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At least 1,063 records · Page 59Linked to original sources
PubMed1995

Site-specific integrated pest management for high value crops: sample units for map generation using the Colorado potato beetle (Coleoptera: Chrysomelidae) as a model system.

Site-specific agriculture uses maps to optimize within-field placement of agricultural practices. This technology introduces the potential to optimize pest management by varying pesticide or other inputs to better match within-field variation in pest density. Current sampling plans are designed to estimate mean density and may not be suitable for mapping, although useful sampling plans could be developed for map generation for integrated pest management. Using Colorado potato beetle, Leptinotarsa decemlineata (Say), adults, larvae, and egg masses as model systems, the influence of the sample unit on map validity was explored. Adapting currently used sampling plans for potato integrated pest management by spatially referencing each sampled stem failed to resolve spatial dependence and resulted in maps with poor reliability. Increasing the sample unit improved resolution of spatial dependence and map reliability for each life stage. A distance-walk sample unit for adult and late instar Colorado potato beetles which has high potential for map generation is introduced. Using this sample unit, generalizations about Colorado potato beetle spatial dependence are made to discuss issues of developing sampling programs for map generation. An iterative process of sampling, spatial analysis, and error analysis is suggested for evaluating sample units for mapping pest density in high value crops.

Animals↗
PubMed2004

Sampling techniques for thrips (Thysanoptera: Thripidae) in preflowering tomato.

Sampling techniques for thrips (Thysanoptera: Thripidae) were compared in preflowering tomato plants at the Coastal Plain Experiment Station in Tifton, GA, in 2000 and 2003, to determine the most effective method of determining abundance of thrips on tomato foliage early in the growing season. Three relative sampling techniques, including a standard insect aspirator, a 946-ml beat cup, and an insect vacuum device, were compared for accuracy to an absolute method and to themselves for precision and efficiency of sampling thrips. Thrips counts of all relative sampling methods were highly correlated (R > 0.92) to the absolute method. The aspirator method was the most accurate compared with the absolute sample according to regression analysis in 2000. In 2003, all sampling methods were considered accurate according to Dunnett's test, but thrips numbers were lower and sample variation was greater than in 2000. In 2000, the beat cup method had the lowest relative variation (RV) or best precision, at 1 and 8 d after transplant (DAT). Only the beat cup method had RV values <25 for all sampling dates. In 2003, the beat cup method had the lowest RV value at 15 and 21 DAT. The beat cup method also was the most efficient method for all sample dates in both years. Frankliniella fusca (Pergande) was the most abundant thrips species on the foliage of preflowering tomato in both years of study at this location. Overall, the best thrips sampling technique tested was the beat cup method in terms of precision and sampling efficiency.

Animals↗
PubMed2003

A statistical sampling algorithm for RNA secondary structure prediction.

An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a representation of the ensemble of probable structures is of interest. We present a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures. The forward step of the algorithm computes the equilibrium partition functions of RNA secondary structures with recent thermodynamic parameters. Using conditional probabilities computed with the partition functions in a recursive sampling process, the backward step of the algorithm quickly generates a statistically representative sample of structures. With cubic run time for the forward step, quadratic run time in the worst case for the sampling step, and quadratic storage, the algorithm is efficient for broad applicability. We demonstrate that, by classifying sampled structures, the algorithm enables a statistical delineation and representation of the Boltzmann ensemble. Applications of the algorithm show that alternative biological structures are revealed through sampling. Statistical sampling provides a means to estimate the probability of any structural motif, with or without constraints. For example, the algorithm enables probability profiling of single-stranded regions in RNA secondary structure. Probability profiling for specific loop types is also illustrated. By overlaying probability profiles, a mutual accessibility plot can be displayed for predicting RNA:RNA interactions. Boltzmann probability-weighted density of states and free energy distributions of sampled structures can be readily computed. We show that a sample of moderate size from the ensemble of an enormous number of possible structures is sufficient to guarantee statistical reproducibility in the estimates of typical sampling statistics. Our applications suggest that the sampling algorithm may be well suited to prediction of mRNA structure and target accessibility. The algorithm is applicable to the rational design of small interfering RNAs (siRNAs), antisense oligonucleotides, and trans-cleaving ribozymes in gene knock-down studies.

