Coalescent simulation in continuous space:Algorithms for large neighbourhood size

Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail

A Comparison of Three Groups of Teacher Trainees\u27 Conceptual and Philosophical Orientations

Problem: The purpose of this study was twofold: first, to determine the differences among the subjects in the three elementary teacher training programs offered at the University of North Dakota (UND) during the spring semester of the 1970-71 school year; and second, to determine the relationships between the Conceptual Systems Test (CST) variables and the Ross Educational Philosophical Inventory (REPI) variables. Procedure: The subjects for this study consisted of juniors and seniors enrolled in the three elementary teacher training programs offered at UND during the spring semester of the 1970-71 school year. The three elementary teacher training programs were: College of Education; New School of Behavioral Studies in Education; and Northern Plains Indian Teacher Corps. On the basis of Harvey’s score profile the conceptual orientations of the 152 subjects were distributed as follows: approximately 51 per cent in System 1; 3 per cent in System 2; 34 per cent in System 3; 9 per cent in System 4; and 3 per cent admixtures. Using the method of highest score on the REPI, the philosophical orientations of the 152 subjects yielded the following distribution: approximately 5 per cent Idealists; 3 per cent Realists; 36 per cent Pragmatists; 44 per cent Existentialists; and 12 per cent with no defined philosophy. Both the CST and the REPI were completed by the subjects during the spring semester of the 1970-71 school year. The statistical procedures utilized in the analyses of the data consisted of: one-way analysis of variance, chi-square test, Dunn\u27s c test for making multiple comparisons among the means, zero-order correlation, and the Veldman method of canonical correlation. The .05 level was used for evaluating the significance of the results. Findings: The findings of the present study are summarized below in the same order in which the research questions and hypothesis were presented: 1. There were significant differences among the programs on the following variables: age, sex, year in program, teaching experience, Divine Fate Control (DFC), Need for People (NFP), Interpersonal Aggression (IA), Anomie, Idealism, Realism, Pragmatism, and Existentialism. 2. There was a significant difference for year in program among the conceptual orientations of the subjects. 3. There were no significant differences for age, sex, year in program, and teaching experience among the philosophical orientations of the subjects. 4. There was a significant canonical relationship between the CST variable, Divine Fate Control, and the REPI variable, Idealism. Conclusion: Concerning the variables of age, sex, and teaching experience, it was concluded that the New School program recruited and trained older, experienced teachers. Also, the New School and Teacher Corps programs attracted more male teacher trainees. On the CST variables, College of Education and Teacher Corps trainees possessed a greater respect for authority; College of Education trainees compared to New School trainees were more influenced by the need to seek group approval for their actions and values; New School and Teacher Corps trainees tended toward interpersonal aggression and Teacher Corps trainees were most affected by impaired social norms. On the REPI variables, no meaningful interpretation could be placed on the higher scores of the Teacher Corps trainees. In considering the conceptual orientations of the subjects, it was concluded that their conceptual development from junior to senior year was in accord with the Conceptual Systems Theory. In considering the relationship between the subjects’ conceptual and philosophical orientations, it xjas concluded that authoritarianism was the mediating link between the positively related Divine Fate Control and Idealism

Coalescent simulation in continuous space

Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation by distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module

Antinuclear antibodies (ANA) in chronic hepatitis C virus infection: correlates of positivity and clinical relevance.

We examined correlates of antinuclear antibody (ANA) positivity (ANA+) in individuals with chronic hepatitis C virus (HCV) infection and the effect of positivity on clinical outcome of HCV. Pretreatment sera from 645 patients from three centres in Sweden (n = 225), the UK (n = 207) and Italy (n = 213) were evaluated by indirect immunofluorescence on Hep-2 cells for ANA pattern and titre by a single laboratory. Liver biopsies were all scored by one pathologist. A total of 258 patients were subsequently treated with interferon monotherapy. There was a significant difference in the prevalence of ANA (1:40) by geographic location: Lund 4.4%, London 8.7%, Padova 10.3% [odds ratio (OR) = 0.66; 95% CI: 0.46-0.94; P = 0.023]. Duration of HCV infection, age at infection, current age, route of infection, viral genotype, alcohol consumption, fibrosis stage and inflammatory score were not correlated with ANA+ or ANA pattern. Female gender was correlated with ANA+ and this association persisted in multivariable analyses (OR = 3.0; P = 0.002). Increased plasma cells were observed in the liver biopsies of ANA-positive individuals compared with ANA-negative individuals, while a trend towards decreased lymphoid aggregates was observed [hazard ratio (HR) = 9.0, P = 0.037; HR = 0.291, P = 0.118, respectively]. No correlations were observed between ANA positivity and nonresponse to therapy (OR = 1.4; P = 0.513), although ANA+ was correlated with faster rates of liver fibrosis, this was not statistically significant (OR = 1.8; P = 0.1452). Low titre ANA+ should not be a contraindication for interferon treatment. Our observation of increased plasma cells in ANA+ biopsies might suggest B-cell polyclonal activity with a secondary clinical manifestation of increased serum immunoglobulins

