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PubMed1993

Data explorer: a prototype expert system for statistical analysis.

The inadequate analysis of medical research data, due mainly to the unavailability of local statistical expertise, seriously jeopardizes the quality of new medical knowledge. Data Explorer is a prototype Expert System that builds on the versatility and power of existing statistical software, to provide automatic analyses and interpretation of medical data. The system draws much of its power by using belief network methods in place of more traditional, but difficult to automate, classical multivariate statistical techniques. Data Explorer identifies statistically significant relationships among variables, and using power-size analysis, belief network inference/learning and various explanatory techniques helps the user understand the importance of the findings. Finally the system can be used as a tool for the automatic development of predictive/diagnostic models from patient databases.

Artificial Intelligence↗
PubMed1996

Biometrics, biomathematics and the morphometric synthesis.

At the core of contemporary morphometrics--the quantitative study of biological shape variation--is a synthesis of two originally divergent methodological styles. One contributory tradition is the multivariate analysis of covariance matrices originally developed as biometrics and now dominant across a broad expanse of applied statistics. This approach, couched solely in the linear geometry of covariance structures, ignores biomathematical aspects of the original measurements. The other tributary emphasizes the direct visualization of changes in biological form. However, making objective the biological meaning of the features seen in those diagrams was always problematical; also, the representation of variation, as distinct from pairwise difference, proved infeasible. To combine these two variants of biomathematical modeling into a valid praxis for quantitative studies of biological shape was a goal earnestly sought though most of this century. That goal was finally achieved in the 1980s when techniques from mathematical statistics, multivariate biometrics, non-Euclidean geometry and computer graphics were combined in a coherent new system of tools for the complete regionalized quantitative analysis of landmark points together with the biomedical images in which they are seen. In this morphometric synthesis, correspondence of landmarks (biologically labeled geometric points, like "bridge of the nose") across specimens is taken as a biomathematical primitive. The shapes of configurations of landmarks are defined as equivalence classes with respect to the Euclidean similarity group and then represented as single points in David Kendall's shape space, a Riemannian manifold with Procrustes distance as metric. All conventional multivariate strategies carry over to the study of shape variation and covariation when shapes are interpreted in the tangent space to the shape manifold at an average shape. For biomathematical interpretation of such analyses, one needs a basis for the tangent space compatible with the reality of local biotheoretical processes and explanations at many different geometric scales, and one needs graphics for visualizing average shape differences and other statistical contrasts there. Both of these needs are managed by the thin-plate spline, a deformation function that has an unusually helpful linear algebra. The spline also links the biometrics of landmarks to deformation analysis of the images from which the landmarks originally arose. This article reviews the history and principal tools of this synthesis in their biomathematical and biometrical context and demonstrates their usefulness in a study of focal neuroanatomical anomalies in schizophrenia.

Anatomy↗
PubMed2006

Dissecting drug and vehicle metabolic effects in rats by a metabonomic approach.

A combined application of high resolution (1)H NMR spectroscopy and multivariate statistical techniques focused on establishing a consistent statistical approach to metabonomic studies was tested. The data reduction, which is preliminary to the application of multivariate analysis to NMR spectra, was carried out by means of two complementary methods: pure Pattern Recognition (PR) and Assigned Signal Analysis (ASA). The simultaneous use of both approaches allowed us to obtain additional information in the analysis of metabonomic data, compared to the use of PR alone. This additional information consists in the possibility of a biochemical interpretation of the effects induced by treatment with xenobiotics, such as drugs or drug vehicles, on the metabolic networks of the systems under investigation. This approach allowed us to ascertain that a single-dose treatment with ST1959 vehicled by Sesame oil affects the production of hepatic glucose associated to an increment of the amino acid ketogenic process.

Algorithms↗
PubMed2005

IR spectroscopy together with multivariate data analysis as a process analytical tool for in-line monitoring of crystallization process and solid-state analysis of crystalline product.

