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PubMed2006

Reduced hippocampal volume correlates with executive dysfunctioning in major depression.

OBJECTIVE: Dysfunction of neuronal plasticity or remodelling seems to contribute to the pathopysiology of major depression and may cause the well-documented hippocampal changes in depression. We aimed to investigate whether reduced hippocampal volumes correlate with executive dysfunctioning or memory dysfunctioning or with depression severity. METHODS: We recruited 34 inpatients with a previous or current episode of major depression from the department of psychiatry at the Ludwig-Maximilians University of Munich, Germany. We examined the 34 patients and 34 healthy control subjects with structural high resolution MRI. We assessed cognitive functions with the Wisconsin Card Sorting Test (WCST) and the Rey Auditory Verbal Learning Test (RAVLT) and severity of depression with the Hamilton Depression Rating Scale. RESULTS: Hippocampal volumes and frontal lobe volumes were significantly smaller in patients, compared with healthy control subjects. Furthermore, lower hippocampal volumes were correlated with poorer performance in the WCST. No significant correlations were found between hippocampal volumes and RAVLT performance or severity of depression. CONCLUSIONS: The present findings emphasize that patients with reduced hippocampal volumes show more executive dysfunctions than their counterparts. Thus, the mechanisms resulting in reduced hippocampal volumes seem to be related to the development of major depression.

Adult↗
PubMed2006

Hippocampal atrophy confounds template-based functional MR imaging measures of hippocampal activation in patients with mild cognitive impairment.

BACKGROUND AND PURPOSE: Functional MR imaging has been used to study patterns of hippocampal activation that distinguish pathologic from normal memory loss in the elderly population. Our objective was to assess whether hippocampal atrophy confounds measurements of hippocampal activation in subjects with mild cognitive impairment (MCI). METHODS: Twenty subjects with MCI and 20 elderly control subjects with objectively normal memory were studied at 4T during a face-name paradigm designed to activate the hippocampus. Hippocampal activation was measured using 2 separate approaches: applying a preset region of interest (ROI) in standardized template space and applying a manually drawn ROI in native subject space. Pearson correlation coefficients were calculated to compare group-dependent relationships between hippocampal volume and activation. Analysis of covariance (ANCOVA) was performed to assess group differences in hippocampal activation during encoding and retrieval. Age and hippocampal volume were included as covariates, as was a term for the interaction between hippocampal volume and group. RESULTS: When hippocampal activation was measured by the template-based method, the correlation coefficient in the right hippocampus of subjects with MCI but not control subjects during retrieval differed significantly from zero. There was a significant (P < .05) group-by-volume interaction in the ANCOVA model. No significant correlations or interactions were demonstrated when activation was measured in native subject space with manually drawn ROIs. CONCLUSION: Our findings suggest a potential confounding relationship between hippocampal volume and activation for subjects with MCI in template-based analyses. Template-based measures of hippocampal activation that do not adequately account for hippocampal atrophy should be used with caution in patients with MCI.

Aged↗
PubMed2006

Normal-appearing white matter changes vary with distance to lesions in multiple sclerosis.

BACKGROUND AND PURPOSE: Multiple sclerosis (MS) disease processes in normal-appearing white matter (NAWM) may be different close to MR-visible lesions than farther from these lesions. We aimed to investigate the relationship of NAWM changes to the distance to the lesions. METHODS: We measured B(1)-corrected T1 and magnetization transfer ratio (MTR) maps in 63 patients with MS (11 primary progressive, 34 relapsing-remitting, 18 secondary progressive). We used histogram analyses to assess the global properties of lesions, of 4 consecutive 1-mm pixel layers of NAWM around the lesions, and of distant NAWM located at least 4-mm from lesions in all directions. In 22 healthy controls, we measured white matter MTR and T1 histograms. Histogram parameters were statistically analyzed by using a linear mixed model. RESULTS: The first and second NAWM pixel layers around the lesions had a significantly lower MTR histogram peak position than distant NAWM, whereas T1 histogram peak position was similar between all types of NAWM. Furthermore, MTR histograms of distant NAWM were statistically indistinguishable from those of control white matter, whereas T1 histograms of distant NAWM had significantly decreased peak height for relapsing-remitting MS and secondary progressive MS and significantly increased peak position for secondary progressive MS. CONCLUSION: Our results may suggest that axonal damage and demyelination in NAWM mainly arise as a secondary result of visible lesions, with the largest effect close to these lesions. NAWM disease farther from the lesions may be mainly characterized by subtle blood-brain barrier damage, with leakage of fibrinogen into the parenchyma and microplaque formation, processes that are detected with T1 but not with MTR.

Adult↗
PubMedDate not supplied

[Value and limits of a statistical aid in typological constructions].

Correspondence analysis has become the favoured method to describe qualitative data. Graphical representation allows to appreciate positions of different modalities between them and in relation with the two factorial design axis. Nevertheless, lecture and interpretation seem to depend on the researcher's assessment who doesn't know always how modalities are jointed. Tri-Deux statistical software directly makes this level readable. Developed by a sociologist engineer from the CNRS, it is free of charge and operates with PC or compatible material. Every time a modality is in attraction with an other (on the basis of independency deviations), one line links the two points: this tool permits to visualize how modalities of analysed variables gather or contrast together. All the connections are not equal, some of them are more important than others. This program allows to draw each connection with a decreasing order according to their weight and to distinguish the highest attractions from the lowest ones. An example with a study allows to understand interest of this method. The aim of this statistical way is researching a possible typology in the analysed corpus. It is necessary to outline, in this method, the significance of an empirical phase when deliverate research of disconnected graphical complexes (clinical entities) leads to rule out non discriminant variables. Analysis consists to study data according to their clinical relevance and to their dynamic cohesion. This time corresponds to a real 'come back to the clinical practice'.(ABSTRACT TRUNCATED AT 250 WORDS)

Cluster Analysis↗
PubMed1997

A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins.

A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four C alpha atoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudodihedral involving four sequential C alpha atoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptide groups. The method provides a reduction in dimensionality, from the usual combination of multiple phi,psi pairs to a single pair, yielding valuable information concerning the structure and dynamics of these important elements. The new two-dimensional surface is explored by reference to 63 selected protein crystal structures together with a comparison of model built peptides representing the common secondary structural elements. Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor.

Aprotinin↗
PubMed1997

Varicose vein clinics: modelling the effects of seasonal variation in referrals.

Data have been collected prospectively on patients referred to a specialist varicose vein clinic between January 1991 and December 1994. A seasonal variation in referral pattern of patients is demonstrated, with more patients being referred in the summer months. Similar fluctuations are seen in the number of patients waiting for first appointment, and the average waiting time for first appointment. Such fluctuations in referral patterns can lead to difficulties in planning. A computer model has been constructed and used to predict future referrals and the effects of seasonal variations upon waiting times for appointments and on efficiency of clinic usage. The computer model accurately predicts numbers of future referrals. The average waiting time for first appointment could be kept constant by arranging more varicose vein clinics in summer than in winter but keeping the overall number of clinics during the year constant. The computer model could be important in planning of specialist clinics, and may play a role when negotiating future contracts. If flexibility can be achieved by exchanging clinics with different seasonal patterns, it may be possible to reduce waiting times within existing resources.

Ambulatory Care Facilities↗
PubMed1989

Computation of diagnostic data from coronary sinus pressure: a comparison between two possible models.

