Threshold Selection Criteria for Quantification of Lumbosacral Cerebrospinal Fluid and Root Volumes from MRI

BACKGROUND AND PURPOSE: The high variability of CSF volumes partly explains the inconsistency of anesthetic effects, but may also be due to image analysis itself. In this study, criteria for threshold selection are anatomically defined. METHODS: T2 MR images (n = 7 cases) were analyzed using 3-dimentional software. Maximal-minimal thresholds were selected in standardized blocks of 50 slices of the dural sac ending caudally at the L5-S1 intervertebral space (caudal blocks) and middle L3 (rostral blocks). Maximal CSF thresholds: threshold value was increased until at least one voxel in a CSF area appeared unlabeled and decreased until that voxel was labeled again: this final threshold was selected. Minimal root thresholds: thresholds values that selected cauda equina root area but not adjacent gray voxels in the CSF-root interface were chosen. RESULTS: Significant differences were found between caudal and rostral thresholds. No significant differences were found between expert and nonexpert observers. Average max/min thresholds were around 1.30 but max/min CSF volumes were around 1.15. Great interindividual CSF volume variability was detected (max/min volumes 1.6-2.7). CONCLUSIONS: The estimation of a close range of CSF volumes which probably contains the real CSF volume value can be standardized and calculated prior to certain intrathecal procedures

Análise de imagem em química analítica: empregando metodologias simples e didáticas para entender e prevenir o escurecimento de tecidos vegetais

A simple and didactic experiment was developed for image monitoring of the browning of fruit tissues caused by the enzyme polyphenol oxidase. The procedure, easy and inexpensive, is a valuable tool to teach and demonstrate the redox reaction between the enzyme and the natural polyphenols. To obtain the browning percentage for apple, pear and banana, digital photographs were employed, and the images were analyzed by means of Monte Carlo methods and digital analysis programs. The effects of several experimental conditions were studied, such as pH, light, temperature and the presence of oxygen or anti-oxidants. It was observed that each fruit presented a different condition that better minimized the oxidation process. The absence of oxygen and the application of a bissulphite solution were sufficient to keep the quality of all fruits tested.

The influence of crystallization conditions on the filtration characteristics of sulphathiazole suspensions

Cooling crystallization is one of the most important purification and separation techniques in the chemical and pharmaceutical industry. The product of the cooling crystallization process is always a suspension that contains both the mother liquor and the product crystals, and therefore the first process step following crystallization is usually solid-liquid separation. The properties of the produced crystals, such as their size and shape, can be affected by modifying the conditions during the crystallization process. The filtration characteristics of solid/liquid suspensions, on the other hand, are strongly influenced by the particle properties, as well as the properties of the liquid phase. It is thus obvious that the effect of the changes made to the crystallization parameters can also be seen in the course of the filtration process. Although the relationship between crystallization and filtration is widely recognized, the number of publications where these unit operations have been considered in the same context seems to be surprisingly small. This thesis explores the influence of different crystallization parameters in an unseeded batch cooling crystallization process on the external appearance of the product crystals and on the pressure filtration characteristics of the obtained product suspensions. Crystallization experiments are performed by crystallizing sulphathiazole (C9H9N3O2S2), which is a wellknown antibiotic agent, from different mixtures of water and n-propanol in an unseeded batch crystallizer. The different crystallization parameters that are studied are the composition of the solvent, the cooling rate during the crystallization experiments carried out by using a constant cooling rate throughout the whole batch, the cooling profile, as well as the mixing intensity during the batch. The obtained crystals are characterized by using an automated image analyzer and the crystals are separated from the solvent through constant pressure batch filtration experiments. Separation characteristics of the suspensions are described by means of average specific cake resistance and average filter cake porosity, and the compressibilities of the cakes are also determined. The results show that fairly large differences can be observed between the size and shape of the crystals, and it is also shown experimentally that the changes in the crystal size and shape have a direct impact on the pressure filtration characteristics of the crystal suspensions. The experimental results are utilized to create a procedure that can be used for estimating the filtration characteristics of solid-liquid suspensions according to the particle size and shape data obtained by image analysis. Multilinear partial least squares regression (N-PLS) models are created between the filtration parameters and the particle size and shape data, and the results presented in this thesis show that relatively obvious correlations can be detected with the obtained models.

