Rapidity Dependence of Strange Particle Ratios in Nuclear Collisions

It was recently found that in sulphur-induced nuclear collisions at 200 A GeV the observed strange hadron abundances can be explained within a thermodynamic model where baryons and mesons separately are in a state of relative chemical equilibrium, with overall strangeness being slightly undersaturated, but distributed among the strange hadron channels according to relative chemical equilibrium with a vanishing strange quark chemical potential. We develop a consistent thermodynamic formulation of the concept of relative chemical equilibrium and show how to introduce into the partition function deviations from absolute chemical equilibrium, e.~g.~an undersaturation of overall strangeness or the breaking of chemical equilibrium between mesons and baryons. We then proceed to test on the available data the hypothesis that the strange quark chemical potential vanishes everywhere, and that the rapidity distributions of all the observed hadrons can be explained in terms of one common, rapidity-dependent function $\mu_{\rm q}(\eta)$ for the baryon chemical potential only. The aim of this study is to shed light on the observed strong rapidity dependence of the strange baryon ratios in the NA36 experiment.Comment: uses REVTeX, 14 pages, 17 ps-figures (uuencoded) added with figures comman

Status of Chemical Equilibrium in Relativistic Heavy Ion Collisions

Recent work on chemical equilibrium in heavy ion collisions is reviewed. The energy dependence of thermal parameters is discussed. The centrality dependence of thermal parameters at SPS energies is presented.Comment: 7 pages, 7 Postscript figure

Bose-Einstein Weights for Event Generators

A simple new algorithm for the calculation of two-particle Bose-Einstein correlations from classical event generators is derived and discussed.Comment: 4 pages, RevTeX, one ps-figur

Multi-boson effects in Bose-Einstein interferometry and the multiplicity distribution

Multi-boson symmetrization effects on two-particle Bose-Einstein interferometry are studied for ensembles with arbitrary multiplicity distributions. This generalizes the previously studied case of a Poissonian input multiplicity distribution. In the general case we find interesting residual correlations which require a modified framework for extracting information on the source geometry from two-particle correlation measurements. In sources with high phase-space densities, multi-boson effects modify the Hanbury Brown-Twiss (HBT) radius parameters and simultaneously generate strong residual correlations. We clarify their effect on the correlation strength (intercept parameter) and thus explain a variety of previously reported puzzling multi-boson symmetrization phenomena. Using a class of analytically solvable Gaussian source models, with and without space-momentum correlations, we present a comprehensive overview of multi-boson symmetrization effects on particle interferometry. For event ensembles of (approximately) fixed multiplicity, the residual correlations lead to a minimum in the correlation function at non-zero relative momentum, which can be practically exploited to search, in a model-independent way, for multi-boson symmetrization effects in high-energy heavy-ion experiments.Comment: 22 pages ReVTex, including 8 postscript figures. Submitted to Annals of Physics (N.Y.

System-size dependence

The final state in The final state in heavy-ion collisions has a higher degree of strangeness saturation than the one produced in collisions between elementary particles like p-p or p-$\bar{p}$. A systematic analysis of this phenomenon is made for C-C, Si-Si and Pb-Pb collisions at the CERN SPS collider and for $Au-Au$ collisions at RHIC and at AGS energies. Strangeness saturation is shown to increase smoothly with the number of participants at AGS, CERN and RHIC energies.Comment: 5 pages, 5 figures, presented at SQM2003 conferenc

Chemical equilibration of strangeness

Thermal models are very useful in the understanding of particle production in general and especially in the case of strangeness. We summarize the assumptions which go into a thermal model calculation and which differ in the application of various groups. We compare the different results to each other. Using our own calculation we discuss the validity of the thermal model and the amount of strangeness equilibration at CERN-SPS energies. Finally the implications of the thermal analysis on the reaction dynamics are discussed.Comment: 23 pages, LaTeX (figures included); Talk given at the Int. Symposium on Strangeness in Quark Matter 1997, Santorini (Greece), April 199

Histological assessment of paxgene tissue fixation and stabilization reagents

Within SPIDIA, an EC FP7 project aimed to improve pre analytic procedures, the PAXgene Tissue System (PAXgene), was designed to improve tissue quality for parallel molecular and morphological analysis. Within the SPIDIA project promising results were found in both genomic and proteomic experiments with PAXgene-fixed and paraffin embedded tissue derived biomolecules. But, for this technology to be accepted for use in both clinical and basic research, it is essential that its adequacy for preserving morphology and antigenicity is validated relative to formalin fixation. It is our aim to assess the suitability of PAXgene tissue fixation for (immuno)histological methods. Normal human tissue specimens (n = 70) were collected and divided into equal parts for fixation either with formalin or PAXgene. Sections of the obtained paraffin-embedded tissue were cut and stained. Morphological aspects of PAXgene-fixed tissue were described and also scored relative to formalin-fixed tissue. Performance of PAXgene-fixed tissue in immunohistochemical and in situ hybridization assays was also assessed relative to the corresponding formalin-fixed tissues. Morphology of PAXgene-fixed paraffin embedded tissue was well preserved and deemed adequate for diagnostics in most cases. Some antigens in PAXgene-fixed and paraffin embedded sections were detectable without the need for antigen retrieval, while others were detected using standard, formalin fixation based, immunohistochemistry protocols. Comparable results were obtained with in situ hybridization and histochemical stains. Basically all assessed histological techniques were found to be applicable to PAXgene-fixed and paraffin embedded tissue. In general results obtained with PAXgene-fixed tissue are comparable to those of formalin-fixed tissue. Compromises made in morphology can be called minor compared to the advantages in the molecular pathology possibilities

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment