Showing papers by "Aix-Marseille University published in 2013"

Astropy: A community Python package for astronomy

Abstract: We present the first public version (v02) of the open-source and community-developed Python package, Astropy This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions Significant functionality is under activedevelopment, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

Abstract: How much does the microbiota influence the host's phenotype? Ridaura et al. ([1241214][1] ; see the Perspective by [ Walker and Parkhill ][2]) obtained uncultured fecal microbiota from twin pairs discordant for body mass and transplanted them into adult germ-free mice. It was discovered that adiposity is transmissible from human to mouse and that it was associated with changes in serum levels of branched-chain amino acids. Moreover, obese-phenotype mice were invaded by members of the Bacteroidales from the lean mice, but, happily, the lean animals resisted invasion by the obese microbiota. [1]: http://www.sciencemag.org/content/341/6150/1241214.full [2]: /lookup/doi/10.1126/science.1243787

Astropy: A Community Python Package for Astronomy

Abstract: We present the first public version (v0.2) of the open-source and community-developed Python package, Astropy. This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as Flexible Image Transport System (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions. Significant functionality is under active development, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools. The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions.

The baryon oscillation spectroscopic survey of sdss-iii

Abstract: The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large-scale structure. BOSS uses 1.5 million luminous galaxies as faint as i = 19.9 over 10,000 deg2 to measure BAO to redshifts z < 0.7. Observations of neutral hydrogen in the Lyα forest in more than 150,000 quasar spectra (g < 22) will constrain BAO over the redshift range 2.15 < z < 3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyα forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance dA to an accuracy of 1.0% at redshifts z = 0.3 and z = 0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyα forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate DA (z) and H –1(z) parameters to an accuracy of 1.9% at z ~ 2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.

Thermo‐plasmonics: using metallic nanostructures as nano‐sources of heat

Abstract: Recent years have seen a growing interest in using metal nanostructures to control temperature on the nanoscale. Under illumination at its plasmonic resonance, a metal nanoparticle features enhanced light absorption, turning it into an ideal nano-source of heat, remotely controllable using light. Such a powerful and flexible photothermal scheme is the basis of thermo-plasmonics. Here, the recent progress of this emerging and fast-growing field is reviewed. First, the physics of heat generation in metal nanoparticles is described, under both continuous and pulsed illumination. The second part is dedicated to numerical and experimental methods that have been developed to further understand and engineer plasmonic-assisted heating processes on the nanoscale. Finally, some of the most recent applications based on the heat generated by gold nanoparticles are surveyed, namely photothermal cancer therapy, nano-surgery, drug delivery, photothermal imaging, protein tracking, photoacoustic imaging, nano-chemistry and optofluidics.

Update on Tick-Borne Rickettsioses around the World: a Geographic Approach

Abstract: Tick-borne rickettsioses are caused by obligate intracellular bacteria belonging to the spotted fever group of the genus Rickettsia. These zoonoses are among the oldest known vector-borne diseases. However, in the past 25 years, the scope and importance of the recognized tick-associated rickettsial pathogens have increased dramatically, making this complex of diseases an ideal paradigm for the understanding of emerging and reemerging infections. Several species of tick-borne rickettsiae that were considered nonpathogenic for decades are now associated with human infections, and novel Rickettsia species of undetermined pathogenicity continue to be detected in or isolated from ticks around the world. This remarkable expansion of information has been driven largely by the use of molecular techniques that have facilitated the identification of novel and previously recognized rickettsiae in ticks. New approaches, such as swabbing of eschars to obtain material to be tested by PCR, have emerged in recent years and have played a role in describing emerging tick-borne rickettsioses. Here, we present the current knowledge on tick-borne rickettsiae and rickettsioses using a geographic approach toward the epidemiology of these diseases.

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Abstract: Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org ) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name “Auxiliary Activities” in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.

Radiographical spinopelvic parameters and disability in the setting of adult spinal deformity: a prospective multicenter analysis.

Abstract: Study design Prospective multicenter study evaluating operative (OP) versus nonoperative (NONOP) treatment for adult spinal deformity (ASD). Objective Evaluate correlations between spinopelvic parameters and health-related quality of life (HRQOL) scores in patients with ASD. Summary of background data Sagittal spinal deformity is commonly defined by an increased sagittal vertical axis (SVA); however, SVA alone may underestimate the severity of the deformity. Spinopelvic parameters provide a more complete assessment of the sagittal plane but only limited data are available that correlate spinopelvic parameters with disability. METHODS.: Baseline demographic, radiographical, and HRQOL data were obtained for all patients enrolled in a multicenter consecutive database. Inclusion criteria were: age more than 18 years and radiographical diagnosis of ASD. Radiographical evaluation was conducted on the frontal and lateral planes and HRQOL questionnaires (Oswestry Disability Index [ODI], Scoliosis Research Society-22r and Short Form [SF]-12) were completed. Radiographical parameters demonstrating highest correlation with HRQOL values were evaluated to determine thresholds predictive of ODI more than 40. Results Four hundred ninety-two consecutive patients with ASD (mean age, 51.9 yr) were enrolled. Patients from the OP group (n = 178) were older (55 vs. 50.1 yr, P Conclusion ASD is a disabling condition. Prospective analysis of consecutively enrolled patients with ASD demonstrated that PT and PI-LL combined with SVA can predict patient disability and provide a guide for patient assessment for appropriate therapeutic decision making. Threshold values for severe disability (ODI > 40) included: PT 22° or more, SVA 47 mm or more, and PI - LL 11° or more.

In vivo recordings of brain activity using organic transistors

Abstract: In vivo electrophysiological recordings of neuronal circuits are necessary for diagnostic purposes and for brain-machine interfaces. Organic electronic devices constitute a promising candidate because of their mechanical flexibility and biocompatibility. Here we demonstrate the engineering of an organic electrochemical transistor embedded in an ultrathin organic film designed to record electrophysiological signals on the surface of the brain. The device, tested in vivo on epileptiform discharges, displayed superior signal-to-noise ratio due to local amplification compared with surface electrodes. The organic transistor was able to record on the surface low-amplitude brain activities, which were poorly resolved with surface electrodes. This study introduces a new class of biocompatible, highly flexible devices for recording brain activity with superior signal-to-noise ratio that hold great promise for medical applications.

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Abstract: The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for “green” biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

Interleukin-18 and IL-18 binding protein.

Abstract: Interleukin-18 (IL-18) is a member of the IL-1 family of cytokines. Similar to IL-1β, IL-18 is synthesized as an inactive precursor requiring processing by caspase-1 into an active cytokine but unlike IL-1β, the IL-18 precursor is constitutively present in nearly all cells in healthy humans and animals. The activity of IL-18 is balanced by the presence of a high affinity, naturally occurring IL-18 binding protein (IL-18BP). In humans, increased disease severity can be associated with an imbalance of IL-18 to IL-18BP such that the levels of free IL-18 are elevated in the circulation. Increasing number of studies have expanded the role of IL-18 in mediating inflammation in animal models of disease using the IL-18BP, IL-18-deficient mice, neutralization of IL-18, or deficiency in the IL-18 receptor alpha chain. A role for IL-18 has been implicated in several autoimmune diseases, myocardial function, emphysema, metabolic syndromes, psoriasis, inflammatory bowel disease, hemophagocytic syndromes, macrophage activation syndrome, sepsis, and acute kidney injury, although in some models of disease, IL-18 is protective. IL-18 plays a major role in the production of interferon-γ from T-cells and natural killer cells. The IL-18BP has been used safely in humans and clinical trials of IL-18BP as well as neutralizing anti-IL-18 antibodies are in clinical trials. This review updates the biology of IL-18 as well as its role in human disease.

Rare species support vulnerable functions in high-diversity ecosystems

Abstract: Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning.

Measurement of form-factor-independent observables in the decay B0→K*0μ+μ-

Abstract: We present a measurement of form-factor-independent angular observables in the decay B-0 -> K*(892)(0)mu(+)mu(-). The analysis is based on a data sample corresponding to an integrated luminosity of 1.0 fb(-1), collected by the LHCb experiment in pp collisions at a center-of-mass energy of 7 TeV. Four observables are measured in six bins of the dimuon invariant mass squared q(2) in the range 0.1 < q(2) < 19.0 GeV2/c(4). Agreement with recent theoretical predictions of the standard model is found for 23 of the 24 measurements. A local discrepancy, corresponding to 3.7 Gaussian standard deviations is observed in one q(2) bin for one of the observables. Considering the 24 measurements as independent, the probability to observe such a discrepancy, or larger, in one is 0.5%.

A dust-obscured massive maximum-starburst galaxy at a redshift of 6.34

Abstract: Massive present-day early-type (elliptical and lenticular) galaxies probably gained the bulk of their stellar mass and heavy elements through intense, dust-enshrouded starbursts--that is, increased rates of star formation--in the most massive dark-matter haloes at early epochs. However, it remains unknown how soon after the Big Bang massive starburst progenitors exist. The measured redshift (z) distribution of dusty, massive starbursts has long been suspected to be biased low in z owing to selection effects, as confirmed by recent findings of systems with redshifts as high as ~5 (refs 2-4). Here we report the identification of a massive starburst galaxy at z = 6.34 through a submillimetre colour-selection technique. We unambiguously determined the redshift from a suite of molecular and atomic fine-structure cooling lines. These measurements reveal a hundred billion solar masses of highly excited, chemically evolved interstellar medium in this galaxy, which constitutes at least 40 per cent of the baryonic mass. A `maximum starburst' converts the gas into stars at a rate more than 2,000 times that of the Milky Way, a rate among the highest observed at any epoch. Despite the overall downturn in cosmic star formation towards the highest redshifts, it seems that environments mature enough to form the most massive, intense starbursts existed at least as early as 880 million years after the Big Bang.

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

Abstract: The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

One hundred years of helicene chemistry. Part 3: applications and properties of carbohelicenes

Abstract: Carbohelicenes are a class of fascinating chiral helical molecules which have a rich history in chemistry. Over a period of almost 100 years, chemists have developed many methods to prepare them in a racemic or in a non-racemic form. They also possess a series of interesting chiral, physical, electronic and optical properties. However, their utilization in chemistry or chemistry-related fields has rarely appeared in a detailed and comprehensive review. It is the purpose of this review to collect fundamental applications and functions involving carbohelicenes in various disciplines such as in materials science, in nanoscience, in biological chemistry and in supramolecular chemistry. From the numerous synthetic methodologies reported up to now, carbohelicenes and their derivatives can be tailor-made for a better involvement in several subfields. Among those domains are: nanosciences, chemosensing, liquid crystals, molecular switches, polymers, foldamers, supramolecular materials, molecular recognition, conductive and opto-electronic materials, nonlinear optics, chirality studies and asymmetric synthesis. Helicene chemistry is now at a developmental stage, where sufficient application data are now collected and are extremely useful. They provide many more ideas for setting up the basis for future innovative applications.

PRIMUS: Constraints on Star Formation Quenching and Galaxy Merging, and the Evolution of the Stellar Mass Function from z = 0-1

Abstract: We measure the evolution of the stellar mass function (SMF) from z = 0−1 using multi-wavelength imaging and spectroscopic redshifts from the PRism MUlti-object Survey (PRIMUS) and the Sloan Digital Sky Survey (SDSS). From PRIMUS we construct an i < 23 flux-limited sample of ∼ 40,000 galaxies at z = 0.2 − 1.0 over five fields totaling ≈ 5.5 deg 2 , and from the SDSS we select ∼ 170,000 galaxies atz = 0.01−0.2 that we analyze consistently with respect to PRIMUS to minimize systematic errors in our evolutionary measurements. We find that the SMF of all galaxies evolves relatively little since z = 1, although we do find evidence for mass assembly downsizing; we measure a ≈ 30% increase in the number density of ∼ 10 10 M⊙ galaxies sincez ≈ 0.6, and a . 10% change in the number density of all & 10 11 M⊙ galaxies since z ≈ 1. Dividing the sample into star-forming and quiescent using an evolving cut in specific star-formation rate, we find that the number density of ∼ 10 10 M⊙ star-forming galaxies stays relatively constant since z ≈ 0.6, whereas the space-density of & 10 11 M⊙ star-forming galaxies decreases by ≈ 50% between z ≈ 1 and z ≈ 0. Meanwhile, the number density of ∼ 10 10 M⊙ quiescent galaxies increases steeply towards low redshift, by a factor of ∼ 2 − 3 since z ≈ 0.6, while the number of massive quiescent galaxies remains approximately constant since z ≈ 1. These results suggest that the rate at which star-forming galaxies are quenched increases with decreasing stellar mass, but that the bulk of the stellar mass buildup within the quiescent population occurs around ∼ 10 10.8 M⊙. In addition, we conclude that mergers do not appear to be a dominant channel for the stellar mass buildup of galaxies at z < 1, even among massive (& 10 11 M⊙) quiescent galaxies. Subject headings: Surveys – galaxies: evolution – galaxies: high-redshift – cosmology: large-scale structure of universe

