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At least 1,225 records · Page 68Linked to original sources
PubMed1984

The National Evaluation of School Nutrition Programs: data analysis methods.

An overview of the analytic methods used in the National Evaluation of School Nutrition Programs is provided. A path model is described that shows the hypothesized relationships between outcome and predictor variables. The outcome variables are participation in the School Nutrition Programs and the effects of participation on family food expenditures and student dietary intake and anthropometric measurements. Individual student participation in the programs is seen as the last of a series of participation decisions that include the school's decision to offer the program and the prices charged for meals. Selection of specific statistical and structural models to present these relationships are discussed. The decision to use ordinary least square estimates of impact rather than a modified two-stage least squares approach is explained.

Anthropometry↗
PubMed1994

Cell abnormalities associated with human papillomavirus-induced squamous intraepithelial cervical lesions. Multivariate data analysis.

One hundred ninety-six cervical scrapings were obtained for simultaneous research of cell abnormalities in Papanicolaou smears and detection of genital human papillomavirus (HPV) genotypes by polymerase chain reaction in extracted DNA from each clinical sample. The samples described by six discriminant cytologic parameters, and a synthetic HPV-presence/absence parameter provided an efficient matrix for multiple correspondence analysis. This statistical analysis displayed a plurality of HPV-related cell abnormalities in squamous intraepithelial lesions, and a high correspondence between HPV infection and the presence of multinucleated squamous cells, morphologically transformed keratinocytes (dyskaryotic cells), koilocytes, and cellular changes related to epithelial maturation. Because of the low proportion of detectable koilocytes in the HPV-infected scrapings, the authors also inferred that cellular changes related to epithelial maturation and morphologically transformed keratinocytes are the most accurate and efficient cell abnormalities, in terms of frequency and correlation, for cytodiagnosis of HPV-induced or associated squamous intraepithelial cervical lesions.

Adolescent↗
PubMed2002

SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis.

SNOMAD is a collection of algorithms for the normalization and standardization of gene expression datasets derived from diverse biological and technological sources. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: (1). Local mean normalization; and (2). Local variance correction (Z-score generation using a locally calculated standard deviation).

Algorithms↗
PubMed2002

Ratio statistics of gene expression levels and applications to microarray data analysis.

MOTIVATION: Expression-based analysis for large families of genes has recently become possible owing to the development of cDNA microarrays, which allow simultaneous measurement of transcript levels for thousands of genes. For each spot on a microarray, signals in two channels must be extracted from their backgrounds. This requires algorithms to extract signals arising from tagged mRNA hybridized to arrayed cDNA locations and algorithms to determine the significance of signal ratios. RESULTS: This paper focuses on estimation of signal ratios from the two channels, and the significance of those ratios. The key issue is the determination of whether a ratio is significantly high or low in order to conclude whether the gene is upregulated or downregulated. The paper builds on an earlier study that involved a hypothesis test based on a ratio statistic under the supposition that the measured fluorescent intensities subsequent to image processing can be assumed to reflect the signal intensities. Here, a refined hypothesis test is considered in which the measured intensities forming the ratio are assumed to be combinations of signal and background. The new method involves a signal-to-noise ratio, and for a high signal-to-noise ratio the new test reduces (with close approximation) to the original test. The effect of low signal-to-noise ratio on the ratio statistics constitutes the main theme of the paper. Finally, and in this vein, a quality metric is formulated for spots. This measure can be used to decide whether or not a spot ratio should be deleted, or to adjust various measurements to reflect confidence in the quality of the measurement. CONTACT: e-dougherty@tamu.edu

Cell Line↗
PubMed2025

NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline.

SUMMARY: Omics profiling has proven of great use for unbiased and comprehensive identification of key features that define biological phenotypes and underlie medical conditions. While each omics profile assists characterization of specific molecular components relevant for the studied phenotype, their joint evaluation can offer deeper insights into the overall mechanistic functioning of biological systems. Here, we introduce an approach where, starting from representative traits (e.g. differentially expressed elements) obtained for each omics profile, we construct and analyze joint interaction networks. The resulting networks rely on the existing knowledge of confident interactions among biological entities. We use these maps to identify and describe central elements, which connect multiple entities characteristic of the studied phenotypes and we leverage MONET network decomposition tool in order to highlight functionally connected network modules. In order to enable broad usage of this approach, we developed the NOODAI software platform, which enables integrative omics analysis through a user-friendly interface. The analysis outcomes are presented both as raw output tables as well as informative summary plots and written reports. Since the MONET tool enables the use of algorithms with strong performance in identifying disease-relevant modules, NOODAI software platform can be of a high value for analyzing clinical multi-omics datasets. AVAILABILITY AND IMPLEMENTATION: NOODAI is freely accessible at https://omics-oracle.com. Source code is available under GPL3 at: https://github.com/TotuTiberiu/NOODAI with the DOI: 10.5281/zenodo.17203984.

Software↗
PubMed2026

BRIDGE: an interactive application for multi-omics data analysis, visualization and integration.

SUMMARY: BRIDGE is a Shiny-based application that provides an accessible, modular platform for individual and integrative multi-omics analysis. Using an independent SQLite database backend, it offers a local, private, and user-friendly environment that requires no prior computational expertise. The application supports proteomics, phospho-proteomics, and RNA-seq analyses through a comprehensive suite of visualization and analytical modules, together with an integrated multi-omics analysis pipeline. Built-in caching and asynchronous processing improve responsiveness, enabling efficient exploration, analysis, and visualization of multi-omics datasets on moderate hardware. AVAILABILITY AND IMPLEMENTATION: BRIDGE is implemented in R using Shiny and is freely available as a Docker container at https://ghcr.io/paulilab/bridge. A public demonstration server with example datasets is available at https://bridge.imp.ac.at. Code and datasets are also available at https://github.com/paulilab/BRIDGE and under DOI: https://doi.org/10.5281/zenodo.20215824.

