Software tools and efficient algorithms for the feature detection, feature tracking, event localization, and visualization of large sets of atmospheric data

Data sets describing the state of the earth's atmosphere are of great importance in the atmospheric sciences. Over the last decades, the quality and sheer amount of the available data increased significantly, resulting in a rising demand for new tools capable of handling and analysing these large, multidimensional sets of atmospheric data. The interdisciplinary work presented in this thesis covers the development and the application of practical software tools and efficient algorithms from the field of computer science, aiming at the goal of enabling atmospheric scientists to analyse and to gain new insights from these large data sets. For this purpose, our tools combine novel techniques with well-established methods from different areas such as scientific visualization and data segmentation. In this thesis, three practical tools are presented. Two of these tools are software systems (Insight and IWAL) for different types of processing and interactive visualization of data, the third tool is an efficient algorithm for data segmentation implemented as part of Insight.Insight is a toolkit for the interactive, three-dimensional visualization and processing of large sets of atmospheric data, originally developed as a testing environment for the novel segmentation algorithm. It provides a dynamic system for combining at runtime data from different sources, a variety of different data processing algorithms, and several visualization techniques. Its modular architecture and flexible scripting support led to additional applications of the software, from which two examples are presented: the usage of Insight as a WMS (web map service) server, and the automatic production of a sequence of images for the visualization of cyclone simulations. The core application of Insight is the provision of the novel segmentation algorithm for the efficient detection and tracking of 3D features in large sets of atmospheric data, as well as for the precise localization of the occurring genesis, lysis, merging and splitting events. Data segmentation usually leads to a significant reduction of the size of the considered data. This enables a practical visualization of the data, statistical analyses of the features and their events, and the manual or automatic detection of interesting situations for subsequent detailed investigation. The concepts of the novel algorithm, its technical realization, and several extensions for avoiding under- and over-segmentation are discussed. As example applications, this thesis covers the setup and the results of the segmentation of upper-tropospheric jet streams and cyclones as full 3D objects. Finally, IWAL is presented, which is a web application for providing an easy interactive access to meteorological data visualizations, primarily aimed at students. As a web application, the needs to retrieve all input data sets and to install and handle complex visualization tools on a local machine are avoided. The main challenge in the provision of customizable visualizations to large numbers of simultaneous users was to find an acceptable trade-off between the available visualization options and the performance of the application. Besides the implementational details, benchmarks and the results of a user survey are presented.

Non Invasive Tools for Early Detection of Autism Spectrum Disorders

Autism Spectrum Disorders (ASDs) describe a set of neurodevelopmental disorders. ASD represents a significant public health problem. Currently, ASDs are not diagnosed before the 2nd year of life but an early identification of ASDs would be crucial as interventions are much more effective than specific therapies starting in later childhood. To this aim, cheap an contact-less automatic approaches recently aroused great clinical interest. Among them, the cry and the movements of the newborn, both involving the central nervous system, are proposed as possible indicators of neurological disorders. This PhD work is a first step towards solving this challenging problem. An integrated system is presented enabling the recording of audio (crying) and video (movements) data of the newborn, their automatic analysis with innovative techniques for the extraction of clinically relevant parameters and their classification with data mining techniques. New robust algorithms were developed for the selection of the voiced parts of the cry signal, the estimation of acoustic parameters based on the wavelet transform and the analysis of the infant’s general movements (GMs) through a new body model for segmentation and 2D reconstruction. In addition to a thorough literature review this thesis presents the state of the art on these topics that shows that no studies exist concerning normative ranges for newborn infant cry in the first 6 months of life nor the correlation between cry and movements. Through the new automatic methods a population of control infants (“low-risk”, LR) was compared to a group of “high-risk” (HR) infants, i.e. siblings of children already diagnosed with ASD. A subset of LR infants clinically diagnosed as newborns with Typical Development (TD) and one affected by ASD were compared. The results show that the selected acoustic parameters allow good differentiation between the two groups. This result provides new perspectives both diagnostic and therapeutic.

Surface-enhanced vibrational techniques for the detection of synthetic organic colorants

The research project object of this thesis is focused on the development of an advanced analytical system based on the combination of an improved thin layer chromatography (TLC) plate coupled with infrared (FTIR) and Raman microscopies for the detection of synthetic dyes. Indeed, the characterization of organic colorants, which are commonly present in mixtures with other components and in a very limited amount, still represents a challenging task in scientific analyses of cultural heritage materials. The approach provides selective spectral fingerprints for each compound, foreseeing the complementary information obtained by micro ATR-RAIRS-FTIR and SERS-Raman analyses, which can be performed on the same separated spot. In particular, silver iodide (AgI) applied on a gold coated slide is proposed as an efficient stationary phase for the discrimination of complex analyte mixtures, such as dyes present in samples of art-historical interest. The gold-AgI-TLC plate shows high performances related both to the chromatographic separation of analytes and to the spectroscopic detection of components. The use of a mid-IR transparent inorganic salt as the stationary phase avoids interferences of the background absorption in FTIR investigations. Moreover, by ATR microscopy measurements performed on the gold-AgI surface, a considerable enhancement in the intensity of spectra is observed. Complementary information can be obtained by Raman analyses, foreseeing a SERS activity of the AgI substrate. The method has been tested for the characterization of a mixture of three synthetic organic colorants widely used in dyeing processes: Brilliant Green (BG1), Rhodamine B (BV10) and Methylene Blue (BB9).

UWB radar sensor networks: Detection algorithms design and experimental analysis

In the last years radar sensor networks for localization and tracking in indoor environment have generated more and more interest, especially for anti-intrusion security systems. These networks often use Ultra Wide Band (UWB) technology, which consists in sending very short (few nanoseconds) impulse signals. This approach guarantees high resolution and accuracy and also other advantages such as low price, low power consumption and narrow-band interference (jamming) robustness. In this thesis the overall data processing (done in MATLAB environment) is discussed, starting from experimental measures from sensor devices, ending with the 2D visualization of targets movements over time and focusing mainly on detection and localization algorithms. Moreover, two different scenarios and both single and multiple target tracking are analyzed.

Endocarditis due to Tropheryma whipplei: rapid detection, limited genetic diversity, and long-term clinical outcome in a local experience

The characteristic features of Whipple's disease include abdominal pain, diarrhoea, wasting, and arthralgias, with the causative agent, Tropheryma whipplei, being detected mainly in intestinal biopsies. PCR technology has led to the identification of T. whipplei in specimens from various other locations, including the central nervous system and the heart. T. whipplei is now recognized as one of the causes of culture-negative endocarditis, and endocarditis can be the only manifestation of the infection with T. whipplei. Although it is considered a rare disease, the true incidence of endocarditis due to T. whipplei is not clearly established. With the increasing use of molecular methods, it is likely that T. whipplei will be more frequently identified. Questions also remain about the genetic variability of T. whipplei strains, optimal diagnostic procedures and therapeutic options. In the present study, we provide clinical data on four new patients with documented endocarditis due to T. whipplei in the context of the available published literature. There was no clinical involvement of the gastrointestinal tract. Genetic analysis of the T. whipplei strains with DNA isolated from the excised heart valves revealed little to no genetic variability. In a selected case, we describe acridine orange staining for early detection of the disease, prompting early adaptation of the antibiotic therapy. We provide long-term follow-up data on the patients. In our hands, an initial 2-week course of intravenous antibiotics followed by cotrimoxazole for at least 1 year was a suitable treatment option for T. whipplei endocarditis.

Assessment of melanocytic skin lesions with a high-definition laser Doppler imaging system

Early detection is a major goal in the management of malignant melanoma. Besides clinical assessment many noninvasive technologies such as dermoscopy, digital dermoscopy and in vivo laser scanner microscopy are used as additional methods. Herein we tested a system to assess lesional perfusion as a tool for early melanoma detection.

Detection of Chlamydia and complement factors in neovascular membranes of patients with age-related macular degeneration

PURPOSE To investigate whether Chlamydia pneumoniae and complement factors were present in surgically removed choroidal neovascular membranes (CNV) of patients with age-related macular degeneration (AMD). METHODS Paraffin sections of 26 CNV were stained for C. pneumoniae or the complement factors H (CFH) and C5, whereas macrophages were identified by positive CD68 staining. Clinical characteristics have been correlated to the immunohistochemical findings. RESULTS C. pneumoniae was found in 68% of the investigated membranes, and 88% of these membranes were also positive for CD68. Staining for CFH and C5 gave a positive reaction in 68 and 41% of the membranes, respectively. Patients with C5-positive membranes had significantly larger CNV mean area and were younger than patients with CFH-positive membranes at the operation time point. CONCLUSIONS Correlations between clinical symptoms and complement factor C5 could be shown. The results strengthen the hypothesis of an involvement of the complement system in AMD.

Detection of exon deletions within an entire gene (CFTR) by relative quantification on the LightCycler

BACKGROUND: Cystic fibrosis (CF) is associated with at least 1 pathogen point sequence variant on each CFTR allele. Some symptomatic patients, however, have only 1 detectable pathogen sequence variant and carry, on the other allele, a large deletion that is not detected by conventional screening methods. METHODS: For relative quantitative real-time PCR detection of large deletions in the CFTR gene, we designed DNA-specific primers for each exon of the gene and primers for a reference gene (beta2-microglobulin). For PCR we used a LightCycler system (Roche) and calculated the gene-dosage ratio of CFTR to beta2-microglobulin. We tested the method by screening all 27 exons in 3 healthy individuals and 2 patients with only 1 pathogen sequence variant. We then performed specific deletion screenings in 10 CF patients with known large deletions and a blinded analysis in which we screened 24 individuals for large deletions by testing 8 of 27 exons. RESULTS: None of the ratios for control samples were false positive (for deletions or duplications); moreover, for all samples from patients with known large deletions, the calculated ratios for deleted exons were close to 0.5. In addition, the results from the blinded analysis demonstrated that our method can also be used for the screening of single individuals. CONCLUSIONS: The LightCycler assay allows reliable and rapid screening for large deletions in the CFTR gene and detects the copy number of all 27 exons.