Crystalline product should exist in optimal polymorphic form. Robust and reliable method for polymorph characterization is of great importance. In this work, infra red (IR) spectroscopy is applied for monitoring of crystallization process in situ. The results show that attenuated total reflection Fourier transform infra red (ATR-FTIR) spectroscopy provides valuable information on process, which can be utilized for more controlled crystallization processes. Diffuse reflectance Fourier transform infra red (DRIFT-IR) is applied for polymorphic characterization of crystalline product using X-ray powder diffraction (XRPD) as a reference technique. In order to fully utilize DRIFT, the application of multivariate techniques are needed, e.g., multivariate statistical process control (MSPC), principal component analysis (PCA) and partial least squares (PLS). The results demonstrate that multivariate techniques provide the powerful tool for rapid evaluation of spectral data and also enable more reliable quantification of polymorphic composition of samples being mixtures of two or more polymorphs. This opens new perspectives for understanding crystallization processes and increases the level of safety within the manufacture of pharmaceutics.

Algorithms↗
PubMedDate not supplied

Knowledge of statistical methods and their implications for clinical practice: a survey of paediatricians.

Improvements in computer software have contributed to an increase in the use of multivariate statistical analyses e.g. multipLe regression in recent times. Our aim was to assess the familiarity with, and understanding of these complex statistical methods among Irish paediatricians. Questionnaires were sent to all paediatric specialist registrars (SpRs) and consultants in the Republic of Ireland. The questionnaire detailed information about clinical practice, and contained a short quiz on statistical methods. 137 questionnaires were distributed, and 62 (45.6%) were returned. Eighty four percent of respondents aimed to read journals weekly but only 46.7% managed to. The commonest journals used were; Archives of Disease in Childhood (93%), Pediatrics (53%), British Medical Journal (46%) and Journal of Paediatrics (45%). 28 of 61 (45.9%) of respondents have had further training in statistics. Only 19% felt they had a clear understanding of regression. Fifty-eight of 62 respondents (93.5%) completed the short test. The average score was 5.1/10. Sixty seven percent of questions on basics were answered correctly, 37.9% of questions on application of tests were answered correctly and 25.8% of questions on regression were answered correctly. Only 3.4% answered all questions on regression correctly. The overall knowledge of advanced statistical methods was poor. There is a poor overall understanding of the concept of regression, despite its increasingly common use.

Health Knowledge, Attitudes, Practice↗
PubMed1996

Analyzing multivariate data in crossover designs using permutation tests.

Studies using crossover designs typically involve observations on a large number of response variables made on each of a relatively small number of subjects. Moreover, investigators often observe the responses longitudinally over time. As the number of variates approaches the number of subjects traditional multivariate statistics based on the concept of statistical distance often are not very powerful, and when that number exceeds the total number of subjects in the study, these tests are not defined. In these situations, statisticians frequently analyze each variate separately and adjust for the multiple testing using a technique suitable for correlated data. In the case of a single variate measured repeatedly, we often make the assumption of a patterned covariance matrix and then conduct a univariate mixed-model analysis. We discuss an alternative approach using a variety of data structures in 2 x 2 crossover designs with (1) univariate response in each treatment period, (2) multivariate response in each treatment period, and (3) longitudinal repeated measures on a single variate in each treatment period.

Cross-Over Studies↗
PubMed1986

Grading scores and survivorship functions in liver cirrhosis: a comparative statistical analysis of various predictive models.

In a group of followed-up liver cirrhotics we evaluated the reliability of prognostic estimates predicted on the basis of a previously described multivariate statistical model (MSM). In the same subjects we also compared theoretical survival estimates obtained by fitting some other liver cirrhosis grading scores (Child-Turcotte's, McCormick's and Orrego's) to prognostic purposes. No statistical difference between actual and MSM-estimated survivorship functions was found (employing a life-table method with Logrank test), thus confirming the prognostic reliability of this multivariate classification model. Such a global and prognosis-correlated index may be recommendable both for comparing different groups of patients, and for assessing treatment effectiveness. Or results also substantially confirm the other investigated classificative methods such as reliable liver cirrhosis severity indexes, although their use for prognostic purposes seems to be less suitable.

Actuarial Analysis↗
PubMed2002

Stromelysin-3 protein expression in invasive breast cancer: relation to proliferation, cell survival and patients' outcome.

