Quantitative Analysis of Mouse Retinal Layers Using Automated Segmentation of Spectral Domain Optical Coherence Tomography Images.

PURPOSE Quantification of retinal layers using automated segmentation of optical coherence tomography (OCT) images allows for longitudinal studies of retinal and neurological disorders in mice. The purpose of this study was to compare the performance of automated retinal layer segmentation algorithms with data from manual segmentation in mice using the Spectralis OCT. METHODS Spectral domain OCT images from 55 mice from three different mouse strains were analyzed in total. The OCT scans from 22 C57Bl/6, 22 BALBc, and 11 C3A.Cg-Pde6b(+)Prph2(Rd2) /J mice were automatically segmented using three commercially available automated retinal segmentation algorithms and compared to manual segmentation. RESULTS Fully automated segmentation performed well in mice and showed coefficients of variation (CV) of below 5% for the total retinal volume. However, all three automated segmentation algorithms yielded much thicker total retinal thickness values compared to manual segmentation data (P < 0.0001) due to segmentation errors in the basement membrane. CONCLUSIONS Whereas the automated retinal segmentation algorithms performed well for the inner layers, the retinal pigmentation epithelium (RPE) was delineated within the sclera, leading to consistently thicker measurements of the photoreceptor layer and the total retina. TRANSLATIONAL RELEVANCE The introduction of spectral domain OCT allows for accurate imaging of the mouse retina. Exact quantification of retinal layer thicknesses in mice is important to study layers of interest under various pathological conditions.

Comparison of proximal femur and vertebral body strength improvements in the FREEDOM trial using an alternative finite element methodology

Denosumab reduced the incidence of new fractures in postmenopausal women with osteoporosis by 68% at the spine and 40% at the hip over 36 months compared with placebo in the FREEDOM study. This efficacy was supported by improvements from baseline in vertebral (18.2%) strength in axial compression and femoral (8.6%) strength in sideways fall configuration at 36 months, estimated in Newtons by an established voxel-based finite element (FE) methodology. Since FE analyses rely on the choice of meshes, material properties, and boundary conditions, the aim of this study was to independently confirm and compare the effects of denosumab on vertebral and femoral strength during the FREEDOM trial using an alternative smooth FE methodology. Unlike the previous FE study, effects on femoral strength in physiological stance configuration were also examined. QCT data for the proximal femur and two lumbar vertebrae were analyzed by smooth FE methodology at baseline, 12, 24, and 36 months for 51 treated (denosumab) and 47 control (placebo) subjects. QCT images were segmented and converted into smooth FE models to compute bone strength. L1 and L2 vertebral bodies were virtually loaded in axial compression and the proximal femora in both fall and stance configurations. Denosumab increased vertebral body strength by 10.8%, 14.0%, and 17.4% from baseline at 12, 24, and 36 months, respectively (p < 0.0001). Denosumab also increased femoral strength in the fall configuration by 4.3%, 5.1%, and 7.2% from baseline at 12, 24, and 36 months, respectively (p < 0.0001). Similar improvements were observed in the stance configuration with increases of 4.2%, 5.2%, and 5.2% from baseline (p ≤ 0.0007). Differences between the increasing strengths with denosumab and the decreasing strengths with placebo were significant starting at 12 months (vertebral and femoral fall) or 24 months (femoral stance). Using an alternative smooth FE methodology, we confirmed the significant improvements in vertebral body and proximal femur strength previously observed with denosumab. Estimated increases in strength with denosumab and decreases with placebo were highly consistent between both FE techniques.

Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features.

Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. MRI sets of 109 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA). Spearman's correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Auto-segmented sub-volumes showed moderate to high agreement with manually delineated volumes (range (r): 0.4 - 0.86). Also, the auto and manual volumes showed similar correlation with VASARI features (auto r = 0.35, 0.43 and 0.36; manual r = 0.17, 0.67, 0.41, for contrast-enhancing, necrosis and edema, respectively). The auto-segmented contrast-enhancing volume and post-contrast abnormal volume showed the highest AUC (0.66, CI: 0.55-0.77 and 0.65, CI: 0.54-0.76), comparable to manually defined volumes (0.64, CI: 0.53-0.75 and 0.63, CI: 0.52-0.74, respectively). BraTumIA and manual tumor sub-compartments showed comparable performance in terms of prognosis and correlation with VASARI features. This method can enable more reproducible definition and quantification of imaging based biomarkers and has potential in high-throughput medical imaging research.

