Analysis of the DRPLA triplet repeat in brain tissue and leukocytes from schizophrenics

This study reports our preliminary experience with interstitial radiofrequencies in the treatment of urological malignancies. Bipolar radiofrequency was interstitially delivered in four freshly removed human kidneys in an ex-vivo model. The kidney was perfused ex-vivo with 37 degrees C saline in order to mimic physiological conditions. Large reproducible and controlled lesions (hypereosinophilia and pyknosis) were observed in the parenchyma between the active needles. Further animal and human clinical studies are planned to precise the place of bipolar RF in the treatment or urological malignancies, and especially in kidney tumors.     

Space-filling experimental designs for constrained design spaces

Conventional space-filling experimental design provides uniform coverage of a hypercube design space. When constraints are imposed, the results may contain many infeasible points. Simply omitting these points leads to fewer feasible points than desired and a design of experiments that is not optimally distributed. In this research, an adaptive method is developed to create space-filling points in arbitrarily constrained spaces. First, a design space reconstruction method is developed to reduce the invalid exploration space and enhance the efficiency of experimental designs. Then, a synthetic criterion of uniformity and feasibility is proposed and optimized by the enhanced stochastic evolutionary method to obtain the initial sampling combination. Finally, an adaptive adjustment strategy of design levels is constructed to obtain the required number of feasible points. Various test cases with convex and non-convex, connected and non-connected design spaces are implemented to verify the efficacy of the proposed method.     

Review of constituent retrieval in optically deep and complex waters from satellite imagery

We provide a comprehensive overview of water constituent retrieval algorithms and underlying definitions and models for optically deep and complex (i.e. case 2) waters using earth observation data. The performance of constituent retrieval algorithms is assessed based on matchup validation experiments published between January 2006 and May 2011. Validation practices range from singular vicarious calibration experiments to comparisons using extensive in situ time series. Band arithmetic and spectral inversion algorithms for all water types are classified using a method based scheme that supports the interpretation of algorithm validity ranges. Based on these ranges we discuss groups of similar algorithms in view of their strengths and weaknesses. Such quantitative literature analysis reveals clear application boundaries. With regard to chlorophyll retrieval, validation of blue–green band ratios in coastal waters is limited to oligotrophic, predominantly ocean waters, while red-NIR ratios apply only at more than 10 mg/m³. Spectral inversion techniques — although not validated to the same extent — are necessary to cover all other conditions. Suspended matter retrieval is the least critical, as long as the wavelengths used in empirical models are increased with concentrations. The retrieval of dissolved organic matter however remains relatively inaccurate and inconsistent, with large differences in the accuracy of comparable methods in similar validation experiments. We conclude that substantial progress has been made in understanding and improving retrieval of constituents in optically deep and complex waters, enabling specific solutions to almost any type of optically complex water. Further validation and intercomparison of spectral inversion procedures are however needed to learn if solutions with a larger validity range are feasible.     

cDNA cloning of a human homologue of the Caenorhabditis elegans cell fate-determining gene mab-21: expression, chromosomal localization and analysis of a highly polymorphic (CAG)n trinucleotide repeat

The two most consistent features of the diseases caused by trinucleotide repeat expansion-neuropsychiatric symptoms and the phenomenon of genetic anticipation-may be present in forms of dementia, hereditary ataxia, Parkinsonism, bipolar affective disorder, schizophrenia and autism. To identify candidate genes for these disorders, we have screened human brain cDNA libraries for the presence of gene fragments containing polymorphic trinucleotide repeats. Here we report the cDNA cloning of CAGR1, originally detected in a retinal cDNA library. The 2743 bp cDNA contains a 1077 bp open reading frame encoding 359 amino acids. This amino acid sequence is homologous (56% amino acid identify and 81% amino acid conservation) to the Caenorhabditis elegans cell fate-determining protein mab-21. CAGR1 is expressed in several human tissues, most prominently in the cerebellum, as a message of approximately 3.0 kb. The gene was mapped to 13q13, just telomeric to D13S220. A 5'-untranslated CAG trinucleotide repeat is highly polymorphic, with repeat length ranging from six to 31 triplets and a heterozygosity of 87-88% in 684 chromosomes from several human populations. One allele from an individual with an atypical movement disorder and bipolar affective disorder type II contains 46 triplets, 15 triplets longer than any other allele detected. Though insufficient data are available to link the long repeat to this clinical phenotype, an expansion mutation of the CAGR1 repeat can be considered a candidate for the etiology of disorders with anticipation or developmental abnormalities, and particularly any such disorders linked to chromosome 13.     

