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At least 1,153 records · Page 64Linked to original sources
PubMed1998

Some new multiple-test procedures for dose finding.

In Tamhane, Hochberg, and Dunnett (1) we focused primarily on step-down test procedures based on contrasts among the sample means to find the minimum effective dose in a dose-response study. In the present article we use the global tests of Bartholomew (2,3) and Hayter (4) in these step-down procedures. We also propose a new step-down procedure that permits tests based on a class of contrasts [step and basin contrasts of Ruberg (5) are examples of such contrasts] that could not be used with the step-down procedures studied in our previous paper because of lack of control of the familywise error rate. A simulation study to compare the four procedures proposed in the present paper with the top four procedures from the previous article is carried out. It is found that the step-down procedure based on Bartholomew's test and the new step-down procedure based on step and modified basin contrasts generally perform better than the other procedures for a wide range of dose-response profiles.

Algorithms↗
PubMed1999

Nonparametric step-down test procedures for finding minimum effective dose.

Nonparametric versions of normal theory step-down multiple-test procedures for inferring minimum effective dose (see Tamhane et al. (1)) were developed and studied by Monte Carlo simulation. Two types of step-down testing procedures were examined. For both procedures, pairwise, linear, or Helmert contrasts of mean ranks were studied. All nonparametric step-down procedures controlled familywise error rate under normal, double exponential, and exponential distributions. Specific recommendations based on power and bias comparisons of nonparametric methods among themselves, with Shirley's (2) test, and with parametric step-down multiple-test procedures are given.

Computer Simulation↗
PubMed1994

A deconvolution method for evaluating indicator-dilution curves.

Characteristics of blood flow in tissue can be measured by administering an intravascular tracer and then deconvolving and analysing the resulting indicator-dilution curves. Existing deconvolution methods are not typically generalizable to a variety of tissues. The authors have developed a more general deconvolution method using simulated indicator-dilution data. This method involves filtering the Fourier transform of indicator-dilution data with a modification of the Wiener filter, an adaptive deconvolution filter. Unlike the Wiener filter, this adaptive filter requires no previous knowledge of the noise frequency spectrum; it is derived by varying the magnitude of the noise spectrum until the oscillations in the deconvolved data fall below an optimal value. The optimal value corresponds to the setting of the noise spectrum that allows the most accurate and precise measurement of vascular characteristics from deconvolved data. Vascular characteristics measured in brain tissues using this deconvolution method on actual indicator-dilution data were similar to established values. It should be possible to use this method on time-concentration data collected from a variety of tissues using a number of different tracer measurement techniques, thereby allowing the accurate characterization of vascular physiology.

Algorithms↗
PubMed1999

Application of distance geometry to 3D visualization of sequence relationships.

SUMMARY: We describe the application of distance geometry methods to the three-dimensional visualization of sequence relationships, with examples for mumps virus SH gene cDNA and prion protein sequences. Sequence-sequence distance measures may be obtained from either a multiple sequence alignment or from sets of pairwise alignments. AVAILABILITY: C/Perl code and HTML/VRML files from http://www.nibsc.ac.uk/dg3dseq/

Algorithms↗
PubMed1988

A microcomputer program to evaluate the saturation of complex solutions with respect to biominerals.

The program described is written in BASIC and enables calculation of ionic activity products and degrees of saturation for solutions with respect to minerals of biological interest. The program takes into account ion-pair formation by association of anions and cations. The number of constituent species, whether or not involved in mineral formation or in ion-pair formation, appears to be unlimited. The computation fulfils the conditions of conservation of matter and electrical neutrality. Successful computation is achieved even for systems with highly unfavourable ratios between cations and anions with high affinities. The program is easily re-orientated towards any mineral/solution system.

Algorithms↗
PubMed1991

Genome inhomogeneity is determined mainly by WW and SS dinucleotides.

According to the hypothesis of the modular structure of DNA, genomes consist of modules of various nature which may differ in statistical characteristics. Statistical analysis helps in revealing the differences in statistical characteristics and predicting the modular structure. In this connection the question about the contribution of each word of length l (l-tuple) to the inhomogeneity of genetic text arises. The notion of stationary (i.e. relatively evenly distributed over a genome) versus non-stationary l-tuples has been introduced previously. In this paper, the dinucleotide distributions for all long sequences from GenBank were analyzed and it was shown that non-stationary dinucleotides are closely associated with polyW and polyS tracts (W denotes 'weak' nucleotides A or T, while S stands for the 'strong' nucleotides G or C). Thus, genome inhomogeneity is shown to be determined mainly by AA, TT, GG, CC, AT, TA, GC and CG dinucleotides. It has been demonstrated that neither 'codon usage' nor the 'isochore model' can account for this phenomenon.

