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PubMed1985

Folding patterns of porin and bacteriorhodopsin.

Porin spans the outer membrane of Escherichia coli with most of the protein embedded within the membrane. It lacks pronounced hydrophobic domains and consists predominantly of beta-pleated sheet. These observations require the accommodation of polar and ionizable residues in an environment that has a low dielectric constant. Owing to a currently limited understanding of the constraints governing membrane protein structure, a minimal approach to structure prediction is proposed that identifies segments causing polypeptides to reverse their direction (turn identification). The application of this procedure avoids hydrophobicity parameters and yields a model of porin which is in good agreement with all experimental data available. The presence of polar and ionizable residues within membrane boundaries implies a dense (saturating) network of hydrogen bond donor and acceptor groups. Application to a paradigm of hydrophobic membrane proteins, bacteriorhodopsin, reveals a pattern consistent with its alpha-helical folding. The postulated structure includes significantly more polar residues in the membrane domain than have been assumed previously, suggesting that there are also hydrogen bonding networks in bacteriorhodopsin. Extensive networks permeating protein interior and surfaces would explain the extraordinary stability and the tight interactions between functional units in the formation of crystalline arrays of both proteins.

Bacterial Outer Membrane Proteins↗
PubMed1995

Identification of a low-risk group of stage I breast cancer patients by cytometrically assessed DNA and nuclear texture parameters.

Image cytometrical measurements were performed on Feulgen-stained cells from 329 stage I breast cancers (pT1pN0,M0,R0). For each patient, several DNA (ploidy, S-phase fraction, exceeding rates, 2c deviation index, ploidy balance, entropy, and histogram typing), morphometric (area and radius of nuclei), and textural parameters (mainly co-occurrence and run-length) were calculated. The prognostic value of these parameters was investigated by multivariate Cox regression analysis, considering a distant recurrence-free survival of 8 years as the prognostic criterion. In the multivariate analysis, one DNA parameter (histogram type) and two textural parameters (co-occurrence and variation of the average heterochromatin area) were proven to have independent prognostic value. Using a linear combination of these variables, a prognostic factor was calculated for each individual patient. Patients were stratified using this factor into several groups according to their risk for distant recurrence. Thus, a low-risk group of stage I patients was identified, remaining distant recurrence-free for 8 years. In addition, a group of patients with a worse prognosis and an 8-year recurrence rate of about 26 per cent was identified, compared with the average distant recurrence rate of all stage I patients of 13 per cent. A combination of DNA and textural parameters can provide powerful prognostic information in stage I breast carcinomas and may allow a better selection of patients for different therapy protocols.

Adult↗
PubMed2000

Identifying predator-prey processes from time-series.

The functional response is a key element in predator-prey models as well as in food chains and food webs. Classical models consider it as a function of prey abundance only. However, many mechanisms can lead to predator dependence, and there is increasing evidence for the importance of this dependence. Identification of the mathematical form of the functional response from real data is therefore a challenging task. In this paper we apply model-fitting to test if typical ecological predator-prey time series data, which contain both observation error and process error, can give some information about the form of the functional response. Working with artificial data (for which the functional response is known) we will show that with moderate noise levels, identification of the model that generated the data is possible. However, the noise levels prevailing in real ecological time-series can give rise to wrong identifications. We will also discuss the quality of parameter estimation by fitting differential equations to such time-series.

Algorithms↗
PubMed1989

Fitting genetic models with LISREL: hypothesis testing.

A brief introduction to the mathematical theory involved in model fitting is provided. The properties of maximum-likelihood estimates are described, and their advantages in fitting structural models are given. Identification of models is considered. Standard errors of parameter estimates are compared with the use of likelihood-ratio (L-R) statistics. For structural modeling, L-R tests are invariant to parameter transformation and give robust tests of significance. Some guidelines for fitting models to data collected from twins are given, with discussion of the relative merits of parsimony and data description.

Computer Simulation↗
PubMed1994

Determining appropriate models for joint control using surface electrical stimulation of soleus in spinal cord injury.

The mechanical impedance of the ankle joint during electrical stimulation of the soleus is studied by applying constant-velocity 10 degrees angular perturbations to the ankle and measuring the resultant torque. Both neurologically intact subjects and spinal cord injured subjects are tested. Lumped, piecewise linear models are developed to predict the torque from the measured displacement and acceleration signals. The commonly used second-order mass-spring-dashpot model fails to predict the changes in torque that occur following imposed movements. A five-element, directionally-dependent piecewise linear model is much better at predicting the measured responses for velocities up to 50 degrees s-1. Numerical least squared error identification techniques are used to estimate the model parameters for three neurologically intact and three spinal cord injured subjects. The average error between the model's response and the measured response across all subjects is 10.9%. There is some evidence that a velocity-dependent non-linear model could produce better results than the directionally-dependent piecewise linear model.

Ankle Joint↗
PubMed1998

Evaluation of nuclide renal dynamic image in diagnosing diabetic nephropathy.

Twenty non-insulin dependent diabetics were given nuclide renal dynamic image examination to investigate its significance in the diagnosis of diabetic nephropathy (DNP). The results showed that 1) the glomerular filtration was hyperfunctioned in the diabetics with less than 5 years course, whereas it was impaired in the diabetics with over 5 years course and 2) nuclide renal dynamic image could reveal the glomerular hyperfiltration without beta 2-microglobulinuria or microalbuminuria, suggesting that it is superior to the clinical biochemical parameters in the diagnosis, especially in the early identification of DNP.

Diabetes Mellitus, Type 2↗
PubMedDate not supplied

A report of the U.S. Environmental Protection Agency Gene-Tox Program. Evaluation of mutagenicity assays for purposes of genetic risk assessment.

For the vast majority of chemicals, mammalian germ-line (MG) mutation data do not exist. The question was examined of how best to utilize results of non-MG genotoxicity assays that are included in the Gene-Tox data base to provide information of the likelihood that genetic damage might be induced in and transmitted by the reproductive cells of exposed human beings. Two approaches were used to assess the relative value of different assays for genetic hazard identification. (1) Test results were weighted according to parameters by which conditions of an assay resemble those encountered in the potential induction of transmitted genetic damage in mammals. For this purpose, 35 assays were grouped into 16 categories that were assigned weights ranging from 1 to 15; there were 2367 chemicals in the data base. This system was evaluated by comparing the sum of weighted test results for each chemical with the outcome of MG-standard (MGst) tests where such had been reported. (MGst tests used were the specific-locus and heritable-translocation assays [SLT and HTT] for gene mutations and chromosome aberrations, respectively.) The weighting system produced a few false positives with respect to the MGst results. It produced no false negatives, but the available evidence is limited by the circumstance that MGst test have evidently been preferentially performed with chemicals that had already been shown to be positive in several other assays. (2) Findings from each MGst test were compared with those from each of the other assays in turn, provided that at least 10 chemicals had been tested in both of the assays. There were 11 such comparisons involving the SLT, and 14 such comparisons involving the HTT. The observed concordance was above random expectation in several comparisons, particularly those involving certain mammalian in vivo tests, but in only one case (HTT vs. unscheduled DNA synthesis in the testis) did the degree of elevation approach statistical significance.

Animals↗
PubMed2004

Comparison of equations describing band broadening in high-performance liquid chromatography.

Several models are well established that describe band broadening in gas and liquid chromatography, including those due to Van Deemter and Knox. Comparison of competing models is complicated if raw data are noisy or if the equations to be fitted to data contain many adjustable parameters. This paper describes a comparison of fitting the Van Deemter, Knox and other equations to low noise data gathered during the separation of propyl- and methylparaben by HPLC. Equations are compared using established statistical methods, including analysis of residuals, inference of parameter estimates and Akaikes Information Criterion for model identification. This work indicates that equations that account for non-linear band broadening at elevated mobile phase velocities are more successful at describing the relationship between height equivalent to a theoretical plate, H, and the velocity of the mobile phase, u.

