Simulating The Cooling Of Medical Ct-Scanners: Part 1: Formulation

CT-scanners are used as an non-invasive detecting method in medical applications as a powerful radiological device. Many patients are used CT-scanners for detecting disease. However CT-scanners required cooling due to the huge heat generated during the operation. In this work we modeled a convection-diffusion cooling process of CT-scan devices. A flow in a rectangular body with symmetry, constant heat flux and constant temperature boundary conditions has been considered. The governing equation has been discredited based on the finite volume method and has been solved using a fully implicit method. This paper is mostly concerned with the problem description and the results presents in part 2 of this paper. Hafshejani M K, Dadjoo F, Alimoradi F, Falavand A, Arad A. Simulating the Cooling of Medical CT-Scanners: Part 1: Formulation. Life Sci J 2012;9(1):1029-1034] (ISSN:1097-8135). http://www.lifesciencesite.com. 14

Demography of Medical Journals in Iran; a Cross-Sectional Study

Introduction: Policymaking in order to increase the quality of medical journals needs having accurate data from their current status. Objective: The present study was designed with the aim of introducing a demographic scheme of Iranian journals in the field of medical sciences. Method: This cross-sectional study was performed on all the medical journals being published in Iran in 2016. The list of all journal titles was extracted by referring to the medical journals databanks (ministry of health, Magiran, IranMedex, Irandoc and…), and the data required for the study were gathered using journals’ homepages or by phone or in person, by attending the journal’s office. Results: Totally, 521 journals were assessed. Publication language used was English in 297 (57%) journals and 515 (98.85%) were open access. 381 (73.1%) journals were published quarterly and the year of starting publication was 2010 onwards in case of 245 (48.0%) of journals. There were 29 (5.56%) journals, which were indexed in all 3 databases of ISI, PubMed and Scopus. Only 4.81% of the journals had an official impact factor announced by Thomson-Reuters or Clarivate Analytics Company. Mean time needed for review of articles was 1.89 ± 1.52 (0.5 – 12) months (n = 146) and mean time interval between accepting an article and its print or electronic publication was 3.63 ± 2.17 (0 – 12) months (n = 144). Rate of membership of these journals in COPE and ICMJE were 40% and 27%, respectively. Conclusion: Most medical journals being published in Iran were English quarterly journals that were regularly published in the fields of general medicine, open access, with university affiliations, centered in the capital, and more than 80% of them had started publishing from 2000 and afterwards

Demography of Medical Journals in Iran; a Cross-Sectional Study

Introduction: Policymaking in order to increase the quality of medical journals needs having accurate data from their current status. Objective: The present study was designed with the aim of introducing a demographic scheme of Iranian journals in the field of medical sciences. Method: This cross-sectional study was performed on all the medical journals being published in Iran in 2016. The list of all journal titles was extracted by referring to the medical journals databanks (ministry of health, Magiran, IranMedex, Irandoc and…), and the data required for the study were gathered using journals’ homepages or by phone or in person, by attending the journal’s office. Results: Totally, 521 journals were assessed. Publication language used was English in 297 (57%) journals and 515 (98.85%) were open access. 381 (73.1%) journals were published quarterly and the year of starting publication was 2010 onwards in case of 245 (48.0%) of journals. There were 29 (5.56%) journals, which were indexed in all 3 databases of ISI, PubMed and Scopus. Only 4.81% of the journals had an official impact factor announced by Thomson-Reuters or Clarivate Analytics Company. Mean time needed for review of articles was 1.89 ± 1.52 (0.5 – 12) months (n = 146) and mean time interval between accepting an article and its print or electronic publication was 3.63 ± 2.17 (0 – 12) months (n = 144). Rate of membership of these journals in COPE and ICMJE were 40% and 27%, respectively. Conclusion: Most medical journals being published in Iran were English quarterly journals that were regularly published in the fields of general medicine, open access, with university affiliations, centered in the capital, and more than 80% of them had started publishing from 2000 and afterwards

Agents.jl: A performant and feature-full agent based modelling software of minimal code complexity

Agent based modelling is a simulation method in which autonomous agents interact with their environment and one another, given a predefined set of rules. It is an integral method for modelling and simulating complex systems, such as socio-economic problems. Since agent based models are not described by simple and concise mathematical equations, code that generates them is typically complicated, large, and slow. Here we present Agents.jl, a Julia-based software that provides an ABM analysis platform with minimal code complexity. We compare our software with some of the most popular ABM software in other programming languages. We find that Agents.jl is not only the most performant, but also the least complicated software, providing the same (and sometimes more) features as the competitors with less input required from the user. Agents.jl also integrates excellently with the entire Julia ecosystem, including interactive applications, differential equations, parameter optimization, and more. This removes any ``extensions library'' requirement from Agents.jl, which is paramount in many other tools

Population size affects adaptation in complex ways: simulations on empirical adaptive landscapes

Do large populations always outcompete smaller ones? Does increasing the mutation rate have a similar effect to increasing the population size, with respect to the adaptation of a population? How important are substitutions in determining the adaptation rate? In this study, we ask how population size and mutation rate interact to affect adaptation on empirical adaptive landscapes. Using such landscapes, we do not need to make many ad hoc assumption about landscape topography, such as about epistatic interactions among mutations or about the distribution of fitness effects. Moreover, we have a better understanding of all the mutations that occur in a population and their effects on the average fitness of the population than we can know in experimental studies. Our results show that the evolutionary dynamics of a population cannot be fully explained by the population mutation rate NμN\mu; even at constant NμN\mu, there can be dramatic differences in the adaptation of populations of different sizes. Moreover, the substitution rate of mutations is not always equivalent to the adaptation rate, because we observed populations adapting to high adaptive peaks without fixing any mutations. Finally, in contrast to some theoretical predictions, even on the most rugged landscapes we study, small population size is never an advantage over larger population size. These result show that complex interactions among multiple factors can affect the evolutionary dynamics of populations, and simple models should be taken with caution

Parallel or convergent evolution in human population genomic data revealed by genotype networks

BACKGROUND: Genotype networks are representations of genetic variation data that are complementary to phylogenetic trees. A genotype network is a graph whose nodes are genotypes (DNA sequences) with the same broadly defined phenotype. Two nodes are connected if they differ in some minimal way, e.g., in a single nucleotide. RESULTS: We analyze human genome variation data from the 1,000 genomes project, and construct haploid genotype (haplotype) networks for 12,235 protein coding genes. The structure of these networks varies widely among genes, indicating different patterns of variation despite a shared evolutionary history. We focus on those genes whose genotype networks show many cycles, which can indicate homoplasy, i.e., parallel or convergent evolution, on the sequence level. CONCLUSION: For 42 genes, the observed number of cycles is so large that it cannot be explained by either chance homoplasy or recombination. When analyzing possible explanations, we discovered evidence for positive selection in 21 of these genes and, in addition, a potential role for constrained variation and purifying selection. Balancing selection plays at most a small role. The 42 genes with excess cycles are enriched in functions related to immunity and response to pathogens. Genotype networks are representations of genetic variation data that can help understand unusual patterns of genomic variation

VCF2Networks: applying genotype networks to single-nucleotide variants data

Summary: A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a representation of the set of genotypes associated with a single phenotype, and they allow one to estimate properties such as the robustness of the phenotype to mutations, and the ability of its associated genotypes to evolve new adaptations. So far, though, genotype networks analysis has rarely been applied to population genetics data. To help fill this gap, here we present VCF2Networks, a tool to determine and study genotype network structure from single-nucleotide variant data. Availability and implementation: VCF2Networks is available at https://bitbucket.org/dalloliogm/vcf2networks. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin