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At least 1,243 records · Page 69Linked to original sources

PubMed2003

Bistability in a size-structured population model of cannibalistic fish--a continuation study.

By numerical continuation of equilibria, we study a size-structured model for the dynamics of a cannibalistic fish population and its alternative resource. Because we model the cannibalistic interaction as dependent on the ratio of cannibal length and victim length, a cannibal experiences a size distribution of potential victims which depends on its own body size. We show how equilibria of the resulting infinite-dimensional dynamical system can be traced with an existing method for numerical continuation for physiologically structured population models. With this approach we found that cannibalism can induce bistability associated with a fold (or, saddle-node) bifurcation. The two stable states can be qualified as 'stunted' and 'piscivorous', respectively. We identify a new ecological mechanism for bistability, in which the energy gain from cannibalism plays a crucial role: Whereas in the stunted population state cannibals consume their victims, on average, while they are very small and yield little energy, in the piscivorous state cannibals consume their victims not before they have become much bigger, which results in a much higher mean yield of cannibalism. We refer to this mechanism as the 'Hansel and Gretel' effect. It is not related to any individual 'choice' or 'strategy', but depends purely on a difference in population size distribution. We argue that studying dynamics of size-structured population models with this new approach of equilibrium continuation extends the insight that can be gleaned from numerical simulations of the model dynamics.

Animals↗

PubMed1989

New model for the secondary structure of the 5' non-coding RNA of poliovirus is supported by biochemical and genetic data that also show that RNA secondary structure is important in neurovirulence.

A secondary structure model for the 5' non-coding RNA of poliovirus has been derived by comparing computer-generated folding patterns of equivalent sequences from a number of related enteroviruses and rhinoviruses and identifying compensating mutations that suggest conservation of a common secondary structure. Although certain elements are similar, the new model differs considerably from a previously published minimal energy structure and is consistent with the observed sensitivity of in vitro RNA transcripts of infectious poliovirus cDNA to RNases and modifying chemicals. The sequence of a neurovirulent revertant of an attenuated mutant provides additional evidence for an interaction between a region known to be important for neurovirulence, sequence 471-483, and nucleotides 528 to 538.

Animals↗

PubMed2004

Visualization of early chromosome condensation: a hierarchical folding, axial glue model of chromosome structure.

Current models of mitotic chromosome structure are based largely on the examination of maximally condensed metaphase chromosomes. Here, we test these models by correlating the distribution of two scaffold components with the appearance of prophase chromosome folding intermediates. We confirm an axial distribution of topoisomerase IIalpha and the condensin subunit, structural maintenance of chromosomes 2 (SMC2), in unextracted metaphase chromosomes, with SMC2 localizing to a 150-200-nm-diameter central core. In contrast to predictions of radial loop/scaffold models, this axial distribution does not appear until late prophase, after formation of uniformly condensed middle prophase chromosomes. Instead, SMC2 associates throughout early and middle prophase chromatids, frequently forming foci over the chromosome exterior. Early prophase condensation occurs through folding of large-scale chromatin fibers into condensed masses. These resolve into linear, 200-300-nm-diameter middle prophase chromatids that double in diameter by late prophase. We propose a unified model of chromosome structure in which hierarchical levels of chromatin folding are stabilized late in mitosis by an axial "glue."

Adenosine Triphosphatases↗

PubMed2006

Structural features of pharmacy function--the analysis using structural equation modeling.

In order to examine the structural features of community pharmacy function and to clarify areas meriting priority in efforts to expand pharmacy functions in the home care field, a questionnaire survey was conducted. Using the distribution of responses regarding the actual conditions entailed in the 16 categories of pharmacy services, factor analysis was carried out. Structural equation modeling was performed and the fitness of the path model constructed to study the interrelatedness of the individual factors extracted by factor analysis was considered. Four factors comprised pharmacy services "dispensing", "supply of goods", "offering home care", and "cooperation in community health and medical programs". The interrelatedness of four pharmacy functions by the result of structural equation modeling indicated the following insights. 1) By strengthening "cooperation in community health and medical programs", it is possible to directly improve the functions of "dispensing", and "offering home care". An improvement in "collecting and utilizing patient information", "providing appropriate instruction", "providing introductions to medical institutions and physicians", and "supplying over-the-counter drugs" can be expected as a result of direct benefits accrued by "cooperation in community health and medical programs". 2) By strengthening "offering home care", it is possible to directly improve "supply of goods". An improvement in "stocking long-term care goods and sanitary goods" can be expected as a result of direct benefits accrued by "offering home care". In conclusion, this study indicated that the areas meriting priority in the expansion and upgrading of pharmacy functions is stronger "cooperation in community health and medical programs".

