COMPARISON OF METHODS TO MAP SELECTED TRAFFIC MARKINGS ON FIRST CLASS ROADS IN THE CZECH REPUBLIC

The article presents conclusions of a comprehensive analysis of pilot data collection using four mapping methods. To validate mapping methods and procedures, we selected three ten-kilometer sections of the first class roads with different geomorphological, vegetative and transportation properties. All sections were measured by aerial photogrammetry using GSD = 4 cm, mobile laser scanning equipment linked with cameras, by geodetic surveying methods, and one section was also measured by UAV. The tested methods mapped selected features of vertical and horizontal traffic markings on the first class roads. The traffic marking measuring sets were analyzed from the perspectives of personnel, time, data, costs, and technological and organizational aspects. All the mapping methods were verified as mentioned above starting from work preparation phase, its terrain realization, captured data processing and detailed analysis, concluding with stating the advantages and disadvantages for each mapping method. One of the analysis outputs was proposals to change and refine road administrator’s regulations. The mapping methods were compared with geodetic measurements. Analyses were also carried out in the context of creating digital data in 3D for the realization of BIM (Building Information Modeling) digital data in connection with the concept of the European Parliament and Council Directive 2014/24 / EU on Public Procurement, and Czech Government Decree 682 on the Concept of Implementation of the BIM Method in the Czech Republic of 25 September 2017 and Decree 958 of the Government of the Czech Republic of 2 November 2016 on the importance of BIM for the construction engineering and proposal of further steps to introduce it in the Czech Republic

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings: We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC based or 583 LTC based contigs. Conclusions/Significance: The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A

Vehicle localization by lidar point correlation improved by change detection

LiDAR sensors are proven sensors for accurate vehicle localization. Instead of detecting and matching features in the LiDAR data, we want to use the entire information provided by the scanners. As dynamic objects, like cars, pedestrians or even construction sites could lead to wrong localization results, we use a change detection algorithm to detect these objects in the reference data. If an object occurs in a certain number of measurements at the same position, we mark it and every containing point as static. In the next step, we merge the data of the single measurement epochs to one reference dataset, whereby we only use static points. Further, we also use a classification algorithm to detect trees. For the online localization of the vehicle, we use simulated data of a vertical aligned automotive LiDAR sensor. As we only want to use static objects in this case as well, we use a random forest classifier to detect dynamic scan points online. Since the automotive data is derived from the LiDAR Mobile Mapping System, we are able to use the labelled objects from the reference data generation step to create the training data and further to detect dynamic objects online. The localization then can be done by a point to image correlation method using only static objects. We achieved a localization standard deviation of about 5 cm (position) and 0.06° (heading), and were able to successfully localize the vehicle in about 93 % of the cases along a trajectory of 13 km in Hannover, Germany

Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

Orientation of oblique airborne image sets - Experiences from the ISPRS/Eurosdr benchmark on multi-platform photogrammetry

During the last decade the use of airborne multi camera systems increased significantly. The development in digital camera technology allows mounting several mid- or small-format cameras efficiently onto one platform and thus enables image capture under different angles. Those oblique images turn out to be interesting for a number of applications since lateral parts of elevated objects, like buildings or trees, are visible. However, occlusion or illumination differences might challenge image processing. From an image orientation point of view those multi-camera systems bring the advantage of a better ray intersection geometry compared to nadir-only image blocks. On the other hand, varying scale, occlusion and atmospheric influences which are difficult to model impose problems to the image matching and bundle adjustment tasks. In order to understand current limitations of image orientation approaches and the influence of different parameters such as image overlap or GCP distribution, a commonly available dataset was released. The originally captured data comprises of a state-of-the-art image block with very high overlap, but in the first stage of the so-called ISPRS/EUROSDR benchmark on multi-platform photogrammetry only a reduced set of images was released. In this paper some first results obtained with this dataset are presented. They refer to different aspects like tie point matching across the viewing directions, influence of the oblique images onto the bundle adjustment, the role of image overlap and GCP distribution. As far as the tie point matching is concerned we observed that matching of overlapping images pointing to the same cardinal direction, or between nadir and oblique views in general is quite successful. Due to the quite different perspective between images of different viewing directions the standard tie point matching, for instance based on interest points does not work well. How to address occlusion and ambiguities due to different views onto objects is clearly a non-solved research problem so far. In our experiments we also confirm that the obtainable height accuracy is better when all images are used in bundle block adjustment. This was also shown in other research before and is confirmed here. Not surprisingly, the large overlap of 80/80% provides much better object space accuracy – random errors seem to be about 2-3fold smaller compared to the 60/60% overlap. A comparison of different software approaches shows that newly emerged commercial packages, initially intended to work with small frame image blocks, do perform very well

Global bundle adjustment with variable orientation point distance for precise mars express orbit reconstruction

