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PubMed2006

Wavelet time-frequency analysis and least squares support vector machines for the identification of voice disorders.

This work describes a novel algorithm to identify laryngeal pathologies, by the digital analysis of the voice. It is based on Daubechies' discrete wavelet transform (DWT-db), linear prediction coefficients (LPC), and least squares support vector machines (LS-SVM). Wavelets with different support-sizes and three LS-SVM kernels are compared. Particularly, the proposed approach, implemented with modest computer requirements, leads to an adequate larynx pathology classifier to identify nodules in vocal folds. It presents over 90% of classification accuracy and has a low order of computational complexity in relation to the speech signal's length.

Adolescent↗
PubMed2004

Integrated wavelet processing and spatial statistical testing of fMRI data.

We introduce an integrated framework for detecting brain activity from fMRI data, which is based on a spatial discrete wavelet transform. Unlike the standard wavelet-based approach for fMRI analysis, we apply the suitable statistical test procedure in the spatial domain. For a desired significance level, this scheme has one remaining degree of freedom, characterizing the wavelet processing, which is optimized according to the principle of minimal approximation error. This allows us to determine the threshold values in a way that does not depend on data. While developing our framework, we make only conservative assumptions. Consequently, the detection of activation is based on strong evidence. We have implemented this framework as a toolbox (WSPM) for the SPM2 software, taking advantage of multiple options and functions of SPM such as the setup of the linear model and the use of the hemodynamic response function. We show by experimental results that our method is able to detect activation patterns; the results are comparable to those obtained by SPM even though statistical assumptions are more conservative.

Attention↗
PubMed2004

Characterizing spatial and temporal features of autobiographical memory retrieval networks: a partial least squares approach.

Conway (Conway, M.A., 1992. A structural model of autobiographical memory. In: Conway, M.A., Spinnler, H., Wagenaar, W.A. (Eds.), Theoretical Perspectives on Autobiological Memory. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. 167-194) proposed that two types of autobiographical memories (AMs) exist within a hierarchical AM system: unique, specific events and repeated, general memories. There is little research on whether retrieval of these AMs relies on different neural substrates. To investigate this issue, we used a multivariate image analysis technique, spatiotemporal partial least squares (PLS), to identify distributed patterns of activity most related to AM tasks that we have found to be associated with a medial and left-lateralized network. Using PLS, specific and general memories were more strongly associated with different parts of this retrieval network. Specific AM retrieval was associated more with activation of regions involved in imagery in episodic memory, including the left precuneus, left superior parietal lobule and right cuneus, whereas general AM retrieval was associated with activation of the right inferior temporal gyrus, right medial frontal cortex, and left thalamus. These two patterns emerged at different lags after stimulus onset, with the general AM pattern peaking between 2 and 6 s, and the specific AM pattern between 6 and 8 s. These lag differences are consistent with Conway's theory which posits that general AMs are the preferred level of entry to the AM system. A seed PLS analysis revealed that the regions functionally connected to the hippocampus during retrieval did not differentiate specific from general AM retrieval, which confirms our earlier univariate analysis indicating that some aspects of the memory retrieval network are shared by these memories.

Adult↗
PubMed2006

Mapping anatomical correlations across cerebral cortex (MACACC) using cortical thickness from MRI.

We introduce MACACC-Mapping Anatomical Correlations Across Cerebral Cortex-to study correlated changes within and across different cortical networks. The principal topic of investigation is whether the thickness of one area of the cortex changes in a statistically correlated fashion with changes in thickness of other cortical regions. We further extend these methods by introducing techniques to test whether different population groupings exhibit significantly varying MACACC patterns. The methods are described in detail and applied to a normal childhood development population (n = 292), and show that association cortices have the highest correlation strengths. Taking Brodmann Area (BA) 44 as a seed region revealed MACACC patterns strikingly similar to tractography maps obtained from diffusion tensor imaging. Furthermore, the MACACC map of BA 44 changed with age, older subjects featuring tighter correlations with BA 44 in the anterior portions of the superior temporal gyri. Lastly, IQ-dependent MACACC differences were investigated, revealing steeper correlations between BA 44 and multiple frontal and parietal regions for the higher IQ group, most significantly (t = 4.0) in the anterior cingulate.

Adolescent↗
PubMed2006

Progressive grey matter atrophy over the first 2-3 years of illness in first-episode schizophrenia: a tensor-based morphometry study.

