Can we improve the statistical analysis of stroke trials? Statistical re-analysis of functional outcomes in stroke trials

Background: Most large acute stroke trials have been neutral. Functional outcome is usually analysed using a yes or no answer, e.g. death or dependency vs. independence. We assessed which statistical approaches are most efficient in analysing outcomes from stroke trials. Methods: Individual patient data from acute, rehabilitation and stroke unit trials studying the effects of interventions which alter functional outcome were assessed. Outcomes included modified Rankin Scale, Barthel Index, and ‘3 questions’. Data were analysed using a variety of approaches which compare two treatment groups. The results for each statistical test for each trial were then compared. Results: Data from 55 datasets were obtained (47 trials, 54,173 patients). The test results differed substantially so that approaches which use the ordered nature of functional outcome data (ordinal logistic regression, t-test, robust ranks test, bootstrapping the difference in mean rank) were more efficient statistically than those which collapse the data into 2 groups (chi square) (ANOVA p<0.001). The findings were consistent across different types and sizes of trial and for the different measures of functional outcome. Conclusions: When analysing functional outcome from stroke trials, statistical tests which use the original ordered data are more efficient and more likely to yield reliable results. Suitable approaches included ordinal logistic regression, t-test, and robust ranks test.

Avaliação da ingestão de alimentos por nipo-brasileiros utilizando análise fatorial

Descreve-se o uso da análise fatorial na avaliação dos hábitos alimentares de nipo-brasileiros. Utilizaram-se dados dietéticos de 1.283 participantes de estudo transversal. A partir de critérios estatísticos e do significado conceitual dos padrões identificados, geraram-se escores que definiram os perfis dietéticos (japonês ou ocidental). Empregou-se o teste t de Student pareado, os modelos de regressão linear e de Poisson para examinar as relações desses escores com, respectivamente, a geração, índice de massa corporal (IMC), perímetro abdominal e a presença de síndrome metabólica. Aqueles de primeira geração, em relação aos de segunda, apresentaram escores maiores para o perfil japonês e menores para o ocidental. O perfil ocidental relacionou-se com o IMC (p = 0,001), perímetro abdominal (p = 0,023) e a síndrome metabólica (p < 0,05). Conclui-se que os escores discriminaram sujeitos que mantêm ou não estilo de vida tradicional japonês e que a incorporação de hábitos ocidentais associou-se a maiores valores de IMC, perímetro abdominal e a presença de síndrome metabólica

Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metastatic disease at the time of diagnosis, which significantly reduces survival rate. Despite extensive research, no molecular markers are currently available for diagnostic or prognostic purposes. Methods: Aiming to identify differentially-expressed genes involved in laryngeal squamous cell carcinoma (LSCC) development and progression, we generated individual Serial Analysis of Gene Expression (SAGE) libraries from a metastatic and non-metastatic larynx carcinoma, as well as from a normal larynx mucosa sample. Approximately 54,000 unique tags were sequenced in three libraries. Results: Statistical data analysis identified a subset of 1,216 differentially expressed tags between tumor and normal libraries, and 894 differentially expressed tags between metastatic and non-metastatic carcinomas. Three genes displaying differential regulation, one down-regulated (KRT31) and two up-regulated (BST2, MFAP2), as well as one with a non-significant differential expression pattern (GNA15) in our SAGE data were selected for real-time polymerase chain reaction (PCR) in a set of HNSCC samples. Consistent with our statistical analysis, quantitative PCR confirmed the upregulation of BST2 and MFAP2 and the downregulation of KRT31 when samples of HNSCC were compared to tumor-free surgical margins. As expected, GNA15 presented a non-significant differential expression pattern when tumor samples were compared to normal tissues. Conclusion: To the best of our knowledge, this is the first study reporting SAGE data in head and neck squamous cell tumors. Statistical analysis was effective in identifying differentially expressed genes reportedly involved in cancer development. The differential expression of a subset of genes was confirmed in additional larynx carcinoma samples and in carcinomas from a distinct head and neck subsite. This result suggests the existence of potential common biomarkers for prognosis and targeted-therapy development in this heterogeneous type of tumor.

