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.     

Efficacy of activated sludge in removing Cryptosporidium parvum oocysts from sewage.

Primary clarifier effluent (procedure B) and final effluent (procedure A) from a wastewater treatment plant were enriched with Cryptosporidium parvum oocysts obtained from the feces of naturally infected calves. Procedure B samples alone were subjected to a laboratory simulation of activated-sludge treatment. Coccidium-free neonatal CD-1 mice were then inoculated intragastrically with procedure A or procedure B samples. Seven days after inoculation, the intensity of oocyst infection in procedure B mice was 91% less than in procedure A mice (controls).     

Measurement of delay discounting using trial-by-trial consequences

DELAY DISCOUNTING IN HUMANS WAS INVESTIGATED USING THREE DIFFERENT PROCEDURES: a frequently used discounting procedure with hypothetical rewards and delays; a procedure with hypothetical rewards and delays compressed down to much smaller values; and a contingent procedure in which each choice had a direct consequence. In the contingent procedure, on every trial, participants actually experienced the delay and obtained the reward amount associated with their choice. Each participant was exposed to all three procedures. Orderly temporal discounting patterns were obtained in all three procedures and described well by a hyperbolic model. Comparisons of the data revealed patterns unique to each procedure. The distributions of the discounting measures differed across the three procedures. In the contingent procedure, several subjects showed no discounting, e.g. complete self-control. Procedural factors in studies of impulsivity are discussed, and suggestions are offered for experiments in which the contingent-discounting procedure may prove useful.     

A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations.

A multiple-tubes procedure is described for using PCR to determine the genotype of a very small DNA sample. The procedure involves dividing the sample among several tubes, then amplifying and typing the contents of each tube separately. The results are analyzed by a statistical procedure which determines whether a genotype can be conclusively assigned to the DNA sample. Simulation studies show that this procedure usually gives correct results even when the number of double-stranded fragments in the sample is as small as 30. The procedure remains effective even in the presence of small amounts of laboratory contamination. We find that the multiple-tubes procedure is superior to the standard one-tube procedure, either when the sample is small or when laboratory contamination is a potential problem; and we recommend its use in these situations. Because the procedure is statistical, it allows the degree of certainty in the result to be quantified and may be useful in other PCR applications as well.     

Efficacy of activated sludge in removing Cryptosporidium parvum oocysts from sewage.

Primary clarifier effluent (procedure B) and final effluent (procedure A) from a wastewater treatment plant were enriched with Cryptosporidium parvum oocysts obtained from the feces of naturally infected calves. Procedure B samples alone were subjected to a laboratory simulation of activated-sludge treatment. Coccidium-free neonatal CD-1 mice were then inoculated intragastrically with procedure A or procedure B samples. Seven days after inoculation, the intensity of oocyst infection in procedure B mice was 91% less than in procedure A mice (controls).     

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.     

Normalizing upper trapezius EMG amplitude: Comparison of ramp and constant force procedures

The present study compared three procedures for normalization of upper trapezius surface electromyographic (EMG) amplitudes: (a) a ramp procedure (providing data in per cent of maximal voluntary contraction, MVC); (b) a constant force procedure based on two reference contractions (two-force procedure) (%MVC) and (c) a procedure expressing muscle activation in per cent of a reference voluntary electrical activity (%RVE). The study also evaluated the repeatability of the ramp and the RVE procedures and estimated the force exertion (%MVC) corresponding to the RVE. To illustrate the ergonomic effect of different normalization procedures, trapezius EMG during two work tasks was compared after normalization by the two-force and the RVE procedures. Fifteen subjects participated in the whole study. We found that force estimates obtained by the ramp procedure equation could be translated to force estimates obtained by the two-force procedure by the equation: %MVC_2force = − 0.6 + 0.9*%MVC_ramp, although with a considerable imprecision due to large inter-individual differences. In the ramp procedure, the intra-individual test-retest coefficient of variation (CV) depended on the force level; it was 45% at 5% MVC and 10% at 30% MVC. The CV of the RVE was 15%. The reference contraction used in the RVE procedure corresponded from 13–79% MVC (median 33%MVC). The load reducing effect of an ergonomic intervention was less obvious with the RVE procedure than with the two-force procedure due to a larger inter-individual variation. The advantages and disadvantages of the different procedures are discussed.     

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.     

An adaptive single-step FDR procedure with applications to DNA microarray analysis

The use of multiple hypothesis testing procedures has been receiving a lot of attention recently by statisticians in DNA microarray analysis. The traditional FWER controlling procedures are not very useful in this situation since the experiments are exploratory by nature and researchers are more interested in controlling the rate of false positives rather than controlling the probability of making a single erroneous decision. This has led to increased use of FDR (False Discovery Rate) controlling procedures. Genovese and Wasserman proposed a single-step FDR procedure that is an asymptotic approximation to the original Benjamini and Hochberg stepwise procedure. In this paper, we modify the Genovese-Wasserman procedure to force the FDR control closer to the level alpha in the independence setting. Assuming that the data comes from a mixture of two normals, we also propose to make this procedure adaptive by first estimating the parameters using the EM algorithm and then using these estimated parameters into the above modification of the Genovese-Wasserman procedure. We compare this procedure with the original Benjamini-Hochberg and the SAM thresholding procedures. The FDR control and other properties of this adaptive procedure are verified numerically.     