Algorithms↗
PubMed1996

The effects of variable mutation rates across sites on the phylogenetic estimation of effective population size or mutation rate of DNA sequences.

Multiple hits at some sites of human mitochondrial DNA sequences suggest that the commonly assumed infinite-sites model can be violated. Under the neutral Wright-Fisher model without recombination and population subdivision, we investigated, by computer simulations, the effect of multiple hits on the estimation of the essential parameter theta = 4Nmu by FU's UPBLUE procedure. We found that with moderate mutation rate heterogeneity, UPBLUE performs very well in terms of unbiasness and efficiency. Under extreme mutation rate heterogeneity, if sample size is reasonably large (e.g., > 60), UPBLUE is still very satisfactory; otherwise we developed a new correction equation. Given knowledge of the degree of mutation rate heterogeneity, the performance of UPBLUE with the new correction equation was tested to be fairly satisfactory: there is almost no bias and the sampling variance is only slightly higher than the theoretical minimum variance. Thus, with an appropriate correction, UPBL.UE is relatively robust to the multiple hits. In genealogies reconstructed by UPGMA, we found that the total length of branches directly linked to the tips is underestimated, and those far away tend to be overestimated, while the total length of all branches is not biased.

Computer Simulation↗
PubMed1997

Marker-assisted introgression of quantitative trait loci.

The use of molecular markers for the introgression of one or several superior QTL alleles into a recipient line is investigated using analytic and simulation results. The positions of the markers devoted to the control of the genotype at the QTLs in a "foreground selection" step are optimized given the confidence interval of the QTL position. Results demonstrate that using at least three markers per QTL allows a good control over several generations. Population sizes that should be recommended for various numbers of QTLs are calculated and are used to determine the limit in the number of QTLs that can be monitored simultaneously. If "background selection" devoted to accelerate the return to the recipient parent genotype outside the QTL regions is applied, the positions of the markers devoted to the control of the QTLs have to be reconsidered. When several QTLs are monitored simultaneously, background selection among the limited number of individuals resulting from the foreground selection step accelerates the increase in genomic similarity with the recipient parent, with only limited costs. Background selection is even more efficient in a pyramidal backcross program where QTLs are first monitored one by one.

Alleles↗
PubMed1996

Model stimulations to estimate malaria risk under climate change.

The current geographic range of malaria is much smaller than its potential range. In many regions there exists a phenomena characterized as "Anophelism without malaria." The vectors are present but malaria transmission does not occur. Vectorial capacity often has been used as a parameter to estimate the susceptibility of an area to malaria. Model computations with global climatological data show that a dynamic concept of vectorial capacity can be used as a comparative risk indicator to predict the current extent and distribution of malarious regions in the world. A sensitivity analysis done in 3 distinct geographic areas shows that the areas of largest change of epidemic potential caused by a temperature increase are those where mosquitoes already occur but where development of the parasite is limited by temperature. Computations with the model presented here predict, with different climate scenarios, an increased malaria risk in areas bordering malaria endemic regions and at higher altitudes within malarious regions under a temperature increase of 2-4 degrees C.

Animals↗
PubMed2004

Isotopica: a tool for the calculation and viewing of complex isotopic envelopes.

The web application Isotopica has been developed as an aid to the interpretation of ions that contain naturally occurring isotopes in a mass spectrum. It allows the calculation of mass values and isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. In addition, Isotopica takes modifications of the input molecule into consideration using a simple and flexible language as a straightforward extension of the molecular formula syntax. This function is especially useful for biomolecules, which are often subjected to additional modifications other than normal constituents, such as the frequently occurring post-translational modification in proteins. The isotopic distribution of any molecule thus defined can be calculated by considering full widths at half maximum or mass resolution. The combined envelope of several overlapping isotopic distributions of a mixture of molecules can be determined after specifying each molecule's relative abundance. The results can be displayed graphically on a local PC using the Isotopica viewer, a standalone application that is downloadable from the sites below, as a complement to the client browser. The m/z and intensity values can also be obtained in the form of a plain ASCII text file. The software has proved to be useful for peptide mass fingerprinting and validating an observed isotopic ion distribution with reference to the theoretical one, even from a multi-component sample. The web server can be accessed at http://bioinformatica.cigb.edu.cu/isotopica and http://coco.protein.osaka-u.ac.jp/isotopica [correction].

