The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets

Use of Single Board Computers as Smart Sensors in the Manufacturing Industry

The continuously growing presence of cyber-physical systems in the industry, especially in the field of processes automation and control, represents the paradigm of the so called fourth industrial revolution, in which the systems are smarter, faster and more optimized by means of artificial intelligence, control systems and sensors networks. The presence of ICT and automation systems guarantees energy and other resources efficiency along the whole value chain of industrial processes. Especially important is the case of the smart sensors, in which a conventional sensor is equipped with interfacing methodologies for signal processing and decision making. In this article the capabilities of using a single board computer as a smart sensor are explored.Postprint (published version

Three qubit entanglement within graphical Z/X-calculus

The compositional techniques of categorical quantum mechanics are applied to analyse 3-qubit quantum entanglement. In particular the graphical calculus of complementary observables and corresponding phases due to Duncan and one of the authors is used to construct representative members of the two genuinely tripartite SLOCC classes of 3-qubit entangled states, GHZ and W. This nicely illustrates the respectively pairwise and global tripartite entanglement found in the W- and GHZ-class states. A new concept of supplementarity allows us to characterise inhabitants of the W class within the abstract diagrammatic calculus; these method extends to more general multipartite qubit states.Comment: In Proceedings HPC 2010, arXiv:1103.226

Depleted uranium is not toxic to rat brain endothelial (RBE4) cells

Abstract: Studies on Gulf War veterans with depleted uranium (DU) fragments embedded in their soft tissues have led to suggestions of possible DU-induced neurotoxicity. We investigated DU uptake into cultured rat brain endothelial cells (RBE4). Following the determination that DU readily enters RBE4 cells, cytotoxic effects were analyzed using assays for cell volume increase, heat shock protein 90 (Hsp90) expression, 3-[4,5-dimethylthiazol-2-yl]-2, 5-diphenyltetrazolium bromide (MTT) reduction, and lactate dehydrogenase (LDH) activity. The results of these studies show that uptake of the U 3 O 8 uranyl chloride form of DU into RBE4 cells is efficient, but there are little or no resulting cytotoxic effects on these cells as detected by common biomarkers. Thus, the present experimental paradigm is rather reassuring and provides no indication for overt cytotoxicity in endothelial cells exposed to DU. Index Entries: Depleted uranium (DU); heavey metal toxicity; blood-brain barrier; endothelium. Article: INTRODUCTION Depleted uranium (DU) is a component of military munitions and is therefore the subject of important toxicity studies. Specifically, the possibility of DU neurotoxicity is under investigation. DU is a dense heavy metal used without reserve in many military applications. Chemically similar to natural uranium, but depleted of much of the radioactivity of the 235 U and 234 U isotopes, DU is a low-specific-activity metal that has several advantages for use as weapons material. Neurotoxicity could potentially arise from the chemical or radioactive properties of DU, and the level of neurotoxicity is as yet undetermined (1-3). Gulf War veterans with DU fragments embedded in their soft tissues were studied and the results suggested that there might be DU-associated effects on behavior and cognition (1-4). Rats embedded with DU fragments accumulated uranium in a range of tissues, with early levels highest in the kidney and a gradual increase in bone accumulation. Brain tissues were found to have far lower levels, with the hippocampus showing high levels among the brain regions following physiologically relevant exposures and cerebellum accumulating the highest levels upon extremely high exposure levels For a blood-borne contaminant to cause neurotoxicity, it must first cross the blood-brain barrier (BBB). This barrier protects the central nervous system (CNS) from toxicants in the blood, and its ability to protect against metal neurotoxicity was reviewed by Zheng et al. (7). The capillaries of the brain are lined with endothelial cells acting as the first line of defense in the BBB. The high degree of tightness of the junctions that link the endothelial cells virtually prevents any paracellular passage from occurring in physiological conditions. In addition, several transport proteins can increase the brain-to-blood efflux of various compounds (e.g., Pglycoproteins or multidrug resistance proteins [MDR] of the ATP-binding cassette [ABC]) (7). The molecula

Can sexual selection drive female life histories? A comparative study on Galliform birds

Sexual selection is an important driver of many of the most spectacular morphological traits that we find in the animal kingdom (for example see Andersson, 1994). As such, sexual selection is most often emphasized as