Chromatography, High Pressure Liquid↗
PubMed2004

Evaluation of 1,3-butadiene dimerization and secondary reactions in the presence and absence of oxygen.

Thermal stability evaluation of exothermic chemical reactions is of great importance to the safer design and operation of chemical processes. Dominant reaction stoichiometries and their thermochemistry parameters are key elements in the evaluation process. Identification of significant reaction pathways under possible process conditions will lead to an understanding of the overall thermodynamic and kinetic behavior. The kinetics of 1,3-butadiene (BD) is an excellent example of conjugated dienes that undergo addition reactions. At elevated temperatures, 1,3-butadiene monomers can dimerize exothermally, and as temperature increases, secondary exothermic reactions will take place. The very high temperature and pressure rates that these reactions can attain may lead to a reaction runaway or even a thermal explosion. BD is a vapor at ambient conditions, usually stored as a pressurized liquid, and is a carcinogen, so the experimental evaluation is potentially difficult and hazardous. In this paper, the thermal stability of BD is evaluated. Dimerization and other secondary reactions are investigated by experimental thermal analysis using an automatic pressure adiabatic calorimeter (APTAC), by theoretical computational quantum chemistry methods, and empirical thermodynamic-energy correlations. A theoretical approach is conducted to predict some of the BD reaction behavior. Results are compared to other literature data obtained using different experimental methods.

Butadienes↗
PubMed2006

Steady-state solutions in mathematical models of atrial cell electrophysiology and their stability.

The steady states of the Fenton-Karma, the Courtemanche and the Nygren cell models were studied by determining the fixed points of the dynamical system describing their cell kinetics. The linear stability of the fixed points was investigated, as well as their response to external stimuli. Symbolic calculations were carried out as far as possible in order to prove the existence of these fixed points. In the Fenton-Karma model, a unique stable fixed point was found, namely the resting state. In contrast, the Courtemanche model had an infinite number of fixed points. A bifurcation diagram was constructed by classifying these fixed points according to a conservation law. Initial conditions were identified, for which the dynamical behavior of the cell was auto-oscillatory. In its original formulation, the Nygren model had no fixed point. After having restored charge conservation, the system was found to have an infinite number of fixed points, resulting in a bifurcation diagram similar to that of the Courtemanche model. The approach proposed in this paper assists in the exploration of the high-dimensional parameter space of the cell models and the identification of the conditions leading to spontaneous pacemaker activity.

Algorithms↗
PubMed2002

High-resolution separation of polychlorinated biphenyls by comprehensive two-dimensional gas chromatography.

Comprehensive two-dimensional gas chromatography (GC x GC) with micro electron-capture detection (microECD) has been optimised for the separation of polychlorinated biphenyl congeners with emphasis on the separation of 12 toxic non- and mono-ortho chlorinated biphenyls (CBs), viz. CBs 77, 81, 105, 114, 118, 123, 126, 156, 157, 167, 169 and 189. The selection of the first- and second-dimension columns and the temperature programme optimisation were carried out with a mixture of 90 CBs and the results are compared with those of one-dimensional GC. A complete separation of all 12 priority CBs was obtained with two column combinations, HP-1-HT-8 and HP-1-SupelcoWax-10. With the HP-1-HT-8 column set, ordered structures show up in the two-dimensional plane, with the number of chlorine substituents and their position (ortho vs. non-ortho) being the main parameters of interest. This can help with congener identification. Estimated detection limits are excellent, i.e. about 10 fg. To illustrate the potential and the versatility of GC x GC-microECD, a cod liver extract and a standard mixture of the 17 most toxic polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans together with 90 CBs were analysed as an application.

Chromatography, Gas↗
PubMed1997

Improved common line-based icosahedral particle image orientation estimation algorithms.

