Phylogenomic analyses data of the avian phylogenomics project.

BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. FINDINGS: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

Modeling the Effects of Habitat Fragmentation on the Movements of the Mongolian Gazelle in the Eastern Mongolian Steppe

The Mongolian gazelle, Procapra gutturosa, resides in the immense and dynamic ecosystem of the Eastern Mongolian Steppe. The Mongolian Steppe ecosystem dynamics, including vegetation availability, change rapidly and dramatically due to unpredictable precipitation patterns. The Mongolian gazelle has adapted to this unpredictable vegetation availability by making long range nomadic movements. However, predicting these movements is challenging and requires a complex model. An accurate model of gazelle movements is needed, as rampant habitat fragmentation due to human development projects - which inhibit gazelles from obtaining essential resources - increasingly threaten this nomadic species. We created a novel model using an Individual-based Neural Network Genetic Algorithm (ING) to predict how habitat fragmentation affects animal movement, using the Mongolian Steppe as a model ecosystem. We used Global Positioning System (GPS) collar data from real gazelles to “train” our model to emulate characteristic patterns of Mongolian gazelle movement behavior. These patterns are: preferred vegetation resources (NDVI), displacement over certain time lags, and proximity to human areas. With this trained model, we then explored how potential scenarios of habitat fragmentation may affect gazelle movement. This model can be used to predict how fragmentation of the Mongolian Steppe may affect the Mongolian gazelle. In addition, this model is novel in that it can be applied to other ecological scenarios, since we designed it in modules that are easily interchanged.

"L'Invitation au voyage" de Baudelaire :une analyse évocative

This paper presents a detailed analysis of Baudelaire's poem ''L'Invitation au voyage''. It aims to understand the general meaning of this poem, showing that Baudelaire's ''voyage'' comes less to an ideal paradise than to a kind of voluptuous purgatory. We associate together dimensions of the poem that are usually treated separately :biographical background, stylistic and intertextual borrowings (orientalized Holland, Goethe's Mignon, popular song and romance, Weber's music, Biblical episodes), formal structure and cognitive effects. Our method is based on Benoît de Cornulier's theory of metrics, Searle and Vanderveken's speech act theory and Marc Dominicy's theory of poetic evocation. As Dominicy's theory is quite recent, our article provides substantial summary and clarification of its main theoretical and methodological hypothesis.

Gene therapy for glioblastoma [correction of gliobestome] multiform: in vivo tumor transduction with the herpes simplex thymidine kinase gene followed by ganciclovir.

Clinical Trial

A phase 1-2 clinical trial of gene therapy for recurrent glioblastoma multiforme by tumor transduction with the herpes simplex thymidine kinase gene followed by ganciclovir.

This study has investigated the effects of herpes simplex thymidine kinase gene (HSV-tk) transfer followed by ganciclovir treatment as adjuvant gene therapy to surgical resection in patients with recurrent glioblastoma multiforme (GBM). The study was open and single-arm, and aimed at assessing the feasibility and safety of the technique and indications of antitumor activity. In 48 patients a suspension of retroviral vector-producing cells (VPCs) was administered by intracerebral injection immediately after tumor resection. Intravenous ganciclovir was infused daily 14 to 27 days after surgery. Patients were monitored for adverse events and for life by regular biosafety assaying. Tumor changes were monitored by magnetic resonance imaging (MRI). Reflux during injection was a frequent occurrence but serious adverse events during the treatment period (days 1-27) were few and of a nature not unexpected in this population. One patient experienced transient neurological disorders associated with postganciclovir MRI enhancement. There was no evidence of replication-competent retrovirus in peripheral blood leukocytes or in tissue samples of reresection or autopsy. Vector DNA was shown in the leukocytes of some patients but not in autopsy gonadal samples. The median survival time was 8.6 months, and the 12-month survival rate was 13 of 48 (27%). On MRI studies, tumor recurrence was absent in seven patients for at least 6 months and for at least 12 months in two patients, one of whom remains recurrence free at more than 24 months. Treatment-characteristic images of injection tracks and intracavity hemoglobin were apparent. In conclusion, the gene therapy is feasible and appears to be satisfactorily safe as an adjuvant to the surgical resection of recurrent GBM, but any benefit appears to be marginal. Investigation of the precise effectiveness of this gene therapy requires prospective, controlled studies.

Measurements and simulations of noise imposed on supercontinuum generated in microstructure fiber

We present experimental and theoretical investigations of the highly nonlinear and broadband noise that exists on supercontinuum spectra generated from launching femtosecond Ti:Sapphire pulses into microstructure fiber.

Erratum: Fundamental amplitude noise limitations to supercontinuum spectra generated in a microstructured fiber (Appl. Phys. B (2003) 77 (269-277))

SCOPUS: er.j

Fundamental Noise Limitations to Supercontinuum Generation in Microstructure Fiber

Broadband noise on supercontinuum spectra generated in microstructure fiber is shown to lead to amplitude fluctuations as large as 50% for certain input laser pulse parameters. We study this noise using both experimental measurements and numerical simulations with a generalized stochastic nonlinear Schrödinger equation, finding good quantitative agreement over a range of input-pulse energies and chirp values. This noise is shown to arise from nonlinear amplification of two quantum noise inputs: the input-pulse shot noise and the spontaneous Raman scattering down the fiber.

