The application of a sequential procedure with elimination as a method for the screening for metabolic diseases

A sequential classification procedure with early elimination, for the screening for metabolic diseases, is presented. Asymptotic properties of the procedure are derived in the Appendix and it is shown that the procedure is asymptotically distribution-free under certain assumptions, and asymptotically at least as efficient as a comparable fixed-sample procedure. With the use of data obtained from 36 mentally retarded patients, the procedure was evaluated by means of a bootstrap simulation. The procedure was then applied to this set of data, with satisfactory results and a considerable economy in observations.     

A two-step procedure for automatic and accurate segmentation of volumetric CLSM biofilm images

This paper presents a robust two-step segmentation procedure for the study of biofilm structure. Without user intervention, the procedure segments volumetric biofilm images generated by a confocal laser scanning microscopy (CLSM). This automated procedure implements an anisotropic diffusion filter as a preprocessing step and a 3D extension of the Otsu method for thresholding. Applying the anisotropic diffusion filter to even low-contrast CLSM images significantly improves the segmentation obtained with the 3D Otsu method. A comparison of the results for several CLSM data sets demonstrated that the accuracy of this procedure, unlike that of the objective threshold selection algorithm (OTS), is not affected by biofilm coverage levels and thus fills an important gap in developing a robust and objective segmenting procedure. The effectiveness of the present segmentation procedure is shown for CLSM images containing different bacterial strains. The image saturation handling capability of this procedure relaxes the constraints on user-selected gain and intensity settings of a CLSM. Therefore, this two-step procedure provides an automatic and accurate segmentation of biofilms that is independent of biofilm coverage levels and, in turn, lays a solid foundation for achieving objective analysis of biofilm structural parameters.     

Population genetic inference using a fixed number of segregating sites: a reassessment

Coalescent theory is commonly used to perform population genetic inference at the nucleotide level. Here, we examine the procedure that fixes the number of segregating sites (henceforth the FS procedure). In this approach a fixed number of segregating sites (S) are placed on a coalescent tree (independently of the total and internode lengths of the tree). Thus, although widely used, the FS procedure does not strictly follow the assumptions of coalescent theory and must be considered an approximation of (i) the standard procedure that uses a fixed population mutation parameter theta, and (ii) procedures that condition on the number of segregating sites. We study the differences in the false positive rate for nine statistics by comparing the FS procedure with the procedures (i) and (ii), using several evolutionary models with single-locus and multilocus data. Our results indicate that for single-locus data the FS procedure is accurate for the equilibrium neutral model, but problems arise under the alternative models studied; furthermore, for multilocus data, the FS procedure becomes inaccurate even for the standard neutral model. Therefore, we recommend a procedure that fixes the theta value (or alternatively, procedures that condition on S and take into account the uncertainty of theta) for analysing evolutionary models with multilocus data. With single-locus data, the FS procedure should not be employed for models other than the standard neutral model.     

A nonparametric test for association with censored data

A nonparametric procedure is proposed for the problem of testing association between two continuous variables when one is subject to arbitrary censoring. The motivation for the procedure derives from our finding that Cox's likelihood procedure may not adequately control the size of the test. The proposed procedure allows the censoring mechanism to depend on the independent variable, is simple computationally, and provides accurate control over the size of the test even for quite small samples. Asymptotic results suggest that it may provide a sensitive alternative to Cox's procedure. An example dealing with survival following operation for myasthenia gravis is provided, wherein a method for testing after adjustment for covariate information is described.     

An Approximate EM Algorithm for Nonlinear Mixed Effects Models

In this article, we construct an approximate EM algorithm to estimate the parameters of a nonlinear mixed effects model. The iterative procedure can be viewed as an iterative method of moments procedure for estimating the variance components and an iterative reweighted least squares estimates for estimating the fixed effects. Therefore, it is valid without the normality assumptions on the random components. A computationally simple method of moments estimates of the model parameters are used as the starting values for our iterative procedure. A simulation study was conducted to compare the performances of the proposed procedure with the procedure proposed by Lindstrom and Bates (1990) for some normal models and nonnormal models.     