Classificação de refrigerantes através de análise de imagens e análise de componentes principais (PCA)

This paper describes an approach for the colour-based classification of RGB (red-green-blue) images, acquired using a common scanner, of commercial carbonated soft drinks. Mean histograms of image colour channels were evaluated for the PCA classification of 29 brands of Guaraná, Cola, and orange flavors. Loadings for principal component axes resulted in different patterns for sample grouping on score plots according to RGB histograms. pH, sorbic acid and sucrose measurements were also correlated to the analyzed brands through PCA score plots of the digitalized images.

Desenhos de estruturas químicas correlacionam-se com propriedades biológicas: MIA-QSAR

Descriptors in multivariate image analysis applied to quantitative structure-activity relationship (MIA-QSAR) are pixels of bidimensional images of chemical structures (drawings), which were used to model the trichomonicidal activities of a series of benzimidazole derivatives. The MIA-QSAR model showed good predictive ability, with r², q² and r val. ext.² of 0.853, 0.519 and 0.778, respectively, which are comparable to the best values obtained by CoMFA e CoMSIA for the same series. A MIA-based analysis was also performed by using images of alphabetic letters with the corresponding numeric ordering as dependent variables, but no correlation was found, supporting that MIA-QSAR is not arbitrary.

Resolução multivariada de curvas com mínimos quadrados alternantes: descrição, funcionamento e aplicações

Multivariate Curve Resolution with Alternating Least Squares (MCR-ALS) is a resolution method that has been efficiently applied in many different fields, such as process analysis, environmental data and, more recently, hyperspectral image analysis. When applied to second order data (or to three-way data) arrays, recovery of the underlying basis vectors in both measurement orders (i.e. signal and concentration orders) from the data matrix can be achieved without ambiguities if the trilinear model constraint is considered during the ALS optimization. This work summarizes different protocols of MCR-ALS application, presenting a case study: near-infrared image spectroscopy.

Imaging and Characterisation of Dirt Particles in Pulp and Paper

Dirt counting and dirt particle characterisation of pulp samples is an important part of quality control in pulp and paper production. The need for an automatic image analysis system to consider dirt particle characterisation in various pulp samples is also very critical. However, existent image analysis systems utilise a single threshold to segment the dirt particles in different pulp samples. This limits their precision. Based on evidence, designing an automatic image analysis system that could overcome this deficiency is very useful. In this study, the developed Niblack thresholding method is proposed. The method defines the threshold based on the number of segmented particles. In addition, the Kittler thresholding is utilised. Both of these thresholding methods can determine the dirt count of the different pulp samples accurately as compared to visual inspection and the Digital Optical Measuring and Analysis System (DOMAS). In addition, the minimum resolution needed for acquiring a scanner image is defined. By considering the variation in dirt particle features, the curl shows acceptable difference to discriminate the bark and the fibre bundles in different pulp samples. Three classifiers, called k-Nearest Neighbour, Linear Discriminant Analysis and Multi-layer Perceptron are utilised to categorize the dirt particles. Linear Discriminant Analysis and Multi-layer Perceptron are the most accurate in classifying the segmented dirt particles by the Kittler thresholding with morphological processing. The result shows that the dirt particles are successfully categorized for bark and for fibre bundles.

