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At least 451 records · Page 25Linked to original sources
PubMed1984

An assay for pattern formation in dictyostelium discoideum using monoclonal antibodies, flow cytometry, and subsequent data analysis.

An assay for determining the proportions of prespore cells in a simple multicellular organism, the slug stage of Dictyostelium discoideum, was established using a prespore-specific monoclonal antibody and a fluorescence-activated cell sorter. Appropriate techniques for data analysis were developed. The effects of slug size and age were determined. Small slugs have a lower percentage of prespore cells than large slugs. The percentage of prespore cells increases and then decreases in slugs aged between a few hours and 9 days. Pronounced effects were observed on the size of cells in aging slugs. In particular unlabelled (mostly prestalk) cells were larger than prespore cells in young slugs, but after 6 days migration they became considerably smaller than prespore cells. The fact that all unlabelled cells were coordinately shifted in size, suggests that these cells (which comprise prestalk, prestalklike, and predisc cells) are related to each other.

Antibodies, Monoclonal↗
PubMed2006

Next station in microarray data analysis: GEPAS.

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.

Cluster Analysis↗
PubMed1999

Classical conditioning of the electrically elicited blink reflex in humans: a new method of data analysis.

The eyeblink conditioning paradigm is a well-established model to study learning processes in humans and animals. Especially results from animal studies have supplied new insight into physiological pathways and brain structures involved in associative motor learning and memory. An important role of the cerebellum and its afferent fiber systems could be shown. Recent studies in humans have given evidence that results of animal experiments can be applied directly to the human condition. A high variation of baseline EMG activity and/or spontaneous blinks may influence the analysis of classical conditioning of the electrically elicited blink reflex in humans. To optimize differentiation between real conditioned responses and stimulus-independent EMG activity, we developed an algorithm which is fully automated and independent of a possible bias of an examiner. In a first step the algorithm decides whether a subject fulfills the criteria of a successful learning process or not. The second step quantifies the learning process. For quantification of the learning process, the following parameters were calculated: number of conditioned responses, onset of conditioning, time and amount of maximal conditioning, speed of conditioning and speed of habituation. According to our criteria, 80% of the healthy volunteers acquired conditioned responses. There is an age-related decline in eyeblink classical conditioning. Analysis of patient groups with different types of lesions will further improve our knowledge and understanding of pathways involved in learning processes in humans. The proposed new algorithm of data analysis takes less than 10 s on a standard computer, is more sensitive and more specific in detecting conditioned responses and, therefore, may further improve the value and reliability of the eyeblink conditioning paradigm in clinical research.

Adult↗
PubMed1992

Clinical assessment of the knowledge base of an expert system for data analysis in laboratory medicine.

Despite the apparent demand for a consultation system, only a few expert systems have been developed for laboratory medicine. Some studies on the diagnostic precision of such systems have been reported, but the efficiency of their knowledge bases has not yet been investigated. An expert system, named BLOOD, for data analysis in a hematology laboratory, which is written in C-Prolog and runs on VAX-station, has already been reported to have excellent diagnostic reliability and ability to cope with the fuzziness involved in clinical diagnostic procedures. A quantitative examination of the knowledge base of BLOOD using real laboratory data from 58 patients diagnosed as having iron deficiency anemia clearly revealed the verbosity of the knowledge base, and proved that it was effective for obtaining a group of essential diagnostic rules.

Anemia, Hypochromic↗
PubMed2006

Statistical practice in high-throughput screening data analysis.

High-throughput screening is an early critical step in drug discovery. Its aim is to screen a large number of diverse chemical compounds to identify candidate 'hits' rapidly and accurately. Few statistical tools are currently available, however, to detect quality hits with a high degree of confidence. We examine statistical aspects of data preprocessing and hit identification for primary screens. We focus on concerns related to positional effects of wells within plates, choice of hit threshold and the importance of minimizing false-positive and false-negative rates. We argue that replicate measurements are needed to verify assumptions of current methods and to suggest data analysis strategies when assumptions are not met. The integration of replicates with robust statistical methods in primary screens will facilitate the discovery of reliable hits, ultimately improving the sensitivity and specificity of the screening process.