The GHZ/W-calculus contains rational arithmetic

Graphical calculi for representing interacting quantum systems serve a number of purposes: compositionally, intuitive graphical reasoning, and a logical underpinning for automation. The power of these calculi stems from the fact that they embody generalized symmetries of the structure of quantum operations, which, for example, stretch well beyond the Choi-Jamiolkowski isomorphism. One such calculus takes the GHZ and W states as its basic generators. Here we show that this language allows one to encode standard rational calculus, with the GHZ state as multiplication, the W state as addition, the Pauli X gate as multiplicative inversion, and the Pauli Z gate as additive inversion.Comment: In Proceedings HPC 2010, arXiv:1103.226

Disentangling the effects of environmental conditions on wintering and breeding grounds on age-specific survival rates in a trans-Saharan migratory raptor

International audienceMigratory species are subject to environmental variability occurring on breeding and wintering grounds. Estimating the relative contribution of environmental factors experienced sequentially during breeding and wintering, and their potential interaction, to the variation of survival is crucial to predict population viability of migratory species. Here we investigated this issue for the Montagu's harrier Circus pygargus, a trans‐Saharan migrant. We analysed capture‐recapture data from a 29‐yr long monitoring of wing‐tagged offspring and adults at two study sites in France (Rochefort‐RO & Maine‐et‐Loire‐ML). The study period covers a climatic shift occurring in the Sahel with increasing rainfall following a period of droughts (Sahel greening). We found that harriers’ adult survival in RO (between 1988 and 2005) varied over time and was sensitive to the interaction between the amount of rainfall in the Sahel and the annual mean breeding success, two proxies of prey availability. The occurrence of adverse conditions on breeding and wintering grounds in the same year decreased survival from 0.70‐0.77 to 0.48 ± 0.05. Juvenile survival in RO was slightly more sensitive to conditions in Europe than in the Sahel. Unexpectedly, lower survival rates were found in years with higher mean breeding success, suggesting compensatory density feedbacks may operate. By contrast, adult survival in ML, monitored between 1999 and 2017, was higher compared to RO (0.76 ± 0.03 vs. 0.66 ± 0.02), remained constant and unaffected by any proxy of prey availability. This difference seems consistent with the fact that harriers in ML experienced better and especially less variable environmental conditions during breeding and wintering seasons compared to RO. Overall, we showed that survival of a migratory bird is sensitive to the level of variability in environmental conditions and that adverse conditions on wintering grounds can amplify the negative effects of conditions during the previous breeding season on birds’ survival

The Serre spectral sequence of a noncommutative fibration for de Rham cohomology

For differential calculi on noncommutative algebras, we construct a twisted de Rham cohomology using flat connections on modules. This has properties similar, in some respects, to sheaf cohomology on topological spaces. We also discuss generalised mapping properties of these theories, and relations of these properties to corings. Using this, we give conditions for the Serre spectral sequence to hold for a noncommutative fibration. This might be better read as giving the definition of a fibration in noncommutative differential geometry. We also study the multiplicative structure of such spectral sequences. Finally we show that some noncommutative homogeneous spaces satisfy the conditions to be such a fibration, and in the process clarify the differential structure on these homogeneous spaces. We also give two explicit examples of differential fibrations: these are built on the quantum Hopf fibration with two different differential structures.Comment: LaTeX, 33 page

Picturing classical and quantum Bayesian inference

We introduce a graphical framework for Bayesian inference that is sufficiently general to accommodate not just the standard case but also recent proposals for a theory of quantum Bayesian inference wherein one considers density operators rather than probability distributions as representative of degrees of belief. The diagrammatic framework is stated in the graphical language of symmetric monoidal categories and of compact structures and Frobenius structures therein, in which Bayesian inversion boils down to transposition with respect to an appropriate compact structure. We characterize classical Bayesian inference in terms of a graphical property and demonstrate that our approach eliminates some purely conventional elements that appear in common representations thereof, such as whether degrees of belief are represented by probabilities or entropic quantities. We also introduce a quantum-like calculus wherein the Frobenius structure is noncommutative and show that it can accommodate Leifer's calculus of `conditional density operators'. The notion of conditional independence is also generalized to our graphical setting and we make some preliminary connections to the theory of Bayesian networks. Finally, we demonstrate how to construct a graphical Bayesian calculus within any dagger compact category.Comment: 38 pages, lots of picture

Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics