriented health behaviors (e.g., regular exercise, U.S. National Action Plan to Improve Health Literacy). Few studies, however, have evaluated the quality of lay material over time (Thomas et al., 2018, Quest). PURPOSE: In order to conduct a repeated-measures study of the quality of physical activity promotion web articles for lay adults, one experienced researcher (JDT) trained undergraduates on how to use the Suitability Assessment of Materials (SAM) protocol (Doak et al., 1996). METHODS: An adapted version of the SAM protocol was used (Thomas & Cardinal, 2020, Quest). Three undergraduates were part of the pilot project (ENT, SAL, CNC; Feb.-Aug. 2020). Each was introduced to the protocol and practiced its methods using six web articles that were written in English and not used in the longitudinal study. Coding by ENT was compared to JDT for analytic purposes; ENT was pre-assigned to evaluate material for the longitudinal study. Per Krippendorff’s alpha and intraclass coefficient measures, ENT showed acceptable between/within coder agreement during the training phase. Jul.-Aug. 2020, ENT then tested his skills further using a random subset of 16 unique web articles that were part of the longitudinal study. RESULTS: ENT between-coder agreement ranged from Good/Substantial (both .68) to Excellent/Almost Perfect (both .86) across the SAM’s main categories. Overall agreement was Excellent/Substantial (range: .76-.77). Within-coder agreement was Excellent/Almost Perfect across all main categories (both ≥ .85). CONCLUSION: This pilot study demonstrates that a novice coder can learn to code material with a high degree of fidelity. This contrasts with speculation that the SAM protocol may be too subjective for good coder agreement. Debriefing revealed key insights: (a) four “rules” that helped the novice coder achieve fidelity (e.g., review notes often) and (b) developer “bad habits” that limit the educational quality of material (e.g., jargon-filled advice). We will discuss our results and practical lessons based on post-hoc text profiles of material sampled in our pilot study

Glass-Like Heat Conduction in High-Mobility Crystalline Semiconductors

The thermal conductivity of polycrystalline semiconductors with type-I clathrate hydrate crystal structure is reported. Ge clathrates (doped with Sr and/or Eu) exhibit lattice thermal conductivities typical of amorphous materials. Remarkably, this behavior occurs in spite of the well-defined crystalline structure and relatively high electron mobility ($\sim 100 cm^2/Vs$). The dynamics of dopant ions and their interaction with the polyhedral cages of the structure are a likely source of the strong phonon scattering.Comment: 4 pages, 3 postscript figures, to be published, Phys. Rev. Let

A combined XAS and XRD Study of the High-Pressure Behaviour of GaAsO4 Berlinite

Combined X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) experiments have been carried out on GaAsO4 (berlinite structure) at high pressure and room temperature. XAS measurements indicate four-fold to six-fold coordination changes for both cations. The two local coordination transformations occur at different rates but appear to be coupled. A reversible transition to a high pressure crystalline form occurs around 8 GPa. At a pressure of about 12 GPa, the system mainly consists of octahedral gallium atoms and a mixture of arsenic in four-fold and six-fold coordinations. A second transition to a highly disordered material with both cations in six-fold coordination occurs at higher pressures and is irreversible.Comment: 8 pages, 5 figures, LaTeX2

Mechanical versus thermodynamical melting in pressure-induced amorphization: the role of defects

We study numerically an atomistic model which is shown to exhibit a one--step crystal--to--amorphous transition upon decompression. The amorphous phase cannot be distinguished from the one obtained by quenching from the melt. For a perfectly crystalline starting sample, the transition occurs at a pressure at which a shear phonon mode destabilizes, and triggers a cascade process leading to the amorphous state. When defects are present, the nucleation barrier is greatly reduced and the transformation occurs very close to the extrapolation of the melting line to low temperatures. In this last case, the transition is not anticipated by the softening of any phonon mode. Our observations reconcile different claims in the literature about the underlying mechanism of pressure amorphization.Comment: 7 pages, 7 figure