Matrix metalloproteinases constitute one of the major extracellular matrix degrading enzymic families implicated in cancer development. Stromelysin-3 in particular, a member of the matrix metalloproteinases belonging to the stromelysins' subgroup, seems to be closely related to invasiveness and tumor progression. In this study, we proceeded to the evaluation of stromelysin-3 protein's expression in paraffin sections of 133 cases of invasive breast carcinomas and statistically estimated its relations with known clinicopathological prognostic parameters and patients' survival, proliferation markers Ki-67 and TopoIIalpha and the antiapoptotic protein bcl-2. Presence of stromelysin-3 was immunodetected, in the 73% of our cases, in stromal cells (65%) and in epithelial tumor cells (26.26%). Stromelysin-3 epithelial positivity presented statistically significant correlations with TopoIIalpha and Ki-67 proliferation indices (P =.042 and P =.031, respectively) and worse disease outcome through multivariate statistics (P =.014). Stromelysin-3 fibroblastic expression was significantly associated with nuclear grade (P =.024), ductal histological type (P =.037), TopoIIalpha (P =.001) and Ki-67 (P =.019), inversely with bcl-2 protein (P =.027) and with adverse overall survival through univariate analysis (P =.017). The subgroup of patients with stromelysin-3 co-expression in stromal and malignant epithelial cells showed statistically significant associations with Ki-67 and TopoIIalpha (P =.019, P <.0001, respectively), an inverse one with bcl-2 protein (P =.027) and furthermore with impaired survival (P =.002) through multivariate analysis. In conclusion, stromelysin-3 protein expression correlated with proliferation indices TopoIIalpha and Ki-67 and the anti-apoptotic protein bcl-2, data confirming stromelysin-3's contribution to breast cancer progression. Moreover its expression was shown to have a direct negative effect on patients' survival, especially in the subgroup of patients with simultaneous epithelial and stromal expression.

Adult↗
PubMed2002

Seminal vesicle involvement in patients with D1 disease predicts early prostate specific antigen recurrence and metastasis after radical prostatectomy and early androgen ablation.

BACKGROUND: Controversy persists regarding the management of patients who present with locally advanced metastatic prostate carcinoma. Although radical prostatectomy is not curative, there is growing evidence that survival may be prolonged when the surgery is combined with early androgen ablation. In the current study, the authors present data with which to evaluate and define factors for disease progression in patients undergoing radical prostatectomy with lymph node positive disease who are treated with early endocrine ablation. METHODS: Data from 40 patients undergoing radical prostatectomy and early androgen ablation between 1987-1998, all of whom had lymph node positive disease, were analyzed. Age, preoperative prostate specific antigen (PSA) level, clinical and pathologic Gleason score, surgical margin, seminal vesicle involvement (SVI), and the number and percentage of involved positive lymph nodes were analyzed to predict PSA progression, metastasis, and death using univariate and multivariate statistical techniques. RESULTS: Univariate analysis identified only SVI as a statistically significant predictor of PSA progression and metastasis. Twenty-seven patients (67.5%) were found to have SVI. Multivariate analysis failed to identify other factors that added significantly to the predictive ability of SVI. Kaplan-Meier estimates of time to PSA recurrence and metastasis demonstrated that SVI was highly predictive of disease progression. The median time to PSA progression for the 27 patients with SVI was 7.5 years compared with no progression reported in the 13 patients without SVI (P = 0.011). CONCLUSIONS: VI is a very powerful predictor of disease progression in patients with lymph node positive disease who undergo radical prostatectomy and early androgen ablation. In the current study, preoperative PSA, clinical or pathologic Gleason scores, and other clinical factors were not found to be predictive of disease outcome.

Adenocarcinoma↗
PubMed1988

Soluble extracts from a lymphoblastoid cell line modulate simian immunodeficiency syndrome (SAIDS) evolution.

Nineteen Macaca fascicularis monkeys were injected with SIV. They were subsequently divided into 5 groups. Four groups of 4 animals were injected with dialysable extracts (DLE) from a lymphoblastoid cell line which had been previously induced with DLE obtained either from the total lymphocyte population, or from the CD4 or CD8 subpopulations of mice immunized with SIV virus. The other three animals which constituted the control group received saline injections. The animals were kept under observation for a 108-day period, and the values of several biological parameters were compared in a multivariant statistical analysis. On the 108th day, the control group was significantly different from the other groups in the multivariant analysis. Furthermore, the CD4/CD8 ratio and the platelets and CD4 cell counts varied significantly between the groups in the univariant analysis. It is thus surmised that DLE obtained from CD8 cells or the total lymphocyte population of immunized animals may exert a modulating effect on the evolution of SAIDS.