We have evaluated two mathematical models to describe the increase in coronary sinus pressure (CSP) following pressure controlled intermittent coronary sinus occlusion (PICSO). The models are evaluated and compared on the basis of human and canine data. Both models were fitted by non-linear least squares algorithms. Next, derived quantities, such as plateau, rise-time and mean integral of the coronary sinus pressure were calculated from the model parameters. Corresponding quantities for the two models were compared with regard to mean values, rate of successful calculation and specific features characterizing the human or canine case. One model was found to be superior for investigational purposes. The other model was found to be more stable in critical situations and is therefore suggested for usage in closed loop regulation of PICSO. Physiologically, the differences in mean values of the derived quantities between the two models were found to be negligible. The formal statistical significance of the differences is but a consequence of the large number of PICSO cycles analysed.

Algorithms↗
PubMed1989

Analysis of progress curves for enzyme-catalysed reactions. Automatic construction of computer programs for fitting integrated rate equations.

The computer analysis of progress curves for enzyme-catalysed reactions involves a series of mathematical and computational tasks. The three most daunting of these are the derivation of an integrated rate equation, solving this equation so that the amount of product formed by the reaction at any time can be calculated, and incorporating this solution into a non-linear-regression computer program. This paper describes the basis of a computer program that greatly simplifies the problem. The proposed mechanism is specified in the familiar kinetic constant form, which is automatically translated into a program capable of fitting this mechanism to a series of experimental progress curves. The approach is illustrated for a reversible reaction with one substrate and one product, and tested with some data obtained for the fumarase reaction. A copy of the program has been deposited as Supplementary Publication SUP 50148 (13 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1989) 257, 5.

Animals↗
PubMed1987

Theorems and implications of a model-independent elimination/distribution function decomposition of linear and some nonlinear drug dispositions. IV. Exact relationship between the terminal log-linear slope parameter beta and drug clearance.

An exact formula relating the terminal log-linear beta parameter and the drug clearance is derived. The expression is valid for drugs with a linear, polyexponential disposition kinetics. The formula is useful for calculating the clearance when the clearance has changed between drug administrations and requires only drug level data from the terminal, log-linear elimination phase in addition to data from a single separate i.v. administration in the same subject. Data from an i.v. administration are necessary in order to apply the disposition decomposition technique to isolate and uniquely define the distribution kinetics in terms of the distribution function h(t). The different clearances can then be calculated from the beta values of the log-linear terminal drug level data and the parameters of h(t). The theoretical basis of the method and its assumptions and limitations are discussed and various pertinent theorems are presented. A computer program enabling an easy implementation of the proposed method is also presented. The mathematical and computational procedures of the method are demonstrated using kinetic data from i.v. and oral administrations of cimetidine, diazepam, and pentobarbital in human subjects. The classical V.beta method of approximating the clearance as the product of volume of distribution and beta is considered for comparison. For the three drugs considered the V.beta method which assumes a single exponential disposition kinetics leads to excessive errors when applied in absolute clearance comparisons. However, when applied in relative comparisons in the form of the "beta correction" the errors cancel out to some extent depending on the magnitude of the distribution kinetic effect. Whenever possible it is advisable to apply the proposed method to avoid such errors.

Cimetidine↗
PubMed1997

ELF magnetic field exposure system with feedback-controlled disturbance rejection.

Extremely low-frequency (ELF) magnetic field exposure systems are usually subject to field disturbances induced by external sources. Here, a method for designing a feedback control system for cancelling the effect of external ELF magnetic field disturbances on the magnetic field over the exposure area is presented. This method was used in the design of a feedback-controlled exposure system for an inverted microscope stage. The effectiveness of the proposed feedback control system for disturbance rejection was verified experimentally and by means of computer simulation.

Computer Simulation↗
PubMed2003

Computing motif correlations in proteins.

Protein motifs, which are specific regions and conserved regions, are found by comparing multiple protein sequences. These conserved regions in general play an important role in protein functions and protein folds, for example, for their binding properties or enzymatic activities. The aim here is to find the existence correlations of protein motifs. The knowledge of protein motif/domain sharing should be important in shedding new light on the biologic functions of proteins and offering a basis in analyzing the evolution in the human genome or other genomes. The protein sequences used here are obtained from the PIR-NREF database and the protein motifs are retrieved from the PROSITE database. We apply data mining approach to discover the occurrence correlations of motif in protein sequences. The correlation of motifs mined can be used in evolution analyses and protein structure prediction. We discuss the latter, i.e., protein structure prediction in this study. The correlations mined are stored and maintained in a database system. The database is now available at http://bioinfo.csie.ncu.edu.tw/ProMotif/.

