Hygrothermal Performance Assessments of Traditional Timber-Framed Houses in Turkey by Numerical Analysis

The aim of this research is to evaluate the hygrothermal performances of traditional timber-framed houses’ exterior walls in Turkey to create a base case scenario of hygrothermal behavior as a datum for conservation and restoration projects. There is a unique range of traditional timber-framed houses in Turkey varied according to geographical, social, economic, and cultural characteristics. They are hybrid constructions whereby an infilled timber-framed system is erected on the masonry walls. They are compositions of rectangular studs of wood and infill materials such as adobe, stone, and brick. Most constructed examples may be classified in groups of four depending on infill materials as follows: (1) timber-framed adobe infill, (2) timber-framed brick infill, (3) timber-framed stone infill, and (4) unfilled timber-framed. Within the scope of the research, one example from each type is selected for hygrothermal performance assessments by applying the simulation program DELPHIN 6.1.1. This research is concentrated on the evaluation of hygrothermal performances of the selected types over 4 years (January 01, 2010–January 01, 2014) by investigating the temperature, relative humidity, U-value, and moisture mass model graphics of the cross-section of the wall samples. 2010 was one of the rainiest years and 2013 was one of the less rainy years in the selected locations for the last 10 years. The findings of this paper indicate that when factors such as construction details, materials, and climatic conditions are varied, there may be humidity-based problems in the selected examples. In that case, intersection points of materials, layers, and their relationships should be re-evaluated to improve the hygrothermal performances of the selected walls for conservation and restoration projects

Deep Spin-Glass Hysteresis Area Collapse and Scaling in the d=3d=3 ±J\pm J Ising Model

We investigate the dissipative loss in the $\pm J$ Ising spin glass in three dimensions through the scaling of the hysteresis area, for a maximum magnetic field that is equal to the saturation field. We perform a systematic analysis for the whole range of the bond randomness as a function of the sweep rate, by means of frustration-preserving hard-spin mean field theory. Data collapse within the entirety of the spin-glass phase driven adiabatically (i.e., infinitely-slow field variation) is found, revealing a power-law scaling of the hysteresis area as a function of the antiferromagnetic bond fraction and the temperature. Two dynamic regimes separated by a threshold frequency $\omega_c$ characterize the dependence on the sweep rate of the oscillating field. For $\omega < \omega_c$, the hysteresis area is equal to its value in the adiabatic limit $\omega = 0$, while for $\omega > \omega_c$ it increases with the frequency through another randomness-dependent power law.Comment: 6 pages, 6 figure

Strongly Asymmetric Tricriticality of Quenched Random-Field Systems

In view of the recently seen dramatic effect of quenched random bonds on tricritical systems, we have conducted a renormalization-group study on the effect of quenched random fields on the tricritical phase diagram of the spin-1 Ising model in $d=3$. We find that random fields convert first-order phase transitions into second-order, in fact more effectively than random bonds. The coexistence region is extremely flat, attesting to an unusually small tricritical exponent $\beta_u$; moreover, an extreme asymmetry of the phase diagram is very striking. To accomodate this asymmetry, the second-order boundary exhibits reentrance.Comment: revtex, 4 pages, 2 figs, submitted to PR

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

Background: Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × -48×). Results: We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency. Conclusion: This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey. © 2014 Alkan et al

Ecuador Paraiso Escondido virus, a new flavivirus isolated from New World sand flies in Ecuador, is the first representative of a novel clade in the genus flavivirus

A new flavivirus, Ecuador Paraiso Escondido virus (EPEV), named after the village where it was discovered, was isolated from sand flies (Psathyromyia abonnenci, formerly Lutzomyia abonnenci) that are unique to the New World. This represents the first sand fly-borne flavivirus identified in the New World. EPEV exhibited a typical flavivirus genome organization. Nevertheless, the maximum pairwise amino acid sequence identity with currently recognized flaviviruses was 52.8%. Phylogenetic analysis of the complete coding sequence showed that EPEV represents a distinct clade which diverged from a lineage that was ancestral to the nonvectored flaviviruses Entebbe bat virus, Yokose virus, and Sokoluk virus and also the Aedes-associated mosquito-borne flaviviruses, which include yellow fever virus, Sepik virus, Saboya virus, and others. EPEV replicated in C6/36 mosquito cells, yielding high infectious titers, but failed to reproduce either in vertebrate cell lines (Vero, BHK, SW13, and XTC cells) or in suckling mouse brains. This surprising result, which appears to eliminate an association with vertebrate hosts in the life cycle of EPEV, is discussed in the context of the evolutionary origins of EPEV in the New World.The flaviviruses are rarely (if ever) vectored by sand fly species, at least in the Old World. We have identified the first representative of a sand fly-associated flavivirus, Ecuador Paraiso Escondido virus (EPEV), in the New World. EPEV constitutes a novel clade according to current knowledge of the flaviviruses. Phylogenetic analysis of the virus genome showed that EPEV roots the Aedes-associated mosquito-borne flaviviruses, including yellow fever virus. In light of this new discovery, the New World origin of EPEV is discussed together with that of the other flaviviruses

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Efficiency and strategy-proofness in object assignment problems with multi-demand preferences

Consider the problem of allocating objects to agents and how much they should pay. Each agent has a preference relation over pairs of a set of objects and a payment. Preferences are not necessarily quasi-linear. Non-quasi-linear preferences describe environments where payments influence agents' abilities to utilize objects. This paper is to investigate the possibility of designing efficient and strategy-proof rules in such environments. A preference relation is single demand if an agent wishes to receive at most one object; it is multi demand if whenever an agent receives one object, an additional object makes him better off. We show that if a domain contains all the single demand preferences and at least one multi demand preference relation, and there are more agents than objects, then no rule satisfies efficiency, strategy-proofness, individual rationality, and no subsidy for losers on the domain

Probabilistic Random Walk Models for Comparative Network Analysis

Graph-based systems and data analysis methods have become critical tools in many fields as they can provide an intuitive way of representing and analyzing interactions between variables. Due to the advances in measurement techniques, a massive amount of labeled data that can be represented as nodes on a graph (or network) have been archived in databases. Additionally, novel data without label information have been gradually generated and archived. Labeling and identifying characteristics of novel data is an important first step in utilizing the valuable data in an effective and meaningful way. Comparative network analysis is an effective computational means to identify and predict the properties of the unlabeled data by comparing the similarities and differences between well-studied and less-studied networks. Comparative network analysis aims to identify the matching nodes and conserved subnetworks across multiple networks to enable a prediction of the properties of the nodes in the less-studied networks based on the properties of the matching nodes in the well-studied networks (i.e., transferring knowledge between networks). One of the fundamental and important questions in comparative network analysis is how to accurately estimate node-to-node correspondence as it can be a critical clue in analyzing the similarities and differences between networks. Node correspondence is a comprehensive similarity that integrates various types of similarity measurements in a balanced manner. However, there are several challenges in accurately estimating the node correspondence for large-scale networks. First, the scale of the networks is a critical issue. As networks generally include a large number of nodes, we have to examine an extremely large space and it can pose a computational challenge due to the combinatorial nature of the problem. Furthermore, although there are matching nodes and conserved subnetworks in different networks, structural variations such as node insertions and deletions make it difficult to integrate a topological similarity. In this dissertation, novel probabilistic random walk models are proposed to accurately estimate node-to-node correspondence between networks. First, we propose a context-sensitive random walk (CSRW) model. In the CSRW model, the random walker analyzes the context of the current position of the random walker and it can switch the random movement to either a simultaneous walk on both networks or an individual walk on one of the networks. The context-sensitive nature of the random walker enables the method to effectively integrate different types of similarities by dealing with structural variations. Second, we propose the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) model. In the CUFID model, we construct an integrated network by inserting pseudo edges between potential matching nodes in different networks. Then, we design the random walk protocol to transit more frequently between potential matching nodes as their node similarity increases and they have more matching neighboring nodes. We apply the proposed random walk models to comparative network analysis problems: global network alignment and network querying. Through extensive performance evaluations, we demonstrate that the proposed random walk models can accurately estimate node correspondence and these can lead to improved and reliable network comparison results

The development of a 16S rRNA gene based PCR for the identification of Streptococcus pneumoniae and comparison with four other species specific PCR assays

<p>Abstract</p> <p>Background</p> <p><it>Streptococcus pneumoniae </it>is one of the most frequently encountered pathogens in humans but its differentiation from closely related but less pathogenic streptococci remains a challenge.</p> <p>Methods</p> <p>This report describes a newly-developed PCR assay (Spne-PCR), amplifying a 217 bp product of the 16S rRNA gene of <it>S. pneumoniae</it>, and its performance compared to other genotypic and phenotypic tests.</p> <p>Results</p> <p>The new PCR assay designed in this study, proved to be specific at 57°C for <it>S. pneumoniae</it>, not amplifying <it>S. pseudopneumoniae </it>or any other streptococcal strain or any strains from other upper airway pathogenic species. PCR assays (psaA, LytA, ply, spn9802-PCR) were previously described for the specific amplification of <it>S. pneumoniae</it>, but <it>psaA</it>-PCR was the only one found not to cross-react with <it>S. pseudopneumoniae</it>.</p> <p>Conclusion</p> <p>Spne-PCR, developed for this study, and psaA-PCR were the only two assays which did not mis-identify <it>S. pseudopneumoniae </it>as <it>S. pneumoniae</it>. Four other PCR assays and the AccuProbe assay were unable to distinguish between these species.</p