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PubMed2004

An accurate and robust method for unsupervised assessment of abdominal fat by MRI.

PURPOSE: To describe and evaluate an automatic and unsupervised method for assessing the quantity and distribution of abdominal adipose tissue by MRI. MATERIAL AND METHODS: A total of 20 patients underwent whole-abdomen MRI. A total of 32 transverse T1-weighted images were acquired from each subject. The data collected were transferred to a dedicated workstation and analyzed by both our unsupervised method and a manual procedure. The proposed methodology allows the automatic processing of MRI axial images, segmenting the adipose tissue by fuzzy clustering approach. The use of an active contour algorithm on image masks provided by the fuzzy clustering algorithm allows the separation of subcutaneous fat from visceral fat. Finally, an automated procedure based on automatic image histogram analysis identifies the visceral fat. RESULTS: The accuracy, reproducibility, and speed of our automatic method were compared with the state-of-the-art manual approach. The unsupervised analysis correlated well with the manual analysis, and was significantly faster than manual tracing. Moreover, the unsupervised method was not affected by intraobserver and interobserver variability. CONCLUSION: The results obtained demonstrate that the proposed method can provide the volume of subcutaneous adipose tissue, visceral adipose tissue, global adipose tissue, and the ratio between subcutaneous and visceral fat in an unsupervised and effective manner.

Abdominal Cavity↗
PubMed2005

Tracking motor unit action potentials in the tibialis anterior during fatigue.

New surface electromyogram (SEMG) techniques offer the potential to advance knowledge of healthy and diseased motor units. Conduction velocity (CV) estimates, obtained from indwelling electrodes, may provide diagnostic information, but the standard method of CV estimation from SEMG may be of only limited value. We developed a motor unit (MU) tracking algorithm to extract motor unit conduction velocity (MUCV) and motor unit action potential (MUAP) amplitude estimates from SEMG. The technique is designed to provide a noninvasive means of accessing fatigue and recruitment behavior of individual MUs. We have applied this MU tracking algorithm to SEMG data recorded during isometric fatiguing contractions of the tibialis anterior (TA) muscle in nine healthy subjects, at 30%-40% maximum voluntary contraction (MVC). The results reveal that MUCVs and MUAP amplitudes of individual MUs can be estimated and tracked across time. Time-related changes in the MU population may also be monitored. Thus, the SEMG technique employed provides insight into the behavior of the underlying muscle at the MU level by noninvasive means.

Action Potentials↗
PubMedDate not supplied

The map comparison problem: tests for the overlap of geographic boundaries.

The quality of environmental studies is often compromised by the use of statistics, such as correlation and regression for example, which presuppose a statistical model, linear or otherwise, between two variables. When investigating hypotheses about relationships among geographically distributed variables, an alternative approach is to measure the amount of boundary overlap. Boundaries are geographic zones of rapid change in the intensity of a variable, and are often of scientific interest in their own right. Examples of boundaries include ecotones, genetic hybrid zones, pollution plumes, and the front of the wave of advance of an epidemic. Boundary overlap describes zones where boundaries from two or more variables coincide, and are useful for evaluating epidemiologic hypotheses relating health to environmental exposures. This paper proposes four statistics of boundary overlap, and explores their performance using simulation models and real data describing ozone concentrations and hospital admissions for respiratory conditions. The statistics are found sensitive to different aspects of boundary overlap, and provide an additional diagnostic tool in the analysis of geographically distributed variables. Overlap statistics are expected to come into increasing use as the installed base of geographic information systems increases.

Air Pollution↗
PubMed2001

Sensitivity of Deinococcus radiodurans to gamma-irradiation: a novel approach by Fourier transform infrared spectroscopy.