Biological Assay↗
PubMed1981

[Data analysis in health insurance].

In the last fifty years four to six mathematical research endeavours of general significance only have been designed in the field of health insurance. It is inconsequent to discuss the changes needed in the insurance system without having at one's disposal minimal mathematically-statistically firm basic figures. The present work first generally defines the mathematical bases in the health insurance field. The purpose of the project, within the first large scale data analysis, is above all the development of concepts for the institutionalized, systematic and periodical exploitation of the data available to health insurance carriers and their testing with econometric models. At the same time, thanks to methods to regularly collect data in the various health care sectors, the dependence of cost factors on medical care supply, on the structure of the insured population and on the cost causes will be studied at periodic intervals. Cheap sampling concepts shall be developed and tested in order to obtain the data which are not gathered directly. In a few fields data collection through surveys will be organized in order to allow for comprehensive interdisciplinary interpretation of the data.

Health Services↗
PubMed2006

A coupled Car-Parrinello molecular dynamics and EXAFS data analysis investigation of aqueous Co(2+).

We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.

Cations, Divalent↗
PubMed1983

Structured exploratory data analysis (SEDA) of finger ridge-count inheritance: I. Major gene index, midparental correlation, and offspring-between-parents function in 125 south Indian families.

Fourteen dermatoglyphic traits measured on 125 Velanadu Brahmin families were analyzed for mode of inheritance using three Structured Exploratory Data Analysis (SEDA) statistics: the major gene index, the offspring between parents function, and the traditional midparental correlation coefficient. Since the traits are integer valued with restricted ranges of variation, we simulated various transmission models with discrete expression to better understand the nature of the SEDA statistics for such variables. In addition, permutation procedures were employed to aid the interpretation of the SEDA results. These analyses suggest that corresponding homologous fingers on the left and right hands exhibit similar transmission characteristics. The relationship of the parent and child total ridge-counts of the two hands separately, as well as their combined total, virtually simulate complete Galtonian blending inheritance. Results for the individual digital ridge-counts as well as the pattern-intensity-index variable also suggest a multifactorial mode of transmission or possibly one involving several genes.

Dermatoglyphics↗
PubMed2006

Easy and rapid method of zygosity determination in transgenic mice by SYBR Green real-time quantitative PCR with a simple data analysis.

Establishment and maintenance of transgenic mouse strains require being able to distinguish homozygous from heterozygous animals. To date, the developed real-time quantitative PCR techniques are often complicated, time-consuming and expensive. Here, we propose a very easy and rapid method with a simple data analysis to determine zygosity in transgenic mice. We show that the real-time quantitative PCR using SYBR Green fluorescent dye can be applied to discriminate two-fold differences in copy numbers of the transgene. Our procedure has to fit only three simple requirements: (1) to design primers capable of detecting one Ct difference for two-fold differences in DNA amounts (2) to measure genomic DNA concentrations accurately and (3) to have a reference animal of known zygosity in each run. Then, if the Ct values for the control gene are similar in all samples, we are able to compare directly the Ct values for the transgene in every sample, and so, to deduce the zygosity status of each mouse relative to the reference animal. This method is really simple and reliable, and it may be valuable as a rapid screening tool for zygosity status in transgenic animals.

Animals↗
PubMed2006

Efficient calculation of interval scores for DNA copy number data analysis.