Adjuvants, Immunologic↗
PubMed1984

Principal components analysis of haematological data from F344 rats with bladder cancer fed N-(ethyl)-all-trans-retinamide.

Several multivariate statistical methods are available which can alleviate the problems of analysing the large volumes of data generated from toxicological experiments. One such technique, principal components analysis, provides a method for exploring the relationships between a number of variables (such as blood parameters) and for eliminating redundant data if strong correlations exist between the characters. It also provides a method for clustering individuals, which may reveal similarities between animals in a treatment group or highlight individual 'outliers'. The application of principal components analysis to a set of haematological data from a trial evaluating the efficacy of a synthetic retinoid against carcinogen-induced bladder cancer in the rat has clearly shown, in two bivariate plots, that while some animals in the carcinogen-treated groups were normal, others were anaemic and that animals fed the synthetic retinoid and killed at 1 year had a microcytic anaemia. A full exploration of the data using conventional univariate statistical analysis would have involved at least 28 graphic representations of the data, as well as the interpretation of more than 130 means and SDs. Principal components analysis provides a valuable additional tool for the statistical analysis and exploration of toxicological data, but it must be used in conjunction with univariate or other multivariate methods if hypothesis testing is required. The use of multivariate techniques in toxicology may best be assessed by their practical application to toxicological data, and this paper presents such an evaluation with the aim of encouraging further exploration of the usefulness of principal components analysis. The raw data on which most analyses have been carried out are given.

Analysis of Variance↗
PubMed2007

A multivariate analysis of neuroanatomic relationships in a genetically informative pediatric sample.

An important component of brain mapping is an understanding of the relationships between neuroanatomic structures, as well as the nature of shared causal factors. Prior twin studies have demonstrated that much of individual differences in human anatomy are caused by genetic differences, but information is limited on whether different structures share common genetic factors. We performed a multivariate statistical genetic analysis on volumetric MRI measures (cerebrum, cerebellum, lateral ventricles, corpus callosum, thalamus, and basal ganglia) from a pediatric sample of 326 twins and 158 singletons. Our results suggest that the great majority of variability in cerebrum, cerebellum, thalamus and basal ganglia is determined by a single genetic factor. Though most (75%) of the variability in corpus callosum was explained by additive genetic effects these were largely independent of other structures. We also observed relatively small but significant environmental effects common to multiple neuroanatomic regions, particularly between thalamus, basal ganglia, and lateral ventricles. These findings are concordant with prior volumetric twin studies and support radial models of brain evolution.

Adolescent↗
PubMed1995

Application of multivariate cluster, discriminate function, and stepwise regression analyses to variable selection and predictive modeling of sperm cryosurvival.

OBJECTIVE: To develop a mathematical model that predicts sperm cryodamage based on the kinematic characteristics of seminal sperm as detected by computer-aided sperm analysis (CASA). DESIGN: Computer-aided sperm analysis was performed on donor semen before and after freezing. An iterative multivariate statistical analysis technique was developed to identify sperm subpopulations and to select the best variables for modeling. Stepwise, multivariate regression was performed on the selected subpopulations to predict the post-thaw percentage of motile sperm from prefreeze kinematic values. SETTING: Andrology laboratories, IVF laboratories, and sperm cryobanks. PARTICIPANTS: Semen donors in an academic research environment. MAIN OUTCOME MEASURES: Identification of predictive kinematic variables; number of sperm subpopulations per sample; number of kinematic variables per subpopulation; prediction error for subpopulation membership; and an equation for prediction of post-thaw percentage of motile sperm from prefreeze CASA variables. RESULTS: The number of subpopulations for each specimen was predicted by 3 to 5 kinematic variables. Straight-line velocity (VSL) and linearity were the most commonly predictive primary variables, whereas curvilinear velocity and amplitude of lateral head displacement were the most commonly predictive secondary variables. The best linear model predicted the post-thaw percentage of motile sperm from the difference in VSL between the subpopulation with the highest value and the subpopulation with the lowest value in each prefreeze specimen. CONCLUSIONS: A small number of consistent kinematic variables accurately described physiologic subpopulations of sperm in prefreeze and post-thaw specimens from different men. An equation based on the characteristics of these subpopulations predicts the post-thaw percentage of motile sperm (i.e., sperm recovery) from simple prefreeze kinematic variables. This equation could improve specimen screening by eliminating the requirements for freezing and thawing in order to identify a specimen's vulnerability to cryodamage.