Algorithms↗
PubMed2006

Testing of high-volume sampler inlets for the sampling of atmospheric radionuclides.

Sampling of air for radioactive particles is one of the most important techniques used to determine the nuclear debris from a nuclear weapon test in the Earth's atmosphere or those particles vented from underground or underwater tests. Massive-flow air samplers are used to sample air for any indication of radionuclides that are a signature of nuclear tests. The International Monitoring System of the Comprehensive Nuclear Test Ban Treaty Organization includes seismic, hydroacoustic, infrasound, and gaseous xenon isotopes sampling technologies, in addition to radionuclide sampling, to monitor for any violation of the treaty. Lovelace Respiratory Research Institute has developed a large wind tunnel to test the outdoor radionuclide samplers for the International Monitoring System. The inlets for these samplers are tested for their collection efficiencies for different particle sizes at various wind speeds. This paper describes the results from the testing of two radionuclide sampling units used in the International Monitoring System. The possible areas of depositional wall losses are identified and the losses in these areas are determined. Sampling inlet type 1 was tested at 2.2 m s wind speed for 5, 10, and 20-microm aerodynamic diameter particles. The global collection efficiency was about 87.6% for 10-microm particles for sampling inlet type 1. Sampling inlet type 2 was tested for three wind speeds at 0.56, 2.2, and 6.6 m s for 5, 10, and 20-microm aerodynamic diameter particles in two different configurations (sampling head lowered and raised). The global collection efficiencies for these configurations for 10-microm particles at 2.2 m s wind speed were 77.4% and 82.5%, respectively. The sampling flow rate was 600 m h for both sampling inlets.

Aerosols↗
PubMed2004

Evaluating the role of patient sample definitions for quality indicators sensitive to nurse staffing patterns.

BACKGROUND: Administrative data are an attractive data source for the construction of quality indicators to assess and monitor quality of nursing care in hospitals. Current approaches to constructing measures from discharge abstracts apply substantial restrictions to exclude patients at high risk or with preexisting conditions. This study evaluates whether broader sample definitions combined with risk adjustment would allow for larger samples and increase analytic power. METHODS: Eight indicators were constructed from discharge abstracts of major surgical and medical patients from 799 hospitals in 11 states using existing definitions: pneumonia, urinary tract infection, decubitus ulcers, central nervous system complications, shock, sepsis, pulmonary failure, and upper gastrointestinal bleeding. We tested the effect of broadening the samples in 4 ways: comparing indicator rates in the broader and restrictive samples; assessing correlations of hospital ranks in the broader and restrictive samples; performing clinical reviews of cases in the added samples; and using different samples in regressions of indicators on nurse staffing variables, adjusting for patient risk. RESULTS: Indicator rates in the broader samples tended to be higher but did not change hospital rankings significantly. Clinical review suggested that many sample restrictions could be dropped. Using indicators based on broader definitions, coefficients on staffing variables increased in magnitude. CONCLUSION: Less restrictive sample definitions were shown to be feasible and increased the sensitivity of the indicators and thus the power of the analysis. Particularly in surgical patients, the samples could be broadened, although more conservative definitions appeared appropriate for medical patients.

Forms and Records Control↗
PubMed2006

Perceptions of the influence of prescription medicine samples on prescribing by family physicians.

BACKGROUND: The provision of free prescription medicine samples is a common and traditional marketing strategy used by pharmaceutical companies, but concerns have been raised about their influence on physician prescribing behavior and patient safety. OBJECTIVE: We sought to investigate the knowledge, attitudes, and behaviors of Australian family physicians regarding the use of sample prescription medications. METHODS: Qualitative and quantitative techniques were used, including (1) mailed questionnaires to family physicians, (2) semistructured interviews with family physicians, and (3) sample cupboard inventories. RESULTS: A number of issues about samples were identified by the questionnaires (208) and interviews (17 doctors), including insufficient labeling, poor record keeping, diversion of stock (personal use by doctors, their families, practice staff and pharmaceutical representatives), and wasting of expired stock. Prescription medicine samples also influenced prescribing behavior. Australian doctors were less likely to provide samples to patients on financial grounds compared with a previous study in the United States on medical residents. Six sample cupboards were inventoried. Median wholesale value of sample cupboards was AUD Dollars 4959 (range Dollars 2395-Dollars 8709), with 6% of stock expired. Very little generic medicine was included in the sample cupboards. CONCLUSIONS: Better methods are needed to meet legislative requirements and to ensure quality use of medicines (and optimal public health) with respect to prescription medicine samples. Doctors and practice staff require training on the appropriate handling and storage of prescription medications. Alternative ways for distribution of sample medications need to be investigated.

