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PubMed1981

Dynamic computed tomography of the brain: techniques, data analysis, and applications.

Rapid sequence computed tomography (CT) scanning has many potential applications in studying intracranial physiologic events. However, visual inspection of these rapid sequence scans fails to extract the large amount of information inherent in the digital data. The concept of corrected mean transit time applied to rapid sequence scans after intravenous bolus injection of contrast material provides quantitative data on relative hemispheric flow. Use of histogram-based areas of interest permits accurate and reproducible identification of anatomic structures including arteries and gray and white matter. Gamma variate curve fit techniques reduce statistical noise. The concept of transit time can be expanded to the creation of functional CT images.

Blood Flow Velocity↗
PubMed2005

Dismal: a spreadsheet for sequential data analysis and HCI experimentation.

Dismal is a spreadsheet that works within GNU Emacs, a widely available programmable editor. Dismal has three features of particular interest to those who study behavior: (1) the ability to manipulate and align sequential data, (2) an open architecture that allows users to expand it to meet their particular needs, and (3) an instrumented and accessible interface for studies of human-computer interaction (HCI). Example uses of each of these capabilities are provided, including cognitive models that have had their sequential behavior aligned with subject's protocols, extensions useful for teaching and doing HCI design, and studies in which keystroke logs from the timing package in Dismal have been used.

Animals↗
PubMed2005

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

BACKGROUND: MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. RESULTS: We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. CONCLUSION: MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454

Algorithms↗
PubMed2005

Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: sample preparation, data analysis, and application to the analysis of complex peptide mixtures.

We report the development of a robust interface for off-line coupling of nano liquid chromatography (LC) to matrix-assisted laser desorption/ionisation-mass spectrometry (MALDI-MS) and its application to the analysis of proteolytic digests of proteins, both isolated and in mixtures. The interface makes use of prestructured MALDI sample supports to concentrate the effluent to a small sample plate area and localize the MALDI sample to a predefined array, thereby enriching the analyte molecules and facilitating automated MALDI-MS analysis. Parameters that influence the preparation of MALDI samples from the LC effluent were evaluated with regard to detection sensitivity, spectra quality, and reproducibility of the method. A procedure for data processing is described. The presented nano LC MALDI-MS system allowed the detection of several peptides from a tryptic digest of bovine serum albumin, at analyzed amounts corresponding to one femtomole of the digested protein. For the identification of native proteins isolated from mouse brain by two-dimensional gel electrophoresis, nano LC MALDI-MS increased the number of detected peptides, thereby allowing identification of proteins that could not be identified by direct MALDI-MS analysis. The ability to identify proteins in complex mixtures was evaluated for the analysis of Escherichia coli 50S ribosomal subunit. Out of the 33 expected proteins, 30 were identified by MALDI tandem time of flight fragment ion fingerprinting.

Animals↗
PubMed1976

Data analysis problems in the area of pharmacokinetics research.

Of interest in compartment analysis is the estimation of kinetic first order rate constants and quantification of the amount of drug present in each compartment at every point in time. From the data pertaining to only one compartment, it is not always possible to estimate all the first order rate parameters of linear and non-linear compartment systems. When multiple varying doses are administered at different intervals of time, the equations quantifying the maximum and minimum amount of drug accumulated in each interval may be used. To obtain estimates of kinetic parameters, statistical adjustments may be used in the kinetic equations.

Humans↗
PubMed2006

[Integrating obtained knowledge from transcriptome data by a new framework for data analysis].

Microarray analyses facilitate the investigation of quantitative information coded in the genome by measuring transcriptome, which records the decoded information from the genome. The state of a cell and differences from other states can be studied through genome information, by comparing one set of transcriptome data to other sets. Clearly, those data should be shared and compared with researchers, and the knowledge should be integrated. Unfortunately, at present data comparisons in microarray analyses are quite difficult; the accuracy as well as the reproducibility is low. The difficulties are originated from data analyses methods. Data comparison requires an intelligent framework, such as that discussed by philosopher Sir Karl R Popper. Frameworks for microarray analyses have been developed by many efforts of bioinformatitians. The frameworks currently used are being inspected and critically discussed. By checking the mathematical models that form the practical frameworks, arbitrariness such as the lack of falsifiability has been pointed out. The paradigm in this field of analyses is also criticized by disagreement with the scientific standard, and it is shown as the origin of errors in analyses. The excessive numbers of frameworks produced in an ad hoc manner has also been criticized, since the existence of so many allows researchers to select different frameworks, discussions beyond frameworks are always difficult. A new framework that uses a parametric model is introduced with an explanation of the bases of the framework and the process of testing. Additionally, differences of obtained results by these frameworks are presented using GeneChip data, in stability of log-ratio measurements and reproducibility of analyses. The possibility of artificial decoding of genome information by an extended framework is also discussed.

Gene Expression Profiling↗
PubMed1984

Prevalence of cervical intraepithelial neoplasia in sexually active teenagers and young adults. Results of data analysis of mass Papanicolaou screening of 796,337 women in the United States in 1981.

One of the largest nationally reported cases of carcinoma in situ in the teenage population of the United States is based on 1 year's computerized data from Cancer Screening Services. In 1981, 796,337 women were screened with an average age of 25.9. Of these, 18,589 (2.33%) had abnormal cytology. In 194,069 (24.3%) of the 796,337 patients aged 15 to 19, 3,651 (1.9%) had abnormal cytology. In 17% of all patients with abnormal cytology biopsy of the cervix was performed. The prevalence rate of dysplasia and carcinoma in situ was 18.8/1,000 for ages 15 to 19 and 28.8/1,000 for ages 20 to 24. Biopsy-proved cases of all grades of cervical intraepithelial neoplasia in the teenage population indicates a prevalence of 13.3/1,000. Sixty cases of grade 3 cervical intraepithelial neoplasia (carcinoma in situ) were diagnosed by biopsy in the teenage population for a projected prevalence rate of 2.6/1,000. No invasive squamous cell carcinoma was found in this age group. This emphasizes the importance of cervical intraepithelial neoplasia as a developing medical and public health problem in this age group and indicates that teenagers of any "permissive society" should be considered as "high risk" and included in screening programs.

Adolescent↗
PubMedDate not supplied

Estimating endogenous treatment effects in retrospective data analysis.

Treatment effect estimation is one of the mainstays of the field of outcomes research. It is, for example, a key component in analyzing the cost-effectiveness of a proposed qualitative intervention. Some outcomes researchers are hesitant to use retrospective data for treatment effect estimation because of the potential endogeneity of the treatment variable. This is unfortunate, given the abundance and other advantages of retrospective data. Others who have used retrospective data have ignored the endogeneity problem, or have not recognized its potential for causing bias in their estimates. In this paper, an econometric method that is unbiased in the presence of endogeneity and therefore broadens the potential for use of retrospective data in the estimation of treatment effects is proposed. This two-stage method is also designed to accommodate nonlinearity in the relationship between the treatment variable and the outcome. An easy to apply GAUSS implementation of the estimator is offered.

Journal Article↗
PubMed1999

A data analysis of the irradiation parameter D10 for bacteria and spores under various conditions.

This paper provides approximate estimates for the irradiation parameter D10 to globally predict the effectiveness of any irradiation process. D10 is often reported to depend on many specific factors, implying that D10 cannot be estimated without exact knowledge of all factors involved. For specific questions these data can of course be useful but only if the conditions reported exactly match the specific question. Alternatively, this study determined the most relevant factors influencing D10, by quantitatively analyzing data from many references. The best first step appeared to be a classification of the data into vegetative bacteria and spores. As expected, spores were found to have significantly higher D10 values (average 2.48 kGy) than vegetative bacteria (average 0.762 kGy). Further analyses of the vegetative bacteria confirmed the expected extreme irradiation resistance of nonpathogenic Deinococcus radiodurans (average 10.4 kGy). Furthermore the analysis identified Enterococcus faecium, Alcaligenes spp., and several members of the Moraxella-Acinetobacter group as having very high resistance at very low temperatures (average 3.65 kGy). After exclusion of high- and low-resistance spores and some specific conditions showing relevant high or low D10 values, the average for spores was estimated to be 2.11 kGy. For vegetative bacteria this average was estimated to be 0.420 kGy. These approximate estimates are not definite, as they depend on the data used in the analyses. It is expected that inclusion of more data will not change the estimates to a great extent. The approximate estimates are therefore useful tools in designing and evaluating irradiation processes.

