LUCIAE 3.0: A new version of a computer program for Firecracker Model and rescattering in relativistic heavy-ion collisions

LUCIAE is a Monte Carlo program that, connected to FRITIOF, implements both the Firecracker Model (FCM), a possible mechanism for collective multi-gluon emission from the colour fields of interacting strings, and the reinteraction of the final state hadrons in relativistic heavy ion collisions. This paper includes a brief presentation of the dynamics of LUCIAE with an emphasis on the new features in this version, as well as a description of the program.Comment: LaTeX, no figur

The QGP phase in relativistic heavy-ion collisions

The dynamics of partons, hadrons and strings in relativistic nucleus-nucleus collisions is analyzed within the novel Parton-Hadron-String Dynamics (PHSD) transport approach, which is based on a dynamical quasiparticle model for partons (DQPM) matched to reproduce recent lattice-QCD results - including the partonic equation of state - in thermodynamic equilibrium. The transition from partonic to hadronic degrees of freedom is described by covariant transition rates for the fusion of quark-antiquark pairs or three quarks (antiquarks), respectively, obeying flavor current-conservation, color neutrality as well as energy-momentum conservation. The PHSD approach is applied to nucleus-nucleus collisions from low SIS to RHIC energies. The traces of partonic interactions are found in particular in the elliptic flow of hadrons as well as in their transverse mass spectra.Comment: To be published by Springer in Proceedings of the International Symposium on `Exciting Physics', Makutsi-Range, South Africa, 13-20 November, 201

Comparison of contact patterns relevant for transmission of respiratory pathogens in Thailand and the Netherlands using respondent-driven sampling

Understanding infection dynamics of respiratory diseases requires the identification and quantification of behavioural, social and environmental factors that permit the transmission of these infections between humans. Little empirical information is available about contact patterns within real-world social networks, let alone on differences in these contact networks between populations that differ considerably on a socio-cultural level. Here we compared contact network data that were collected in the Netherlands and Thailand using a similar online respondent-driven method. By asking participants to recruit contact persons we studied network links relevant for the transmission of respiratory infections. We studied correlations between recruiter and recruited contacts to investigate mixing patterns in the observed social network components. In both countries, mixing patterns were assortative by demographic variables and random by total numbers of contacts. However, in Thailand participants reported overall more contacts which resulted in higher effective contact rates. Our findings provide new insights on numbers of contacts and mixing patterns in two different populations. These data could be used to improve parameterisation of mathematical models used to design control strategies. Although the spread of infections through populations depends on more factors, found similarities suggest that spread may be similar in the Netherlands and Thailand

Quantifying the Detrimental Impacts of Land-Use and Management Change on European Forest Bird Populations

The ecological impacts of changing forest management practices in Europe are poorly understood despite European forests being highly managed. Furthermore, the effects of potential drivers of forest biodiversity decline are rarely considered in concert, thus limiting effective conservation or sustainable forest management. We present a trait-based framework that we use to assess the detrimental impact of multiple land-use and management changes in forests on bird populations across Europe. Major changes to forest habitats occurring in recent decades, and their impact on resource availability for birds were identified. Risk associated with these changes for 52 species of forest birds, defined as the proportion of each species' key resources detrimentally affected through changes in abundance and/or availability, was quantified and compared to their pan-European population growth rates between 1980 and 2009. Relationships between risk and population growth were found to be significantly negative, indicating that resource loss in European forests is an important driver of decline for both resident and migrant birds. Our results demonstrate that coarse quantification of resource use and ecological change can be valuable in understanding causes of biodiversity decline, and thus in informing conservation strategy and policy. Such an approach has good potential to be extended for predictive use in assessing the impact of possible future changes to forest management and to develop more precise indicators of forest health

Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens

© 2015 Brabec et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The attached file is the published version of the article

D-MaPs - DNA-microarray projects: Web-based software for multi-platform microarray analysis

The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix). Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus) submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner). In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core

arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies

Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing number of projects have mapped CNAs using high-resolution microarray based techniques. So far, no single resource does provide a global collection of readily accessible oncoge- nomic array data. Methodology/Principal Findings: We here present arrayMap, a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides a platform for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. To date, the resource incorporates more than 40,000 arrays in 224 cancer types extracted from several resources, including the NCBI's Gene Expression Omnibus (GEO), EBIs ArrayExpress (AE), The Cancer Genome Atlas (TCGA), publication supplements and direct submissions. For the majority of the included datasets, probe level and integrated visualization facilitate gene level and genome wide data re- view. Results from multi-case selections can be connected to downstream data analysis and visualization tools. Conclusions/Significance: To our knowledge, currently no data source provides an extensive collection of high resolution oncogenomic CNA data which readily could be used for genomic feature mining, across a representative range of cancer entities. arrayMap represents our effort for providing a long term platform for oncogenomic CNA data independent of specific platform considerations or specific project dependence. The online database can be accessed at http://www.arraymap.org.Comment: 17 pages, 5 inline figures, 3 tables, supplementary figures/tables split into 4 PDF files; manuscript submitted to PLoS ON

Time trends of chest pain symptoms and health related quality of life in coronary artery disease

BACKGROUND: There is at present a lack of knowledge of time trends in health related quality of life (HRQL) in common patients with coronary artery disease (CAD) treated in ordinary care. The objective of this study is to assess and compare time trends of health related quality of life (HRQL) and chest pain in patients with coronary artery disease. METHODS: 253 consecutive CAD patients in Stockholm County, Sweden – 197 males/56 females; 60 ± 8 years – were followed during two years. Perceived chest pain symptoms and three global assessments of HRQL were assessed at baseline, after one and after two years. EuroQol-5 dimension (EQ-5D) with a predefined focus on function and symptoms; the broader tapping global estimates of HRQL; EuroQol VAS (EQ-VAS) and Cardiac Health Profile (CHP) were used. Chest pain was ranked according to Canadian Cardiovascular Society (CCS). Change in HRQL was analysed by a repeated measurements ANOVA and chest pain symptoms were analysed by Friedman non-parametric ANOVA. RESULTS: Perceived chest pain decreased during the two years (p < 0.00022); CCS 0: 41–51%; CCS 1: 19–15%; CCS 2: 31–27%; CCS 3: 5–4% and CCS 4: 4–2%. By contrast, HRQL did not change: EQ-5D: 0.76 (CI 0.73–0.79) -0.78 (CI 0.75–0.81), EQ-VAS: 0.68 (CI 0.66–0.71)-0.68 (CI 0.65–0.71) and CHP: 0.66 (CI 0.64–0.69) -0.66 (CI 0.64–0.69). CONCLUSION: HRQL did not increase despite a reduction in the severity of chest pain during two years. This implies that the major part of HRQL in these consecutive ordinary patients with CAD is unresponsive to change in chest pain symptoms