Multiomics↗
PubMed2005

MAGIC Tool: integrated microarray data analysis.

SUMMARY: Several programs are now available for analyzing the large datasets arising from cDNA microarray experiments. Most programs are expensive commercial packages or require expensive third party software. Some are freely available to academic researchers, but are limited to one operating system. MicroArray Genome Imaging and Clustering Tool (MAGIC Tool) is an open source program that works on all major platforms, and takes users 'from tiff to gif'. Several unique features of MAGIC Tool are particularly useful for research and teaching. AVAILABILITY: http://www.bio.davidson.edu/MAGIC

Algorithms↗
PubMed2006

Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques.

MOTIVATION: We present a study of antigen expression signals from a newly developed high-throughput protein microarray technique. These signals are a measure of antibody-antigen binding activity and provide a basis for understanding humoral immune responses to various infectious agents and supporting vaccine and diagnostic development. RESULTS: We investigate the characteristics of these expression profiles and show that noise models, normalization, variance estimation and differential expression analysis techniques developed in the context of DNA microarray analysis can be adapted and applied to these protein arrays. Using a high-dimensional dataset containing measurements of expression profiles of antibody reactivity against each protein (295 antigens and 9 controls) in 42 malaria (Plasmodium falciparum) protein arrays derived from 22 donors with various clinical presentations of malaria, we present a methodology for the analysis and identification of significantly expressed antigens targeted by immune responses for individual sera, groups of sera and across stages of infection. We also conduct a short study highlighting the top immunoreactive antigens where we identify three novel high priority antigens for future evaluation. AVAILABILITY: All software programs (in R) used for the analysis described in this paper are freely available for academic purposes at www.igb.uci.edu/servers/servers.html.

Algorithms↗
PubMed2000

Experience with the elective transfer of two embryos under the conditions of the german embryo protection law: results of a retrospective data analysis of 2573 transfer cycles.

The German embryo protection law (Embryonenschutzgesetz, ESchG) does not allow embryo selection. Therefore, only as many oocytes at the pronuclear stage (PN), as are planned to be transferred, are allowed to be cultured. It is not known whether, under these conditions, it is possible to reduce the number of embryos for transfer without a corresponding reduction of the overall pregnancy rate (PR). We retrospectively analysed 2573 consecutive transfer cycles following either in-vitro fertilization (IVF) or IVF/intracytoplasmic sperm injection. Out of these cycles, 234, 329 and 792 were performed with one, two, and three embryos respectively, because only that number was available (non-elective transfer). Another 123 and 1095 transfer cycles were performed with two and three embryos, respectively, which were selected from a higher number of PN oocytes (elective transfer). The clinical ongoing PR were 3.9, 9.1 and 17.7% respectively for the groups with non-elective transfer of 1, 2 and 3 embryos, and 22.0 and 22.5% for the groups with elective transfers with two and three embryos, respectively. There was no statistically significant difference in PR between the two elective embryo transfer groups up to the age of 40 years. The multiple pregnancy rate was reduced by 7.9%. The reduction of the number of embryos transferred from three to two can be performed even under the conditions of the ESchG without an effect on the overall PR.

Abortion, Spontaneous↗
PubMed1990

The use of residuals for longitudinal data analysis: the example of child growth.

Health impact evaluations often measure changes in health status over part of a total life experience. The effects on health up to and including the start of the evaluation, which are embodied in the measure of initial health status, need to be removed while examining the effects that other variables exert during the evaluation period on final health status. Statistical models, which include initial health status as a covariate while examining the effects of other variables during the evaluation, confound the effects of a determinant during evaluation with preevaluation effects, because they do not differentiate between effects produced at different times by the same determinant. A residual model removes the preevaluation effects by regressing final health status on initial health status. The residuals from this regression are then regressed on the other predictor variables. In this paper, standard covariate adjustment, which includes all effects simultaneously, is compared with a two-part residual model using child growth as an example. The simultaneous model over- and underpredicts growth relative to the residual model depending on the age and initial body size of a child. In general, whenever initial (preintervention) and final (postintervention) measures of health outcome exist, the residual model should be considered on the basis of biologic and epidemiologic consideration, not solely on statistical optimality.

Anthropometry↗
PubMed2006

Data analysis from a multi-centre, comparative study of angiographic examinations leading to practical guidelines for the optimisation of patient doses.

In this study, patient doses were analysed against exposure parameters and procedure protocol. Patient doses were measured in seven hospitals for a standard diagnostic vascular examination. Image quality was assessed using the contrast-detail phantom from Nijmegen (CD-DISC 2.0). A link between dose and image quality was investigated. Image quality strongly depends on the preset dose level. The higher the dose level, the better the image quality, but also the higher the patient dose. However, no clear correlation was found between total dose-area product (DAP) or effective dose and image quality. A large range in patient dose was found: DAP (22-130 Gy cm2) and effective dose (3.9-16.8 mSv). A difference in number of frames was also found in the different centres, owing to different frame rates (3-2-1 frames per second) and use of oblique projections. Differences in doses and exposure settings offer the possibility of optimising patient doses in angiography and interventional radiology.

Angiography↗