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PubMed2003

Group imaging of task-related changes in cortical synchronisation using nonparametric permutation testing.

Synthetic aperture magnetometry (SAM) is a nonlinear beamformer technique for producing 3D images of cortical activity from magnetoencephalography data. We have previously shown how SAM images can be spatially normalised and averaged to form a group image. In this paper we show how nonparametric permutation methods can be used to make robust statistical inference about group SAM data. Data from a biological motion direction discrimination experiment were analysed using both a nonparametric analysis toolbox (SnPM) and a conventional parametric approach utilising Gaussian field theory. In data from a group of six subjects, we were able to show robust group activation at the P < 0.05 (corrected) level using the nonparametric methods, while no significant clusters were found using the conventional parametric approach. Activation was found using SnPM in several regions of right occipital-temporal cortex, including the superior temporal sulcus, V5/MT, the fusiform gyrus, and the lateral occipital complex.

Adult↗
PubMed1999

Robust retrieval of three-dimensional structures from image stacks.

Robust high-breakdown-point location estimators are employed to analyze image stacks under the piecewise constant image structure model. To reduce the effect of bias along the Z-axis, the class parameters are extracted using three consecutive slices, The segmentation algorithm first determines the most reliable seed regions, which are then used in a region-growing procedure supported by local evidence. The robustness and stability of the proposed technique is shown with both synthetic and real data, the latter consisting of one MRI and one confocal microscopy set. The performance of the algorithm is consistent with the ground truth obtained with manual segmentation by physicians.

Algorithms↗
PubMedDate not supplied

Optimal design of an enzymatic reactor for flow injection analysis.

A simulation procedure for the optimization of enzymatic reactors used in sandwich flow injection systems is evaluated. The system is modeled as a plug-flow reactor with axial dispersion. To calibrate it, dispersion coefficients can be evaluated using residence time distribution techniques; meanwhile, enzymatic kinetics must be determined for the system considered, according to the values of the substrate conversion attained. The model has been linked to an optimization routine based on the Powell algorithm. The proposed approach has been evaluated in a system performing simultaneous determinations of glucose and glycerol, considered the common carbon sources in a fermentation process.

Biotechnology↗
PubMed2006

Paper and plastic in daily diary research: Comment on Green, Rafaeli, Bolger, Shrout, and Reis (2006).

The authors applaud A. S. Green, E. Rafaeli, N. Bolger, P. E. Shrout, and H. T. Reis's (2006) response to one-sided comparisons of paper versus electronic (plastic) diary methods and hope that it will stimulate more balanced considerations of the issues involved. The authors begin by highlighting areas of agreement and disagreement with Green et al. The authors review briefly the broader literature that has compared paper and plastic diaries, noting how recent comparisons have relied on study designs and methods that favor investigators' allegiances. The authors note some sorely needed data for the evaluation of the implications of paper versus plastic for the internal and external validity of research. To facilitate evaluation of the existing literature and assist in the design of future studies, the authors offer a balanced comparison of paper and electronic diary methods across a range of applications. Finally, the authors propose 2 study designs that offer fair comparisons of paper and plastic diary methods.

Adolescent↗
PubMed2001

The family based association test method: strategies for studying general genotype--phenotype associations.

With possibly incomplete nuclear families, the family based association test (FBAT) method allows one to evaluate any test statistic that can be expressed as the sum of products (covariance) between an arbitrary function of an offspring's genotype with an arbitrary function of the offspring's phenotype. We derive expressions needed to calculate the mean and variance of these test statistics under the null hypothesis of no linkage. To give some guidance on using the FBAT method, we present three simple data analysis strategies for different phenotypes: dichotomous (affection status), quantitative and censored (eg, the age of onset). We illustrate the approach by applying it to candidate gene data of the NIMH Alzheimer Disease Initiative. We show that the RC-TDT is equivalent to a special case of the FBAT method. This result allows us to generalise the RC-TDT to dominant, recessive and multi-allelic marker codings. Simulations compare the resulting FBAT tests to the RC-TDT and the S-TDT. The FBAT software is freely available.

Alzheimer Disease↗
PubMed2003

[Growth of sporadic vestibular schwannomas correlates with Ki-67 proliferation index].