Adult↗
PubMedDate not supplied

Compliance with saliva sampling protocols: electronic monitoring reveals invalid cortisol daytime profiles in noncompliant subjects.

OBJECTIVE: Ambulatory saliva collections for subsequent analysis of free cortisol levels are now frequently applied to measure adrenocortical activity in healthy subjects and patient populations. Despite the prime importance of accurate timing of saliva collection outside the laboratory, no data are available on the compliance of study participants following a given sampling protocol. This study investigated how accurately subjects adhered to the instructions to collect six saliva samples throughout 1 day. METHODS: Subjects were instructed to collect six saliva samples throughout 1 day (directly after awakening, 30 minutes after awakening, 11 AM, 3 PM, 8 PM, 10 PM). Objective compliance was measured using an electronic monitoring device given to the subjects either with ("informed" N = 23) or without ("noninformed" N = 24) their knowledge of the nature of the device. Data on subjective compliance were obtained by self-report. RESULTS: Thirty-one subjects (74%) were found to comply with the sampling instructions, and 11 (26%) failed at least once to obtain the saliva sample at the correct time of day. Nine of the 11 noncompliant subjects (82%) had two or more noncompliant samples. Fifty-five percent (6 of 11) of the noncompliant subjects took sample 2 outside the sampling window. The circadian cortisol profile differed significantly between compliant and noncompliant subjects (F = 7.98, p =.007). The most important effect of compliance was seen in the rise of cortisol at awakening. Compliant subjects showed a robust increase, whereas noncompliant individuals had only minimal changes from baseline at 30 minutes after awakening (t = 2.89, p =.007). Thus the steepness of the circadian cortisol decline was greater for compliant subjects (t = 2.10, p =.043). Furthermore, the informed group adhered more closely to the sampling protocol than the noninformed subjects (p =.001). Self-reported compliance also differed significantly between study groups (p =.03). In the noninformed group, self-reported sampling accuracy was significantly higher than objectively measured compliance (p =.03); the two measures were similar in the informed group (p = NS). CONCLUSIONS: A significant number of subjects did not obtain saliva samples reliably in an ambulatory setting. This can partially invalidate the cortisol results and mask potential differences between subject groups of interest. We therefore recommend the use of electronic monitoring devices or other suitable methods and that study participants be informed about the device when ambulatory saliva collection is performed.

Adolescent↗
PubMed2004

Is bilateral protected specimen brush sampling necessary for the accurate diagnosis of ventilator-associated pneumonia?

BACKGROUND: Clinical acumen alone is unreliable in establishing a diagnosis of ventilator-associated pneumonia (VAP) and controversy exists over which diagnostic tools should be utilized to confirm a clinical suspicion of VAP. The purpose of this study was to determine the reliability of blind protected specimen brush (PSB) sampling in the diagnosis of VAP and if bilateral PSB sampling is necessary. METHODS: Prospective study comparing blind PSB sampling with bronchoscopic directed PSB sampling in thirty-four consecutive SICU patients with a clinical suspicion of VAP. All patients underwent blind PSB sampling followed by bronchoscopic directed contralateral PSB sampling. RESULTS: Twenty-four of 34 patients (71%) were diagnosed to have VAP. The concordance rate between blind and directed PSB samples was 53% (18/34). When blind PSB was positive (15/34), the contralateral sample yielded a different microorganism in three patients (9%). When blind PSB was negative (19/34), infection was present in the contralateral lung in nine patients (26%). Blind PSB sampling alone was inaccurate in 35% of patients. CONCLUSIONS: The low concordance between blind and directed PSB suggests the need to sample both lung fields. Bilateral PSB sampling can identify unsuspected pathogenic microorganisms in the contralateral lung.