Characterization of Chelonus inanitus polydnavirus segments: sequences and analysis, excision site and demonstration of clustering

Polydnaviruses (genera Ichnovirus and Bracovirus) have a segmented genome of circular double-stranded DNA molecules, replicate in the ovary of parasitic wasps and are essential for successful parasitism of the host. Here we show the first detailed analysis of various segments of a bracovirus, the Chelonus inanitus virus (CiV). Four segments were sequenced and two of them, CiV12 and CiV14, were found to be closely related while CiV14.5 and CiV16.8 were unrelated. CiV12, CiV14.5 and CiV16.8 are unique while CiV14 occurs also nested in another larger segment. All four segments are predicted to contain genes and predictions could be substantiated in most cases. Comparison with databases revealed no significant similarities at either the nucleotide or amino acid level. Inverted repeats with identities between 77% and 92% and lengths between 26 bp and 100 bp were found on all segments outside of predicted genes. Hybridization experiments indicate that CiV12 and CiV14 are both flanked by other virus segments, suggesting that proviral CiV segments are clustered in the genome of the wasp. The integration/excision site of CiV14 was analysed and compared to that of CiV12. On both termini of proviral CiV12 and CiV14 as well as in the excised circular molecule and the rejoined DNA a very similar repeat of 14 bp was found. A model to illustrate where the terminal repeats might recombine to yield the circular molecule is presented. Excision of CiV12 and CiV14 is restricted to the female and sets in at a very specific time-point in pupal-adult development.

Presence of polydnavirus transcripts in an egg-larval parasitoid and its lepidopterous host

The parasitoid Chelonus inanitus (Braconidae, Hymenoptera) oviposits into eggs of Spodoptera littoralis (Noctuidae, Lepidoptera) and, along with the egg, also injects polydnaviruses and venom, which are prerequisites for successful parasitoid development. The parasitoid larva develops within the embryonic and larval stages of the host, which enters metamorphosis precociously and arrests development in the prepupal stage. Polydnaviruses are responsible for the developmental arrest and interfere with the host's endocrine system in the last larval instar. Polydnaviruses have a segmented genome and are transmitted as a provirus integrated in the wasp's genome. Virions are only formed in female wasps and no virus replication is seen in the parasitized host. Here it is shown that very small amounts of viral transcripts were found in parasitized eggs and early larval instars of S. littoralis. Later on, transcript quantities increased and were highest in the late last larval instar for two of the three viral segments tested and in the penultimate to early last larval instar for the third segment. These are the first data on the occurrence of viral transcripts in the host of an egg-larval parasitoid and they are different from data reported for hosts of larval parasitoids, where transcript levels are already high shortly after parasitization. The analysis of three open reading frames by RT-PCR revealed viral transcripts in parasitized S. littoralis and in female pupae of C. inanitus, indicating the absence of host specificity. For one open reading frame, transcripts were also seen in male pupae, suggesting transcription from integrated viral DNA.

Fully Automatic Segmentation of Hip CT Images

Automatic segmentation of the hip joint with pelvis and proximal femur surfaces from CT images is essential for orthopedic diagnosis and surgery. It remains challenging due to the narrowness of hip joint space, where the adjacent surfaces of acetabulum and femoral head are hardly distinguished from each other. This chapter presents a fully automatic method to segment pelvic and proximal femoral surfaces from hip CT images. A coarse-to-fine strategy was proposed to combine multi-atlas segmentation with graph-based surface detection. The multi-atlas segmentation step seeks to coarsely extract the entire hip joint region. It uses automatically detected anatomical landmarks to initialize and select the atlas and accelerate the segmentation. The graph based surface detection is to refine the coarsely segmented hip joint region. It aims at completely and efficiently separate the adjacent surfaces of the acetabulum and the femoral head while preserving the hip joint structure. The proposed strategy was evaluated on 30 hip CT images and provided an average accuracy of 0.55, 0.54, and 0.50 mm for segmenting the pelvis, the left and right proximal femurs, respectively.

