VIRTUAL RECONSTRUCTION OF THE ALMAQAH TEMPLE OF YEHA IN ETHIOPIA BY TERRESTRIAL LASER SCANNING

In autumn 2009 the Almaqah Temple of Yeha in Ethiopia has been recorded by terrestrial laser scanning and digital photogrammetry in cooperation between the Sana'a Branch of the Orient Department of the German Archaeological Institute and the HafenCity University Hamburg. The temple dates from the 7th Century BC and is one of the best preserved buildings of Sabaean architecture in Africa. As a basis for all future project works a geodetic network was established in UTM-coordinates by GPS measurements. The geodata collected will form the basis for all future work on the temple. The deformations of the facades were determined for restoration issues and the existing parts of the temple were modelled by meshing (3D triangulation). Using the scanned point cloud and a technical analysis of the building the Propylon, which is no longer existent today, was virtually reconstructed. In future, the data will also be included in the master plan for touristic development of the region of Axum and Yeha in northern Ethiopia

Robust probabilistic superposition and comparison of protein structures

<p>Abstract</p> <p>Background</p> <p>Protein structure comparison is a central issue in structural bioinformatics. The standard dissimilarity measure for protein structures is the root mean square deviation (RMSD) of representative atom positions such as α-carbons. To evaluate the RMSD the structures under comparison must be superimposed optimally so as to minimize the RMSD. How to evaluate optimal fits becomes a matter of debate, if the structures contain regions which differ largely - a situation encountered in NMR ensembles and proteins undergoing large-scale conformational transitions.</p> <p>Results</p> <p>We present a probabilistic method for robust superposition and comparison of protein structures. Our method aims to identify the largest structurally invariant core. To do so, we model non-rigid displacements in protein structures with outlier-tolerant probability distributions. These distributions exhibit heavier tails than the Gaussian distribution underlying standard RMSD minimization and thus accommodate highly divergent structural regions. The drawback is that under a heavy-tailed model analytical expressions for the optimal superposition no longer exist. To circumvent this problem we work with a scale mixture representation, which implies a weighted RMSD. We develop two iterative procedures, an Expectation Maximization algorithm and a Gibbs sampler, to estimate the local weights, the optimal superposition, and the parameters of the heavy-tailed distribution. Applications demonstrate that heavy-tailed models capture differences between structures undergoing substantial conformational changes and can be used to assess the precision of NMR structures. By comparing Bayes factors we can automatically choose the most adequate model. Therefore our method is parameter-free.</p> <p>Conclusions</p> <p>Heavy-tailed distributions are well-suited to describe large-scale conformational differences in protein structures. A scale mixture representation facilitates the fitting of these distributions and enables outlier-tolerant superposition.</p

Dysmorphometrics: the modelling of morphological abnormalities

<p>Abstract</p> <p>Background</p> <p>The study of typical morphological variations using quantitative, morphometric descriptors has always interested biologists in general. However, unusual examples of form, such as abnormalities are often encountered in biomedical sciences. Despite the long history of morphometrics, the means to identify and quantify such unusual form differences remains limited.</p> <p>Methods</p> <p>A theoretical concept, called dysmorphometrics, is introduced augmenting current geometric morphometrics with a focus on identifying and modelling form abnormalities. Dysmorphometrics applies the paradigm of detecting form differences as outliers compared to an appropriate norm. To achieve this, the likelihood formulation of landmark superimpositions is extended with outlier processes explicitly introducing a latent variable coding for abnormalities. A tractable solution to this augmented superimposition problem is obtained using Expectation-Maximization. The topography of detected abnormalities is encoded in a dysmorphogram.</p> <p>Results</p> <p>We demonstrate the use of dysmorphometrics to measure abrupt changes in time, asymmetry and discordancy in a set of human faces presenting with facial abnormalities.</p> <p>Conclusion</p> <p>The results clearly illustrate the unique power to reveal unusual form differences given only normative data with clear applications in both biomedical practice & research.</p

Clinico-radiological features, molecular spectrum, and identification of prognostic factors in developmental and epileptic encephalopathy due to inosine triphosphate pyrophosphatase (ITPase) deficiency

Developmental and epileptic encephalopathy 35 (DEE 35) is a severe neurological condition caused by biallelic variants in ITPA, encoding inosine triphosphate pyrophosphatase, an essential enzyme in purine metabolism. We delineate the genotypic and phenotypic spectrum of DEE 35, analyzing possible predictors for adverse clinical outcomes. We investigated a cohort of 28 new patients and reviewed previously described cases, providing a comprehensive characterization of 40 subjects. Exome sequencing was performed to identify underlying ITPA pathogenic variants. Brain MRI (magnetic resonance imaging) scans were systematically analyzed to delineate the neuroradiological spectrum. Survival curves according to the Kaplan–Meier method and log-rank test were used to investigate outcome predictors in different subgroups of patients. We identified 18 distinct ITPA pathogenic variants, including 14 novel variants, and two deletions. All subjects showed profound developmental delay, microcephaly, and refractory epilepsy followed by neurodevelopmental regression. Brain MRI revision revealed a recurrent pattern of delayed myelination and restricted diffusion of early myelinating structures. Congenital microcephaly and cardiac involvement were statistically significant novel clinical predictors of adverse outcomes. We refined the molecular, clinical, and neuroradiological characterization of ITPase deficiency, and identified new clinical predictors which may have a potentially important impact on diagnosis, counseling, and follow-up of affected individuals

Clinico-radiological features, molecular spectrum, and identification of prognostic factors in developmental and epileptic encephalopathy due to inosine triphosphate pyrophosphatase (ITPase) deficiency.