Deinococcus radiodurans is a red-pigmented coccus known to be particularly resistant to both chemical and radiative agents. Fourier transform infrared (FT-IR) spectroscopy was used as a convenient and easy-to-run method to monitor damage induced in this bacterium by ionizing radiations. First, stationary-phase cultures were submitted to increasing doses of gamma-irradiation ((137)Cs source). Beyond a threshold of 11 kGy, striking changes occurred in spectra of irradiated samples compared with unirradiated ones, especially in the 1750-900 cm(-1) region, which is spectroscopically assigned to amide I and II components, nucleotide bases, the phosphodiester backbone, and the sugar ring. Second, bacterial cultures were postirradiation reincubated. After a reincubation time of 15 h, the oxidative stress was in part overwhelmed, and the growth of D. radiodurans again occurred, although some biocellular components remained altered. Consequently, FT-IR analysis is an accurate means to rapidly visualize biomolecular changes undergone by cells both after gamma-irradiation and during the repair mechanism.

Algorithms↗
PubMed2002

Effective diameters for collisions of fractal-like aggregates: recommendations for improved aerosol coagulation frequency predictions.

Fractal-like aggregate (FA-) drag has been previously calculated/correlated/reported, but "mobility diameter" information is not sufficient to make rational calculations of Brownian coagulation rates (for, say, population-balance modeling). Indeed, until now, only conjectures about gyration-radius scaling behavior have been used to predict FA-FA collision cross sections! But such "scaling relations" are untrustworthy even for FA momentum-, energy-, and mass-transfer purposes, and improved FA-collision rate constants (appearing as "kernels" in the coagulation balance integro-PDE) are overdue. Our premise is that FA collision rates in the free-molecule regime can be predicted using a gas-kinetic type formulation. If (a) carrier gas mean free path and FA persistence length are much larger than any characteristic FA size, (b) FA number density is low, (c) FA velocity and position are uncorrelated, and (d) there is a "hard-sphere" interaction between primary particles of different FAs, such a theory is developed/applied here. We introduce an effective collision diameter, , depending on the geometries of the two participating FAs. Quasi-MC calculations are reported for large ensembles of pairs of FAs, each computer-generated using a tunable cluster-cluster (CC)-algorithm. Our results differ from frequently used theoretical estimates based only on FA gyration (or mobility) radii and D(f). They also confirm that, if the size disparity of the colliding FAs is large, obtained by simply assigning individual diameters to each FA are significantly overestimated. Modified collision rate expressions for FA-coagulation modeling are suggested.

Journal Article↗
PubMed1996

A global taxonomy of loops in globular proteins.

A bank of loops from three to eight amino acid residues long has been constituted. On the basis of statistical analysis of occurrences of conformations and residue, loops could be divided into two parts: the side residues directly bonded to the secondary structure flanking element, and the inner part. The conformations of the side residues are correlated to the nature of their neighboring flanks, while the inner residues adopt conformations uncorrelated from one residue to the next; thus they are unrelated to the flanks. Two zones in the Ramachandran plot are important: alpha L and beta P. In particular, the high occurrence of alpha L, mainly occupied by glycine residues, is necessary to induce flexibility and thus allow loops to comply with the geometrical constraints of the flanks. An algorithm of clustering has been used to aggregate loops of the same length within families of similar 3D structures. At each position in each cluster, sequence and conformational signatures have been deduced if the occurrence of a residue (or a conformation) is higher than an equiprobable distribution over all clusters. The result is that some positions favor particular amino acids and conformations, which are typical of a cluster although not unique. This is an indication of a relation between structure and sequence in loops. A taxonomy is proposed that classifies the various clusters. It relies on two terms: the mean distance between the first and last C alpha in one cluster and, perpendicular to this line, the distance to the center of gravity of the cluster. It is noteworthy that the differently populated clusters represented in such 2D plots can be separated. Thus, although the conformations of loops in globular proteins could cover a continuum, it has been possible to cluster them into a limited number of well populated families and superfamilies. This basic feature of protein architecture could be further exploited to better predict their geometry.

Amino Acids↗
PubMed1999

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

We report the tertiary structure predictions for 95 proteins ranging in size from 17 to 160 residues starting from known secondary structure. Predictions are obtained from global minimization of an empirical potential function followed by the application of a refined atomic overlap potential. The minimization strategy employed represents a variant of the Monte Carlo plus minimization scheme of Li and Scheraga applied to a reduced model of the protein chain. For all of the cases except beta-proteins larger than 75 residues, a native-like structure, usually 4-6 A root-mean-square deviation from the native, is located. For beta-proteins larger than 75 residues, the energy gap between native-like structures and the lowest energy structures produced in the simulation is large, so that low RMSD structures are not generated starting from an unfolded state. This is attributed to the lack of an explicit hydrogen bond term in the potential function, which we hypothesize is necessary to stabilize large assemblies of beta-strands.

