135,125 research outputs found
Special features of RAD Sequencing data:implications for genotyping
No full textRestriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools
Identification of a sex-linked SNP marker in the salmon louse (Lepeophtheirus salmonis) using RAD sequencing
No full textThe salmon louse (Lepeophtheirus salmonis (Krøyer, 1837)) is a parasitic copepod that can, if untreated, cause considerable damage to Atlantic salmon (Salmo salar Linnaeus, 1758) and incurs significant costs to the Atlantic salmon mariculture industry. Salmon lice are gonochoristic and normally show sex ratios close to 1:1. While this observation suggests that sex determination in salmon lice is genetic, with only minor environmental influences, the mechanism of sex determination in the salmon louse is unknown. This paper describes the identification of a sex-linked Single Nucleotide Polymorphism (SNP) marker, providing the first evidence for a genetic mechanism of sex determination in the salmon louse. Restriction site-associated DNA sequencing (RAD-seq) was used to isolate SNP markers in a laboratory-maintained salmon louse strain. A total of 85 million raw Illumina 100 base paired-end reads produced 281,838 unique RAD-tags across 24 unrelated individuals. RAD marker Lsa101901 showed complete association with phenotypic sex for all individuals analysed, being heterozygous in females and homozygous in males. Using an allele-specific PCR assay for genotyping, this SNP association pattern was further confirmed for three unrelated salmon louse strains, displaying complete association with phenotypic sex in a total of 96 genotyped individuals. The marker Lsa101901 was located in the coding region of the prohibitin-2 gene, which showed a sex-dependent differential expression, with mRNA levels determined by RT-qPCR about 1.8-fold higher in adult female than adult male salmon lice. This study's observations of a novel sex-linked SNP marker are consistent with sex determination in the salmon louse being genetic and following a female heterozygous system. Marker Lsa101901 provides a tool to determine the genetic sex of salmon lice, and could be useful in the development of control strategies
An investigation into the applicability of the RAD methodology when applied to the development of an information system
No full textWithin any software-related environment many tools, techniques and SDMs (Software Development Methodologies) can be applied to help control the software development lifecycle. The aim of this thesis is to assess the applicability of the RAD (Rapid Application Development) SDM to software development when designing an MIS (Management Information System) for Philips Components Washington. Both positive and negative characteristics of the approach were examined. This thesis provides detailed conclusions on each of the identified characteristics together with more general analysis of the use of SDMs. Research into several SDMs has been carried out in parallel with the development of the MIS, however the RAD SDM was predominantly used throughout the project. This study has been carried out through the analysis of information requirements around the Philips factory with an aim to providing one central system by which all production figures can be collated and reported upon. Prior to this study no standards for the choice of SDM were in place for software design, however previous SDMs used tended to be more traditional and structured in nature. Through this study, additional areas of analysis have been identified in order to further investigate the RAD SDM. Recommendations have also been provided for any future software projects that Philips may undertake with the application of the RAD methodology
Mapping and Validation of the Major Sex-Determining Region in Nile Tilapia (Oreochromis niloticus L.) Using RAD Sequencing
No full textSex in Oreochromis niloticus (Nile tilapia) is principally determined by an XX/XY locus but other genetic and environmental factors also influence sex ratio. Restriction Associated DNA (RAD) sequencing was used in two families derived from crossing XY males with females from an isogenic clonal line, in order to identify Single Nucleotide Polymorphisms (SNPs) and map the sex-determining region(s). We constructed a linkage map with 3,802 SNPs, which corresponded to 3,280 informative markers, and identified a major sex-determining region on linkage group 1, explaining nearly 96% of the phenotypic variance. This sex-determining region was mapped in a 2 cM interval, corresponding to approximately 1.2 Mb in the O. niloticus draft genome. In order to validate this, a diverse family (4 families; 96 individuals in total) and population (40 broodstock individuals) test panel were genotyped for five of the SNPs showing the highest association with phenotypic sex. From the expanded data set, SNPs Oni23063 and Oni28137 showed the highest association, which persisted both in the case of family and population data. Across the entire dataset all females were found to be homozygous for these two SNPs. Males were heterozygous, with the exception of five individuals in the population and two in the family dataset. These fish possessed the homozygous genotype expected of females. Progeny sex ratios (over 95% females) from two of the males with the "female" genotype indicated that they were neomales (XX males). Sex reversal induced by elevated temperature during sexual differentiation also resulted in phenotypic males with the "female" genotype. This study narrows down the region containing the main sex-determining locus, and provides genetic markers tightly linked to this locus, with an association that persisted across the population. These markers will be of use in refining the production of genetically male O. niloticus for aquaculture
A comparative treatment planning study of intensity modulated radiotherapy and 3-D conformal radiotherapy for head & neck cancer
No full text2nd International Conference on Radiation and Dosimetry in Various Fields of Research, RAD 2014 --27 May 2014 through 30 May 2014 -- --The purpose of this study was to investigate the main differences and the advantages of Intensity Modulated Radiation Therapy (IMRT) in comparison to 3D Conformal Radiotherapy (3DCRT) for head&neck (h&n) patients. In this work, treatment plans of 20 h&n patients treated between 01.01.2011 - 01.01.2012 in Radiation Oncology Department at Cukurova University were prepared for both two treatment techniques and compared statistically. Target volumes described by radiation oncologists were classified according to the taken doses and the defined area planning target volume (PTV) as PTV1, PTV2 and PTV3. Dose values of minimum, maximum and V95% of the target volumes were determined as percentage for each specific definitions and the dose values of organ at risk (OAR) were determined as Gray (Gy). Each result for these two techniques was compared in Eclipse Treatment Planning System (TPS) and the results were discussed according to the p values with using Student's t-test. Additionally, factor of Compatibility Index (Conformity Index, CI) was used to determine the extent which high dose region was compatible with PTV. Radiotherapy compatibility index is a very useful method to quantitatively determine the quality of radiotherapy treatment plans and to show the relationship between isodose distributions and the target volume. © 2014 RAD Conference Proceedings. All rights reserved
RAD-51 foci levels and distribution in wild type, <i>rad-54</i>, <i>dpy-28</i>, and <i>mnT12 (</i>+/–IR).
No full text(A) Histogram shows the distribution of RAD-51 foci at the center versus the arms of the chromosomes in rad-54 mutants compared to wild-type exposed to IR (60 Gy). rad-54 mutants show similar distribution of RAD-51 foci compared to wild-type throughout pachytene. Comparisons among different zones scored not significant by Fisher’s exact test, see S2 File. (B) Histogram depicts the mean number of RAD-51 foci/nucleus observed in different zones of dpy-28 mutant germlines compared to wild-type exposed to IR (60Gy). X-axis shows the position along the germline: PMT-premeiotic tip (germ cells in mitosis), L/Z- leptotene/zygotene, EP- early pachytene, MP- mid-pachytene, and LP- late pachytene. Mean number is indicated above each bar. At least 6 gonads were scored per genotype. Error bars represent SEM from technical repeats for each of two biological replicates. (C) Histogram shows the distribution of RAD-51 foci at the center versus the arms of the chromosomes in dpy-28 mutants compared to wild-type +/- IR (60 Gy). A similar distribution of RAD-51 foci is observed in dpy-28 mutants compared to wild-type throughout pachytene. Percentages are indicated above each bar graph. (D) Histogram depicts the mean number of RAD-51 foci/nucleus observed in different zones of mnT12 mutant germlines exposed to IR (60 Gy) compared to wild-type worms. X-axis shows the position along the germline. Mean number is indicated above each bar graph. At least 6 gonads were scored per genotype. Error bars represent SEM from technical repeats for each of two biological replicates. Comparisons between wild-type and mnT12 mutant worms scored not significant by the two-tailed Mann-Whitney test, 95% C.I., see S1 File. (E) Histogram shows the distribution of RAD-51 foci in the center versus the arm regions of the chromosomes in mnT12 mutants exposed to IR (60 Gy) compared to wild-type worms. mnT12 mutant worms show similar distribution of RAD-51 foci compared to wild-type throughout pachytene. Comparisons among different zones scored not significant by Fisher’s exact test, see S2 File. (TIF)</p
PROTON BORON CAPTURE THERAPY: DOSE CALCULATIONS AND A POSSIBLE NEW MEASUREMENT
No full textSince a few decades, proton therapy is being widely used for cancer treatment, with minimal dose to healthy tissues and surrounding organs. Recent studies have suggested that the efficacy of proton therapy could be enhanced if natural boron is selectively accumulated in the tumor tissues. Such an increase is attributed to the protonboron fusion reaction that leads to the production of low-energy α-particles (~2.9 MeV), a mechanism that resembles the well-known Boron Neutron Capture Therapy. However, analytical calculations and detailed Monte Carlo simulations with GEANT4, both in a macro- and micro-dosimetry approach, indicate that the effect of the p+11B→3α reaction, at the standard Boron concentration levels (less than 100 ppm), is orders of magnitude lower than the one of the primary proton beam inside the tissues. In an attempt to solve this discrepancy, an experimental campaign will be carried out with a low-energy proton beam at the CNA laboratory, in Seville. In this talk, we present the latest results of detailed calculations and Geant4 simulations of the dose related to PBCT and describe the concept at the basis of the proposed experimental activity on the PBCT efficacy
Uma Análise de Debaixo das Rodas de Hermann Hesse: os acréscimos pelo tradutor
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Comunicação e Expressão, Programa de Pós-graduação em Estudos da Tradução, Florianópolis, 2011Esta pesquisa compara a tradução brasileira "Debaixo das Rodas" (1971) com o original Unterm Rad (1906) de Hermann Hesse a partir dos acréscimos aos diálogos e trechos narrativos pelo tradutor Álvaro Cabral. Com base na prototipologia textual proposta por Snell-Hornby (1995), na qual a análise da tradução é feita de maneira interdisciplinar, a recepção do projeto literário de Hesse em relação ao romance escolar Unterm Rad na Alemanha como em outros países onde foi mais lido (PFEIFER, 1977; VAHLBUSCH, 2009) auxilia a configuração do contexto da tradução brasileira. Na interface entre a Literatura Comparada e os Estudos da Tradução, o percurso de uma obra literária do cânone a partir de sua cultura fonte e sua passagem por outras culturas alvo exemplica a discussão sobre a compreensão do texto fonte pelo tradutor (REISS, 2000). Da mesma forma, na análise dos aspectos extralinguísticos e funcionais dos textos fonte e alvo, podem se ilustrar tendências e estratégias tradutórias que se