Evaluation of diversity, specialization, and gene specificity in transcriptomes

The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. Recently we proposed an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. This approach can be useful for the determination and measure of transcriptional networks. We defined transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either housekeeping or highly specific genes and clarifying the meaning of these concepts in the literature. Tissue specialization is measured by average gene specificity. Visualization of the positions of transcriptomes in a system of diversity and specialization coordinates makes it possible to understand at a glance their interrelations, summarizing in a powerful way which transcriptomes are richer in diversity of expressed genes, or which are relatively more specialized. This enlightens the relation among transcriptomes, allowing a better understanding of their changes through the development of the organism or in response to environmental stimuli. We present statistical tools based on resampling procedures to obtain confidence intervals for the parameters as well as perform statistical test. These approaches are illustrated with a human dataset

What majority decisions are possible

Suppose we are given a family of choice functions on pairs from a given finite set (with at least three elements) closed under permutations of the given set. The set is considered the set of alternatives (say candidates for an office). The question is, what are the choice functions c on pairs of this set of the following form: for some (finite) family of ``voters'', each having a preference, i.e., a choice from each pair from the given family, c{x,y} is chosen by the preference of the majority of voters. We give full characterization

VAMDC as a Resource for Atomic and Molecular Data and the New Release of VALD

The Virtual Atomic and Molecular Data Centre (VAMDC) (M.L. Dubernet et al. 2010, JQSRT 111, 2151) is an EU-FP7 e-infrastructure project devoted to building a common electronic infrastructure for the exchange and distribution of atomic and molecular data. It involves two dozen teams from six EU member states (Austria, France, Germany, Italy, Sweden, United Kingdom) as well as Russia, Serbia, and Venezuela. Within VAMDC scientists from many different disciplines in atomic and molecular physics collaborate with users of their data and also with scientists and engineers from the information and communication technology community. In this presentation an overview of the current status of VAMDC and its capabilities will be provided. In the second part of the presentation I will focus on one of the databases which have become part of the VAMDC platform, the Vienna Atomic Line Data Base (VALD). VALD has developed into a well-known resource of atomic data for spectroscopy particularly in astrophysics. A new release, VALD-3, will provide numerous improvements over its predecessor. This particularly relates to the data contents where new sets of atomic data for both precision spectroscopy (i.e., with data for observed energy levels) as well as opacity calculations (i.e., with data involving predicted energy levels) have been included. Data for selected diatomic molecules have been added and a new system for data distribution and data referencing provides for more convenience in using the upcoming third release of VALD.Comment: 8 pages, 1 tabl

The Belgian repository of fundamental atomic data and stellar spectra (BRASS). I. Cross-matching atomic databases of astrophysical interest

Fundamental atomic parameters, such as oscillator strengths, play a key role in modelling and understanding the chemical composition of stars in the universe. Despite the significant work underway to produce these parameters for many astrophysically important ions, uncertainties in these parameters remain large and can propagate throughout the entire field of astronomy. The Belgian repository of fundamental atomic data and stellar spectra (BRASS) aims to provide the largest systematic and homogeneous quality assessment of atomic data to date in terms of wavelength, atomic and stellar parameter coverage. To prepare for it, we first compiled multiple literature occurrences of many individual atomic transitions, from several atomic databases of astrophysical interest, and assessed their agreement. Several atomic repositories were searched and their data retrieved and formatted in a consistent manner. Data entries from all repositories were cross-matched against our initial BRASS atomic line list to find multiple occurrences of the same transition. Where possible we used a non-parametric cross-match depending only on electronic configurations and total angular momentum values. We also checked for duplicate entries of the same physical transition, within each retrieved repository, using the non-parametric cross-match. We report the cross-matched transitions for each repository and compare their fundamental atomic parameters. We find differences in log(gf) values of up to 2 dex or more. We also find and report that ~2% of our line list and Vienna Atomic Line Database retrievals are composed of duplicate transitions. Finally we provide a number of examples of atomic spectral lines with different log(gf) values, and discuss the impact of these uncertain log(gf) values on quantitative spectroscopy. All cross-matched atomic data and duplicate transitions are available to download at brass.sdf.org.Comment: 18 pages, 12 figures, 9 tables. Accepted for publication in A&