Developmental and epileptic encephalopathy 35 (DEE 35) is a severe neurological condition caused by biallelic variants in ITPA, encoding inosine triphosphate pyrophosphatase, an essential enzyme in purine metabolism. We delineate the genotypic and phenotypic spectrum of DEE 35, analyzing possible predictors for adverse clinical outcomes. We investigated a cohort of 28 new patients and reviewed previously described cases, providing a comprehensive characterization of 40 subjects. Exome sequencing was performed to identify underlying ITPA pathogenic variants. Brain MRI (magnetic resonance imaging) scans were systematically analyzed to delineate the neuroradiological spectrum. Survival curves according to the Kaplan-Meier method and log-rank test were used to investigate outcome predictors in different subgroups of patients. We identified 18 distinct ITPA pathogenic variants, including 14 novel variants, and two deletions. All subjects showed profound developmental delay, microcephaly, and refractory epilepsy followed by neurodevelopmental regression. Brain MRI revision revealed a recurrent pattern of delayed myelination and restricted diffusion of early myelinating structures. Congenital microcephaly and cardiac involvement were statistically significant novel clinical predictors of adverse outcomes. We refined the molecular, clinical, and neuroradiological characterization of ITPase deficiency, and identified new clinical predictors which may have a potentially important impact on diagnosis, counseling, and follow-up of affected individuals

3D MODEL OF AL ZUBARAH FORTRESS IN QATAR - TERRESTRIAL LASER SCANNING VS. DENSE IMAGE MATCHING

In September 2011 the fortress Al Zubarah, built in 1938 as a typical Arabic fortress and restored in 1987 as a museum, was recorded by the HafenCity University Hamburg using terrestrial laser scanning with the IMAGER 5006h and digital photogrammetry for the Qatar Museum Authority within the framework of the Qatar Islamic Archaeology and Heritage Project. One goal of the object recording was to provide detailed 2D/3D documentation of the fortress. This was used to complete specific detailed restoration work in the recent years. From the registered laser scanning point clouds several cuttings and 2D plans were generated as well as a 3D surface model by triangle meshing. Additionally, point clouds and surface models were automatically generated from digital imagery from a Nikon D70 using the open-source software Bundler/PMVS2, free software VisualSFM, Autodesk Web Service 123D Catch beta, and low-cost software Agisoft PhotoScan. These outputs were compared with the results from terrestrial laser scanning. The point clouds and surface models derived from imagery could not achieve the same quality of geometrical accuracy as laser scanning (i.e. 1&ndash;2 cm)

MONITORING AND DEFORMATION ANALYSIS OF GROYNES USING TLS AT THE RIVER ELBE

To enter the Port of Hamburg, one of Europe’s busiest ports all vessels need to navigate around 145 km along the Elbe river, a tide influenced navigation channel. To protect the Elbe shoreline from erosion and to channel the waterway groynes (rigid hydraulic structures) have been built along the river. In the past years since ca. 2001 there has been a large increase in damage of groynes structural integrity at parts of the German waterways. The reason for this was determined in the ever growing size of container vessels passing by and inducing long periodical primary waves which have such a force that they erode the groynes rock structure. To analyse and improve the groynes structural resistance for vessel-induced long periodical wave loads an in-situ study is carried out at Juelssand, located at the Elbe river estuary. Over a period of two years the change of the geometrical structure of two different groyne shapes is monitored automatically by utilising two terrestrial laser scanners mounted in protective housings, located each on a 12 m high platform. The self-contained monitoring systems perform scanning of the two groynes one to two times a day at low tide, as the structures are fully submerged at high tide. The long-periodical wave loads are also determined using pressure sensors in each groyne. To correlate the captured data with vessel events and analyse the effects, vessel related parameters are recorded utilizing the Automatic Identification System (AIS). This paper describes the automated processes for the data acquisition and focusses on the deformation that is calculated using current, extended and new algorithms of the Point Cloud Library. It shows the process chain from the acquisition of raw scan files from an elevated station to the filtering of point cloud, the registration, the calculation of pointwise changes and the aggregation to a grid for later correlation with ship parameters. When working outdoor in all kinds of weather conditions, the processes and equipment need to be robust and account for various cases and situations. This is especially applicable for the algorithms, which need to be adaptable to different scenarios like wet surfaces or snow and unwelcome objects ranging from flotsam to birds sitting on the groyne. At the current stage of the research, deformation in the magnitude of a couple of decimetres is observable. The orientation and location of the deformation is on the seaward side and corresponds to the lower distance of vessels leaving the harbour