View subspaces for indexing and retrieval of 3D models

View-based indexing schemes for 3D object retrieval are gaining popularity since they provide good retrieval results. These schemes are coherent with the theory that humans recognize objects based on their 2D appearances. The viewbased techniques also allow users to search with various queries such as binary images, range images and even 2D sketches. The previous view-based techniques use classical 2D shape descriptors such as Fourier invariants, Zernike moments, Scale Invariant Feature Transform-based local features and 2D Digital Fourier Transform coefficients. These methods describe each object independent of others. In this work, we explore data driven subspace models, such as Principal Component Analysis, Independent Component Analysis and Nonnegative Matrix Factorization to describe the shape information of the views. We treat the depth images obtained from various points of the view sphere as 2D intensity images and train a subspace to extract the inherent structure of the views within a database. We also show the benefit of categorizing shapes according to their eigenvalue spread. Both the shape categorization and data-driven feature set conjectures are tested on the PSB database and compared with the competitor view-based 3D shape retrieval algorithmsComment: Three-Dimensional Image Processing (3DIP) and Applications (Proceedings Volume) Proceedings of SPIE Volume: 7526 Editor(s): Atilla M. Baskurt ISBN: 9780819479198 Date: 2 February 201

Biophysical studies of lipid membranes by solid state NMR and molecular dynamics simulations

Biological membranes separate the cell interior from the outside and have diverse functions from signal transduction, apoptosis to transportations of ions and small molecules in and out of the cell. Most of these functions are fulfilled by proteins incorporated in the membrane. However, lipids as the main component of membrane not only serve as structural element for bilayer formation but they are also directly involved e.g. signalling processes and bilayer properties are important to mediate protein interactions. To fully understand the role of lipids, it is necessary to develop a molecular understanding of how certain membrane components modify bulk bilayer structure and dynamics. Membranes are known to have many different motions in different conditions and time scales. Temperature, pH, water content and many other conditions change membrane dynamics in a high degree. In addition to this, time scales of motions in membranes vary from ns to ms range corresponding to fast motion and slow motion, respectively. Therefore, membranes are needed to be studied systematically by varying the conditions and using methods to investigate motions in various time scales separately. The aim of this study was therefore perform a combined solid-state NMR / molecular dynamics study on model membranes. Different substrates, such as potential drugs, polarizing agents and signaling lipids were incorporated into bilayers and their location within the membrane and their effect onto the membrane was probed. NSAIDs (non-steroidal anti-inflammatory drugs), pirinixic acid derivatives, ceramides and polarizing agents were the substrates for membranes in this study. There were several experimental methods that were applied in order to investigate effects of these substrates on membrane dynamics. Different kind of phospholipids including POPC, DMPC and DPPC were used. In addition to experimental work, with the information gathered from solid state NMR experiments molecular dynamics simulations were performed to obtain more information about the membranes at the molecular level. As a result, combination of solid-state NMR with molecular dynamics simulations provides very systematic way of investigating membrane dynamics in a large range of time scales. Pirinixic acid derivatives were special interest of this study because of their activity on peroxisome proliferator-activated receptor (PPAR) as an agonist as well as on enzymes of microsomal prostaglandin E2 synthase-1 (PGE2s) -1 and 5-lipoxygenase (5-LO) as dual inhibitor. Two potent pirinixic acid derivatives, 2-(4-chloro-6-(quinolin-6-ylamino)pyrimidin-2-ylthio)octanoic acid (compound 2) and 2-(4-chloro-6-(quinolin-6-ylamino)pyrimidin-2-ylthio)octanoate (compound 3), have been worked and their insertion depts were investigated by combining of solid state NMR and molecular dynamics simulations. Both experimental and theoretical results pointed out that compound 3 was inserted the phospholipid bilayer more deeply than 2. NSAIDs – lipid mixtures have been also studied here. It is known that consumption of NSAIDs as in mixture with lipids results much fewer side effects than consumption of the drugs alone. Thus, it is crucial to understand interactions of NSAIDs with lipids and investigate the possible complex formation of drugs with lipids. In this study, interactions of three widely used NSAIDs, ibuprofen, diclofenac and piroxicam, with DPPC were investigated by solid-state NMR. 1H and 31P NMR results depicted that ibuprofen and diclofenac had interactions with lipids, which is an indication of drug-lipid complex formation whereas piroxicam didn’t show any interactions with lipids suggesting that no complex formation occurred in the case of piroxicam. Ceramides are known to play key roles in many cell processes and many studies showed that the functions of ceramides are related with the ceramide effects on biological membranes. Therefore, in this study, influences of ceramides on biophysics of lipid bilayers were investigated by using various solid state NMR techniques and molecular dynamics simulations. Results from molecular dynamics simulations clearly showed that ceramide and lipids have strong interactions. More evidences about ceramide-lipid interactions were provided from 1H and 14N NMR results. In addition, it was indicated by both simulation and experimental methods that ceramide increased the rigidity of DMPC by increasing chain order parameters. BTbk is a biradical, which is used as polarizing agent for dynamic nuclear polarization (DNP) experiments and found to be more efficient than other widely used polarizing agents such as TOTAPOL. Since it is a hydrophobic compound, which prefers to stay inside lipid bilayer it is important to investigate the location and orientation of bTbk along the bilayer in order to understand its enhancement profile in DNP measurements. In this study, both NMR relaxation time measurements and molecular dynamics simulations revealed that bTbk tends to stay more close to hydrophobic chain of lipids than the interfacial part of lipids at bilayer surface. In the first part of this work, a brief introduction on lipid membranes as well as a theoretical summary on both methods of solid-state NMR and molecular dynamics simulations is given. Then, in the second part methodology is introduced for both solid-state NMR spectrometer and theoretical calculations. Afterwards, results of different membrane systems are discussed in the following parts for both solid state NMR and MD. Finally, in the last part, a summary and the conclusion of the overall results together with some future plans are explained.Biologische Membranen stellen eine Permeabilitätsbarriere zwischen dem Inneren und dem Äußeren von Zellen dar, die im Wesentlichen über die eingebetteten Membranproteine gesteuert wird. Für die mit der Membran assoziierten funktionalen Prozesse spielen aber auch Lipidbestandteile eine wichtige Rolle, was deren genaue Charakterisierung erforderlich macht. Beispiele hierfür sind u.a. laterale Phasentrennung/Rafts, Auflösung von Doppelschichtphasen bei der Zellfusion, die Rolle bestimmter Lipidbestandteile als sekundäre Botenstoffe, Modulierung der Aktivität von Membranproteinen über spezifische Lipidinteraktionen oder veränderte physikalische Membranparameter oder auch die Interaktion lipophiler Pharmaka mit Lipiden. Festkörper-NMR bietet einen idealen Zugang zu diesen Fragestellungen, da diese Technik direkte Experimente an verschiedensten Lipidphasen zulässt sowie über eine sehr große dynamische Bandbreite verfügt, über die mit geeigneten Experimenten viele dynamische Prozesse in der Membran detektiert werden können. Komplementär zu Festkörper-NMR können MD-Simulationen an vollständigen Lipiddoppelschichten zum Einsatz gebracht werden, um entweder Vorhersagen machen zu können, die mittels NMR überprüft werden können, oder um im Falle von unvollständigen NMR Datensätzen zu einem vollständigeren molekularen Bild des betrachteten Systems zu gelangen. Ziel dieser Dissertation war es daher, einen kombinierten FK-NMR/MD-Simulationsansatz für die Untersuchung kleiner Moleküle in der Lipidmembran zu etablieren und an mehreren Beispielen zu demonstrieren...