Amino Acid Sequence↗
PubMed1991

Electrostatic screening in molecular dynamics simulations.

The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties like pK shifts, the effects of charged groups on redox potentials and binding constants of metal ions. To test how well the screening of the electrostatic potential describes the dynamical trajectory of a macromolecular system, a series of comparative simulations have been carried out on a protein system which explicitly included water molecules and a system in vacuo. For the system without solvent the results of using (i) the standard potential form were compared with results of (ii) the potential where the Coulomb term was modified by the inclusion of a distance dependent dielectric, epsilon (r), to model the screening effect of bulk water, and (iii) standard potential modified by reducing the charge on ionized residue side chains. All molecular dynamics simulations have been carried out on bovine pancreatic trypsin inhibitor. Comparisons between the resulting trajectories, averaged structures, hydrogen bonding patterns and properties such as solvent accessible surface area and radius of gyration are described. The results show that the dynamical behaviour of the protein calculated with a screened electrostatic term compares more favourably with the time-dependent structural changes of the full system with explicitly included water than the standard vacuum simulation.

Animals↗
PubMed1993

Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins.

A modelled tertiary structure for the dimeric HLH domain of the E47 protein is presented. Structural information was obtained from the aligned sequences of > 40 members of the HLH family. The information was used to model each monomer as an alpha-helical hairpin, with knobs-into-holes packing of side-chains as found in antiparallel coiled-coil. The dimer forms a four-helix bundle with additional knobs-into-holes packing at the dimer interface. The size and electrostatic properties of core-forming residues are all accounted for in the model. The model does not violate any known properties of protein structure. The monomers are related by two-fold rotational symmetry, in agreement with the observed DNA-binding sites which are imperfect inverted repeats. The N-terminal basic region, in which DNA binding and base specificity reside, forms the first part of helix 1. A prediction based on the model structure is that the HLH domains do not bind to DNA in its B form but require a partially unwound conformation in order to enter the major groove.

Amino Acid Sequence↗
PubMed2005

Using the circumstances of symptom experience to assess the severity of urgency in the overactive bladder.

PURPOSE: We identified a method for quantifying the symptoms of the overactive bladder that addresses the assessment of urgency. MATERIALS AND METHODS: An observational study of a cohort was used. Data were collected prospectively from 5,423 consultations on 1,797 patients (158 males and 1,639 females) being assessed and treated for the overactive bladder. The study was conducted during 5 years. The reported frequencies and incontinence episodes were recorded. Using ranked ordinal scales (none, mild, moderate, severe) the symptoms of urgency and urge incontinence associated with waking and rising, hearing running water, arriving home ("latchkey"), cold weather and when feeling tired or worried were noted. The experiences of urgency and urge incontinence, without reference to the circumstances in which they were experienced were similarly assessed and if on treatment, they were asked to grade their overall response. RESULTS: Reported urinary frequency and incontinence episodes were strongly associated with patient grading of response to treatment. Therefore, the symptoms assessed on the scale of none, mild, moderate and severe were compared with disease severity by using reported frequency and incontinence episodes. The description of the symptoms with reference to the situations in which they were experienced showed clear associations with frequency and incontinence, falling along a progressive scale. An overall pattern could be detected in that at points on the scale of none, mild, moderate and severe, the least frequency and incontinence tended to be associated with waking, rising and latchkey symptoms. Next followed symptoms precipitated by running water and cold weather. Aggravation by fatigue or worry was associated with the greatest disease severity (ANOVA F = 8.9, p <0.001). This scale covered a wide range from frequencies of 7 to 15 times daily and incontinence episodes through 0 to 4 times daily. CONCLUSIONS: Qualifying the experience of urgency and urge incontinence, according to the circumstances in which these symptoms are experienced, seems to offer a promising new method for assessing the severity of urgency and urge incontinence.

Activities of Daily Living↗
PubMed2005

Molecular dynamics simulations of nanoindentation and nanotribology.

We present results of parallel molecular dynamics simulations of nanoindentation and nanotribology experiments. The models we have developed describe both the sample and the indenter atomistically and model the effect of the cantilevers in an atomic force microscope through the use of springs. We show that the simulations are in good qualitative agreement with experiment and help to elucidate many of the mechanisms that take place during these processes. In particular, we illustrate the role that dislocations play both in nanoindentation and also in stick-slip. Further to this we show how real-time visualization and computational steering have been employed in these simulations to capture the dynamical events that take place.

Computer Simulation↗
PubMed1989

Computation of the passive electrical parameters of neurons using a system model.

