A Machine Checked Model of Idempotent MGU Axioms For Lists of Equational Constraints

We present formalized proofs verifying that the first-order unification algorithm defined over lists of satisfiable constraints generates a most general unifier (MGU), which also happens to be idempotent. All of our proofs have been formalized in the Coq theorem prover. Our proofs show that finite maps produced by the unification algorithm provide a model of the axioms characterizing idempotent MGUs of lists of constraints. The axioms that serve as the basis for our verification are derived from a standard set by extending them to lists of constraints. For us, constraints are equalities between terms in the language of simple types. Substitutions are formally modeled as finite maps using the Coq library Coq.FSets.FMapInterface. Coq's method of functional induction is the main proof technique used in proving many of the axioms.Comment: In Proceedings UNIF 2010, arXiv:1012.455

A Search for Multi-Planet Systems Using the Hobby-Eberly Telescope

Extrasolar multiple-planet systems provide valuable opportunities for testing theories of planet formation and evolution. The architectures of the known multiple-planet systems demonstrate a fascinating level of diversity, which motivates the search for additional examples of such systems in order to better constrain their formation and dynamical histories. Here we describe a comprehensive investigation of 22 planetary systems in an effort to answer three questions: 1) Are there additional planets? 2) Where could additional planets reside in stable orbits? and 3) What limits can these observations place on such objects? We find no evidence for additional bodies in any of these systems; indeed, these new data do not support three previously announced planets (HD 20367b: Udry et al. 2003, HD 74156d: Bean et al. 2008, and 47 UMa c: Fischer et al. 2002). The dynamical simulations show that nearly all of the 22 systems have large regions in which additional planets could exist in stable orbits. The detection-limit computations indicate that this study is sensitive to close-in Neptune-mass planets for most of the systems targeted. We conclude with a discussion on the implications of these non-detections.Comment: Accepted to ApJS. Includes 39 pages of radial-velocity data table

Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA

This article includes supplemental data. Please visit http://www.fasebj.org to obtain this information.Multiple recent publications on RNA sequencing (RNA-seq) have demonstrated the power of next-generation sequencing technologies in whole-transcriptome analysis. Vendor-specific protocols used for RNA library construction often require at least 100 ng total RNA. However, under certain conditions, much less RNA is available for library construction. In these cases, effective transcriptome profiling requires amplification of subnanogram amounts of RNA. Several commercial RNA amplification kits are available for amplification prior to library construction for next-generation sequencing, but these kits have not been comprehensively field evaluated for accuracy and performance of RNA-seq for picogram amounts of RNA. To address this, 4 types of amplification kits were tested with 3 different concentrations, from 5 ng to 50 pg, of a commercially available RNA. Kits were tested at multiple sites to assess reproducibility and ease of use. The human total reference RNA used was spiked with a control pool of RNA molecules in order to further evaluate quantitative recovery of input material. Additional control data sets were generated from libraries constructed following polyA selection or ribosomal depletion using established kits and protocols. cDNA was collected from the different sites, and libraries were synthesized at a single site using established protocols. Sequencing runs were carried out on the Illumina platform. Numerous metrics were compared among the kits and dilutions used. Overall, no single kit appeared to meet all the challenges of small input material. However, it is encouraging that excellent data can be recovered with even the 50 pg input total RNA

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

Acknowledgments This work was funded in part by the William and Melinda Gates Foundation, award 42917 to JPN and OCS; US National Institutes of Health grants 5R01HG005220 to HCB, 5R01HG004885 to MP; US National Science Foundation Graduate Research Fellowship award DGE0750616 to JNP; AWW and JP are funded by The Wellcome Trust (Grant No. WT098051).Peer reviewedPublisher PD