DNA amplifications and deletions characterize cancer genome and are often related to disease evolution. Microarray-based techniques for measuring these DNA copy-number changes use fluorescence ratios at arrayed DNA elements (BACs, cDNA, or oligonucleotides) to provide signals at high resolution, in terms of genomic locations. These data are then further analyzed to map aberrations and boundaries and identify biologically significant structures. We develop a statistical framework that enables the casting of several DNA copy number data analysis questions as optimization problems over real-valued vectors of signals. The simplest form of the optimization problem seeks to maximize phi(I) = Sigmanu(i)/radical|I| over all subintervals I in the input vector. We present and prove a linear time approximation scheme for this problem, namely, a process with time complexity O (nepsilon(-2)) that outputs an interval for which phi(I) is at least Opt/alpha(epsilon), where Opt is the actual optimum and alpha(epsilon) --> 1 as epsilon --> 0. We further develop practical implementations that improve the performance of the naive quadratic approach by orders of magnitude. We discuss properties of optimal intervals and how they apply to the algorithm performance. We benchmark our algorithms on synthetic as well as publicly available DNA copy number data. We demonstrate the use of these methods for identifying aberrations in single samples as well as common alterations in fixed sets and subsets of breast cancer samples.

Algorithms↗
PubMed2004

A novel method for displaying gait and clinical movement analysis data.

Plotting kinematic and kinetic data of a patient's movement patterns relative to normative values (i.e., mean and +/-1 S.D.) is a common method used by clinicians to visually assess deviations and interpret the patient's gait analysis data. This method of data interpretation is often time consuming and complex, especially when the process requires the inspection of a plethora of line graphs for numerous variables that are displayed across several report pages. In this paper we propose an alternate method for displaying movement pattern deviations relative to normative data by color-coding the magnitude and the direction of the deviation. An advantage of this approach is that a single page summary of all the deviation magnitudes can be displayed simultaneously, in a manner that is concise, visually effective and reduces complexity. The purpose of this paper is to describe the algorithmic development of the color-coding method.

Algorithms↗
PubMed1982

Interactive computer programs in sequence data analysis.

We present interactive computer programs for the analysis of nucleic acid sequences. In order to handle these programs, minimum computer experience is sufficient. The nucleotide sequence of the human gamma globin gene complex is used as an example to illustrate the data analysis.

Base Sequence↗
PubMed2006

Relationship between ozone and temperature during the 2003 heat wave in France: consequences for health data analysis.

BACKGROUND: PAPRICA is a research program designed to estimate the impact on the health of patients with chronic respiratory insufficiency of a prevention strategy based on notification of ozone pollution. The first year of this study was conducted during the 2003 heat wave, and high temperatures were therefore considered as a confounding factor in the data analysis. The aim of the present study was to assess the relationship between ozone and temperature in order to propose a methodology to distinguish between the effects of ozone and temperature on the impact of a prevention strategy with regard to ozone pollution. METHODS: Multivariate analyses were used to identify associated climate and ozone pollution profiles. This descriptive method is of great value to highlight the complexity of interactions between these parameters. RESULTS: Ozone concentration and temperature were strongly correlated, but the health impact of ozone pollution alone will be evaluated by focusing on situations characterized by ozone concentrations above 110 mug/m3/8h (air quality guidelines to protect human health defined by the French legislation) and temperatures lower than 26 degrees C, below the discomfort threshold. CONCLUSION: The precise relationship between ambient ozone concentration and temperature identified during the PAPRICA 2003 study period will be used in analysing the PAPRICA health data.

Air Pollution↗
PubMed1999

Linewidth analysis of spin labels in liquids. I. Theory and data analysis.

We present a method of simulating the EPR spectra of spin labels in liquids using direct convolution of hyperfine splitting with Lorentzian linewidths. The aim is to simulate the experimental lineshape by considering all spectrometer characteristics as well as inhomogeneous and homogeneous linewidth effects. A major advance in this method is the correction for the broadening produced by Zeeman modulation commonly used to obtain EPR signals; this allows experimenters much more freedom to optimize their experimental conditions for the best signal-to-noise ratio. Microwave power broadening (saturation) effects on the EPR lines are significant even at very low observer levels. Successful simulation requires that all contributions from unresolved hyperfine splittings be explicitly included. Inhomogeneous broadening is dealt with by including all spins that interact with the electron (as a set of superhyperfine interactions); there is no "effective Gaussian" to substitute for the correct superhyperfine interactions. The effects of spin exchange on the linewidth and lineshape can be observed and must be taken into account in order to extract the fundamental linewidths.

