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PubMed2004

Mathematical basis for the optimization of single cell-line screening on multi-well plates.

Screening of stably transfected cells on multi-well plates is most efficient when a maximum number of wells contain a single colony. The multinomial distribution has been used to derive a novel equation that relates the number of wells containing a specified number of cell-lines and the total number of viable cells loaded on the plate. To test its validity, Chinese hamster ovary cells were transfected with a gene coding for the M2 muscarinic cholinergic receptor and screened on 96-well plates. The observed and predicted numbers of wells containing a single cell-line were indistinguishable. This approach therefore can be used to optimize the conditions for screening transfected cells.

Algorithms↗
PubMed2003

Processivity of the single-headed kinesin KIF1A through biased binding to tubulin.

Conventional isoforms of the motor protein kinesin behave functionally not as 'single molecules' but as 'two molecules' paired. This dimeric structure poses a barrier to solving its mechanism. To overcome this problem, we used an unconventional kinesin KIF1A (refs 5, 6) as a model molecule. KIF1A moves processively as an independent monomer, and can also work synergistically as a functional dimer. Here we show, by measuring its movement with an optical trapping system, that a single ATP hydrolysis triggers a single stepping movement of a single KIF1A monomer. The step size is distributed stochastically around multiples of 8 nm with a gaussian-like envelope and a standard deviation of 15 nm. On average, the step is directional to the microtubule's plus-end against a load force of up to 0.15 pN. As the source for this directional movement, we show that KIF1A moves to the microtubule's plus-end by approximately 3 nm on average on binding to the microtubule, presumably by preferential binding to tubulin on the plus-end side. We propose a simple physical formulation to explain the movement of KIF1A.

Adenosine Diphosphate↗
PubMed2000

Escherichia coli genome is composed of two distinct types of nucleotide sequences.

We calculated correlations of the nucleotide distributions along the E. coli genome. Subsequent cluster analysis of the correlation distributions showed that the genome was composed of two qualitatively different types of nucleotide sequences. The first type exhibited strong correlations of the genomic distributions of A with T and G with C, and high anticorrelations of A with C and G with T. In contrast, the second type was characterized by weak or negligible correlations typical of randomized sequences. Both types of sequences were almost equally abundant in the E. coli genome and their length varied from several hundred nucleotides to about 70 kilobases. They were not disjunct with respect to their (G + C) content but the high correlations and anticorrelations were rather characteristic for (A + T)-rich genomic segments. We offer possible explanations of the mosaic structure of the E. coli genome.

Base Composition↗
PubMed2001

Relationships between passive sampler and continuous ozone (O3 ) measurement data in ecological effects research.

In ecological effects research, there is a rapid increase in the application of passive sampling techniques for measuring ambient ozone (O3) concentrations. Passive samplers provide data on cumulative exposures of a plant to a pollutant. However, O3 is not an accumulative contaminant within the plant tissue, and use of prolonged passive sampling durations cannot account for the dynamics of the occurrences of O3 that have a significant influence on the plant response. Therefore, a stochastic Weibull probability model was previously developed and applied to a site in Washington State (1650 m MSL) to simulate the cumulative exposure data from a passive sampler, to mimic the corresponding frequency distributions of hourly O3 concentrations that would otherwise have been obtained by continuous monitoring. At that site the correlation between the actual passive sampler and the continuous monitor data was R2 = 0.74. The simulation of the hourly O3 data was based on and compared with the results obtained from a colocated continuous monitor. In this paper we report the results of the model application to data from an unrelated monitoring site (New Hampshire, 476 m MSL) with poor correlation between the passive sampling and continuous monitoring (R2 = 0.24). In addition, as opposed to the previous work, we provide comparisons of the frequency distributions of the hourly O3 concentrations obtained by the simulation and the actual continuous monitoring. In spite of the major difference in the R2 values, at both sites the simulation provided very satisfactory results within the 95% confidence interval, suggesting its broad applicability. The final objective of this overall approach is to develop a generic model that can simulate reasonably well the occurrences of ambient O3 concentrations that are dependent upon the elevation of the measurement site and the synoptic and local meteorology. Such an effort would extend the relative utility of the passive sampling data in explaining stochastic plant responses.