Influence of the condition of the adjacent tooth surface on fluorescence measurements for the detection of approximal caries

The aim of this study was to test whether the status of the adjacent tooth surface has an influence on the signal of a new laser fluorescence (LF) device for the detection of approximal caries. Seventy-eight teeth were selected from a pool of extracted permanent human molars, frozen at -20 degrees C until use. Before being measured the teeth were defrosted, cleaned, and any calculus removed. As a control, a defined approximal surface of each tooth was measured with the LF device holding the tip with the detecting- and the reverse-side on it, but without a neighboring tooth contacting the surface. The proximal site under examination was then placed adjacent to a tooth, which had deep dentinal caries, a composite restoration, a provisional ZnO-Eugenol restoration, or a ceramic restoration. The adjacent tooth with the ZnO-Eugenol restoration, the composite restoration, and the dentinal caries all demonstrated a statistically significant increase of LF readings on sound tooth surfaces. Teeth with enamel or dentinal caries were only slightly (and not statistically significantly) influenced by the different types of neighboring surfaces compared with the control LF readings. It can be concluded that caries detection of approximal tooth surfaces with the new LF system might be influenced by the condition of the adjacent tooth surface.

Comparison of different radiography systems in an experimental study for detection of forearm fractures and evaluation of the Müller-AO and Frykman classification for distal radius fractures

OBJECTIVES: We sought to compare the diagnostic performance of screen-film radiography, storage-phosphor radiography, and a flat-panel detector system in detecting forearm fractures and to classify distal radius fractures according to the Müller-AO and Frykman classifications compared with the true extent, depicted by anatomic preparation. MATERIALS AND METHODS: A total of 71 cadaver arms were fractured in a material testing machine creating different fractures of the radius and ulna as well as of the carpal bones. Radiographs of the complete forearm were evaluated by 3 radiologists, and anatomic preparation was used as standard of reference in a receiver operating curve analysis. RESULTS: The highest diagnostic performance was obtained for the detection of distal radius fractures with area under the receiver operating curve (AUC) values of 0.959 for screen-film radiography, 0.966 for storage-phosphor radiography, and 0.971 for the flat-panel detector system (P > 0.05). Exact classification was slightly better for the Frykman (kappa values of 0.457-0.478) compared with the Müller-AO classification (kappa values of 0.404-0.447), but agreement can be considered as moderate for both classifications. CONCLUSIONS: The 3 imaging systems showed a comparable diagnostic performance in detecting forearm fractures. A high diagnostic performance was demonstrated for distal radius fractures and conventional radiography can be routinely performed for fracture detection. However, compared with anatomic preparation, depiction of the true extent of distal radius fractures was limited and the severity of distal radius fractures tends to be underestimated.

Detection of approximal caries with a new laser fluorescence device

The laser device DIAGNOdent developed for the detection of occlusal caries has limited value on approximal surfaces. The aim of this study was to develop and to test a new laser fluorescence (LF) device for the detection of approximal caries. Light with a wavelength of 655 nm was transported to the approximal surface using two different sapphire fibre tips. Seventy-five teeth were selected from a pool of extracted permanent human molars, frozen at -20 degrees C until use. Before being measured, they were defrosted, cleaned and calculus was removed with a scaler. The molars were set in blocks simulating the contact area of adults. Bitewing radiographs were obtained using Kodak Insight films. After two independent assessments with the new LF device, the teeth were histologically prepared, and assessed for caries extension. Using the laser, specificity values for D1 threshold (outer half of enamel), D2 threshold (inner half of enamel), D3 threshold (dentine) ranged between 0.81 and 0.93, sensitivity between 0.84 and 0.92 with no difference between the two tips. Bitewing radiography showed an inferior performance compared to LF (p<0.05). Intraex aminer reproducibility was high (kappa>.74). The new LF system might be a useful additional tool in detecting approximal caries. Because of its good reproducibility, it could be used to monitor caries regression or progression on approximal surfaces.

Single-exposure dual-energy subtraction chest radiography: detection of pulmonary nodules and masses in clinical practice

The purpose of this retrospective study was to evaluate the impact of energy subtraction (ES) chest radiography on the detection of pulmonary nodules and masses in daily routine. Seventy-seven patients and 25 healthy subjects were examined with a single exposure digital radiography system. Five blinded readers evaluated first the non-subtracted PA and lateral chest radiographs alone and then together with the subtracted PA soft tissue images. The size, location and number of lung nodules or masses were registered with the confidence level. CT was used as standard of reference. For the 200 total lesions, a sensitivity of 33.5-52.5% was found at non-subtracted and a sensitivity of 43.5-58.5% at energy-subtracted radiography, corresponding to a significant improvement in four of five readers (p < 0.05). However, in three of five readers the rate of false positives was higher with ES. With ES, sensitivity, but not the area under the alternative free-response receiver operating characteristics (AFROC) curve, showed a good correlation with reader experience (R = 0.90, p = 0.026). In four of five readers, the diagnostic confidence improved with ES (p = 0.0036). We conclude that single-exposure digital ES chest radiography improves detection of most pulmonary nodules and masses, but identification of nodules <1 cm and false-positive findings remain a problem.