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Protection elicited by two glutamine auxotrophs of Mycobacterium tuberculosis and in vivo growth phenotypes of the four unique glutamine synthetase mutants in a murine model.

We generated four individual glutamine synthetase (GS) mutants (DeltaglnA1, DeltaglnA2, DeltaglnA3, and DeltaglnA4) and one triple mutant (DeltaglnA1EA2) of Mycobacterium tuberculosis to investigate the roles of GS enzymes. Subcutaneous immunization with the DeltaglnA1EA2 and DeltaglnA1 glutamine auxotrophic mutants conferred protection on C57BL/6 mice against an aerosol challenge with virulent M. tuberculosis, which was comparable to that provided by Mycobacterium bovis BCG vaccination.

Animals↗

Path analytical study of the short version of the WHO Quality of Life Instrument.

BACKGROUND: Using confirmatory factor analysis, we have shown that the 8 factors we derived from the responses of 118 Nigerian psychiatric patients to the short version of the WHO Quality of Life Instrument had greater structural integrity than the 4- and 6-domain models of the WHO. OBJECTIVES: Using path analysis to assess the structural integrity of the model we generated from the relationships among the 8 factors, we proposed a model of QOL from which targets for subjective QOL interventions could be delineated. METHOD: The model was generated by multiple regression analysis with the item on overall QOL (OQOL) as dependent variable and the 8 domains as predictors. Path analysis was done by Analysis of Moment Structures, with a maximum likelihood ratio as method of estimation. RESULTS: Our model had high Cronbach's alphas and met the criteria for the following fit indices: relative chi2 (1.9), goodness of fit (0.92) and comparative fit index (0.91). Hence, we propose that subjective QOL is primarily mediated by satisfaction with life, informational need, opportunity for experience, and instrumental need. CONCLUSION: Subjective QOL encompasses satisfaction with life circumstances, fulfillment of needs, and opportunity for experience, which should be targets for QOL interventions.

Adolescent↗

A universal algorithm for an improved finite element mesh generation Mesh quality assessment in comparison to former automated mesh-generators and an analytic model.

The FE-modeling of complex anatomical structures is not solved satisfyingly so far. Voxel-based as opposed to contour-based algorithms allow an automated mesh generation based on the image data. Nonetheless their geometric precision is limited. We developed an automated mesh-generator that combines the advantages of voxel-based generation with improved representation of the geometry by displacement of nodes on the object-surface. Models of an artificial 3D-pipe-section and a skullbase were generated with different mesh-densities using the newly developed geometric, unsmoothed and smoothed voxel generators. Compared to the analytic calculation of the 3D-pipe-section model the normalized RMS error of the surface stress was 0.173-0.647 for the unsmoothed voxel models, 0.111-0.616 for the smoothed voxel models with small volume error and 0.126-0.273 for the geometric models. The highest element-energy error as a criterion for the mesh quality was 2.61x10(-2) N mm, 2.46x10(-2) N mm and 1.81x10(-2) N mm for unsmoothed, smoothed and geometric voxel models, respectively. The geometric model of the 3D-skullbase resulted in the lowest element-energy error and volume error. This algorithm also allowed the best representation of anatomical details. The presented geometric mesh-generator is universally applicable and allows an automated and accurate modeling by combining the advantages of the voxel-technique and of improved surface-modeling.

Algorithms↗

Doubly stochastic coherence via noise-induced symmetry in bistable neural models.

The generation of coherent dynamics due to noise in an activator-inhibitor system describing bistable neural dynamics is investigated. We show that coherence can be induced in deterministically asymmetric regimes via symmetry restoration by multiplicative noise, together with the action of additive noise which induces jumps between the two stable steady states. The phenomenon is thus doubly stochastic, because both noise sources are necessary. This effect can be understood analytically in the frame of a small-noise expansion and is confirmed experimentally in a nonlinear electronic circuit. Finally, we show that spatial coupling enhances this coherent behavior in a form of system-size coherence resonance.

Membrane Potentials↗

Estimating the life-span of oligodendrocytes from clonal data on their development in cell culture.

