Speckle noise and dynamic range in coronagraphic images

This paper is concerned with the theoretical properties of high contrast coronagraphic images in the context of exoplanet searches. We derive and analyze the statistical properties of the residual starlight in coronagraphic images, and describe the effect of a coronagraph on the speckle and photon noise. Current observations with coronagraphic instruments have shown that the main limitations to high contrast imaging are due to residual quasi-static speckles. We tackle this problem in this paper, and propose a generalization of our statistical model to include the description of static, quasi-static and fast residual atmospheric speckles. The results provide insight into the effects on the dynamic range of wavefront control, coronagraphy, active speckle reduction, and differential speckle calibration. The study is focused on ground-based imaging with extreme adaptive optics, but the approach is general enough to be applicable to space, with different parameters.Comment: 31 pages, 18 figure

Prediction of the production of oil palms (Elaeis guineensis Jacq.) by inflorescences and bunches counting method in the Dabou region (Cote d'Ivoire)

Knowledge of the expected production for the next six months allows the managers of agro-industrial plantations of oil palms to better organize their technical and financial management. However, the estimation methods must be easy to apply, yet sufficiently accurate. This study was initiated in order to contribute to the development of a model for the estimation of oil palm production on the one hand and to evaluate the sensitivity of the method face the data necessary for this forecast. These data are of two types: the actual production data and the inflorescence and bunch count data. The experiment was carried out on the experimental station Robert-Michaux of the CNRA of Dabou, located in the South-East of the Côte d'Ivoire. The proposed methodology is based on the duration of plan formation and maturation. It takes 5.5 to 6 months between the exit of the female inflorescence and the harvest of the corresponding ripe bunch. Counting of bunches and female inflorescences in the crown provides information on the number of rips bunches to be harvested in the next six months. The evolution of the average weight of bunches harvested previously makes it possible to predict the average weight of bunches that will be harvested during the same period. The model makes it possible to estimate the tonnage of production for the next six months provided that, for a plantation unit, it can be applied to representative samples of the whole. The yield is translated into production at different scales taking into account planting density. The estimated production variations and those of the previous production make it possible to estimate production in the months to come. The results are very satisfactory, with error accuracy of 9 %. They demonstrate the economic and technical interest of such a method in the case of production sites with little information on the conditions of oil palm cultivation

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

MRI sensing based on the displacement of paramagnetic ions from chelated complexes

We introduce a mechanism for ion sensing by MRI in which analytes compete with paramagnetic ions for binding to polydentate chelating agents. Displacement of the paramagnetic ions results in alteration of solvent interaction parameters and consequent changes in relaxivity and MRI contrast. The MRI changes can be tuned by the choice of chelator. As an example, we show that calcium-dependent displacement of Mn[superscript 2+] ions bound to EGTA and BAPTA results in a T[subscript 1]-weighted MRI signal increase, whereas displacement from calmodulin results in a signal decrease. The changes are ion selective and can be explained using relaxivity theory. The ratio of T[subscript 2] to T[subscript 1] relaxivity is also calcium-dependent, indicating the feasibility of “ratiometric” analyte detection, independent of the probe concentration. Measurement of paramagnetic ion displacement effects could be used to determine analyte ion concentrations with spatial resolution in opaque specimens.National Institutes of Health (U.S.) (grant DP2-OD2441)National Institutes of Health (U.S.) (grant R01-GM65519)McGovern Institute for Brain Research at MIT. Neurotechnology (MINT) Progra

Adaptive optics in high-contrast imaging

The development of adaptive optics (AO) played a major role in modern astronomy over the last three decades. By compensating for the atmospheric turbulence, these systems enable to reach the diffraction limit on large telescopes. In this review, we will focus on high contrast applications of adaptive optics, namely, imaging the close vicinity of bright stellar objects and revealing regions otherwise hidden within the turbulent halo of the atmosphere to look for objects with a contrast ratio lower than 10^-4 with respect to the central star. Such high-contrast AO-corrected observations have led to fundamental results in our current understanding of planetary formation and evolution as well as stellar evolution. AO systems equipped three generations of instruments, from the first pioneering experiments in the nineties, to the first wave of instruments on 8m-class telescopes in the years 2000, and finally to the extreme AO systems that have recently started operations. Along with high-contrast techniques, AO enables to reveal the circumstellar environment: massive protoplanetary disks featuring spiral arms, gaps or other asymmetries hinting at on-going planet formation, young giant planets shining in thermal emission, or tenuous debris disks and micron-sized dust leftover from collisions in massive asteroid-belt analogs. After introducing the science case and technical requirements, we will review the architecture of standard and extreme AO systems, before presenting a few selected science highlights obtained with recent AO instruments.Comment: 24 pages, 14 figure