Remote sensing of water quality in an Australian tropical freshwater impoundment using matrix inversion and MERIS images

The purpose of this study was to investigate how semi-analytical inversion techniques developed for the remote sensing of water quality parameters (chlorophyll a, tripton and coloured dissolved organic matter (CDOM)) in inland waters could be adapted or improved for application to Australian tropical and sub-tropical water bodies. The Matrix Inversion Method (MIM) with a semi-analytic model of the anisotropy of the in-water light field was applied to MERIS images of Burdekin Falls Dam, Australia, a tropical freshwater impoundment. Specific attention was required to improve the atmospheric correction of the MERIS data. The performance of the conventional three band exact solution of the MIM was compared to that of over-determined solutions that used constant and differential weighting for each sensor band.The results of the application of the MIM algorithm showed that the best weighting scheme had a mean chlorophyll a retrieval difference of 1.0 μgl^− 1, the three band direct matrix inversion scheme had a mean difference of 4.2 μgl^− 1 and the constant weight scheme had a mean difference of 5.5 μgl^− 1. For tripton, the best performed weighting scheme had a mean difference of 1.2 mgl^− 1, the three band scheme had a mean difference of 3.4 mgl^− 1 and the constant weight scheme had a mean difference of 1.8 mgl^− 1. For the CDOM retrieval, the mean difference was found to be 0.12 m^− 1 for the best performed weighting scheme, 0.25 m^− 1 for the three band scheme and 0.52 m^− 1 for the constant weight scheme. It was found that significant improvements in the accuracy and precision of retrieved water quality parameter values can be obtained by using differentially weighted, over-determined systems of equations, rather than exact solutions. These more reliable estimates of water quality parameters will allow water resource managers to improve their monitoring regimes.     

A physics based retrieval and quality assessment of bathymetry from suboptimal hyperspectral data

In order to retrieve bathymetry, substratum type and the concentrations of the optically active constituents of the water column, an integrated physics based mapping approach was applied to airborne hyperspectral data of Moreton Bay, Australia. The remotely sensed data were sub-optimal due to high and mid-level cloud covers. Critical to the correct interpretation of the resultant coastal bathymetry map was the development of a quality control procedure based on additional outputs of the integrated physics based mapping approach and the characteristics of the instrument. These two outputs were: an optical closure term which defines differences between the image and model based remote sensing signal; and an estimate of the relative contribution of the substratum signal to the remote sensing signal. This quality control procedure was able to identify those pixels with a reliable retrieval of depth and to detect thin and thick clouds and their shadows, which were subsequently masked out from further analysis. The derived coastal bathymetry in depths ranging 4-13 m for the mapped area was within ± 15% of boat-based multi-beam acoustic mapping survey of the same area. The agreement between the imaging spectrometry and the acoustic datasets varies as a function of the contribution of the bottom visibility to the remote sensing signal. As expected, there was greater agreement in shallower clear water (± 0.67 m) than quasi-optically deep water (± 1.35 m). The quantitative identification and screening of the optically deep waters and the quasi-optically deep waters led to improved precision in the depth retrieval. These results suggest that the physics based mapping approach adopted in this study performs well for retrieving water column depths in coastal waters in water depths ranging 4-13 m for the area and conditions studied, even with sub-optimal imagery.     

Structural characterization of Mycobacterium tuberculosis lipoarabinomannans by the combination of capillary electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) associated with capillary electrophoresis (CE) has been used for structural characterization of mannooligosaccharide caps from Mycobacterium tuberculosis H37rv mannosylated lipoarabinomannans (ManLAMs). The mannooligosaccharide caps were released by mild acid hydrolysis, labeled with 1-aminopyrene-3,6,8-trisulfonate (APTS) prior to being separated by CE, collected, and analyzed by MALDI-TOF-MS and post-source decay experiments. This approach was optimized using standard APTS-labeled oligosaccharides. With the selected (9:1) mixture of 2,5-dihydroxybenzoic acid (DHB) and 5-methoxysalicylic acid (MSA) as matrix and the on-probe sample cleanup procedure with cation-exchange resin, standard APTS-maltotriose was successfully detected down to 50 fmol using linear-mode negative MALDI-TOF-MS. Moreover, using extraction delay time, only 100 and 500 fmol of this standard were required, respectively, to obtain accurate reflectron mass measurements and sequence determination through post-source decay experiments. Applied to only 5 microg (294 pmol) of M. tuberculosis ManLAMs, this analytical approach allowed successful mass characterization of the mannooligosaccharide cap structures from the deprotonated molecular ions [M - H]- and the y-type ion fragments obtained in post-source decay experiments. This powerful analytical approach opens new insights into both the characterization of oligosaccharides and the capping motifs displayed by ManLAMs purified from mycobacteria isolated from tubercular patients without in vitro culturing.