Occupational mobility chains and the role of job opportunities for upward, lateral and downward mobility in Switzerland

This paper addresses the rarely studied relationship between job vacancies and inter-firm upward, lateral, and downward status mobility in an occupationally segmented labor market, taking Switzerland as the example. To conceptualize mobility mechanisms in this type of labor market, we introduce the concept of “occupational mobility chains” and test its validity. This concept provides the backdrop for developing time-dependent measures of individual job opportunities based on Swiss Job Monitor data. We link these measures with career data taken from the Swiss Life History Study and employ event history analysis to test different propositions of the ways in which status mobility is contingent on the number and the status of vacant positions. Results support our assumption that in occupationally segmented labor markets vacant positions affect status mobility only to the degree that they are located within workers’ occupational mobility chains.

Particle Accelerators and Detectors for medical Diagnostics and Therapy

This Habilitationsschrift (Habilitation thesis) is focused on my research activities on medical applications of particle physics and was written in 2013 to obtain the Venia Docendi (Habilitation) in experimental physics at the University of Bern. It is based on selected publications, which represented at that time my major scientific contributions as an experimental physicist to the field of particle accelerators and detectors applied to medical diagnostics and therapy. The thesis is structured in two parts. In Part I, Chapter 1 presents an introduction to accelerators and detectors applied to medicine, with particular focus on cancer hadrontherapy and on the production of radioactive isotopes. In Chapter 2, my publications on medical particle accelerators are introduced and put into their perspective. In particular, high frequency linear accelerators for hadrontherapy are discussed together with the new Bern cyclotron laboratory. Chapter 3 is dedicated to particle detectors with particular emphasis on three instruments I contributed to propose and develop: segmented ionization chambers for hadrontherapy, a proton radiography apparatus with nuclear emulsion films, and a beam monitor detector for ion beams based on doped silica fibres. Selected research and review papers are contained in Part II. For copyright reasons, they are only listed and not reprinted in this on-line version. They are available on the websites of the journals.

T1ρ MRI detects cartilage damage in asymptomatic individuals with a cam deformity

Hips with a cam deformity are at risk for early cartilage degeneration, mainly in the anterolateral region of the joint. T1ρ MRI is a described technique for assessment of proteoglycan content in hyaline cartilage and subsequently early cartilage damage. In this study, 1.5 Tesla T1ρ MRI was performed on 20 asymptomatic hips with a cam deformity and compared to 16 healthy control hips. Cam deformity was defined as an alpha angle at 1:30 o'clock position over 60° and/or at 3:00 o'clock position over 50.5°. Hip cartilage was segmented and divided into four regions of interest (ROIs): anterolateral, anteromedial, posterolateral and posteromedial quadrants. Mean T1ρ value of the entire weight bearing cartilage in hips with a cam deformity (34.0 ± 4.6 ms) was significantly higher compared to control hips (31.3 ± 3.2 ms, p = 0.050). This difference reached significance in the anterolateral (p = 0.042) and posteromedial quadrants (p = 0.041). No significant correlation between the alpha angle and T1ρ values was detected. The results indicate cartilage damage occurs in hips with a cam deformity before symptoms occur. A significant difference in T1ρ values was found in the anterolateral quadrant, the area of direct engagement of the deformity, and in the posteromedial quadrant. To conclude, T1ρ MRI can detect early chondral damage in asymptomatic hips with a cam deformity. This article is protected by copyright. All rights reserved.