Holocene Varved Lake Sediments as Records of Palaeoenvironmental Change and Geomagnetic Palaeosecular Variation in Eastern Finland

This dissertation discusses Holocene palaeoenvironmental and palaeomagnetic secular variation (PSV) records reconstructed from sediments preserved in Lake Lehmilampi (63º37´N, 29º06´E) and Lake Kortejärvi (63º37´N, 28º56´E) in eastern Finland. Several piston and freeze cores were obtained from both lakes for varve and magnetic analyses. Sediment samples were impregnated in low-viscosity epoxy and physical parameters of varves, including varve thickness and relative grey-scale values, were recorded using x-ray densitometry combined with semiautomatic digital image analysis. On average, varve records of Lehmilampi and Kortejärvi cover 5122 and 3902 years, respectively. Past solar activity, as estimated by residual ₁₄C data, compares favourably with varve thicknesses from Lehmilampi during the last 2000 years. This indicates the potential of clastic-organic varves to record sensitively climatic variations. Bulk magnetic parameters, including magnetic susceptibility together with natural, anhysteretic and isothermal remanent magnetizations, were measured to describe mineral magnetic properties and geomagnetic palaeosecular variation recorded in the sediments. Main stages in the development of the investigated lakes are reflected in the variations in the mineral magnetic records, sediment lithology and composition. Similar variations in magnetic parameters and sediment organic matter suggest contribution of bacterial magnetite in the magnetic assemblages of Lehmilampi. Inclination and relative declination records yielded largely consistent results, attesting to the great potential of these sediments to preserve directional palaeosecular variation in high resolution. The PSV data from Lehmilampi and Kortejärvi were stacked into North Karelian PSV stack, which may be used for dating homogenous lake sediments in the same regional context. Reconstructed millennial variations in relative palaeointensity results are approximately in agreement with those seen in the absolute palaeointensity data from Europe. Centennial variations in the relative palaeointensity, however, are influenced by environmental changes. Caution is recommended when using varved lake sediments in reconstructing relative palaeointensity.

Digital surface area assessment of broiler chickens

Surface area (SA) of poultry is an important parameter for heat and mass transfer calculations. Optical approaches, such as the moiré technique (MT), are non-destructive, result in accuracy and speed gains, and preserve the object integrity. The objective of this research was to develop and validate a new protocol for estimating the surface area (SA) of broiler chickens based on the MT. Sixty-six Ross breed broiler chickens (twenty-seven male, thirty-nine female, ages spanning all growth phases) were used in this study. The dimensions (length, width and height) and body mass of randomly selected broiler chickens were evaluated in the laboratory. Chickens were illuminated by a light source, and grids were projected onto the chickens to allow their shape to be determined and recorded. Next, the skin and feathers of the chickens were removed to allow SA to be determined by conventional means. These measurements were then used for calibration and validation. The MT for image analysis was a reliable means of evaluating the three-dimensional shape and SA of broiler chickens. This technique, which is neither invasive nor destructive, is a good alternative to the conventional destructive methods.

Detection of soybean planted areas through orbital images based on culture spectral dynamics

The soybean is important to the economy of Brazil, so the estimation of the planted area and the production with higher antecedence and reliability becomes essential. Techniques related to Remote Sensing may help to obtain this information at lower cost and less subjectivity in relation to traditional surveys. The aim of this study is to estimate the planted area with soybean culture in the crop of 2008/2009 in cities in the west of the state of Paraná, in Brazil, based on the spectral dynamics of the culture and through the use of the specific system of analysis for images of Landsat 5/TM satellite. The obtained results were satisfactory, because the classification supervised by Maximum Verisimilitude - MaxVer along with the techniques of the specific system of analysis for satellite images has allowed an estimate of soybean planted area (soybean mask), obtaining values ​​of the metrics of Global Accuracy with an average of 79.05% and Kappa Index over 63.50% in all cities. The monitoring of a reference area was of great importance for determining the vegetative phase in which the culture is more different from the other targets, facilitating the choice of training samples (ROIs) and avoiding misclassifications.

