Arrow plot and CA maps on microarray preprocessing methods

Microarray allow to monitoring simultaneously thousands of genes, where the abundance of the transcripts under a same experimental condition at the same time can be quantified. Among various available array technologies, double channel cDNA microarray experiments have arisen in numerous technical protocols associated to genomic studies, which is the focus of this work. Microarray experiments involve many steps and each one can affect the quality of raw data. Background correction and normalization are preprocessing techniques to clean and correct the raw data when undesirable fluctuations arise from technical factors. Several recent studies showed that there is no preprocessing strategy that outperforms others in all circumstances and thus it seems difficult to provide general recommendations. In this work, it is proposed to use exploratory techniques to visualize the effects of preprocessing methods on statistical analysis of cancer two-channel microarray data sets, where the cancer types (classes) are known. For selecting differential expressed genes the arrow plot was used and the graph of profiles resultant from the correspondence analysis for visualizing the results. It was used 6 background methods and 6 normalization methods, performing 36 pre-processing methods and it was analyzed in a published cDNA microarray database (Liver) available at http://genome-www5.stanford.edu/ which microarrays were already classified by cancer type. All statistical analyses were performed using the R statistical software.

Comparison of Methods and Co-Registration Maps of EEG and fMRI in Occipital Lobe Epilepsy

Clinically childhood occipital lobe epilepsy (OLE) manifests itself with distinct syndromes. The traditional EEG recordings have not been able to overcome the difficulty in correlating the ictal clinical symptoms to the onset in particular areas of the occipital lobes. To understand these syndromes it is important to map with more precision the epileptogenic cortical regions in OLE. Experimentally, we studied three idiopathic childhood OLE patients with EEG source analysis and with the simultaneous acquisition of EEG and fMRI, to map the BOLD effect associated with EEG spikes. The spatial overlap between the EEG and BOLD results was not very good, but the fMRI suggested localizations more consistent with the ictal clinical manifestations of each type of epileptic syndrome. Since our first results show that by associating the BOLD effect with interictal spikes the epileptogenic areas are mapped to localizations different from those calculated from EEG sources and that by using different EEG/fMRI processing methods our results differ to some extent, it is very important to compare the different methods of processing the localization of activation and develop a good methodology for obtaining co-registration maps of high resolution EEG with BOLD localizations.

Effect of processing on antioxidant potential and total phenolics content in beet (Beta vulgaris L.)

The antioxidant capacity of beet is associated with non-nutritive constituents, such as phenolic compounds. The purpose of this research was to evaluate the effect of two different heat-processing techniques (drying and canned) on the antioxidant potential (ABTS) and phenolics content of beets. A forced air circulation dehydrator was used for the drying. Drying at high temperatures (100 + 90 °C/5.6 hours; 90 °C/6 hours) increased the antioxidant potential of the processed products while mild drying conditions decreased it (80 °C/6 hours; 100 + 70 °C/6 hours) or had no effect on it (70 °C/7 hours; 100 + 80 °C/6 hours). For the canned products, the antioxidant potential did not differ according to the pH (4.2 to 3.8) for any of the four acids tested. Some processing methods influenced the antioxidant potential of the processed products, and this was also dependent on changes in the total phenolics content.

Variation of glucoraphanin and glucobrassicin: anticancer components in Brassica during processing

Effects of cold storage and three common cooking practices, blanching, sauteing, and microwave cooking at different time intervals, on the content of glucosinolate (GSL) anticancer components in six Brassica vegetables were investigated. Eleven GSLs including progoitrin, glucoraphanin, sinigrin, glucoalyssin, gluconapin, glucobrassicanapin, glucoerucin, glucobrassicin, 4-methoxyglucobrassicin, gluconasturtiin, and neoglucobrassicin were quantified using LC-MS and HPLC. Storage at 4 ºC indicated no significant loss of GSLs in broccoli, kohlrabi, and cabbage, and approximately 90-100% of the total concentration of aliphatic and indolyl GSLs were detected. Interestingly, glucoraphanin and glucobrassicin, known as a cancer prevention agents, increased approximately above 50% in broccoli, kohlrabi, and cabbage, while the amount of glucobrassicin decreased by 5% in cauliflower for 5 days at 4 ºC. Blanching of broccoli at 120 sec significantly (36%) decreased total GSLs; however, sautéing and microwaving decreased by13-26%. Individual GSLs have different response at blanching. These findings suggest that different processing methods for each vegetable would be preferred to preserve the nutritional qualities.