Cell Survival↗
PubMedDate not supplied

[Prevalence of Neisseria meningitidis carriers among the population of Cerdanyola (Barcelona)].

OBJECTIVE: To determine the prevalence of Neisseria meningitidis (N. meningitidis) from healthy carriers and its resistance to penicillin in Cerdanyola population. To asses which risk factors were associated with healthy carriers and compare some epidemiologic characteristics between people with penicillin sensitive and penicillin resistant strains. METHODS: Cross-sectional seasonal study of 1500 individuals selected from day care centers, schools, colleges, cultural and working centers, located in different areas of Cerdanyola. We performed throat smears and immediate culture onto selective media for isolation of N. meningitidis. Data were evaluated by univariate and multivariate statistical analysis using the SPSS statistical package. RESULTS: One hundred and ninety-one (12.7%) individuals harbored N. meningitidis strains. In logistic regression multivariate analysis, meningococcal carriage significantly increased for the age group 14-18 years (OR = 4.55 with respect to the reference group, 0-3 years), in the spring (OR = 2.29), male sex (OR = 1.67), and active smoking (OR = 1.45, intervals of 10 cigarettes/day), while meningococcal carriage significantly decreased in the group under 4 years at age (OR = 0.55), with prior use of antibiotics (OR = 0.58) and with bigger housing space (OR = 0.84 for 10 m2/person). A 42% of N. meningitidis strains in carriers from this population showed decreased sensitivity to penicillin (MIC > 0.1 microgram/ml). We have not found significantly association between the variables studied and penicillin resistance among carriers of N. meningitidis. CONCLUSIONS: Age, spring season, sex, active smoking and overcrowded housing are significantly associated to carrier state. Prior use of antibiotics decreased to carrier state. According to our findings, reducing smoking habits and improving housing conditions may be useful measures to reduce the prevalence of carriers.

Adolescent↗
PubMed1999

Patients younger than 40 years with gastric carcinoma: Helicobacter pylori genotype and associated gastritis phenotype.

BACKGROUND: In the general population, Helicobacter pylori (H. pylori), particularly the cagA positive strain, has been associated with intestinal-type gastric carcinoma. Gastric carcinomas are rarely observed in patients age < or = 40 years. Host-related factors have been thought to be more important than environmental agents in these early-onset cancers. The aim of this study was to ascertain the possible role of H. pylori infection and that of cagA positive strains in the development of gastric carcinoma in these young patients. METHODS: In this case-control study, 105 gastric carcinoma patients (male-to-female ratio = 1.1; mean age, 34.4 years; range, 16-40 years) and an equal number of controls (matched for gender and age) were retrospectively selected from the same geographic area. The phenotypes of gastritis and H. pylori were histologically assessed, and the presence of the ureC gene, which is indicative of H. pylori infection, and the cagA genotype were determined by polymerase chain reaction. Gastric carcinoma risk was calculated by both univariate and multivariate statistical methods, taking into account the cancer phenotype, the gastritis phenotype detected in both patients and controls, and the H. pylori genotype. RESULTS: For 74 diffuse and 31 intestinal gastric carcinomas, multivariate logistic regression analysis produced results consistent with those of univariate statistical tests, showing a significant association between gastric carcinoma and both H. pylori infection (odds ratio [OR] = 2.79; 95% confidence interval [CI] = 1.52-5.11) and cagA positive status (OR = 2.94; 95% CI = 1.56-5.52). CONCLUSIONS: In young Italian patients with gastric carcinoma, the significant association with cagA positive H. pylori infection suggests that the bacterium has an etiologic role in both diffuse-type and intestinal-type gastric carcinoma.

Adenocarcinoma↗
PubMed2002

Characterisation of NMHCs in a French urban atmosphere: overview of the main sources.