Biopolttoaineiden leijutusominaisuuksien karakterisointi

Tässä diplomityössä selvitettiin biopolttoaineiden ominaisuuksia leijutuksen kannalta. Ensiksi tutkittavat biopolttoaineet, hake ja turve, seulottiin ja seulotut näytteet analysoitiin. Seuraavaksi turvetta ja haketta leijutettiin eri nopeuksilla ja eri leijutusnopeuksilla saadut näytteet analysoitiin kuva-analysilla. Partikkeleista selvitettiin runsaasti mittoja, kuten keskihalkaisija, pinta-ala ja muotokerroin. Kirjallisuudesta löytyvien korrelaatioiden avulla laskettiin leijutettujen partikkelien vastuskertoimet ja terminaalinopeudet. Korrelaatioiden tuloksia verrattiin mittaustuloksiin. Tässä työssä myös laskettiin kyseisiin biopolttoaineisiin vaikuttavat ominaisvoimat leijutuksessa sekä laskettiin korjauskerroin, jota käytettiin ominaisvoimien korjaamiseen. Referenssiaineina käytettiin hiekkaa ja lasikuulia.

A Farewell to Flat Biology. Three-dimensional Cell Culture Models in Cancer Drug Target Identification and Validation

Cells of epithelial origin, e.g. from breast and prostate cancers, effectively differentiate into complex multicellular structures when cultured in three-dimensions (3D) instead of conventional two-dimensional (2D) adherent surfaces. The spectrum of different organotypic morphologies is highly dependent on the culture environment that can be either non-adherent or scaffold-based. When embedded in physiological extracellular matrices (ECMs), such as laminin-rich basement membrane extracts, normal epithelial cells differentiate into acinar spheroids reminiscent of glandular ductal structures. Transformed cancer cells, in contrast, typically fail to undergo acinar morphogenic patterns, forming poorly differentiated or invasive multicellular structures. The 3D cancer spheroids are widely accepted to better recapitulate various tumorigenic processes and drug responses. So far, however, 3D models have been employed predominantly in the Academia, whereas the pharmaceutical industry has yet to adopt a more widely and routine use. This is mainly due to poor characterisation of cell models, lack of standardised workflows and high throughput cell culture platforms, and the availability of proper readout and quantification tools. In this thesis, a complete workflow has been established entailing well-characterised 3D cell culture models for prostate cancer, a standardised 3D cell culture routine based on high-throughput-ready platform, automated image acquisition with concomitant morphometric image analysis, and data visualisation, in order to enable large-scale high-content screens. Our integrated suite of software and statistical analysis tools were optimised and validated using a comprehensive panel of prostate cancer cell lines and 3D models. The tools quantify multiple key cancer-relevant morphological features, ranging from cancer cell invasion through multicellular differentiation to growth, and detect dynamic changes both in morphology and function, such as cell death and apoptosis, in response to experimental perturbations including RNA interference and small molecule inhibitors. Our panel of cell lines included many non-transformed and most currently available classic prostate cancer cell lines, which were characterised for their morphogenetic properties in 3D laminin-rich ECM. The phenotypes and gene expression profiles were evaluated concerning their relevance for pre-clinical drug discovery, disease modelling and basic research. In addition, a spontaneous model for invasive transformation was discovered, displaying a highdegree of epithelial plasticity. This plasticity is mediated by an abundant bioactive serum lipid, lysophosphatidic acid (LPA), and its receptor LPAR1. The invasive transformation was caused by abrupt cytoskeletal rearrangement through impaired G protein alpha 12/13 and RhoA/ROCK, and mediated by upregulated adenylyl cyclase/cyclic AMP (cAMP)/protein kinase A, and Rac/ PAK pathways. The spontaneous invasion model tangibly exemplifies the biological relevance of organotypic cell culture models. Overall, this thesis work underlines the power of novel morphometric screening tools in drug discovery.