This paper presents a new method to analyze clonal data on oligodendrocyte development in cell culture. The process of oligodendrocyte generation from precursor cells is modelled as a multi-type Bellman-Harris branching process as suggested in an earlier paper [K. Boucher, A. Zorin, A.Y. Yakovlev, M. Mayer-Proschel, M. Noble, An alternative stochastic model of generation of oligodendrocytes in cell culture, J. Math. Biol. 43 (2001) 22]. This model has been extended to allow for death of oligodendrocytes as well as a dissimilar distribution of the first mitotic cycle duration as compared to the subsequent cycles of precursor cells, which lengths are assumed to be independent and identically distributed random variables. Since the time-span of oligodendrocytes is not directly observable in clonal data, plausible parametric assumptions are invoked to make estimation problems tractable. In particular, the time to cell death follows a two-parameter gamma distribution, while the lapse of time between the event of cell death and the event of cell disintegration is assumed to be exponentially distributed. A simulated pseudo maximum likelihood method for estimation of model parameters has been developed using simulation-based approximations of the expected numbers and variance-covariance matrices for different types of cells. Finite sample properties of the estimation procedure are studied by computer simulations. The proposed method is illustrated with an analysis of the clonal development of O-2A progenitor cells isolated from the rat optic nerve and the corpus callosum.

Animals↗

Requirements for generating sigmoidal time-course aggregation in nucleation-dependent polymerization model.

Requirements for generating remarkable sigmoidal time-course of aggregation are found in the nucleation-dependent polymerization model by a numerical calculation method; i.e. there are optimum values of the kinetic constants to afford prominent sigmoidal character by inducing slightly unfavorable nucleation. However, if the nucleus formation is too unfavorable, sigmoidal character is again decreased. This result is in contrast to the generally accepted idea that sigmoid is induced by thermodynamically unfavorable nucleation phase.

Amyloid↗

Insights into cancer from transgenic mouse models.

The generation of mice designed to overexpress activated forms of oncogenes or carrying targeted mutations in tumour suppressor genes, has allowed scientists to causally link the function of these genes with specific tumour processes, such as proliferation, apoptosis, angiogenesis or metastasis. In addition, these mice have been interbred to assess the extent of cooperativity between different genetic lesions in disease progression, leading to a greater understanding of the multi-stage nature of tumourigenesis. The effect of genetic mutations is often influenced by the genetic background of the mouse and by analysing strain-dependent phenotypes, modifier loci have been identified. Although genetic mutations in mouse and humans do not always lead to the same tumour spectrum, the underlying molecular mechanisms are frequently relevant to both species. Furthermore, new technical approaches creating conditional mouse mutants which develop tumours in a tissue-specific manner, will allow the effect of mutation of certain genes to be studied in specific tissues, free from the fatal effects of the mutation in other clinically less relevant tissues. Several exising mouse strains have already been used to develop and test new therapies and conditional mutagenesis will undoubtedly increase the potential use of transgenic mice in understanding and treating cancer.

Animals↗

Survey of genetically engineered mouse models for prostate cancer: analyzing the molecular basis of prostate cancer development, progression, and metastasis.

Genetically engineered mouse models have been generated to study the molecular basis of prostate cancer (PCa) development, progression, and metastasis. Selection of a prostate-specific promoter, such as the probasin (PB) and prostate specific antigen (PSA) promoters, is critical for generating sufficient levels of transgene expression to elicit a phenotypic response. To date, target genes have included growth factors, cell cycle regulators, pro- and anti-apoptotic proteins, steroid hormone and growth factor receptors, oncogenes, tumor suppressors, and homeobox genes. The experimental approaches used to generate these mouse models include overexpression of the transgene, knock-out/knock-in of transgene expression and conditional regulation of expression using Cre/lox technology. This review summarizes the promoters, which have been utilized to create genetically engineered mouse models for PCa. Furthermore, the effects of gene disruption on promoting low- and high-grade intraepithelial neoplasia (LGPIN and HGPIN, respectively), locally invasive carcinoma and metastatic lesions will be discussed. To date, the PB-Cre4 x PTENloxp/loxp model appears to be the only model that represents the entire continuum of prostate adenocarcinoma development, tumor progression, and metastasis, although models that develop prostatic neuroendocrine (NE) cancer can be generated by disrupting one genetic event. Indeed, analysis of bigenic mouse models indicates that two genetic events are generally required for progression from HGPIN to locally invasive adenocarcinoma and that two to five genetic events can promote metastasis to distant sites. Studying the effects of genetic perturbation on PCa biology will increase our understanding of the disease process and potentially provide targets for developing novel therapeutic approaches.

