Horse spleen segmentation technique as large animal model of preclinical trials

The parenchymal distribution of the splenic artery was studied in order to obtain anatomical basis for partial splenectomy. Thirty two spleens were studied, 26 spleens of healthy horses weighing 320 to 450kg, aged 3 to 12 years and 6 spleens of fetus removed from slaughterhouse. The spleens were submitted to arteriography and scintigraphy in order to have their vascular pattern examined and compared to the external aspect of the organ aiming establish anatomo-surgical segments. All radiographs were photographed with a digital camera and the digital images were submitted to a measuring system for comparative analysis of areas of dorsal and ventral anatomo-surgical segments. Anatomical investigations into the angioarchitecture of the equine spleen showed a paucivascular area, which coincides with a thinner external area, allowing the organ to be divided in two anatomo-surgical segments of approximately 50% of the organ each.

Biphasic positive airway pressure minimizes biological impact on lung tissue in mild acute lung injury independent of etiology

Abstract Introduction Biphasic positive airway pressure (BIVENT) is a partial support mode that employs pressure-controlled, time-cycled ventilation set at two levels of continuous positive airway pressure with unrestricted spontaneous breathing. BIVENT can modulate inspiratory effort by modifying the frequency of controlled breaths. Nevertheless, the optimal amount of inspiratory effort to improve respiratory function while minimizing ventilator-associated lung injury during partial ventilatory assistance has not been determined. Furthermore, it is unclear whether the effects of partial ventilatory support depend on acute lung injury (ALI) etiology. This study aimed to investigate the impact of spontaneous and time-cycled control breaths during BIVENT on the lung and diaphragm in experimental pulmonary (p) and extrapulmonary (exp) ALI. Methods This was a prospective, randomized, controlled experimental study of 60 adult male Wistar rats. Mild ALI was induced by Escherichia coli lipopolysaccharide either intratracheally (ALIp) or intraperitoneally (ALIexp). After 24 hours, animals were anesthetized and further randomized as follows: (1) pressure-controlled ventilation (PCV) with tidal volume (Vt) = 6 ml/kg, respiratory rate = 100 breaths/min, PEEP = 5 cmH2O, and inspiratory-to-expiratory ratio (I:E) = 1:2; or (2) BIVENT with three spontaneous and time-cycled control breath modes (100, 75, and 50 breaths/min). BIVENT was set with two levels of CPAP (Phigh = 10 cmH2O and Plow = 5 cmH2O). Inspiratory time was kept constant (Thigh = 0.3 s). Results BIVENT was associated with reduced markers of inflammation, apoptosis, fibrogenesis, and epithelial and endothelial cell damage in lung tissue in both ALI models when compared to PCV. The inspiratory effort during spontaneous breaths increased during BIVENT-50 in both ALI models. In ALIp, alveolar collapse was higher in BIVENT-100 than PCV, but decreased during BIVENT-50, and diaphragmatic injury was lower during BIVENT-50 compared to PCV and BIVENT-100. In ALIexp, alveolar collapse during BIVENT-100 and BIVENT-75 was comparable to PCV, while decreasing with BIVENT-50, and diaphragmatic injury increased during BIVENT-50. Conclusions In mild ALI, BIVENT had a lower biological impact on lung tissue compared to PCV. In contrast, the response of atelectasis and diaphragmatic injury to BIVENT differed according to the rate of spontaneous/controlled breaths and ALI etiology.

Mechanical Alterations in airway smooth muscle after interaction with indoor pollutant – A mathematical model.