desenvolveram e vem sendo estudadas nos últimos 40 anos em Teorias e Estudos da Tradução.This research compares the Brazilian translation Debaixo das Rodas (1971) with its original Unterm Rad (1906) by Hermann Hesse, taking into consideration the additions made by the translator Álvaro Cabral to the dialogues and narrative passages. Based on the textual prototypology proposed by Snell-Hornby (1995), in which the analysis of translation is interdisciplinary, the reception of Hesse's literary project regarding his school romance in Germany, as well as in other countries where it was most read (PFEIFER, 1977; VAHLBUSCH, 2009), helps setting the context of the Brazilian translation. At the interface between Comparative Literature and Translation Studies, the history of the canons# literary work from its source culture and its passage through other target cultures illustrates the discussion on the understanding of the source text by the translator (REISS, 2000). Likewise, translation strategies can be explained by the analysis of the functional and extralinguistic aspects of the source and target texts in the development of Translation Studies in the last 40 years
Investigation the Response of Rapeseed Cultivars to Moisture Regimes in Different Growth Stages
No full textIn order to evaluate the response of rapeseed cultivars to moisture regimes and correlation analysis in different growth stages, a field experiment was conducted in 2006-7 in seed and plant improvement institute of Karaj, Iran. Results showed that number of pods per plant, pod length, stem diameter, 1000-seed weight, oil seed content and branch numbers per plant were reduced significantly under water deficit stress. Also, grain yield was decreased more than biological yield and this resulted in decreased harvest index. Correlation coefficient analysis revealed that number of pods per plant, number of seeds per main and secondary pod, 1000-seed weight, pod length, biological yield and oil seed content had positive and significant correlation with seed yield. Stopping the irrigation from flowering stage also had undesirable effect on seed yield and its components. Among cultivars, Opera cultivar produced more seed yield (4053 kg ha-1) than the others under normal irrigation and under water deficit stress conditions, Zarfam cultivar had the maximum seed yield during stem elongation (3569 kg ha-1), flowering (2135 kg ha-1) and podding stages (2476 kg ha-1). Okapi had the least changes of oil content than other cultivars. Based on the result of this study can be concluded that Zarfam cultivar had better capability to tolerate drought stress and could produce greater seed yield under stress condition
Flexural strengthening of reinforced concrete beams with NSM-CFRP bars using mechanical interlocking
No full textFlexural strengthening of reinforced concrete (RC) beams using near-surface-mounted (NSM) technique has become an attractive alternative for rehabilitation using fiber reinforced polymer (FRP) materials. Previous studies have recommended using available anchoring techniques to overcome premature bonding failure. In this study, mechanical interlocking grooves were utilized to delay or prevent debonding failure. The first part of the study aimed to investigate the bond characteristics for NSM-CFRP bars by conducting several pullout tests on No. 6, No.10, and No.13 CFRP bars. Results indicate that mechanical interlocking grooves can significantly enhance the bonding capacity and prevent or delay premature bonding failure. In the second part, the proposed NSM CFRP strengthening technique was used to strengthen nine RC beams. In addition to longitudinal grooves, the proposed technique consisted of 6 mm wide lateral grooves (or mechanical interlocking) placed at 76 mm on center along the entire length of the strengthened beams. Steel reinforcement ratios of 0.7% and 0.4% were selected. All beam specimens were tested under four-point bending until failure. Results showed that strengthening was more effective for specimens with a lower steel reinforcement ratio. Percentages of enhancement in flexural strength were between 34-68% and 60–128% for specimens with 0.7% and 0.4% steel reinforcement ratios, respectively. Finally, a simple empirical model was created for the experimental results. Theoretical results showed reasonable agreement with the experimental results. However, the maximum load carrying capacity and flexural stiffness were overestimated for beams with a total reinforcement ratio (steel plus CFRP) larger than 1.1%
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