The spatial regulation of meiotic recombination hotspots: are all DSB hotspots crossover hotspots?

PubMed

Serrentino, Maria-Elisabetta; Borde, Valérie

2012-07-15

A key step for the success of meiosis is programmed homologous recombination, during which crossovers, or exchange of chromosome arms, take place. Crossovers increase genetic diversity but their main function is to ensure accurate chromosome segregation. Defects in crossover number and position produce aneuploidies that represent the main cause of miscarriages and chromosomal abnormalities such as Down's syndrome. Recombination is initiated by the formation of programmed double strand breaks (DSBs), which occur preferentially at places called DSB hotspots. Among all DSBs generated, only a small fraction is repaired by crossover, the other being repaired by other homologous recombination pathways. Crossover maps have been generated in a number of organisms, defining crossover hotspots. With the availability of genome-wide maps of DSBs as well as the ability to measure genetically the repair outcome at several hotspots, it is becoming more and more clear that not all DSB hotspots behave the same for crossover formation, suggesting that chromosomal features distinguish different types of hotspots. Copyright © 2012. Published by Elsevier Inc.

Investigation of iron spin crossover pressure in Fe-bearing MgO using hybrid functional

NASA Astrophysics Data System (ADS)

Cheng, Ya; Wang, Xianlong; Zhang, Jie; Yang, Kaishuai; Zhang, Chuanguo; Zeng, Zhi; Lin, Haiqin

2018-04-01

Pressure-induced spin crossover behaviors of Fe-bearing MgO were widely investigated by using an LDA  +  U functional for describing the strongly correlated Fe–O bonding. Moreover, the simulated spin crossover pressures depend on the applied U values, which are sensitive to environments and parameters. In this work, the spin crossover pressures of (Mg1‑x ,Fe x )O are investigated by using the hybrid functional with a uniform parameter. Our results indicate that the spin crossover pressures increase with increasing iron concentration. For example, the spin crossover pressure of (Mg0.03125,Fe0.96875)O and FeO was 56 GPa and 127 GPa, respectively. The calculated crossover pressures agreed well with the experimental observations. Therefore, the hybrid functional should be an effective method for describing the pressure-induced spin crossover behaviors in transition metal oxides.

The role of crossover operator in evolutionary-based approach to the problem of genetic code optimization.

PubMed

Błażej, Paweł; Wnȩtrzak, Małgorzata; Mackiewicz, Paweł

2016-12-01

One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time. Therefore, heuristic methods should be applied to search the space of possible solutions. Evolutionary algorithms (EA) seem to be ones of such promising approaches. This class of methods is founded both on mutation and crossover operators, which are responsible for creating and maintaining the diversity of candidate solutions. These operators possess dissimilar characteristics and consequently play different roles in the process of finding the best solutions under given criteria. Therefore, the effective searching for the potential solutions can be improved by applying both of them, especially when these operators are devised specifically for a given problem. To study this subject, we analyze the effectiveness of algorithms for various combinations of mutation and crossover probabilities under three models of the genetic code assuming different restrictions on its structure. To achieve that, we adapt the position based crossover operator for the most restricted model and develop a new type of crossover operator for the more general models. The applied fitness function describes costs of amino acid replacement regarding their polarity. Our results indicate that the usage of crossover operators can significantly improve the quality of the solutions. Moreover, the simulations with the crossover operator optimize the fitness function in the smaller number of generations than simulations without this operator. The optimal genetic codes without restrictions on their structure minimize the costs about 2.7 times better than the canonical genetic code. Interestingly, the optimal codes are dominated by amino acids characterized by polarity close to its average value for all amino acids. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Meiotic recombination hotspots - a comparative view.

PubMed

Choi, Kyuha; Henderson, Ian R

2015-07-01

During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Extended precedence preservative crossover for job shop scheduling problems

NASA Astrophysics Data System (ADS)

Ong, Chung Sin; Moin, Noor Hasnah; Omar, Mohd

2013-04-01

Job shop scheduling problems (JSSP) is one of difficult combinatorial scheduling problems. A wide range of genetic algorithms based on the two parents crossover have been applied to solve the problem but multi parents (more than two parents) crossover in solving the JSSP is still lacking. This paper proposes the extended precedence preservative crossover (EPPX) which uses multi parents for recombination in the genetic algorithms. EPPX is a variation of the precedence preservative crossover (PPX) which is one of the crossovers that perform well to find the solutions for the JSSP. EPPX is based on a vector to determine the gene selected in recombination for the next generation. Legalization of children (offspring) can be eliminated due to the JSSP representation encoded by using permutation with repetition that guarantees the feasibility of chromosomes. The simulations are performed on a set of benchmarks from the literatures and the results are compared to ensure the sustainability of multi parents recombination in solving the JSSP.

Genetic algorithm with maximum-minimum crossover (GA-MMC) applied in optimization of radiation pattern control of phased-array radars for rocket tracking systems.

PubMed

Silva, Leonardo W T; Barros, Vitor F; Silva, Sandro G

2014-08-18

In launching operations, Rocket Tracking Systems (RTS) process the trajectory data obtained by radar sensors. In order to improve functionality and maintenance, radars can be upgraded by replacing antennas with parabolic reflectors (PRs) with phased arrays (PAs). These arrays enable the electronic control of the radiation pattern by adjusting the signal supplied to each radiating element. However, in projects of phased array radars (PARs), the modeling of the problem is subject to various combinations of excitation signals producing a complex optimization problem. In this case, it is possible to calculate the problem solutions with optimization methods such as genetic algorithms (GAs). For this, the Genetic Algorithm with Maximum-Minimum Crossover (GA-MMC) method was developed to control the radiation pattern of PAs. The GA-MMC uses a reconfigurable algorithm with multiple objectives, differentiated coding and a new crossover genetic operator. This operator has a different approach from the conventional one, because it performs the crossover of the fittest individuals with the least fit individuals in order to enhance the genetic diversity. Thus, GA-MMC was successful in more than 90% of the tests for each application, increased the fitness of the final population by more than 20% and reduced the premature convergence.

Genetic Algorithm with Maximum-Minimum Crossover (GA-MMC) Applied in Optimization of Radiation Pattern Control of Phased-Array Radars for Rocket Tracking Systems

PubMed Central

Silva, Leonardo W. T.; Barros, Vitor F.; Silva, Sandro G.

2014-01-01

In launching operations, Rocket Tracking Systems (RTS) process the trajectory data obtained by radar sensors. In order to improve functionality and maintenance, radars can be upgraded by replacing antennas with parabolic reflectors (PRs) with phased arrays (PAs). These arrays enable the electronic control of the radiation pattern by adjusting the signal supplied to each radiating element. However, in projects of phased array radars (PARs), the modeling of the problem is subject to various combinations of excitation signals producing a complex optimization problem. In this case, it is possible to calculate the problem solutions with optimization methods such as genetic algorithms (GAs). For this, the Genetic Algorithm with Maximum-Minimum Crossover (GA-MMC) method was developed to control the radiation pattern of PAs. The GA-MMC uses a reconfigurable algorithm with multiple objectives, differentiated coding and a new crossover genetic operator. This operator has a different approach from the conventional one, because it performs the crossover of the fittest individuals with the least fit individuals in order to enhance the genetic diversity. Thus, GA-MMC was successful in more than 90% of the tests for each application, increased the fitness of the final population by more than 20% and reduced the premature convergence. PMID:25196013

The Effect of School Uniform on Incidental Physical Activity among 10-Year-Old Children

ERIC Educational Resources Information Center

Norrish, Hannah; Farringdon, Fiona; Bulsara, Max; Hands, Beth

2012-01-01

The school setting provides a unique opportunity to promote physical activity in children by ensuring adequate time, appropriate facilities and education guidance is offered. However school uniform design could also limit physical activity. A repeated measures crossover design was used to compare school recess and lunchtime physical activity over…

JavaGenes: Evolving Graphs with Crossover

NASA Technical Reports Server (NTRS)

Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

2000-01-01

Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

Invisible hand effect in an evolutionary minority game model

NASA Astrophysics Data System (ADS)

Sysi-Aho, Marko; Saramäki, Jari; Kaski, Kimmo

2005-03-01

In this paper, we study the properties of a minority game with evolution realized by using genetic crossover to modify fixed-length decision-making strategies of agents. Although the agents in this evolutionary game act selfishly by trying to maximize their own performances only, it turns out that the whole society will eventually be rewarded optimally. This “invisible hand” effect is what Adam Smith over two centuries ago expected to take place in the context of free market mechanism. However, this behaviour of the society of agents is realized only under idealized conditions, where all agents are utilizing the same efficient evolutionary mechanism. If on the other hand part of the agents are adaptive, but not evolutionary, the system does not reach optimum performance, which is also the case if part of the evolutionary agents form a uniformly acting “cartel”.

Pedigree data analysis with crossover interference.

PubMed Central

Browning, Sharon

2003-01-01

We propose a new method for calculating probabilities for pedigree genetic data that incorporates crossover interference using the chi-square models. Applications include relationship inference, genetic map construction, and linkage analysis. The method is based on importance sampling of unobserved inheritance patterns conditional on the observed genotype data and takes advantage of fast algorithms for no-interference models while using reweighting to allow for interference. We show that the method is effective for arbitrarily many markers with small pedigrees. PMID:12930760

Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference

PubMed Central

Phillips, Dylan; Wnetrzak, Joanna; Nibau, Candida; Barakate, Abdellah; Ramsay, Luke; Wright, Frank; Higgins, James D.; Perry, Ruth M.; Jenkins, Glyn

2013-01-01

In barley (Hordeum vulgare L.), chiasmata (the physical sites of genetic crossovers) are skewed towards the distal ends of chromosomes, effectively consigning a large proportion of genes to recombination coldspots. This has the effect of limiting potential genetic variability, and of reducing the efficiency of map-based cloning and breeding approaches for this crop. Shifting the sites of recombination to more proximal chromosome regions by forward and reverse genetic means may be profitable in terms of realizing the genetic potential of the species, but is predicated upon a better understanding of the mechanisms governing the sites of these events, and upon the ability to recognize real changes in recombination patterns. The barley MutL Homologue (HvMLH3), a marker for class I interfering crossovers, has been isolated and a specific antibody has been raised. Immunolocalization of HvMLH3 along with the synaptonemal complex transverse filament protein ZYP1, used in conjunction with fluorescence in situ hybridization (FISH) tagging of specific barley chromosomes, has enabled access to the physical recombination landscape of the barley cultivars Morex and Bowman. Consistent distal localization of HvMLH3 foci throughout the genome, and similar patterns of HvMLH3 foci within bivalents 2H and 3H have been observed. A difference in total numbers of HvMLH3 foci between these two cultivars has been quantified, which is interpreted as representing genotypic variation in class I crossover frequency. Discrepancies between the frequencies of HvMLH3 foci and crossover frequencies derived from linkage analysis point to the existence of at least two crossover pathways in barley. It is also shown that interference of HvMLH3 foci is relatively weak compared with other plant species. PMID:23554258

Genetic algorithms applied to the scheduling of the Hubble Space Telescope

NASA Technical Reports Server (NTRS)

Sponsler, Jeffrey L.

1989-01-01

A prototype system employing a genetic algorithm (GA) has been developed to support the scheduling of the Hubble Space Telescope. A non-standard knowledge structure is used and appropriate genetic operators have been created. Several different crossover styles (random point selection, evolving points, and smart point selection) are tested and the best GA is compared with a neural network (NN) based optimizer. The smart crossover operator produces the best results and the GA system is able to evolve complete schedules using it. The GA is not as time-efficient as the NN system and the NN solutions tend to be better.

Mobile transporter path planning

NASA Technical Reports Server (NTRS)

Baffes, Paul; Wang, Lui

1990-01-01

The use of a genetic algorithm (GA) for solving the mobile transporter path planning problem is investigated. The mobile transporter is a traveling robotic vehicle proposed for the space station which must be able to reach any point of the structure autonomously. Elements of the genetic algorithm are explored in both a theoretical and experimental sense. Specifically, double crossover, greedy crossover, and tournament selection techniques are examined. Additionally, the use of local optimization techniques working in concert with the GA are also explored. Recent developments in genetic algorithm theory are shown to be particularly effective in a path planning problem domain, though problem areas can be cited which require more research.

Automatic Combination of Operators in a Genetic Algorithm to Solve the Traveling Salesman Problem.

PubMed

Contreras-Bolton, Carlos; Parada, Victor

2015-01-01

Genetic algorithms are powerful search methods inspired by Darwinian evolution. To date, they have been applied to the solution of many optimization problems because of the easy use of their properties and their robustness in finding good solutions to difficult problems. The good operation of genetic algorithms is due in part to its two main variation operators, namely, crossover and mutation operators. Typically, in the literature, we find the use of a single crossover and mutation operator. However, there are studies that have shown that using multi-operators produces synergy and that the operators are mutually complementary. Using multi-operators is not a simple task because which operators to use and how to combine them must be determined, which in itself is an optimization problem. In this paper, it is proposed that the task of exploring the different combinations of the crossover and mutation operators can be carried out by evolutionary computing. The crossover and mutation operators used are those typically used for solving the traveling salesman problem. The process of searching for good combinations was effective, yielding appropriate and synergic combinations of the crossover and mutation operators. The numerical results show that the use of the combination of operators obtained by evolutionary computing is better than the use of a single operator and the use of multi-operators combined in the standard way. The results were also better than those of the last operators reported in the literature.

Automatic Combination of Operators in a Genetic Algorithm to Solve the Traveling Salesman Problem

PubMed Central

2015-01-01

Genetic algorithms are powerful search methods inspired by Darwinian evolution. To date, they have been applied to the solution of many optimization problems because of the easy use of their properties and their robustness in finding good solutions to difficult problems. The good operation of genetic algorithms is due in part to its two main variation operators, namely, crossover and mutation operators. Typically, in the literature, we find the use of a single crossover and mutation operator. However, there are studies that have shown that using multi-operators produces synergy and that the operators are mutually complementary. Using multi-operators is not a simple task because which operators to use and how to combine them must be determined, which in itself is an optimization problem. In this paper, it is proposed that the task of exploring the different combinations of the crossover and mutation operators can be carried out by evolutionary computing. The crossover and mutation operators used are those typically used for solving the traveling salesman problem. The process of searching for good combinations was effective, yielding appropriate and synergic combinations of the crossover and mutation operators. The numerical results show that the use of the combination of operators obtained by evolutionary computing is better than the use of a single operator and the use of multi-operators combined in the standard way. The results were also better than those of the last operators reported in the literature. PMID:26367182

Repression of harmful meiotic recombination in centromeric regions

PubMed Central

Nambiar, Mridula; Smith, Gerald R.

2016-01-01

During the first division of meiosis, segregation of homologous chromosomes reduces the chromosome number by half. In most species, sister chromatid cohesion and reciprocal recombination (crossing-over) between homologous chromosomes are essential to provide tension to signal proper chromosome segregation during the first meiotic division. Crossovers are not distributed uniformly throughout the genome and are repressed at and near the centromeres. Rare crossovers that occur too near or in the centromere interfere with proper segregation and can give rise to aneuploid progeny, which can be severely defective or inviable. We review here how crossing-over occurs and how it is prevented in and around the centromeres. Molecular mechanisms of centromeric repression are only now being elucidated. However, rapid advances in understanding crossing-over, chromosome structure, and centromere functions promise to explain how potentially deleterious crossovers are avoided in certain chromosomal regions while allowing beneficial crossovers in others. PMID:26849908

Effect of sex, age and genetics on crossover interference in cattle

PubMed Central

Wang, Zhiying; Shen, Botong; Jiang, Jicai; Li, Jinquan; Ma, Li

2016-01-01

Crossovers generated by homologous recombination ensure proper chromosome segregation during meiosis. Crossover interference results in chiasmata being more evenly distributed along chromosomes, but the mechanism underlying crossover interference remains elusive. Based on large pedigrees of Holstein and Jersey cattle with genotype data, we extracted three-generation families, including 147,327 male and 71,687 female meioses in Holstein, and 108,163 male and 37,008 female meioses in Jersey, respectively. We identified crossovers in these meioses and fitted the Housworth-Stahl “interference-escape” model to study crossover interference patterns in the cattle genome. Our result reveals that the degree of crossover interference is stronger in females than in males. We found evidence for inter-chromosomal variation in the level of crossover interference, with smaller chromosomes exhibiting stronger interference. In addition, crossover interference levels decreased with maternal age. Finally, sex-specific GWAS analyses identified one locus near the NEK9 gene on chromosome 10 to have a significant effect on crossover interference levels. This locus has been previously associated with recombination rate in cattle. Collectively, this large-scale analysis provided a comprehensive description of crossover interference across chromosome, sex and age groups, identified associated candidate genes, and produced useful insights into the mechanism of crossover interference. PMID:27892966

Genetic parameters for uniformity of harvest weight and body size traits in the GIFT strain of Nile tilapia.

PubMed

Marjanovic, Jovana; Mulder, Han A; Khaw, Hooi L; Bijma, Piter

2016-06-10

Animal breeding programs have been very successful in improving the mean levels of traits through selection. However, in recent decades, reducing the variability of trait levels between individuals has become a highly desirable objective. Reaching this objective through genetic selection requires that there is genetic variation in the variability of trait levels, a phenomenon known as genetic heterogeneity of environmental (residual) variance. The aim of our study was to investigate the potential for genetic improvement of uniformity of harvest weight and body size traits (length, depth, and width) in the genetically improved farmed tilapia (GIFT) strain. In order to quantify the genetic variation in uniformity of traits and estimate the genetic correlations between level and variance of the traits, double hierarchical generalized linear models were applied to individual trait values. Our results showed substantial genetic variation in uniformity of all analyzed traits, with genetic coefficients of variation for residual variance ranging from 39 to 58 %. Genetic correlation between trait level and variance was strongly positive for harvest weight (0.60 ± 0.09), moderate and positive for body depth (0.37 ± 0.13), but not significantly different from 0 for body length and width. Our results on the genetic variation in uniformity of harvest weight and body size traits show good prospects for the genetic improvement of uniformity in the GIFT strain. A high and positive genetic correlation was estimated between level and variance of harvest weight, which suggests that selection for heavier fish will also result in more variation in harvest weight. Simultaneous improvement of harvest weight and its uniformity will thus require index selection.

Does Cannabis Onset Trigger Cocaine Onset? A Case-Crossover Approach

PubMed Central

O’Brien, Megan S.; Comment, Leah Andrews; Liang, Kung Yee; Anthony, James C.

2016-01-01

Psychiatric researchers tend to select the discordant co-twin design when they seek to hold constant genetic influence while estimating exposure-associated disease risk. The epidemiologic case-crossover research design developed for the past two decades represents a viable alternative, not often seen in psychiatric studies. Here, we turn to the epidemiologic case-crossover approach to examine the idea that cannabis onset is a proximal trigger for cocaine use, with the power of ‘subject-as-own-control’ research used to hold constant antecedent characteristics of the individual drug user, including genetic influence and other traits experienced up to the time of the observed hazard and control intervals. Data are from newly incident cocaine users identified in the 2002–2006 U.S. National Surveys on Drug Use and Health. Among these cocaine users, 48 had both cannabis onset and cocaine onset in the same month-long hazard interval; the expected value is 30 users, based on the control interval we had pre-specified for case-crossover estimation (estimated relative risk, RR = 1.6; exact mid-p = 0.042). Within the framework of a subject-as-own-control design, the evidence is consistent with the hypothesis that cannabis onset is a proximal trigger for cocaine use, with genetic influences (and many environmental conditions and processes) held constant. Limitations are noted and implications discussed. PMID:22228642

Learning Intelligent Genetic Algorithms Using Japanese Nonograms

ERIC Educational Resources Information Center

Tsai, Jinn-Tsong; Chou, Ping-Yi; Fang, Jia-Cen

2012-01-01

An intelligent genetic algorithm (IGA) is proposed to solve Japanese nonograms and is used as a method in a university course to learn evolutionary algorithms. The IGA combines the global exploration capabilities of a canonical genetic algorithm (CGA) with effective condensed encoding, improved fitness function, and modified crossover and…

Genetic recombination as a major cause of mutagenesis in the human globin gene clusters.