DNA Sequence Representation methods

DNA sequence representation methods are used to denote a gene structure effectively and help in similarities/dissimilarities analysis of coding sequences. Many different kinds of representations have been proposed in the literature. They can be broadly classified into Numerical, Graphical, Geometrical and Hybrid representation methods. DNA structure and function analysis are made easy with graphical and geometrical representation methods since it gives visual representation of a DNA structure. In numerical method, numerical values are assigned to a sequence and digital signal processing methods are used to analyze the sequence. Hybrid approaches are also reported in the literature to analyze DNA sequences. This paper reviews the latest developments in DNA Sequence representation methods. We also present a taxonomy of various methods. A comparison of these methods where ever possible is also done

Effects of processing on the structure of zein/oleic acid films investigated by X-ray diffraction

Zein films plasticized with oleic acid were formed by solution casting, by the stretching of moldable resins, and by blown film extrusion. The effects of the forming process on film structure were investigated by X-ray diffraction. Wide-angle X-ray scattering (WAXS) patterns showed d-spacings at 4.5 and 10 angstrom, which were attributed to the zein alpha-helix backbone and inter-helix packing, respectively. The 4.5.angstrom d-spacing remained stable under processing while the 10 angstrom d-spacing varied with processing treatment. Small-angle X-ray scattering (SAXS) detected a long-range periodicity for the formed films but not for unprocessed zein, which suggests that the forming process-promoted film structure development is possibly aided by oleic acid. The SAXS d-spacing varied among the samples (130-238 angstrom) according to zein origin and film-forming method. X-ray scattering data suggest that the zein molecular structure resists processing but the zein supramolecular arrangements in the formed films are dependent on processing methods.

Effects of food processing and fibre content on the digestibility, energy intake and biochemical parameters of Blue-and-gold macaws (Ara ararauna L. - Aves, Psittacidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Bioimaging of animal embryogenesis: mathematical methods and computational algorithms

Some fundamental biological processes such as embryonic development have been preserved during evolution and are common to species belonging to different phylogenetic positions, but are nowadays largely unknown. The understanding of cell morphodynamics leading to the formation of organized spatial distribution of cells such as tissues and organs can be achieved through the reconstruction of cells shape and position during the development of a live animal embryo. We design in this work a chain of image processing methods to automatically segment and track cells nuclei and membranes during the development of a zebrafish embryo, which has been largely validates as model organism to understand vertebrate development, gene function and healingrepair mechanisms in vertebrates. The embryo is previously labeled through the ubiquitous expression of fluorescent proteins addressed to cells nuclei and membranes, and temporal sequences of volumetric images are acquired with laser scanning microscopy. Cells position is detected by processing nuclei images either through the generalized form of the Hough transform or identifying nuclei position with local maxima after a smoothing preprocessing step. Membranes and nuclei shapes are reconstructed by using PDEs based variational techniques such as the Subjective Surfaces and the Chan Vese method. Cells tracking is performed by combining informations previously detected on cells shape and position with biological regularization constraints. Our results are manually validated and reconstruct the formation of zebrafish brain at 7-8 somite stage with all the cells tracked starting from late sphere stage with less than 2% error for at least 6 hours. Our reconstruction opens the way to a systematic investigation of cellular behaviors, of clonal origin and clonal complexity of brain organs, as well as the contribution of cell proliferation modes and cell movements to the formation of local patterns and morphogenetic fields.

Investigation of Solid-State Shear Pulverization Processing Parameters for Polyethylene-Clay Nanocomposites

Investigates multiple processing parameters, includingpolymer type, filler type, processing technique, severity of SSSP (Solid-state shear pulverization)processing, and postprocessing, of SSSP. HDPE and LLDPE polymers with pristine clay and organo-clay samples are explored. Effects on crystallization, high-temperature behavior, mechanicalproperties, and gas barrier properties are examined. Thermal, mechanical, and morphological characterization is conducted to determine polymer/filler compatibility and superior processing methods for the polymer-clay nanocomposites.

Characterization of Biodegradable Polymer Nanocomposites Fabricated via Solid-State Processing

Biodegradable polymer/clay nanocomposites were prepared withpristine and organically modified montmorillonite in polylactic acid (PLA) and polycaprolactone (PCL) polymer matrices. Nanocomposites were fabricated using extrusion and SSSP to compare the effects of melt-state and solid-state processing on the morphology of the final nanocomposite. Characterization of various material properties was performed on prepared biodegradable polymer/clay nanocomposites to evaluate property enhancements from different clays and/or processing methods.

EXTRACTION OF PICTORIAL ENERGY INFORMATION FROM CAMPUS UNMETERED BUILDINGS USING IMAGE PROCESSING TECHNIQUES

In recent years, advanced metering infrastructure (AMI) has been the main research focus due to the traditional power grid has been restricted to meet development requirements. There has been an ongoing effort to increase the number of AMI devices that provide real-time data readings to improve system observability. Deployed AMI across distribution secondary networks provides load and consumption information for individual households which can improve grid management. Significant upgrade costs associated with retrofitting existing meters with network-capable sensing can be made more economical by using image processing methods to extract usage information from images of the existing meters. This thesis presents a new solution that uses online data exchange of power consumption information to a cloud server without modifying the existing electromechanical analog meters. In this framework, application of a systematic approach to extract energy data from images replaces the manual reading process. One case study illustrates the digital imaging approach is compared to the averages determined by visual readings over a one-month period.