BACKGROUND: Sporadic vestibular schwannoma show a wide variability of their growth rate. Some tumors might remain quiescent for a long time without symptoms and other tumors might suddenly enlarge. Sometimes during surgical removal of tumors, it is useful to have a parameter for the prediction of the further growth potential of the schwannoma, especially if tumor resection results in functional impairment of the facial nerve. An often used histological parameter for growth rate of tumor cells is the proliferation index. METHODS AND PATIENTS: In our study we observed a series of 50 patients with neurinoma of the vestibular nerve by "wait and scan". After the first magnetic resonance imaging (MRI) all patients were controlled by a second MRI. The time between the MRIs ranged between 3 and 26 months (median 9). In 45 of 50 patients a surgical removal of the tumor by transtemporal approach followed. RESULTS: The proliferation index (Ki-67) was identified in the histological tumor specimens. The next step was the correlation of proliferation index and "tumor doubling time" (TDT). The volume of the tumors was provided by measuring three diameters of the tumors in MRI and calculating the volume with a formula. The volume of the tumors were used to calculate tumor growth and TDT. 10 patients showed no tumor growth during follow up. The average TDT in 40 cases was 22 months (SD 16). In 33 cases we were able to determine a proliferation index, which showed an average score of 1.99 %. Statistical analysis showed a correlation between proliferation index and TDT with a coefficient of - 0.42 (s: 0.014). In two cases with relevant clinical tumor growth (TDT: 12 months), the MIB-1 index was nearly 0 % in different areas of the tumor specimen. May be in these cases, the cell proliferation declined just before operation. On the other hand we found one patient with a high proliferation index of 3.3 % and a rather long TDT of 19 months. CONCLUSIONS: The determination of proliferation can serve as a further decision guidance during surgery of vestibular schwannoma.

Cell Division↗
PubMed1995

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations.

Absolute binding free energies for three inhibitors of HIV-1 proteinase were estimated from molecular dynamics simulations by a recently reported linear approximation procedure. The results were in fairly good agreement with experimental binding data. Two of the inhibitors were very similar and, for comparison, their relative free energies of binding were also calculated by free energy perturbation methods, giving virtually the same result. Effects of cut-off radii and charge states of the protein model were examined. The effects of pH on binding of one of the inhibitors were predicted.

Computer Simulation↗
PubMed1991

The use of modified constellation graph method for computer-aided classification of congenital heart diseases.

This paper describes a new method of data reduction and classification in a multidimensional symptom space for diagnostic aid of congenital heart diseases. The algorithm developed here is to reduce interactively a multidimensional symptom space to sectorial regions representing each disease in a semicircle using the modified constellation graph method. This method enables us to classify patients using the angle in the semicircle as a single classifying parameter with an accuracy of about 90%, that is, with little overlapping between disease sectors. Comparing this method with conventional factor analysis, we have found the former far more effective than the latter for disease region separation.

Algorithms↗
PubMed2001

Electric fields in the human body resulting from 60-Hz contact currents.

Contact currents occur when a person touches conductive surfaces at different potentials and completes a path for current flow through the body. Such currents provide an additional coupling mechanism to that, due to the direct field effect between the human body and low-frequency external fields. The scalar potential finite difference method, with minor modifications, is applied to assess current density and electric field within excitable tissue and bone marrow due to contact current. An anatomically correct adult model is used, as well as a proportionally downsized child model. Three pathways of contact current are modeled: hand to opposite hand and both feet, hand to hand only, and hand to both feet. Because of its larger size relative to the child, the adult model has lower electric field and current-density values in tissues/unit of contact current. For a contact current of 1 mA [the occupational reference level set by the International Commission on Non-ionizing Protection (ICNIRP)], the current density in brain does not exceed the basic restriction of 10 mA/m2. The restriction is exceeded slightly in the spine, and by a factor of more than 2 in the heart. For a contact current of 0.5 mA (ICNIRP general public reference level), the basic restriction of 2 mA/m2 is exceeded several-fold in the spine and heart. Several microamperes of contact current produces tens of mV/m within the child's lower arm bone marrow.

Adult↗
PubMedDate not supplied

Integer programming approaches to haplotype inference by pure parsimony.

In 2003, Gusfield introduced the Haplotype Inference by Pure Parsimony (HIPP) problem and presented an integer program (IP) that quickly solved many simulated instances of the problem. Although it solved well on small instances, Gusfield's IP can be of exponential size in the worst case. Several authors have presented polynomial-sized IPs for the problem. In this paper, we further the work on IP approaches to HIPP. We extend the existing polynomial-sized IPs by introducing several classes of valid cuts for the IP. We also present a new polynomial-sized IP formulation that is a hybrid between two existing IP formulations and inherits many of the strengths of both. Many problems that are too complex for the exponential-sized formulations can still be solved in our new formulation in a reasonable amount of time. We provide a detailed empirical comparison of these IP formulations on both simulated and real genotype sequences. Our formulation can also be extended in a variety of ways to allow errors in the input or model the structure of the population under consideration.

Algorithms↗
PubMed2003

A phenomenological model for the responses of auditory-nerve fibers. II. Nonlinear tuning with a frequency glide.