Adenocarcinoma↗

Blastoid mantle cell lymphoma: evidence for nonrandom cytogenetic abnormalities additional to t(11;14) and generation of a mouse model.

Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32), which is associated with cyclin D1 hyperexpression and a poor prognosis. MCL cases have been shown to progress to a more aggressive disease but the molecular events responsible of this phenomenon have not been determined. We have established two cell lines from the pleural effusions of two patients with MCL that we have used for further cytogenetic characterization to better define the incidence and nature of secondary chromosome abnormalities using multicolor fluorescence in situ hybridization, whole chromosome paint, and specific probes. Both cell lines grew independently without growth factors. Using CCND1/IGH-specific probes, patient UPN1 was found to have a masked t(11;14). Numerous and complex chromosomal abnormalities were found in both cell lines affecting chromosomes 2, 8, 13, 18, 22, X, and Y. These abnormalities included 8p losses, suggesting the presence of an anti-oncogene in this region, rearrangements of 8q24, MYC gene, and translocations involving 8, X, and Y chromosomes, which might be significant in the pathogenesis of MCL progression. The use of the cell lines (UPN1) allowed us to generate a mouse model of human MCL, mimicking a disseminated lymphoma and leading to the death of the animals in 4 weeks. This blastoid MCL model could be of major interest to determine molecular events involved in MCL progression, allowing isolation of involved genes and their functional characterization, and to study the effects of new chemotherapy regimens in mouse models.

Animals↗

Modeling of lamb waves generated by integrated transducers in composite plates using a coupled finite element-normal modes expansion method

Thin piezoelectric transducers attached to or embedded within composite structures could be used for in situ structural health monitoring. For plate-shaped structures, the useful ultrasonic vibration modes are Lamb waves. Preliminary testing has already demonstrated the suitability and practical feasibility of such integrated transducers, but better control of the generation of Lamb modes seems to be necessary. Therefore, an original modeling approach has been developed, which can be used to design and optimize these "sensitive materials." This modeling technique allows the determination of the amplitude of each Lamb mode excited in a composite plate with surface-bonded or bulk-embedded piezoelectric elements. The method consists of a coupling of the finite element method (FEM) and the normal modes expansion method. The limited finite element mesh of the transducer and its vicinity enables the computation of the mechanical field created by the transducer, which is then introduced as a forcing function into the normal modes equations. The adequacy and accuracy of this modeling method have been numerically and experimentally verified.

Journal Article↗

The generation effect and the modeling of associations in memory.

The search of associative memory (SAM) model of Gillund and Shiffrin (1984) was applied to data of two experiments that examined the generation effect (Slamecka & Graf, 1978). Subjects studied a list of related word pairs, in which they either read both words in the pair or generated the right- hand response term using the left-hand stimulus term plus the response word fragment as generation cues. Experiment 1 manipulated encoding condition within subjects and used an incidental learning procedure. Experiment 2 manipulated encoding condition between subjects and used an intentional learning procedure. Memory was tested with recognition, cued recall, and free recall. A higher order association model gave a better and more parsimonious fit to the results than did an item-level association model. The relationship between various versions of SAM and current accounts of the generation effect are discussed, particulary the two-factor theory of Hirshman and Bjork (1988).

Adult↗

Can pre-operative computed tomography predict resectability of ovarian carcinoma at primary laparotomy?

