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Demography and computer simulation in historic village population reconstruction.

"Demographic anthropology has given rise to methodological advances in the analysis of single community populations. However, the obstacles of small data bases and incomplete vital-event registration remain. This paper details one approach to these problems; the principles of community demography are incorporated with computer simulation methodology, with the goals of validating the internal consistency of and determining demographic secular trends from data commonly utilized in anthropological investigations." The approach is tested on data for the 250 inhabitants of Old Crow Village, Yukon Territory, Canada, in 1978.

Americas↗

A test of crystal structure prediction of small organic molecules.

A collaborative workshop was held in May 1999 at the Cambridge Crystallographic Data Centre to test how well currently available methods of crystal structure prediction perform when given only the atomic connectivity for an organic compound. A blind test was conducted on a selection of four compounds and a wide range of methodologies representing, the principal computer programs currently available were used. There were 11 participants who were allowed to propose at most three structures for each compound. No program gave consistently reliable results. However, seven proposed structures were close to an experimental one and were classified as "correct". One compound occurred in two polymorphs, but only one form was predicted correctly among the calculated structures. The basic problem with lattice energy based methods of crystal structure prediction is that many structures are found within a few kJ mol(-1) of the global minimum. The fine detail of the force-field methodology and parametrization influences the energy ranking within each method. Nevertheless, present methods may be useful in providing a set of structures as possible polymorphs for a given molecular structure.

Journal Article↗

Three-dimensional reconstruction of the myofiber pattern in the fetal and neonatal mouse heart.

A methodology for three-dimensional reconstruction from serial sections and interactive computer graphics is described briefly. This methodology was applied to study the morphogenesis of the cardiac myofiber pattern in the fetal and neonatal mouse heart (ventricles). Few organized in-plane myofibers were found in the myocardial wall before 12 days postconception, but many fibers were observed in the very numerous trabeculae at all times up to birth. However, beginning at about 12 days, the number of fibers in the myocardial wall increases rapidly: these are seen predominantly in the transverse plane. The neonatal mouse heart, especially the left ventricle, resembles a small adult muscular artery. But the global myofiber pattern in the mouse heart at these stages appears to be more complex than might be inferred from earlier studies of the local myofiber pattern at a few sites in the ventricles of a few species of adult mammals. In particular, the pattern in and adjacent to the interventricular septum appears quite complex.

Animals↗

Measurement of acute tolerance to alcohol in human subjects.

Acute tolerance can be defined as a decrease in response to alcohol within a single exposure to the drug, which occurs independently of changes in blood alcohol concentrations (BACs). BACs change over time in most human alcohol administration studies, and computational techniques that account for these changes must be used to measure the rate of acute tolerance development. The most widely used acute tolerance measure in human research is often called the Mellanby effect, and involves the comparison of responses at the same BAC on the ascending and descending limbs of the blood alcohol curve. We compared the Mellanby measure with two other measures of acute tolerance: a conceptually similar area under the curve measure, and a slope function approach that used data only from the descending limb of the blood alcohol curve. The measures were intercorrelated and discussed with regard to empirical and conceptual issues. Exploratory comparisons of those with and without a family history of alcoholism are reported. Methodological recommendations for the computation of acute tolerance are made. The results suggest new methods for measuring the rate of acquisition of acute tolerance, and suggest areas for future research on tolerance-proneness and risk for alcoholism.

Adult↗

Biomarkers in Barrett's esophagus.