AFP蛋白芯片技术的检测流程优化

目的:通过优化现有的蛋白芯片检测过程,在保证检测准确性的同时缩短甲胎蛋白(Alpha Fetal protein,AFP)的检测时间,提高检测效率,为原发性肝癌的筛查提供经济、便捷、省时、有效的检测方法。方法:本研究在传统蛋白芯片检测流程(1-1.5小时)的基础上,通过优化检测流程将检测时间缩短至18分钟,并且通过和传统方法进行比较,评价该优化方法的检测效能。结果:与传统蛋白芯片检测方法相比,本优化方法的检测时间缩短至18分钟。重复检测同一样本,传统方法 AFP水平为16.50±1.172ng/m L,优化方法 AFP水平为18.33±1.029 ng/m L,结果无明显统计学差异(P=0.251)。结论:本研究成功地优化了AFP的蛋白芯片检测流程,在缩短检测时间的同时,保证了检测的准确率,是一种经济省时易操作的AFP检测方法。     

Displacement imprinted polymer receptor analysis (DIPRA) for chlorophenolic contaminants in drinking water and packaging materials

The preparation of a molecularly imprinted polymer (MIP) for pentachlorophenol is described together with two alternative reporter derivatives for use in a displacement imprinted polymer receptor analysis (DIPRA) format procedure. In this procedure, alternative reporter molecules were rebound to the synthetic receptor sites and their displacement by the target analyte was employed as the basis of a simple procedure for the measurement of chlorophenols in water and packaging material samples. Water samples were extracted using the standard procedure (EPA 528) and a detection limit of 0.5 microg l(-1) was achieved using the DIPRA detection method, with good agreement between the displacement technique and GC-ECD analysis. A variety of packaging materials, extracted using a buffered detergent solution were also analysed using the DIPRA procedure and showed good agreement with GC results. In addition, investigation of the cross-reactivity of a range of pesticides and materials commonly encountered in environmental analysis indicated the procedure gave good discrimination between pesticides bearing a chlorophenolic moiety and other materials. The procedure is considered highly suitable for use as a rapid field-test method or for incorporation into a test kit device.     

Rapid glutamate decarboxylase assay for detection of Escherichia coli.

A rapid test procedure for the enzyme glutamate decarboxylase was developed for detection of Escherichia coli. The assay procedure was able to confirm the presence of E. coli in enteric broth cultures with 95% specificity for both pure cultures and environmental samples. The procedure was capable of detecting survivors among chlorine-exposed cells.     

Inverse analysis of constitutive models: biological soft tissues

The paper describes a procedure for estimating the material parameters of biological soft tissue by fitting model prediction to experimental load-deformation data. This procedure minimizes the error between data and theoretical model prediction through systematically adjusting the parameters in the latter. The procedure uses commercially available software and is not specific to any particular model; nevertheless, for illustration purposes, we employ a six parameter fibril-reinforced poroelastic cartilage model. We are able to estimate any and all of these parameters by the procedure. Convergence of the parameters and convergence of the arbitrary initial stress relaxation to the data was demonstrated in all cases. Though we illustrate the optimization procedure here for unconfined compression only, it can be adapted easily to other experimental configurations such as confined compression, indentation and tensile test. Furthermore, the procedure can be applied in other areas of biomechanics where material parameters need to be extracted from experimental data.     

Regulatory affairs and biotechnology in Europe II.

This paper describes the EEC regulatory requirements for the preparation and execution of a community concertation "High Tech" procedure and compares this "High Tech" procedure with the Multi-State procedure. According to a decision of the European Commission enforced in July 1987, medicinal products, derived from high technology methods have been grouped in two categories: A. and B. Category A. concerns biotechnology products made by R-DNA techniques and by manipulation of mammalian cells. Category B. comprises all other products made by high technology. Before applying for an EEC marketing licence (e.g. submission for registration) one must ascertain whether a product is most appropriate in Category A. or B. and one should contact a licencing authority at an early stage to discuss the planned submission. Various procedures for submission have to be followed: 1. for the so-called "High Tech" products and especially products derived from biotechnology with therapeutic applications (Category A.), it is mandatory that one of the Member States accepts the submission. 2. The "High Tech" procedure is derived from the so-called "2-country" (Multi-State) procedure, in which for the latter procedure a marketing licence in one of the Member States (except Portugal) is required before application in other Member States. The Multi-State and "High Tech" (other products: Category B.) procedures are optional. When the procedures are started, all Member States concerned are involved in evaluation of full or abbreviated dossiers through mediation of the European Commission represented by the CPMP (Committee for Proprietary Medicinal Products), Brussels, Belgium. No application for a marketing licence of Category A. products is allowed without mediation of the CPMP. For Category B. products the applicant may opt for a national submission in one or more of the Member States without using the "High Tech" procedure. However, after consultation with the competent authority in one of the Member States, a "High Tech" procedure for Category B. products might still be advisable, but the applicant is not required to follow this procedure. Both the "High Tech" and the Multi-State procedure are currently executed by the mediation of a rapporteur, who liaises with the applicant from the start of the "High Tech" procedure. Ideally, the applicant should contact a licencing authority some 6 to 9 months before an application is planned: to ensure that the near future submission is acceptable. The institution of a rapporteur (appointed by the licencing authority in the country from where the procedure has recently been established) is introduced for the Multi-State procedure.(ABSTRACT TRUNCATED AT 400 WORDS)     