Little is known about the structural brain changes that occur over the first few years of schizophrenia, or how these changes differ from those associated with healthy brain development in adolescence and early adulthood. In this study, we aimed to identify regional differences in grey matter (GM) volume between patients with first-episode schizophrenia (FES) and matched healthy controls, both at the time of the patients' first psychotic episode (baseline condition) and 2-3 years subsequently (follow-up condition). Forty-one patients with FES and 47 matched healthy controls underwent a T1-weighted structural MRI scan. Of these participants, 25 FES patients and 26 controls returned 2-3 years later for a follow-up scan. Voxel-based morphometry in SPM2 was used to identify the regions of GM difference between the groups in the baseline condition, while tensor-based morphometry was used to identify the longitudinal change within subject over the follow-up interval. The FES patients exhibited widespread GM reductions in the frontal, parietal, and temporal cortices and cerebellum in the baseline condition, as well as more circumscribed regions of GM increase, particularly in the occipital lobe. Furthermore, the FES subjects were observed to lose considerably more GM over the follow-up interval than the controls, especially in the parietal and temporal cortices. We argue that the progressive GM atrophy we have found to be associated with the onset of schizophrenia arises from a dysfunction in the dramatic period of healthy brain development typically associated with adolescence.

Adolescent↗
PubMed2006

A simulation model for the study of the within-animal infection dynamics of E. coli O157.

Escherichia coli 0157 can cause serious illness, even death, in humans. There is some consensus that the main reservoirs of this harmful bacterium are the rumens and intestines of cattle. Hence, a stochastic model of the bovine gut was developed to investigate the in vivo population dynamics of E. coli O157. Because bacterial numbers can reach minimal levels, a stochastic system was considered, with a birth-death process being used to represent bacterial growth and decay dynamics throughout the gastrointestinal tract. Reinfection through ingestion of bacteria present in the environment was allowed to occur and the required clustered distribution of inter-event times was implemented through the use of a random hazard doubly stochastic Poisson process. Due to the inclusion of multiple compartments, a feedback mechanism and an interest in the non-equilibrium dynamics of the process, it was not possible to obtain an analytical representation of the process and therefore, a simulation study was used to obtain results. The within-animal model can be used to explore the efficacy of control measures which act at an individual animal level.

Animals↗
PubMed1990

Analysis of the kinetic hairpin transfer model for parvoviral DNA replication.

All linear DNA molecules face special problems in replicating their 5' ends, as DNA polymerases add nucleotides only to pre-existing strands with free 3'-OH groups. Parvoviruses, a group of small animal viruses with a linear single-stranded DNA genome, cope with this problem by having palindromic terminal sequences that can fold back on themselves to form hairpin structures essential in priming DNA replication. The 3' terminal sequence that initiates replication becomes reversed in orientation during the process, and if the palindrome is imperfect, two different, reverse-complementary terminal sequences are generated. The relative abundances of the terminal sequence orientations at each end of the DNA molecules can be measured and give information about the replication process. From such clues, we developed a "kinetic hairpin transfer model" based on differential rates of hairpin formation and inversion processes depending on the conformations of the 3' termini. Numerical studies showed that this simple idea can account for the diverse pattern of DNA distributions observed in the family Parvoviridae. In this paper, we simplify the model to a set of coupled linear first-order ordinary differential equations in order to delineate its essential properties by Perron-Frobenius theory. Secondly, we examine our assumption of linear kinetics by modeling enzyme catalysis of the component steps of the hairpin transfer process. We show that the rate-determining step of the process is the binding of initiation complex to the self-priming hairpin structures. Furthermore, we find that if the replication machinery is saturated by DNA substrate late in an infection, the differential equations become non-linear but the steady-state DNA distribution is still given by the solution of our original linear equations.

Computer Simulation↗
PubMed1995

Comparison of simulated and in-vivo plasma levels of cilastatin following intravenous in-line drug administration.

The primary objective of this work was to establish a method to simulate the plasma levels of cilastatin, a model drug, following an intravenous in-line delivery scheme. In-vivo data in dogs obtained from this work were used to demonstrate the validity of the proposed approach. The in-line drug delivery system consists of a drug containing device which is placed between a large volume parenteral and a patient. Numerous advantages have been identified for this automatic in-line reconstitution delivery system. The numerical convolution integral algorithm was used in this work to perform plasma profile simulation. The results indicated that the simulated cilastatin plasma profile following in-line delivery closely agreed with the in-vivo data.

Animals↗
PubMed2005

Ventilatory and hemodynamic changes during retroperitoneal and transperitoneal laparoscopic nephrectomy: a prospective real-time comparison.