The viscoelasticity of mammalian lung is determined by the mechanical properties and structural regulation of the airway smooth muscle (ASM). The exposure to polluted air may deteriorate these properties with harmful consequences to individual health. Formaldehyde (FA) is an important indoor pollutant found among volatile organic compounds. This pollutant permeates through the smooth muscle tissue forming covalent bonds between proteins in the extracellular matrix and intracellular protein structure changing mechanical properties of ASM and inducing asthma symptoms, such as airway hyperresponsiveness, even at low concentrations. In the experimental scenario, the mechanical effect of FA is the stiffening of the tissue, but the mechanism behind this effect is not fully understood. Thus, the aim of this study is to reproduce the mechanical behavior of the ASM, such as contraction and stretching, under FA action or not. For this, it was created a two-dimensional viscoelastic network model based on Voronoi tessellation solved using Runge-Kutta method of fourth order. The equilibrium configuration was reached when the forces in different parts of the network were equal. This model simulates the mechanical behavior of ASM through of a network of dashpots and springs. This dashpot-spring mechanical coupling mimics the composition of the actomyosin machinery of ASM through the contraction of springs to a minimum length. We hypothesized that formation of covalent bonds, due to the FA action, can be represented in the model by a simple change in the elastic constant of the springs, while the action of methacholine (MCh) reduce the equilibrium length of the spring. A sigmoid curve of tension as a function of MCh doses was obtained, showing increased tension when the muscle strip was exposed to FA. Our simulations suggest that FA, at a concentration of 0.1 ppm, can affect the elastic properties of the smooth muscle ¯bers by a factor of 120%. We also analyze the dynamic mechanical properties, observing the viscous and elastic behavior of the network. Finally, the proposed model, although simple, incorporates the phenomenology of both MCh and FA and reproduces experimental results observed with in vitro exposure of smooth muscle to FA. Thus, this new mechanical approach incorporates several well know features of the contractile system of the cells in a tissue level model. The model can also be used in different biological scales.

Mechanical alterations in airway smooth muscle after interaction with indoor pollutant - A mathematical model

The viscoelasticity of mammalian lung is determined by the mechanical properties and structural regulation of the airway smooth muscle (ASM). The exposure to polluted air may deteriorate these properties with harmful consequences to individual health. Formaldehyde (FA) is an important indoor pollutant found among volatile organic compounds. This pollutant permeates through the smooth muscle tissue forming covalent bonds between proteins in the extracellular matrix and intracellular protein structure changing mechanical properties of ASM and inducing asthma symptoms, such as airway hyperresponsiveness, even at low concentrations. In the experimental scenario, the mechanical effect of FA is the stiffening of the tissue, but the mechanism behind this effect is not fully w1derstood. Thus, the aim of this study is to reproduce the mechanical behavior of the ASM, such as contraction and stretching, under FA action or not. For this, it was created a two-dimensional viscoelastic network model based on Voronoi tessellation solved using Runge-Kutta method of fourth order. The equilibrium configuration was reached when the forces in different parts of the network were equal. This model simulates the mechanical behavior of ASM through of a network of dashpots and springs. This dashpot-spring mechanical coupling mimics the composition of the actomyosin machinery of ASM through the contraction of springs to a minimum length. We hypothesized that formation of covalent bonds, due to the FA action, can be represented in the model by a simple change in the elastic constant of the springs, while the action of methacholinc (MCh) reduce the equilibrium length of the spring. A sigmoid curve of tension as a function of MCh doses was obtained, showing increased tension when the muscle strip was exposed to FA. Our simulations suggest that FA, at a concentration of 0.1 ppm, can affect the elastic properties of the smooth muscle fibers by a factor of 120%. We also analyze the dynamic mechanical properties, observing the viscous and elastic behavior of the network. Finally, the proposed model, although simple, ir1corporates the phenomenology of both MCh and FA and reproduces experirnental results observed with ir1 vitro exposure of smooth muscle to .FA. Thus, this new mechanical approach incorporates several well know features of the contractile system of the cells ir1 a tissue level model. The model can also be used in different biological scales.

Endotoxin exposure during sensitization to Blomia tropicalis allergens shifts TH2 immunity towards a TH17-mediated airway neutrophilic inflammation: role of TLR4 and TLR2