The photogrammetric bundle adjustment of line scanner image data requires a precise description of the time-dependent image orientation. For this task exterior orientation parameters of discrete points are used to model position and viewing direction of a camera trajectory via polynomials. This paper investigates the influence of the distance between these orientation points on the quality of trajectory modeling. A new method adapts the distance along the trajectory to the available image information. Compared to a constant distance as used previously, a better reconstruction of the exterior orientation is possible, especially when image quality changes within a strip. In our research we use image strips of the High Resolution Stereo Camera (HRSC), taken to map the Martian surface. Several experiments on the global image data set have been carried out to investigate how the bundle adjustment improves the image orientation, if the new method is employed. For evaluation the forward intersection errors of 3D points derived from HRSC images, as well as their remaining height differences to the MOLA DTM are used. In 13.5 % (515 of 3,828) of the image strips, taken during this ongoing mission over the last 12 years, high frequency image distortions were found. Bundle adjustment with a constant orientation point distance was able to reconstruct the orbit in 239 (46.4 %) cases. A variable orientation point distance increased this number to 507 (98.6 %).German Federal Ministry for Economic Affairs and Energy (BMWi)German Aerospace Center (DLR)/50 QM 130

Pléiades project: Assessment of georeferencing accuracy, image quality, pansharpening performence and DSM/DTM quality

Pléiades 1A and 1B are twin optical satellites of Optical and Radar Federated Earth Observation (ORFEO) program jointly running by France and Italy. They are the first satellites of Europe with sub-meter resolution. Airbus DS (formerly Astrium Geo) runs a MyGIC (formerly Pléiades Users Group) program to validate Pléiades images worldwide for various application purposes. The authors conduct three projects, one is within this program, the second is supported by BEU Scientific Research Project Program, and the third is supported by TÜBİTAK. Assessment of georeferencing accuracy, image quality, pansharpening performance and Digital Surface Model/Digital Terrain Model (DSM/DTM) quality subjects are investigated in these projects. For these purposes, triplet panchromatic (50 cm Ground Sampling Distance (GSD)) and VNIR (2 m GSD) Pléiades 1A images were investigated over Zonguldak test site (Turkey) which is urbanised, mountainous and covered by dense forest. The georeferencing accuracy was estimated with a standard deviation in X and Y (SX, SY) in the range of 0.45m by bias corrected Rational Polynomial Coefficient (RPC) orientation, using ~170 Ground Control Points (GCPs). 3D standard deviation of ±0.44m in X, ±0.51m in Y, and ±1.82m in Z directions have been reached in spite of the very narrow angle of convergence by bias corrected RPC orientation. The image quality was also investigated with respect to effective resolution, Signal to Noise Ratio (SNR) and blur coefficient. The effective resolution was estimated with factor slightly below 1.0, meaning that the image quality corresponds to the nominal resolution of 50cm. The blur coefficients were achieved between 0.39-0.46 for triplet panchromatic images, indicating a satisfying image quality. SNR is in the range of other comparable space borne images which may be caused by de-noising of Pléiades images. The pansharpened images were generated by various methods, and are validated by most common statistical metrics and also visual interpretation. The generated DSM and DTM were achieved with ±1.6m standard deviation in Z (SZ) in relation to a reference DTM.Airbus Defence and SpaceBEU/2014-47912266-01TÜBİTAK/114Y38

Genomic Diversity in Two Related Plant Species with and without Sex Chromosomes - Silene latifolia and S. vulgaris

Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood.We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family.Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes

The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades – Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes

Increasing Incidence of Geomyces destructans Fungus in Bats from the Czech Republic and Slovakia

BACKGROUND: White-nose syndrome is a disease of hibernating insectivorous bats associated with the fungus Geomyces destructans. It first appeared in North America in 2006, where over a million bats died since then. In Europe, G. destructans was first identified in France in 2009. Its distribution, infection dynamics, and effects on hibernating bats in Europe are largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: We screened hibernacula in the Czech Republic and Slovakia for the presence of the fungus during the winter seasons of 2008/2009 and 2009/2010. In winter 2009/2010, we found infected bats in 76 out of 98 surveyed sites, in which the majority had been previously negative. A photographic record of over 6000 hibernating bats, taken since 1994, revealed bats with fungal growths since 1995; however, the incidence of such bats increased in Myotis myotis from 2% in 2007 to 14% by 2010. Microscopic, cultivation and molecular genetic evaluations confirmed the identity of the recently sampled fungus as G. destructans, and demonstrated its continuous distribution in the studied area. At the end of the hibernation season we recorded pathologic changes in the skin of the affected bats, from which the fungus was isolated. We registered no mass mortality caused by the fungus, and the recorded population decline in the last two years of the most affected species, M. myotis, is within the population trend prediction interval. CONCLUSIONS/SIGNIFICANCE: G. destructans was found to be widespread in the Czech Republic and Slovakia, with an epizootic incidence in bats during the most recent years. Further development of the situation urgently requires a detailed pan-European monitoring scheme