PubMed

Borg, Joseph; Georgitsi, Marianthi; Aleporou-Marinou, Vassiliki; Kollia, Panagoula; Patrinos, George P

2009-12-01

Homologous recombination is a frequent phenomenon in multigene families and as such it occurs several times in both the alpha- and beta-like globin gene families. In numerous occasions, genetic recombination has been previously implicated as a major mechanism that drives mutagenesis in the human globin gene clusters, either in the form of unequal crossover or gene conversion. Unequal crossover results in the increase or decrease of the human globin gene copies, accompanied in the majority of cases with minor phenotypic consequences, while gene conversion contributes either to maintaining sequence homogeneity or generating sequence diversity. The role of genetic recombination, particularly gene conversion in the evolution of the human globin gene families has been discussed elsewhere. Here, we summarize our current knowledge and review existing experimental evidence outlining the role of genetic recombination in the mutagenic process in the human globin gene families.

Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals.

PubMed

Dumont, Beth L

2017-01-01

The segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the parameters that shape patterns of recombination rate evolution across species. Here, I use cytogenetic methods for in situ imaging of crossovers in karyotypically diverse house mice (Mus musculus domesticus) and voles (genus Microtus) to test how chromosome number and configuration constrain the distribution of crossovers in a genome. I show that the global distribution of crossovers in house mice is thresholded by a minimum of one crossover per chromosome arm, whereas the crossover landscape in voles is defined by a more relaxed requirement of one crossover per chromosome. I extend these findings in an evolutionary metaanalysis of published recombination and karyotype data for 112 mammalian species and demonstrate that the physical scale of the genomic crossover distribution has undergone multiple independent shifts from one crossover per chromosome arm to one per chromosome during mammalian evolution. Together, these results indicate that the chromosomal scale constraint on crossover rates is itself a trait that evolves among species, a finding that casts light on an important source of crossover rate variation in mammals. Copyright © 2017 by the Genetics Society of America.

Algebraic, geometric, and stochastic aspects of genetic operators

NASA Technical Reports Server (NTRS)

Foo, N. Y.; Bosworth, J. L.

1972-01-01

Genetic algorithms for function optimization employ genetic operators patterned after those observed in search strategies employed in natural adaptation. Two of these operators, crossover and inversion, are interpreted in terms of their algebraic and geometric properties. Stochastic models of the operators are developed which are employed in Monte Carlo simulations of their behavior.

Evolutionary algorithms for multi-objective optimization: fuzzy preference aggregation and multisexual EAs

NASA Astrophysics Data System (ADS)

Bonissone, Stefano R.

2001-11-01

There are many approaches to solving multi-objective optimization problems using evolutionary algorithms. We need to select methods for representing and aggregating preferences, as well as choosing strategies for searching in multi-dimensional objective spaces. First we suggest the use of linguistic variables to represent preferences and the use of fuzzy rule systems to implement tradeoff aggregations. After a review of alternatives EA methods for multi-objective optimizations, we explore the use of multi-sexual genetic algorithms (MSGA). In using a MSGA, we need to modify certain parts of the GAs, namely the selection and crossover operations. The selection operator groups solutions according to their gender tag to prepare them for crossover. The crossover is modified by appending a gender tag at the end of the chromosome. We use single and double point crossovers. We determine the gender of the offspring by the amount of genetic material provided by each parent. The parent that contributed the most to the creation of a specific offspring determines the gender that the offspring will inherit. This is still a work in progress, and in the conclusion we examine many future extensions and experiments.

Genetic Recombination at the Buff Spore Color Locus in SORDARIA BREVICOLLIS. II. Analysis of Flanking Marker Behavior in Crosses between Buff Mutants.

PubMed

Sang, H; Whitehouse, H L

1983-02-01

Aberrant asci containing one or more wild-type spores were selected from crosses between pairs of alleles of the buff locus in the presence of closely linked flanking markers. Data were obtained relating to the site of aberrant segregation and the position of any associated crossover giving recombination of flanking markers. Aberrant segregation at a proximal site within the buff gene may be associated with a crossover proximal to the site of aberrant segregation or, with equal frequency, with a crossover distal to the site of the second mutant present in the cross. Similarly, segregation at a distal site may be associated with a crossover distal to the site or, with lower frequency, with a crossover proximal to the site of the proximal mutant present in the cross. Crossovers between the alleles were rare. This evidence for the relationship between hybrid DNA and crossing over is discussed in terms of current models for the mechanism of recombination.

Orbital Transfer Vehicle Engine Technology High Velocity Ratio Diffusing Crossover

NASA Technical Reports Server (NTRS)

Lariviere, Brian W.

1992-01-01

High speed, high efficiency head rise multistage pumps require continuous passage diffusing crossovers to effectively convey the pumped fluid from the exit of one impeller to the inlet of the next impeller. On Rocketdyne's Orbital Transfer Vehicle (OTV), the MK49-F, a three stage high pressure liquid hydrogen turbopump, utilizes a 6.23 velocity ratio diffusing crossover. This velocity ratio approaches the diffusion limits for stable and efficient flow over the operating conditions required by the OTV system. The design of the high velocity ratio diffusing crossover was based on advanced analytical techniques anchored by previous tests of stationary two-dimensional diffusers with steady flow. To secure the design and the analytical techniques, tests were required with the unsteady whirling characteristics produced by an impeller. A tester was designed and fabricated using a 2.85 times scale model of the MK49-F turbopumps first stage, including the inducer, impeller, and the diffusing crossover. Water and air tests were completed to evaluate the large scale turbulence, non-uniform velocity, and non-steady velocity on the pump and crossover head and efficiency. Suction performance tests from 80 percent to 124 percent of design flow were completed in water to assess these pump characteristics. Pump and diffuser performance from the water and air tests were compared with the actual MK49-F test data in liquid hydrogen.

DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis.

PubMed

Yelina, Nataliya E; Lambing, Christophe; Hardcastle, Thomas J; Zhao, Xiaohui; Santos, Bruno; Henderson, Ian R

2015-10-15

During meiosis, homologous chromosomes undergo crossover recombination, which is typically concentrated in narrow hot spots that are controlled by genetic and epigenetic information. Arabidopsis chromosomes are highly DNA methylated in the repetitive centromeres, which are also crossover-suppressed. Here we demonstrate that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. However, loss of CG DNA methylation maintenance in met1 triggers epigenetic crossover remodeling at the chromosome scale, with pericentromeric decreases and euchromatic increases in recombination. We used recombination mutants that alter interfering and noninterfering crossover repair pathways (fancm and zip4) to demonstrate that remodeling primarily involves redistribution of interfering crossovers. Using whole-genome bisulfite sequencing, we show that crossover remodeling is driven by loss of CG methylation within the centromeric regions. Using cytogenetics, we profiled meiotic DNA double-strand break (DSB) foci in met1 and found them unchanged relative to wild type. We propose that met1 chromosome structure is altered, causing centromere-proximal DSBs to be inhibited from maturation into interfering crossovers. These data demonstrate that DNA methylation is sufficient to silence crossover hot spots and plays a key role in establishing domains of meiotic recombination along chromosomes. © 2015 Yelina et al.; Published by Cold Spring Harbor Laboratory Press.

Effect of sex, age, and breed on genetic recombination features in cattle

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is a fundamental biological process which generates genetic diversity, affects fertility, and influences evolvability. Here we investigate the roles of sex, age, and breed in cattle recombination features, including recombination rate, location and crossover interference. Usin...

Combinatorial optimization problem solution based on improved genetic algorithm

NASA Astrophysics Data System (ADS)

Zhang, Peng

2017-08-01

Traveling salesman problem (TSP) is a classic combinatorial optimization problem. It is a simplified form of many complex problems. In the process of study and research, it is understood that the parameters that affect the performance of genetic algorithm mainly include the quality of initial population, the population size, and crossover probability and mutation probability values. As a result, an improved genetic algorithm for solving TSP problems is put forward. The population is graded according to individual similarity, and different operations are performed to different levels of individuals. In addition, elitist retention strategy is adopted at each level, and the crossover operator and mutation operator are improved. Several experiments are designed to verify the feasibility of the algorithm. Through the experimental results analysis, it is proved that the improved algorithm can improve the accuracy and efficiency of the solution.

A Randomized, Double-Blind, Crossover Comparison of MK-0929 and Placebo in the Treatment of Adults with ADHD

ERIC Educational Resources Information Center

Rivkin, Anna; Alexander, Robert C.; Knighton, Jennifer; Hutson, Pete H.; Wang, Xiaojing J.; Snavely, Duane B.; Rosah, Thomas; Watt, Alan P.; Reimherr, Fred W.; Adler, Lenard A.

2012-01-01

Objective: Preclinical models, receptor localization, and genetic linkage data support the role of D4 receptors in the etiology of ADHD. This proof-of-concept study was designed to evaluate MK-0929, a selective D4 receptor antagonist as treatment for adult ADHD. Method: A randomized, double-blind, placebo-controlled, crossover study was conducted…

Low-light divergence in photovoltaic parameter fluctuations

NASA Astrophysics Data System (ADS)

Shvydka, Diana; Karpov, V. G.; Compaan, A. D.

2003-03-01

We study statistics of the major photovoltaic (PV) parameters, such as open-circuit voltage, short-circuit current, etc., versus light intensity on a set of nominally identical thin-film CdTe/CdS solar cells. A crossover light intensity is found, below which the relative fluctuations of the PV parameters diverge inversely proportional to the square root of the light intensity. We propose a model in which the observed fluctuations are due to lateral nonuniformities in the device structure. The crossover is attributed to the lateral nonuniformity screening length exceeding the device size. From the practical standpoint, our study introduces a simple uniformity diagnostic technique.

GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

PubMed

Curtis, Farren; Li, Xiayue; Rose, Timothy; Vázquez-Mayagoitia, Álvaro; Bhattacharya, Saswata; Ghiringhelli, Luca M; Marom, Noa

2018-04-10

We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.

Fuel management optimization using genetic algorithms and code independence

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeChaine, M.D.; Feltus, M.A.

1994-12-31

Fuel management optimization is a hard problem for traditional optimization techniques. Loading pattern optimization is a large combinatorial problem without analytical derivative information. Therefore, methods designed for continuous functions, such as linear programming, do not always work well. Genetic algorithms (GAs) address these problems and, therefore, appear ideal for fuel management optimization. They do not require derivative information and work well with combinatorial. functions. The GAs are a stochastic method based on concepts from biological genetics. They take a group of candidate solutions, called the population, and use selection, crossover, and mutation operators to create the next generation of bettermore » solutions. The selection operator is a {open_quotes}survival-of-the-fittest{close_quotes} operation and chooses the solutions for the next generation. The crossover operator is analogous to biological mating, where children inherit a mixture of traits from their parents, and the mutation operator makes small random changes to the solutions.« less

Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic recombination maps have been developed in numerous plant species since late the 1980s, very few of these maps have provided the necessary resolution needed to investiga...

Improved bioavailability of calcium in genetically-modified carrots

USDA-ARS?s Scientific Manuscript database

Osteoporosis is one of the world's most prevalent nutritional disorders, and inadequate absorbed calcium is a known contributor to the pathophysiology of this condition. In a cross-over study of 15 male and 15 female young adults, we used a dual stable isotope method with 42Ca-labeled genetically-mo...

Genetic Algorithm Phase Retrieval for the Systematic Image-Based Optical Alignment Testbed

NASA Technical Reports Server (NTRS)

Rakoczy, John; Steincamp, James; Taylor, Jaime

2003-01-01

A reduced surrogate, one point crossover genetic algorithm with random rank-based selection was used successfully to estimate the multiple phases of a segmented optical system modeled on the seven-mirror Systematic Image-Based Optical Alignment testbed located at NASA's Marshall Space Flight Center.

REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans

PubMed Central

Chung, George; Rose, Ann M.; Petalcorin, Mark I.R.; Martin, Julie S.; Kessler, Zebulin; Sanchez-Pulido, Luis; Ponting, Chris P.; Yanowitz, Judith L.; Boulton, Simon J.

2015-01-01

The Caenorhabditis elegans gene rec-1 was the first genetic locus identified in metazoa to affect the distribution of meiotic crossovers along the chromosome. We report that rec-1 encodes a distant paralog of HIM-5, which was discovered by whole-genome sequencing and confirmed by multiple genome-edited alleles. REC-1 is phosphorylated by cyclin-dependent kinase (CDK) in vitro, and mutation of the CDK consensus sites in REC-1 compromises meiotic crossover distribution in vivo. Unexpectedly, rec-1; him-5 double mutants are synthetic-lethal due to a defect in meiotic double-strand break formation. Thus, we uncovered an unexpected robustness to meiotic DSB formation and crossover positioning that is executed by HIM-5 and REC-1 and regulated by phosphorylation. PMID:26385965

Performance impact of mutation operators of a subpopulation-based genetic algorithm for multi-robot task allocation problems.

PubMed

Liu, Chun; Kroll, Andreas

2016-01-01

Multi-robot task allocation determines the task sequence and distribution for a group of robots in multi-robot systems, which is one of constrained combinatorial optimization problems and more complex in case of cooperative tasks because they introduce additional spatial and temporal constraints. To solve multi-robot task allocation problems with cooperative tasks efficiently, a subpopulation-based genetic algorithm, a crossover-free genetic algorithm employing mutation operators and elitism selection in each subpopulation, is developed in this paper. Moreover, the impact of mutation operators (swap, insertion, inversion, displacement, and their various combinations) is analyzed when solving several industrial plant inspection problems. The experimental results show that: (1) the proposed genetic algorithm can obtain better solutions than the tested binary tournament genetic algorithm with partially mapped crossover; (2) inversion mutation performs better than other tested mutation operators when solving problems without cooperative tasks, and the swap-inversion combination performs better than other tested mutation operators/combinations when solving problems with cooperative tasks. As it is difficult to produce all desired effects with a single mutation operator, using multiple mutation operators (including both inversion and swap) is suggested when solving similar combinatorial optimization problems.

Dynamics of a magnetic active Brownian particle under a uniform magnetic field.

PubMed

Vidal-Urquiza, Glenn C; Córdova-Figueroa, Ubaldo M

2017-11-01

The dynamics of a magnetic active Brownian particle undergoing three-dimensional Brownian motion, both translation and rotation, under the influence of a uniform magnetic field is investigated. The particle self-propels at a constant speed along its magnetic dipole moment, which reorients due to the interplay between Brownian and magnetic torques, quantified by the Langevin parameter α. In this work, the time-dependent active diffusivity and the crossover time (τ^{cross})-from ballistic to diffusive regimes-are calculated through the time-dependent correlation function of the fluctuations of the propulsion direction. The results reveal that, for any value of α, the particle undergoes a directional (or ballistic) propulsive motion at very short times (t≪τ^{cross}). In this regime, the correlation function decreases linearly with time, and the active diffusivity increases with it. It the opposite time limit (t≫τ^{cross}), the particle moves in a purely diffusive regime with a correlation function that decays asymptotically to zero and an active diffusivity that reaches a constant value equal to the long-time active diffusivity of the particle. As expected in the absence of a magnetic field (α=0), the crossover time is equal to the characteristic time scale for rotational diffusion, τ_{rot}. In the presence of a magnetic field (α>0), the correlation function, the active diffusivity, and the crossover time decrease with increasing α. The magnetic field regulates the regimes of propulsion of the particle. Here, the field reduces the period of time at which the active particle undergoes a directional motion. Consequently, the active particle rapidly reaches a diffusive regime at τ^{cross}≪τ_{rot}. In the limit of weak fields (α≪1), the crossover time decreases quadratically with α, while in the limit of strong fields (α≫1) it decays asymptotically as α^{-1}. The results are in excellent agreement with those obtained by Brownian dynamics simulations.

Dynamics of a magnetic active Brownian particle under a uniform magnetic field

NASA Astrophysics Data System (ADS)

Vidal-Urquiza, Glenn C.; Córdova-Figueroa, Ubaldo M.

2017-11-01

The dynamics of a magnetic active Brownian particle undergoing three-dimensional Brownian motion, both translation and rotation, under the influence of a uniform magnetic field is investigated. The particle self-propels at a constant speed along its magnetic dipole moment, which reorients due to the interplay between Brownian and magnetic torques, quantified by the Langevin parameter α . In this work, the time-dependent active diffusivity and the crossover time (τcross)—from ballistic to diffusive regimes—are calculated through the time-dependent correlation function of the fluctuations of the propulsion direction. The results reveal that, for any value of α , the particle undergoes a directional (or ballistic) propulsive motion at very short times (t ≪τcross ). In this regime, the correlation function decreases linearly with time, and the active diffusivity increases with it. It the opposite time limit (t ≫τcross ), the particle moves in a purely diffusive regime with a correlation function that decays asymptotically to zero and an active diffusivity that reaches a constant value equal to the long-time active diffusivity of the particle. As expected in the absence of a magnetic field (α =0 ), the crossover time is equal to the characteristic time scale for rotational diffusion, τrot. In the presence of a magnetic field (α >0 ), the correlation function, the active diffusivity, and the crossover time decrease with increasing α . The magnetic field regulates the regimes of propulsion of the particle. Here, the field reduces the period of time at which the active particle undergoes a directional motion. Consequently, the active particle rapidly reaches a diffusive regime at τcross≪τrot . In the limit of weak fields (α ≪1 ), the crossover time decreases quadratically with α , while in the limit of strong fields (α ≫1 ) it decays asymptotically as α-1. The results are in excellent agreement with those obtained by Brownian dynamics simulations.

REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans.

PubMed

Chung, George; Rose, Ann M; Petalcorin, Mark I R; Martin, Julie S; Kessler, Zebulin; Sanchez-Pulido, Luis; Ponting, Chris P; Yanowitz, Judith L; Boulton, Simon J

2015-09-15

The Caenorhabditis elegans gene rec-1 was the first genetic locus identified in metazoa to affect the distribution of meiotic crossovers along the chromosome. We report that rec-1 encodes a distant paralog of HIM-5, which was discovered by whole-genome sequencing and confirmed by multiple genome-edited alleles. REC-1 is phosphorylated by cyclin-dependent kinase (CDK) in vitro, and mutation of the CDK consensus sites in REC-1 compromises meiotic crossover distribution in vivo. Unexpectedly, rec-1; him-5 double mutants are synthetic-lethal due to a defect in meiotic double-strand break formation. Thus, we uncovered an unexpected robustness to meiotic DSB formation and crossover positioning that is executed by HIM-5 and REC-1 and regulated by phosphorylation. © 2015 Chung et al.; Published by Cold Spring Harbor Laboratory Press.

Genetic algorithms using SISAL parallel programming language

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tejada, S.

1994-05-06

Genetic algorithms are a mathematical optimization technique developed by John Holland at the University of Michigan [1]. The SISAL programming language possesses many of the characteristics desired to implement genetic algorithms. SISAL is a deterministic, functional programming language which is inherently parallel. Because SISAL is functional and based on mathematical concepts, genetic algorithms can be efficiently translated into the language. Several of the steps involved in genetic algorithms, such as mutation, crossover, and fitness evaluation, can be parallelized using SISAL. In this paper I will l discuss the implementation and performance of parallel genetic algorithms in SISAL.

A Swarm Optimization Genetic Algorithm Based on Quantum-Behaved Particle Swarm Optimization.

PubMed

Sun, Tao; Xu, Ming-Hai

2017-01-01

Quantum-behaved particle swarm optimization (QPSO) algorithm is a variant of the traditional particle swarm optimization (PSO). The QPSO that was originally developed for continuous search spaces outperforms the traditional PSO in search ability. This paper analyzes the main factors that impact the search ability of QPSO and converts the particle movement formula to the mutation condition by introducing the rejection region, thus proposing a new binary algorithm, named swarm optimization genetic algorithm (SOGA), because it is more like genetic algorithm (GA) than PSO in form. SOGA has crossover and mutation operator as GA but does not need to set the crossover and mutation probability, so it has fewer parameters to control. The proposed algorithm was tested with several nonlinear high-dimension functions in the binary search space, and the results were compared with those from BPSO, BQPSO, and GA. The experimental results show that SOGA is distinctly superior to the other three algorithms in terms of solution accuracy and convergence.