A simultaneous procedure facilitates acquisition under an optimal interstimulus interval in artificial neural networks and rats

In a computer simulation, a neural network first received a simultaneous procedure, where the interstimulus interval (ISI) was 0 time-steps (ts). Output activations were near zero under this procedure. The network then received a forward-delay procedure where the ISI was 8 ts. Output activations increased to the near-maximum level faster than those of a control network that first received an explicitly unpaired procedure. Comparable results were obtained with rats that first received trials where a retractable lever was presented for 3s concurrently with access to water. Low-lever pressing was observed under this procedure. The rats then received trials where the lever was followed 15s after by water. Lever pressing appeared faster than a control group that received the 15-s ISI after an explicitly unpaired procedure. The model used in the simulation explains these results as connection-weight increments that promote little output activations in a simultaneous procedure, but facilitate acquisition in an optimal ISI.     

Stepwise Variable Selection in Classification Problems

Two variable selection procedures are evaluated for classification problems: a forward stepwise discrimination procedure, and a stepwise procedure preceded by a preliminary screening of variables on the basis of individual t statistics. Expected probability of correct classification is used as the measure of performance. A comparison is made of the procedures using samples from multi-variate normal populations and from several nonnormal populations. The study demonstrated some situations where the use of all variables is preferable to the use of a stepwise discriminant procedure stopping after a few steps, though usually the latter procedure was superior in performance. However where the stepwise procedure performed better than using all variables, the modified stepwise procedure performed still better. The use of modified stepwise procedures in which not all the covariances of the problem need be estimated seems promising.     

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.     

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.     

生物大分子结晶学中的刚体修正方法

刚体修正方法是修正生物大分子初结构的取向和位置的一个很有效的方法.本文简要地介绍了Fourier搜索法,CORELS刚体修正法及TRAREF刚体修正法三种方法,并给出了它们在不同的蛋白质结构测定中应用的结果.     

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.     

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.     

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.     

Development of a simple and high-throughput method for detecting aflatoxins production in culture media

Aims: To develop a simple, high‐throughput and inexpensive procedure to detect and quantify aflatoxins into the culture media of growing mycelia. Methods and Results: Fungal conidia (Aspergillus flavus) were inoculated into the wells of a microplate containing 200 μl of different formulations of coconut‐derived liquid medium. Time‐dependent production of aflatoxins in the culture media was evaluated by a procedure relying on the UV‐induced fluorescence emission by the toxin, using a microplate reader. These data were validated by comparison with the outputs of a conventional HPLC‐based procedure. Determinations of aflatoxin concentration, according to the fluorimetric procedure, were performed either by withdrawing samples from the plates or by direct ‘in situ’ readings, the latter method reinforcing the high‐throughput feature of the procedure. Fluorescence enhancers (cyclodextrins) did not ameliorate the sensitivity of the procedure to low concentrations of the toxin into the medium. The efficacy of the procedure was also validated by testing the effect on toxin yield of adding an antioxidant agent (α‐lipoic acid) to the medium. Conclusions: We give evidence that our improved procedure is reliable and suitable to analyse aflatoxin accumulation time course in coconut‐derived culture medium. Significance and Impact of the Study: This study shows that our procedure may profitably be used to give insights into the mechanisms of regulation of mycotoxin production and, consequently, to implement different strategies for the containment of aflatoxin contamination of food and feed commodities.     

Multiple testing with discrete data: Proportion of true null hypotheses and two adaptive FDR procedures

We consider multiple testing with false discovery rate (FDR) control when p values have discrete and heterogeneous null distributions. We propose a new estimator of the proportion of true null hypotheses and demonstrate that it is less upwardly biased than Storey's estimator and two other estimators. The new estimator induces two adaptive procedures, that is, an adaptive Benjamini–Hochberg (BH) procedure and an adaptive Benjamini–Hochberg–Heyse (BHH) procedure. We prove that the adaptive BH (aBH) procedure is conservative nonasymptotically. Through simulation studies, we show that these procedures are usually more powerful than their nonadaptive counterparts and that the adaptive BHH procedure is usually more powerful than the aBH procedure and a procedure based on randomized p‐value. The adaptive procedures are applied to a study of HIV vaccine efficacy, where they identify more differentially polymorphic positions than the BH procedure at the same FDR level.     

Cryopreservation of mammalian embryos: Derivation of a method

In 1972, a procedure was derived to cryopreserve mouse embryos. Over the past four decades, this procedure has been adapted to freeze embryos of more than twenty-five mammalian species. Cryopreservation of embryos has become a routine procedure in both veterinary and human medicine, having been used to freeze millions of embryos of mice and cattle, and many hundreds of thousands of human embryos. After transfer into appropriate foster mothers, cryopreserved embryos have developed into innumerable live offspring. This article describes the background that led to the derivation of the procedure and the events that transpired during its development. The first successful embryo cryopreservation procedure was developed by collaboration of three investigators, each bringing a special expertise and perspective to the project.