Community Pharmacy Services↗

PubMed2005

Pallidal index on MRI as a target organ dose of manganese: structural equation model analysis.

We have used a structural equation model (SEM) to analyze the interrelationships among exposure markers, magnetic resonance imaging (MRI) signal index, and neurobehavioral effects. Based on exposure groups, we assessed blood manganese, MRI measurements of pallidal index (PI), and neurobehavioral core test battery (WHO-NCTB) on 111 male workers occupationally exposed to manganese, including welders, smelter workers, and welding rod manufacturing workers. Latent variables were constructed to represent the neurobehavioral effects in an integrated way. The structural equation model revealed that airborne manganese and blood manganese contribute to PI significantly. Manganese exposure in the ambient air may lead to an increase in the internal dose, not only indirectly, by increasing blood manganese level, but also directly, independent of blood concentration. PI significantly contributed to a decrease in neurobehavioral test scores. We found that airborne manganese contributed to PI, and that PI is the most effective predictor of neurobehavioral performance, after adjusting for age and level of education. In conclusion, PI on MRI reflects target organ dose of occupational manganese exposure.

Accidents, Occupational↗

PubMed2003

Molecular modeling of ion channels: structural predictions.

Recent advances in membrane protein crystallography have greatly increased structural information of channels permeating metal ions. Structural bioinformatics techniques and molecular dynamics calculations are providing structural models of ion channels for which the three-dimensional structure is not known. Most of the reported structure prediction studies focus on K(+) channels and are based on the KcsA K(+) channel structure.

Computational Biology↗

PubMedDate not supplied

[Structure of histone fragments and their models. I. Structural features of N-terminal oligopeptides of histone H4].

Circular dichroism (CD) and infrared spectroscopy (IRS) studies of aqueous solutions of fourth N-terminal peptides of histone H4 with different chain length were carried out under various conditions. It was shown that all studied peptides had conformation of extended left-handed helix as well as poly-1-proline II at the acidic and neutral pH, in moderate ionic strength (0,15), in 80% ethanol, 0,2 M sodium dodecylsulphate, in 8 M urea and 5 M guanidinum hydrochloride. This conformation was changed by raising temperature, under transition to the range of basic pH and in the concentrated solutions of CaCl2 (5M).

Amino Acid Sequence↗

PubMed1998

Marginal versus conditional versus 'structural source' models: a rationale for an alternative to log-linear methods for capture-recapture estimates.

Log-linear models for capture-recapture type data are widely used for estimating sizes of populations. Log-linear methods model conditional interactions between the sources. Often, however, the marginal associations are more appropriate and easier for the practitioner to conceptualize. Analyses here of previously published data on cases of spina bifida in upstate New York are used to show how the assumption that sources are conditionally independent can give biased estimates if in fact the sources are marginally independent. A plausible model for the structural sources of interactions between the sources of information about spina bifida cases is developed which implies marginal independence of two of the sources rather than conditional independence. Estimates of the population total based on marginal independence are derived and give larger estimates of the population total than those derived based upon conditional dependence. When investigators can in fact model the likely underlying relationships of the sources in the population, we suggest considering modelling the potential interdependencies of the sources, which we term 'structural source modeling'.

Birth Certificates↗

PubMed2003

A test for deviation from island-model population structure.

The neutral island model forms the basis for several estimation models that relate patterns of genetic structure to microevolutionary processes. Estimates of gene flow are often based on this model and may be biased when the model's assumptions are violated. An appropriate test for violations is to compare FST scores for individual loci to a null distribution based on the average FST taken over multiple loci. A parametric bootstrap method is described here based on Wright's beta-distribution to generate null distributions of FST for each locus. These null distributions account for error introduced by sampling populations, individuals and loci, and also biological sources of error, including variable alleles/locus and inbreeding. Confidence limits can be obtained directly from these distributions. Significant deviations from the island model may be the result of selection, deviations from the island model's migration pattern, nonequilibrium conditions, or other deviations from island-model assumptions. Only strong biases are likely to be detected because of the inherently large sampling variation of FST. Nevertheless, a coefficient, Nb, describing bias in the spread of the beta-distribution in units comparable to the gene flow parameter, Nm, can be obtained for each locus. In samples from populations of the butterfly Coenonympha tullia, the loci Idh-1, Mdh-1, Pgi and Pgm showed significantly lower FST than expected.