Regulation of Meiotic Recombination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory p. Copenhaver

Meiotic recombination results in the heritable rearrangement of DNA, primarily through reciprocal exchange between homologous chromosome or gene conversion. In plants these events are critical for ensuring proper chromosome segregation, facilitating DNA repair and providing a basis for genetic diversity. Understanding this fundamental biological mechanism will directly facilitate trait mapping, conventional plant breeding, and development of genetic engineering techniques that will help support the responsible production and conversion of renewable resources for fuels, chemicals, and the conservation of energy (1-3). Substantial progress has been made in understanding the basal recombination machinery, much of which is conserved in organisms as diversemore » as yeast, plants and mammals (4, 5). Significantly less is known about the factors that regulate how often and where that basal machinery acts on higher eukaryotic chromosomes. One important mechanism for regulating the frequency and distribution of meiotic recombination is crossover interference - or the ability of one recombination event to influence nearby events. The MUS81 gene is thought to play an important role in regulating the influence of interference on crossing over. The immediate goals of this project are to use reverse genetics to identify mutants in two putative MUS81 homologs in the model plant Arabidopsis thaliana, characterize those mutants and initiate a novel forward genetic screen for additional regulators of meiotic recombination. The long-term goal of the project is to understand how meiotic recombination is regulated in higher eukaryotes with an emphasis on the molecular basis of crossover interference. The ability to monitor recombination in all four meiotic products (tetrad analysis) has been a powerful tool in the arsenal of yeast geneticists. Previously, the qrt mutant of Arabidopsis, which causes the four pollen products of male meiosis to remain attached, was developed as a facile system for assaying recombination using tetrad analysis in a higher eukaryotic system (6). This system enabled the measurement of the frequency and distribution of recombination events at a genome wide level in wild type Arabidopsis (7), construction of genetic linkage maps which include positions for each centromere (8), and modeling of the strength and pattern of interference (9). This proposal extends the use of tetrad analysis in Arabidopsis by using it as the basis for assessing the phenotypes of mutants in genes important for recombination and the regulation of crossover interference and performing a novel genetic screen. In addition to broadening our knowledge of a classic genetic problem - the regulation of recombination by crossover interference - this proposal also provides broader impact by: generating pedagogical tools for use in hands-on classroom experience with genetics, building interdisciplinary collegial partnerships, and creating a platform for participation by junior scientists from underrepresented groups. There are three specific aims: (1) Isolate mutants in Arabidopsis MUS81 homologs using T-DNA and TILLING (2) Characterize recombination levels and interference in mus81 mutants (3) Execute a novel genetic screen, based on tetrad analysis, for genes that regulate meiotic recombination« less

Dielectrophoretic spectroscopy using a microscopic electrode array

NASA Astrophysics Data System (ADS)

Kirmani, Syed Abdul Mannan; Gudagunti, Fleming Dackson; Velmanickam, Logeeshan; Nawarathna, Dharmakeerthi; Lima, Ivan T.

2017-02-01

Dielectrophoresis (DEP) is a commonly used technique in biomedical engineering to manipulate biomolecules. DEP is defined as the force acting on dielectric particles when they are exposed to non-uniform electric fields. DEP effect can be divided in three categories: positive (dielectric particles are attracted to the electrodes), negative, and zero force DEP. The cross-over frequency is the frequency in which the DEP force is equal to zero. The cross-over frequency depends on the conductivity and the permittivity of the particles and of the suspended medium. The DEP cross-over frequency has been utilized in detecting/quantifying biomolecules. A manual procedure is commonly used to estimate the cross-over frequency of biomolecules. Therefore, the accuracy of this detection method is significantly limited. To address this issue, we designed and tested an automated procedure to carry out DEP spectroscopy in dielectric particles dissolved in a biological buffer solution. Our method efficiently measures the effect of the DEP force through a live video feed from the microscope camera and performs real-time image processing. It records the change in the fluorescence emission as the system automatically scans the electric frequency of the function generator over a specified time interval. We demonstrated the effectiveness of the method by extracting the crossover frequencies and the DEP spectrum of polystyrene beads with blue color dye (1000 nm diameter) and green fluorescent polystyrene beads with 500 nm diameter using this procedure. This approach can lead to the development of a biosensor with significantly higher sensitivity than existing detection methods.

Genetic mapping of centromeres in the nine Citrus clementina chromosomes using half-tetrad analysis and recombination patterns in unreduced and haploid gametes.

PubMed

Aleza, Pablo; Cuenca, José; Hernández, María; Juárez, José; Navarro, Luis; Ollitrault, Patrick

2015-03-08

Mapping centromere locations in plant species provides essential information for the analysis of genetic structures and population dynamics. The centromere's position affects the distribution of crossovers along a chromosome and the parental heterozygosity restitution by 2n gametes is a direct function of the genetic distance to the centromere. Sexual polyploidisation is relatively frequent in Citrus species and is widely used to develop new seedless triploid cultivars. The study's objectives were to (i) map the positions of the centromeres of the nine Citrus clementina chromosomes; (ii) analyse the crossover interference in unreduced gametes; and (iii) establish the pattern of genetic recombination in haploid clementine gametes along each chromosome and its relationship with the centromere location and distribution of genic sequences. Triploid progenies were derived from unreduced megagametophytes produced by second-division restitution. Centromere positions were mapped genetically for all linkage groups using half-tetrad analysis. Inference of the physical locations of centromeres revealed one acrocentric, four metacentric and four submetacentric chromosomes. Crossover interference was observed in unreduced gametes, with variation seen between chromosome arms. For haploid gametes, a strong decrease in the recombination rate occurred in centromeric and pericentromeric regions, which contained a low density of genic sequences. In chromosomes VIII and IX, these low recombination rates extended beyond the pericentromeric regions. The genomic region corresponding to a genetic distance < 5cM from a centromere represented 47% of the genome and 23% of the genic sequences. The centromere positions of the nine citrus chromosomes were genetically mapped. Their physical locations, inferred from the genetic ones, were consistent with the sequence constitution and recombination pattern along each chromosome. However, regions with low recombination rates extended beyond the pericentromeric regions of some chromosomes into areas richer in genic sequences. The persistence of strong linkage disequilibrium between large numbers of genes promotes the stability of epistatic interactions and multilocus-controlled traits over successive generations but also maintains multi-trait associations. Identification of the centromere positions will allow the development of simple methods to analyse unreduced gamete formation mechanisms in a large range of genotypes and further modelling of genetic inheritance in sexual polyploidisation breeding schemes.

The impact of insecticide-treated school uniforms on dengue infections in school-aged children: study protocol for a randomised controlled trial in Thailand.

PubMed

Wilder-Smith, Annelies; Byass, Peter; Olanratmanee, Phanthip; Maskhao, Pongsri; Sringernyuang, Luechai; Logan, James G; Lindsay, Steve W; Banks, Sarah; Gubler, Duane; Louis, Valérie R; Tozan, Yesim; Kittayapong, Pattamaporn

2012-11-15

There is an urgent need to protect children against dengue since this age group is particularly sensitive to the disease. Since dengue vectors are active mainly during the day, a potential target for control should be schools where children spend a considerable amount of their day. School uniforms are the cultural norm in most developing countries, worn throughout the day. We hypothesise that insecticide-treated school uniforms will reduce the incidence of dengue infection in school-aged children. Our objective is to determine the impact of impregnated school uniforms on dengue incidence. A randomised controlled trial will be conducted in eastern Thailand in a group of schools with approximately 2,000 students aged 7-18 years. Pre-fabricated school uniforms will be commercially treated to ensure consistent, high-quality insecticide impregnation with permethrin. A double-blind, randomised, crossover trial at the school level will cover two dengue transmission seasons. Practical issues and plans concerning intervention implementation, evaluation, analysing and interpreting the data, and possible policy implications arising from the trial are discussed. clinicaltrial.gov. NCT01563640.

Research and application of multi-agent genetic algorithm in tower defense game

NASA Astrophysics Data System (ADS)

Jin, Shaohua

2018-04-01

In this paper, a new multi-agent genetic algorithm based on orthogonal experiment is proposed, which is based on multi-agent system, genetic algorithm and orthogonal experimental design. The design of neighborhood competition operator, orthogonal crossover operator, Son and self-learning operator. The new algorithm is applied to mobile tower defense game, according to the characteristics of the game, the establishment of mathematical models, and finally increases the value of the game's monster.

Low Light Diagnostics in Thin-Film Photovoltaics

NASA Astrophysics Data System (ADS)

Shvydka, Diana; Karpov, Victor; Compaan, Alvin

2003-03-01

We study statistics of the major photovoltaic (PV) parameters such as open circuit voltage, short circuit current and fill factor vs. light intensity on a set of nominally identical CdTe/CdS solar cells. We found the most probable parameter values to change with the light intensity as predicted by the standard diode model, while their relative fluctuations increase dramatically under low light. The crossover light intensity is found below which the relative fluctuations of the PV parameters diverge inversely proportional to the square root of the light intensity. We propose a model where the observed fluctuations are due to lateral nonuniformities in the device structure. In particular, the crossover is attributed to the lateral nonuniformity screening length exceeding the device size. >From the practical standpoint, our study introduces a simple uniformity diagnostic technique.

Crossing over...Markov meets Mendel.

PubMed

Mneimneh, Saad

2012-01-01

Chromosomal crossover is a biological mechanism to combine parental traits. It is perhaps the first mechanism ever taught in any introductory biology class. The formulation of crossover, and resulting recombination, came about 100 years after Mendel's famous experiments. To a great extent, this formulation is consistent with the basic genetic findings of Mendel. More importantly, it provides a mathematical insight for his two laws (and corrects them). From a mathematical perspective, and while it retains similarities, genetic recombination guarantees diversity so that we do not rapidly converge to the same being. It is this diversity that made the study of biology possible. In particular, the problem of genetic mapping and linkage-one of the first efforts towards a computational approach to biology-relies heavily on the mathematical foundation of crossover and recombination. Nevertheless, as students we often overlook the mathematics of these phenomena. Emphasizing the mathematical aspect of Mendel's laws through crossover and recombination will prepare the students to make an early realization that biology, in addition to being experimental, IS a computational science. This can serve as a first step towards a broader curricular transformation in teaching biological sciences. I will show that a simple and modern treatment of Mendel's laws using a Markov chain will make this step possible, and it will only require basic college-level probability and calculus. My personal teaching experience confirms that students WANT to know Markov chains because they hear about them from bioinformaticists all the time. This entire exposition is based on three homework problems that I designed for a course in computational biology. A typical reader is, therefore, an instructional staff member or a student in a computational field (e.g., computer science, mathematics, statistics, computational biology, bioinformatics). However, other students may easily follow by omitting the mathematically more elaborate parts. I kept those as separate sections in the exposition.

Crossing Over…Markov Meets Mendel

PubMed Central

Mneimneh, Saad

2012-01-01

Chromosomal crossover is a biological mechanism to combine parental traits. It is perhaps the first mechanism ever taught in any introductory biology class. The formulation of crossover, and resulting recombination, came about 100 years after Mendel's famous experiments. To a great extent, this formulation is consistent with the basic genetic findings of Mendel. More importantly, it provides a mathematical insight for his two laws (and corrects them). From a mathematical perspective, and while it retains similarities, genetic recombination guarantees diversity so that we do not rapidly converge to the same being. It is this diversity that made the study of biology possible. In particular, the problem of genetic mapping and linkage—one of the first efforts towards a computational approach to biology—relies heavily on the mathematical foundation of crossover and recombination. Nevertheless, as students we often overlook the mathematics of these phenomena. Emphasizing the mathematical aspect of Mendel's laws through crossover and recombination will prepare the students to make an early realization that biology, in addition to being experimental, IS a computational science. This can serve as a first step towards a broader curricular transformation in teaching biological sciences. I will show that a simple and modern treatment of Mendel's laws using a Markov chain will make this step possible, and it will only require basic college-level probability and calculus. My personal teaching experience confirms that students WANT to know Markov chains because they hear about them from bioinformaticists all the time. This entire exposition is based on three homework problems that I designed for a course in computational biology. A typical reader is, therefore, an instructional staff member or a student in a computational field (e.g., computer science, mathematics, statistics, computational biology, bioinformatics). However, other students may easily follow by omitting the mathematically more elaborate parts. I kept those as separate sections in the exposition. PMID:22629235

Genetic Evolution of Shape-Altering Programs for Supersonic Aerodynamics

NASA Technical Reports Server (NTRS)

Kennelly, Robert A., Jr.; Bencze, Daniel P. (Technical Monitor)

2002-01-01

Two constrained shape optimization problems relevant to aerodynamics are solved by genetic programming, in which a population of computer programs evolves automatically under pressure of fitness-driven reproduction and genetic crossover. Known optimal solutions are recovered using a small, naive set of elementary operations. Effectiveness is improved through use of automatically defined functions, especially when one of them is capable of a variable number of iterations, even though the test problems lack obvious exploitable regularities. An attempt at evolving new elementary operations was only partially successful.

Genetic algorithms and their use in Geophysical Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, Paul B.

1999-04-01

Genetic algorithms (GAs), global optimization methods that mimic Darwinian evolution are well suited to the nonlinear inverse problems of geophysics. A standard genetic algorithm selects the best or ''fittest'' models from a ''population'' and then applies operators such as crossover and mutation in order to combine the most successful characteristics of each model and produce fitter models. More sophisticated operators have been developed, but the standard GA usually provides a robust and efficient search. Although the choice of parameter settings such as crossover and mutation rate may depend largely on the type of problem being solved, numerous results show thatmore » certain parameter settings produce optimal performance for a wide range of problems and difficulties. In particular, a low (about half of the inverse of the population size) mutation rate is crucial for optimal results, but the choice of crossover method and rate do not seem to affect performance appreciably. Optimal efficiency is usually achieved with smaller (< 50) populations. Lastly, tournament selection appears to be the best choice of selection methods due to its simplicity and its autoscaling properties. However, if a proportional selection method is used such as roulette wheel selection, fitness scaling is a necessity, and a high scaling factor (> 2.0) should be used for the best performance. Three case studies are presented in which genetic algorithms are used to invert for crustal parameters. The first is an inversion for basement depth at Yucca mountain using gravity data, the second an inversion for velocity structure in the crust of the south island of New Zealand using receiver functions derived from teleseismic events, and the third is a similar receiver function inversion for crustal velocities beneath the Mendocino Triple Junction region of Northern California. The inversions demonstrate that genetic algorithms are effective in solving problems with reasonably large numbers of free parameters and with computationally expensive objective function calculations. More sophisticated techniques are presented for special problems. Niching and island model algorithms are introduced as methods to find multiple, distinct solutions to the nonunique problems that are typically seen in geophysics. Finally, hybrid algorithms are investigated as a way to improve the efficiency of the standard genetic algorithm.« less

Genetic algorithms and their use in geophysical problems

NASA Astrophysics Data System (ADS)

Parker, Paul Bradley

Genetic algorithms (GAs), global optimization methods that mimic Darwinian evolution are well suited to the nonlinear inverse problems of geophysics. A standard genetic algorithm selects the best or "fittest" models from a "population" and then applies operators such as crossover and mutation in order to combine the most successful characteristics of each model and produce fitter models. More sophisticated operators have been developed, but the standard GA usually provides a robust and efficient search. Although the choice of parameter settings such as crossover and mutation rate may depend largely on the type of problem being solved, numerous results show that certain parameter settings produce optimal performance for a wide range of problems and difficulties. In particular, a low (about half of the inverse of the population size) mutation rate is crucial for optimal results, but the choice of crossover method and rate do not seem to affect performance appreciably. Also, optimal efficiency is usually achieved with smaller (<50) populations. Lastly, tournament selection appears to be the best choice of selection methods due to its simplicity and its autoscaling properties. However, if a proportional selection method is used such as roulette wheel selection, fitness scaling is a necessity, and a high scaling factor (>2.0) should be used for the best performance. Three case studies are presented in which genetic algorithms are used to invert for crustal parameters. The first is an inversion for basement depth at Yucca mountain using gravity data, the second an inversion for velocity structure in the crust of the south island of New Zealand using receiver functions derived from teleseismic events, and the third is a similar receiver function inversion for crustal velocities beneath the Mendocino Triple Junction region of Northern California. The inversions demonstrate that genetic algorithms are effective in solving problems with reasonably large numbers of free parameters and with computationally expensive objective function calculations. More sophisticated techniques are presented for special problems. Niching and island model algorithms are introduced as methods to find multiple, distinct solutions to the nonunique problems that are typically seen in geophysics. Finally, hybrid algorithms are investigated as a way to improve the efficiency of the standard genetic algorithm.

Pairing fluctuations and the superfluid density through the BCS-BEC crossover

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, E.; Griffin, A.; Fukushima, N.

2006-12-15

We derive an expression for the superfluid density of a uniform two-component Fermi gas through the BCS-BEC crossover in terms of the thermodynamic potential in the presence of an imposed superfluid flow. Treating the pairing fluctuations in a Gaussian approximation following the approach of Nozieres and Schmitt-Rink, we use this definition of {rho}{sub s} to obtain an explicit result which is valid at finite temperatures and over the full BCS-BEC crossover. It is crucial that the BCS gap {delta}, the chemical potential {mu}, and {rho}{sub s} all include the effect of fluctuations at the same level in a self-consistent manner.more » We show that the normal fluid density {rho}{sub n}{identical_to}n-{rho}{sub s} naturally separates into a sum of contributions from Fermi BCS quasiparticles ({rho}{sub n}{sup F}) and Bose collective modes ({rho}{sub n}{sup B}). The expression for {rho}{sub n}{sup F} is just Landau's formula for a BCS Fermi superfluid but now calculated over the BCS-BEC crossover. The expression for the Bose contribution {rho}{sub n}{sup B} is more complicated and only reduces to Landau's formula for a Bose superfluid in the extreme BEC limit, where all the fermions have formed stable Bose pairs and the Bogoliubov excitations of the associated molecular Bose condensate are undamped. In a companion paper, we present numerical calculations of {rho}{sub s} using an expression equivalent to the one derived in this paper, over the BCS-BEC crossover, including unitarity, and at finite temperatures.« less

A Link between Meiotic Prophase Progression and CrossoverControl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlton, Peter M.; Farruggio, Alfonso P.; Dernburg, Abby F.

2005-07-06

During meiosis, most organisms ensure that homologous chromosomes undergo at least one exchange of DNA, or crossover, to link chromosomes together and accomplish proper segregation. How each chromosome receives a minimum of one crossover is unknown. During early meiosis in Caenorhabditis elegans and many other species, chromosomes adopt a polarized organization within the nucleus, which normally disappears upon completion of homolog synapsis. Mutations that impair synapsis even between a single pair of chromosomes in C. elegans delay this nuclear reorganization. We quantified this delay by developing a classification scheme for discrete stages of meiosis. Immunofluorescence localization of RAD-51 protein revealedmore » that delayed meiotic cells also contained persistent recombination intermediates. Through genetic analysis, we found that this cytological delay in meiotic progression requires double-strand breaks and the function of the crossover-promoting heteroduplex HIM-14 (Msh4) and MSH-5. Failure of X chromosome synapsis also resulted in impaired crossover control on autosomes, which may result from greater numbers and persistence of recombination intermediates in the delayed nuclei. We conclude that maturation of recombination events on chromosomes promotes meiotic progression, and is coupled to the regulation of crossover number and placement. Our results have broad implications for the interpretation of meiotic mutants, as we have shown that asynapsis of a single chromosome pair can exert global effects on meiotic progression and recombination frequency.« less

Comparison of application of various crossovers in solving inhomogeneous minimax problem modified by Goldberg model

NASA Astrophysics Data System (ADS)

Kobak, B. V.; Zhukovskiy, A. G.; Kuzin, A. P.

