Multivariate analysis applied to clinical analysis data

Dissertação para obtenção do Grau de Mestre em Engenharia e Gestão Industrial

Multivariate modelling of responses to conditional items: New possibilities for latent class analysis

Questionnaire data may contain missing values because certain questions do not apply to all respondents. For instance, questions addressing particular attributes of a symptom, such as frequency, triggers or seasonality, are only applicable to those who have experienced the symptom, while for those who have not, responses to these items will be missing. This missing information does not fall into the category 'missing by design', rather the features of interest do not exist and cannot be measured regardless of survey design. Analysis of responses to such conditional items is therefore typically restricted to the subpopulation in which they apply. This article is concerned with joint multivariate modelling of responses to both unconditional and conditional items without restricting the analysis to this subpopulation. Such an approach is of interest when the distributions of both types of responses are thought to be determined by common parameters affecting the whole population. By integrating the conditional item structure into the model, inference can be based both on unconditional data from the entire population and on conditional data from subjects for whom they exist. This approach opens new possibilities for multivariate analysis of such data. We apply this approach to latent class modelling and provide an example using data on respiratory symptoms (wheeze and cough) in children. Conditional data structures such as that considered here are common in medical research settings and, although our focus is on latent class models, the approach can be applied to other multivariate models.

A comparative analysis of self-determined evaluations of work performance and support needs by adults with mental retardation in supported work and in sheltered workshop environments

The purpose of this study was to determine if there was a difference in the self-determined evaluations of work performance and support needs by adults with mental retardation in supported employment and in sheltered workshop environments. The instrument, Job Observation and Behavior Scale: Opportunity for Self-Determination (JOBS: OSD; Brady, Rosenberg, & Frain, 2006), was administered to 38 adults with mental retardation from sheltered workshops and 32 adults with mental retardation from supported employment environments. Cross-tabulations with Chi-square tests and independent samples t-tests were conducted to evaluate differences between the two groups, sheltered workshop and supported work. Two Multivariate Analyses of Variance (MANOVAs) were conducted to determine the effect of work environment on Quality of Performance (QP) and Types of Support (TS) test scores and their subscales. ^ This study found that there were significant differences between the groups on the QP Behavior and Job Duties subscales. The sheltered workshop group perceived themselves as performing significantly better on job duties than the supported work group. Conversely, the supported work group perceived themselves to have better behavior than the sheltered workshop group. However, there were no significant differences between groups in their perception of support needs for the three subscales. ^ The findings imply that work environment affects the self-determined evaluations of work performance by adults with mental retardation. Recommendations for further study include (a) detailing the characteristics of supported work and sheltered workshops that support and/or discourage self-determined behaviors, (b) exploring the behavior of adults with mental retardation in sheltered workshops and supported work environments, and (c) analysis of the support needs for and understanding of them by adults with mental retardation in sheltered workshops and in supported work environments. ^

Analysis Of The Fluorescence Of Body Fluids On Different Surfaces And Times.

The use of screening techniques, such as an alternative light source (ALS), is important for finding biological evidence at a crime scene. The objective of this study was to evaluate whether biological fluid (blood, semen, saliva, and urine) deposited on different surfaces changes as a function of the age of the sample. Stains were illuminated with a Megamaxx™ ALS System and photographed with a Canon EOS Utility™ camera. Adobe Photoshop™ was utilized to prepare photographs for analysis, and then ImageJ™ was used to record the brightness values of pixels in the images. Data were submitted to analysis of variance using a generalized linear mixed model with two fixed effects (surface and fluid). Time was treated as a random effect (through repeated measures) with a first-order autoregressive covariance structure. Means of significant effects were compared by the Tukey test. The fluorescence of the analyzed biological material varied depending on the age of the sample. Fluorescence was lower when the samples were moist. Fluorescence remained constant when the sample was dry, up to the maximum period analyzed (60 days), independent of the substrate on which the fluid was deposited, showing the novelty of this study. Therefore, the forensic expert can detect biological fluids at the crime scene using an ALS even several days after a crime has occurred.

In vitro analysis of thermocompaction time and gutta-percha type on quality of main canal and lateral canals filling

The aim of this study was to evaluate the quality of filling in main and lateral root canals performed with the McSpadden technique, regarding the time spent on the procedure and the type of gutta-percha employed. Fifty simulated root canals, made with six lateral canals placed two apiece in the cervical, middle and apical thirds of the root, were divided into 5 groups. Group A: McSpadden technique with conventional gutta-percha, performed with sufficient time for canal filling; Group B: McSpadden technique with conventional gutta-percha, performed in twice the mean time used in Group A; Group C: McSpadden technique with TP gutta-percha, performed with sufficient time for canal filling; Group D: McSpadden technique with TP gutta-percha, performed in twice the mean time used in Group C; Group E: lateral condensation technique. Images of the filled root canals were taken using a stereomicroscope and analyzed using the Leica QWIN Pro software for filling material flow, gutta-percha filling extension and sealer flow. Data were analyzed by analysis of variance (ANOVA) and Tukey test (p < 0.05). The best values of penetration in lateral canals in the middle third occurred in the groups where TP gutta-percha was used. However, in the apical third, group B showed the best values. Although a longer time of compactor use allows greater penetration of the filling material into the lateral canals, the presence of voids resulted in bad quality radiographic images, suggesting porosity. The best quality of filling material was observed in Group A (McSpadden technique with conventional Gutta-Percha, performed with sufficient time for root canal filling).

Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila

Background: We characterized variation and chemical composition of epicuticular hydrocarbons (CHCs) in the seven species of the Drosophila buzzatii cluster with gas chromatography/mass spectrometry. Despite the critical role of CHCs in providing resistance to desiccation and involvement in communication, such as courtship behavior, mating, and aggregation, few studies have investigated how CHC profiles evolve within and between species in a phylogenetic context. We analyzed quantitative differences in CHC profiles in populations of the D. buzzatii species cluster in order to assess the concordance of CHC differentiation with species divergence. Results: Thirty-six CHC components were scored in single fly extracts with carbon chain lengths ranging from C(29) to C(39), including methyl-branched alkanes, n alkenes, and alkadienes. Multivariate analysis of variance revealed that CHC amounts were significantly different among all species and canonical discriminant function (CDF) analysis resolved all species into distinct, non-overlapping groups. Significant intraspecific variation was found in different populations of D. serido suggesting that this taxon is comprised of at least two species. We summarized CHC variation using CDF analysis and mapped the first five CHC canonical variates (CVs) onto an independently derived period (per) gene + chromosome inversion + mtDNA COI gene for each sex. We found that the COI sequences were not phylogenetically informative due to introgression between some species, so only per + inversion data were used. Positive phylogenetic signal was observed mainly for CV1 when parsimony methods and the test for serial independence (TFSI) were used. These results changed when no outgroup species were included in the analysis and phylogenetic signal was then observed for female CV3 and/or CV4 and male CV4 and CV5. Finally, removal of divergent populations of D. serido significantly increased the amount of phylogenetic signal as up to four out of five CVs then displayed positive phylogenetic signal. Conclusions: CHCs were conserved among species while quantitative differences in CHC profiles between populations and species were statistically significant. Most CHCs were species-, population-, and sex-specific. Mapping CHCs onto an independently derived phylogeny revealed that a significant portion of CHC variation was explained by species' systematic affinities indicating phylogenetic conservatism in the evolution of these hydrocarbon arrays, presumptive waterproofing compounds and courtship signals as in many other drosophilid species.

A 1-year longitudinal study of severe traumatic brain injury in Australia using the Sickness Impact Profile

Objective: To document outcome and to investigate patterns of physical and psychosocial recovery in the first year following severe traumatic brain injury (TBI) in an Australian patient sample. Design: A longitudinal prospective study of a cohort of patients, with data collection at 3, 6, 9, and 12 months post injury. Setting: A head injury rehabilitation unit in a large metropolitan public hospital. Patients: A sample of 55 patients selected from 120 consecutive admissions with severe TBI. Patients who were more than 3 months post injury on admission, who remained confused, or who had severe communication deficits or a previous neurologic disorder were excluded. Interventions: All subjects participated in a multidisciplinary inpatient rehabilitation program, followed by varied participation in outpatient rehabilitation and community-based sen ices. Main Outcome Measures: The Sickness impact Profile (SIP) provided physical, psychosocial, and total dysfunction scores at each follow-up. Outcome at 1 year was measured by the Disability Rating Scale. Results: Multivariate analysis of variance indicated that the linear trend of recovery over time was less for psychosocial dysfunction than for physical dysfunction (F(1,51) = 5.87, P < .02). One rear post injury, 22% of subjects had returned to their previous level of employability, and 42% were able to live independently. Conclusions: Recovery from TBI in this Australian sample followed a pattern similar to that observed in other countries, with psychosocial dysfunction being more persistent. Self-report measures such as the SIP in TBI research are limited by problems of diminished self-awareness.

On cluster analysis of complex and heterogeneous data

3rd SMTDA Conference Proceedings, 11-14 June 2014, Lisbon Portugal.