This article provides a framework for clinicians who are attempting the difficult task of interpreting the Barrett's biomarker literature with the goal of improving care for their patients. Although many articles. including more that 60 proposed biomarkers, have been published on this subject, only a few describe phase 3 and 4 studies that are of interest to the clinical gastroenterologist (Table 1). For year, dysplasia grade has been the sole means of risk stratification for patients with BE, and it likely will continue to be used in the foreseeable future. The current authors believe that dysplasia classification can be valuable using the team management approach and quality controls described previously. Significant problems, however, have emerged in phase 2 through 4 studies of dysplasia that make it imperative for the Barrett's field to incorporate additional biomarkers as they are validated. These problems include poor reproducibility of dysplasia interpretations, poor predictive value for negative, indefinite, and low-grade dysplasia, and inconsistent results for HGD in different centers, all of which makes it virtually impossible to develop national guidelines for surveillance. Some studies have even suggested that endoscopic biopsy surveillance using dysplasia may not be worthwhile. Currently, flow cytometric tetraploidy and aneuploidy have progressed furthest in biomarker validation (see Table 1). With proper handling, endoscopic biopsy specimens can be shipped to reference laboratories that have the instruments, computer analytic methods, and expertise to reproducibly detect tetraploidy and aneuploidy. The results of phase 4 studies indicate that flow cytometry appears to be useful in detecting a subset of patients who do not have HGD and yet have an increased risk of progression to cancer that cannot be identified by dysplasia grade. For many reasons, the authors anticipate that the number of validated biomarkers will increase substantially in the future. Biopsy repositories are now readily available for phase 3 studies that can evaluate and compare biomarkers. There are initiatives for multi-institutional Barrett's Centers of Excellence that could provide rapid progress in biomarker evaluation. In addition to new candidate biomarkers, the human genome project has provided high-throughput methodologies and methods for computer analysis of data, which can provide the volume and quality control required for clinically useful biomarkers. Currently, 17p (p53) LOH has progressed the furthest among molecular biomarkers. The authors do not recommend its routine clinical use at the present time, however. Finally, it is likely that clinicians will want to follow the results of clinical treatment-response studies and epidemiologic studies that evaluate relationship between clinical interventions or environmental risk and protective factors and surrogate endpoints, especially if the endpoints are progessing well along the phases of biomarker validation. These studies are likely to be of clinical interest because they may becoming the basis for randomized clinical trials to prevent cancer in BE.

Adenocarcinoma↗

Computer-assisted measurement of retinal vessel diameters in the Beaver Dam Eye Study: methodology, correlation between eyes, and effect of refractive errors.

OBJECTIVE: Narrowed retinal arterioles may independently predict cardiovascular disease. We describe a computer-assisted method to measure retinal vessel diameters from digitized fundus photographs in a large population, and examine the correlation of retinal vessel diameters between eyes and whether refractive errors affect these measurements. DESIGN AND POPULATION: Population-based, cross-sectional study in Beaver Dam, Wisconsin (n = 4926; age, 43-84 years). METHODS: Retinal photographs were digitized, and all arterioles and venules located in an area 0.5 to 1 disc diameter from the optic disc were measured with the aid of computer software. MAIN OUTCOME MEASURES: Summary of retinal arteriolar and venular diameters, and the ratio of their diameters (arteriole:venule ratio [AVR]). RESULTS: Correlation between right and left eyes was substantial for retinal arteriolar diameters (Pearson correlation coefficient, rho = 0.71) and venular diameters (rho = 0.74), and moderate for the AVR (rho = 0.49). The inverse association of higher blood pressure and smaller retinal arteriolar diameters was similar using data from either one eye or two eyes; arteriolar diameters decreased by 4.1 microm (right eyes), 4.0 microm (left eyes), and 4.0 microm (mean of both eyes) with each 10-mmHg increase in mean arterial blood pressure. A myopic refraction was associated with smaller retinal vessel diameters; arteriolar diameters decreased by 2.8 microm and venular diameters by 3.3 microm with each -1.0-diopter shift towards myopia. However, the pattern and strength of the association of blood pressure and retinal vessel diameters were not altered by variations in refractive errors. CONCLUSIONS: There is good correlation of retinal vessel diameters between eyes. A myopic refraction is associated with smaller retinal vessel diameters. The association of retinal arteriolar diameters and blood pressure seems similar using data from either one eye or two eyes, and is minimally affected by refraction. These data suggest that measurement of retinal vessel diameters from one eye without regard to its refractive status may provide adequate information indicative of a person's retinal vessel caliber if information from two eyes and refraction is unavailable.