Some reflections on acquisition, processing and analysis of statistical data in forest soils

Beyond the classical statistical approaches (determination of basic statistics, regression analysis, ANOVA, etc.) a new set of applications of different statistical techniques has increasingly gained relevance in the analysis, processing and interpretation of data concerning the characteristics of forest soils. This is possible to be seen in some of the recent publications in the context of Multivariate Statistics. These new methods require additional care that is not always included or refered in some approaches. In the particular case of geostatistical data applications it is necessary, besides to geo-reference all the data acquisition, to collect the samples in regular grids and in sufficient quantity so that the variograms can reflect the spatial distribution of soil properties in a representative manner. In the case of the great majority of Multivariate Statistics techniques (Principal Component Analysis, Correspondence Analysis, Cluster Analysis, etc.) despite the fact they do not require in most cases the assumption of normal distribution, they however need a proper and rigorous strategy for its utilization. In this work, some reflections about these methodologies and, in particular, about the main constraints that often occur during the information collecting process and about the various linking possibilities of these different techniques will be presented. At the end, illustrations of some particular cases of the applications of these statistical methods will also be presented.

JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Assessing food dietary intakes in Japanese-Brazilians using factor analysis

We describe the use of factor analysis for assessing food habits in Japanese-Brazilians. Dietary data from 1,283 participants of a cross-sectional study were used. Besides statistical criteria, we also used the conceptual meaning of identified profiles to obtain scores for dietary patterns (Japanese or Western profile). Paired Student t test, linear regression and Poisson models were used to verify the existence of relationship between these scores and generation, body mass index (BMI), waist circumference and presence of metabolic syndrome, respectively. First generation subjects had higher mean Japanese profile scores and lower Western profile scores than those of second generation. The Western dietary pattern was associated with BMI (p = 0.001), waist circumference (p = 0.023) and metabolic syndrome (p < 0.05). We concluded that these scores were able to discriminate subjects who maintained their traditional Japanese lifestyle or otherwise, and that the incorporation of a Western lifestyle is associated to high values of BMI, waist circumference and presence of metabolic syndrome.

Territorial Strategic Planning as a support instrument for Regional and Local Development: a comparative analysis between Lisbon and Barcelona Metropolitan Areas

MARQUES, B.P. (2011) "Territorial Strategic Planning as a support instrument for Regional and Local Development: a comparative analysis between Lisbon and Barcelona Metropolitan Areas", in Atas do 17.º Congresso da APDR, do 5.º Congresso de Gestão e Conservação da Natureza e do Congresso Internacional da APDR/AECR, Bragança e Zamora, pp. 1265-1272, ISBN 978-989-96353-2-6.

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Sexual dimorphism of the human mandible: demonstration by elliptical Fourier analysis.

A new quantitative approach of the mandibular sexual dimorphism, based on computer-aided image analysis and elliptical Fourier analysis of the mandibular outline in lateral view is presented. This method was applied to a series of 117 dentulous mandibles from 69 male and 48 female individuals native of Rhenish countries. Statistical discriminant analysis of the elliptical Fourier harmonics allowed the demonstration of a significant sexual dimorphism in 97.1% of males and 91.7% of females, i.e. in a higher proportion than in previous studies using classical metrical approaches. This original method opens interesting perspectives for increasing the accuracy of sex identification in current anthropological practice and in forensic procedures.

(210)Po poisoning as possible cause of death: forensic investigations and toxicological analysis of the remains of Yasser Arafat.