Intraspecific ecomorphological variations in Poecilia reticulata (Actinopterygii, Cyprinodontiformes): comparing populations of distinct environments

ABSTRACT Morphological variations, according to the principles of ecomorphology, can be related to different aspects of the organism way of life, such as occupation of habitats and feeding behavior. The present study sought to examine the intraspecific variation in two populations of Poecilia reticulata Peters, 1859, that occur in two types of environments, a lotic (Maringá Stream) and a lentic (Jaboti Lake). Due to a marked sexual dimorphism, males and females were analyzed separately. Thus, the proposed hypotheses were that the populations that occur in distinct environments present morphological differences. The morphological variables were obtained using morphometric measurements and the ecomorphological indexes. The data were summarized in a Principal Component Analysis (PCA). A Multivariate Analysis of Variance (Manova) was made to verify significant differences in morphology between the populations. Males and females showed similar ecomorphological patterns according to the environment they occur. In general the population from Maringá Stream had fins with major areas, and the Jaboti Lake population eyes located more dorsally. Additionally, others morphological differences such as wider mouth of the males from Maringá Stream, wider heads on Jaboti Lake females and more protractible mouths on males from Jaboti Lake suggest a set of environmental variables that can possibly influence the ecomorphological patterns of the populations, as the water current, availability of food resources and predation. In summary, the initial hypotheses could be confirmed, evidencing the occurrence of distinct ecomorphotypes in the same species according to the environment type.

Clinicopathologic analysis of acute myeloid leukemia arising from chronic myelomonocytic leukemia.

Acute myeloid leukemia arising from chronic myelomonocytic leukemia is currently classified as acute myeloid leukemia with myelodysplasia-related changes, a high-risk subtype. However, the specific features of these cases have not been well described. We studied 38 patients with chronic myelomonocytic leukemia who progressed to acute myeloid leukemia. We compared the clinicopathologic and genetic features of these cases with 180 patients with de novo acute myeloid leukemia and 34 patients with acute myeloid leukemia following myelodysplastic syndromes. We also examined features associated with progression from chronic myelomonocytic leukemia to acute myeloid leukemia by comparing the progressed chronic myelomonocytic leukemia cases with a cohort of chronic myelomonocytic leukemia cases that did not transform to acute myeloid leukemia. Higher white blood cell count, marrow cellularity, karyotype risk score, and Revised International Prognostic Scoring System score were associated with more rapid progression from chronic myelomonocytic leukemia to acute myeloid leukemia. Patients with acute myeloid leukemia ex chronic myelomonocytic leukemia were older (P<0.01) and less likely to receive aggressive treatment (P=0.02) than de novo acute myeloid leukemia patients. Most cases showed monocytic differentiation and fell into the intermediate acute myeloid leukemia karyotype risk group; 55% had normal karyotype and 17% had NPM1 mutation. Median overall survival was 6 months, which was inferior to de novo acute myeloid leukemia (17 months, P=0.002) but similar to post myelodysplastic syndrome acute myeloid leukemia. On multivariate analysis of all acute myeloid leukemia patients, only age and karyotype were independent prognostic variables for overall survival. Our findings indicate that acute myeloid leukemia following chronic myelomonocytic leukemia displays aggressive behavior and support placement of these cases within the category of acute myeloid leukemia with myelodysplasia-related changes. The poor prognosis of these patients may be related to an older population and lack of favorable-prognosis karyotypes that characterize many de novo acute myeloid leukemia cases.

Spatial variation of dung beetle assemblages associated with forest structure in remnants of southern Brazilian Atlantic Forest

ABSTRACT The Brazilian Atlantic Forest is one of the world's biodiversity hotspots, and is currently highly fragmented and disturbed due to human activities. Variation in environmental conditions in the Atlantic Forest can influence the distribution of species, which may show associations with some environmental features. Dung beetles (Coleoptera: Scarabaeinae) are insects that act in nutrient cycling via organic matter decomposition and have been used for monitoring environmental changes. The aim of this study is to identify associations between the spatial distribution of dung beetle species and Atlantic Forest structure. The spatial distribution of some dung beetle species was associated with structural forest features. The number of species among the sampling sites ranged widely, and few species were found in all remnant areas. Principal coordinates analysis indicated that species composition, abundance and biomass showed a spatially structured distribution, and these results were corroborated by permutational multivariate analysis of variance. The indicator value index and redundancy analysis showed an association of several dung beetle species with some explanatory environmental variables related to Atlantic Forest structure. This work demonstrated the existence of a spatially structured distribution of dung beetles, with significant associations between several species and forest structure in Atlantic Forest remnants from Southern Brazil.

Clinical relevance of CD44 cell-surface expression and N-myc gene amplification in a multicentric analysis of 121 pediatric neuroblastomas.