Adult↗

Development of an avidin-biotin amplified enzyme-linked immunoassay for detection of DNA adducts of the human bladder carcinogen 4-aminobiphenyl.

4-Aminobiphenyl (ABP) is a known human urinary bladder carcinogen which is present in tobacco smoke and may be ubiquitous in the environment. As a biological monitor of carcinogen exposure, we have developed an immunological method for measuring the predominant carcinogen-DNA adduct of ABP, N-(deoxyguanosin-8-yl)-ABP (dG-C8-ABP). Rabbits were immunized with keyhole limpet hemocyanin (KLH) conjugate prepared by a periodate oxidation and coupling of N-(guanosin-8-yl)-ABP (rG-C8-ABP) to the protein. The resulting polyclonal antisera was systematically characterized using dual inhibitor methodology augmented by specialized computer and software support; and a competitive avidin-biotin enzyme-linked immunoassay (A-B ELISA) assay employing polyclonal rabbit anti-KLH-(rG-C8-ABP) was developed. Under the assay conditions described, the detection limit for dG-C8-ABP was 18 fmol/well. The relative lack of reactivity toward ABP, N-acetyl-4-aminobiphenyl, N-(deoxyadenosin-8-yl)-ABP, N-(deoxyguanosin-8-yl)-2-aminofluorene and deoxyguanosine as inhibitors indicated that primary specificity involves epitopes found on the purine and biphenyl rings. Results emphasize the need to define polyclonal anti-adduct sera operationally in the context of the antigen/assay system used to evaluate it. Assay sensitivity was achieved by decreasing the amount of antibody and solid-phase antigen in the competitive portion of the assay and the use of avidin-biotin as well as enzymatic amplification. This methodology is a useful alternative to other ultrasensitive techniques and should be directly applicable to the detection of ABP-DNA adducts in exposed human populations.

Aminobiphenyl Compounds↗

In silico modelling--pharmacophores and hERG channel models.

In computational drug design, modelling studies are undertaken following two main strategies that depend on which information is available. If experimental data exist only for the molecules displaying the biological property of interest, a so-called ligand-based approach is taken; if information is available on the macromolecular target(s) of the compounds (e.g. proteins' 3D structures), target-based studies can be carried out. Recently, in the field of hERG K+-channel blocking drugs, pharmacophoric (ligand-based) studies started appearing aimed at determining the physicochemical features associated with the channel block, and also at predicting the hERG blocking potential of compounds. However, partial homology models (target-based) of the hERG channel have also been built and used as working tools to interpret electrophysiological and mutagenesis studies. Here, we review some of the ligand- and target-based in silico studies carried out on hERG, focusing on both their main characteristics and their meaning. In addition, we discuss some methodological aspects of the computational work that in our opinion should be considered, in view of the construction of reliable models possibly able to predict the functional behaviour of the channel system and the blocking potential of drugs.

Amino Acid Sequence↗

Hemispheric asymmetries on computed tomographic scans in schizophrenia and mania. A controlled study and a critical review.

A major reason for reassessing hemispheric asymmetries in schizophrenics by computed tomography is the methodologic shortcomings of previously published measurement techniques. We used completely blind measurements, multiple measurements performed by two independent examiners of each region of the brain, and an SE of measurement with a confidence level of P less than .01 to define significant asymmetry. The frequency of reversed occipital asymmetry was significantly higher in the 36 schizophrenic than in the 18 manic right-handed male patients. Furthermore, when all of the previously published techniques were applied to these patients, the frequency of such a reversal was consistently higher in the schizophrenic than in the manic group. Further investigation of hemispheric asymmetries in schizophrenics is warranted.

Anthropometry↗

Combining structure-based drug design and pharmacophores.

Development towards integrated computer-aided drug design methodologies is presented by utilising crystal structure complexes to produce structure-based pharmacophores. These novel pharmacophores represent the ligand features that are involved in interactions with the target protein, as well as the space around the ligand occupied by the protein. The protein-ligand complexes can also yield information about all interactions that ligands could potentially form with the binding site, as well as about the size of the binding cavity. Together, these describe a 'superligand', which can also be viewed as a pharmacophore. Various types of novel pharmacophores are discussed and compared, using HIV-1 reverse transcriptase (RT) as the target protein, and their application in database searching is presented.

Binding Sites↗

Towards NeuroML: model description methods for collaborative modelling in neuroscience.

Biological nervous systems and the mechanisms underlying their operation exhibit astonishing complexity. Computational models of these systems have been correspondingly complex. As these models become ever more sophisticated, they become increasingly difficult to define, comprehend, manage and communicate. Consequently, for scientific understanding of biological nervous systems to progress, it is crucial for modellers to have software tools that support discussion, development and exchange of computational models. We describe methodologies that focus on these tasks, improving the ability of neuroscientists to engage in the modelling process. We report our findings on the requirements for these tools and discuss the use of declarative forms of model description--equivalent to object-oriented classes and database schema--which we call templates. We introduce NeuroML, a mark-up language for the neurosciences which is defined syntactically using templates, and its specific component intended as a common format for communication between modelling-related tools. Finally, we propose a template hierarchy for this modelling component of NeuroML, sufficient for describing models ranging in structural levels from neuron cell membranes to neural networks. These templates support both a framework for user-level interaction with models, and a high-performance framework for efficient simulation of the models.

Animals↗

Structural requirements for the induction of the SOS repair in bacteria by nitrated polycyclic aromatic hydrocarbons and related chemicals.

The CASE (computer-automated structure evaluation) methodology was used to investigate the structural basis of the SOS-inducing activity of 56 nitrated polycyclic aromatic hydrocarbons (nitroarenes, nPAH) and the unsubstituted parent PAH molecules. Based upon the presence and/or absence of structural features, CASE identified 5 activating (biophores) and 4 inactivating (biophobes) fragments responsible for the SOS-inducing activity. Based upon these fragments, CASE correctly calculated the genotoxicity of 94.6% of the molecules in the training set (sensitivity = 0.85, specificity = 1.0). Disregarding the questionable experimental results of the unexpected very weak direct-acting activity of the unsubstituted benzo[a]pyrene, dibenzo[a,h]anthracene and 7,12-dimethylbenz[a]anthracene, the concordance of the prediction was 100%, i.e., sensitivity = 1.0, specificity = 1.0. Additionally, the quantitative analysis of the SOS-inducing potency showed a good correlation between the experimental and predicted results. The present analyses indicate an identity in the structural determinants responsible for SOS induction in E. coli PQ37 (SOS chromotest) and mutagenicity in Salmonella typhimurium.

Computer Simulation↗

Clinical predictors of abnormal computed tomography scans in paediatric head injury.

OBJECTIVE: To evaluate whether clinical features associated with head injury in children can be correlated with an abnormal computed tomography (CT) scan. METHODOLOGY: Three hundred and eleven children aged 14 years or younger admitted with a diagnosis of acute head injury were studied retrospectively. RESULTS: A Glasgow Coma Scale (GCS) score of 12 or lower and the presence of focal neurological deficits were significant predictors of an abnormal CT scan. Ninety-five per cent of those with abnormal CT scans and 100% of those with intracranial injury could be identified by the presence of one or more of the nine clinical findings, particularly by a GCS score of 12 or lower, and the presence of focal neurological deficits. Identification was also possible to a lesser degree by loss of consciousness, ataxia, amnesia, drowsiness, headache, seizure or vomiting. CONCLUSION: Use of CT scans can be limited to children with ongoing specific symptoms and/or focal neurological signs. The implementation of guidelines in the management of head injuries in children could have a substantial effect on clinical practice and health-care costs.