Modifications are described for the center and angular parameter estimation algorithms of common line-based particle image orientation determination which is an essential step in the three-dimensional reconstruction of icosahedral virus particles. The modifications incorporate a variety of image processing, pattern recognition, and statistical tools resulting in objective and automated orientation estimation algorithms. The modified algorithms were tested using electron cryo-microscopic particle images of three different virus specimens, with sizes 400-1250 A in diameter, covering a broad range of defocus values. Evaluation of these modified algorithms shows significant improvement over the previous algorithms. The center and angular parameters were estimated with higher accuracy allowing the identification of a larger number of particle orientations. Usage of the modified estimation algorithms resulted in the identification of particle orientations which could not to be identified using the algorithms before modification. Furthermore, these improvements have resulted in the determination of a better quality and a higher resolution three-dimensional reconstruction. The improved algorithms have been developed into a software package which can be obtained via the world wide web at http://ncmi.bioch.bcm.tmc.edu/pthuman.

Algorithms↗
PubMed1997

Natural history and management of the asymptomatic, moderately stenotic internal carotid artery.

PURPOSE: Although it has been widely accepted as the evidence supporting prophylactic carotid endarterectomy, aspects of the Asymptomatic Carotid Atherosclerosis Study have left unease among clinicians who must decide which individuals without symptoms should undergo surgery. Additional confusion has been created by the fact that the several large randomized trials investigating the efficacy of carotid endarterectomy have classified and analyzed different categories of carotid stenosis. In an effort to provide more information on the natural history of asymptomatic, moderate carotid artery stenosis (50% to 79%), we have reviewed data on approximately 500 arteries. METHODS: Records of our vascular laboratory from 1990 to 1992 were reviewed. We identified 425 patients with asymptomatic, moderate carotid artery stenosis; 71 patients had bilateral stenoses in this category, resulting in 496 arteries for study. RESULTS: The mean length of follow-up was 38 +/- 18 months. New ipsilateral strokes occurred in 16 (3.8%) patients. New ipsilateral transient ischemic attacks occurred in 25 (5.9%) patients. Documented progression of stenosis occurred in 48 (17%) of the 282 arteries for which a repeat duplex examination was available. Arteries that progressed to > 80% stenosis were significantly more likely to have caused strokes than those that remained in the 50% to 79% range (10.4% vs 2.1%, p < 0.02). Conversely, arteries that remained stable in the degree of stenosis were significantly more likely to have remained asymptomatic than those that progressed (92.7% vs 62.5%, p < 0.001). With life-table analysis the estimated cumulative ipsilateral stroke rate was 0.85% at 1 year, 3.6% at 3 years, and 5.4% at 5 years. The respective estimated cumulative transient ischemic attack rates were 1.9%, 5.5%, and 6.3%. The respective estimated cumulative rates for progression of stenosis were 4.9%, 16.7%, and 26.5%. Life-table comparison of ipsilateral stroke revealed a significantly higher cumulative rate among arteries that progressed in the degree of stenosis than among those that remained stable (p < 0.001). CONCLUSIONS: Based on the low rate of permanent neurologic events in these cases, prophylactic carotid endarterectomy for the asymptomatic, moderately stenotic internal carotid artery cannot currently be recommended. The only factor that appears to predict increased risk for future stroke is progression of stenosis. Careful follow-up with serial repeat duplex examinations must be performed in these patients. Until there are widely accepted duplex parameters that can provide all clinicians with accurate identification of arteries with narrowing corresponding to 60% stenosis as defined by the Asymptomatic Carotid Atherosclerosis Study, all surgeons will need to be aware of specifically how their noninvasive laboratories are deriving their results. For the many laboratories that continue to use the University of Washington criteria, 80% should remain the level above which prophylactic carotid endarterectomy is warranted.

Aged↗
PubMed2002

A computer system for acoustic analysis of pathological voices and laryngeal diseases screening.