Immunohistochemical evaluation of fibrillar components of the extracellular matrix of transversalis fascia and anterior abdominal rectus sheath in men with inguinal hernia

OBJECTIVE: to evaluate the role of fibrillar extracellular matrix components in the pathogenesis of inguinal hernias. METHODS: samples of the transverse fascia and of the anterior sheath of the rectus abdominis muscle were collected from 40 men aged between 20 and 60 years with type II and IIIA Nyhus inguinal hernia and from 10 fresh male cadavers (controls) without hernia in the same age range. The staining technique was immunohistochemistry for collagen I, collagen III and elastic fibers; quantification of fibrillar components was performed with an image analysis processing software. RESULTS: no statistically significant differences were found in the amount of elastic fibers, collagen I and collagen III, and the ratio of collagen I / III among patients with inguinal hernia when compared with subjects without hernia. CONCLUSION: the amount of fibrillar extracellular matrix components did not change in patients with and without inguinal hernia.

PTEN expression in patients with carcinoma of the cervix and its association with p53, Ki-67 and CD31

PURPOSE: To investigate protein expression and mutations in phosphatase and tensin homolog (PTEN) in patients with stage IB cervical squamous cell carcinoma (CSCC) and the association with clinical-pathologic features, tumor p53 expression, cell proliferation and angiogenesis.METHODS:Women with stage IB CSCC (n=20 - Study Group) and uterine myoma (n=20 - Control Group), aged 49.1±1.7 years (mean±standard deviation, range 27-78 years), were prospectively evaluated. Patients with cervical cancer were submitted to Piver-Rutledge class III radical hysterectomy and pelvic lymphadenectomy and patients in the Control Group underwent vaginal hysterectomy. Tissue samples from the procedures were stained with hematoxylin and eosin for histological evaluation. Protein expression was detected by immunohistochemistry. Staining for PTEN, p53, Ki-67 and CD31 was evaluated. The intensity of PTEN immunostaining was estimated by computer-assisted image analysis, based on previously reported protocols. Data were analyzed using the Student's t-test to evaluate significant differences between the groups. Level of significance was set at p<0.05.RESULTS:The PTEN expression intensity was lower in the CSCC group than in the Control (benign cervix) samples (150.5±5.2 versus 204.2±2.6; p<0.001). Our study did not identify any mutations after sequencing all nine PTEN exons. PTEN expression was not associated with tumor expression of p53 (p=0.9), CD31 (p=0.8) or Ki-67 (p=0.3) or clinical-pathologic features in patients with invasive carcinoma of the cervix.CONCLUSIONS: Our findings demonstrate that the PTEN protein expression is significantly diminished in CSCC.

Effects of topical 0.2% Cyclosporine A on corneal neovascularization induced by xenologous amniotic membrane implantation into a corneal stroma micropocket of rats

The objective of the study was to evaluate the topical effects of 0.2% Cyclosporine A (CsA) on corneal neovascularization of rats following surgical implantation of equine amniotic membrane into a corneal stroma micropocket. The implantation of xenologous amniotic membrane was performed bilaterally in 90 rats. In the same day of the surgery each right eye started receiving topical CsA twice a day. The left eye received no medication and served as a control. The evaluation of corneal neovascularization was performed by computerized image analysis and histopathological evaluation at 1, 3, 7, 15, 30 and 60 days postoperatively. For the image analysis 10 animals were used per time period, and for the histopathological examination, five animals were used per time period. Image analysis found that corneal neovascularization began on the 3rd postoperative day, reached its peak on the 7th day, and then progressively and rapidly decreased. Statistic analysis indicated that neovascularization of the CsA treated eye on the 7th day was significantly higher than that observed in untreated eyes. On the 30th day, however, this pattern was reversed with the neovascularization observed in the CsA treated eyes declining to the low levels observed on the 3rd day. The degree of neovascularization in the untreated eyes on the 30th day declined to the baseline levels found on day 3 at the 60th day. Histopathological analysis indicated that deposition of collagen in the implanted tissue was completed by the 15th day. Therefore, we concluded that (1) equine amniotic membrane in rat corneal stroma produced an intense neovascularization until the 15th day postoperatively and then regressed, (2) deposition of collagen of the implanted tissue was completed on the 15th day postoperatively, and (3) use of CsA was associated with increase in the corneal neovascularization initially, followed by a quick and intense regression.