OBJECTIVE: To assess the ability of computed tomography in predicting whether suspected ovarian cancer could be fully excised at primary laparotomy. DESIGN: Retrospective analysis of patient notes and pre-operative computed tomography scans. Setting A UK NHS cancer centre. POPULATION: Seventy-seven women who underwent laparotomy for an ovarian tumour and who had had a pre-operative computed tomography scan. METHODS: Women who had a computed tomography scan before laparotomy for an ovarian tumour were identified. Analysis was undertaken to determine the accuracy of computed tomography in predicting malignancy, stage and residual disease. The computed tomography parameters significantly associated with residual disease were determined by a chi2 analysis. These parameters, in addition to age and CA125, were used to generate a predictive model. This model was further refined by stepwise logistic regression and a clinical scoring index was generated. MAIN OUTCOME MEASURES: To identify those computed tomography parameters significantly associated with residual disease and to use these with CA125 and age to generate a useful clinical scoring index to predict residual disease in suspected ovarian cancer. RESULTS: Seventy-seven women underwent a laparotomy for an ovarian tumour and had a pre-operative computed tomography scan. Fifty-one of these women had malignant disease and twenty-five of these women had residual disease remaining. The sensitivity of computed tomography in predicting malignancy was 90% with a specificity of 85% and the overall accuracy of computed tomography for predicting stage of disease was 73% (37/51). The overall sensitivity of computed tomography in predicting residual disease was 88%, the specificity was 92% and the positive predictive value was 85%. The parameters on computed tomography that were significantly (P < 0.05) associated with residual disease were ascites, omental cake, mesenteric disease, paracolic gutter deposits, diaphragmatic deposits and pleural effusion. The predictive model generated was more accurate than computed tomography alone (sensitivity 88%, specificity 98%, positive predictive value 95%). Using stepwise logistic regression enabled the predictive model to be simplified to include mesenteric disease, omental cake, age and CA125 without any change in sensitivity or specificity and this model was used to generate a scoring index. CONCLUSION: This study shows that prediction of resectability by computed tomography is excellent and is further improved by the generation of a predictive model, which can be used to generate a simple scoring index. This scoring system now needs to be tested prospectively to ensure that its performance remains as good in an independent sample population.

Adult↗

A profile hidden Markov model for signal peptides generated by HMMER.

SUMMARY: Although the HMMER package is widely used to produce profile hidden Markov models (profile HMMs) for protein domains, it has been difficult to create a profile HMM for signal peptides. Here we describe an approach for building a complex model of eukaryotic signal peptides by the standard HMMER package. Signal peptide prediction with this model gives a 95.6% sensitivity and 95.7% specificity. AVAILABILITY: The profile HMM for signal peptides, data sets, and the scripts for analyzing data are available for non-commercial use at http://share.gene.com/.

Amino Acid Sequence↗

Development of a structural model for the cytoplasmic domain of an integrin.

The cytoplasmic tails of integrin heterodimers play central roles in controlling the activation states of integrins and in transmitting intracellular signals. Despite their short length, no structure of any integrin cytoplasmic domain has been determined. Therefore, molecular models for the cytoplasmic domain of alpha(IIb)beta3, the major platelet integrin, were generated, including models for the individual cytoplasmic tails, the binary alphaIIb-calcium complex, and the ternary alphaIIb-beta3-calcium complex. Structural analysis of circular dichroism spectra were compiled with data obtained from short homologous sequences within crystallized proteins, and with secondary structural predictions to develop starting models for each subunit. These models were subjected to a series of energy minimization and molecular dynamic simulations to generate final models. AlphaIIb was predicted to be ordered at its N-terminus and its C-terminus could accommodate a cation in a multicoordinated complex. The structure of beta3 was dominated by a beta-turn at its NPXY motif (beta3 744-747). In docking of alphaIIb to different sites within beta3, the conformation of the beta3 juxta-transmembrane (beta3 716-721) was greatly altered. This region was confirmed to be a conformational 'hot-spot' by circular dichroism. The conformational flexibility of this juxta-transmembrane region, which is highly conserved amongst integrins, is ideally located to regulate signaling.