PURPOSE: Nephrectomies are currently performed via the transperitoneal or retroperitoneal laparoscopic approach. We compared the ventilatory and hemodynamic effects of these approaches. MATERIALS AND METHODS: After institutional ethics committee approval was obtained patients requiring nephrectomy in a 9-month period were prospectively allocated to the retroperitoneal (24) or transperitoneal (15) approach. All were initially ventilated in the volume controlled mode (10 ml kg tidal volume). Intraoperative fingertip, pulse derived arterial oxygen saturation less than 97%, end tidal CO2 partial pressure greater than 40 mm Hg and peak inspiratory pressure greater than 36 cm H2O necessitated changes in ventilatory parameters, as deemed necessary by the anesthetist. If tidal volume decreased greater than 25% of baseline, pressure controlled ventilation was begun instead. RESULTS: Peak inspiratory and plateau pressures increased for the transperitoneal approach by approximately 30% more than in the retroperitoneal group (p <0.05). Volume controlled ventilation was changed to pressure controlled ventilation in 8 transperitoneal vs zero retroperitoneal cases (p <0.05). Heart rate, and systolic and diastolic blood pressure increased by approximately 13% more in the transperitoneal than in the retroperitoneal group (p <0.05). CONCLUSIONS: Nephrectomy via the retroperitoneal laparoscopic approach interferes with ventilatory and hemodynamic functions less than nephrectomy via the transperitoneal approach.

Adult↗
PubMed2004

Integration of outer hair cell activity in a one-dimensional cochlear model.

Recently, significant progress has been made in understanding the contribution of the mammalian cochlear outer hair cells (OHCs) to normal auditory signal processing. In the present paper an outer hair cell model is incorporated in a complete, time-domain, one-dimensional cochlear model. The two models control each other through cochlear partition movement and pressure. An OHC gain (gamma) is defined to indicate the outer hair cell contribution at each location along the cochlear partition. Its value ranges from 0 to 1: gamma=0 represents a cochlea with no active OHCs, gamma=1 represents a nonrealistic cochlea that becomes unstable at resonance frequencies, and gamma=0.5 represents an ideal cochlea. The model simulations reveal typical normal and abnormal excitation patterns according to the value of gamma. The model output is used to estimate normal and hearing-impairment audiograms. High frequency loss is predicted by the model, when the OHC gain is relatively small at the basal part of the cochlear partition. The model predicts phonal trauma audiograms, when the OHC gain is random along the cochlear partition. A maximum threshold shift of about 60 dB is obtained at 4 kHz.

Animals↗
PubMedDate not supplied

Improvement of decisions regarding hemodialysis patients by urea kinetic modeling.

The potentials for improving decisions about adequacy of dialysis (AD) and daily protein intake (DPI) by urea kinetic modeling (UKM) were examined. Four nephrologists evaluated AD, DPI, and metabolic stability in 62 patients. UKM was done three times; but the results were not revealed. Clinicians' decisions were then compared with UKM measures of effective dialysis (Kt/V) and protein catabolic rate (pcr). Detection of inadequately treated patients by the clinicians was poor (28%, Kt/V less than 1.0; and 40%, Kt/V less than 0.9). Specificities of the clinicians' decisions were 0.96 and 0.92, respectively. Combining pcr and consensus decisions, 59 patients could be assigned a probable DPI. Using this as "gold standard," the average clinician detected 77% of 13 low DPIs. Single or triple pcr determinations alone detected 77% or 62%, respectively. Specificities were 0.91, 0.85, and 1.0. Simulated decision making suggested that combining pcr with clinical evaluation in a logical way would lead to detection of most patients with low DPI. Qualitative data from individual patient cases causing controversies are presented and discussed. It is concluded the UKM should be used routinely to assess the adequacy of dialysis and daily protein intake.

Adult↗
PubMed2005

Automated generation of heuristics for biological sequence comparison.

BACKGROUND: Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. We introduce bounded sparse dynamic programming (BSDP) to allow rapid approximation to exhaustive alignment. This is used within a framework whereby the alignment algorithms are described in terms of their underlying model, to allow automated development of efficient heuristic implementations which may be applied to a general set of sequence comparison problems. RESULTS: The speed and accuracy of this approach compares favourably with existing methods. Examples of its use in the context of genome annotation are given. CONCLUSIONS: This system allows rapid implementation of heuristics approximating to many complex alignment models, and has been incorporated into the freely available sequence alignment program, exonerate.

Algorithms↗
PubMed2002

[A 3D FEM model for calculation of electromagnetic fields in transmagnetic stimulation].

We developed a realistic finite elements method (FEM) model of the brain for the calculation of electromagnetic fields in transcranial magnetic stimulation (TMS). A focal butterfly stimulation coil was X-rayed, parameterized, and modeled. The magnetic field components of the TMS coil were calculated and compared for validation to pointwise measurements of the magnetic fields with a Hall sensor. We found a mean deviation of 7.4% at an axial distance of 20 mm to the coil. A 3D brain model with the biological tissues of white and gray matter, bone, and cerebrospinal fluid was developed. At a current sweep of 1000 A in 120 microseconds, the maximum induced current density in gray matter was 177 mA/m2 and the strongest electric field gradient covered an area of 40 mm x 53 mm.