Experimental evidence and epidemiological studies indicate that exposure to endotoxin lipopolysaccharide (eLPS) or other TLR agonists prevent asthma. We have previously shown in the OVA-model of asthma that eLPS administration during alum-based allergen sensitization blocked the development of lung TH2 immune responses via MyD88 pathway and IL-12/IFN-γ axis. In the present work we determined the effect of eLPS exposure during sensitization to a natural airborne allergen extract derived from the house dust mite Blomia tropicalis (Bt). Mice were subcutaneously sensitized with Bt allergens co-adsorbed onto alum with or without eLPS and challenged twice intranasally with Bt. Cellular and molecular parameters of allergic lung inflammation were evaluated 24 h after the last Bt challenge. Exposure to eLPS but not to ultrapure LPS (upLPS) preparation during sensitization to Bt allergens decreased the influx of eosinophils and increased the influx of neutrophils to the airways. Inhibition of airway eosinophilia was not observed in IFN-γdeficient mice while airway neutrophilia was not observed in IL-17RA-deficient mice as well in mice lacking MyD88, CD14, TLR4 and, surprisingly, TLR2 molecules. Notably, exposure to a synthetic TLR2 agonist (PamCSK4) also induced airway neutrophilia that was dependent on TLR2 and TLR4 molecules. In the OVA model, exposure to eLPS or PamCSK4 suppressed OVA-induced airway inflammation. Our results suggest that B. tropicalis allergens engage TLR4 that potentiates TLR2 signaling. This dual TLR activation during sensitization results in airway neutrophilic inflammation associated with increased frequency of lung TH17 cells. Our work highlight the complex interplay between bacterial products, house dust mite allergens and TLR signaling in the induction of different phenotypes of airway inflammation.

Role of M2 muscarinic receptor in the airway response to methacholine of mice selected for minimal or maximal acute inflammatory response

Airway smooth muscle constriction induced by cholinergic agonists such as methacholine (MCh), which is typically increased in asthmatic patients, is regulated mainly by muscle muscarinic M3 receptors and negatively by vagal muscarinic M2 receptors. Here we evaluated basal (intrinsic) and allergen-induced (extrinsic) airway responses to MCh. We used two mouse lines selected to respond maximally (AIRmax) or minimally (AIRmin) to innate inflammatory stimuli. We found that in basal condition AIRmin mice responded more vigorously to MCh than AIRmax. Treatment with a specific M2 antagonist increased airway response of AIRmax but not of AIRmin mice. The expression of M2 receptors in the lung was significantly lower in AIRmin compared to AIRmax animals. AIRmax mice developed a more intense allergic inflammation than AIRmin, and both allergic mouse lines increased airway responses to MCh. However, gallamine treatment of allergic groups did not affect the responses to MCh. Our results confirm that low or dysfunctional M2 receptor activity is associated with increased airway responsiveness to MCh and that this trait was inherited during the selective breeding of AIRmin mice and was acquired by AIRmax mice during allergic lung inflammation

Dynamic texture segmentation based on deterministic partially self-avoiding walks

Recently there has been a considerable interest in dynamic textures due to the explosive growth of multimedia databases. In addition, dynamic texture appears in a wide range of videos, which makes it very important in applications concerning to model physical phenomena. Thus, dynamic textures have emerged as a new field of investigation that extends the static or spatial textures to the spatio-temporal domain. In this paper, we propose a novel approach for dynamic texture segmentation based on automata theory and k-means algorithm. In this approach, a feature vector is extracted for each pixel by applying deterministic partially self-avoiding walks on three orthogonal planes of the video. Then, these feature vectors are clustered by the well-known k-means algorithm. Although the k-means algorithm has shown interesting results, it only ensures its convergence to a local minimum, which affects the final result of segmentation. In order to overcome this drawback, we compare six methods of initialization of the k-means. The experimental results have demonstrated the effectiveness of our proposed approach compared to the state-of-the-art segmentation methods.

Dynamic texture analysis and segmentation using deterministic partially self-avoiding walks

Dynamic texture is a recent field of investigation that has received growing attention from computer vision community in the last years. These patterns are moving texture in which the concept of selfsimilarity for static textures is extended to the spatiotemporal domain. In this paper, we propose a novel approach for dynamic texture representation, that can be used for both texture analysis and segmentation. In this method, deterministic partially self-avoiding walks are performed in three orthogonal planes of the video in order to combine appearance and motion features. We validate our method on three applications of dynamic texture that present interesting challenges: recognition, clustering and segmentation. Experimental results on these applications indicate that the proposed method improves the dynamic texture representation compared to the state of the art.

Pattern-based segmentation of digital documents: model and implementation

This thesis proposes a new document model, according to which any document can be segmented in some independent components and transformed in a pattern-based projection, that only uses a very small set of objects and composition rules. The point is that such a normalized document expresses the same fundamental information of the original one, in a simple, clear and unambiguous way. The central part of my work consists of discussing that model, investigating how a digital document can be segmented, and how a segmented version can be used to implement advanced tools of conversion. I present seven patterns which are versatile enough to capture the most relevant documents’ structures, and whose minimality and rigour make that implementation possible. The abstract model is then instantiated into an actual markup language, called IML. IML is a general and extensible language, which basically adopts an XHTML syntax, able to capture a posteriori the only content of a digital document. It is compared with other languages and proposals, in order to clarify its role and objectives. Finally, I present some systems built upon these ideas. These applications are evaluated in terms of users’ advantages, workflow improvements and impact over the overall quality of the output. In particular, they cover heterogeneous content management processes: from web editing to collaboration (IsaWiki and WikiFactory), from e-learning (IsaLearning) to professional printing (IsaPress).