A blackboard architecture for a hybrid CBR system for scientific software

This paper describes the use of a blackboard architecture for building a hybrid case based reasoning (CBR) system. The Smartfire fire field modelling package has been built using this architecture and includes a CBR component. It allows the integration into the system of qualitative spatial reasoning knowledge from domain experts. The system can be used for the automatic set-up of fire field models. This enables fire safety practitioners who are not expert in modelling techniques to use a fire modelling tool. The paper discusses the integrating powers of the architecture, which is based on a common knowledge representation comprising a metric diagram and place vocabulary and mechanisms for adaptation and conflict resolution built on the Blackboard.

Validations of high-rank syntaxa in Potamogetonetea and Scheuchzerio-Caricetea fuscae

This paper presents the validation of five syntaxonomic concepts –two orders (Callitricho hamulatae-Ranunculetalia aquatilis, Zannichellietalia pedicellatae) and three alliances (Ranunculion aquatilis, Nelumbion nuciferae and Caricion viridulo-trinervis).

Descriptions and validation of the names of some high-rank syntaxa in the European Asplenietea trichomanis and Polypodietea

The paper presents the description of one new order (Asplenietalia septentrionalo-cuneifolii) and two new alliances (Arenarion bertolonii and Physoplexido comosae- Saxifragion petraeae). In addition, the syntaxon Asplenietalia lanceolato-obovati is here formally raised to the order level and the name Hypno-Polypodietalia vulgaris is validated.

Nomenclature and syntaxonomic notes on some high-rank syntaxa of the European grassland vegetation

We present descriptions of a new order (Ranunculo cortusifolii-Geranietalia reuteri and of a new alliance (Stachyo lusitanicae-Cheirolophion sempervirentis) for the herbaceous fringe communities of Macaronesia and of the southwestern Iberian Peninsula, respectively. A new alliance, the Polygalo mediterraneae-Bromion erecti (mesophilous post-cultural grasslands), was introduced for the Peninsular Italy. We further validate and typify the Armerietalia rumelicae (perennial grasslands supported by nutrient-poor on siliceous bedrocks at altitudes characterized by the submediterranean climate of central-southern Balkan Peninsula), the Securigero-Dasypyrion villosae (lawn and fallow-land tall-grass annual vegetation of Italy), and the Cirsio vallis-demoni-Nardion (acidophilous grasslands on siliceous substrates of the Southern Italy). Nomenclatural issues (validity, legitimacy, synonymy, formal corrections) have been discussed and clarified for the following names: Brachypodio-Brometalia, Bromo pannonici-Festucion csikhegyensis, Corynephoro-Plantaginion radicatae, Heleochloion, Hieracio-Plantaginion radicatae, Nardetea strictae, Nardetalia strictae, Nardo-Callunetea, Nardo-Galion saxatilis, Oligo-Bromion, Paspalo-Heleochloetalia, Plantagini-Corynephorion and Scorzoneret alia villosae. 

Validations and descriptions of European syntaxa of vegetation dominated by lichens, bryophytes and algae

Fourty-two high-rank syntaxa and seven associations of the thallophyte system of syntaxa are either described as new or validated in this paper. Among those, there are the following nine classes: Aspicilietea candidae, Caulerpetea racemosae, Desmococcetea olivacei, Entophysalidetea deustae, Gloeocapsetea sanguineae, Mesotaenietea berggrenii, Naviculetea gregariae, Porpidietea zeoroidis, Roccelletea phycopsis. Eleven orders and ten alliances as well as three associations are described or validated: the Aspicilietalia verruculosae (incl. Aspicilion mashiginensis and Teloschistion contortuplicati), the Caulerpetalia racemosae (incl. Caulerpion racemosae), the Desmococcetalia olivacei (incl. Desmococcion olivacei), the Dirinetalia massiliensis, the Fucetalia vesiculosi (incl. Ascophyllion nodosi), the Gloeocapsetalia sanguineae, the Lecideetalia confluescentis (incl. Lecideion confluescentis), the Mesotaenietalia berggrenii (incl. Mesotaenion berggrenii, Mesotaenietum berggrenii and Chloromonadetum nivalis), the Naviculetalia gregariae (incl. Oscillatorion limosae and Oscillatorietum limosae), the Porpidietalia zeoroidis (incl. Porpidion zeoroidis), and the Roccelletalia fuciformis (incl. Paralecanographion grumulosae). Further, five orders, seven alliances and four associations, classified in known classes, were described as well. These include: the Bacidinetalia phacodis, the Agonimion octosporae and the Dendrographetalia decolorantis (all in the Arthonio radiatae-Lecidelletea elaeochromae), the Staurothelion solventis (in the Aspicilietea lacustris), the Pediastro duplicis-Scenedesmion quadricaudae and the Pediastro duplicis-Scenedesmetum quadricaudae (both in the Asterionelletea formosae), the Peccanion coralloidis and the Peltuletalia euplocae (both in the Collematetea cristati), the Laminarion hyperboreae, the Saccorhizo polyschidi-Laminarietum and the Alario esculenti-Himanthalietum elongatae (all in the Cystoseiretea crinitae), the Delesserietalia sanguinei, the Delesserion sanguinei and the Delesserietum sanguineae (all in the Lithophylletea soluti), as well as the the Rinodino confragosae-Rusavskietalia elegantis and the Rhizocarpo geographici-Rusavskion elegantis (both in the Rhizocarpetea geographici).