Computer Simulation↗
PubMed2004

Improving technology for collecting platelets by apheresis: five-year experience in one blood center.

Over the past decade, newly introduced methods for apheresis platelet collection have led to increased collection yields. This has resulted in "splitting," which allows transfusion of 2 patients from 1 high-yield collection. Although many small studies exist, no large studies have described the impact of methodological changes on routine blood center collections. We constructed a database containing selected parameters from 45,224 apheresis collections spanning July 1997 to April 2002, using Gambro BCT Spectra (Lakewood, CO), Fenwal CS-3000+ (Baxter Healthcare Corp, Fenwal Division, Deerfield, IL), and Baxter Amicus instruments. A Baker 9110+ hematology analyzer (Bio Chem Immunosystems, Inc., Allentown, PA) was used for platelet counting. Monthly average collection yields, distribution yields (product platelet contents after splitting), and split rates (the fraction of donations which may be split) were determined. The monthly mean collection yield and split rate correlated very closely. Both rose throughout the study period. The split rate climbed from 25% to 70% by study end. However, mean monthly distribution yields decreased by 7% because split and unsplit platelet yields both rose as split rates rose. Overcollections with the Amicus correlated with underestimation of donors' true preprocedure platelet counts during machine programming. Undercollections occurred in donors with low counts and, with-single needle Amicus, microcytic platelet collection. These results may assist in the optimization of an apheresis program. Increased collection yields correlated with cell separator type, dual-needle access, donor platelet count >250 x 10(9)/L, programming with true preprocedure platelet counts and capacity for triple product preparation from collection yields exceeding 2-bag storage capacity.

Blood Banks↗
PubMed2006

Genetic polymorphisms of 15 STR loci of Chinese Dongxiang and Salar ethnic minority living in Qinghai Province of China.

Fifteen autosomal STRs loci were analyzed from two samples of 178 healthy unrelated autochthonous individuals of Chinese Dongxiang and Salar ethnic minority groups using a multiplex PCR system. Allele frequencies distribution and statistical parameters for all STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA, were determined by the AmpFISTR Identifiler Kit. The observed genotype frequencies and expected of genotype frequencies were evaluated by chi(2)-test and the Fisher exact tests. chi(2)-test showed that the agreement with Hardy-Weinberg equilibrium (p>0.05) was for all studied STR loci of two populations. The data in the present study can be used greatly for routine forensic application in the region, and enrich Chinese ethnical genetic informational resources.

Alleles↗
PubMed2001

Indigenous domestic breeds as reservoirs of genetic diversity: the Argentinean Creole cattle.

Contrary to highly selected commercial breeds, indigenous domestic breeds are composed of semi-wild or feral populations subjected to reduced levels of artificial selection. As a consequence, many of these breeds have become locally adapted to a wide range of environments, showing high levels of phenotypic variability and increased fitness under natural conditions. Genetic analyses of three loci associated with milk production (alpha(S1)-casein, kappa-casein and prolactin) and the locus BoLA-DRB3 of the major histocompatibility complex indicated that the Argentinean Creole cattle (ACC), an indigenous breed from South America, maintains high levels of genetic diversity and population structure. In contrast to the commercial Holstein breed, the ACC showed considerable variation in heterozygosity (H(e)) and allelic diversity (A) across populations. As expected, bi-allelic markers showed extensive variation in He whereas the highly polymorphic BoLA-DRB3 showed substantial variation in A, with individual populations having 39-74% of the total number of alleles characterized for the breed. An analysis of molecular variance (AMOVA) of nine populations throughout the distribution range of the ACC revealed that 91.9-94.7% of the total observed variance was explained by differences within populations whereas 5.3-8.1% was the result of differences among populations. In addition, the ACC breed consistently showed higher levels of genetic differentiation among populations than Holstein. Results from this study emphasize the importance of population genetic structure within domestic breeds as an essential component of genetic diversity and suggest that indigenous breeds may be considered important reservoirs of genetic diversity for commercial domestic species.

Alleles↗
PubMed2000

Bacterial thermal death kinetics based on probability distributions: the heat destruction of Clostridium botulinum and Salmonella Bedford.

Despite the long history and excellent record of inactivation models used in thermal processing, there are relatively few approaches that attempt to describe the kinetics commonly observed. There are even fewer examples of models that allow the user to deal with the environmental conditions that influence these kinetics. We describe an approach that assumes a distribution of inactivation times within a population of bacterial cells. The concept allows for alternative interpretations of death kinetics and provides excellent descriptions of data generated with two important foodborne pathogens, Clostridium botulinum and Salmonella Bedford. The Salmonella Bedford data set used is unusual and perhaps unique in that it provides information where more than 50% of the population survival has been measured. These measurements are often overlooked or missed in experimental work but are essential when using a vitalistic approach, enabling calculation of a 50% lethal dose for destruction of bacteria. Use of the normal or Prentice distribution provided better fits to the data than other models commonly used to describe thermal death. There was no obvious bias in the fits even though significant tailing was evident. In addition, the procedure described allows data from all the conditions to be fitted rather than individual independent series. This enables a single equation to be derived that can be judged against the whole domain of the data. Approaches that provide accurate and unbiased descriptions of thermal death are likely to become increasingly important to ensure the safety of more marginal heat processes.

Clostridium botulinum↗
PubMed2002

Size distribution measurement of vesicles by atomic force microscopy.

Vesicles have been utilized as nanoscale vehicles for reagents including potential drug delivery systems. When used to deliver drugs, vesicle size and the size distribution are important factors in the determination of the dosage, cell specificity, and rate of clearance from the body. Current size measurement techniques for vesicles are electron microscopy and dynamic light scattering, but their results are not equal. Therefore atomic force microscopy was attempted as another size measurement technique. After adsorption of the vesicles from a low-concentration solution of vesicles on mica substrate, each vesicle is generally found as a flattened structure. The diameters of vesicles in these solutions and their distribution have been successfully estimated from the surface area of the flattened structure of each vesicle. At higher concentrations, we have found a monolayer crammed with dome-shaped vesicles on the substrate. The diameters of vesicles in these solutions have also been successfully estimated from the surface area of the dome-shaped structure of each vesicle. Diameters of vesicles in solution estimated from two different vesicle concentrations are not close to those reported by electron microscope studies but are close to those reported by dynamic light scattering studies.

Adsorption↗
PubMed2002

Equity and health: a perspective on nonrandom distribution of health in the population.

The nonrandom distribution of ill health across and within populations is cause for ethical concern. Systematic differences in health across populations and subpopulations are a result of interactions among many types of influences operating on broad ecological, community, and individual levels. The operation of this web of influences potentiates health disadvantage for some populations and subpopulations and, conversely, enhances resilience to health threats in more advantaged populations. Understanding the genesis of inequity requires an appreciation of the dynamics of these interactions. Thus, research directed at elucidating the causes of inequity in order to facilitate policy changes requires the adoption of conceptual frameworks to guide more efficient and effective future scientific inquiry concerning this worldwide imperative.

Americas↗
PubMed1996

[Examples of pitfalls in statistical analysis--2. Parametric and nonparametric analyses].

When conducting statistical analysis, it is essential to use parametric and nonparametric analyses which properly accord with the attributions of data. What is often overlooked, however, is the need to select the most suitable method of spatistical analysis for the model of the studies. Parametric analysis certainly cannot be relied upon in all situations to yield the best resolutions, and even if we strictly distinguish between the use of parametric and that of nonparametric analyses, we still have done nothing to improve the resolutions themselves. In this article, I discuss several frequently asked questions by presenting an example in which I use parametric analysis on data that should be analyzed by nonparametric analysis.

Drug-Related Side Effects and Adverse Reactions↗
PubMed2004

Clinical significance of health status assessment measures in head and neck cancer: what do quality-of-life scores mean?

OBJECTIVES: To determine the magnitude of clinically significant differences in domain scores for a quality-of-life questionnaire specific to head and neck cancer; and to demonstrate a clinically relevant method of presenting head and neck cancer-specific quality-of-life data using cutoff scores and clinical anchors. DESIGN: Anchor-based and distribution-based techniques for determining clinically significant differences in health-related quality-of-life scores were used. SETTING: University-based tertiary care hospital. PATIENTS: A total of 421 patients with head and neck cancer enrolled in a longitudinal outcomes project. MAIN OUTCOME MEASURES: The Head and Neck Cancer Inventory; clinical anchor health status in the domains of speech, eating, and social disruption; and distribution-based clinically significant score differences. RESULTS: Clinical anchor health states representing incremental levels of dysfunction were significantly correlated with domain scores for eating, speech, and social disruption. The anchor-based clinically important difference magnitudes were consistent with the values obtained using distribution-based techniques. For mean domain scores (minimum, 0; maximum, 100), differences of approximately 4, 10, and 14 or greater represented small, intermediate, and large clinically significant differences, respectively. Stratifying mean domain scores into low (0-30), intermediate (31-69), and high (70-100) categories allowed presentation of the health-related quality-of-life data in a clinically relevant format. CONCLUSIONS: This study provides benchmarks for small, intermediate, and large clinically significant changes in scores and demonstrates the presentation of health-related quality-of-life data in a clinically useful format.

Benchmarking↗
PubMed2002

[Multifactorial analysis of results of the open and endo-biliary surgical treatment of patients with obstructive jaundice due to the distal obstruction of the bile ducts].

The were analyzed the results of treatment of patients with the obstructive jaundice (OJ) due to obstruction of the biliary ducts distal part using surgical and endobiliary decompression using the variation statistics methods (distribution of patients on groups depending on the values of the investigated parameters, calculation of the mean values, evaluation of the authenticity of the indexes distinction), the multifactoral correlative-regressive analysis, the complex evaluation of indexes and probit-analysis. The dependence of results of treatment from value of clinical parameters was established, their prognostic significance was determined. The content of the bilirubin more than 300 mmol/l in distal level of affection of biliferous ducts cause high probability of the postoperative complications occurrence (coefficient of determination 34.8%), determining necessity of performance of draining endobiliary intervention on the first stage of surgical treatment. The dependence of lethality from age of patients and duration of the OJ was noted.

Bilirubin↗
PubMed2003

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction.

MOTIVATION: Feature subset selection is an important preprocessing step for classification. In biology, where structures or processes are described by a large number of features, the elimination of irrelevant and redundant information in a reasonable amount of time has a number of advantages. It enables the classification system to achieve good or even better solutions with a restricted subset of features, allows for a faster classification, and it helps the human expert focus on a relevant subset of features, hence providing useful biological knowledge. RESULTS: We present a heuristic method based on Estimation of Distribution Algorithms to select relevant subsets of features for splice site prediction in Arabidopsis thaliana. We show that this method performs a fast detection of relevant feature subsets using the technique of constrained feature subsets. Compared to the traditional greedy methods the gain in speed can be up to one order of magnitude, with results being comparable or even better than the greedy methods. This makes it a very practical solution for classification tasks that can be solved using a relatively small amount of discriminative features (or feature dependencies), but where the initial set of potential discriminative features is rather large.

Algorithms↗
PubMed2003

A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases.

We present a new probability-based method for protein identification using tandem mass spectra and protein databases. The method employs a hypergeometric distribution to model frequencies of matches between fragment ions predicted for peptide sequences with a specific (M + H)+ value (at some mass tolerance) in a protein sequence database and an experimental tandem mass spectrum. The hypergeometric distribution constitutes null hypothesis-all peptide matches to a tandem mass spectrum are random. It is used to generate a score characterizing the randomness of a database sequence match to an experimental tandem mass spectrum and to determine the level of significance of the null hypothesis. For each tandem mass spectrum and database search, a peptide is identified that has the least probability of being a random match to the spectrum and the corresponding level of significance of the null hypothesis is determined. To check the validity of the hypergeometric model in describing fragment ion matches, we used chi2 test. The distribution of frequencies and corresponding hypergeometric probabilities are generated for each tandem mass spectrum. No proteolytic cleavage specificity is used to create the peptide sequences from the database. We do not use any empirical probabilities in this method. The scores generated by the hypergeometric model do not have a significant molecular weight bias and are reasonably independent of database size. The approach has been implemented in a database search algorithm, PEP_PROBE. By using a large set of tandem mass spectra derived from a set of peptides created by digestion of a collection of known proteins using four different proteases, a false positive rate of 5% is demonstrated.

Amino Acid Sequence↗
PubMed2006

A distribution free summarization method for Affymetrix GeneChip arrays.

MOTIVATION: Affymetrix GeneChip arrays require summarization in order to combine the probe-level intensities into one value representing the expression level of a gene. However, probe intensity measurements are expected to be affected by different levels of non-specific- and cross-hybridization to non-specific transcripts. Here, we present a new summarization technique, the Distribution Free Weighted method (DFW), which uses information about the variability in probe behavior to estimate the extent of non-specific and cross-hybridization for each probe. The contribution of the probe is weighted accordingly during summarization, without making any distributional assumptions for the probe-level data. RESULTS: We compare DFW with several popular summarization methods on spike-in datasets, via both our own calculations and the 'Affycomp II' competition. The results show that DFW outperforms other methods when sensitivity and specificity are considered simultaneously. With the Affycomp spike-in datasets, the area under the receiver operating characteristic curve for DFW is nearly 1.0 (a perfect value), indicating that DFW can identify all differentially expressed genes with a few false positives. The approach used is also computationally faster than most other methods in current use. AVAILABILITY: The R code for DFW is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗
PubMed2006

[Comparison of open versus percutaneous treatment for humeral head fracture].

BACKGROUND: The hypothesis of this study was that percutaneous techniques lower the risk of post-traumatic avascular necrosis. MATERIALS AND METHODS: In this retrospective study 83 patients were followed up clinically and radiologically for signs of avascular necrosis and nonunion after open or percutaneous treatment of proximal humerus fractures. Mean age was 50 years. Fractures were classified in 22 patients (26.5%) as two part, in 21 patients (25.3%) as three part, in 39 patients (47%) as four part, and in 1 patient (1.2%) as fracture dislocation (Neer classification). Fractures were treated in 12 patients (14.5%) by ORIF (open reduction and internal fixation) and in 71 patients (85.5%) by CRPF (closed reduction and percutaneous fixation). Both groups were statistically equally distributed according to fracture type (Mann-Whitney U, p=0.267) and age (One-way-Annova, p=0.740). The postoperative regime did not differ between the two groups. RESULTS: Patients suffered significantly more avascular necrosis after open treatment [five patients (50%) versus eight patients (12.7%) in the percutaneous group, Mann-Whitney, p=0.004]. The risk for avascular necrosis and nonunion increased with age. Mean age of patients with avascular necrosis was 57 years, and the age of patients with nonunion was 67 years. CONCLUSION: Percutaneous treatment of humeral head fractures seems to be a reliable method for lowering the risk of avascular necrosis in young patients.

Adult↗
PubMed2003

Doubly distributional population codes: simultaneous representation of uncertainty and multiplicity.

Perceptual inference fundamentally involves uncertainty, arising from noise in sensation and the ill-posed nature of many perceptual problems. Accurate perception requires that this uncertainty be correctly represented, manipulated, and learned about. The choices subjects make in various psychophysical experiments suggest that they do indeed take such uncertainty into account when making perceptual inferences, posing the question as to how uncertainty is represented in the activities of neuronal populations. Most theoretical investigations of population coding have ignored this issue altogether; the few existing proposals that address it do so in such a way that it is fatally conflated with another facet of perceptual problems that also needs correct handling: multiplicity (that is, the simultaneous presence of multiple distinct stimuli). We present and validate a more powerful proposal for the way that population activity may encode uncertainty, both distinctly from and simultaneously with multiplicity.

Action Potentials↗