Automatic clothes segmentation for soft biometrics

[EN]During the last decade, researchers have verified that clothing can provide information for gender recognition. However, before extracting features, it is necessary to segment the clothing region. We introduce a new clothes segmentation method based on the application of the GrabCut technique over a trixel mesh, obtaining very promising results for a close to real time system. Finally, the clothing features are combined with facial and head context information to outperform previous results in gender recognition with a public database.

Stripe based clothes segmentation

[EN]In this paper, a clothes segmentation method for fashion parsing is described. This method does not rely in a previous pose estimation but people segmentation. Therefore, novel and classic segmentation techniques have been considered and improved in order to achieve accurate people segmentation. Unlike other methods described in the literature, the output is the bounding box and the predominant color of the different clothes and not a pixel level segmentation. The proposal is based on dividing the person area into an initial fixed number of stripes, that are later fused according to similar color distribution. To assess the quality of the proposed method the experiments are carried out with the Fashionista dataset that is widely used in the fashion parsing community.

Statistical methods for analysis and processing of medical ultrasound: applications to segmentation and restoration

In this thesis two major topics inherent with medical ultrasound images are addressed: deconvolution and segmentation. In the first case a deconvolution algorithm is described allowing statistically consistent maximum a posteriori estimates of the tissue reflectivity to be restored. These estimates are proven to provide a reliable source of information for achieving an accurate characterization of biological tissues through the ultrasound echo. The second topic involves the definition of a semi automatic algorithm for myocardium segmentation in 2D echocardiographic images. The results show that the proposed method can reduce inter- and intra observer variability in myocardial contours delineation and is feasible and accurate even on clinical data.

Über das Vermessen tubulärer Strukturen in der Computertomographie

Die chronisch obstruktive Lungenerkrankung (engl. chronic obstructive pulmonary disease, COPD) ist ein Überbegriff für Erkrankungen, die zu Husten, Auswurf und Dyspnoe (Atemnot) in Ruhe oder Belastung führen - zu diesen werden die chronische Bronchitis und das Lungenemphysem gezählt. Das Fortschreiten der COPD ist eng verknüpft mit der Zunahme des Volumens der Wände kleiner Luftwege (Bronchien). Die hochauflösende Computertomographie (CT) gilt bei der Untersuchung der Morphologie der Lunge als Goldstandard (beste und zuverlässigste Methode in der Diagnostik). Möchte man Bronchien, eine in Annäherung tubuläre Struktur, in CT-Bildern vermessen, so stellt die geringe Größe der Bronchien im Vergleich zum Auflösungsvermögen eines klinischen Computertomographen ein großes Problem dar. In dieser Arbeit wird gezeigt wie aus konventionellen Röntgenaufnahmen CT-Bilder berechnet werden, wo die mathematischen und physikalischen Fehlerquellen im Bildentstehungsprozess liegen und wie man ein CT-System mittels Interpretation als lineares verschiebungsinvariantes System (engl. linear shift invariant systems, LSI System) mathematisch greifbar macht. Basierend auf der linearen Systemtheorie werden Möglichkeiten zur Beschreibung des Auflösungsvermögens bildgebender Verfahren hergeleitet. Es wird gezeigt wie man den Tracheobronchialbaum aus einem CT-Datensatz stabil segmentiert und mittels eines topologieerhaltenden 3-dimensionalen Skelettierungsalgorithmus in eine Skelettdarstellung und anschließend in einen kreisfreien Graphen überführt. Basierend auf der linearen System Theorie wird eine neue, vielversprechende, integral-basierte Methodik (IBM) zum Vermessen kleiner Strukturen in CT-Bildern vorgestellt. Zum Validieren der IBM-Resultate wurden verschiedene Messungen an einem Phantom, bestehend aus 10 unterschiedlichen Silikon Schläuchen, durchgeführt. Mit Hilfe der Skelett- und Graphendarstellung ist ein Vermessen des kompletten segmentierten Tracheobronchialbaums im 3-dimensionalen Raum möglich. Für 8 zweifach gescannte Schweine konnte eine gute Reproduzierbarkeit der IBM-Resultate nachgewiesen werden. In einer weiteren, mit IBM durchgeführten Studie konnte gezeigt werden, dass die durchschnittliche prozentuale Bronchialwandstärke in CT-Datensätzen von 16 Rauchern signifikant höher ist, als in Datensätzen von 15 Nichtrauchern. IBM läßt sich möglicherweise auch für Wanddickenbestimmungen bei Problemstellungen aus anderen Arbeitsgebieten benutzen - kann zumindest als Ideengeber dienen. Ein Artikel mit der Beschreibung der entwickelten Methodik und der damit erzielten Studienergebnisse wurde zur Publikation im Journal IEEE Transactions on Medical Imaging angenommen.