Animals↗

PubMed2005

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.

MOTIVATION: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases. RESULTS: SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3. AVAILABILITY: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/

Algorithms↗

PubMed2006

Structural equation models of memory performance across noise conditions and age groups.

Competing models of declarative memory were tested with structural equation models to analyze whether a second-order latent variable structure for episodic and semantic memory was invariant across age groups and across noise exposure conditions. Data were taken from three previous experimental noise studies that were performed with the same design, procedure, and dependent measures, and with participants from four age groups (13-14, 18-20, 35-45, and 55-65 years). Two noise conditions, road traffic noise and meaningful irrelevant speech, were compared to a quiet control group. The structural models put to the test were taken from Nyberg et al. (2003), which employed several memory tests that were the same as ours and studied age-groups that partly overlapped with our groups. In addition we also varied noise exposure conditions. Our analyses replicated and supported the second-order semantic-episodic memory models in Nyberg et al. (2003). The latent variable structures were invariant across age groups, with the exception of our youngest group, which by itself showed a less clear latent structure. The obtained structures were also invariant across noise exposure conditions. We also noted that our text memory items, which did not have a counterpart in the study by Nyberg et al. (2003), tend to form a separate latent variable loading on episodic memory.

Adolescent↗

PubMed1994

Evidence for a ternary complex formed between flavodoxin and cytochrome c3: 1H-NMR and molecular modeling studies.

Small electron-transfer proteins such as flavodoxin (16 kDa) and the tetraheme cytochrome c3 (13 kDa) have been used to mimic, in vitro, part of the complex electron-transfer chain operating between substrate electron donors and respiratory electron acceptors, in sulfate-reducing bacteria (Desulfovibrio species). The nature and properties of the complex formed between these proteins are revealed by 1H-NMR and molecular modeling approaches. Our previous study with the Desulfovibrio vulgaris proteins [Moura, I., Moura, J.J. G., Santos, M.H., & Xavier, A. V. (1980) Cienc. Biol. (Portugal) 5, 195-197; Stewart, D.E. LeGall, J., Moura, I., Moura, J. J. G., Peck, H.D. Jr., Xavier, A. V., Weiner, P. K., & Wampler, J.E. (1988) Biochemistry 27, 2444-2450] indicated that the complex between cytochrome c3 and flavodoxin could be monitored by changes in the NMR signals of the heme methyl groups of the cytochrome and that the electrostatic surface charge (Coulomb's law) on the two proteins favored interaction between one unique heme of the cytochrome with flavodoxin. If the interaction is indeed driven by the electrostatic complementarity between the acidic flavodoxin and a unique positive region of the cytochrome c3, other homologous proteins from these two families of proteins might be expected to interact similarly. In this study, three homologous Desulfovibrio cytochromes c3 were used, which show a remarkable variation in their individual isoelectric points (ranging from 5.5 to 9.5). On the basis of data obtained from protein-protein titrations followed at specific proton NMR signals (i.e., heme methyl resonances), a binding model for this complex has been developed with evaluation of stoichiometry and binding constants. This binding model involves one site on the cytochromes c3 and two sites on the flavodoxin, with formation of a ternary complex at saturation. In order to understand the potential chemical form of the binding model, a structural model for the hypothetical ternary complex, formed between one molecule of Desulfovibrio salexigens flavodoxin and two molecules of cytochrome c3, is proposed. These molecular models of the complexes were constructed on the basis of complementarity of Coulombic electrostatic surface potentials, using the available X-ray structures of the isolated proteins and, when required, model structures (D. salexigens flavodoxin and Desulfovibrio desulfuricans ATCC 27774 cytochrome c3) predicted by homology modeling.

Amino Acid Sequence↗

PubMed1984

Life events and depression in women: a structural equation model.

A non-recursive structural equation model designed to examine the reciprocal relationship between life event reports and depressive symptoms in women is presented. The model was fitted to data from a 2-year longitudinal study of life events and depression in a sample of women with 5-year-old children. The findings suggest that life event reports may be influenced by mental state; however, even when this tendency is taken into account, there is still a substantial relationship between life events and depressive symptoms in women. This indicates that it is unlikely that the life events/depression correlation can be explained simply by a tendency for depressed women to over-report life events.

Adaptation, Psychological↗

PubMed2002

When constraints interact: a caution about reference variables, identification constraints, and scale dependencies in structural equation modeling.