Algorithms↗
PubMed2003

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.

Algorithms↗
PubMed2001

Determination of regional pulmonary parenchymal strain during normal respiration using spin inversion tagged magnetization MRI.

In clinical practice, the assessment of lung mechanics is limited to a global physiological evaluation, which measures, in the aggregate, the contributions of the pulmonary parenchyma, pleura, and chest wall. In this study, we used an MR imaging methodology which applies two-dimensional bands of inverted magnetization directly onto the pulmonary parenchyma, thus allowing for the quantification of local pulmonary tissue deformation, or strain, throughout inhalation. Our results showed that the magnitude of strain was maximal at the base and apex of the lung, but was curtailed at the hilum, the anatomical site of the poorly mobile bronchial and vascular insertions. In-plane shear strain mapping showed mostly positive shear strain, predominant at the apex throughout inhalation, and increasing with expanding lung volume. Anisotropy mapping showed that superior-inferior axial strain was greater than medial-lateral axial strain at the apex and base, while the opposite was true for the middle lung field. This study demonstrates that localized pulmonary deformation can be measured in vivo with tagging MRI, and quantified by applying finite strain definitions from continuum mechanics.

Adult↗
PubMed1992

Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4.

Recently we developed methods for the construction of knowledge-based mean fields from a data base of known protein structures. As shown previously, this approach can be used to calculate ensembles of probable conformations for short fragments of polypeptide chains. Here we develop procedures for the assembly of short fragments to complete three-dimensional models of polypeptide chains. The amino acid sequence of a given protein is decomposed into all possible overlapping fragments of a given length, and an ensemble of probable conformations is calculated for each fragment. The fragments are assembled to a complete model by choosing appropriate conformations from the individual ensembles and by averaging over equivalent angles. Finally a consistent model is obtained by rebuilding the conformation from the average angles. From the average angles the local variability of the structure can be calculated, which is a useful criterion for the reliability of the model. The procedure is applied to the calculation of the local backbone conformations of myoglobin and lysozyme whose structures have been solved by X-ray analysis and thymosin beta 4, a polypeptide of 43 amino acid residues whose structure was recently investigated by NMR spectroscopy. We demonstrate that substantial fractions of the calculated local backbone conformations are similar to the experimentally determined structures.

Amino Acid Sequence↗
PubMed2003

Free energy calculations for the relative binding affinity between DNA and lambda-repressor.

The change in the binding free energy between DNA and lambda-repressor resulting from a base substitution, thymine (T)-->deoxyuracil (abbreviated as U), was evaluated by the free energy perturbation method on the basis of molecular dynamics simulations for the DNA-lambda-repressor complex in water with all degrees of freedom and including long-range Coulomb interactions. The binding free energy change that we calculated (1.47 +/- 0.40 kcal/mol) was in good agreement with an experimental value (1.8 kcal/mol). We clarified why the small difference between T and U (CH(3) in T is replaced with H in U) caused such a significant change in the binding free energy: The substitution of CH(3) in T with H in U lowered the dissociated-state free energy level due to the gain of the hydration free energy. Furthermore, the T-->U substitution raised the free energy level in the associated state due to the loss of the favored van der Waals (vdW) interactions with the lambda-repressor amino acid residues. In other words, the amino acid residues of lambda-repressor can recognize the CH(3) in T through the vdW interactions with the CH(3). This recognition is enhanced in a water environment, because the hydrophobic CH(3) prefers the amino acid residues of lambda-repressor to water molecules.

Binding Sites↗