Adolescent↗

Evolutionary computation in medicine: an overview.

The term evolutionary computation encompasses a host of methodologies inspired by natural evolution that are used to solve hard problems. This paper provides an overview of evolutionary computation as applied to problems in the medical domains. We begin by outlining the basic workings of six types of evolutionary algorithms: genetic algorithms, genetic programming, evolution strategies, evolutionary programming, classifier systems, and hybrid systems. We then describe how evolutionary algorithms are applied to solve medical problems, including diagnosis, prognosis, imaging, signal processing, planning, and scheduling. Finally, we provide an extensive bibliography, classified both according to the medical task addressed and according to the evolutionary technique used.

Algorithms↗

Cardiac electrophysiological experiments in numero, Part I: Concepts and strategies of mathematical and computer models.

This article is the first of three articles that review mathematical and computer models of the heart and describe their construction, development, research potential, and clinical utility. This article explains the methodological principles of mathematical and computer simulation of biomedical systems. The strategies of model construction, testing, and application are presented; the advantages and limitations of computer simulation studies are explained, and the basic value of computer simulation for cardiological research and practice is discussed.

Cardiac Pacing, Artificial↗

Rectal methohexital sedation for computed tomography imaging of stable pediatric emergency department patients.

OBJECTIVE: Rapid onset of sleep, brief duration of action, and ease of administration are properties that make rectal methohexital (MXT) an attractive choice for sedating stable pediatric emergency department (ED) patients for computed tomography (CT) imaging. METHODOLOGY: One hundred stable patients between 3 and 60 months of age who presented to any of 3 participating EDs and required sedation to undergo CT scanning were given 25 mg/kg of rectal MXT approximately 15 minutes before their imaging. Vital signs and oxygen saturation were recorded at regular intervals. Data collected included indication for CT imaging, time to achieve sleep, time to reach discharge criteria, adequacy of sedation, adverse effects, and parental satisfaction. RESULTS: Ninety-five percent of the patients were adequately sedated with rectal MXT. It took an average of 8 minutes to achieve full sedation and the duration of action averaged 79.3 minutes. Ten percent had transient side effects, but all recovered completely. None required intubation. Parental satisfaction was 90%. CONCLUSION: Rectal MXT compares favorably to other methods of nonintravenous sedation for CT scanning of stable pediatric ED patients in terms of rapidity of onset and reliability but does cause a significant amount of transient respiratory depression. Its use requires careful monitoring of oxygen saturation and should be used only in a setting where physicians skilled in airway management are present. If these requirements are met, it may be a good choice for the relatively noninvasive sedation of pediatric ED patients undergoing painless but anxiety-provoking procedures.methohexital, pediatric procedure sedation, rectal administration, computerized tomography imaging.

Administration, Rectal↗

Statistical analysis of the estimation of distance measures.

Distance functions serve for quantitative evaluation of the degree of similarity, shape content, symmetry, chirality, and so on. We have developed a general methodology and a general computational tool for the estimation of the value of the distance function and of the error in that estimation, which originates in the experimental uncertainty in the location of the set of points of the studied structure (such as that expressed by the atomic displacement factor in X-ray data analysis).

Journal Article↗

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory provides a good approximation to Poisson electrostatic solvation energy calculations if one uses the same definitions of molecular volume for each. In this work, we present a new and improved analytic method for reproducing the Lee-Richards molecular volume, which is the most common volume definition for Poisson calculations. Overall, 1% errors are achieved for absolute solvation energies of a large set of proteins and relative solvation energies of protein conformations. We also introduce an accurate SASA approximation that uses the same machinery employed by our GB method and requires a small addition of computational cost. The combined methodology is shown to yield an efficient and accurate implicit solvent representation for simulations of biopolymers.

Algorithms↗