927 resultados para secondary structure detection
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Antibody microarrays are of great research interest because of their potential application as biosensors for high-throughput protein and pathogen screening technologies. In this active area, there is still a need for novel structures and assemblies providing insight in binding interactions such as spherical and annulus-shaped protein structures, e.g. for the utilization of curved surfaces for the enhanced protein-protein interactions and detection of antigens. Therefore, the goal of the presented work was to establish a new technique for the label-free detection of bio-molecules and bacteria on topographically structured surfaces, suitable for antibody binding.rnIn the first part of the presented thesis, the fabrication of monolayers of inverse opals with 10 μm diameter and the immobilization of antibodies on their interior surface is described. For this purpose, several established methods for the linking of antibodies to glass, including Schiff bases, EDC/S-NHS chemistry and the biotin-streptavidin affinity system, were tested. The employed methods included immunofluorescence and image analysis by phase contrast microscopy. It could be shown that these methods were not successful in terms of antibody immobilization and adjacent bacteria binding. Hence, a method based on the application of an active-ester-silane was introduced. It showed promising results but also the need for further analysis. Especially the search for alternative antibodies addressing other antigens on the exterior of bacteria will be sought-after in the future.rnAs a consequence of the ability to control antibody-functionalized surfaces, a new technique employing colloidal templating to yield large scale (~cm2) 2D arrays of antibodies against E. coli K12, eGFP and human integrin αvβ3 on a versatile useful glass surface is presented. The antibodies were swept to reside around the templating microspheres during solution drying, and physisorbed on the glass. After removing the microspheres, the formation of annuli-shaped antibody structures was observed. The preserved antibody structure and functionality is shown by binding the specific antigens and secondary antibodies. The improved detection of specific bacteria from a crude solution compared to conventional “flat” antibody surfaces and the setting up of an integrin-binding platform for targeted recognition and surface interactions of eukaryotic cells is demonstrated. The structures were investigated by atomic force, confocal and fluorescence microscopy. Operational parameters like drying time, temperature, humidity and surfactants were optimized to obtain a stable antibody structure.
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This study evaluated the performance of the DIAGNOdent pen laser fluorescence device (LFpen) in comparison with visual examination (VE), bitewing radiographs (BW) and visual examination combined with bitewing radiographs (VEBW) in detecting secondary approximal caries associated with composite restorations. In total, 60 approximal surfaces from 43 permanent molars with composite restorations were assessed twice by two examiners using the LFpen, VE, BW and VEBW. After histological preparation and hardness measurements, the sample was assigned to either a crown or root caries group, depending on the location of the lesions as the gold standard. For crown caries at D1, the highest values of specificity and sensitivity were observed for the LFpen at a cutoff value of 18 (1.00) and for the VEBW (0.89). At D3 (cutoff of 30), the LFpen showed the highest values of sensitivity and specificity. For root caries, the LFpen and VEBW showed the highest values of specificity (0.54), sensitivity (0.81) and accuracy (0.69). The Spearman rank correlation coefficients for crown/root caries with histology were 0.54/0.37 (LFpen), 0.29/0.10 (BW), 0.29/0.18 (VE) and 0.23/0.37 (VEBW). For the LFpen, the ICC varied from 0.80 (interexaminer) to 0.97 (intraexaminer B); the kappa value was 0.19 for BW and 0.35 for VE (interexaminer). Intraexaminer kappa values for BW were 0.25 (A) and 0.29 (B), and those for VE were 0.31 (A) and 0.32 (B). The LFpen device exhibited a performance comparable to that of conventional methods but with higher interexaminer reproducibility. Therefore, the LFpen should be considered an auxiliary method for the detection of secondary approximal caries associated with composite restorations.
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To compare the performance of LFpen (DIAGNOdent pen) with two different wedge-shaped tips to conventional bitewing radiography (BW) for detecting proximal secondary caries at the cervical margin of amalgam restorations in vitro.
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To evaluate these factors, the scale of perceived influences on the election of a specialized plan of studies, IPEP, was built and in this study its factorial structure and reliability were evaluated. The instrument was applied to 115 students, chosen by quote sampling. They were students of a subsidized private secondary school from the city of Chillan, Chile. An exploratory factorial analysis identified eight factors in the scale IPEP: Academic projection, Personal development, Maintenance of the social environment, Academic requirements, Satisfaction of others' expectations, Vocational information, Image of the plan and Family pressure. The results present an initial factorial structure, that empirically and theoretically adequate, whose factors were reliable and conceptually useful. These factors distinguish psychogenic and sociogenic aspects of the vocational process, and allow to initiate diagnostic and investigative actions in relation to this early vocational election that is established in secondary schools of the Chilean educational system
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To evaluate these factors, the scale of perceived influences on the election of a specialized plan of studies, IPEP, was built and in this study its factorial structure and reliability were evaluated. The instrument was applied to 115 students, chosen by quote sampling. They were students of a subsidized private secondary school from the city of Chillan, Chile. An exploratory factorial analysis identified eight factors in the scale IPEP: Academic projection, Personal development, Maintenance of the social environment, Academic requirements, Satisfaction of others' expectations, Vocational information, Image of the plan and Family pressure. The results present an initial factorial structure, that empirically and theoretically adequate, whose factors were reliable and conceptually useful. These factors distinguish psychogenic and sociogenic aspects of the vocational process, and allow to initiate diagnostic and investigative actions in relation to this early vocational election that is established in secondary schools of the Chilean educational system
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To evaluate these factors, the scale of perceived influences on the election of a specialized plan of studies, IPEP, was built and in this study its factorial structure and reliability were evaluated. The instrument was applied to 115 students, chosen by quote sampling. They were students of a subsidized private secondary school from the city of Chillan, Chile. An exploratory factorial analysis identified eight factors in the scale IPEP: Academic projection, Personal development, Maintenance of the social environment, Academic requirements, Satisfaction of others' expectations, Vocational information, Image of the plan and Family pressure. The results present an initial factorial structure, that empirically and theoretically adequate, whose factors were reliable and conceptually useful. These factors distinguish psychogenic and sociogenic aspects of the vocational process, and allow to initiate diagnostic and investigative actions in relation to this early vocational election that is established in secondary schools of the Chilean educational system
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On the orbiter of the Rosetta spacecraft, the Cometary Secondary Ion Mass Analyser (COSIMA) will provide new in situ insights about the chemical composition of cometary grains all along 67P/Churyumov–Gerasimenko (67P/CG) journey until the end of December 2015 nominally. The aim of this paper is to present the pre-calibration which has already been performed as well as the different methods which have been developed in order to facilitate the interpretation of the COSIMA mass spectra and more especially of their organic content. The first step was to establish a mass spectra library in positive and negative ion mode of targeted molecules and to determine the specific features of each compound and chemical family analyzed. As the exact nature of the refractory cometary organic matter is nowadays unknown, this library is obviously not exhaustive. Therefore this library has also been the starting point for the research of indicators, which enable to highlight the presence of compounds containing specific atom or structure. These indicators correspond to the intensity ratio of specific peaks in the mass spectrum. They have allowed us to identify sample containing nitrogen atom, aliphatic chains or those containing polyaromatic hydrocarbons. From these indicators, a preliminary calibration line, from which the N/C ratio could be derived, has also been established. The research of specific mass difference could also be helpful to identify peaks related to quasi-molecular ions in an unknown mass spectrum. The Bayesian Positive Source Separation (BPSS) technique will also be very helpful for data analysis. This work is the starting point for the analysis of the cometary refractory organic matter. Nevertheless, calibration work will continue in order to reach the best possible interpretation of the COSIMA observations.
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Horse ferricytochrome c (cyt c) undergoes exchange of one of its axial heme ligands (Met-80) for one or more non-native ligands under denaturing conditions. We have used 1H NMR spectroscopy to detect two conformations of paramagnetic cyt c with non-native heme ligation through a range of urea concentrations. One non-native form is an equilibrium unfolding intermediate observed under partially denaturing conditions and is attributed to replacement of Met-80 with one or more Lys side chains. The second non-native form, in which the native Met ligand is replaced by a His, is observed under strongly denaturing conditions. Thermodynamic analysis of these data indicates a relatively small ΔG (17 kJ/mol) for the transition from native to the Lys-ligated intermediate and a significantly larger ΔG (47 kJ/mol) for the transition from native to the His-ligated species. Although CD and fluorescence data indicate that the equilibrium unfolding of cyt c is a two-state process, these NMR results implicate an intermediate with His-Lys ligation.
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Sequence analysis of peptides naturally presented by major histocompatibility complex (MHC) class I molecules has revealed allele-specific motifs in which the peptide length and the residues observed at certain positions are restricted. Nevertheless, peptides containing the standard motif often fail to bind with high affinity or form physiologically stable complexes. Here we present the crystal structure of a well-characterized antigenic peptide from ovalbumin [OVA-8, ovalbumin-(257-264), SIINFEKL] in complex with the murine MHC class I H-2Kb molecule at 2.5-A resolution. Hydrophobic peptide residues Ile-P2 and Phe-P5 are packed closely together into binding pockets B and C, suggesting that the interplay of peptide anchor (P5) and secondary anchor (P2) residues can couple the preferred sequences at these positions. Comparison with the crystal structures of H-2Kb in complex with peptides VSV-8 (RGYVYQGL) and SEV-9 (FAPGNYPAL), where a Tyr residue is used as the C pocket anchor, reveals that the conserved water molecule that binds into the B pocket and mediates hydrogen bonding from the buried anchor hydroxyl group could not be likewise positioned if the P2 side chain were of significant size. Based on this structural evidence, H-2Kb has at least two submotifs: one with Tyr at P5 (or P6 for nonamer peptides) and a small residue at P2 (i.e., Ala or Gly) and another with Phe at P5 and a medium-sized hydrophobic residue at P2 (i.e., Ile). Deciphering of these secondary submotifs from both crystallographic and immunological studies of MHC peptide binding should increase the accuracy of T-cell epitope prediction.
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1049-D
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This thesis consisted of two major parts, one determining the masking characteristics of pixel noise and the other investigating the properties of the detection filter employed by the visual system. The theoretical cut-off frequency of white pixel noise can be defined from the size of the noise pixel. The empirical cut-off frequency, i.e. the largest size of noise pixels that mimics the effect of white noise in detection, was determined by measuring contrast energy thresholds for grating stimuli in the presence of spatial noise consisting of noise pixels of various sizes and shapes. The critical i.e. minimum number of noise pixels per grating cycle needed to mimic the effect of white noise in detection was found to decrease with the bandwidth of the stimulus. The shape of the noise pixels did not have any effect on the whiteness of pixel noise as long as there was at least the minimum number of noise pixels in all spatial dimensions. Furthermore, the masking power of white pixel noise is best described when the spectral density is calculated by taking into account all the dimensions of noise pixels, i.e. width, height, and duration, even when there is random luminance only in one of these dimensions. The properties of the detection mechanism employed by the visual system were studied by measuring contrast energy thresholds for complex spatial patterns as a function of area in the presence of white pixel noise. Human detection efficiency was obtained by comparing human performance with an ideal detector. The stimuli consisted of band-pass filtered symbols, uniform and patched gratings, and point stimuli with randomised phase spectra. In agreement with the existing literature, the detection performance was found to decline with the increasing amount of detail and contour in the stimulus. A measure of image complexity was developed and successfully applied to the data. The accuracy of the detection mechanism seems to depend on the spatial structure of the stimulus and the spatial spread of contrast energy.
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Classification procedures, including atmospheric correction satellite images as well as classification performance utilizing calibration and validation at different levels, have been investigated in the context of a coarse land-cover classification scheme for the Pachitea Basin. Two different correction methods were tested against no correction in terms of reflectance correction towards a common response for pseudo-invariant features (PIF). The accuracy of classifications derived from each of the three methods was then assessed in a discriminant analysis using crossvalidation at pixel, polygon, region, and image levels. Results indicate that only regression adjusted images using PIFs show no significant difference between images in any of the bands. A comparison of classifications at different levels suggests though that at pixel, polygon, and region levels the accuracy of the classifications do not significantly differ between corrected and uncorrected images. Spatial patterns of land-cover were analyzed in terms of colonization history, infrastructure, suitability of the land, and landownership. The actual use of the land is driven mainly by the ability to access the land and markets as is obvious in the distribution of land cover as a function of distance to rivers and roads. When considering all rivers and roads a threshold distance at which disproportional agro-pastoral land cover switches from over represented to under represented is at about 1km. Best land use suggestions seem not to affect the choice of land use. Differences in abundance of land cover between watersheds are more prevailing than differences between colonist and indigenous groups.
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We consider an LTE network where a secondary user acts as a relay, transmitting data to the primary user using a decode-and-forward mechanism, transparent to the base-station (eNodeB). Clearly, the relay can decode symbols more reliably if the employed precoder matrix indicators (PMIs) are known. However, for closed loop spatial multiplexing (CLSM) transmit mode, this information is not always embedded in the downlink signal, leading to a need for effective methods to determine the PMI. In this thesis, we consider 2x2 MIMO and 4x4 MIMO downlink channels corresponding to CLSM and formulate two techniques to estimate the PMI at the relay using a hypothesis testing framework. We evaluate their performance via simulations for various ITU channel models over a range of SNR and for different channel quality indicators (CQIs). We compare them to the case when the true PMI is known at the relay and show that the performance of the proposed schemes are within 2 dB at 10% block error rate (BLER) in almost all scenarios. Furthermore, the techniques add minimal computational overhead over existent receiver structure. Finally, we also identify scenarios when using the proposed precoder detection algorithms in conjunction with the cooperative decode-and-forward relaying mechanism benefits the PUE and improves the BLER performance for the PUE. Therefore, we conclude from this that the proposed algorithms as well as the cooperative relaying mechanism at the CMR can be gainfully employed in a variety of real-life scenarios in LTE networks.