Phase Transition and Monopoles Densities in a Nearest Neighbors Two-Dimensional Spin Ice Model

In this work, we show that, due to the alternating orientation of the spins in the ground state of the artificial square spin ice, the influence of a set of spins at a certain distance of a reference spin decreases faster than the expected result for the long range dipolar interaction, justifying the use of the nearest neighbor two dimensional square spin ice model as an effective model. Using an extension of the model presented in ref. [Scientific Reports 5, 15875 (2015)], considering the influence of the eight nearest neighbors of each spin on the lattice, we analyze the thermodynamics of the model and study the monopoles and string densities dependence as a function of the temperature.Comment: 11 pages, 8 figure

Determination of Selected Polyaromatic Hydrocarbons by Gas Chromatography-Mass Spectrometry for the Analysis of Wood to Establish the cause of Sinking of an Old Vessel (Scauri wreck) by Fire

The aimof this paper was to establish the cause of sinking of an old wooden vessel by polycyclic aromatic hydrocarbon (PAH) analyses because wood combustion is a source of PAHs. In particular, the molecular PAH patterns generated by each source are like fingerprints and it is possible to determine the processes that generate PAHs by studying their distribution in wood samples. The relative abundance of high molecular weight PAHs, together with the PAH compound ratios and with total index (proposed by us) has demonstrated that samples owe their PAHs in wood archaeological material to a predominant single mode of origin, i.e. combustion processes, therefore we can say that the sinking of the vessel was caused by a fire

Genetic heterogeneity and trans regulators of gene expression

Heterogeneity poses a challenge to linkage mapping. Here, we apply a latent class extension of Haseman-Elston regression to expression phenotypes with significant evidence of linkage to trans regulators in 14 large pedigrees. We test for linkage, accounting for heterogeneity, and classify individual families as "linked" and "unlinked" on the basis of their contribution to the overall evidence of linkage

Facilitating Pupil Thinking About Information Literacy

Whilst information literacy is frequently taught through the imposition on learners of an established framework, this paper suggests a different approach by taking a lead from James Herring’s ideas. Specifically, it provides guidance to school-based information professionals who would like to encourage their pupils to devise their own flexible, information literacy models which are unique to them. Drawing on existing material in information science and wider thought, it proposes areas for coverage and considers how information professionals may support the dynamic process of model construction. It is recommended that those who are intent on facilitating the creation of personal information literacy models help pupils to identify the roles they take on in their lives, to reflect on the information needs that result, to ascertain the information they require in particular situations, to explore their information-seeking activities, to consider means by which information can be captured and to give thought as to how the information they have accessed may be used. This framework is, however, by no means rigid and readers are, of course, free to make their own adjustments

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data

[v2; ref status: indexed, http://f1000r.es/301]Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling of the methylation levels is done from the alignments. A huge effort has been made to quickly and correctly align the reads and many different algorithms and programs to do this have been created. However, the second step is just as crucial and non-trivial, but much less attention has been paid to the final inference of the methylation states. Important error sources do exist, such as sequencing errors, bisulfite failure, clonal reads, and single nucleotide variants. We developed MethylExtract, a user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources. MethylExtract detects variation (SNVs – Single Nucleotide Variants) in a similar way to VarScan, a very sensitive method extensively used in SNV and genotype calling based on non-bisulfite-treated reads. The usefulness of MethylExtract is shown by means of extensive benchmarking based on artificial bisulfite-treated reads and a comparison to a recently published method, called Bis-SNP. MethylExtract is able to detect SNVs within High-Throughput Sequencing experiments of bisulfite treated DNA at the same time as it generates high quality methylation maps. This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation. An exclusive feature of MethylExtract, in comparison with existing software, is the possibility to assess the bisulfite failure in a statistical way. The source code, tutorial and artificial bisulfite datasets are available at http://bioinfo2.ugr.es/MethylExtract/ and http://sourceforge.net/projects/methylextract/, and also permanently accessible from 10.5281/zenodo.7144.This work was supported by the Spanish Government [BIO2008-01353 to JLO and BIO2010-20219 to MH], and Basque country 'AE' grant (GB)

A geographical population analysis of dental trauma in school-children aged 12 and 15 in the city of Curitiba-Brazil