Adolescent↗
PubMed2000

Bootstrap confidence intervals for adaptive cluster sampling.

Consider a collection of spatially clustered objects where the clusters are geographically rare. Of interest is estimation of the total number of objects on the site from a sample of plots of equal size. Under these spatial conditions, adaptive cluster sampling of plots is generally useful in improving efficiency in estimation over simple random sampling without replacement (SRSWOR). In adaptive cluster sampling, when a sampled plot meets some predefined condition, neighboring plots are added to the sample. When populations are rare and clustered, the usual unbiased estimators based on small samples are often highly skewed and discrete in distribution. Thus, confidence intervals based on asymptotic normal theory may not be appropriate. We investigated several nonparametric bootstrap methods for constructing confidence intervals under adaptive cluster sampling. To perform bootstrapping, we transformed the initial sample in order to include the information from the adaptive portion of the sample yet maintain a fixed sample size. In general, coverages of bootstrap percentile methods were closer to nominal coverage than the normal approximation.

Animals↗
PubMed2006

Detection and characterization of hepatitis A virus in water samples in Thailand.

AIMS: Outbreaks of hepatitis A in Thailand have been reported continuely and associated with water supply. However, the genetic analysis of hepatitis A virus (HAV) in water is limited. This study described the application of virus concentration method and reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) to detect HAV RNA and analyse the genetic sequence of the virus in environmental water samples. METHODS AND RESULTS: The HAV from water samples was concentrated by using a developed virus concentration method (adsorption-elution and subsequent speedVac reconcentration) and the viral RNA was detected by RT-nested PCR followed by sequencing of the amplified DNA products. Detection limit of HAV determined by the RT-nested PCR was 1.29 radioimmunofocus assay (RIFA) units ml(-1). The DNA band appeared at 183 basepairs. No cross-reactivity was observed in the presence of other enteric viruses (poliovirus and rotavirus). A total of 180 water samples were collected, concentrated, and detected for HAV. The HAV was found in 6/40 (15%) of water samples collected from a swamp and 3/30 (10%) collected from a canal. Ten river samples and 100 tap water samples stored in containers for drinking and domestic uses were negative for HAV. In sequence analysis of the DNA products and alignment with the HAV sequence deposited in the GenBank, six water samples showed the nucleotide sequence associated with HAV. The 120 nucleotides in the N-terminal VP1 region obtained from two swamp samples showed 95 and 96.7% identity to HAV genotype IA. In nearly all water samples where HAV was present bacterial indicators (faecal coliforms and Escherichia coli) were found for faecal contamination. CONCLUSIONS: A coupled virus concentration method and RT-nested PCR was successfully applied to examine HAV in water samples collected from various sources. DNA sequencing of nested PCR products showed the genotype IA associated with HAV that is predominate in Thailand. SIGNIFICANCE AND IMPACT OF THE STUDY: This research is the first study of genetic sequence of HAV in water samples in Thailand. The presence of naturally occurring HAV might pose a potential health risk for people.

Environmental Monitoring↗
PubMed2005

Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites.

The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error-checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.

Animals↗
PubMed2005

The application of sample pooling methods for determining AUC, AUMC and mean residence times in pharmacokinetic studies.

For high-throughput screening in drug development, methods that can reduce analytical work are desirable. Pooling of plasma samples from an individual subject in the time domain to yield a single sample for analysis has been used to estimate the area under the concentration-time curve (AUC). We describe a pooling procedure for the estimation of the area under the first moment curve (AUMC). The mean residence time (MRT), and where intravenous dosing has been used, the steady-state volume of distribution can then be determined. Plasma samples from pharmacokinetic studies in dogs and humans analyzed in our laboratory were used to validate the pooling approach. Each plasma sample containing a prokinetic macrolide and three of its metabolites was first analyzed separately, and AUCs and AUMCs were calculated using the linear trapezoidal rule. The procedures for the estimation of AUC by sample pooling have been reported by Riad et al. [Pharm. Res. (1991) vol. 8, pp. 541-543]. For the estimation of AUMC, the volume taken from each of n samples to form a pooled sample is proportional to t(n)(t(n+1) - t(n-1)), except at t0 where the aliquot volume is 0 and at t(last) where the aliquot volume is proportional to t(last)(t(last) - t((last)-1)). AUMC to t(last) is equal to C(pooled) x T2/2, where T is the overall experimental time (t(last) - t0). The ratio between AUMC and AUC yields the mean residence time (MRT). Bivariate (orthogonal) regression analysis was used to assess agreement between the pooling method and the linear trapezoidal rule. Bias and root mean square error were used to validate the pooling method. Orthogonal regression analysis of the AUMC values determined by pooling (y-axis) and those estimated by the linear trapezoidal rule (x-axis) yielded a slope of 1.08 and r2 of 0.994 for the dog samples; slope values ranged from 0.862 to 0.928 and r2 values from 0.838 to 0.988 for the human samples. Bias, expressed as percentage, ranged from -25.1% to 14.8% with an overall average of 1.40%. The results support the use of a pooled-sample technique in quantitating the average plasma concentration to estimate areas under the curve and areas under the first moment curve over the sampling time period. Mean residence times can then be calculated.

Algorithms↗
PubMed1995

The toothpick method in relation to other plaque sampling techniques for evaluating mutans streptococci.

The aim of the present study was to compare the use of toothpicks with other sampling methods for determination of mutans streptococci on different tooth surfaces. In nine persons with > 10(5) CFU per ml saliva of mutans streptococci, plaque samples were taken from 90 buccal and lingual surfaces, 108 occlusal surfaces and 90 approximal surfaces with toothpicks. The prevalence of mutans streptococci on these tooth surfaces was compared with samples taken at four 1-week intervals on the same tooth surfaces with a carver (buccal/lingual surfaces), a needle (occlusal surfaces) or a dental floss (approximal surfaces). Each sample was plated on MSB agar and the presence of mutans streptococci was expressed on a scale varying from 0 to 4. On two of the sampling occasions the amount of plaque, mirrored by total viable counts on blood agar, was also determined. Only for buccal/lingual plaque samples was a difference in total counts between methods noted and then with higher total recoveries obtained after sampling with toothpicks. More surfaces were found to be positive for mutans streptococci when samples were taken with a toothpick than with a carver, needle or floss. On surfaces positive for mutans streptococci the colonization score was higher in samples taken with a toothpick than with a carver or a needle while samples taken with a floss showed a tendency to higher levels of mutans streptococci than samples collected with a toothpick. The data indicate that the results indicate that the results obtained by using toothpicks for evaluating the prevalence of mutans streptococci on individual tooth surfaces compare favorably with the other methods tested.

Adult↗
PubMed2005

Temporal effects of 3 commonly used anticoagulants on hematologic and biochemical variables in blood samples from macaws and Burmese pythons.

BACKGROUND: Few studies have been done to evaluate anticoagulants for use with blood samples from birds and reptiles. Heparin currently is the most commonly used anticoagulant in practice, but may adversely affect blood cell staining and quantitation. OBJECTIVE: The purpose of this study was to evaluate the effects of lithium heparin, K3-EDTA, and sodium citrate, with and without the addition of albumin, on hematologic variables in macaw (Ara sp) and python (Python molurus bivittatus) blood samples. METHODS: Blood samples from 10 macaws and 10 Burmese pythons were collected in heparin-coated syringes and placed into tubes containing either lithium heparin, K3-EDTA, or sodium citrate with and without the addition of 0.25 mL of a 22% bovine serum albumin solution. Cell lysis was determined by counting the number of lysed cells/200 WBCs in Wright's-Giemsa-stained blood smears and by qualitative evaluation of pink plasma in microhematocrit tubes. A CBC was done after 3, 12, and 24 hours of storage at 4 degrees C in anticoagulant-containing tubes and results were compared with those obtained at 0 hour for the heparin-coated syringe sample. A biochemical panel also was done at each time point in similarly stored lithium-heparin samples. RESULTS: Hemolysis was significantly increased in citrated samples from both macaws and pythons beginning at 12 hours. At 24 hours, 19 of 30 (63%) macaw samples in all anticoagulants had >100 lysed cells/200 WBCs. There were no significant differences in hematologic values in samples from pythons collected in heparin or EDTA at any time point. No significant differences were found in the number of lysed cells or in other hematologic data in samples with albumin. Glucose concentration decreased and potassium concentration increased significantly over time in heparinized blood samples. CONCLUSIONS: Based on the results of this study, whole blood samples anticoagulated with lithium heparin or EDTA should be evaluated within 12 hours (macaws) or 24 hours (pythons) of collection and stored at 4 degrees C for best results. Citrate should be avoided as it may result in increased cell lysis. The addition of albumin does not prevent cell lysis.

