GreenPhylDB: A Gene Family Database for plant functional Genomics

With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in functional genomics. The release of various annotated genomes of plants, such as _O. sativa_ and _A. thaliana_, has allowed setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally processed by phylogenetic analysis to infer orthologs and paralogs that will be particularly helpful to study genome evolution. Previously, each cluster has to be curated (i.e. properly named and classified) using different sources of information. A web interface for plant gene families’ curation was developed for that purpose. This interface, accessible on GreenPhylDB ("http://greenphyl.cirad.fr":http://greenphyl.cirad.fr), centralizes external references (e.g. InterPro, KEGG, Swiss-Prot, PIRSF, Pubmed) related to all gene members of the clusters and shows statistics and automatic analysis. We believe that this synthetic view of data available for a gene cluster, combined with basic guidelines, is an efficient way to provide reliable method for gene family annotations

Anisotropic Pauli spin blockade in hole quantum dots

We present measurements on gate-defined double quantum dots in Ge-Si core-shell nanowires, which we tune to a regime with visible shell filling in both dots. We observe a Pauli spin blockade and can assign the measured leakage current at low magnetic fields to spin-flip cotunneling, for which we measure a strong anisotropy related to an anisotropic g-factor. At higher magnetic fields we see signatures for leakage current caused by spin-orbit coupling between (1,1)-singlet and (2,0)-triplet states. Taking into account these anisotropic spin-flip mechanisms, we can choose the magnetic field direction with the longest spin lifetime for improved spin-orbit qubits

Visual Saliency Based on Fast Nonparametric Multidimensional Entropy Estimation

Bottom-up visual saliency can be computed through information theoretic models but existing methods face significant computational challenges. Whilst nonparametric methods suffer from the curse of dimensionality problem and are computationally expensive, parametric approaches have the difficulty of determining the shape parameters of the distribution models. This paper makes two contributions to information theoretic based visual saliency models. First, we formulate visual saliency as center surround conditional entropy which gives a direct and intuitive interpretation of the center surround mechanism under the information theoretic framework. Second, and more importantly, we introduce a fast nonparametric multidimensional entropy estimation solution to make information theoretic-based saliency models computationally tractable and practicable in realtime applications. We present experimental results on publicly available eyetracking image databases to demonstrate that the proposed method is competitive to state of the art

Graphene Transport at High Carrier Densities using a Polymer Electrolyte Gate

We report the study of graphene devices in Hall-bar geometry, gated with a polymer electrolyte. High densities of 6 $\times 10^{13}/cm^{2}$ are consistently reached, significantly higher than with conventional back-gating. The mobility follows an inverse dependence on density, which can be correlated to a dominant scattering from weak scatterers. Furthermore, our measurements show a Bloch-Gr\"uneisen regime until 100 K (at 6.2 $\times10^{13}/cm^{2}$), consistent with an increase of the density. Ubiquitous in our experiments is a small upturn in resistivity around 3 $\times10^{13}/cm^{2}$, whose origin is discussed. We identify two potential causes for the upturn: the renormalization of Fermi velocity and an electrochemically-enhanced scattering rate.Comment: 13 pages, 4 figures, Published Versio

Comparative quantitative survey of patient experience in Barrett's oesophagus and other gastrointestinal disorders

Objective To assess health-related quality of life in patients with non-dysplastic Barrett’s oesophagus (NDBO) and endoscopically treated dysplastic Barrett’s oesophagus (DBO). Design This quantitative, self-administered questionnaire study was conducted across three National Health Service hospitals. Data were collected from three other cohorts; gastro-oesophageal reflux disease (GORD), colonic polyp surveillance and healthy individuals. Fisher’s exact and Spearman’s rank correlation tests were used for analysis. Propensity score matching adjusted for age, sex and comorbidities. Results 687 participants were eligible for analysis (NDBO n=306, DBO n=49, GORD n=132, colonic polyps n=152 and healthy n=48). 53% of NDBO participants reported similarly high cancer worry, comparable to DBO (50%, p=0.933) and colonic polyp participants (51%, p=0.355). Less cancer worry was reported in GORD participants (43.4%, p=0.01 vs NDBO). NDBO participants reported anxiety in 15.8% and depression in 8.6% of cases, which was similar to the other disease cohorts. Moderate or severe heartburn or acid regurgitation was found in 11% and 10%, respectively, in the NDBO cohort, comparable to DBO participants (heartburn 2% p=0.172, acid regurgitation 4% p=0.31) but lower (better) than GORD participants (heartburn 31% p=<0.001, acid regurgitation 25% p=0.001). NDBO participants with moderate or severe GORD symptoms were associated with higher rates of anxiety (p=<0.001), depression (p=<0.001) and cancer worry (p=<0.001). NDBO patients appropriately perceiving their cancer risk as low had lower rates of cancer worry (p=<0.001). Conclusion This study provides insight into the problems Barrett’s oesophagus patients may face. Future care pathways must be more patient focussed to address misconceptions of cancer risk, oesophageal cancer related worry and GORD symptom control