Acinetobacter↗
PubMedDate not supplied

Modeling time-to-tumor data: analysis of the ED01 study.

The ED01 study is an experiment conducted by the National Center for Toxicological Research (NCTR) of the FDA in which over 24,000 mice were exposed to the known carcinogen 2-acetylaminofluorene. The details of the experiment and analysis of the results by NCTR are documented in Staffa and Mehlman (1979). The analysis by the ED01 task force of the Society of Toxicology is in disagreement with NCTR on several issues, and is reported in Fundam. Appl. Toxicol. 1:26-128. The results given in this paper are from a separate analysis aimed at adequately and parsimoniously representing the functional relationship of dose and time to the carcinogenic response. A very general non-parametric approach is applied to the data on sacrificed animals, which eliminates any complications due to a change in protocol and avoids the difficulties in combining sacrifice and non-sacrifice data. It is shown that for either liver neoplasms or bladder neoplasms as the toxicological endpoint, any model which has a factorable hazard function (one that can be factored into the product of a function of dose exclusively and a function of time exclusively) is too simplistic to accurately describe the response over the entire experimental range of dose and time. The lack of fit of the liver neoplasm data to a time-dose product model is due to data at the highest time (month 33). If these data are excluded then a factorable hazard function fits the data well, with the function of dose following a J-shaped curve and the function of time being either a simple power of time or a polynomial in time. For a power of time, the resultant probability distribution is Weibull over time with dose affecting the scale parameter, and this result is consistent with the empirical equation of Druckrey (1967). Both of the functional forms described fit the data significantly better than the previously suggested Hartley-Sielken model which utilized polynomials in both dose and time. The lack of fit of bladder neoplasms to a model with a factorable hazard function is not due to just the data at month 33 or the data at months 24 and 33 combined. Unfortunately, from the viewpoint of model fitting, the response of bladder neoplasms is fairly insensitive to changes in time and dose, except at the high extremes. This leaves only a small number of observations which are actually very useful in model validation and comparison, which means that one could only hope to discriminate between gross differences of fit.(ABSTRACT TRUNCATED AT 400 WORDS)

2-Acetylaminofluorene↗
PubMed2003

Wage policy in the health care sector: a panel data analysis of nurses' labour supply.

Shortage of nurses is a problem in several countries. It is an unsettled question whether increasing wages constitute a viable policy for extracting more labour supply from nurses. In this paper we use a unique matched panel data set of Norwegian nurses covering the period 1993-1998 to estimate wage elasticities. The data set includes detailed information on 19,638 individuals over 6 years totalling 69,122 observations. The estimated wage elasticity after controlling for individual heterogeneity, sample selection and instrumenting for possible endogeneity is 0.21. Individual and institutional features are statistically significant and important for working hours. Contractual arrangements as represented by shift work are also important for hours of work, and omitting information about this common phenomenon will underestimate the wage effect.

Adult↗
PubMed1976

Insulin kinetics after portal and peripheral injection of [125I] insulin. I. Data analysis and modeling.

The kinetics of insulin are commonly investigated by intravenous administration of labeled hormone, whereas native insulin is removed by the liver to some extent before mixing in the systemic circulation. A mathematical model has been developed which makes it possible to interpret the experimental data obtained by peripheral plasma sampling after portal and peripheral injection of the tracer. Equations are given that allow for the computation of metabolic clearance rate, initial distribution volume, production rate, and body mass of insulin. It is demonstrated that hepatic extraction can be calculated from the difference between the clearance rate values obtained after portal and peripheral injection of the tracer; an estimate of total hepatic catabolism is also derived. The assumptions and limitations underlying this mathematical analysis are discussed.

Infusions, Parenteral↗