The physical gravitational degrees of freedom

When constructing general relativity (GR), Einstein required 4D general covariance. In contrast, we derive GR (in the compact, without boundary case) as a theory of evolving 3-dimensional conformal Riemannian geometries obtained by imposing two general principles: 1) time is derived from change; 2) motion and size are relative. We write down an explicit action based on them. We obtain not only GR in the CMC gauge, in its Hamiltonian 3 + 1 reformulation but also all the equations used in York's conformal technique for solving the initial-value problem. This shows that the independent gravitational degrees of freedom obtained by York do not arise from a gauge fixing but from hitherto unrecognized fundamental symmetry principles. They can therefore be identified as the long-sought Hamiltonian physical gravitational degrees of freedom.Comment: Replaced with published version (minor changes and added references

Laryngeal and respiratory patterns in patients with paradoxical vocal fold motion

SummaryThe purposes of this study were to determine the differences in spirometric measures obtained from patients with endoscopically-documented paradoxical vocal fold motion (PVFM) and to compare them to a group of normal subjects without endoscopically-documented paradoxical vocal fold motion during non-provocative breathing and following speech. Thirty eight subjects with documented paradoxical vocal fold motion using transnasal flexible laryngoscopy (TFL) and no history of asthma and 21 normal subjects with documented normal breathing patterns and normal findings on endoscopy underwent flow-volume loop studies. Endoscopic judgments of vocal fold motion from three breathing conditions were made by two observers. The results of the endoscopic judgments indicate that paradoxical motion occurs whether breathing through the nose or mouth in the PVFM subjects, mainly after speaking and inhalation. In addition, the spirometry results indicated that the inspiratory measure of FIVC%, FVC% and FIV0.5/FIVC were significantly lower in the PVFM group compared to the normal subjects. The data supports the hypothesis that in patients with PVFM, inspiratory spirometric values play a role in identifying patients with PVFM. The finding of vocal fold closure following a speech utterance in the majority of the PVFM subjects but not in the normal control group warrants further investigation

Stability analysis of electrical powered wheelchair-mounted robotic-assisted transfer device

The ability of people with disabilities to live in their homes and communities with maximal independence often hinges, at least in part, on their ability to transfer or be transferred by an assistant. Because of limited resources and the expense of personal care, robotic transfer assistance devices will likely be in great demand. An easy-to-use system for assisting with transfers, attachable to electrical powered wheelchairs (EPWs) and readily transportable, could have a significant positive effect on the quality of life of people with disabilities. We investigated the stability of our newly developed Strong Arm, which is attached and integrated with an EPW to assist with transfers. The stability of the system was analyzed and verified by experiments applying different loads and using different system configurations. The model predicted the distributions of the system’s center of mass very well compared with the experimental results. When real transfers were conducted with 50 and 75 kg loads and an 83.25 kg dummy, the current Strong Arm could transfer all weights safely without tip-over. Our modeling accurately predicts the stability of the system and is suitable for developing better control algorithms to enhance the safety of the device

The influence of paediatric HIV infection on circulating B cell subsets and CXCR5+ T helper cells

Antiretroviral therapy (ART) only partially restores HIV-induced alterations in lymphocyte populations. We assessed B and T cell phenotypes in a cohort of children from a single centre in the United Kingdom with perinatally acquired HIV compared to healthy controls. The majority of HIV infected children (44 of 56) were on fully suppressive combination ART. Children with perinatally acquired HIV had significantly lower memory B and CD4(+) CD45RO(+) CXCR5(+) [follicular T helper cell (Tfh)-like] T cell percentages. Detectable viraemia was associated with higher CD21(-) (activated and exhausted/tissue-like memory) B cells. A greater proportion of life spent on suppressive ART was associated with higher memory B cell percentages. These results suggest that early and sustained suppressive ART may preserve B and T cell phenotypes in perinatally acquired HIV and limit deficits in humoral immunity. A lower proportion of circulating Tfh-like cells in HIV infected children appears to be independent of HIV treatment history and ongoing HIV viraemia and warrants further investigation