Continuous hourly air quality data involving 37 C2-C9 non-methane hydrocarbons (NMHC) over 4 years are reported for the first time in Lille metropol, northern France, at two urban roadside and background sites. The data have been analysed in two complementary steps: univariate statistics which define the spatial and temporal characteristics of NMHC by constructing the seasonal and daily concentration profiles, and multivariate statistics based on principal component analysis (PCA). A number of important sources have been clearly identified depending on the season: (1) motor vehicle exhaust, which dominates the NMHC distribution and particularly in winter, even for isoprene; (2) wintertime stationary combustion and activities related to fossil fuel consumption in general, such as natural gas leakage of ethane and propane; (3) summertime evaporative emissions from fuel and solvent; and (4) summertime biogenic emissions through isoprene behaviour and their dependence on temperature.

Journal Article↗
PubMed2005

The independent impact of extended pattern biopsy on prostate cancer stage migration.

PURPOSE: There are many factors impacting stage migration for prostate cancer. The number of prostate core biopsies is known to increase detection of prostate cancers. It is still unknown whether the number of biopsies is an independent predictor of tumor size. This is important as a number of studies show that tumor volume is an independent predictor of cancer progression. MATERIALS AND METHODS: Using the University of California, San Francisco Urologic Oncology database, a retrospective review of 378 patients undergoing radical prostatectomy by a single surgeon during 2000 to 2003 was performed. Patient and tumor specific variables including age, prostate specific antigen (PSA), number of biopsies, biopsy Gleason grade, tumor volume in the surgical specimen and surgical specimen tumor grade were studied. Univariate and multivariate statistical methods including multiple and logistic regression were used to characterize patients by the number of biopsy cores. Tests of significance to identify predictors of tumor size were based on the partial F statistic and the likelihood ratio test. RESULTS: A total of 317 eligible patients were studied, of whom 119 had 6 biopsies and 198 had more than 6 biopsies. The 2 groups of patients were evenly matched in terms of age, PSA and Gleason sum, with no statistically significant differences observed. On univariate analysis, mean tumor volume was larger for patients receiving 6 core biopsies vs greater than 6 core biopsies (3.85 vs 2.04 cc, p = 0.0009). Additionally, statistically significant differences were observed when comparing median tumor volumes, as well as excluding extremely large volume tumors. On multivariate analysis the number of biopsies performed (6 vs more than 6), was an independent predictor of tumor size (p = 0.006), controlling for primary Gleason score, Gleason sum, PSA as a continuous or categorical variable, year of biopsy and year of surgery. CONCLUSIONS: The use of extended pattern prostate biopsy templates results in the detection of smaller volume prostate cancers, independent of PSA and Gleason grade. These biopsy templates have contributed to the downward stage migration of prostate cancer detection and may possibly contribute to the risk of over detection.

Adult↗
PubMed2006

Effect of c-Met expression on survival in head and neck squamous cell carcinoma.

The proto-oncogene c-Met has been suggested to be associated with progression of squamous cell carcinoma of the head and neck. The aims of the present study were to assess the prevalence of c-Met expression in oral squamous cell carcinoma (OSCC) and to verify whether c-Met can be considered a marker of prognosis in these patients. In a retrospective study, a cohort of 84 OSCC patients was investigated for c-Met expression and its cellular localization by immunohistochemistry. After grouping for c-Met expression, OSCC patients were statistically analyzed for the variables age, gender, histological grading, tumor node metastasis, staging and overall survival rate. Univariate and multivariate statistics were used for data analysis. Sixty-nine cases (82.2%) of OSCC showed immunopositivity, with a mainly membranous expression and scattered areas also showing a cytoplasmic localization, whereas 15 cases (17.8%) did not show c-Met. No statistical association was found between c-Met expression and any variables considered at baseline, apart from the higher number of c-Met positivity in females (p = 0.026). Among positive tumors, well-differentiated areas showed low or absent cytoplasmic expression, while low-differentiated areas showed both membranous and cytoplasmic positivity. In terms of prognostic significance, c-Met expression was found to have an independent association with a poorer overall survival rate (p = 0.036). On the basis of these results, it is possible to suggest c-Met as an early marker of poor prognosis, a hallmark of aggressive biological behavior in OSCC, suggested to be useful in identifying cases of OSCC before the relapse.

Adolescent↗