Automatic classification of high resolution satellite imagery - A case study for urban areas in the Kingdom of Saudi Arabia

Updating topographic geospatial databases is often performed based on current remotely sensed images. To automatically extract the object information (labels) from the images, supervised classifiers are being employed. Decisions to be taken in this process concern the definition of the classes which should be recognised, the features to describe each class and the training data necessary in the learning part of classification. With a view to large scale topographic databases for fast developing urban areas in the Kingdom of Saudi Arabia we conducted a case study, which investigated the following two questions: (a) which set of features is best suitable for the classification?; (b) what is the added value of height information, e.g. derived from stereo imagery? Using stereoscopic GeoEye and Ikonos satellite data we investigate these two questions based on our research on label tolerant classification using logistic regression and partly incorrect training data. We show that in between five and ten features can be recommended to obtain a stable solution, that height information consistently yields an improved overall classification accuracy of about 5%, and that label noise can be successfully modelled and thus only marginally influences the classification results

Building monitoring with differential dsms

The monitoring of building activity (erection of new buildings, demolishing buildings and especially the change of building heights) by manual inspection of space and aerial images is time consuming and a source of errors. A detection of building changes based on the comparison of digital surface models (DSMs) is more reliable. For this study DSMs have been generated based on aerial images, an IKONOS and a GeoEye-1 stereo pair taken from 2007 up to 2009. By pixel based matching with dynamic programming, semiglobal matching and least squares matching the visible surface has been determined. Semiglobal matching leads to sharp building shapes, while the area based least squares matching smoothes the height model and has more problems in areas with little or without contrast. As is shown in the investigation building changes and building height changes in the range of one floor can in many cases be determined with all methods, however building shapes are better determined using semiglobal matching

Do RARA/PML fusion gene deletions confer resistance to ATRA-based therapy in patients with acute promyelocytic leukemia?

Acute promyelocytic leukemia (APL) is characterized by the translocation t(15;17)(q22;q21), resulting in the promyelocytic leukemia (PML)-retinoic acid receptor alpha (RARA) fusion protein in 95% cases whereas variant translocations involving PLZF (11q23), NPM (5q35), NUMA (11q13) and STAT5b (17q23) account for the rest. Leukemias with PML-RARA translocations respond well to all-trans retinoic acid (ATRA) or arsenic trioxide (ATO) therapy whereas those with PLZF-RARA fusions respond poorly. Although primary resistance to ATRA is rare, secondary or acquired resistance is frequently observed in patients treated with ATRA alone or in combination with other chemotherapy regimens. However, molecular abnormalities mediating resistance to ATRA therapy are underexplored. Here, we report two cases of APL with RARA-PML deletions on der(17) or der(15), which displayed clinical evidence of primary and secondary resistance to therapy, respectively

The spectrum of myelodysplastic syndromes post-solid organ transplantation: A single institutional experience

An increased incidence of acute myeloid leukemia (AML) has recently been documented in patients post-solid organ transplantation but the incidence and types of myelodysplastic syndromes (MDS) occurring in this patient population are not known. We identified 5 patients (3M, 2F, age 48–64 years) who developed MDS ranging from 1.8 to 25 years (median 4.2 years) post-solid organ transplantation, only 2 patients had received azathioprine. The cumulative incidence of MDS in heart and lung transplant recipients at 15 years was 0.5% and 1.8%, respectively, which is markedly higher compared to the general population. Low-risk types of MDS predominated, 3 of 5 patients are alive (median 3.9 years) since diagnosis. Deletions of chromosome 20q, which have not been previously reported in post-transplant MDS/AML, were identified in 3 cases. Our findings expand the morphologic and cytogenetic spectrum of MDS occurring post-solid organ transplantation and suggest that mechanisms beside azathioprine toxicity might be important in disease pathogenesis

The genetic landscape of dural marginal zone lymphomas

The dura is a rare site of involvement by marginal zone lymphoma (MZL) and the biology of dural MZL is not well understood. We performed genome-wide DNA copy number and targeted mutational analysis of 14 dural MZL to determine the genetic landscape of this entity. Monoallelic and biallelic inactivation of TNFAIP3 by mutation (n=5) or loss (n=1) was observed in 6/9 (67%) dural MZL exhibiting plasmacytic differentiation, including 3 IgG4+ cases. In contrast, activating NOTCH2 mutations were detected in 4/5 (80%) dural MZL displaying variable monocytoid morphology. Inactivating TBL1XR1 mutations were identified in all NOTCH2 mutated cases. Recurrent mutations in KLHL6 (n=2) and MLL2 (n=2) were also detected. Gains at 6p25.3 (n=2) and losses at 1p36.32 (n=3) were common chromosomal imbalances, with loss of heterozygosity (LOH) of these loci observed in a subset of cases. Translocations involving the IGH or MALT1 genes were not identified. Our results indicate genetic similarities between dural MZL and other MZL subtypes. However, recurrent and mutually exclusive genetic alterations of TNFAIP3 and NOTCH2 appear to be associated with distinct disease phenotypes in dural MZL

Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome

The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species

Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome.

The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species

INFLUENCE OF DEM IN WATERSHED MANAGEMENT AS FLOOD ZONATION MAPPING

Despite of valuable efforts from working groups and research organizations towards flood hazard reduction through its program, still minimal diminution from these hazards has been realized. This is mainly due to the fact that with rapid increase in population and urbanization coupled with climate change, flood hazards are becoming increasingly catastrophic. Therefore there is a need to understand and access flood hazards and develop means to deal with it through proper preparations, and preventive measures. To achieve this aim, Geographical Information System (GIS), geospatial and hydrological models were used as tools to tackle with influence of flash floods in the Kingdom of Saudi Arabia due to existence of large valleys (Wadis) which is a matter of great concern. In this research paper, Digital Elevation Models (DEMs) of different resolution (30m, 20m,10m and 5m) have been used, which have proven to be valuable tool for the topographic parameterization of hydrological models which are the basis for any flood modelling process. The DEM was used as input for performing spatial analysis and obtaining derivative products and delineate watershed characteristics of the study area using ArcGIS desktop and its Arc Hydro extension tools to check comparability of different elevation models for flood Zonation mapping. The derived drainage patterns have been overlaid over aerial imagery of study area, to check influence of greater amount of precipitation which can turn into massive destructions. The flow accumulation maps derived provide zones of highest accumulation and possible flow directions. This approach provide simplified means of predicting extent of inundation during flood events for emergency action especially for large areas because of large coverage area of the remotely sensed data