Moment inversion problem for piecewise D-finite functions

We consider the problem of exact reconstruction of univariate functions with jump discontinuities at unknown positions from their moments. These functions are assumed to satisfy an a priori unknown linear homogeneous differential equation with polynomial coefficients on each continuity interval. Therefore, they may be specified by a finite amount of information. This reconstruction problem has practical importance in Signal Processing and other applications. It is somewhat of a ``folklore'' that the sequence of the moments of such ``piecewise D-finite''functions satisfies a linear recurrence relation of bounded order and degree. We derive this recurrence relation explicitly. It turns out that the coefficients of the differential operator which annihilates every piece of the function, as well as the locations of the discontinuities, appear in this recurrence in a precisely controlled manner. This leads to the formulation of a generic algorithm for reconstructing a piecewise D-finite function from its moments. We investigate the conditions for solvability of the resulting linear systems in the general case, as well as analyze a few particular examples. We provide results of numerical simulations for several types of signals, which test the sensitivity of the proposed algorithm to noise

Dallas with balls: televized sport, soap opera and male and female pleasures

Two of the most popular of television genres, soap opera and sports coverage have been very much differentiated along gender lines in terms of their audiences. Soap opera has been regarded very much as a 'gynocentric' genre with a large female viewing audience while the audiences for television sport have been predominantly male. Gender differentiation between the genres has had implications for the popular image of each. Soap opera has been perceived as inferior; as mere fantasy and escapism for women while television sports has been perceived as a legitimate, even edifying experience for men. In this article the authors challenge the view that soap opera and television sport are radically different and argue that they are, in fact, very similar in a number of significant ways. They suggest that both genres invoke similar structures of feeling and sensibility in their respective audiences and that television sport is a 'male soap opera'. They consider the ways in which the viewing context of each genre is related to domestic life and leisure, the ways in which the textual structure and conventions of each genre invoke emotional identification, and finally, the ways in which both genres re-affirm gender identities

Double di ffential fragmentation cross sections measurements of 95 MeV/u 12C on thin targets for hadrontherapy

During therapeutic treatment with heavy ions like carbon, the beam undergoes nuclear fragmentation and secondary light charged particles, in particular protons and alpha particles, are produced. To estimate the dose deposited into the tumors and the surrounding healthy tissues, an accurate prediction on the fluences of these secondary fragments is necessary. Nowadays, a very limited set of double di ffential carbon fragmentation cross sections are being measured in the energy range used in hadrontherapy (40 to 400 MeV/u). Therefore, new measurements are performed to determine the double di ffential cross section of carbon on di erent thin targets. This work describes the experimental results of an experiment performed on May 2011 at GANIL. The double di ffential cross sections and the angular distributions of secondary fragments produced in the 12C fragmentation at 95 MeV/u on thin targets (C, CH2, Al, Al2O3, Ti and PMMA) have been measured. The experimental setup will be precisely described, the systematic error study will be explained and all the experimental data will be presented.Comment: Submitted to PR

Orbital textures and charge density waves in transition metal dichalcogenides

Low-dimensional electron systems, as realized naturally in graphene or created artificially at the interfaces of heterostructures, exhibit a variety of fascinating quantum phenomena with great prospects for future applications. Once electrons are confined to low dimensions, they also tend to spontaneously break the symmetry of the underlying nuclear lattice by forming so-called density waves; a state of matter that currently attracts enormous attention because of its relation to various unconventional electronic properties. In this study we reveal a remarkable and surprising feature of charge density waves (CDWs), namely their intimate relation to orbital order. For the prototypical material 1T-TaS2 we not only show that the CDW within the two-dimensional TaS2-layers involves previously unidentified orbital textures of great complexity. We also demonstrate that two metastable stackings of the orbitally ordered layers allow to manipulate salient features of the electronic structure. Indeed, these orbital effects enable to switch the properties of 1T-TaS2 nanostructures from metallic to semiconducting with technologically pertinent gaps of the order of 200 meV. This new type of orbitronics is especially relevant for the ongoing development of novel, miniaturized and ultra-fast devices based on layered transition metal dichalcogenides