Tissue resolved, gene structure refined equine transcriptome.

BackgroundTranscriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.ResultsThis equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.ConclusionsWe have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome

Holographic Reconstruction and Renormalization in Asymptotically Ricci-flat Spacetimes

In this work we elaborate on an extension of the AdS/CFT framework to a subclass of gravitational theories with vanishing cosmological constant. By building on earlier ideas, we construct a correspondence between Ricci-flat spacetimes admitting asymptotically hyperbolic hypersurfaces and a family of conformal field theories on a codimension two manifold at null infinity. By truncating the gravity theory to the pure gravitational sector, we find the most general spacetime asymptotics, renormalize the gravitational action, reproduce the holographic stress tensors and Ward identities of the family of CFTs and show how the asymptotics is mapped to and reconstructed from conformal field theory data. In even dimensions, the holographic Weyl anomalies identify the bulk time coordinate with the spectrum of central charges with characteristic length the bulk Planck length. Consistency with locality in the bulk time direction requires a notion of locality in this spectrum.Comment: 44 pages, 4 figures. v2: minor changes in section

Is the biology of breast cancer changing? A study of hormone receptor status 1984-1986 and 1996-1997

Using archived tumours, those from 1984-1986 and 1996-1997 underwent immunohistochemistry for hormone receptors and grade analysis. A significant shift towards more ER-positive and low-grade disease was found; this appears to reflect screening practices, but could still influence survival

Entropy of three-dimensional asymptotically flat cosmological solutions

The thermodynamics of three-dimensional asymptotically flat cosmological solutions that play the same role than the BTZ black holes in the anti-de Sitter case is derived and explained from holographic properties of flat space. It is shown to coincide with the flat-space limit of the thermodynamics of the inner black hole horizon on the one hand and the semi-classical approximation to the gravitational partition function associated to the entropy of the outer horizon on the other. This leads to the insight that it is the Massieu function that is universal in the sense that it can be computed at either horizon.Comment: 16 pages Latex file, v2: references added, cosmetic changes, v3: 1 reference adde

Black Branes in a Box: Hydrodynamics, Stability, and Criticality

We study the effective hydrodynamics of neutral black branes enclosed in a finite cylindrical cavity with Dirichlet boundary conditions. We focus on how the Gregory-Laflamme instability changes as we vary the cavity radius R. Fixing the metric at the cavity wall increases the rigidity of the black brane by hindering gradients of the redshift on the wall. In the effective fluid, this is reflected in the growth of the squared speed of sound. As a consequence, when the cavity is smaller than a critical radius the black brane becomes dynamically stable. The correlation with the change in thermodynamic stability is transparent in our approach. We compute the bulk and shear viscosities of the black brane and find that they do not run with R. We find mean-field theory critical exponents near the critical point.Comment: 23 pages, 3 figures. v2: added comments on first-order phase transitio

Quantizing higher-spin gravity in free-field variables

We study the formulation of massless higher-spin gravity on AdS$_3$ in a gauge in which the fundamental variables satisfy free field Poisson brackets. This gauge choice leaves a small portion of the gauge freedom unfixed, which should be further quotiented out. We show that doing so leads to a bulk version of the Coulomb gas formalism for $W_N$ CFT's: the generators of the residual gauge symmetries are the classical limits of screening charges, while the gauge-invariant observables are classical $W_N$ charges. Quantization in these variables can be carried out using standard techniques and makes manifest a remnant of the triality symmetry of $W_\infty[\lambda]$. This symmetry can be used to argue that the theory should be supplemented with additional matter content which is precisely that of the Prokushkin-Vasiliev theory. As a further application, we use our formulation to quantize a class of conical surplus solutions and confirm the conjecture that these are dual to specific degenerate $W_N$ primaries, to all orders in the large central charge expansion.Comment: 31 pages + appendices. V2: typos corrected, reference adde

The action for higher spin black holes in three dimensions

In the context of (2+1)--dimensional Chern-Simons SL(N,R)\times SL(N,R) gauge fields and spin N black holes we compute the on-shell action and show that it generates sensible and consistent thermodynamics. In particular, the Chern-Simons action solves the integrability conditions recently considered in the literature.Comment: Paper shortened and generalized. Main results unchanged. 25 pages, Latex, no figure

In vivo measurement of surface pressures and retraction distances applied on abdominal organs during surgery

This study undertook the in vivo measurement of surface pressures applied by the fingers of the surgeon during typical representative retraction movements of key human abdominal organs during both open and hand-assisted laparoscopic surgery. Surface pressures were measured using a flexible thin-film pressure sensor for 35 typical liver retractions to access the gall bladder, 36 bowel retractions, 9 kidney retractions, 8 stomach retractions, and 5 spleen retractions across 12 patients undergoing open and laparoscopic abdominal surgery. The maximum and root mean square surface pressures were calculated for each organ retraction. The maximum surface pressures applied to these key abdominal organs are in the range 1 to 41 kPa, and the average maximum surface pressure for all organs and procedures was 14 ± 3 kPa. Surface pressure relaxation during the retraction hold period was observed. Generally, the surface pressures are higher, and the rate of surface pressure relaxation is lower, in the more confined hand-assisted laparoscopic procedures than in open surgery. Combined video footage and pressure sensor data for retraction of the liver in open surgery enabled correlation of organ retraction distance with surface pressure application. The data provide a platform to design strategies for the prevention of retraction injuries. They also form a basis for the design of next-generation organ retraction and space creation surgical devices with embedded sensors that can further quantify intraoperative retraction forces to reduce injury or trauma to organs and surrounding tissues