2018-05-01

This paper considers one of the classical NP complete problems - an inhomogeneous minimax problem. When solving such large-scale problem, there appear difficulties in obtaining an exact solution. Therefore, let us propose getting an optimum solution in an acceptable time. Among a wide range of genetic algorithm models, let us choose the modified Goldberg model, which earlier was successfully used by authors in solving NP complete problems. The classical Goldberg model uses a single-point crossover and a singlepoint mutation, which somewhat decreases the accuracy of the obtained results. In the article, let us propose using a full two-point crossover with various mutations previously researched. In addition, the work studied the necessary probability to apply it to the crossover in order to obtain results that are more accurate. Results of the computation experiment showed that the higher the probability of a crossover, the higher the quality of both the average results and the best solutions. In addition, it was found out that the higher the values of the number of individuals and the number of repetitions, the closer both the average results and the best solutions to the optimum. The paper shows how the use of a full two-point crossover increases the accuracy of solving an inhomogeneous minimax problem, while the time for getting the solution increases, but remains polynomial.

Paternal alcoholism and offspring conduct disorder: evidence for the 'common genes' hypothesis.

PubMed

Haber, Jon R; Jacob, Theodore; Heath, Andrew C

2005-04-01

Not only are alcoholism and externalizing disorders frequently comorbid, they often co-occur in families across generations; for example, paternal alcoholism predicts offspring conduct disorder just as it does offspring alcoholism. To clarify this relationship, the current study examined the 'common genes' hypothesis utilizing a children-of-twins research design. Participants were male monozygotic (MZ) and dizygotic (DZ) twins from the Vietnam Era Twin Registry who were concordant or discordant for alcohol dependence together with their offspring and the mothers of those offspring. All participants were conducted through a structured psychiatric interview. Offspring risk of conduct disorder was examined as a function of alcoholism genetic risk (due to paternal and co-twin alcohol dependence) and alcoholism environmental risk (due to being reared by a father with an alcohol dependence diagnosis). After controlling for potentially confounding variables, the offspring of alcohol-dependent fathers were significantly more likely to exhibit conduct disorder diagnoses than were offspring of nonalcohol-dependent fathers, thus indicating diagnostic crossover in generational family transmission. Comparing offspring at high genetic and high environmental risk with offspring at high genetic and low environmental risk indicated that genetic factors were most likely responsible for the alcoholism-conduct disorder association. The observed diagnostic crossover (from paternal alcoholism to offspring conduct disorder) across generations in the context of both high and low environmental risk (while genetic risk remained high) supported the common genes hypothesis.

Optimization of laminated stacking sequence for buckling load maximization by genetic algorithm

NASA Technical Reports Server (NTRS)

Le Riche, Rodolphe; Haftka, Raphael T.

1992-01-01

The use of a genetic algorithm to optimize the stacking sequence of a composite laminate for buckling load maximization is studied. Various genetic parameters including the population size, the probability of mutation, and the probability of crossover are optimized by numerical experiments. A new genetic operator - permutation - is proposed and shown to be effective in reducing the cost of the genetic search. Results are obtained for a graphite-epoxy plate, first when only the buckling load is considered, and then when constraints on ply contiguity and strain failure are added. The influence on the genetic search of the penalty parameter enforcing the contiguity constraint is studied. The advantage of the genetic algorithm in producing several near-optimal designs is discussed.

Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster

PubMed Central

Singh, Nadia D.; Aquadro, Charles F.; Clark, Andrew G.

2009-01-01

Accurate assessment of local recombination rate variation is crucial for understanding the recombination process and for determining the impact of natural selection on linked sites. In Drosophila, local recombination intensity has been estimated primarily by statistical approaches, estimating the local slope of the relationship between the physical and genetic maps. However, these estimates are limited in resolution, and as a result, the physical scale at which recombination intensity varies in Drosophila is largely unknown. While there is some evidence suggesting as much as a 40-fold variation in crossover rate at a local scale in D. pseudoobscura, little is known about the fine-scale structure of recombination rate variation in D. melanogaster. Here, we experimentally examine the fine-scale distribution of crossover events in a 1.2 Mb region on the D. melanogaster X chromosome using a classic genetic mapping approach. Our results show that crossover frequency is significantly heterogeneous within this region, varying ~ 3.5 fold. Simulations suggest that this degree of heterogeneity is sufficient to affect levels of standing nucleotide diversity, although the magnitude of this effect is small. We recover no statistical association between empirical estimates of nucleotide diversity and recombination intensity, which is likely due to the limited number of loci sampled in our population genetic dataset. However, codon bias is significantly negatively correlated with fine-scale recombination intensity estimates, as expected. Our results shed light on the relevant physical scale to consider in evolutionary analyses relating to recombination rate, and highlight the motivations to increase the resolution of the recombination map in Drosophila. PMID:19504037

Experimental evolution of recombination and crossover interference in Drosophila caused by directional selection for stress-related traits.

PubMed

Aggarwal, Dau Dayal; Rashkovetsky, Eugenia; Michalak, Pawel; Cohen, Irit; Ronin, Yefim; Zhou, Dan; Haddad, Gabriel G; Korol, Abraham B

2015-11-27

Population genetics predicts that tight linkage between new and/or pre-existing beneficial and deleterious alleles should decrease the efficiency of natural selection in finite populations. By decoupling beneficial and deleterious alleles and facilitating the combination of beneficial alleles, recombination accelerates the formation of high-fitness genotypes. This may impose indirect selection for increased recombination. Despite the progress in theoretical understanding, interplay between recombination and selection remains a controversial issue in evolutionary biology. Even less satisfactory is the situation with crossover interference, which is a deviation of double-crossover frequency in a pair of adjacent intervals from the product of recombination rates in the two intervals expected on the assumption of crossover independence. Here, we report substantial changes in recombination and interference in three long-term directional selection experiments with Drosophila melanogaster: for desiccation (~50 generations), hypoxia, and hyperoxia tolerance (>200 generations each). For all three experiments, we found a high interval-specific increase of recombination frequencies in selection lines (up to 40-50% per interval) compared to the control lines. We also discovered a profound effect of selection on interference as expressed by an increased frequency of double crossovers in selection lines. Our results show that changes in interference are not necessarily coupled with increased recombination. Our results support the theoretical predictions that adaptation to a new environment can promote evolution toward higher recombination. Moreover, this is the first evidence of selection for different recombination-unrelated traits potentially leading, not only to evolution toward increased crossover rates, but also to changes in crossover interference, one of the fundamental features of recombination.

The impact of insecticide-treated school uniforms on dengue infections in school-aged children: study protocol for a randomised controlled trial in Thailand

PubMed Central

2012-01-01

Background There is an urgent need to protect children against dengue since this age group is particularly sensitive to the disease. Since dengue vectors are active mainly during the day, a potential target for control should be schools where children spend a considerable amount of their day. School uniforms are the cultural norm in most developing countries, worn throughout the day. We hypothesise that insecticide-treated school uniforms will reduce the incidence of dengue infection in school-aged children. Our objective is to determine the impact of impregnated school uniforms on dengue incidence. Methods A randomised controlled trial will be conducted in eastern Thailand in a group of schools with approximately 2,000 students aged 7–18 years. Pre-fabricated school uniforms will be commercially treated to ensure consistent, high-quality insecticide impregnation with permethrin. A double-blind, randomised, crossover trial at the school level will cover two dengue transmission seasons. Discussion Practical issues and plans concerning intervention implementation, evaluation, analysing and interpreting the data, and possible policy implications arising from the trial are discussed. Trial registration clinicaltrial.gov. Registration number: NCT01563640 PMID:23153360

The exposure-crossover design is a new method for studying sustained changes in recurrent events.

PubMed

Redelmeier, Donald A

2013-09-01

To introduce a new design that explores how an acute exposure might lead to a sustained change in the risk of a recurrent outcome. The exposure-crossover design uses self-matching to control within-person confounding due to genetics, personality, and all other stable patient characteristics. The design is demonstrated using population-based individual-level health data from Ontario, Canada, for three separate medical conditions (n > 100,000 for each) related to the risk of a motor vehicle crash (total outcomes, >2,000 for each). The exposure-crossover design yields numerical risk estimates during the baseline interval before an intervention, the induction interval immediately ahead of the intervention, and the subsequent interval after the intervention. Accompanying graphs summarize results, provide an intuitive display to readers, and show risk comparisons (absolute and relative). Self-matching increases statistical efficiency, reduces selection bias, and yields quantitative analyses. The design has potential limitations related to confounding, artifacts, pragmatics, survivor bias, statistical models, potential misunderstandings, and serendipity. The exposure-crossover design may help in exploring selected questions in epidemiology science. Copyright © 2013 Elsevier Inc. All rights reserved.

Single-crossover recombination in discrete time.

PubMed

von Wangenheim, Ute; Baake, Ellen; Baake, Michael

2010-05-01

Modelling the process of recombination leads to a large coupled nonlinear dynamical system. Here, we consider a particular case of recombination in discrete time, allowing only for single crossovers. While the analogous dynamics in continuous time admits a closed solution (Baake and Baake in Can J Math 55:3-41, 2003), this no longer works for discrete time. A more general model (i.e. without the restriction to single crossovers) has been studied before (Bennett in Ann Hum Genet 18:311-317, 1954; Dawson in Theor Popul Biol 58:1-20, 2000; Linear Algebra Appl 348:115-137, 2002) and was solved algorithmically by means of Haldane linearisation. Using the special formalism introduced by Baake and Baake (Can J Math 55:3-41, 2003), we obtain further insight into the single-crossover dynamics and the particular difficulties that arise in discrete time. We then transform the equations to a solvable system in a two-step procedure: linearisation followed by diagonalisation. Still, the coefficients of the second step must be determined in a recursive manner, but once this is done for a given system, they allow for an explicit solution valid for all times.

Fuel management optimization using genetic algorithms and expert knowledge

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeChaine, M.D.; Feltus, M.A.

1996-09-01

The CIGARO fuel management optimization code based on genetic algorithms is described and tested. The test problem optimized the core lifetime for a pressurized water reactor with a penalty function constraint on the peak normalized power. A bit-string genotype encoded the loading patterns, and genotype bias was reduced with additional bits. Expert knowledge about fuel management was incorporated into the genetic algorithm. Regional crossover exchanged physically adjacent fuel assemblies and improved the optimization slightly. Biasing the initial population toward a known priority table significantly improved the optimization.

Evolving aerodynamic airfoils for wind turbines through a genetic algorithm

NASA Astrophysics Data System (ADS)

Hernández, J. J.; Gómez, E.; Grageda, J. I.; Couder, C.; Solís, A.; Hanotel, C. L.; Ledesma, JI

2017-01-01

Nowadays, genetic algorithms stand out for airfoil optimisation, due to the virtues of mutation and crossing-over techniques. In this work we propose a genetic algorithm with arithmetic crossover rules. The optimisation criteria are taken to be the maximisation of both aerodynamic efficiency and lift coefficient, while minimising drag coefficient. Such algorithm shows greatly improvements in computational costs, as well as a high performance by obtaining optimised airfoils for Mexico City's specific wind conditions from generic wind turbines designed for higher Reynolds numbers, in few iterations.

Circular Data Images for Directional Data

NASA Technical Reports Server (NTRS)

Morpet, William J.

2004-01-01

Directional data includes vectors, points on a unit sphere, axis orientation, angular direction, and circular or periodic data. The theoretical statistics for circular data (random points on a unit circle) or spherical data (random points on a unit sphere) are a recent development. An overview of existing graphical methods for the display of directional data is given. Cross-over occurs when periodic data are measured on a scale for the measurement of linear variables. For example, if angle is represented by a linear color gradient changing uniformly from dark blue at -180 degrees to bright red at +180 degrees, the color image will be discontinuous at +180 degrees and -180 degrees, which are the same location. The resultant color would depend on the direction of approach to the cross-over point. A new graphical method for imaging directional data is described, which affords high resolution without color discontinuity from "cross-over". It is called the circular data image. The circular data image uses a circular color scale in which colors repeat periodically. Some examples of the circular data image include direction of earth winds on a global scale, rocket motor internal flow, earth global magnetic field direction, and rocket motor nozzle vector direction vs. time.

Inversion for Refractivity Parameters Using a Dynamic Adaptive Cuckoo Search with Crossover Operator Algorithm

PubMed Central

Zhang, Zhihua; Sheng, Zheng; Shi, Hanqing; Fan, Zhiqiang

2016-01-01

Using the RFC technique to estimate refractivity parameters is a complex nonlinear optimization problem. In this paper, an improved cuckoo search (CS) algorithm is proposed to deal with this problem. To enhance the performance of the CS algorithm, a parameter dynamic adaptive operation and crossover operation were integrated into the standard CS (DACS-CO). Rechenberg's 1/5 criteria combined with learning factor were used to control the parameter dynamic adaptive adjusting process. The crossover operation of genetic algorithm was utilized to guarantee the population diversity. The new hybrid algorithm has better local search ability and contributes to superior performance. To verify the ability of the DACS-CO algorithm to estimate atmospheric refractivity parameters, the simulation data and real radar clutter data are both implemented. The numerical experiments demonstrate that the DACS-CO algorithm can provide an effective method for near-real-time estimation of the atmospheric refractivity profile from radar clutter. PMID:27212938

Leaf-level gas-exchange uniformity and photosynthetic capacity among loblolly pine (Pinus taeda L.) genotypes of contrasting inherent genetic variation

Treesearch

Michael J. Aspinwall; John S. King; Steven E. McKeand; Jean-Christophe Domec

2011-01-01

Variation in leaf-level gas exchange among widely planted genetically improved loblolly pine (Pinus taeda L.) genotypes could impact stand-level water use, carbon assimilation, biomass production, C allocation, ecosystem sustainability and biogeochemical cycling under changing environmental conditions. We examined uniformity in leaf-level light-saturated photosynthesis...

Increasing Prediction the Original Final Year Project of Student Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Saragih, Rijois Iboy Erwin; Turnip, Mardi; Sitanggang, Delima; Aritonang, Mendarissan; Harianja, Eva

2018-04-01

Final year project is very important forgraduation study of a student. Unfortunately, many students are not seriouslydidtheir final projects. Many of studentsask for someone to do it for them. In this paper, an application of genetic algorithms to predict the original final year project of a studentis proposed. In the simulation, the data of the final project for the last 5 years is collected. The genetic algorithm has several operators namely population, selection, crossover, and mutation. The result suggest that genetic algorithm can do better prediction than other comparable model. Experimental results of predicting showed that 70% was more accurate than the previous researched.

Characterization of recombination features and the genetic basis in multiple cattle breeds

USDA-ARS?s Scientific Manuscript database

Background: Crossover generated by meiotic recombination is a fundamental event which facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination between species, but the characterization of recombination between bovine breeds remains elusive. Cattle p...

Automatic Molecular Design using Evolutionary Techniques

NASA Technical Reports Server (NTRS)

Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

1998-01-01

Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.

ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci

PubMed Central

2010-01-01

Background Growing interest and burgeoning technology for discovering genetic mechanisms that influence disease processes have ushered in a flood of genetic association studies over the last decade, yet little heritability in highly studied complex traits has been explained by genetic variation. Non-additive gene-gene interactions, which are not often explored, are thought to be one source of this "missing" heritability. Methods Stochastic methods employing evolutionary algorithms have demonstrated promise in being able to detect and model gene-gene and gene-environment interactions that influence human traits. Here we demonstrate modifications to a neural network algorithm in ATHENA (the Analysis Tool for Heritable and Environmental Network Associations) resulting in clear performance improvements for discovering gene-gene interactions that influence human traits. We employed an alternative tree-based crossover, backpropagation for locally fitting neural network weights, and incorporation of domain knowledge obtainable from publicly accessible biological databases for initializing the search for gene-gene interactions. We tested these modifications in silico using simulated datasets. Results We show that the alternative tree-based crossover modification resulted in a modest increase in the sensitivity of the ATHENA algorithm for discovering gene-gene interactions. The performance increase was highly statistically significant when backpropagation was used to locally fit NN weights. We also demonstrate that using domain knowledge to initialize the search for gene-gene interactions results in a large performance increase, especially when the search space is larger than the search coverage. Conclusions We show that a hybrid optimization procedure, alternative crossover strategies, and incorporation of domain knowledge from publicly available biological databases can result in marked increases in sensitivity and performance of the ATHENA algorithm for detecting and modelling gene-gene interactions that influence a complex human trait. PMID:20875103

Pharmacogenetics of Methylphenidate Response in Preschoolers with ADHD

ERIC Educational Resources Information Center

McGough, James; McCracken, James; Swanson, James; Riddle, Mark; Kollins, Scott; Greenhill, Laurence; Abikoff, Howard; Davies, Mark; Chuang, Shirley; Wigal, Tim; Wigal, Sharon; Posner, Kelly; Skrobala, Anne; Kastelic, Elizabeth; Ghuman, Jaswinder; Cunningham, Charles; Shigawa, Sharon; Moyzis, Robert; Vitiello, Benedetto

2006-01-01

Objective: The authors explored genetic moderators of symptom reduction and side effects in methylphenidate-treated preschool-age children diagnosed with attention-deficit/hyperactivity disorder (ADHD). Method: DNA was isolated from 81 subjects in a double-blind, placebo-controlled, crossover methylphenidate titration. Parents and teachers…

Genetic analysis of eight loci tightly linked to neurofibromatosis 1

PubMed Central

Stephens, Karen; Green, Philip; Riccardi, Vincent M.; Ng, Siu; Rising, Marcia; Barker, David; Darby, John K.; Falls, Kathleen M.; Collins, Francis S.; Willard, Huntington F.; Donis-Keller, Helen

1989-01-01

The genetic locus for neurofibromatosis 1 (NF1) has recently been mapped to the pericentromeric region of chromosome 17. We have genotyped eight previously identified RFLP probes on 50 NF1 families to determine the placement of the NF1 locus relative to the RFLP loci. Thirty-eight recombination events in the pericentromeric region were identified, eight involving crossovers between NF1 and loci on either chromosomal arm. Multipoint linkage analysis resulted in the unique placement of six loci at odds >100:1 in the order of pter–A10-41–EW301–NF1–EW207–CRI-L581–CRI-L946–qter. Owing to insufficient crossovers, three loci–D17Z1, EW206, and EW203–could not be uniquely localized. In this region female recombination rates were significantly higher than those of males. These data were part of a joint study aimed at the localization of both NF1 and tightly linked pericentromeric markers for chromosome 17. PMID:2491775

An Improved Heuristic Method for Subgraph Isomorphism Problem

NASA Astrophysics Data System (ADS)

Xiang, Yingzhuo; Han, Jiesi; Xu, Haijiang; Guo, Xin

2017-09-01

This paper focus on the subgraph isomorphism (SI) problem. We present an improved genetic algorithm, a heuristic method to search the optimal solution. The contribution of this paper is that we design a dedicated crossover algorithm and a new fitness function to measure the evolution process. Experiments show our improved genetic algorithm performs better than other heuristic methods. For a large graph, such as a subgraph of 40 nodes, our algorithm outperforms the traditional tree search algorithms. We find that the performance of our improved genetic algorithm does not decrease as the number of nodes in prototype graphs.

Disclosing genetic information to at-risk relatives: new Australian privacy principles, but uniformity still elusive.

PubMed

Otlowski, Margaret F A

2015-04-06

There is growing understanding of the need for genetic information to be shared with genetic relatives in some circumstances. Since 2006, s 95AA of the Privacy Act 1988 (Cwlth) has permitted the disclosure of genetic information to genetic relatives without the patient's consent, provided that the health practitioner reasonably believes that disclosure is necessary to lessen or prevent a serious threat to the life, health or safety of the genetic relatives. Enabling guidelines were introduced in 2009. These were limited to the private sector, and excluded doctors working in the public sector at both Commonwealth and state and territory levels. Privacy legislation was amended in March 2014, and new Australian Privacy Principles, which replace the National Privacy Principles and Information Privacy Principles, now cover the collection and use of personal information. The Privacy Act and the Australian Privacy Principles now extend to practitioners employed by the Commonwealth but not to health practitioners working in state and territory public hospitals. In this article, I review these legislative developments and highlight the implications of the lack of uniformity and the consequent need for a collaborative, uniform approach by states and territories.