Extraction of subjective properties in image processing

Most of the present digital images processing methods are related with objective characterization of external properties as shape, form or colour. This information concerns objective characteristics of different bodies and is applied to extract details to perform several different tasks. But in some occasions, some other type of information is needed. This is the case when the image processing system is going to be applied to some operation related with living bodies. In this case, some other type of object information may be useful. As a matter of fact, it may give additional knowledge about its subjective properties. Some of these properties are object symmetry, parallelism between lines and the feeling of size. These types of properties concerns more to internal sensations of living beings when they are related with their environment than to the objective information obtained by artificial systems. This paper presents an elemental system able to detect some of the above-mentioned parameters. A first mathematical model to analyze these situations is reported. This theoretical model will give the possibility to implement a simple working system. The basis of this system is the use of optical logic cells, previously employed in optical computing.

Computational methods for the detection of facial palsy

We are developing a telemedicine application which offers automated diagnosis of facial (Bell's) palsy through a Web service. We used a test data set of 43 images of facial palsy patients and 44 normal people to develop the automatic recognition algorithm. Three different image pre-processing methods were used. Machine learning techniques (support vector machine, SVM) were used to examine the difference between the two halves of the face. If there was a sufficient difference, then the SVM recognized facial palsy. Otherwise, if the halves were roughly symmetrical, the SVM classified the image as normal. It was found that the facial palsy images had a greater Hamming Distance than the normal images, indicating greater asymmetry. The median distance in the normal group was 331 (interquartile range 277-435) and the median distance in the facial palsy group was 509 (interquartile range 334-703). This difference was significant (P

Signal processing techniques for ultrasonic inspection

This thesis discusses the need for nondestructive testing and highlights some of the limitations in present day techniques. Special interest has been given to ultrasonic examination techniques and the problems encountered when they are applied to thick welded plates. Some suggestions are given using signal processing methods. Chapter 2 treats the need for nondestructive testing as seen in the light of economy and safety. A short review of present day techniques in nondestructive testing is also given. The special problems using ultrasonic techniques for welded structures is discussed in Chapter 3 with some examples of elastic wave propagation in welded steel. The limitations in applying sophisticated signal processing techniques to ultrasonic NDT~ mainly found in the transducers generating or receiving the ultrasound. Chapter 4 deals with the different transducers used. One of the difficulties with ultrasonic testing is the interpretation of the signals encountered. Similar problems might be found with SONAR/RADAR techniques and Chapter 5 draws some analogies between SONAR/RADAR and ultrasonic nondestructive testing. This chapter also includes a discussion on some on the techniques used in signal processing in general. A special signal processing technique found useful is cross-correlation detection and this technique is treated in Chapter 6. Electronic digital compute.rs have made signal processing techniques easier to implement -Chapter 7 discusses the use of digital computers in ultrasonic NDT. Experimental equipment used to test cross-correlation detection of ultrasonic signals is described in Chapter 8. Chapter 9 summarises the conclusions drawn during this investigation.

Compatibilisation of heterogeneous polymer blends by reactive processing

Functionalisation of polystyrene, PS, and ethylene-co-propylene-co-cyclopentadiene terpolymer, EPDM, with acrylic acid, AA, in a melt reactive processing procedure, in the presence of peroxide, trigonox 101, and coagents, Divinyl benzene, DVB (for PS), and trimethylolpropane triacrylate, TRIS (for EPDM), were successfully carried out. The level of grafting of the AA, as determined by infrared analysis, was significantly enhanced by the coagents. The grafting reaction of AA takes place simultaneously with homopolymerisation of the monomers, melt degradation and crosslinking reactions of the polymers. The extent of these competing reactions were inferred from measurements of melt flow index and insoluble gel content. Through a judicious use of both the peroxide and the coagent, particularly TRIS, unwanted side reactions were minimized. Five different processing methods were investigated for both functionalisation experiments; the direct addition of the pre-mixed polymer with peroxide and reactive modifiers was found to give optimum condition for grafting. The functionalised PS, F-PS, and EPDM, F-EPD, and maleinised polypropylene carrying a potential antioxidant, N-(4-anilinophenyl maleimide), F-PP were melt blended in binary mixtures of F-PS/F-EPD and F-PP/F-EPD in the presence (or absence) of organic diamines which act as an interlinking agent, e.g, Ethylene Diamine, EDA, and Hexamethylene Diamine, HEMDA. The presence of an interlinking agent, particularly HEMDA shows significant enhancement in the mechanical properties of the blend, suggesting that the copolymer formed has acted as compatibiliser to the otherwise incompatible polymer pairs. The functionalised and amidised blends, F and A-PSIEPDM (SPOI) and F and A-PPIEPDM (SPD2) were subsequently used as compatibiliser concentrates in the corresponding PSIEPDM and PPIEPDM blends containing various weight propotion of the homopolymers. The SPD1 caused general decreased in tensile strength, albeit increased in drop impact strength particularly in blend containing high PS content (80%). The SPD2 was particularly effective in enhancing impact strength in blends containing low weight ratio of PP (<70%). The SPD2 was also a good thermal antioxidant albeit less effective than commercial antioxidant. In all blends the evidence of compatibility was examined by scanning electron microscopy.