Computer Simulation↗
PubMedDate not supplied

Use of MEDUSA-based data analysis and capillary HPLC-ion-trap mass spectrometry to examine complex immunoaffinity extracts of RBAp48.

To examine the Jurkat cell interaction partners of RbAp48, we digested entire immunoaffinity extracts with trypsin and identified potential interacting proteins using one- and two-dimensional microcapillary HPLC-ion-trap mass spectrometry. An Oracle-based automated data analysis system (MEDUSA) was used to compare quadruplicate anti-RbAp48 antibody affinity extracts with two sets of quadruplicate control extracts. The anti-RbAp48 extracts contained over 40 difference 1D gel bands. We identified all known proteins of the NuRD/Mi-2 complex including human p66. Three potential homologues of members of this complex were also found, suggesting that there may be more than one variant of this complex. Eleven proteins associated with RNA binding or pre-mRNA splicing were observed. Four other proteins, including a putative tumor suppressor, were identified, as were 18 ribosomal proteins. There was little overlap with RbAp48-interacting proteins defined by yeast two-hybrid methods. These results demonstrate the analysis of a complex immunoaffinity extract and suggest a more complex cellular role for RbAp48 than previously documented.

Amino Acid Sequence↗
PubMed1994

Categorical data analysis of the effect on bull fertility of butylated hydroxytoluene addition to semen extenders prior to freezing.

Butylated hydroxytoluene is an antioxidant that has antiviral properties and sustains sperm viability during freezing and thawing. A field trial involving 11 bulls and 19,000 AI was conducted to determine whether addition of .5 mM butylated hydroxytoluene to whole milk extender during seminal processing affected bull fertility as estimated by nonreturn rates generated by cows bred to the bulls. Effects of bull, batch of semen nested within bull, treatment, and month of AI were studied. Nonreturn rates were recorded for each month for every bull, batch of semen (ejaculates pooled on a given day), and treatment combination. Because some bulls had < 6 batches of semen, the original experimental design was reduced to two smaller designs. Categorical data analysis with maximum likelihood estimation was used for analysis of nonreturn rates. The results from three models were used to interpret the data. The nonreturn rates were approximately 73.9% for the butylated hydroxytoluene treatment and 74.1% for the control. In all models, bull effect was significant, but batch, month of AI, and treatment had no effect on bull fertility. Addition of .5 mM butylated hydroxytoluene to whole milk extender during semen processing did not affect bull nonreturn rates.

Animals↗
PubMed2004

Classification and correlation of St. John's wort extracts by nuclear magnetic resonance spectroscopy, multivariate data analysis and pharmacological activity.

The use of proton NMR spectroscopy allows the analysis of complex multi-component mixtures such as plant extracts by simultaneous quantification of all proton-bearing compounds and consequently all relevant substance classes. Since the spectra obtained are too complicated to be analysed visually, the classification of spectra was carried out using multivariate statistical methods. The spectroscopic data of various extracts of St. John's wort (Hypericum perforatum) samples derived from 4 different accessions extracted with 6 distinct solvents were chemometrically evaluated and calibrated using the partial least square (PLS) algorithm. In a first approach, we found a consistent correlation for the spectroscopic pattern of the extracts and the corresponding IC (50) values derived from non-selective binding to opioid receptors. Consequently, the multivariate data analysis was used to predict the pharmacological efficacy of further St. John's wort extracts on the basis of their proton NMR spectra. In a second approach a PLS 2 model was used to predict the biological activity for eight St. John's wort extracts based on two pharmacological data sets: (i) non-selective binding to opioid receptors and (ii) antagonist effect at corticotrophin-releasing factor type 1 (CRF (1)) receptors. The PLS 2 model confirmed the useful application of the presented approach to assess the quality of medicinal herbs and extracts by spectroscopic analysis derived from bioactivity-related quality parameters.

Humans↗