Time-domain analysis of voltage responses to current pulse stimulation has been used to estimate the electrotonic parameters of neurons using the signal model. Errors are likely to accumulate from various steps of the analysis due to noise and electrode artifacts. A system model, which has inherent noise immunity and filtering properties, is presented here. This model employs frequency-domain analysis of the input impedance of a neuronal model (an RC cable). The resistances and capacitances of the system model are estimated from the cell-input impedance using an optimization strategy. Using the expression for the input impedance, any specified number of equalizing time constants can be computed exactly. The accessibility to these equalizing time constants 1) provides greater insight into the charge equalization along the length and circumference of the cable, and 2) improves the estimation of all other passive parameters including the electrotonic length. Thus, the system model approach allows information to be extracted more directly and accurately than the signal model approach.

Animals↗
PubMed2002

Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences.

We have developed an alignment-independent method for classification of G-protein coupled receptors (GPCRs) according to the principal chemical properties of their amino acid sequences. The method relies on a multivariate approach where the primary amino acid sequences are translated into vectors based on the principal physicochemical properties of the amino acids and transformation of the data into a uniform matrix by applying a modified autocross-covariance transform. The application of principal component analysis to a data set of 929 class A GPCRs showed a clear separation of the major classes of GPCRs. The application of partial least squares projection to latent structures created a highly valid model (cross-validated correlation coefficient, Q(2) = 0.895) that gave unambiguous classification of the GPCRs in the training set according to their ligand binding class. The model was further validated by external prediction of 535 novel GPCRs not included in the training set. Of the latter, only 14 sequences, confined in rapidly expanding GPCR classes, were mispredicted. Moreover, 90 orphan GPCRs out of 165 were tentatively identified to GPCR ligand binding class. The alignment-independent method could be used to assess the importance of the principal chemical properties of every single amino acid in the protein sequences for their contributions in explaining GPCR family membership. It was then revealed that all amino acids in the unaligned sequences contributed to the classifications, albeit to varying extent; the most important amino acids being those that could also be determined to be conserved by using traditional alignment-based methods.

Amino Acids↗
PubMed2003

Simulation of ultrasonic focus aberration and correction through human tissue.

Ultrasonic focusing in two dimensions has been investigated by calculating the propagation of ultrasonic pulses through cross-sectional models of human abdominal wall and breast. Propagation calculations used a full-wave k-space method that accounts for spatial variations in density, sound speed, and frequency-dependent absorption and includes perfectly matched layer absorbing boundary conditions. To obtain a distorted receive wavefront, propagation from a point source through the tissue path was computed. Receive focusing used an angular spectrum method. Transmit focusing was accomplished by propagating a pressure wavefront from a virtual array through the tissue path. As well as uncompensated focusing, focusing that employed time-shift compensation and time-shift compensation after backpropagation was investigated in both transmit and receive and time reversal was investigated for transmit focusing in addition. The results indicate, consistent with measurements, that breast causes greater focus degradation than abdominal wall. The investigated compensation methods corrected the receive focus better than the transmit focus. Time-shift compensation after backpropagation improved the focus from that obtained using time-shift compensation alone but the improvement was less in transmit focusing than in receive focusing. Transmit focusing by time reversal resulted in lower sidelobes but larger mainlobes than the other investigated transmit focus compensation methods.

Abdomen↗
PubMed2003

Surface response of a viscoelastic medium to subsurface acoustic sources with application to medical diagnosis.

The response at the surface of an isotropic viscoelastic medium to buried fundamental acoustic sources is studied theoretically, computationally and experimentally. Finite and infinitesimal monopole and dipole sources within the low audible frequency range (40-400 Hz) are considered. Analytical and numerical integral solutions that account for compression, shear and surface wave response to the buried sources are formulated and compared with numerical finite element simulations and experimental studies on finite dimension phantom models. It is found that at low audible frequencies, compression and shear wave propagation from point sources can both be significant, with shear wave effects becoming less significant as frequency increases. Additionally, it is shown that simple closed-form analytical approximations based on an infinite medium model agree well with numerically obtained "exact" half-space solutions for the frequency range and material of interest in this study. The focus here is on developing a better understanding of how biological soft tissue affects the transmission of vibro-acoustic energy from biological acoustic sources below the skin surface, whose typical spectral content is in the low audible frequency range. Examples include sound radiated from pulmonary, gastro-intestinal and cardiovascular system functions, such as breath sounds, bowel sounds and vascular bruits, respectively.

Auscultation↗