Animals↗
PubMed2006

Comparison of biochemical values in serum and plasma, fresh and frozen plasma, and hemolyzed samples from orange-winged Amazon parrots (Amazona amazonica).

BACKGROUND: To the authors' knowledge, on the basis of sample type, storage condition, or hemolysis, differences in serum and plasma biochemical values have not been evaluated in orange-winged Amazon parrots (Amazona amazonica). OBJECTIVES: The purpose of this study was to compare values for biochemical analytes in serum vs plasma, fresh vs frozen plasma, and nonhemolyzed vs hemolyzed samples in orange-winged Amazon parrots. We also compared differences in serum and plasma yield from whole-blood aliquots. METHODS: Fifteen biochemical analytes were evaluated in paired serum and plasma, fresh and frozen plasma, nonhemolyzed and hemolyzed serum and plasma samples from orange-winged Amazon parrots (n = 10) using a wet reagent analyzer. Hemolysis was assessed qualitatively (visually) and quantitatively (hemoglobin [Hgb] measured spectrophotometrically). Serum and plasma yields from 500-microl whole-blood aliquots were determined from centrifuged samples. RESULTS: Analyte values significantly differed among sample groups, but were still within published reference intervals, with the exception of increases in potassium concentration in markedly hemolyzed serum and plasma samples. Clinically important changes in hemolyzed serum and plasma samples included increases in potassium, phosphorus, and albumin concentrations and lactate dehydrogenase activity. The degree of hemolysis assigned qualitatively did not correlate with quantitative Hgb concentration. A significantly greater yield of plasma (288 +/- 13 microL) than serum (241 +/- 44 microL) was obtained. CONCLUSIONS: Significant differences may occur in different sample types, however, only changes in potassium, phosphorus, albumin, and lactate dehydrogenase values in hemolyzed samples were considered clinically relevant. Lack of agreement between qualitative and quantitative Hgb concentration indicates the unreliability of visual estimation. Based on higher sample yield, and lack of clinically relevant differences from serum, plasma is a better sample choice for clinical chemistry analysis in birds.

Amazona↗
PubMed1999

Classifier design for computer-aided diagnosis: effects of finite sample size on the mean performance of classical and neural network classifiers.

Classifier design is one of the key steps in the development of computer-aided diagnosis (CAD) algorithms. A classifier is designed with case samples drawn from the patient population. Generally, the sample size available for classifier design is limited, which introduces variance and bias into the performance of the trained classifier, relative to that obtained with an infinite sample size. For CAD applications, a commonly used performance index for a classifier is the area, Az, under the receiver operating characteristic (ROC) curve. We have conducted a computer simulation study to investigate the dependence of the mean performance, in terms of Az, on design sample size for a linear discriminant and two nonlinear classifiers, the quadratic discriminant and the backpropagation neural network (ANN). The performances of the classifiers were compared for four types of class distributions that have specific properties: multivariate normal distributions with equal covariance matrices and unequal means, unequal covariance matrices and unequal means, and unequal covariance matrices and equal means, and a feature space where the two classes were uniformly distributed in disjoint checkerboard regions. We evaluated the performances of the classifiers in feature spaces of dimensionality ranging from 3 to 15, and design sample sizes from 20 to 800 per class. The dependence of the resubstitution and hold-out performance on design (training) sample size (Nt) was investigated. For multivariate normal class distributions with equal covariance matrices, the linear discriminant is the optimal classifier. It was found that its Az-versus-1/Nt curves can be closely approximated by linear dependences over the range of sample sizes studied. In the feature spaces with unequal covariance matrices where the quadratic discriminant is optimal, the linear discriminant is inferior to the quadratic discriminant or the ANN when the design sample size is large. However, when the design sample is small, a relatively simple classifier, such as the linear discriminant or an ANN with very few hidden nodes, may be preferred because performance bias increases with the complexity of the classifier. In the regime where the classifier performance is dominated by the 1/Nt term, the performance in the limit of infinite sample size can be estimated as the intercept (1/Nt= 0) of a linear regression of Az versus 1/Nt. The understanding of the performance of the classifiers under the constraint of a finite design sample size is expected to facilitate the selection of a proper classifier for a given classification task and the design of an efficient resampling scheme.