Revisiting SIFT for plant foliage in RGB images acquired on a turntable

In this work, SIFT features are revisited for their use in two applications of computer vision for plant analysis. The first application is the reconstruction of 3D models of plants through tracking homologue points in successive intensity images. The second application is to provide a new global descriptor that gives a measure of the level of self-similariy of foliage for plants of different architectures and foliar appearance. In order to properly exploit SIFT descriptors in relation to these applications, we discuss two aspects of the classical SIFT keypoint matching practice. On the one hand we propose to match detected keypoints based on a scale criterion. On the other hand, we drop the ratio rule while matching keypoints in two images and propose the use of a spatial proximity filter instead

SHREC 2010 - Shape Retrieval Contest of Range Scans

The SHREC’10 Shape Retrieval Contest of Range Scans aims at comparing algorithms that match a range scan to complete 3D models in a target database. The queries are range scans of real objects, and the objective is to retrieve complete 3D models that are of the same class. This problem is essential to current and future vision systems that perform shape based matching and classification of the objects in the environment. Two groups have participated in the contest. They have provided rank lists for the query set, which is composed of 120 range scan

Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability.

Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functions in promoter-proximal pausing and elongation processivity. Spt5 was also recognized for its roles in the transcription of expanded-repeat genes that are related to neurodegenerative diseases. Recently, a set of Spt5-Pol II small molecule inhibitors (SPIs) were reported, which selectively inhibit mutant huntingtin gene transcription. Inhibition mechanisms as well as interaction sites of these SPIs with Pol II and Spt5 are not entirely known. In this study, we predicted the binding sites of three selected SPIs at the Pol II-Spt5 interface by docking and molecular dynamics simulations. Two molecules out of three demonstrated strong binding with Spt5 and Pol II, while the other molecule was more loosely bound and sampled multiple binding sites. Strongly bound SPIs indirectly affected RNA and DNA dynamics at the exit site as DNA became more flexible while RNA was stabilized by increased interactions with Spt5. Our results suggest that the transcription inhibition mechanism induced by SPIs can be related to Spt5-nucleic acid interactions, which were altered to some extent with strong binding of SPIs