Amino Acid Sequence↗

Models of respiratory rhythm generation in the pre-Bötzinger complex. II. Populations Of coupled pacemaker neurons.

We have proposed models for the ionic basis of oscillatory bursting of respiratory pacemaker neurons in the pre-Bötzinger complex. In this paper, we investigate the frequency control and synchronization of these model neurons when coupled by excitatory amino-acid-mediated synapses and controlled by convergent synaptic inputs modeled as tonic excitation. Simulations of pairs of identical cells reveal that increasing tonic excitation increases the frequency of synchronous bursting, while increasing the strength of excitatory coupling between the neurons decreases the frequency of synchronous bursting. Low levels of coupling extend the range of values of tonic excitation where synchronous bursting is found. Simulations of a heterogeneous population of 50-500 bursting neurons reveal coupling effects similar to those found experimentally in vitro: coupling increases the mean burst duration and decreases the mean burst frequency. Burst synchronization occurred over a wide range of intrinsic frequencies (0.1-1 Hz) and even in populations where as few as 10% of the cells were intrinsically bursting. Weak coupling, extreme parameter heterogeneity, and low levels of depolarizing input could contribute to the desynchronization of the population and give rise to quasiperiodic states. The introduction of sparse coupling did not affect the burst synchrony, although it did make the interburst intervals more irregular from cycle to cycle. At a population level, both parameter heterogeneity and excitatory coupling synergistically combine to increase the dynamic input range: robust synchronous bursting persisted across a much greater range of parameter space (in terms of mean depolarizing input) than that of a single model cell. This extended dynamic range for the bursting cell population indicates that cellular heterogeneity is functionally advantageous. Our modeled system accounts for the range of intrinsic frequencies and spiking patterns of inspiratory (I) bursting cells found in the pre-Bötzinger complex in neonatal rat brain stem slices in vitro. There is a temporal dispersion in the spiking onset times of neurons in the population, predicted to be due to heterogeneity in intrinsic neuronal properties, with neurons starting to spike before (pre-I), with (I), or after (late-I) the onset of the population burst. Experimental tests for a number of the model's predictions are proposed.

Animals↗

Properties of phylogenetic trees generated by Yule-type speciation models.

We investigate some discrete structural properties of evolutionary trees generated under simple null models of speciation, such as the Yule model. These models have been used as priors in Bayesian approaches to phylogenetic analysis, and also to test hypotheses concerning the speciation process. In this paper we describe new results for three properties of trees generated under such models. Firstly, for a rooted tree generated by the Yule model we describe the probability distribution on the depth (number of edges from the root) of the most recent common ancestor of a random subset of k species. Next we show that, for trees generated under the Yule model, the approximate position of the root can be estimated from the associated unrooted tree, even for trees with a large number of leaves. Finally, we analyse a biologically motivated extension of the Yule model and describe its distribution on tree shapes when speciation occurs in rapid bursts.

Animals↗

An elbow joint movement control model with visual feedback.

A motor program generator control model is proposed to simulate neuromuscular control. Three muscles (Biceps, Triceps, Brachialis) driving elbow joint flexion in a plane are simulated by integrating their nonlinear dynamic property and spinal neural circuitry. The motor descending commands are described by a visual feedback signal from the joint and an excitation signal for the motor neuron pool. The visual feedback signal mimics the gamma command whereas the excitation signal mimics another descending co-activation command. The gamma command is expressed as the output of a PID controller with the visual feedback error signal as the input. The gamma command and the motoneuron pool background activity are the inputs to the motoneuron pool model coupled with the Renshaw cell recurrent inhibitions. The output of the motoneuron pool model mimics the alpha command feeding directly to the muscle dynamics. A movement is produced by reducing the error signal between goal position and actual position and altering excitation signal properly. The simulation results show that a burst pattern of excitation signal and a PID controller can accurately trace the terminal goal and generate a smooth movement with a bell shaped velocity profile. The muscle activation signals have the characteristic similar to the smoothed EMG. Changing different parameters of the PID can cause the same effects as the stimulus pulse intensity or duration modulation.

Elbow Joint↗