Genetic diversity within honeybee colonies increases signal production by waggle-dancing foragers

PubMed Central

Mattila, Heather R; Burke, Kelly M; Seeley, Thomas D

2008-01-01

Recent work has demonstrated considerable benefits of intracolonial genetic diversity for the productivity of honeybee colonies: single-patriline colonies have depressed foraging rates, smaller food stores and slower weight gain relative to multiple-patriline colonies. We explored whether differences in the use of foraging-related communication behaviour (waggle dances and shaking signals) underlie differences in foraging effort of genetically diverse and genetically uniform colonies. We created three pairs of colonies; each pair had one colony headed by a multiply mated queen (inseminated by 15 drones) and one colony headed by a singly mated queen. For each pair, we monitored the production of foraging-related signals over the course of 3 days. Foragers in genetically diverse colonies had substantially more information available to them about food resources than foragers in uniform colonies. On average, in genetically diverse colonies compared with genetically uniform colonies, 36% more waggle dances were identified daily, dancers performed 62% more waggle runs per dance, foragers reported food discoveries that were farther from the nest and 91% more shaking signals were exchanged among workers each morning prior to foraging. Extreme polyandry by honeybee queens enhances the production of worker–worker communication signals that facilitate the swift discovery and exploitation of food resources. PMID:18198143

JavaGenes and Condor: Cycle-Scavenging Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Langhirt, Eric; Livny, Miron; Ramamurthy, Ravishankar; Soloman, Marvin; Traugott, Steve

2000-01-01

A genetic algorithm code, JavaGenes, was written in Java and used to evolve pharmaceutical drug molecules and digital circuits. JavaGenes was run under the Condor cycle-scavenging batch system managing 100-170 desktop SGI workstations. Genetic algorithms mimic biological evolution by evolving solutions to problems using crossover and mutation. While most genetic algorithms evolve strings or trees, JavaGenes evolves graphs representing (currently) molecules and circuits. Java was chosen as the implementation language because the genetic algorithm requires random splitting and recombining of graphs, a complex data structure manipulation with ample opportunities for memory leaks, loose pointers, out-of-bound indices, and other hard to find bugs. Java garbage-collection memory management, lack of pointer arithmetic, and array-bounds index checking prevents these bugs from occurring, substantially reducing development time. While a run-time performance penalty must be paid, the only unacceptable performance we encountered was using standard Java serialization to checkpoint and restart the code. This was fixed by a two-day implementation of custom checkpointing. JavaGenes is minimally integrated with Condor; in other words, JavaGenes must do its own checkpointing and I/O redirection. A prototype Java-aware version of Condor was developed using standard Java serialization for checkpointing. For the prototype to be useful, standard Java serialization must be significantly optimized. JavaGenes is approximately 8700 lines of code and a few thousand JavaGenes jobs have been run. Most jobs ran for a few days. Results include proof that genetic algorithms can evolve directed and undirected graphs, development of a novel crossover operator for graphs, a paper in the journal Nanotechnology, and another paper in preparation.

Genetic-evolution-based optimization methods for engineering design

NASA Technical Reports Server (NTRS)

Rao, S. S.; Pan, T. S.; Dhingra, A. K.; Venkayya, V. B.; Kumar, V.

1990-01-01

This paper presents the applicability of a biological model, based on genetic evolution, for engineering design optimization. Algorithms embodying the ideas of reproduction, crossover, and mutation are developed and applied to solve different types of structural optimization problems. Both continuous and discrete variable optimization problems are solved. A two-bay truss for maximum fundamental frequency is considered to demonstrate the continuous variable case. The selection of locations of actuators in an actively controlled structure, for minimum energy dissipation, is considered to illustrate the discrete variable case.

The Frenkel Line: a direct experimental evidence for the new thermodynamic boundary

DOE PAGES

Bolmatov, Dima; Zhernenkov, Mikhail; Zav’yalov, Dmitry; ...

2015-11-05

We report that supercritical fluids play a significant role in elucidating fundamental aspects of liquid matter under extreme conditions. They have been extensively studied at pressures and temperatures relevant to various industrial applications. However, much less is known about the structural behaviour of supercritical fluids and no structural crossovers have been observed in static compression experiments in any temperature and pressure ranges beyond the critical point. The structure of supercritical state is currently perceived to be uniform everywhere on the pressure-temperature phase diagram, and to change only in a monotonic way even moving around the critical point, not only alongmore » isotherms or isobars. Conversely, we observe structural crossovers for the first time in a deeply supercritical sample through diffraction measurements in a diamond anvil cell and discover a new thermodynamic boundary on the pressure-temperature diagram. We explain the existence of these crossovers in the framework of the phonon theory of liquids using molecular dynamics simulations. The obtained results are of prime importance since they imply a global reconsideration of the mere essence of the supercritical phase. Furthermore, this discovery may pave the way to new unexpected applications and to the exploration of exotic behaviour of confined fluids relevant to geo- and planetary sciences.« less

Plasticity of Meiotic Recombination Rates in Response to Temperature in Arabidopsis

PubMed Central

Lloyd, Andrew; Morgan, Chris; H. Franklin, F. Chris

2018-01-01

Meiotic recombination shuffles genetic information from sexual species into gametes to create novel combinations in offspring. Thus, recombination is an important factor in inheritance, adaptation, and responses to selection. However, recombination is not a static parameter; meiotic recombination rate is sensitive to variation in the environment, especially temperature. That recombination rates change in response to both increases and decreases in temperature was reported in Drosophila a century ago, and since then in several other species. But it is still unclear what the underlying mechanism is, and whether low- and high-temperature effects are mechanistically equivalent. Here, we show that, as in Drosophila, both high and low temperatures increase meiotic crossovers in Arabidopsis thaliana. We show that, from a nadir at 18°, both lower and higher temperatures increase recombination through additional class I (interfering) crossovers. However, the increase in crossovers at high and low temperatures appears to be mechanistically at least somewhat distinct, as they differ in their association with the DNA repair protein MLH1. We also find that, in contrast to what has been reported in barley, synaptonemal complex length is negatively correlated with temperature; thus, an increase in chromosome axis length may account for increased crossovers at low temperature in A. thaliana, but cannot explain the increased crossovers observed at high temperature. The plasticity of recombination has important implications for evolution and breeding, and also for the interpretation of observations of recombination rate variation among natural populations. PMID:29496746

Brief Report: Initial Trial of Alpha7-Nicotinic Receptor Stimulation in Two Adult Patients with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Olincy, Ann; Blakeley-Smith, Audrey; Johnson, Lynn; Kem, William R.; Freedman, Robert

2016-01-01

Abnormalities in CHRNA7, the alpha7-nicotinic receptor gene, have been reported in autism spectrum disorder. These genetic abnormalities potentially decrease the receptor's expression and diminish its functional role. This double-blind, placebo-controlled crossover study in two adult patients investigated whether an investigational…

Crossover versus mutation: a comparative analysis of the evolutionary strategy of genetic algorithms applied to combinatorial optimization problems.

PubMed

Osaba, E; Carballedo, R; Diaz, F; Onieva, E; de la Iglesia, I; Perallos, A

2014-01-01

Since their first formulation, genetic algorithms (GAs) have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test.

Crossover versus Mutation: A Comparative Analysis of the Evolutionary Strategy of Genetic Algorithms Applied to Combinatorial Optimization Problems

PubMed Central

Osaba, E.; Carballedo, R.; Diaz, F.; Onieva, E.; de la Iglesia, I.; Perallos, A.

2014-01-01

Since their first formulation, genetic algorithms (GAs) have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test. PMID:25165731

A Multi-Stage Reverse Logistics Network Problem by Using Hybrid Priority-Based Genetic Algorithm

NASA Astrophysics Data System (ADS)

Lee, Jeong-Eun; Gen, Mitsuo; Rhee, Kyong-Gu

Today remanufacturing problem is one of the most important problems regarding to the environmental aspects of the recovery of used products and materials. Therefore, the reverse logistics is gaining become power and great potential for winning consumers in a more competitive context in the future. This paper considers the multi-stage reverse Logistics Network Problem (m-rLNP) while minimizing the total cost, which involves reverse logistics shipping cost and fixed cost of opening the disassembly centers and processing centers. In this study, we first formulate the m-rLNP model as a three-stage logistics network model. Following for solving this problem, we propose a Genetic Algorithm pri (GA) with priority-based encoding method consisting of two stages, and introduce a new crossover operator called Weight Mapping Crossover (WMX). Additionally also a heuristic approach is applied in the 3rd stage to ship of materials from processing center to manufacturer. Finally numerical experiments with various scales of the m-rLNP models demonstrate the effectiveness and efficiency of our approach by comparing with the recent researches.

Srs2 promotes synthesis-dependent strand annealing by disrupting DNA polymerase δ-extending D-loops

PubMed Central

Liu, Jie; Ede, Christopher; Wright, William D; Gore, Steven K; Jenkins, Shirin S; Freudenthal, Bret D; Todd Washington, M; Veaute, Xavier; Heyer, Wolf-Dietrich

2017-01-01

Synthesis-dependent strand annealing (SDSA) is the preferred mode of homologous recombination in somatic cells leading to an obligatory non-crossover outcome, thus avoiding the potential for chromosomal rearrangements and loss of heterozygosity. Genetic analysis identified the Srs2 helicase as a prime candidate to promote SDSA. Here, we demonstrate that Srs2 disrupts D-loops in an ATP-dependent fashion and with a distinct polarity. Specifically, we partly reconstitute the SDSA pathway using Rad51, Rad54, RPA, RFC, DNA Polymerase δ with different forms of PCNA. Consistent with genetic data showing the requirement for SUMO and PCNA binding for the SDSA role of Srs2, Srs2 displays a slight but significant preference to disrupt extending D-loops over unextended D-loops when SUMOylated PCNA is present, compared to unmodified PCNA or monoubiquitinated PCNA. Our data establish a biochemical mechanism for the role of Srs2 in crossover suppression by promoting SDSA through disruption of extended D-loops. DOI: http://dx.doi.org/10.7554/eLife.22195.001 PMID:28535142

Randomized pharmacokinetic cross-over study comparing two curcumin preparations in plasma and rectal tissue of healthy human volunteers

PubMed Central

Asher, Gary N.; Xie, Ying; Moaddel, Ruin; Sanghvi, Mitesh; Dossou, Katina S.S.; Kashuba, Angela D. M.; Sandler, Robert S.; Hawke, Roy L.

2016-01-01

Curcumin is poorly absorbed driving interest in new preparations. However, little is known about pharmacokinetics and tissue bioavailability between formulations. In this randomized, crossover study we evaluated the relationship between steady-state plasma and rectal tissue curcuminoid concentrations using standard and phosphatidylcholine curcumin extracts. There was no difference in the geometric mean plasma AUCs when adjusted for the 10-fold difference in curcumin dose between the two formulations. Phosphatidylcholine curcumin extract yielded only 20–30% plasma demethoxycurcumin and bisdemethoxycurcumin conjugates compared to standard extract, yet yielded 20-fold greater hexahydrocurcumin. When adjusting for curcumin dose, tissue curcumin concentrations were 5-fold greater for the phosphatidylcholine extract. Improvements in curcuminoid absorption due to phosphatidylcholine are not uniform across the curcuminoids. Furthermore, curcuminoid exposures in the intestinal mucosa are most likely due to luminal exposure rather than plasma disposition. Finally, once-daily dosing is sufficient to maintain detectable curcuminoids at steady-state in both plasma and rectal tissues. PMID:27503249

Optimisation of groundwater level monitoring networks using geostatistical modelling based on the Spartan family variogram and a genetic algorithm method

NASA Astrophysics Data System (ADS)

Parasyris, Antonios E.; Spanoudaki, Katerina; Kampanis, Nikolaos A.

2016-04-01

Groundwater level monitoring networks provide essential information for water resources management, especially in areas with significant groundwater exploitation for agricultural and domestic use. Given the high maintenance costs of these networks, development of tools, which can be used by regulators for efficient network design is essential. In this work, a monitoring network optimisation tool is presented. The network optimisation tool couples geostatistical modelling based on the Spartan family variogram with a genetic algorithm method and is applied to Mires basin in Crete, Greece, an area of high socioeconomic and agricultural interest, which suffers from groundwater overexploitation leading to a dramatic decrease of groundwater levels. The purpose of the optimisation tool is to determine which wells to exclude from the monitoring network because they add little or no beneficial information to groundwater level mapping of the area. Unlike previous relevant investigations, the network optimisation tool presented here uses Ordinary Kriging with the recently-established non-differentiable Spartan variogram for groundwater level mapping, which, based on a previous geostatistical study in the area leads to optimal groundwater level mapping. Seventy boreholes operate in the area for groundwater abstraction and water level monitoring. The Spartan variogram gives overall the most accurate groundwater level estimates followed closely by the power-law model. The geostatistical model is coupled to an integer genetic algorithm method programmed in MATLAB 2015a. The algorithm is used to find the set of wells whose removal leads to the minimum error between the original water level mapping using all the available wells in the network and the groundwater level mapping using the reduced well network (error is defined as the 2-norm of the difference between the original mapping matrix with 70 wells and the mapping matrix of the reduced well network). The solution to the optimization problem (the best wells to retain in the monitoring network) depends on the total number of wells removed; this number is a management decision. The water level monitoring network of Mires basin has been optimized 6 times by removing 5, 8, 12, 15, 20 and 25 wells from the original network. In order to achieve the optimum solution in the minimum possible computational time, a stall generations criterion was set for each optimisation scenario. An improvement made to the classic genetic algorithm was the change of the mutation and crossover fraction in respect to the change of the mean fitness value. This results to a randomness in reproduction, if the solution converges, to avoid local minima, or, in a more educated reproduction (higher crossover ratio) when there is higher change in the mean fitness value. The choice of integer genetic algorithm in MATLAB 2015a poses the restriction of adding custom selection and crossover-mutation functions. Therefore, custom population and crossover-mutation-selection functions have been created to set the initial population type to custom and have the ability to change the mutation crossover probability in respect to the convergence of the genetic algorithm, achieving thus higher accuracy. The application of the network optimisation tool to Mires basin indicates that 25 wells can be removed with a relatively small deterioration of the groundwater level map. The results indicate the robustness of the network optimisation tool: Wells were removed from high well-density areas while preserving the spatial pattern of the original groundwater level map. Varouchakis, E. A. and D. T. Hristopulos (2013). "Improvement of groundwater level prediction in sparsely gauged basins using physical laws and local geographic features as auxiliary variables." Advances in Water Resources 52: 34-49.

Homologous genetic recombination in the yellow head complex of nidoviruses infecting Penaeus monodon shrimp.

PubMed

Wijegoonawardane, Priyanjalie K M; Sittidilokratna, Nusra; Petchampai, Natthida; Cowley, Jeff A; Gudkovs, Nicholas; Walker, Peter J

2009-07-20

Yellow head virus (YHV) is a highly virulent pathogen of Penaeus monodon shrimp. It is one of six known genotypes in the yellow head complex of nidoviruses which also includes mildly pathogenic gill-associated virus (GAV, genotype 2) and four other genotypes (genotypes 3-6) that have been detected only in healthy shrimp. In this study, comparative phylogenetic analyses conducted on replicase- (ORF1b) and glycoprotein- (ORF3) gene amplicons identified 10 putative natural recombinants amongst 28 viruses representing all six genotypes from across the Indo-Pacific region. The approximately 4.6 kb genomic region spanning the two amplicons was sequenced for three putative recombinant viruses from Vietnam (genotype 3/5), the Philippines (genotype 5/2) and Indonesia (genotype 3/2). SimPlot analysis using these and representative parental virus sequences confirmed that each was a recombinant genotype and identified a recombination hotspot in a region just upstream of the ORF1b C-terminus. Maximum-likelihood breakpoint analysis predicted identical crossover positions in the Vietnamese and Indonesian recombinants, and a crossover position 12 nt upstream in the Philippine recombinant. Homologous genetic recombination in the same genome region was also demonstrated in recombinants generated experimentally in shrimp co-infected with YHV and GAV. The high frequency with which natural recombinants were identified indicates that genetic exchange amongst genotypes is occurring commonly in Asia and playing a significant role in expanding the genetic diversity in the yellow head complex. This is the first evidence of genetic recombination in viruses infecting crustaceans and has significant implications for the pathogenesis of infection and diagnosis of these newly emerging invertebrate pathogens.

An Improved Hierarchical Genetic Algorithm for Sheet Cutting Scheduling with Process Constraints

PubMed Central

Rao, Yunqing; Qi, Dezhong; Li, Jinling

2013-01-01

For the first time, an improved hierarchical genetic algorithm for sheet cutting problem which involves n cutting patterns for m non-identical parallel machines with process constraints has been proposed in the integrated cutting stock model. The objective of the cutting scheduling problem is minimizing the weighted completed time. A mathematical model for this problem is presented, an improved hierarchical genetic algorithm (ant colony—hierarchical genetic algorithm) is developed for better solution, and a hierarchical coding method is used based on the characteristics of the problem. Furthermore, to speed up convergence rates and resolve local convergence issues, a kind of adaptive crossover probability and mutation probability is used in this algorithm. The computational result and comparison prove that the presented approach is quite effective for the considered problem. PMID:24489491

An improved hierarchical genetic algorithm for sheet cutting scheduling with process constraints.

PubMed

Rao, Yunqing; Qi, Dezhong; Li, Jinling

2013-01-01

For the first time, an improved hierarchical genetic algorithm for sheet cutting problem which involves n cutting patterns for m non-identical parallel machines with process constraints has been proposed in the integrated cutting stock model. The objective of the cutting scheduling problem is minimizing the weighted completed time. A mathematical model for this problem is presented, an improved hierarchical genetic algorithm (ant colony--hierarchical genetic algorithm) is developed for better solution, and a hierarchical coding method is used based on the characteristics of the problem. Furthermore, to speed up convergence rates and resolve local convergence issues, a kind of adaptive crossover probability and mutation probability is used in this algorithm. The computational result and comparison prove that the presented approach is quite effective for the considered problem.

Differential effects of the mismatch repair genes MSH2 and MSH3 on homeologous recombination in Saccharomyces cerevisiae.

PubMed

Selva, E M; Maderazo, A B; Lahue, R S

1997-12-01

The products of the yeast mismatch repair genes MSH2 and MSH3 participate in the inhibition of genetic recombination between homeologous (divergent) DNA sequences. In strains deficient for these genes, homeologous recombination rates between repeated elements are elevated due to the loss of this inhibition. In this study, the effects of these mutations were further analyzed by quantitation of mitotic homeologous recombinants as crossovers, gene conversions or exceptional events in wild-type, msh2, msh3 and msh2 msh3 mutant strains. When homeologous sequences were present as a direct repeat in one orientation, crossovers and gene conversions were elevated in msh2, msh3 and msh2 msh3 strains. The increases were greater in the msh2 msh3 double mutant than in either single mutant. When the order of the homeologous sequences was reversed, the msh2 mutation again yielded increased rates of crossovers and gene conversions. However, in an msh3 strain, gene conversions occurred at higher levels but interchromosomal crossovers were not increased and intrachromosomal crossovers were reduced relative to wild type. The msh2 msh3 double mutant behaved like the msh2 single mutant in this orientation. Control strains harboring homologous duplications were largely but not entirely unaffected in mutant strains, suggesting specificity for the mismatched intermediates of homeologous recombination. In all strains, very few (< 10%) recombinants could be attributed to exceptional events. These results suggest that MSH2 and MSH3 can function differentially to control homeologous exchanges.

Serum a- and b-carotene concentrations qualitatively respond to sustained carrot feeding

USDA-ARS?s Scientific Manuscript database

b-Carotene is a predominant source of vitamin A in developing countries. Genetically selected ‘‘high carotene’’ carrots could have an impact on the vitamin A and antioxidant status of people if widely adopted. A 3 3 3 crossover study in humans (n = 10) evaluated the difference in uptake and clearanc...

Exotic germplasm introgression effect on agronomic and fiber properties of upland cotton

USDA-ARS?s Scientific Manuscript database

Genetic diversity is an important breeder’s tool for selection and improvement in crop cultivar development. Any successful breeding program depends on selecting superior quality parents. Lack of genetic diversity limits the potential of the breeder in selecting elite parents. Genetic uniformity pre...

High-Resolution Mapping of Two Types of Spontaneous Mitotic Gene Conversion Events in Saccharomyces cerevisiae

PubMed Central

Yim, Eunice; O’Connell, Karen E.; St. Charles, Jordan; Petes, Thomas D.

2014-01-01

Gene conversions and crossovers are related products of the repair of double-stranded DNA breaks by homologous recombination. Most previous studies of mitotic gene conversion events have been restricted to measuring conversion tracts that are <5 kb. Using a genetic assay in which the lengths of very long gene conversion tracts can be measured, we detected two types of conversions: those with a median size of ∼6 kb and those with a median size of >50 kb. The unusually long tracts are initiated at a naturally occurring recombination hotspot formed by two inverted Ty elements. We suggest that these long gene conversion events may be generated by a mechanism (break-induced replication or repair of a double-stranded DNA gap) different from the short conversion tracts that likely reflect heteroduplex formation followed by DNA mismatch repair. Both the short and long mitotic conversion tracts are considerably longer than those observed in meiosis. Since mitotic crossovers in a diploid can result in a heterozygous recessive deleterious mutation becoming homozygous, it has been suggested that the repair of DNA breaks by mitotic recombination involves gene conversion events that are unassociated with crossing over. In contrast to this prediction, we found that ∼40% of the conversion tracts are associated with crossovers. Spontaneous mitotic crossover events in yeast are frequent enough to be an important factor in genome evolution. PMID:24990991

Germplasm Release: Tissue Culture-Derived Curly Top-Resistant Genetic Stock

USDA-ARS?s Scientific Manuscript database

The USDA-ARS sugarbeet research program at Kimberly is focused on discovering novel genes for resistance to beet curly top and other economically important diseases. It is vital in genetics research to develop uniform breeding lines and genetic stocks to study inheritance, gene transfer (through co...

Phase Reconstruction from FROG Using Genetic Algorithms[Frequency-Resolved Optical Gating

DOE Office of Scientific and Technical Information (OSTI.GOV)

Omenetto, F.G.; Nicholson, J.W.; Funk, D.J.

1999-04-12

The authors describe a new technique for obtaining the phase and electric field from FROG measurements using genetic algorithms. Frequency-Resolved Optical Gating (FROG) has gained prominence as a technique for characterizing ultrashort pulses. FROG consists of a spectrally resolved autocorrelation of the pulse to be measured. Typically a combination of iterative algorithms is used, applying constraints from experimental data, and alternating between the time and frequency domain, in order to retrieve an optical pulse. The authors have developed a new approach to retrieving the intensity and phase from FROG data using a genetic algorithm (GA). A GA is a generalmore » parallel search technique that operates on a population of potential solutions simultaneously. Operators in a genetic algorithm, such as crossover, selection, and mutation are based on ideas taken from evolution.« less

In silico modelling of directed evolution: Implications for experimental design and stepwise evolution.

PubMed

Wedge, David C; Rowe, William; Kell, Douglas B; Knowles, Joshua

2009-03-07

We model the process of directed evolution (DE) in silico using genetic algorithms. Making use of the NK fitness landscape model, we analyse the effects of mutation rate, crossover and selection pressure on the performance of DE. A range of values of K, the epistatic interaction of the landscape, are considered, and high- and low-throughput modes of evolution are compared. Our findings suggest that for runs of or around ten generations' duration-as is typical in DE-there is little difference between the way in which DE needs to be configured in the high- and low-throughput regimes, nor across different degrees of landscape epistasis. In all cases, a high selection pressure (but not an extreme one) combined with a moderately high mutation rate works best, while crossover provides some benefit but only on the less rugged landscapes. These genetic algorithms were also compared with a "model-based approach" from the literature, which uses sequential fixing of the problem parameters based on fitting a linear model. Overall, we find that purely evolutionary techniques fare better than do model-based approaches across all but the smoothest landscapes.

Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes

PubMed Central

Dreissig, Steven; Fuchs, Jörg; Himmelbach, Axel; Mascher, Martin; Houben, Andreas

2017-01-01

Meiotic recombination is a fundamental mechanism to generate novel allelic combinations which can be harnessed by breeders to achieve crop improvement. The recombination landscape of many crop species, including the major crop barley, is characterized by a dearth of recombination in 65% of the genome. In addition, segregation distortion caused by selection on genetically linked loci is a frequent and undesirable phenomenon in double haploid populations which hampers genetic mapping and breeding. Here, we present an approach to directly investigate recombination at the DNA sequence level by combining flow-sorting of haploid pollen nuclei of barley with single-cell genome sequencing. We confirm the skewed distribution of recombination events toward distal chromosomal regions at megabase resolution and show that segregation distortion is almost absent if directly measured in pollen. Furthermore, we show a bimodal distribution of inter-crossover distances, which supports the existence of two classes of crossovers which are sensitive or less sensitive to physical interference. We conclude that single pollen nuclei sequencing is an approach capable of revealing recombination patterns in the absence of segregation distortion. PMID:29018459

A genetic algorithm solution to the unit commitment problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kazarlis, S.A.; Bakirtzis, A.G.; Petridis, V.

1996-02-01

This paper presents a Genetic Algorithm (GA) solution to the Unit Commitment problem. GAs are general purpose optimization techniques based on principles inspired from the biological evolution using metaphors of mechanisms such as natural selection, genetic recombination and survival of the fittest. A simple Ga algorithm implementation using the standard crossover and mutation operators could locate near optimal solutions but in most cases failed to converge to the optimal solution. However, using the Varying Quality Function technique and adding problem specific operators, satisfactory solutions to the Unit Commitment problem were obtained. Test results for systems of up to 100 unitsmore » and comparisons with results obtained using Lagrangian Relaxation and Dynamic Programming are also reported.« less

Ensemble of hybrid genetic algorithm for two-dimensional phase unwrapping

NASA Astrophysics Data System (ADS)

Balakrishnan, D.; Quan, C.; Tay, C. J.

2013-06-01

The phase unwrapping is the final and trickiest step in any phase retrieval technique. Phase unwrapping by artificial intelligence methods (optimization algorithms) such as hybrid genetic algorithm, reverse simulated annealing, particle swarm optimization, minimum cost matching showed better results than conventional phase unwrapping methods. In this paper, Ensemble of hybrid genetic algorithm with parallel populations is proposed to solve the branch-cut phase unwrapping problem. In a single populated hybrid genetic algorithm, the selection, cross-over and mutation operators are applied to obtain new population in every generation. The parameters and choice of operators will affect the performance of the hybrid genetic algorithm. The ensemble of hybrid genetic algorithm will facilitate to have different parameters set and different choice of operators simultaneously. Each population will use different set of parameters and the offspring of each population will compete against the offspring of all other populations, which use different set of parameters. The effectiveness of proposed algorithm is demonstrated by phase unwrapping examples and advantages of the proposed method are discussed.

In situ synthesis of nanocomposite membranes: comprehensive improvement strategy for direct methanol fuel cells.

PubMed

Rao, Siyuan; Xiu, Ruijie; Si, Jiangju; Lu, Shanfu; Yang, Meng; Xiang, Yan

2014-03-01

In situ synthesis is a powerful approach to control nanoparticle formation and consequently confers extraordinary properties upon composite membranes relative to conventional doping methods. Herein, uniform nanoparticles of cesium hydrogen salts of phosphotungstic acid (CsPW) are controllably synthesized in situ in Nafion to form CsPW–Nafion nanocomposite membranes with both improved proton conductivity and methanol-crossover suppression. A 101.3% increase of maximum power density has been achieved relative to pristine Nafion in a direct methanol fuel cell (DMFC), indicating a potential pathway for large-scale fabrication of DMFC alternative membranes.

Randomized Pharmacokinetic Crossover Study Comparing 2 Curcumin Preparations in Plasma and Rectal Tissue of Healthy Human Volunteers.

PubMed

Asher, Gary N; Xie, Ying; Moaddel, Ruin; Sanghvi, Mitesh; Dossou, Katina S S; Kashuba, Angela D M; Sandler, Robert S; Hawke, Roy L

2017-02-01

Curcumin is poorly absorbed, which is interest in new preparations. However, little is known about variations in its pharmacokinetics and tissue bioavailability between formulations. In this randomized, crossover study we evaluated the relationship between steady-state plasma and rectal tissue curcuminoid concentrations using standard and phosphatidylcholine curcumin extracts. There was no difference in the geometric mean plasma AUCs when adjusted for the 10-fold difference in curcumin dose between the 2 formulations. Phosphatidylcholine curcumin extract yielded only 20% to 30% plasma demethoxycurcumin and bisdemethoxycurcumin conjugates compared to standard extract, yet yielded 20-fold greater hexahydrocurcumin. When adjusting for curcumin dose, tissue curcumin concentrations were 5-fold greater for the phosphatidylcholine extract. Improvements in curcuminoid absorption due to phosphatidylcholine are not uniform across the curcuminoids. Furthermore, curcuminoid exposures in the intestinal mucosa are most likely due to luminal exposure rather than to plasma disposition. Finally, once-daily dosing is sufficient to maintain detectable curcuminoids at steady state in both plasma and rectal tissues. © 2016, The American College of Clinical Pharmacology.

Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain.

PubMed

Moreno, I M; Malpica, J M; Díaz-Pendón, J A; Moriones, E; Fraile, A; García-Arenal, F

2004-01-05

The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection.

The Decision Support System (DSS) Application to Determination of Diabetes Mellitus Patient Menu Using a Genetic Algorithm Method

NASA Astrophysics Data System (ADS)

Zuliyana, Nia; Suseno, Jatmiko Endro; Adi, Kusworo

2018-02-01

Composition of foods containing sugar in people with Diabetes Mellitus should be balanced, so an app is required for facilitate the public and nutritionists in determining the appropriate food menu with calorie requirement of diabetes patient. This research will be recommended to determination of food variation for using Genetic Algorithm. The data used is nutrient content of food obtained from Tabel Komposisi Pangan Indonesia (TKPI). The requirement of caloric value the patient can be used the PERKENI 2015 method. Then the data is processed to determine the best food menu consisting of energy (E), carbohydrate (K), fat (L) and protein (P) requirements. The system is comparised with variation of Genetic Algorithm parameters is the total of chromosomes, Probability of Crossover (Pc) and Probability of Mutation (Pm). Maximum value of the probability generation of crossover and probability of mutation will be the more variations of food that will come out. For example, patient with gender is women aged 61 years old, height 160 cm, weight 55 kg, will be resulted number of calories: (E=1621.4, K=243.21, P=60.80, L=45.04), with the gene=4, chromosomes=3, generation=3, Pc=0.2, and Pm=0.2. The result obtained is the three varians: E=1607.25, K=198.877, P=95.385, L=47.508), (E=1633.25, K=196.677, P=85.885, L=55.758), (E=1630.90, K=177.455, P=85.245, L=64.335).

Superfluid density and condensate fraction in the BCS-BEC crossover regime at finite temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukushima, N.; Ohashi, Y.; Faculty of Science and Technology, Keio University, Hiyoshi, Yokohama 223

2007-03-15

The superfluid density is a fundamental quantity describing the response to a rotation as well as in two-fluid collisional hydrodynamics. We present extensive calculations of the superfluid density {rho}{sub s} in the BCS-BEC crossover regime of a uniform superfluid Fermi gas at finite temperatures. We include strong-coupling or fluctuation effects on these quantities within a Gaussian approximation. We also incorporate the same fluctuation effects into the BCS single-particle excitations described by the superfluid order parameter {delta} and Fermi chemical potential {mu}, using the Nozieres-Schmitt-Rink approximation. This treatment is shown to be necessary for consistent treatment of {rho}{sub s} over themore » entire BCS-BEC crossover. We also calculate the condensate fraction N{sub c} as a function of the temperature, a quantity which is quite different from the superfluid density {rho}{sub s}. We show that the mean-field expression for the condensate fraction N{sub c} is a good approximation even in the strong-coupling BEC regime. Our numerical results show how {rho}{sub s} and N{sub c} depend on temperature, from the weak-coupling BCS region to the BEC region of tightly bound Cooper pair molecules. In a companion paper [Phys. Rev. A 74, 063626 (2006)], we derive an equivalent expression for {rho}{sub s} from the thermodynamic potential, which exhibits the role of the pairing fluctuations in a more explicit manner.« less

Cold-Water Immersion for Hyperthermic Humans Wearing American Football Uniforms.

PubMed

Miller, Kevin C; Swartz, Erik E; Long, Blaine C

2015-08-01

Current treatment recommendations for American football players with exertional heatstroke are to remove clothing and equipment and immerse the body in cold water. It is unknown if wearing a full American football uniform during cold-water immersion (CWI) impairs rectal temperature (Trec) cooling or exacerbates hypothermic afterdrop. To determine the time to cool Trec from 39.5°C to 38.0°C while participants wore a full American football uniform or control uniform during CWI and to determine the uniform's effect on Trec recovery postimmersion. Crossover study. Laboratory. A total of 18 hydrated, physically active, unacclimated men (age = 22 ± 3 years, height = 178.8 ± 6.8 cm, mass = 82.3 ± 12.6 kg, body fat = 13% ± 4%, body surface area = 2.0 ± 0.2 m(2)). Participants wore the control uniform (undergarments, shorts, crew socks, tennis shoes) or full uniform (control plus T-shirt; tennis shoes; jersey; game pants; padding over knees, thighs, and tailbone; helmet; and shoulder pads). They exercised (temperature approximately 40°C, relative humidity approximately 35%) until Trec reached 39.5°C. They removed their T-shirts and shoes and were then immersed in water (approximately 10°C) while wearing each uniform configuration; time to cool Trec to 38.0°C (in minutes) was recorded. We measured Trec (°C) every 5 minutes for 30 minutes after immersion. Time to cool from 39.5°C to 38.0°C and Trec. The Trec cooled to 38.0°C in 6.19 ± 2.02 minutes in full uniform and 8.49 ± 4.78 minutes in control uniform (t17 = -2.1, P = .03; effect size = 0.48) corresponding to cooling rates of 0.28°C·min(-1) ± 0.12°C·min(-1) in full uniform and 0.23°C·min(-1) ± 0.11°C·min(-1) in control uniform (t17 = 1.6, P = .07, effect size = 0.44). The Trec postimmersion recovery did not differ between conditions over time (F1,17 = 0.6, P = .59). We speculate that higher skin temperatures before CWI, less shivering, and greater conductive cooling explained the faster cooling in full uniform. Cooling rates were considered ideal when the full uniform was worn during CWI, and wearing the full uniform did not cause a greater postimmersion hypothermic afterdrop. Clinicians may immerse football athletes with hyperthermia wearing a full uniform without concern for negatively affecting body-core cooling.

Thermosensory processing in the Drosophila brain

PubMed Central

Liu, Wendy W.; Mazor, Ofer; Wilson, Rachel I.

2014-01-01

In Drosophila, just as in vertebrates, changes in external temperature are encoded by bidirectional opponent thermoreceptor cells: some cells are excited by warming and inhibited by cooling, whereas others are excited by cooling and inhibited by warming1,2. The central circuits that process these signals are not understood. In Drosophila, a specific brain region receives input from thermoreceptor cells2,3. Here we show that distinct genetically-identified projection neurons (PNs) in this brain region are excited by cooling, warming, or both. The PNs excited by cooling receive mainly feedforward excitation from cool thermoreceptors. In contrast, the PNs excited by warming (“warm-PNs”) receive both excitation from warm thermoreceptors and crossover inhibition from cool thermoreceptors via inhibitory interneurons. Notably, this crossover inhibition elicits warming-evoked excitation, because warming suppresses tonic activity in cool thermoreceptors. This in turn disinhibits warm-PNs and sums with feedforward excitation evoked by warming. Crossover inhibition could cancel non-thermal activity (noise) that is positively-correlated among warm and cool thermoreceptor cells, while reinforcing thermal activity which is anti-correlated. Our results show how central circuits can combine signals from bidirectional opponent neurons to construct sensitive and robust neural codes. PMID:25739502

Genetic Algorithms to Optimizatize Lecturer Assessment's Criteria

NASA Astrophysics Data System (ADS)

Jollyta, Deny; Johan; Hajjah, Alyauma

2017-12-01

The lecturer assessment criteria is used as a measurement of the lecturer's performance in a college environment. To determine the value for a criteriais complicated and often leads to doubt. The absence of a standard valuefor each assessment criteria will affect the final results of the assessment and become less presentational data for the leader of college in taking various policies relate to reward and punishment. The Genetic Algorithm comes as an algorithm capable of solving non-linear problems. Using chromosomes in the random initial population, one of the presentations is binary, evaluates the fitness function and uses crossover genetic operator and mutation to obtain the desired crossbreed. It aims to obtain the most optimum criteria values in terms of the fitness function of each chromosome. The training results show that Genetic Algorithm able to produce the optimal values of lecturer assessment criteria so that can be usedby the college as a standard value for lecturer assessment criteria.

Using microsatellites to understand the physical distribution of recombination on soybean chromosomes.

PubMed

Ott, Alina; Trautschold, Brian; Sandhu, Devinder

2011-01-01

Soybean is a major crop that is an important source of oil and proteins. A number of genetic linkage maps have been developed in soybean. Specifically, hundreds of simple sequence repeat (SSR) markers have been developed and mapped. Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information. The objectives of this investigation were to use SSR markers in developing a connection between genetic and physical maps and to determine the physical distribution of recombination on soybean chromosomes. A total of 2,188 SSRs were used for sequence-based physical localization on soybean chromosomes. Linkage information was used from different maps to create an integrated genetic map. Comparison of the integrated genetic linkage maps and sequence based physical maps revealed that the distal 25% of each chromosome was the most marker-dense, containing an average of 47.4% of the SSR markers and 50.2% of the genes. The proximal 25% of each chromosome contained only 7.4% of the markers and 6.7% of the genes. At the whole genome level, the marker density and gene density showed a high correlation (R(2)) of 0.64 and 0.83, respectively with the physical distance from the centromere. Recombination followed a similar pattern with comparisons indicating that recombination is high in telomeric regions, though the correlation between crossover frequency and distance from the centromeres is low (R(2) = 0.21). Most of the centromeric regions were low in recombination. The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average. The number of recombination hotspots varied from 1 to 12 per chromosome. A high correlation of 0.83 between the distribution of SSR markers and genes suggested close association of SSRs with genes. The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes.

Genetic effects on transpiration, canopy conductance, stomatal sensitivity to vapour pressure deficit, and cavitation resistance in loblolly pine

Treesearch

Michael J Aspinwall; John S King; Jean-Christophe Domec; Steven E McKeand; Isik Fikret

2011-01-01

Physiological uniformity and genetic effects on canopy-level gas-exchange and hydraulic function could impact loblolly pine (Pinus taeda L.) plantation sustainability and ecosystem dynamics under projected changes in climate. Over a 1-year period, we examined genetic effects on mean and maximum mid-day canopy conductance (Gs, Gsmax...

Branch-pipe-routing approach for ships using improved genetic algorithm

NASA Astrophysics Data System (ADS)

Sui, Haiteng; Niu, Wentie

2016-09-01

Branch-pipe routing plays fundamental and critical roles in ship-pipe design. The branch-pipe-routing problem is a complex combinatorial optimization problem and is thus difficult to solve when depending only on human experts. A modified genetic-algorithm-based approach is proposed in this paper to solve this problem. The simplified layout space is first divided into threedimensional (3D) grids to build its mathematical model. Branch pipes in layout space are regarded as a combination of several two-point pipes, and the pipe route between two connection points is generated using an improved maze algorithm. The coding of branch pipes is then defined, and the genetic operators are devised, especially the complete crossover strategy that greatly accelerates the convergence speed. Finally, simulation tests demonstrate the performance of proposed method.

Study of genetic direct search algorithms for function optimization

NASA Technical Reports Server (NTRS)

Zeigler, B. P.

1974-01-01

The results are presented of a study to determine the performance of genetic direct search algorithms in solving function optimization problems arising in the optimal and adaptive control areas. The findings indicate that: (1) genetic algorithms can outperform standard algorithms in multimodal and/or noisy optimization situations, but suffer from lack of gradient exploitation facilities when gradient information can be utilized to guide the search. (2) For large populations, or low dimensional function spaces, mutation is a sufficient operator. However for small populations or high dimensional functions, crossover applied in about equal frequency with mutation is an optimum combination. (3) Complexity, in terms of storage space and running time, is significantly increased when population size is increased or the inversion operator, or the second level adaptation routine is added to the basic structure.