Algorithms↗
PubMed2000

Correlator beware: correlation has limited selectivity for fMRI data analysis.

Groups of time-courses created from fMRI data by the frequently used correlation analysis are often highly heterogeneous. This heterogeneity is due to the limited selectivity of correlation when trying to match brain time-courses to an externally imposed activation paradigm. Thus, this process unnecessarily generates many type I errors (false positives). Furthermore, as a consequence of the heterogeneity, time-courses identified and grouped by correlation may in fact describe different activations. After demonstrating this inadequacy, we give one particular approach to partition such a heterogeneous group into internally more homogeneous subgroups, using Kendall's coefficient of concordance W, and show its applicability and application to both simulated and in vivo data. Such group partition and "purification" will help subsequent inferential methods to deal more efficiently with false positives.

Algorithms↗
PubMed2004

Genetic diversity amongst landraces of a dioecious vegetatively propagated plant, betelvine (Piper betle L.).

Betelvine (Piper betle L., family Piperaceae) is an important, traditional and widely cultivated crop of India. The cultivators and consumers recognize more than 100 cultivars (landraces) based on regional and organoleptic considerations, while in terms of phytochemical constituents only five groups have been identified for all the landraces. Since betelvine is an obligate vegetatively propagated species, genomic changes, if any, may have become 'fixed' in the landraces. We carried out random amplified polymorphic DNA (RAPD) analysis in several landraces considered in four groups, namely, 'Kapoori', 'Bangla', 'Sanchi' and 'Others' in order to ascertain their genetic diversity. On the basis of the data from eleven RAPD primers, we distinguished genetic variation within and among the four groups of landraces. The results indicate the 'Kapoori' group is the most diverse. The neighbour joining (NJ) tree after a bootstrap (500 replicate) test of robustness clearly shows the four groups to be well separated. Interestingly, all known male or female betelvine landraces have separated in the NJ tree indicating an apparent gender-based distinction among the betelvines.

Algorithms↗
PubMed1989

The effects of prolonged opioidergic blockade on LH pulsatile secretion during the menstrual cycle.

Although considerable evidence points towards a pivotal role for the endogenous opioid peptides (EOP) in the neuroendocrine regulation of GnRH-LH secretion, the effects of prolonged opioidergic blockade on LH pulsatile activity during the menstrual cycle have not been thoroughly investigated. Accordingly, 10 women in the early follicular phase (EFP, days 3 and 4), 10 women in the late follicular phase (LFP, days 9 to 13) and 7 women in the midluteal phase (MLP, days 6 to 8 after LH surge) were studied on two consecutive days before and during opioidergic blockade imposed by an opiate receptor antagonist, naloxone. Blood samples were obtained at 15 min intervals for 8 h during saline (150 mmol/l at 50 ml/h) or naloxone (30 micrograms/kg/h) infusions. Furthermore, sequential 24-h infusions of saline or naloxone (30 micrograms/kg/h) were performed in 6 other women (two each in the EFP, LFP, and MLP). LH hormone series were analyzed for significant pulses by the Cluster pulse algorithm. While 8-h naloxone infusions did not change any of the LH pulse characteristics (frequency, amplitude, transverse mean, duration) in the EFP, they elevated significantly (p less than 0.05) the LH pulse frequencies, pulse amplitudes and transverse mean levels in the LFP. In the MLP, the LH pulse amplitudes were significantly (p less than 0.05) increased, but pulse frequencies and transverse mean levels remained unchanged. While the 24-h naloxone infusions did not alter any of the pulse characteristics in the EFP, they elicited a robust increase in LH pulsatile activity in the LFP, composed of a progressive rise in LH pulse amplitudes and transverse mean levels.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2001

Multi-element sewer slime impact pattern--a quantitative characteristic enabling identification of the source of heavy metal discharges into sewer systems.