Food Recognition for Dietary Assessment Using Deep Convolutional Neural Networks

Diet management is a key factor for the prevention and treatment of diet-related chronic diseases. Computer vision systems aim to provide automated food intake assessment using meal images. We propose a method for the recognition of already segmented food items in meal images. The method uses a 6-layer deep convolutional neural network to classify food image patches. For each food item, overlapping patches are extracted and classified and the class with the majority of votes is assigned to it. Experiments on a manually annotated dataset with 573 food items justified the choice of the involved components and proved the effectiveness of the proposed system yielding an overall accuracy of 84.9%.

GoCARB: Smartphone-App zur Kohlenhydratberechnung bei Typ-1-Diabetes

Smartphone-App zur Kohlenhydratberechnung Neue Technologien wie Blutzuckersensoren und moderne Insulinpumpen prägten die Therapie des Typ-1-Diabetes (T1D) in den letzten Jahren in wesentlichem Ausmaß. Smartphones sind aufgrund ihrer rasanten technischen Entwicklung eine weitere Plattform für Applikationen zur Therapieunterstützung bei T1D. GoCARB Hierbei handelt es sich um ein zur Kohlenhydratberechnung entwickeltes System für Personen mit T1D. Die Basis für Endanwender stellt ein Smartphone mit Kamera dar. Zur Berechnung werden 2 mit dem Smartphone aus verschiedenen Winkeln aufgenommene Fotografien einer auf einem Teller angerichteten Mahlzeit benötigt. Zusätzlich ist eine neben dem Teller platzierte Referenzkarte erforderlich. Die Grundlage für die Kohlenhydratberechnung ist ein Computer-Vision-gestütztes Programm, das die Mahlzeiten aufgrund ihrer Farbe und Textur erkennt. Das Volumen der Mahlzeit wird mit Hilfe eines dreidimensional errechneten Modells bestimmt. Durch das Erkennen der Art der Mahlzeiten sowie deren Volumen kann GoCARB den Kohlenhydratanteil unter Einbeziehung von Nährwerttabellen berechnen. Für die Entwicklung des Systems wurde eine Bilddatenbank von mehr als 5000 Mahlzeiten erstellt und genutzt. Resümee Das GoCARB-System befindet sich aktuell in klinischer Evaluierung und ist noch nicht für Patienten verfügbar.

Motivational profiles of sporting event volunteers

This article presents an approach for segmenting sporting event volunteers according to differences in their motives. Empirical data were obtained from a sample of 1169 volunteers who registered for the 2014 European Athletics Championships in Zürich. They completed the ‘Volunteer Motivation Scale for International Sporting Events’ (VMS-ISE) questionaire. The validity of the VMS-ISE was replicated by confirmatory factor analysis and the data were cluster analysed to identify distinct motivation-based volunteer profiles. These segmented volunteers on the basis of mutually exclusive motivational characteristics. The external validity of the four motivation-based types (‘community supporters’, ‘material incentive seekers’, ‘social networkers’ and ‘career and personal growth orienteers’) was confirmed with socio-economic, sport-related and volunteer activity-related variables. It is concluded that motivation-based segmentation represents a useful way of gaining a clearer understanding of the patterns underlying the heterogeneity of sporting events volunteers.

Retinal slit lamp video mosaicking

Purpose To this day, the slit lamp remains the first tool used by an ophthalmologist to examine patient eyes. Imaging of the retina poses, however, a variety of problems, namely a shallow depth of focus, reflections from the optical system, a small field of view and non-uniform illumination. For ophthalmologists, the use of slit lamp images for documentation and analysis purposes, however, remains extremely challenging due to large image artifacts. For this reason, we propose an automatic retinal slit lamp video mosaicking, which enlarges the field of view and reduces amount of noise and reflections, thus enhancing image quality. Methods Our method is composed of three parts: (i) viable content segmentation, (ii) global registration and (iii) image blending. Frame content is segmented using gradient boosting with custom pixel-wise features. Speeded-up robust features are used for finding pair-wise translations between frames with robust random sample consensus estimation and graph-based simultaneous localization and mapping for global bundle adjustment. Foreground-aware blending based on feathering merges video frames into comprehensive mosaics. Results Foreground is segmented successfully with an area under the curve of the receiver operating characteristic curve of 0.9557. Mosaicking results and state-of-the-art methods were compared and rated by ophthalmologists showing a strong preference for a large field of view provided by our method. Conclusions The proposed method for global registration of retinal slit lamp images of the retina into comprehensive mosaics improves over state-of-the-art methods and is preferred qualitatively.