Modern optical astronomy: technology and impact of interferometry

The present `state of the art' and the path to future progress in high spatial resolution imaging interferometry is reviewed. The review begins with a treatment of the fundamentals of stellar optical interferometry, the origin, properties, optical effects of turbulence in the Earth's atmosphere, the passive methods that are applied on a single telescope to overcome atmospheric image degradation such as speckle interferometry, and various other techniques. These topics include differential speckle interferometry, speckle spectroscopy and polarimetry, phase diversity, wavefront shearing interferometry, phase-closure methods, dark speckle imaging, as well as the limitations imposed by the detectors on the performance of speckle imaging. A brief account is given of the technological innovation of adaptive-optics (AO) to compensate such atmospheric effects on the image in real time. A major advancement involves the transition from single-aperture to the dilute-aperture interferometry using multiple telescopes. Therefore, the review deals with recent developments involving ground-based, and space-based optical arrays. Emphasis is placed on the problems specific to delay-lines, beam recombination, polarization, dispersion, fringe-tracking, bootstrapping, coherencing and cophasing, and recovery of the visibility functions. The role of AO in enhancing visibilities is also discussed. The applications of interferometry, such as imaging, astrometry, and nulling are described. The mathematical intricacies of the various `post-detection' image-processing techniques are examined critically. The review concludes with a discussion of the astrophysical importance and the perspectives of interferometry.Comment: 65 pages LaTeX file including 23 figures. Reviews of Modern Physics, 2002, to appear in April issu

Dual-modality gene reporter for in vivo imaging

The ability to track cells and their patterns of gene expression in living organisms can increase our understanding of tissue development and disease. Gene reporters for bioluminescence, fluorescence, radionuclide, and magnetic resonance imaging (MRI) have been described but these suffer variously from limited depth penetration, spatial resolution, and sensitivity. We describe here a gene reporter, based on the organic anion transporting protein Oatp1a1, which mediates uptake of a clinically approved, Gd(3+)-based, hepatotrophic contrast agent (gadolinium-ethoxybenzyl-diethylenetriamine pentaacetic acid). Cells expressing the reporter showed readily reversible, intense, and positive contrast (up to 7.8-fold signal enhancement) in T1-weighted magnetic resonance images acquired in vivo. The maximum signal enhancement obtained so far is more than double that produced by MRI gene reporters described previously. Exchanging the Gd(3+) ion for the radionuclide, (111)In, also allowed detection by single-photon emission computed tomography, thus combining the spatial resolution of MRI with the sensitivity of radionuclide imaging

A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation.

Although anaplastic large-cell lymphomas (ALCL) carrying anaplastic lymphoma kinase (ALK) have a relatively good prognosis, aggressive forms exist. We have identified a novel translocation, causing the fusion of the TRAF1 and ALK genes, in one patient who presented with a leukemic ALK+ ALCL (ALCL-11). To uncover the mechanisms leading to high-grade ALCL, we developed a human patient-derived tumorgraft (hPDT) line. Molecular characterization of primary and PDT cells demonstrated the activation of ALK and nuclear factor kB (NFkB) pathways. Genomic studies of ALCL-11 showed the TP53 loss and the in vivo subclonal expansion of lymphoma cells, lacking PRDM1/Blimp1 and carrying c-MYC gene amplification. The treatment with proteasome inhibitors of TRAF1-ALK cells led to the downregulation of p50/p52 and lymphoma growth inhibition. Moreover, a NFkB gene set classifier stratified ALCL in distinct subsets with different clinical outcome. Although a selective ALK inhibitor (CEP28122) resulted in a significant clinical response of hPDT mice, nevertheless the disease could not be eradicated. These data indicate that the activation of NFkB signaling contributes to the neoplastic phenotype of TRAF1-ALK ALCL. ALCL hPDTs are invaluable tools to validate the role of druggable molecules, predict therapeutic responses and implement patient specific therapies

Lumazine Synthase Protein Nanoparticle-Gd(III)-DOTA Conjugate as a T1 contrast agent for high-field MRI

With the applications of magnetic resonance imaging (MRI) at higher magnetic fields increasing, there is demand for MRI contrast agents with improved relaxivity at higher magnetic fields. Macromolecule-based contrast agents, such as protein-based ones, are known to yield significantly higher r(1) relaxivity at low fields, but tend to lose this merit when used as T-1 contrast agents (r(1)/r(2) = 0.5 similar to 1), with their r(1) decreasing and r(2) increasing as magnetic field strength increases. Here, we developed and characterized an in vivo applicable magnetic resonance (MR) positive contrast agent by conjugating Gd(III)-chelating agent complexes to lumazine synthase isolated from Aquifex aeolicus (AaLS). The r(1) relaxivity of Gd(III)-DOTA-AaLS-R108C was 16.49 mM(-1)s(-1) and its r(1)/r(2) ratio was 0.52 at the magnetic field strength of 7 T. The results of 3D MR angiography demonstrated the feasibility of vasculature imaging within 2 h of intravenous injection of the agent and a significant reduction in T-1 values were observed in the tumor region 7 h post-injection in the SCC-7 flank tumor model. Our findings suggest that Gd(III)-DOTA-AaLS-R108C could serve as a potential theranostic nanoplatform at high magnetic field strength.open0