The capability of sewer slime to accumulate heavy metals from municipal wastewater can be exploited to identify the sources of sewage sludge pollution. Former investigations of sewer slime looked for a few elements only and could, therefore, not account for deviations of the enrichment efficiency of the slime or for irregularities from sampling. Results of ICP-MS multi element determinations were analyzed by multivariate statistical methods. A new dimensionless characteristic "sewer slime impact" is proposed, which is zero for unloaded samples. Patterns expressed in this data format specifically extract the information required to identify the type of pollution and polluter quicker and with less effort and cost than hitherto.

Algorithms↗
PubMed1990

P-A-I-N reviews.

Explore the source record for details and available documents.

Algorithms↗
PubMed1991

Covering events in eigenimages of biomolecules.

Multivariate statistical analysis of a large set of micrographs of biological macromolecules involves the computation of eigenimages representing principal features, on the basis of which similar views of the complexes can be grouped. It is not generally clear what these eigenimages represent physically and which ones should be used in the classification process. In this paper, hierarchical maximum entropy discretisation and event covering are used to (1) detect statistically significant relationships in the eigenimages, (2) select the most relevant eigenimages for classifying biomolecular projections, and (3) build a prototype of the biomolecular complex under study.

Algorithms↗
PubMed2005

Macroergonomics: analysis and design of work systems.

Attending to the larger system components such as organizational design and management is not novel for ergonomists. In Europe, there has been a strong tradition to investigate ergonomic problems within a holistic, systems context. "Macroergonomics" builds upon this tradition by providing specific methods and tools that yield large-scale results. It is believed that meaningful and large-scale results are needed in today's competitive and turbulent work environments. Macroergonomics is defined, its history is uncovered and focus is given to a key methodology, macroergonomic analysis and design. Case studies are used to validate the method and illustrate that performance results in the 60-90% range can be expected.

Algorithms↗
PubMed2006

Novel technology for rapid species-specific detection of Bacillus spores.

There is an urgent need for a small, inexpensive sensor that can rapidly detect bio-warfare agents with high specificity. Bacillus anthracis, the causative agent of anthrax, would be a perilous disease-causing organism in the event of a release. Currently, most anthrax detection research is based on nucleic acid detection, immunoassays and mass spectrometry, with few detection levels reported below 10(5) spores. Here, we show the ability to distinguish Bacillus spores to a level approaching 10(3) spores, below the reported median infectious dose of B. anthracis, using pyrolysis--micromachined differential mobility spectrometry and novel pattern recognition algorithms that combine lead cluster mapping with genetic algorithms.

Algorithms↗
PubMedDate not supplied

Information maximization for exploring neural coding in hippocampus and lateral septum.

A central problem in neural coding is to understand what are the features of the stimulus that are encoded by the neural activity. Assuming that neuronal coding is optimized for information transmission, we can use mutual information maximization for extracting the relevant features encoded in certain activity patterns. We show that this algorithm can be successfully applied to the study of different encoding strategies for location and direction of movement in hippocampal and lateral septal cells. Using this approach, we find that in lateral septum, a significant amount of information about location can be encoded in patterns that are not place-fields.

Algorithms↗
PubMed2005

Classification of carotid artery Doppler signals in the early phase of atherosclerosis using complex-valued artificial neural network.

In this study, carotid arterial Doppler ultrasound signals were acquired from left carotid arteries of 38 patients and 40 healthy volunteers. The patient group had an established diagnosis of the early phase of atherosclerosis through coronary or aortofemoropopliteal angiographies. Results were classified using complex-valued artificial neural network (CVANN). Principal component analysis (PCA) and fuzzy c-means clustering (FCM) algorithm were used to make a CVANN system more effective. For this aim, before classifying with CVANN, PCA method was used for feature extraction in PCA-CVANN architecture and FCM algorithm was used for data set reduction in FCM-CVANN architecture. Training and test data were selected randomly using 10-fold cross validation. PCA-CVANN and FCM-CVANN architectures classified healthy and unhealthy subjects for training and test data with about 100% correct classification rate. These results shown that PCA-CVANN and FCM-CVANN classified Doppler signals successfully.

Adult↗