The First HET Planet: A Companion to HD 37605

We report the first detection of a planetary-mass companion to a star using the High Resolution Spectrograph (HRS) of the Hobby-Eberly Telescope (HET). The HET-HRS now gives routine radial velocity precision of 2-3 m/s for high SNR observations of quiescent stars. The planetary-mass companion to the metal-rich K0V star HD37605 has an orbital period of 54.23 days, an orbital eccentricity of 0.737, and a minimum mass of 2.84 Jupiter masses. The queue-scheduled operation of the Hobby-Eberly Telescope enabled us to discovery of this relatively short-period planet with a total observation time span of just two orbital periods. The ability of queue-scheduled large-aperture telescopes to respond quickly to interesting and important results demonstrates the power of this new approach in searching for extra-solar planets as well as in other ares of research requiring rapid response time critical observations.Comment: 4 Pages, 2 figures. Accepted in Astrophysical Journal Letters, http://austral.as.utexas.edu/planets/hd37605/hd37605.htm

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

SummaryBMP and Wnt signaling pathways control essential cellular responses through activation of the transcription factors SMAD (BMP) and TCF (Wnt). Here, we show that regeneration of hematopoietic lineages following acute injury depends on the activation of each of these signaling pathways to induce expression of key blood genes. Both SMAD1 and TCF7L2 co-occupy sites with master regulators adjacent to hematopoietic genes. In addition, both SMAD1 and TCF7L2 follow the binding of the predominant lineage regulator during differentiation from multipotent hematopoietic progenitor cells to erythroid cells. Furthermore, induction of the myeloid lineage regulator C/EBPα in erythroid cells shifts binding of SMAD1 to sites newly occupied by C/EBPα, whereas expression of the erythroid regulator GATA1 directs SMAD1 loss on nonerythroid targets. We conclude that the regenerative response mediated by BMP and Wnt signaling pathways is coupled with the lineage master regulators to control the gene programs defining cellular identity

Flowing afterglow apparatus for the study of ion-molecule reactions at high temperatures

We describe two versions of a high temperature flowing afterglow apparatus. With a stainless steel flow tube wrapped with heating tape we have obtained data over the range 300-1300 K. In a version with a ceramic flow tube in a commercial furnace we have obtained data over the range 300-1600 K. The ceramic version is designed to take data up to 1800 K, but we have encountered experimental problems at the upper temperature range. The design modifications to a standard flowing afterglow needed to make measurements at elevated temperatures are described in detail, as are problems associated with operating at elevated temperatures. Samples of data are given. (C) 1996 American Institute of Physics

The Distances to Open Clusters from Main-Sequence Fitting. III. Improved Accuracy with Empirically Calibrated Isochrones

We continue our series of papers on open cluster distances with a critical assessment of the accuracy of main-sequence fitting using isochrones that employ empirical corrections to the color-temperature relations. We use four nearby open clusters with multicolor photometry and accurate metallicities and present a new metallicity for Praesepe ([Fe/H] = +0.11 +/- 0.03) from high-resolution spectra. The internal precision of distance estimates is about a factor of 5 better than the case without the color calibrations. After taking into account all major systematic errors, we obtain distances accurate to about 2%-3% when there exists a good metallicity estimate. Metallicities accurate to better than 0.1 dex may be obtained from BVIcKs photometry alone. We also derive a helium abundance for the Pleiades of Y = 0.279 +/- 0.015, which is equal within the errors to the Sun's initial helium abundance and that of the Hyades. Our best estimates of distances are (m - M)_0 = 6.33 +/- 0.04, 8.03 +/- 0.04, and 9.61 +/- 0.03 to Praesepe, NGC 2516, and M67, respectively. Our Pleiades distance at the spectroscopic metallicity, (m - M)_0 = 5.66 +/- 0.01 (internal) +/- 0.05 (systematic), is in excellent agreement with several geometric distance measurements. We have made calibrated isochrones for -0.3 <= [Fe/H] <= +0.2 available at http://www.astronomy.ohio-state.edu/iso/ .Comment: 28 pages, 23 figures; accepted for publication in the Ap