Brain↗
PubMed2004

Analysis of the estimators of the average coefficient of dominance of deleterious mutations.

We investigate the sources of bias that affect the most commonly used methods of estimation of the average degree of dominance (h) of deleterious mutations, focusing on estimates from segregating populations. The main emphasis is on the effect of the finite size of the populations, but other sources of bias are also considered. Using diffusion approximations to the distribution of gene frequencies in finite populations as well as stochastic simulations, we assess the behavior of the estimators obtained from populations at mutation-selection-drift balance under different mutational scenarios and compare averages of h for newly arisen and segregating mutations. Because of genetic drift, the inferences concerning newly arisen mutations based on the mutation-selection balance theory can have substantial upward bias depending upon the distribution of h. In addition, estimates usually refer to h weighted by the homozygous deleterious effect in different ways, so that inferences are complicated when these two variables are negatively correlated. Due to both sources of bias, the widely used regression of heterozygous on homozygous means underestimates the arithmetic mean of h for segregating mutations, in contrast to their repeatedly assumed equality in the literature. We conclude that none of the estimators from segregating populations provides, under general conditions, a useful tool to ascertain the properties of the degree of dominance, either for segregating or for newly arisen deleterious mutations. Direct estimates of the average h from mutation-accumulation experiments are shown to suffer some bias caused by purging selection but, because they do not require assumptions on the causes maintaining segregating variation, they appear to give a more reliable average dominance for newly arisen mutations.

Computer Simulation↗
PubMed2002

[A method for worst-case study of coupling between medical equipment].

The increasing use of electronic devices in operating theatres and intensive-care units leads to possible interactions of such devices and consequently to serious immunity problems. This paper presents a numerical near field worst-case-study of the coupling between coagulators and ECG devices under consideration of the human body. For this purpose a special body model has been developed which meets the geometrical dimensions given in DIN 33402 part 2. The model's electrical properties correspond to a weighted average of those of different tissues of the human body. Different parameters (coagulation frequency, positions of electrodes, etc.) are considered.

Adult↗
PubMed2002

Pre and post 3D modeling of scoliotic patients operated with in situ contouring technique.

A three-dimensional segmental analysis was performed on the stereoradiographic reconstructions of ten right thoracic scoliotic patients. From the quantitative model of the spine and pelvis, the vertebral and intervertebral orientations were computed pre and post operatively. These orientations allow to determine the apical and junctional zones of the high thoracic, thoracic and lumbar curves. The apical zone corresponds to the maximum of vertebral axial rotation. Pre operatively, the tendency was T7 for the thoracic transverse apex with 20 AE of axial rotation. The junctional zone corresponds to the maximum of vertebral lateral rotation and the maximum of intervertebral axial rotation. The tendency was T5 and T12 for the junctional vertebrae of the thoracic curve with, at both levels, 30 AE of vertebral lateral rotation and 10 AE of intervertebral axial rotation. The surgical correction obtained by in situ contouring technique was evaluated through these 3D orientations. The vertebral axial rotation at the high thoracic, thoracic and lumbar apex was corrected with respectively 52%, 60% and 60%.

Adolescent↗
PubMed2006

MR imaging anatomy in neurodegeneration: a robust volumetric parcellation method of the frontal lobe gyri with quantitative validation in patients with dementia.

BACKGROUND AND PURPOSE: Brain volumetry is widely used for evaluating tissue degeneration; however, the parcellation methods are rarely validated and use arbitrary planes to mark boundaries of brain regions. The goal of this study was to develop, validate, and apply an MR imaging tracing method for the parcellation of 3 major gyri of the frontal lobe, which uses only local landmarks intrinsic to the structures of interest, without the need for global reorientation or the use of dividing planes or lines. METHODS: Studies were performed on 25 subjects--healthy controls and subjects diagnosed with Lewy body dementia and Alzheimer disease--with significant variation in the underlying gyral anatomy and state of atrophy. The protocol was evaluated by using multiple observers tracing scans of subjects diagnosed with neurodegenerative disease and those aging normally, and the results were compared by spatial overlap agreement. To confirm the results, observers marked the same locations in different brains. We illustrated the variabilities of the key boundaries that pose the greatest challenge to defining consistent parcellations across subjects. RESULTS: The resulting gyral volumes were evaluated, and their consistency across raters was used as an additional assessment of the validity of our marking method. The agreement on a scale of 0-1 was found to be 0.83 spatial and 0.90 volumetric for the same rater and 0.85 spatial and 0.90 volumetric for 2 different raters. The results revealed that the protocol remained consistent across different neurodegenerative conditions. CONCLUSION: Our method provides a simple and reliable way for the volumetric evaluation of frontal lobe neurodegeneration and can be used as a resource for larger comparative studies as well as a validation procedure of automated algorithms.

Aged↗