A system for acoustic analysis of pathological voices is proposed. The vocalized part of the voice signal is separated and all glottal cycles are traced by means of a cross-correlation detector. Based on the so determined beginning and duration of all glottal cycles, shimmer, jitter, several harmonics-to-noise ratios and other widely used acoustic parameters are calculated. New parameters are also introduced for estimation of the turbulent noise in voice signals (Turbulent Noise Index - TNI) and for the "breathy" voice characterization (Normalized First Harmonic Energy - NFHE). These parameters are applied for laryngeal pathology detection. An identification accuracy of 96.1% by the K-nearest neighbors' method has been achieved. The system is clinically tested.

Algorithms↗
PubMed1999

Laser ablation of gall bladder stones.

Study of laser interaction with calculi is presented. A system of Nd-Yag and Ho-Yag pulsed lasers were used to produce fluorescence and plasma signals at the stone surface surrounded by saline and bile fluids. Fourth harmonic from Nd-Yag laser was transmitted to the samples by graded UV optical fibres. Gall bladder stones of various compositions were subjected to the high power Ho-Yag laser. Temporal transients and spectral evolution of plasma and fluorescence signals were monitored by a streak camera. A profile of acoustic pressures generated by shock waves was recorded with sensitive hydrophones placed in the surrounding fluids. Ablation threshold, cavitation process and fluorescence dependence on the laser parameters were studied in detail. Potential of stone identification by fluorescence and possible hydrodynamic model for ablation of biological samples is discussed.

Bile Duct Diseases↗
PubMed2006

Discovery and optimization of anthranilic acid sulfonamides as inhibitors of methionine aminopeptidase-2: a structural basis for the reduction of albumin binding.

Methionine aminopeptidase-2 (MetAP2) is a novel target for cancer therapy. As part of an effort to discover orally active reversible inhibitors of MetAP2, a series of anthranilic acid sulfonamides with micromolar affinities for human MetAP2 were identified using affinity selection by mass spectrometry (ASMS) screening. These micromolar hits were rapidly improved to nanomolar leads on the basis of insights from protein crystallography; however, the compounds displayed extensive binding to human serum albumin and had limited activity in cellular assays. Modifications based on structural information on the binding of lead compounds to both MetAP2 and domain III of albumin allowed the identification of compounds with significant improvements in both parameters, which showed good cellular activity in both proliferation and methionine processing assays.

Aminopeptidases↗
PubMed2004

[Multi-center study of the Jenaer model of the temporal bone].

BACKGROUND: Preparing exercises at the temporal bone are a prerequisite for the knowledge of the anatomical special features of this region and for learning the fundamentals of the tympanic cavity surgery. Since however fewer human temporal bones are available, the search for back-up models already took place in the last years. METHODS: Based on the experiences of the handling and visualization of CT data for the 3D-implant construction in the ent department Jena a temporal bone model was developed. The model was sent away to surgeons of different training. On the basis of identification of anatomical structures and evaluation of general parameters by means of a point system the model was evaluated. RESULTS AND CONCLUSIONS: The Jenaer temporal bone model is suitable as entrance into the preparing exercises. The anatomical structures are good to identify for the beginner. The handling with drill and chisel can be learned.

Attitude of Health Personnel↗
PubMed2002

Guidelines for using body composition measurement in patients with human immunodeficiency virus infection.

Wasting remains a significant condition of human immunodeficiency virus (HIV) infection despite antiretroviral treatment. Early identification requires the measurement of various body composition parameters, particularly body cell mass (BCM). Anthropometry may provide some useful information. Cost and complexity issues make many body composition techniques unsuitable for the clinical setting. Bioelectrical impedance analysis (BIA) may be the best method available to caregivers for monitoring serial changes in BCM over time and for determining the occurrence of wasting. It is not useful, however, for detecting body composition changes in patients with fat redistribution syndromes. Portability, low cost, ease of use, and patient acceptance make anthropometry and BIA ideally suited for the clinical setting.

Anthropometry↗