Automated Segmentation and Non-Rigid Registration for the Quantitative Evaluation of Myocardial Perfusion from Magnetic Resonance Images

Myocardial perfusion quantification by means of Contrast-Enhanced Cardiac Magnetic Resonance images relies on time consuming frame-by-frame manual tracing of regions of interest. In this Thesis, a novel automated technique for myocardial segmentation and non-rigid registration as a basis for perfusion quantification is presented. The proposed technique is based on three steps: reference frame selection, myocardial segmentation and non-rigid registration. In the first step, the reference frame in which both endo- and epicardial segmentation will be performed is chosen. Endocardial segmentation is achieved by means of a statistical region-based level-set technique followed by a curvature-based regularization motion. Epicardial segmentation is achieved by means of an edge-based level-set technique followed again by a regularization motion. To take into account the changes in position, size and shape of myocardium throughout the sequence due to out of plane respiratory motion, a non-rigid registration algorithm is required. The proposed non-rigid registration scheme consists in a novel multiscale extension of the normalized cross-correlation algorithm in combination with level-set methods. The myocardium is then divided into standard segments. Contrast enhancement curves are computed measuring the mean pixel intensity of each segment over time, and perfusion indices are extracted from each curve. The overall approach has been tested on synthetic and real datasets. For validation purposes, the sequences have been manually traced by an experienced interpreter, and contrast enhancement curves as well as perfusion indices have been computed. Comparisons between automatically extracted and manually obtained contours and enhancement curves showed high inter-technique agreement. Comparisons of perfusion indices computed using both approaches against quantitative coronary angiography and visual interpretation demonstrated that the two technique have similar diagnostic accuracy. In conclusion, the proposed technique allows fast, automated and accurate measurement of intra-myocardial contrast dynamics, and may thus address the strong clinical need for quantitative evaluation of myocardial perfusion.

Airway Basal Cell Vascular Endothelial Growth Factor-mediated Cross-Talk Regulates Endothelial Cell Dependent Growth Support of Human Airway Basal Cells

The human airway epithelium is a pseudostratified heterogenous layer comprised of cili-ated, secretory, intermediate and basal cells. As the stem/progenitor population of the airway epi-thelium, airway basal cells differentiate into ciliated and secretory cells to replenish the airway epithelium during physiological turnover and repair. Transcriptome analysis of airway basal cells revealed high expression of vascular endothelial growth factor A (VEGFA), a gene not typically associated with the function of this cell type. Using cultures of primary human airway basal cells, we demonstrate that basal cells express all of the 3 major isoforms of VEGFA (121, 165 and 189) but lack functional expression of the classical VEGFA receptors VEGFR1 and VEGFR2. The VEGFA is actively secreted by basal cells and while it appears to have no direct autocrine function on basal cell growth and proliferation, it functions in a paracrine manner to activate MAPK signaling cascades in endothelium via VEGFR2 dependent signaling pathways. Using a cytokine- and serum-free co-culture system of primary human airway basal cells and human endothelial cells revealed that basal cell secreted VEGFA activated endothelium to ex-press mediators that, in turn, stimulate and support basal cell proliferation and growth. These data demonstrate novel VEGFA mediated cross-talk between airway basal cells and endothe-lium, the purpose of which is to modulate endothelial activation and in turn stimulate and sustain basal cell growth.