The late president of the Palestinian Authority, Yasser Arafat, died in November 2004 in Percy Hospital, one month after having experienced a sudden onset of symptoms that included severe nausea, vomiting, diarrhoea and abdominal pain and which were followed by multiple organ failure. In spite of numerous investigations performed in France, the pathophysiological mechanisms at the origin of the symptoms could not be identified. In 2011, we found abnormal levels of polonium-210 ((210)Po) in some of Arafat's belongings that were worn during his final hospital stay and which were stained with biological fluids. This finding led to the exhumation of Arafat's remains in 2012. Significantly higher (up to 20 times) activities of (210)Po and lead-210 ((210)Pb) were found in the ribs, iliac crest and sternum specimens compared to reference samples from the literature (p-value <1%). In all specimens from the tomb, (210)Po activity was supported by a similar activity of (210)Pb. Biokinetic calculations demonstrated that a (210)Pb impurity, as identified in a commercial source of 3MBq of (210)Po, may be responsible for the activities measured in Arafat's belongings and remains 8 years after his death. The absence of myelosuppression and hair loss in Mr Arafat's case compared to Mr Litvinenko's, the only known case of malicious poisoning with (210)Po, could be explained by differences in the time delivery-scheme of intake. In conclusion, statistical Bayesian analysis combining all the evidence gathered in our forensic expert report moderately supports the proposition that Mr Arafat was poisoned by (210)Po.

A statistical evaluation of the field emission for copper oxide nanostructures

A statistical data analysis methodology was developed to evaluate the field emission properties of many samples of copper oxide nanostructured field emitters. This analysis was largely done in terms of Seppen-Katamuki (SK) charts, field strength and emission current. Some physical and mathematical models were derived to describe the effect of small electric field perturbations in the Fowler-Nordheim (F-N) equation, and then to explain the trend of the data represented in the SK charts. The field enhancement factor and the emission area parameters showed to be very sensitive to variations in the electric field for most of the samples. We have found that the anode-cathode distance is critical in the field emission characterization of samples having a non-rigid nanostructure. (C) 2007 Elsevier B.V. All rights reserved.

Analysis of simple hardware efficiency for temperature measurement in agriculture and environment

This work focuses basically on the design and analysis of simple and low cost hardware systems efficiency for temperature measurement in agricultural area. The main objective is to prove quantitatively, through statistical data analysis, to what extent a simple hardware designed with inexpensive components can be used safely in the indoor temperature measurement in farm buildings, such as greenhouses, warehouse or silos. To verify the of simple hardware efficiency, its data were compared with data from measurements with a high performance LabVIEW platform. This work proved that a simple hardware based on a microcontroller and the LM35 sensor can perform well. It presented a good accuracy but a relatively low precision that can be improved when performed some consecutive signal sampling and then used its average value. Although there are many papers that explain these components, this work has the distinction of presenting a data analysis in numerical form and using high performance systems to ensure critical data comparison.

Probing the anomalous extinction of four young star clusters: the use of colour-excess, main-sequence fitting and fractal analysis

Aims. We studied four young star clusters to characterise their anomalous extinction or variable reddening and asses whether they could be due to contamination by either dense clouds or circumstellar effects. Methods. We evaluated the extinction law (R-V) by adopting two methods: (i) the use of theoretical expressions based on the colour-excess of stars with known spectral type; and (ii) the analysis of two-colour diagrams, where the slope of the observed colour distribution was compared to the normal distribution. An algorithm to reproduce the zero-age main-sequence (ZAMS) reddened colours was developed to derive the average visual extinction (A(V)) that provides the closest fit to the observational data. The structure of the clouds was evaluated by means of a statistical fractal analysis, designed to compare their geometric structure with the spatial distribution of the cluster members. Results. The cluster NGC 6530 is the only object of our sample affected by anomalous extinction. On average, the other clusters suffer normal extinction, but several of their members, mainly in NGC 2264, seem to have high R-V, probably because of circumstellar effects. The ZAMS fitting provides A(V) values that are in good agreement with those found in the literature. The fractal analysis shows that NGC 6530 has a centrally concentrated distribution of stars that differs from the substructures found in the density distribution of the cloud projected in the A(V) map, suggesting that the original cloud was changed by the cluster formation. However, the fractal dimension and statistical parameters of Berkeley 86, NGC 2244, and NGC 2264 indicate that there is a good cloud-cluster correlation, when compared to other works based on an artificial distribution of points.