Computer Simulation↗
PubMed1996

Comparison of Vero cell assay and PCR as indicators of the presence of verocytotoxigenic Escherichia coli in bovine and human fecal samples.

Comparisons were made between Vero cell assay (VCA) and PCR as indicators for the detection of verocytotoxigenic Escherichia coli (VTEC; also known as Shiga-like toxin-producing E. coli) and as predictors of VTEC isolation from bovine and human fecal samples. Fecal samples were collected as part of a survey on the prevalence of VTEC on dairy farms in southern Ontario (J. B. Wilson et al., J. Infect. Dis., 174:1021-1027, 1996). A total of 2,655 samples were examined by VCA and PCR, 2,153 originating from cattle and 502 originating from humans. Overall, 36.2% of the samples were positive in the VCA and 38.7% were positive by PCR. Of the VCA-positive samples screened, 41.6% yielded a VTEC isolate. For both human and bovine samples, a significant positive association between PCR result and VCA titer (P = 0.0001) was found. In addition, there was a significant positive association between the PCR result and VTEC isolation from VCA-positive samples for cattle (odds ratio = 9.1, P < 0.0001). For bovine samples positive in the VCA, VCA titer was significantly associated with the probability of obtaining a VTEC isolate. Agreement between VCA and PCR was good for both bovine and human samples (kappa = 0.69 and 0.64, respectively). The sensitivity and specificity of the PCR with respect to the VCA for bovine samples were 82.0 and 86.5%, respectively, and those for human samples were 59.3 and 98.1%, respectively. Although correlation between VCA and PCR results was not absolute, when used in conjunction, these tests complemented one another as predictors of VTEC isolation.

Animals↗
PubMed1992

Detection of Mycobacterium tuberculosis in clinical samples by using polymerase chain reaction and a nonradioactive detection system.

A test based on the polymerase chain reaction (PCR) was developed for the detection of the Mycobacterium tuberculosis complex in clinical samples. In this test, a 245-bp sequence of the insertion element IS986 was amplified and detected by agarose gel electrophoresis in the presence of ethidium bromide and by Southern blot and dot blot hybridization by using a 188-bp digoxigenin-labeled probe. We tested clinical specimens from 227 patients suspected of having tuberculosis. These included 102 cerebrospinal fluid, 48 sputum, 18 pleural fluid, 5 bronchoalveolar lavage, 18 blood, 7 pus, 8 bone marrow, and 6 urine samples and 15 tissue biopsy specimens. We also tested sputum samples from 75 patients with diseases other than tuberculosis. Sputum samples were first decontaminated, and all samples were treated with proteinase K-detergent solution to extract the DNA. Part of each sample was spiked with M. tuberculosis to provide a semiquantitative assay and to control for the loss of mycobacteria or interference with the PCR which may cause false-negative results. One femtogram of M. tuberculosis DNA could be detected. PCR was positive for all 32 culture-positive (for M. tuberculosis) and Ziehl-Neelsen staining (ZN)-positive samples, 10 of 12 culture-positive and ZN-negative samples, and all 4 culture-negative and ZN-positive samples. PCR detected M. tuberculosis complex bacteria in 35 of 178 culture- and ZN-negative samples. Clinical data supported the diagnosis of tuberculosis in the majority of the 35 patients from whom those samples were obtained.

Base Sequence↗