PURPOSE: In contrast to other human tumors, a repression of the cell-surface glycoprotein CD44 on neuroblastoma is a marker of aggressiveness that usually correlates to N-myc amplification. We thus compared the prognostic value of both markers in the initial staging of 121 children treated for neuroblastoma in collaborative institutions. METHODS: Frozen samples were analyzed by a rapid and well-standardized technique of immunostaining with monoclonal antibodies (MoAbs) against epitopes in the CD44 constant region. RESULTS: In this retrospective series, CD44 was expressed on 102 specimens and strongly correlated with favorable tumor stages and histology, younger age, and normal N-myc copy numbers. In univariate analysis, CD44 expression and normal N-myc were the most powerful markers of favorable clinical outcome (P < 10(-6) and chi 2 = 65.40 and P < 10(-6) and chi 2 = 42.56, respectively), but analysis of CD44 affords significant prognostic discrimination in subgroups of patients with or without N-myc-amplified tumors. In the subgroup of stage IV neuroblastomas, CD44 was the only significant prognostic marker (P < .02, chi 2 = 5.76), whereas N-myc status was not discriminant. In multivariate analysis of five factors, ie, N-myc amplification, CD44 expression, age, tumor stage, and histology, the only independent prognostic factors of event-free survival were CD44 expression and tumor stage. CONCLUSION: The analysis of CD44 cell-surface expression must be recommended as an additional biologic marker in the initial staging of the disease.

Evaluation of ammonia volatilization losses by adjusted parameters of a logistic function

The dynamics of N losses in fertilizer by ammonia volatilization is affected by several factors, making investigation of these dynamics more complex. Moreover, some features of the behavior of the variable can lead to deviation from normal distribution, making the main commonly adopted statistical strategies inadequate for data analysis. Thus, the purpose of this study was to evaluate the patterns of cumulative N losses from urea through ammonia volatilization in order to find a more adequate and detailed way of assessing the behavior of the variable. For that reason, changes in patterns of ammonia volatilization losses as a result of applying different combinations of two soil classes [Planossolo and Chernossolo (Typic Albaqualf and Vertic Argiaquolls)] and different rates of urea (50, 100 and 150 kg ha-1 N), in the presence or absence of a urease inhibitor, were evaluated, adopting a 2 × 3 × 2 factorial design with four replications. Univariate and multivariate analysis of variance were performed using the adjusted parameter values of a logistic function as a response variable. The results obtained from multivariate analysis indicated a prominent effect of the soil class factor on the set of parameters, indicating greater relevance of soil adsorption potential on ammonia volatilization losses. Univariate analysis showed that the parameters related to total N losses and rate of volatilization were more affected by soil class and the rate of urea applied. The urease inhibitor affected only the rate and inflection point parameters, decreasing the rate of losses and delaying the beginning of the process, but had no effect on total ammonia losses. Patterns of ammonia volatilization losses provide details on behavior of the variable, details which can be used to develop and adopt more accurate techniques for more efficient use of urea.

Analysis of vineyard differential management zones and relation to vine development, grape maturity and quality

The objective of research was to analyse the potential of Normalized Difference Vegetation Index (NDVI) maps from satellite images, yield maps and grapevine fertility and load variables to delineate zones with different wine grape properties for selective harvesting. Two vineyard blocks located in NE Spain (Cabernet Sauvignon and Syrah) were analysed. The NDVI was computed from a Quickbird-2 multi-spectral image at veraison (July 2005). Yield data was acquired by means of a yield monitor during September 2005. Other variables, such as the number of buds, number of shoots, number of wine grape clusters and weight of 100 berries were sampled in a 10 rows × 5 vines pattern and used as input variables, in combination with the NDVI, to define the clusters as alternative to yield maps. Two days prior to the harvesting, grape samples were taken. The analysed variables were probable alcoholic degree, pH of the juice, total acidity, total phenolics, colour, anthocyanins and tannins. The input variables, alone or in combination, were clustered (2 and 3 Clusters) by using the ISODATA algorithm, and an analysis of variance and a multiple rang test were performed. The results show that the zones derived from the NDVI maps are more effective to differentiate grape maturity and quality variables than the zones derived from the yield maps. The inclusion of other grapevine fertility and load variables did not improve the results.

Analysis of Brazilian consumer preference of filled chocolate

Chocolate is the most popular product made from cocoa. It is mainly consumed with fillings, such as fondant, hydrogenated fat or fruits. This work aimed at assessing the sensory acceptability of chocolate filled with strawberry, orange or passion fruit pulps, mixed in fondant, in a hydrogenated fat base and as truffles. Ninety four consumers participated in the test using a 10 cm hedonic scale to rate the overall liking of the samples. Two-way analysis of variance and the Internal Preference Mapping technique were used to analyze the data. Results showed a good overall liking for almost all samples, especially for strawberry and passion fruit truffles, which obtained 8.4 and 8.8 global means, respectively (p < 0.05), in liking ratings, followed by the hydrogenated fat and fondant fillings. The Internal Preference Map presented two dimensions explaining 72.5% of the variation found. Regarding the flavors, strawberry - traditional in chocolate and confectionary in Brazil - and passion fruit obtained better acceptance, unlike the orange fillings, which showed significantly lower ratings (p < 0.05). The orange fondant filling obtained a global mean of 6.5.