A computational model was developed to simulate the responses of auditory-nerve (AN) fibers in cat. The model's signal path consisted of a time-varying bandpass filter; the bandwidth and gain of the signal path were controlled by a nonlinear feed-forward control path. This model produced realistic response features to several stimuli, including pure tones, two-tone combinations, wideband noise, and clicks. Instantaneous frequency glides in the reverse-correlation (revcor) function of the model's response to broadband noise were achieved by carefully restricting the locations of the poles and zeros of the bandpass filter. The pole locations were continuously varied as a function of time by the control signal to change the gain and bandwidth of the signal path, but the instantaneous frequency profile in the revcor function was independent of sound pressure level, consistent with physiological data. In addition, this model has other important properties, such as nonlinear compression, two-tone suppression, and reasonable Q10 values for tuning curves. The incorporation of both the level-independent frequency glide and the level-dependent compressive nonlinearity into a phenomenological model for the AN was the primary focus of this work. The ability of this model to process arbitrary sound inputs makes it a useful tool for studying peripheral auditory processing.

Auditory Pathways↗
PubMed1994

Molecular computation of solutions to combinatorial problems.

The tools of molecular biology were used to solve an instance of the directed Hamiltonian path problem. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This experiment demonstrates the feasibility of carrying out computations at the molecular level.

Algorithms↗
PubMed2006

Magnetic resonance imaging and magnetic resonance spectroscopy study of deficits in hippocampal structure in fire victims with recent-onset posttraumatic stress disorder.

OBJECTIVE: To explore hippocampal structural abnormalities in fire victims with recent-onset posttraumatic stress disorder (PTSD). METHOD: We compared 12 patients with recent-onset PTSD diagnosed according to DSM-IV criteria 6 to 8 months after a major fire with 12 individuals without PTSD who were victims of the same fire accident. Voxel-based morphometry (VBM) and magnetic resonance spectroscopy (MRS) were combined to examine hippocampal structural abnormalities in patients with recent-onset PTSD. RESULTS: Results of VBM showed that the grey matter density of the left hippocampus was lower in the group with PTSD than it was in the group without PTSD. Results of MRS showed that the ratio of N-acetyl asparate and creatine in the left hippocampus was significantly lower in patients with PTSD than in control subjects. CONCLUSION: Patients with recent-onset PTSD had hippocampal structural abnormalities.

Adult↗
PubMed2005

On the classic and modern theories of matching.

Classic matching theory, which is based on Herrnstein's (1961) original matching equation and includes the well-known quantitative law of effect, is almost certainly false. The theory is logically inconsistent with known experimental findings, and experiments have shown that its central constant-k assumption is not tenable. Modern matching theory, which is based on the power function version of the original matching equation, remains tenable, although it has not been discussed or studied extensively. The modern theory is logically consistent with known experimental findings, it predicts the fact and details of the violation of the classic theory's constant-k assumption, and it accurately describes at least some data that are inconsistent with the classic theory.

Animals↗
PubMed2005

Quantified aneurysm shape and rupture risk.

OBJECT: The authors investigated whether quantified shape or size indices could better discriminate between ruptured and unruptured aneurysms. METHODS: Several custom algorithms were created to quantifiy the size and shape indices of intracranial aneurysms by using three-dimensional computerized tomography angiography models of the brain vasculature. Data from 27 patients with ruptured or unruptured aneurysms were evaluated in a blinded fashion to determine whether aneurysm size or shape better discriminated between the ruptured and unruptured groups. Five size and eight shape indices were calculated for each aneurysm. Two-tailed independent Student t-tests (significance p < 0.05) were used to determine statistically significant differences between ruptured and unruptured aneurysm groups for all 13 indices. Receiver-operating characteristic-area under curve analyses were performed for all indices to quantify the predictability of each index and to identify optimal threshold values. None of the five size indices were significantly different between the ruptured and unruptured aneurysms. Five of the eight shape indices were significantly different between the two lesion groups, and two other shape indices showed a trend toward discriminating between ruptured and unruptured aneurysms, although these differences did not reach statistical significance. CONCLUSIONS: Quantified shape is more effective than size in discriminating between ruptured and unruptured aneurysms. Further investigation will determine whether quantified aneurysm shape will prove to be a reliable predictor of aneurysm rupture.

Adult↗
PubMed1999

Outpatient health care statistics data warehouse--logical design.

Outpatient Health Care Statistics on a state level is a central point where all relevant statistic data are collected from various sources from all over the country. Various and complex requirements for processing and reporting data makes Outpatient Health Care Statistics on a state level a perfect example for efficient implementing of Data warehouse technology. The research investigates logical design of data warehouse with a special attention on a different data modeling technique in various phases of a logical data warehouse design. The research shows that a requirement for processing statistical data determines the design decision and thus the scope and semantic value of final data warehouse.

Ambulatory Care↗