Qualifikationsnachfrage und Arbeitsmarkteintritt in der Schweiz: Arbeit im erlernten Beruf, Berufswechsel oder Arbeitslosigkeit

Berufsorientierte Bildungssysteme sind auf die Vermittlung von spezialisierten beruflichen Qualifikationen ausgelegt. Werden diese nach Abschluss einer beruflichen Grundbildung auf dem Arbeitsmarkt wenig nachgefragt, riskieren die Absolventen, die erworbenen berufsspezifischen Qualifikationen nicht verwerten zu können. Dies trifft nicht nur zu, wenn Arbeitsmarkteinsteiger arbeitslos werden, sondern auch, wenn sie den Beruf wechseln müssen. Für die drei verschiedenen Optionen des Arbeitsmarkteinstiegs – Arbeit im erlernten Beruf, Berufswechsel und Arbeitslosigkeit – wird erstens untersucht, welche Bedeutung das individuell passende und das fachfremde Stellenangebot hat. Zweitens wird analysiert, wie eine unterschiedlich ausgeprägte Nachfrage nach fachspezifischen Qualifikationen die Bedeutung ausbildungsbezogener und individueller Merkmale für den Berufseinstieg verändert. Die Schweiz mit ihrem berufsorientierten Bildungssystem und berufsfachlich segmentieren Arbeitsmarkt dient als empirische Referenz. Die multinominalen logistischen Regressionsmodelle basieren auf den Daten des Schweizer Jugendpanels PISA2000/TREE. Die Individualdaten von Lehrabgänger werden auf Berufsebene, zeitpunkt- und regionsspezifisch mit dem individuell passenden und fachfremden Stellenangebot verknüpft, das auf den Stelleninseratendaten des Stellenmarktmonitors Schweiz (SMM) beruht. Dank dieser Verknüpfung von Angebot und Nachfrage nach beruflichen Qualifikationen auf der Mikroebene kann zum ersten Mal die grundlegende Bedeutung der Personalnachfrage für den Berufseinstieg nachgewiesen werden.

Temporal association between childhood leukaemia and population growth in Swiss municipalities.

The population mixing hypothesis proposes that childhood leukaemia (CL) might be a rare complication of a yet unidentified subclinical infection. Large population influxes into previously isolated rural areas may foster localised epidemics of the postulated infection causing a subsequent increase of CL. While marked population growth after a period of stability was central to the formulation of the hypothesis and to the early studies on population mixing, there is a lack of objective criteria to define such growth patterns. We aimed to determine whether periods of marked population growth coincided with increases in the risk of CL in Swiss municipalities. We identified incident cases of CL aged 0-15 years for the period 1985-2010 from the Swiss Childhood Cancer Registry. Annual data on population counts in Swiss municipalities were obtained for 1980-2010. As exposures, we defined (1) cumulative population growth during a 5-year moving time window centred on each year (1985-2010) and (2) periods of 'take-off growth' identified by segmented linear regression. We compared CL incidence across exposure categories using Poisson regression and tested for effect modification by degree of urbanisation. Our study included 1500 incident cases and 2561 municipalities. The incident rate ratio (IRR) comparing the highest to the lowest quintile of 5-year population growth was 1.18 (95 % CI 0.96, 1.46) in all municipalities and 1.33 (95 % CI 0.93, 1.92) in rural municipalities (p value interaction 0.36). In municipalities with take-off growth, the IRR comparing the take-off period (>6 % annual population growth) with the initial period of low or negative growth (<2 %) was 2.07 (95 % CI 0.95, 4.51) overall and 2.99 (1.11, 8.05) in rural areas (p interaction 0.52). Our study provides further support for the population mixing hypothesis and underlines the need to distinguish take-off growth from other growth patterns in future research.