Ten years of landscape genetics

Abstract: Landscape genetics is now ten years old. It has stimulated research into the effect of landscapes on evolutionary processes. This review describes the main topics that have contributed most significantly to the progress of landscape genetics, such as conceptual and methodological developments in spatial and temporal patterns of gene flow, seascape genetics, and landscape genomics. We then suggest perspectives for the future, investigating what the field will contribute to the assessment of global change and conservation in general and to the management of tropical and urban areas in particular. To address these urgent topics, future work in landscape genetics should focus on a better integration of neutral and adaptive genetic variation and their interplay with species distribution and the environment.

Mechanics of epithelial tissue homeostasis and morphogenesis.

Abstract: Epithelia are robust tissues that support the structure of embryos and organs and serve as effective barriers against pathogens. Epithelia also chemically separate different physiological environments. These vital functions require tight association between cells through the assembly of junctions that mechanically stabilize the tissue. Remarkably, epithelia are also dynamic and can display a fluid behavior. Cells continuously die or divide, thereby allowing functional tissue homeostasis. Epithelial cells can change shape or intercalate as tissues deform during morphogenesis. We review the mechanical basis of tissue robustness and fluidity, with an emphasis on the pivotal role of junction dynamics. Tissue fluidity emerges from local active stresses acting at cell interfaces and allows the maintenance of epithelial organization during morphogenesis and tissue renewal.

Cervical spine alignment, sagittal deformity, and clinical implications: A review

Abstract: This paper is a narrative review of normal cervical alignment, methods for quantifying alignment, and how alignment is associated with cervical deformity, myelopathy, and adjacent-segment disease (ASD), with discussions of health-related quality of life (HRQOL). Popular methods currently used to quantify cervical alignment are discussed including cervical lordosis, sagittal vertical axis, and horizontal gaze with the chin-brow to vertical angle. Cervical deformity is examined in detail as deformities localized to the cervical spine affect, and are affected by, other parameters of the spine in preserving global sagittal alignment. An evolving trend is defining cervical sagittal alignment. Evidence from a few recent studies suggests correlations between radiographic parameters in the cervical spine and HRQOL. Analysis of the cervical regional alignment with respect to overall spinal pelvic alignment is critical. The article details mechanisms by which cervical kyphotic deformity potentially leads to ASD and discusses previous studies that suggest how postoperative sagittal malalignment may promote ASD. Further clinical studies are needed to explore the relationship of cervical malalignment and the development of ASD. Sagittal alignment of the cervical spine may play a substantial role in the development of cervical myelopathy as cervical deformity can lead to spinal cord compression and cord tension. Surgical correction of cervical myelopathy should always take into consideration cervical sagittal alignment, as decompression alone may not decrease cord tension induced by kyphosis. Awareness of the development of postlaminectomy kyphosis is critical as it relates to cervical myelopathy. The future direction of cervical deformity correction should include a comprehensive approach in assessing global cervicalpelvic relationships. Just as understanding pelvic incidence as it relates to lumbar lordosis was crucial in building our knowledge of thoracolumbar deformities, T-1 incidence and cervical sagittal balance can further our understanding of cervical deformities. Other important parameters that account for the cervical-pelvic relationship are surveyed in detail, and it is recognized that all such parameters need to be validated in studies that correlate HRQOL outcomes following cervical deformity correction.