DNA probe attachment on plastic surfaces and microfluidic hybridization array channel devices with sample oscillation

DNA probe immobilization on plastic surfaces and device assembly are both critical to the fabrication of microfluidic hybridization array channel (MHAC) devices. Three oligonucleotide (oligo) probe immobilization procedures were investigated for attaching oligo probes on four different types of plastic surfaces (polystyrene, polycarbonate, poly(methylmethacrylate), and polypropylene). These procedures are the Surmodics procedure, the cetyltrimethylammonium bromide (CTAB) procedure, and the Reacti-Bind procedure. To determine the optimal plastic substrate and attachment chemistry for array fabrication, we investigated plastic hydrophobicity, intrinsic fluorescence, and oligo attachment efficiency. The Reacti-Bind procedure is least effective for attaching oligo probes in the microarray format. The CTAB procedure performs well enough to use in array fabrication, and the concentration of CTAB has a significant effect on oligo immobilization efficiency. We also found that use of amine-modified oligo probes resulted in better immobilization efficiency than use of unmodified oligos with the CTAB procedure. The oligo probe immobilization on plastic surfaces by the Surmodics procedure is the most effective with regard to probe spot quality and hybridization sensitivity. A DNA hybridization assay on such a device results in a limit of detection of 12pM. Utilizing a CO(2) IR laser machining and adhesive layer approach, we have developed an improved procedure for realizing a DNA microarray inside a microfluidic channel. This device fabrication procedure allows for more feasible spot placement in the channel and reduced sample adsorption by adhesive tapes used in the fabrication procedure. We also demonstrated improved hybridization kinetics and increased detection sensitivity in MHAC devices by implementing sample oscillation inside the channel. A limit of detection of 5pM has been achieved in MHAC devices with sample oscillation.     

A family of Bayes multiple testing procedures

Under the model of independent test statistics, we propose atwo-parameter family of Bayes multiple testing procedures. Thetwo parameters can be viewed as tuning parameters. Using theBenjamini–Hochberg step-up procedure for controlling falsediscovery rate as a baseline for conservativeness, we choosethe tuning parameters to compromise between the operating characteristicsof that procedure and a less conservative procedure that focuseson alternatives that a priori might be considered likely ormeaningful. The Bayes procedures do not have the theoreticaland practical shortcomings of the popular stepwise procedures.In terms of the number of mistakes, simulations for two examplesindicate that over a large segment of the parameter space, theBayes procedure is preferable to the step-up procedure. Anotherdesirable feature of the procedures is that they are computationallyfeasible for any number of hypotheses.     

Does it matter what a hospital is “high volume” for? Specificity of hospital volume-outcome associations for surgical procedures: analysis of administrative data

Objective To determine whether the improved outcome of a surgical procedure in high volume hospitals is specific to the volume of the same procedure.Design and setting Analysis of secondary data in Ontario, Canada.Participants Patients having an oesophagectomy, colorectal resection for cancer, pancreaticoduodenectomy, major lung resection for cancer, or repair of an unruptured abdominal aortic aneurysm between 1994 and 1999.Main outcome measures Odds ratio for death within 30 days of surgery in relation to the hospital volume of the same surgical procedure and the hospital volume of the other four procedures. Estimates were adjusted for age, sex, and comorbidity and accounted for hospital level clustering.Results With the exception of colorectal resection, 30 day mortality seemed to be inversely related not only to the hospital volume of the same procedure but also to the hospital volume of most of the other procedures. In some cases the effect of the volume of a different procedure was stronger than the effect of the volume of the same procedure. For example, the association of mortality from pancreaticoduodenectomy with hospital volume of lung resection (odds ratio for death in hospitals with a high volume of lung resection compared with low volume 0.36, 95% confidence interval 0.23 to 0.57) was much stronger than the association of mortality from pancreaticoduodenectomy with hospital volume of pancreaticoduodenectomy (0.76, 0.44 to 1.32).Conclusion The inverse association between high volume of procedure and risk of operative death is not specific to the volume of the procedure being studied.     

Rapid and sensitive procedure for the separation and quantitation of - and -serine in rat brain using gas chromatography-mass spectrometry

A very simple and rapid GC-MS procedure for the separation and quantitation of - and -serine has been developed utilizing a conventional bonded-phase capillary column. The procedure involves initial esterification with isobutanol followed by acylation with the chiral derivatizing reagent S-(−)-N-(heptafluorobutyryl)prolyl chloride (HPC). This procedure requires neither extraction nor clean-up steps and is sensitive to 50 pg on-column. Total time of the procedure is under 3 h and derivatives are stable at room temperature for at least 5 days, making this procedure ideal for automated injections. A simple, one-day synthesis of HPC is described which yields >99.9% optical purity.     

Accurate and rapid estimation of phosphene thresholds (REPT)

To calibrate the intensity of transcranial magnetic stimulation (TMS) at the occipital pole, the phosphene threshold is used as a measure of cortical excitability. The phosphene threshold (PT) refers to the intensity of magnetic stimulation that induces illusory flashes of light (phosphenes) on a proportion of trials. The existing PT estimation procedures lack the accuracy and mathematical rigour of modern threshold estimation methods. We present an improved and automatic procedure for estimating the PT which is based on the well-established Ψ Bayesian adaptive staircase approach. To validate the new procedure, we compared it with another commonly used procedure for estimating the PT. We found that our procedure is more accurate, reliable, and rapid when compared with an existing PT measurement procedure. The new procedure is implemented in Matlab and works automatically with the Magstim Rapid(2) stimulator using a convenient graphical user interface. The Matlab program is freely available for download.     

Detection of human papilloma virus DNA sequences by polymerase chain reaction

We have developed a polymerase chain reaction-based procedure for reproducible detection of the E6-E7 gene in human papilloma virus DNA sequences using formalin-fixed, paraffin-embedded tissue sections. This procedure is a simple one-step procedure which does not require any elaborate hybridization following polymerase chain reaction amplification. The protocol combines modified tissue treatment and proper primer selection for efficient amplification of target DNA in a highly specific manner allowing identification in ethidium bromide-stained gels. The procedure described here is useful for a variety of tissue preparations, particularly formalin-fixed, paraffin-embedded archival tissues.     

Inference Procedures for Assessing Interobserver Agreement among Multiple Raters

We propose a new procedure for constructing inferences about a measure of interobserver agreement in studies involving a binary outcome and multiple raters. The proposed procedure, based on a chi-square goodness-of-fit test as applied to the correlated binomial model (Bahadur, 1961, in Studies in Item Analysis and Prediction, 158-176), is an extension of the goodness-of-fit procedure developed by Donner and Eliasziw (1992, Statistics in Medicine 11, 1511-1519) for the case of two raters. The new procedure is shown to provide confidence-interval coverage levels that are close to nominal over a wide range of parameter combinations. The procedure also provides a sample-size formula that may be used to determine the required number of subjects and raters for such studies.     

Method for Measuring Mineralization in Lake Sediments

A method is described for measuring the mineralization of an organic solute ((14)C-glucose) by the heterotrophic indigenous bacteria in lake sediments. Since there is no suitable procedure for the determination of in situ microbial activities in sediments, the procedure described is probably the best devised so far and may serve as a base for a more definitive procedure.     

Increased permeability-oedema and atelectasis in pulmonary dysfunction after trauma and surgery: a prospective cohort study

We have developed a two-step procedure for preparing the skin before peripheral venous catheter (PVC) insertions. This procedure involves two successive swabbings with wipes soaked in alcoholic antiseptic. We investigated whether this two-step procedure was as effective and safe as the standard four-step procedure – washing with detergent, rinsing, drying, applying antiseptic – by carrying out a multicentre randomised equivalence study comparing the frequency of precursor signs of infection at the site of insertion for the two skin preparation procedures. The study was carried out over an eight-month period, and 248 PVC insertion sites were evaluated. The two-step procedure was used for 130 subjects and the standard procedure for 118. Taking into account all the confounding factors predisposing patients to the complications studied, the characteristics of the two groups of patients were found to be similar, with no significant differences noted. The incidence of precursor signs of infection was 11 % 24 hours after PVC insertion (27/248), 25 % at 48 hours (50/203) and at 29 % at 72 hours (34/119). Eleven patients had complications necessitating the withdrawal of the PVC: sensitivity of the insertion site, with redness and/or slight swelling and/or a palpable venous cord. No major complications were observed in this study. The frequency of local complications associated with PVCs reported in this study, whether simple or severe, was not affected by the skin preparation procedure used for PVC insertion (two-step or four-step procedure).     

A Two-Way Analysis of Covariance Model for Classification of Stability Data

This paper proposes a procedure for testing and classifying data with multiple factors. A two-way analysis of covariance is used to classify the differences among the batches as well as another factor such as package type and/or product strength. In the test procedure, slopes and intercepts of the main effects are tested using a combination of simultaneous and sequential F-tests. Based on the test procedure results, the data are classified into one of four different groups. For each group, shelf life can be calculated accordingly. We examine if the procedure produces satisfactory control of the probability of a Type I error and the power of detecting the difference of degradation rates and intercepts for different nominal levels. The method is evaluated with a Monte Carlo simulation study. The proposed procedure is compared with the current FDA procedure using real data.