In traditional approaches to structural equations modeling, variances of latent endogenous variables cannot be specified or constrained directly and, consequently, are not identified, unless certain precautions are taken. The usual method for achieving identification has been to fix one factor loading for each endogenous latent variable at unity. An alternative approach is to fix variances using newer constrained estimation algorithms. This article examines the philosophy behind such constraints and shows how their appropriate use is neither as straightforward nor as noncontroversial as portrayed in textbooks and computer manuals. The constraints on latent variable variances can interact with other model constraints to interfere with the testing of certain kinds of hypotheses and can yield incorrect standardized solutions with some popular software.

Humans↗

PubMed2006

On the use of structural equation modeling in health communication research.

Structural equation modeling (SEM) is a multivariate technique suited for testing proposed relations between variables. In this article, the authors discuss the potential for SEM as a tool to advance health communication research both statistically and conceptually. Specifically, the authors discuss the advantages that latent variable modeling in SEM affords researchers by extracting measurement error. In addition, they argue that SEM is useful in understanding communication as a complex set of relations between variables. Moreover, the authors articulate the possibility for examining communication as an agent, mediator, and an outcome. Finally, they review the application of SEM to recursive models, interactions, and confirmatory factor analysis.

Communication↗

PubMed1999

Can structural equation models inform blood pressure research?

OBJECTIVE: To show how structural equation models might be used to better understand the ways in which risk factors influence blood pressure. METHODS: Nine measurements on 2009 women and 1518 men for whom there was complete data both at time 1 and at time 8 of the Framingham Heart Study were used to test a hypothetical model of how risk factors such as age, obesity, smoking, vital capacity, and heart rate influence each other and blood pressure. The hypothetical model was translated into structural equations and tested against the data. RESULTS: The hypothetical model fits the data for women at time 1 very well with a chi2=15.41 which, with 14 degrees of freedom, has P=0.32 and indicates there is no difference between the covariance structure generated by the hypothetical model and the covariance structure generated by the data. The same model was tested for women at time 8 and for men at times 1 and 8 also and fit almost as well. Age and percentage of ideal weight of subjects exert the strongest influence on systolic blood pressure, whereas the effect of age on diastolic blood pressure seems less consistent. Smoking has no direct effect on blood pressure, but it does have a small effect on heart rate and a negative effect on obesity, suggesting, perhaps, that, while it has no direct effect, it does play an indirect role. CONCLUSIONS: Structural equation models can be used by researchers trying to understand how risk factors can influence blood pressure in complex ways. The methodology is especially appropriate for testing competing conceptual models.

Blood Pressure↗

PubMed1998

Use of structural equation modeling to test the construct validity of the SF-36 Health Survey in ten countries: results from the IQOLA Project. International Quality of Life Assessment.

A crucial prerequisite to the use of the SF-36 Health Survey in multinational studies is the reproduction of the conceptual model underlying its scoring and interpretation. Structural equation modeling (SEM) was used to test these aspects of the construct validity of the SF-36 in ten IQOLA countries: Denmark, France, Germany, Italy, the Netherlands, Norway, Spain, Sweden, the United Kingdom, and the United States. Data came from general population surveys fielded to gather normative data. Measurement and structural models developed in the United States were cross-validated in random halves of the sample in each country. SEM analyses supported the eight first-order factor model of health that underlies the scoring of SF-36 scales and two second-order factors that are the basis for summary physical and mental health measures. A single third-order factor was also observed in support of the hypothesis that all responses to the SF-36 are generated by a single, underlying construct--health. In addition, a third second-order factors, interpreted as general well-being, was shown to improve the fit of the model. This model (including eight first-order factors, three second-order factors, and one third-order factor) was cross-validated using a holdout sample within the United States and in each of the nine other countries. These results confirm the hypothesized relationships between SF-36 items and scales and justify their scoring in each country using standard algorithms. Results also suggest that SF-36 scales and summary physical and mental health measures will have similar interpretations across countries. The practical implications of a third second-order SF-36 factor (general well-being) warrant further study.

Cross-Cultural Comparison↗

PubMed2005

Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.

Despite the advantages provided by the enormous recent increases in the availability of structural information, functional assignment for the large number of proteins represented in the sequence and structural genomics projects remains a pressing problem for genomic era biology. This section describes work relevant to this problem from several perspectives, including new approaches that take advantage of combined structure and sequence-based classification. Leveraging of genomic context and evolutionary information to improve classification and predictive power is a second prominent theme in the papers represented here. Finally, issues in building a database for linking sequence, structural, and functional information are explored.

Genomics↗