<p>Abstract</p> <p>Background</p> <p>The study presents a geographical analysis of dental trauma in a population of 12 and 15 year-old school-children, in the city of Curitiba, Brazil (n = 1581), using a database obtained in the period 2005-2006. The main focus is to analyze dental trauma using a geographic information system as a tool for integrating social, environmental and epidemiological data.</p> <p>Methods</p> <p>Geostatistical analysis of the database and thematic maps were generated showing the distribution of dental trauma cases according to Curitiba's Health Districts and other variables of interest. Dental trauma spatial variation was assessed using a generalized additive model in order to identify and control the individual risk-factors and thus determine whether spatial variation is constant or not throughout the Health Districts and the place of residence of individuals. In addition, an analysis was made of the coverage of dental trauma cases taking the spatial distribution of Curitiba's primary healthcare centres.</p> <p>Results</p> <p>The overall prevalence of dental trauma was 37.1%, with 53.1% in males and 46.7% in females. The spatial analysis confirms the hypothesis that there is significant variation in the occurrence of dental trauma, considering the place of residence in the population studied (Monte Carlo test, p = 0,006). Furthermore, 28.7% of cases had no coverage by the primary healthcare centres.</p> <p>Conclusions</p> <p>The effect of the place of residence was highly significant in relation to the response variable. The delimitation of areas, as a basis for case density, enables the qualification of geographical territories where actions can be planned based on priority criteria. Promotion, control and rehabilitation actions, applied in regions of higher prevalence of dental trauma, can be more effective and efficient, thus providing healthcare refinement.</p

Gene-Gene and Gene-Environmental Interactions of Childhood Asthma: A Multifactor Dimension Reduction Approach

Background: The importance of gene-gene and gene-environment interactions on asthma is well documented in literature, but a systematic analysis on the interaction between various genetic and environmental factors is still lacking. Methodology/Principal Findings: We conducted a population-based, case-control study comprised of seventh-grade children from 14 Taiwanese communities. A total of 235 asthmatic cases and 1,310 non-asthmatic controls were selected for DNA collection and genotyping. We examined the gene-gene and gene-environment interactions between 17 singlenucleotide polymorphisms in antioxidative, inflammatory and obesity-related genes, and childhood asthma. Environmental exposures and disease status were obtained from parental questionnaires. The model-free and non-parametrical multifactor dimensionality reduction (MDR) method was used for the analysis. A three-way gene-gene interaction was elucidated between the gene coding glutathione S-transferase P (GSTP1), the gene coding interleukin-4 receptor alpha chain (IL4Ra) and the gene coding insulin induced gene 2 (INSIG2) on the risk of lifetime asthma. The testing-balanced accuracy on asthma was 57.83 % with a cross-validation consistency of 10 out of 10. The interaction of preterm birth and indoor dampness had the highest training-balanced accuracy at 59.09%. Indoor dampness also interacted with many genes, including IL13, beta-2 adrenergic receptor (ADRB2), signal transducer and activator of transcription 6 (STAT6). We also used likelihood ratio tests for interaction and chi-square tests to validate our results and all tests showed statistical significance

Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees

Identifying microbial pathogens with zoonotic potential in wild-living primates can be important to human health, as evidenced by human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2) and Ebola virus. Simian foamy viruses (SFVs) are ancient retroviruses that infect Old and New World monkeys and apes. Although not known to cause disease, these viruses are of public health interest because they have the potential to infect humans and thus provide a more general indication of zoonotic exposure risks. Surprisingly, no information exists concerning the prevalence, geographic distribution, and genetic diversity of SFVs in wild-living monkeys and apes. Here, we report the first comprehensive survey of SFVcpz infection in free-ranging chimpanzees (Pan troglodytes) using newly developed, fecal-based assays. Chimpanzee fecal samples (n = 724) were collected at 25 field sites throughout equatorial Africa and tested for SFVcpz-specific antibodies (n = 706) or viral nucleic acids (n = 392). SFVcpz infection was documented at all field sites, with prevalence rates ranging from 44% to 100%. In two habituated communities, adult chimpanzees had significantly higher SFVcpz infection rates than infants and juveniles, indicating predominantly horizontal rather than vertical transmission routes. Some chimpanzees were co-infected with simian immunodeficiency virus (SIVcpz); however, there was no evidence that SFVcpz and SIVcpz were epidemiologically linked. SFVcpz nucleic acids were recovered from 177 fecal samples, all of which contained SFVcpz RNA and not DNA. Phylogenetic analysis of partial gag (616 bp), pol-RT (717 bp), and pol-IN (425 bp) sequences identified a diverse group of viruses, which could be subdivided into four distinct SFVcpz lineages according to their chimpanzee subspecies of origin. Within these lineages, there was evidence of frequent superinfection and viral recombination. One chimpanzee was infected by a foamy virus from a Cercopithecus monkey species, indicating cross-species transmission of SFVs in the wild. These data indicate that SFVcpz (i) is widely distributed among all chimpanzee subspecies; (ii) is shed in fecal samples as viral RNA; (iii) is transmitted predominantly by horizontal routes; (iv) is prone to superinfection and recombination; (v) has co-evolved with its natural host; and (vi) represents a sensitive marker of population structure that may be useful for chimpanzee taxonomy and conservation strategies