An Adaptive Immune Genetic Algorithm for Edge Detection

NASA Astrophysics Data System (ADS)

Li, Ying; Bai, Bendu; Zhang, Yanning

An adaptive immune genetic algorithm (AIGA) based on cost minimization technique method for edge detection is proposed. The proposed AIGA recommends the use of adaptive probabilities of crossover, mutation and immune operation, and a geometric annealing schedule in immune operator to realize the twin goals of maintaining diversity in the population and sustaining the fast convergence rate in solving the complex problems such as edge detection. Furthermore, AIGA can effectively exploit some prior knowledge and information of the local edge structure in the edge image to make vaccines, which results in much better local search ability of AIGA than that of the canonical genetic algorithm. Experimental results on gray-scale images show the proposed algorithm perform well in terms of quality of the final edge image, rate of convergence and robustness to noise.

Genetic Algorithm for Optimization: Preprocessing with n Dimensional Bisection and Error Estimation

NASA Technical Reports Server (NTRS)

Sen, S. K.; Shaykhian, Gholam Ali

2006-01-01

A knowledge of the appropriate values of the parameters of a genetic algorithm (GA) such as the population size, the shrunk search space containing the solution, crossover and mutation probabilities is not available a priori for a general optimization problem. Recommended here is a polynomial-time preprocessing scheme that includes an n-dimensional bisection and that determines the foregoing parameters before deciding upon an appropriate GA for all problems of similar nature and type. Such a preprocessing is not only fast but also enables us to get the global optimal solution and its reasonably narrow error bounds with a high degree of confidence.

A GA based penalty function technique for solving constrained redundancy allocation problem of series system with interval valued reliability of components

NASA Astrophysics Data System (ADS)

Gupta, R. K.; Bhunia, A. K.; Roy, D.

2009-10-01

In this paper, we have considered the problem of constrained redundancy allocation of series system with interval valued reliability of components. For maximizing the overall system reliability under limited resource constraints, the problem is formulated as an unconstrained integer programming problem with interval coefficients by penalty function technique and solved by an advanced GA for integer variables with interval fitness function, tournament selection, uniform crossover, uniform mutation and elitism. As a special case, considering the lower and upper bounds of the interval valued reliabilities of the components to be the same, the corresponding problem has been solved. The model has been illustrated with some numerical examples and the results of the series redundancy allocation problem with fixed value of reliability of the components have been compared with the existing results available in the literature. Finally, sensitivity analyses have been shown graphically to study the stability of our developed GA with respect to the different GA parameters.

Operational rooted cuttings in southern pines

Treesearch

Joe Weber; Hank Stelzer

2002-01-01

Use of rooted cuttings for planting of pine trees has become increasingly popular. Vegetative propagation can deliver planting stock of higher genetic quality, increasing productivity and shortening rotations. Clonal forestry can also provide stands of higher uniformity, which can reduce logging and processing cost and yield a much more uniform product. One of the...

Identification of a key recombinant narrows the CADASIL gene region to 8 cM and argues against allelism of CADASIL and familial hemiplegic migraine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dichgans, M.; Mayer, M.; Straube, A.

1996-02-15

This article reports on new information regarding the genetic mapping of the human CADASIL gene region. Previously, the gene had been mapped to human chromosome 19q12. Using the identification of a chromosomal crossover, the region has been refined to an 8-cM interval. 11 refs., 2 figs., 1 tab.

Amplified fragment length polymorphism analysis to assess crossover interference and homozygosity in gynogenetic diploid Pacific abalone (Haliotis discus hannai).

PubMed

Nie, H-T; Li, Q; Kong, L-F

2014-06-01

Recombination analysis in gynogenetic diploids is a powerful tool for assessing the degree of inbreeding, investigating crossover events and understanding chiasma interference during meiosis. To estimate the marker-centromere recombination rate, the inheritance pattern of 654 amplified fragment length polymorphism (AFLP) markers was examined in the 72-h veliger larvae of two meiogynogenetic diploid families in the Pacific abalone (Haliotis discus hannai). The second-division segregation frequency (y) of the AFLP loci ranged from 0.00 to 0.96, with 23.9% of loci showing y-values higher than 0.67, evidencing the existence of interference. The average recombination frequency across the 654 AFLP loci was 0.45, allowing estimation of the fixation index of 0.55, indicating that meiotic gynogenesis could provide an effective means of rapid inbreeding in the Pacific abalone. The AFLP loci have a small proportion (4.4%) of y-values greater than 0.90, suggesting that a relatively low or intermediate degree of chiasma interference occurred in the abalone chromosomes. The information obtained in this study will enhance our understanding of the abalone genome and will be useful for genetic studies in the species. © 2014 Stichting International Foundation for Animal Genetics.

Optimal design and management of chlorination in drinking water networks: a multi-objective approach using Genetic Algorithms and the Pareto optimality concept

NASA Astrophysics Data System (ADS)

Nouiri, Issam

2017-11-01

This paper presents the development of multi-objective Genetic Algorithms to optimize chlorination design and management in drinking water networks (DWN). Three objectives have been considered: the improvement of the chlorination uniformity (healthy objective), the minimization of chlorine booster stations number, and the injected chlorine mass (economic objectives). The problem has been dissociated in medium and short terms ones. The proposed methodology was tested on hypothetical and real DWN. Results proved the ability of the developed optimization tool to identify relationships between the healthy and economic objectives as Pareto fronts. The proposed approach was efficient in computing solutions ensuring better chlorination uniformity while requiring the weakest injected chlorine mass when compared to other approaches. For the real DWN studied, chlorination optimization has been crowned by great improvement of free-chlorine-dosing uniformity and by a meaningful chlorine mass reduction, in comparison with the conventional chlorination.

Physical characteristics of genetically-altered wheat related to technological protein separation

USDA-ARS?s Scientific Manuscript database

Wheat protein is a technologically challenging substrate for food and non-food applications because of its compositional diversity and susceptibility to denaturation. Genetic modification could be used to create cultivars capable of producing more uniform or focused and novel protein compositions t...

In Vitro Propagation and Conservation of Withania somnifera (Dunal) L.

PubMed

Fatima, Nigar; Ahmad, Naseem; Anis, Mohammad

2016-01-01

Plant tissue culture offers several techniques for rapid clonal propagation, germplasm conservation, regeneration of genetically manipulated superior clones, production of phyto-constituents, and ex vitro conservation of valuable phytodiversity. An improved and efficient micropropagation protocol for Withania somnifera (L.), a drug-producing medicinal plant, using juvenile explants (nodal explants) has been developed. Highest multiplication and subsequent elongation of shoots is observed on MS medium containing BA and NAA. The regenerated microshoots roots best on ½ MS medium containing NAA, established in earthen pots containing garden soil and are maintained in the greenhouse with 95 % survival rate. Genetic uniformity of micropropagated plants is confirmed by PCR-based DNA fingerprinting techniques, viz., RAPD and ISSR. No variation is observed in DNA fingerprinting patterns among the micropropagated plants, which are similar to that of the donor plant illustrating their genetic uniformity.

Structured parenting of toddlers at high versus low genetic risk: two pathways to child problems.

PubMed

Leve, Leslie D; Harold, Gordon T; Ge, Xiaojia; Neiderhiser, Jenae M; Shaw, Daniel; Scaramella, Laura V; Reiss, David

2009-11-01

Little is known about how parenting might offset genetic risk to prevent the onset of child problems during toddlerhood. We used a prospective adoption design to separate genetic and environmental influences and test whether associations between structured parenting and toddler behavior problems were conditioned by genetic risk for psychopathology. The sample included 290 linked sets of adoptive families and birth mothers and 95 linked birth fathers. Genetic risk was assessed via birth mother and birth father psychopathology (anxiety, depression, antisociality, and drug use). Structured parenting was assessed via microsocial coding of adoptive mothers' behavior during a cleanup task. Toddler behavior problems were assessed with the Child Behavior Checklist. Controlling for temperamental risk at 9 months, there was an interaction between birth mother psychopathology and adoptive mothers' parenting on toddler behavior problems at 18 months. The interaction indicated two pathways to child problems: structured parenting was beneficial for toddlers at high genetic risk but was related to behavior problems for toddlers at low genetic risk. This crossover interaction pattern was replicated with birth father psychopathology as the index of genetic risk. The effects of structured parenting on toddler behavior problems varied as a function of genetic risk. Children at genetic risk might benefit from parenting interventions during toddlerhood that enhance structured parenting.

High-throughput measurement of recombination rates and genetic interference in Saccharomyces cerevisiae.

PubMed

Raffoux, Xavier; Bourge, Mickael; Dumas, Fabrice; Martin, Olivier C; Falque, Matthieu

2018-06-01

Allelic recombination owing to meiotic crossovers is a major driver of genome evolution, as well as a key player for the selection of high-performing genotypes in economically important species. Therefore, we developed a high-throughput and low-cost method to measure recombination rates and crossover patterning (including interference) in large populations of the budding yeast Saccharomyces cerevisiae. Recombination and interference were analysed by flow cytometry, which allows time-consuming steps such as tetrad microdissection or spore growth to be avoided. Moreover, our method can also be used to compare recombination in wild-type vs. mutant individuals or in different environmental conditions, even if the changes in recombination rates are small. Furthermore, meiotic mutants often present recombination and/or pairing defects affecting spore viability but our method does not involve growth steps and thus avoids filtering out non-viable spores. Copyright © 2018 John Wiley & Sons, Ltd.

The rate of meiotic gene conversion varies by sex and age

PubMed Central

Halldorsson, Bjarni V.; Hardarson, Marteinn T.; Kehr, Birte; Styrkarsdottir, Unnur; Gylfason, Arnaldur; Thorleifsson, Gudmar; Zink, Florian; Jonasdottir, Adalbjorg; Jonasdottir, Aslaug; Sulem, Patrick; Masson, Gisli; Thorsteinsdottir, Unnur; Helgason, Agnar; Kong, Augustine; Gudbjartsson, Daniel F.; Stefansson, Kari

2016-01-01

Meiotic recombination involves a combination of gene conversion and crossover events that along with mutations produce germline genetic diversity. Here, we report the discovery of 3,176 SNP and 61 indel gene conversions. Our estimate of the non-crossover (NCO) gene conversion rate (G) is 7.0 for SNPs and 5.8 for indels per Mb per generation, and the GC bias is 67.6%. For indels we demonstrate a 65.6% preference for the shorter allele. NCO gene conversions from mothers are longer than those from fathers and G is 2.17 times greater in mothers. Notably, G increases with the age of mothers, but not fathers. A disproportionate number of NCO gene conversions in older mothers occur outside double strand break (DSB) regions and in regions with relatively low GC content. This points to age-related changes in the mechanisms of meiotic gene conversions in oocytes. PMID:27643539

The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen.

PubMed

Croll, Daniel; Lendenmann, Mark H; Stewart, Ethan; McDonald, Bruce A

2015-11-01

Recombination has an impact on genome evolution by maintaining chromosomal integrity, affecting the efficacy of selection, and increasing genetic variability in populations. Recombination rates are a key determinant of the coevolutionary dynamics between hosts and their pathogens. Historic recombination events created devastating new pathogens, but the impact of ongoing recombination in sexual pathogens is poorly understood. Many fungal pathogens of plants undergo regular sexual cycles, and sex is considered to be a major factor contributing to virulence. We generated a recombination map at kilobase-scale resolution for the haploid plant pathogenic fungus Zymoseptoria tritici. To account for intraspecific variation in recombination rates, we constructed genetic maps from two independent crosses. We localized a total of 10,287 crossover events in 441 progeny and found that recombination rates were highly heterogeneous within and among chromosomes. Recombination rates on large chromosomes were inversely correlated with chromosome length. Short accessory chromosomes often lacked evidence for crossovers between parental chromosomes. Recombination was concentrated in narrow hotspots that were preferentially located close to telomeres. Hotspots were only partially conserved between the two crosses, suggesting that hotspots are short-lived and may vary according to genomic background. Genes located in hotspot regions were enriched in genes encoding secreted proteins. Population resequencing showed that chromosomal regions with high recombination rates were strongly correlated with regions of low linkage disequilibrium. Hence, genes in pathogen recombination hotspots are likely to evolve faster in natural populations and may represent a greater threat to the host. Copyright © 2015 by the Genetics Society of America.

A Randomized Crossover Design to Assess Learning Impact and Student Preference for Active and Passive Online Learning Modules.

PubMed

Prunuske, Amy J; Henn, Lisa; Brearley, Ann M; Prunuske, Jacob

Medical education increasingly involves online learning experiences to facilitate the standardization of curriculum across time and space. In class, delivering material by lecture is less effective at promoting student learning than engaging students in active learning experience and it is unclear whether this difference also exists online. We sought to evaluate medical student preferences for online lecture or online active learning formats and the impact of format on short- and long-term learning gains. Students participated online in either lecture or constructivist learning activities in a first year neurologic sciences course at a US medical school. In 2012, students selected which format to complete and in 2013, students were randomly assigned in a crossover fashion to the modules. In the first iteration, students strongly preferred the lecture modules and valued being told "what they need to know" rather than figuring it out independently. In the crossover iteration, learning gains and knowledge retention were found to be equivalent regardless of format, and students uniformly demonstrated a strong preference for the lecture format, which also on average took less time to complete. When given a choice for online modules, students prefer passive lecture rather than completing constructivist activities, and in the time-limited environment of medical school, this choice results in similar performance on multiple-choice examinations with less time invested. Instructors need to look more carefully at whether assessments and learning strategies are helping students to obtain self-directed learning skills and to consider strategies to help students learn to value active learning in an online environment.

Cold-Water Immersion for Hyperthermic Humans Wearing American Football Uniforms

PubMed Central

Miller, Kevin C.; Swartz, Erik E.; Long, Blaine C.

2015-01-01

Context Current treatment recommendations for American football players with exertional heatstroke are to remove clothing and equipment and immerse the body in cold water. It is unknown if wearing a full American football uniform during cold-water immersion (CWI) impairs rectal temperature (Trec) cooling or exacerbates hypothermic afterdrop. Objective To determine the time to cool Trec from 39.5°C to 38.0°C while participants wore a full American football uniform or control uniform during CWI and to determine the uniform's effect on Trec recovery postimmersion. Design Crossover study. Setting Laboratory. Patients or Other Participants A total of 18 hydrated, physically active, unacclimated men (age = 22 ± 3 years, height = 178.8 ± 6.8 cm, mass = 82.3 ± 12.6 kg, body fat = 13% ± 4%, body surface area = 2.0 ± 0.2 m2). Intervention(s) Participants wore the control uniform (undergarments, shorts, crew socks, tennis shoes) or full uniform (control plus T-shirt; tennis shoes; jersey; game pants; padding over knees, thighs, and tailbone; helmet; and shoulder pads). They exercised (temperature approximately 40°C, relative humidity approximately 35%) until Trec reached 39.5°C. They removed their T-shirts and shoes and were then immersed in water (approximately 10°C) while wearing each uniform configuration; time to cool Trec to 38.0°C (in minutes) was recorded. We measured Trec (°C) every 5 minutes for 30 minutes after immersion. Main Outcome Measure(s) Time to cool from 39.5°C to 38.0°C and Trec. Results The Trec cooled to 38.0°C in 6.19 ± 2.02 minutes in full uniform and 8.49 ± 4.78 minutes in control uniform (t17 = −2.1, P = .03; effect size = 0.48) corresponding to cooling rates of 0.28°C·min−1 ± 0.12°C·min−1 in full uniform and 0.23°C·min−1 ± 0.11°C·min−1 in control uniform (t17 = 1.6, P = .07, effect size = 0.44). The Trec postimmersion recovery did not differ between conditions over time (F1,17 = 0.6, P = .59). Conclusions We speculate that higher skin temperatures before CWI, less shivering, and greater conductive cooling explained the faster cooling in full uniform. Cooling rates were considered ideal when the full uniform was worn during CWI, and wearing the full uniform did not cause a greater postimmersion hypothermic afterdrop. Clinicians may immerse football athletes with hyperthermia wearing a full uniform without concern for negatively affecting body-core cooling. PMID:26090706

Haemophilia A: carrier detection and prenatal diagnosis by linkage analysis using DNA polymorphism.

PubMed Central

Tuddenham, E G; Goldman, E; McGraw, A; Kernoff, P B

1987-01-01

Restriction fragment length polymorphisms (RFLPs) within or close to the factor VIII locus are very useful for genetic linkage analysis. Such RFLPs allow a mutant allele to be tracked in a family, segregating haemophilia A even when, as is usually the case, the precise mutation causing failure to synthesise factor VIII is unknown. To date two markers tightly linked to the factor VIII locus have been described, one of which is highly polymorphic and therefore informative in most kindreds. A significant crossover rate, however, does not make diagnosis absolute. Three intragenic RFLPs have been defined, which, taken together, are informative in about 70% of women, providing virtually deterministic genetic diagnosis. PMID:2889753

Targetable genetic features of primary testicular and primary central nervous system lymphomas

PubMed Central

Chapuy, Bjoern; Roemer, Margaretha G. M.; Stewart, Chip; Tan, Yuxiang; Abo, Ryan P.; Zhang, Liye; Dunford, Andrew J.; Meredith, David M.; Thorner, Aaron R.; Jordanova, Ekaterina S.; Liu, Gang; Feuerhake, Friedrich; Ducar, Matthew D.; Illerhaus, Gerald; Gusenleitner, Daniel; Linden, Erica A.; Sun, Heather H.; Homer, Heather; Aono, Miyuki; Pinkus, Geraldine S.; Ligon, Azra H.; Ligon, Keith L.; Ferry, Judith A.; Freeman, Gordon J.; van Hummelen, Paul; Golub, Todd R.; Getz, Gad; Rodig, Scott J.; de Jong, Daphne; Monti, Stefano

2016-01-01

Primary central nervous system lymphomas (PCNSLs) and primary testicular lymphomas (PTLs) are extranodal large B-cell lymphomas (LBCLs) with inferior responses to current empiric treatment regimens. To identify targetable genetic features of PCNSL and PTL, we characterized their recurrent somatic mutations, chromosomal rearrangements, copy number alterations (CNAs), and associated driver genes, and compared these comprehensive genetic signatures to those of diffuse LBCL and primary mediastinal large B-cell lymphoma (PMBL). These studies identify unique combinations of genetic alterations in discrete LBCL subtypes and subtype-selective bases for targeted therapy. PCNSLs and PTLs frequently exhibit genomic instability, and near-uniform, often biallelic, CDKN2A loss with rare TP53 mutations. PCNSLs and PTLs also use multiple genetic mechanisms to target key genes and pathways and exhibit near-uniform oncogenic Toll-like receptor signaling as a result of MYD88 mutation and/or NFKBIZ amplification, frequent concurrent B-cell receptor pathway activation, and deregulation of BCL6. Of great interest, PCNSLs and PTLs also have frequent 9p24.1/PD-L1/PD-L2 CNAs and additional translocations of these loci, structural bases of immune evasion that are shared with PMBL. PMID:26702065

Genetic diversity, morphological uniformity and polyketide production in dinoflagellates (Amphidinium, Dinoflagellata).

PubMed

Murray, Shauna A; Garby, Tamsyn; Hoppenrath, Mona; Neilan, Brett A

2012-01-01

Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a 'model' dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the diversity of 'cryptic' species of Amphidinium that are morphologically similar to A. carterae, including the very similar species Amphidinium massartii, based on light and electron microscopy, two nuclear gene regions (LSU rDNA and ITS rDNA) and one mitochondrial gene region (cytochrome b). We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families. Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species. We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them.

Genetic Diversity, Morphological Uniformity and Polyketide Production in Dinoflagellates (Amphidinium, Dinoflagellata)

PubMed Central

Hoppenrath, Mona; Neilan, Brett A.

2012-01-01

Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a ‘model’ dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the diversity of ‘cryptic’ species of Amphidinium that are morphologically similar to A. carterae, including the very similar species Amphidinium massartii, based on light and electron microscopy, two nuclear gene regions (LSU rDNA and ITS rDNA) and one mitochondrial gene region (cytochrome b). We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families. Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species. We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them. PMID:22675531

Uniform Selection as a Primary Force Reducing Population Genetic Differentiation of Cavitation Resistance across a Species Range

PubMed Central

Lamy, Jean-Baptiste; Bouffier, Laurent; Burlett, Régis; Plomion, Christophe; Cochard, Hervé; Delzon, Sylvain

2011-01-01

Background Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. Methodology We assessed cavitation resistance (P 50), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F ST) and quantitative genetic differentiation (Q ST), for retrospective identification of the evolutionary forces acting on these traits. Results/Discussion In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h2 ns = 0.43±0.18, CVA = 4.4%). Q ST was significantly lower than F ST, indicating uniform selection for P 50, rather than genetic drift. Putative mechanisms underlying QST

Wheat Landrace Genome Diversity

PubMed Central

Wingen, Luzie U.; West, Claire; Leverington-Waite, Michelle; Collier, Sarah; Orford, Simon; Goram, Richard; Yang, Cai-Yun; King, Julie; Allen, Alexandra M.; Burridge, Amanda; Edwards, Keith J.; Griffiths, Simon

2017-01-01

Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focusing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating biparental populations was developed, mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity. A modern spring elite variety, “Paragon,” was used as common reference parent. Genetic maps were constructed following identical rules to make them comparable. In total, 1611 linkage groups were identified, based on recombination from an estimated 126,300 crossover events over the whole NAM panel. A consensus map, named landrace consensus map (LRC), was constructed and contained 2498 genetic loci. These newly developed genetics tools were used to investigate the rules underlying genome fluidity or rigidity, e.g., by comparing marker distances and marker orders. In general, marker order was highly correlated, which provides support for strong synteny between bread wheat accessions. However, many exceptional cases of incongruent linkage groups and increased marker distances were also found. Segregation distortion was detected for many markers, sometimes as hot spots present in different populations. Furthermore, evidence for translocations in at least 36 of the maps was found. These translocations fell, in general, into many different translocation classes, but a few translocation classes were found in several accessions, the most frequent one being the well-known T5B:7B translocation. Loci involved in recombination rate, which is an interesting trait for plant breeding, were identified by QTL analyses using the crossover counts as a trait. In total, 114 significant QTL were detected, nearly half of them with increasing effect from the nonreference parents. PMID:28213475

Plant Sex Chromosomes.

PubMed

Charlesworth, Deborah

2016-04-29

Although individuals in most flowering plant species, and in many haploid plants, have both sex functions, dioecious species-in which individuals have either male or female functions only-are scattered across many taxonomic groups, and many species have genetic sex determination. Among these, some have visibly heteromorphic sex chromosomes, and molecular genetic studies are starting to uncover sex-linked markers in others, showing that they too have fully sex-linked regions that are either too small or are located in chromosomes that are too small to be cytologically detectable from lack of pairing, lack of visible crossovers, or accumulation of heterochromatin. Detailed study is revealing that, like animal sex chromosomes, plant sex-linked regions show evidence for accumulation of repetitive sequences and genetic degeneration. Estimating when recombination stopped confirms the view that many plants have young sex-linked regions, making plants of great interest for studying the timescale of these changes.

Inverting the parameters of an earthquake-ruptured fault with a genetic algorithm

NASA Astrophysics Data System (ADS)

Yu, Ting-To; Fernàndez, Josè; Rundle, John B.

1998-03-01

Natural selection is the spirit of the genetic algorithm (GA): by keeping the good genes in the current generation, thereby producing better offspring during evolution. The crossover function ensures the heritage of good genes from parent to offspring. Meanwhile, the process of mutation creates a special gene, the character of which does not exist in the parent generation. A program based on genetic algorithms using C language is constructed to invert the parameters of an earthquake-ruptured fault. The verification and application of this code is shown to demonstrate its capabilities. It is determined that this code is able to find the global extreme and can be used to solve more practical problems with constraints gathered from other sources. It is shown that GA is superior to other inverting schema in many aspects. This easy handling and yet powerful algorithm should have many suitable applications in the field of geosciences.

Why sampling scheme matters: the effect of sampling scheme on landscape genetic results

Treesearch

Michael K. Schwartz; Kevin S. McKelvey

2008-01-01

There has been a recent trend in genetic studies of wild populations where researchers have changed their sampling schemes from sampling pre-defined populations to sampling individuals uniformly across landscapes. This reflects the fact that many species under study are continuously distributed rather than clumped into obvious "populations". Once individual...

Rayleigh wave dispersion curve inversion by using particle swarm optimization and genetic algorithm

NASA Astrophysics Data System (ADS)

Buyuk, Ersin; Zor, Ekrem; Karaman, Abdullah

2017-04-01

Inversion of surface wave dispersion curves with its highly nonlinear nature has some difficulties using traditional linear inverse methods due to the need and strong dependence to the initial model, possibility of trapping in local minima and evaluation of partial derivatives. There are some modern global optimization methods to overcome of these difficulties in surface wave analysis such as Genetic algorithm (GA) and Particle Swarm Optimization (PSO). GA is based on biologic evolution consisting reproduction, crossover and mutation operations, while PSO algorithm developed after GA is inspired from the social behaviour of birds or fish of swarms. Utility of these methods require plausible convergence rate, acceptable relative error and optimum computation cost that are important for modelling studies. Even though PSO and GA processes are similar in appearence, the cross-over operation in GA is not used in PSO and the mutation operation is a stochastic process for changing the genes within chromosomes in GA. Unlike GA, the particles in PSO algorithm changes their position with logical velocities according to particle's own experience and swarm's experience. In this study, we applied PSO algorithm to estimate S wave velocities and thicknesses of the layered earth model by using Rayleigh wave dispersion curve and also compared these results with GA and we emphasize on the advantage of using PSO algorithm for geophysical modelling studies considering its rapid convergence, low misfit error and computation cost.

Dependence of the Contact Resistance on the Design of Stranded Conductors

PubMed Central

Zeroukhi, Youcef; Napieralska-Juszczak, Ewa; Vega, Guillaume; Komeza, Krzysztof; Morganti, Fabrice; Wiak, Slawomir

2014-01-01

During the manufacturing process multi-strand conductors are subject to compressive force and rotation moments. The current distribution in the multi-strand conductors is not uniform and is controlled by the transverse resistivity. This is mainly determined by the contact resistance at the strand crossovers and inter-strand contact resistance. The surface layer properties, and in particular the crystalline structure and degree of oxidation, are key parameters in determining the transverse resistivity. The experimental set-ups made it possible to find the dependence of contact resistivity as a function of continuous working stresses and cable design. A study based on measurements and numerical simulation is made to identify the contact resistivity functions. PMID:25196112

Improved classification accuracy by feature extraction using genetic algorithms

NASA Astrophysics Data System (ADS)

Patriarche, Julia; Manduca, Armando; Erickson, Bradley J.

2003-05-01

A feature extraction algorithm has been developed for the purposes of improving classification accuracy. The algorithm uses a genetic algorithm / hill-climber hybrid to generate a set of linearly recombined features, which may be of reduced dimensionality compared with the original set. The genetic algorithm performs the global exploration, and a hill climber explores local neighborhoods. Hybridizing the genetic algorithm with a hill climber improves both the rate of convergence, and the final overall cost function value; it also reduces the sensitivity of the genetic algorithm to parameter selection. The genetic algorithm includes the operators: crossover, mutation, and deletion / reactivation - the last of these effects dimensionality reduction. The feature extractor is supervised, and is capable of deriving a separate feature space for each tissue (which are reintegrated during classification). A non-anatomical digital phantom was developed as a gold standard for testing purposes. In tests with the phantom, and with images of multiple sclerosis patients, classification with feature extractor derived features yielded lower error rates than using standard pulse sequences, and with features derived using principal components analysis. Using the multiple sclerosis patient data, the algorithm resulted in a mean 31% reduction in classification error of pure tissues.

Honey bee nest thermoregulation: diversity promotes stability.

PubMed

Jones, Julia C; Myerscough, Mary R; Graham, Sonia; Oldroyd, Benjamin P

2004-07-16

A honey bee colony is characterized by high genetic diversity among its workers, generated by high levels of multiple mating by its queen. Few clear benefits of this genetic diversity are known. Here we show that brood nest temperatures in genetically diverse colonies (i.e., those sired by several males) tend to be more stable than in genetically uniform ones (i.e., those sired by one male). One reason this increased stability arises is because genetically determined diversity in workers' temperature response thresholds modulates the hive-ventilating behavior of individual workers, preventing excessive colony-level responses to temperature fluctuations.

Crossover from the coffee-ring effect to the uniform deposit caused by irreversible cluster-cluster aggregation

NASA Astrophysics Data System (ADS)

Crivoi, A.; Zhong, X.; Duan, Fei

2015-09-01

The coffee-ring effect for particle deposition near the three-phase line after drying a pinned sessile colloidal droplet has been suppressed or attenuated in many recent studies. However, there have been few attempts to simulate the mitigation of the effect in the presence of strong particle-particle attraction forces. We develop a three-dimensional stochastic model to investigate the drying process of a pinned colloidal sessile droplet by considering the sticking between particles, which was observed in the experiments. The Monte Carlo simulation results show that by solely promoting the particle-particle attraction in the model, the final deposit shape is transformed from the coffee ring to the uniform film deposition. This phenomenon is modeled using the colloidal aggregation technique and explained by the "Tetris principle," meaning that unevenly shaped or branched particle clusters rapidly build up a sparse structure spanning throughout the entire domain in the drying process. The influence of the controlled parameters is analyzed as well. The simulation is reflected by the drying patterns of the nanofluid droplets through the surfactant control in the experiments.

Silviculture of varietal loblolly pine plantations: second year impacts of spacing and silvicultural treatments on varieties with differing crown ideotypes

Treesearch

Lance A. Vickers; Thomas R. Fox; Jose L. Stape; Timothy J. Albaugh

2012-01-01

A long-term study has been established to address the following objectives: 1) Evaluate the crown ideotype approach to clonal testing in loblolly pine; 2) Determine impacts of increasing genetic uniformity on growth and uniformity of loblolly pine plantations; 3) Compare growth response, carbon allocation patterns (above and below ground), and ecophysiological...

Superfluid transition temperature in a trapped gas of Fermi atoms with a Feshbach resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohashi, Y.; Institute of Physics, University of Tsukuba, Ibaraki 305; Griffin, A.

2003-03-01

We investigate strong-coupling effects on the superfluid phase transition in a gas of Fermi atoms with a Feshbach resonance. The Feshbach resonance describes a composite quasiboson that can give rise to an additional pairing interaction between the Fermi atoms. This attractive interaction becomes stronger as the threshold energy 2{nu} of the Feshbach resonance two-particle bound state is lowered. In a recent paper, we showed that in the uniform Fermi gas, this tunable pairing interaction naturally leads to a crossover from a BCS state to a Bose-Einstein condensate (BEC) of the Nozieres and Schmitt-Rink kind, in which the BCS-type superfluid phasemore » transition continuously changes into the BEC type as the threshold energy is decreased. In this paper, we extend our previous work by including the effect of a harmonic trap potential, treated within the local-density approximation. We also give results for both weak and strong coupling to the Feshbach resonance. We show that the BCS-BEC crossover phenomenon strongly modifies the shape of the atomic density profile at the superfluid phase-transition temperature T{sub c}, reflecting the change of the dominant particles going from Fermi atoms to composite bosons. In the BEC regime, these composite bosons are shown to first appear well above T{sub c}. We also discuss the 'phase diagram' above T{sub c} as a function of the tunable threshold energy 2{nu}. We introduce a characteristic temperature T*(2{nu}) describing the effective crossover in the normal phase from a Fermi gas of atoms to a gas of stable molecules.« less

Improvement of Predictive Ability by Uniform Coverage of the Target Genetic Space

PubMed Central

Bustos-Korts, Daniela; Malosetti, Marcos; Chapman, Scott; Biddulph, Ben; van Eeuwijk, Fred

2016-01-01

Genome-enabled prediction provides breeders with the means to increase the number of genotypes that can be evaluated for selection. One of the major challenges in genome-enabled prediction is how to construct a training set of genotypes from a calibration set that represents the target population of genotypes, where the calibration set is composed of a training and validation set. A random sampling protocol of genotypes from the calibration set will lead to low quality coverage of the total genetic space by the training set when the calibration set contains population structure. As a consequence, predictive ability will be affected negatively, because some parts of the genotypic diversity in the target population will be under-represented in the training set, whereas other parts will be over-represented. Therefore, we propose a training set construction method that uniformly samples the genetic space spanned by the target population of genotypes, thereby increasing predictive ability. To evaluate our method, we constructed training sets alongside with the identification of corresponding genomic prediction models for four genotype panels that differed in the amount of population structure they contained (maize Flint, maize Dent, wheat, and rice). Training sets were constructed using uniform sampling, stratified-uniform sampling, stratified sampling and random sampling. We compared these methods with a method that maximizes the generalized coefficient of determination (CD). Several training set sizes were considered. We investigated four genomic prediction models: multi-locus QTL models, GBLUP models, combinations of QTL and GBLUPs, and Reproducing Kernel Hilbert Space (RKHS) models. For the maize and wheat panels, construction of the training set under uniform sampling led to a larger predictive ability than under stratified and random sampling. The results of our methods were similar to those of the CD method. For the rice panel, all training set construction methods led to similar predictive ability, a reflection of the very strong population structure in this panel. PMID:27672112

Genetic characterization of human herpesvirus type 1: Full-length genome sequence of strain obtained from an encephalitis case from India.

PubMed

Bondre, Vijay P; Sankararaman, Vasudha; Andhare, Vijaysinh; Tupekar, Manisha; Sapkal, Gajanan N

2016-11-01

Human herpes simplex virus 1 (HSV-1) is the most common cause of sporadic encephalitis in humans that contributes to >10 per cent of the encephalitis cases occurring worldwide. Availability of limited full genome sequences from a small number of isolates resulted in poor understanding of host and viral factors responsible for variable clinical outcome. In this study genetic relationship, extent and source of recombination using full-length genome sequence derived from a newly isolated HSV-1 isolate was studied in comparison with those sampled from patients with varied clinical outcome. Full genome sequence of HSV-1 isolated from cerebrospinal fluid (CSF) of a patient with acute encephalitis syndrome (AES) by inoculation in baby hamster kidney-21 (BHK-21) cells was determined using next-generation sequencing (NGS) technology. Phylogenetic analysis of the newly generated sequence in comparison with 33 additional full-length genomes defined genetic relationship with worldwide distributed strains. The bootscan and similarity plot analysis defined recombination crossovers and similarities between newly isolated Indian HSV-1 with six Asian and a total of 34 worldwide isolated strains. Mapping of 376,332 reads amplified from HSV-1 DNA by NGS generated full-length genome of 151,024 bp from newly isolated Indian HSV-1. Phylogenetic analysis classified worldwide distributed strains into three major evolutionary lineages correlating to their geographic distribution. Lineage 1 containing strains were isolated from America and Europe; lineage 2 contained all the strains from Asian countries along with the North American KOS and RE strains whereas the South African isolates were distributed into two groups under lineage 3. Recombination analysis confirmed events of recombination in Indian HSV-1 genome resulting from mixing of different strains evolved in Asian countries. Our results showed that the full-length genome sequence generated from an Indian HSV-1 isolate shared close genetic relationship with the American KOS and Chinese CR38 strains which belonged to the Asian genetic lineage. Recombination analysis of Indian isolate demonstrated multiple recombination crossover points throughout the genome. This full-length genome sequence amplified from the Indian isolate would be helpful to study HSV evolution, genetic basis of differential pathogenesis, host-virus interactions and viral factors contributing towards differential clinical outcome in human infections.

Genetic characterization of human herpesvirus type 1: Full-length genome sequence of strain obtained from an encephalitis case from India

PubMed Central

Bondre, Vijay P.; Sankararaman, Vasudha; Andhare, Vijaysinh; Tupekar, Manisha; Sapkal, Gajanan N.

2016-01-01

Background & objectives: Human herpes simplex virus 1 (HSV-1) is the most common cause of sporadic encephalitis in humans that contributes to >10 per cent of the encephalitis cases occurring worldwide. Availability of limited full genome sequences from a small number of isolates resulted in poor understanding of host and viral factors responsible for variable clinical outcome. In this study genetic relationship, extent and source of recombination using full-length genome sequence derived from a newly isolated HSV-1 isolate was studied in comparison with those sampled from patients with varied clinical outcome. Methods: Full genome sequence of HSV-1 isolated from cerebrospinal fluid (CSF) of a patient with acute encephalitis syndrome (AES) by inoculation in baby hamster kidney-21 (BHK-21) cells was determined using next-generation sequencing (NGS) technology. Phylogenetic analysis of the newly generated sequence in comparison with 33 additional full-length genomes defined genetic relationship with worldwide distributed strains. The bootscan and similarity plot analysis defined recombination crossovers and similarities between newly isolated Indian HSV-1 with six Asian and a total of 34 worldwide isolated strains. Results: Mapping of 376,332 reads amplified from HSV-1 DNA by NGS generated full-length genome of 151,024 bp from newly isolated Indian HSV-1. Phylogenetic analysis classified worldwide distributed strains into three major evolutionary lineages correlating to their geographic distribution. Lineage 1 containing strains were isolated from America and Europe; lineage 2 contained all the strains from Asian countries along with the North American KOS and RE strains whereas the South African isolates were distributed into two groups under lineage 3. Recombination analysis confirmed events of recombination in Indian HSV-1 genome resulting from mixing of different strains evolved in Asian countries. Interpretation & conclusions: Our results showed that the full-length genome sequence generated from an Indian HSV-1 isolate shared close genetic relationship with the American KOS and Chinese CR38 strains which belonged to the Asian genetic lineage. Recombination analysis of Indian isolate demonstrated multiple recombination crossover points throughout the genome. This full-length genome sequence amplified from the Indian isolate would be helpful to study HSV evolution, genetic basis of differential pathogenesis, host-virus interactions and viral factors contributing towards differential clinical outcome in human infections. PMID:28361829

New knowledge-based genetic algorithm for excavator boom structural optimization

NASA Astrophysics Data System (ADS)

Hua, Haiyan; Lin, Shuwen

2014-03-01

Due to the insufficiency of utilizing knowledge to guide the complex optimal searching, existing genetic algorithms fail to effectively solve excavator boom structural optimization problem. To improve the optimization efficiency and quality, a new knowledge-based real-coded genetic algorithm is proposed. A dual evolution mechanism combining knowledge evolution with genetic algorithm is established to extract, handle and utilize the shallow and deep implicit constraint knowledge to guide the optimal searching of genetic algorithm circularly. Based on this dual evolution mechanism, knowledge evolution and population evolution can be connected by knowledge influence operators to improve the configurability of knowledge and genetic operators. Then, the new knowledge-based selection operator, crossover operator and mutation operator are proposed to integrate the optimal process knowledge and domain culture to guide the excavator boom structural optimization. Eight kinds of testing algorithms, which include different genetic operators, are taken as examples to solve the structural optimization of a medium-sized excavator boom. By comparing the results of optimization, it is shown that the algorithm including all the new knowledge-based genetic operators can more remarkably improve the evolutionary rate and searching ability than other testing algorithms, which demonstrates the effectiveness of knowledge for guiding optimal searching. The proposed knowledge-based genetic algorithm by combining multi-level knowledge evolution with numerical optimization provides a new effective method for solving the complex engineering optimization problem.

Development and evaluation of a high density genotyping 'Axiom_Arachis' array with 58K SNPs for accelerating genetics and breeding in groundnut

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applicatio...

Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait

Treesearch

Craig S. Echt; L.L. DeVerno; M. Anzidei; G.G. Vendramin

1998-01-01

Variation in paternally inherited chloroplast microsatellite (cpSSR) DNA was used to study population genetic structure in red pine (Pinus resinosa Ait.), a species characterized by morphological uniformity, no allozyme variation, and limited RAPD variation. Using nine cpSSR loci, a total of 23 chloroplast haplotypes and 25 cpSSR alleles were were...

DNA nanotechnology: a future perspective

PubMed Central

2013-01-01

In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology. PMID:23497147

Application of methylation in improving plasmid transformation into Helicobacter pylori.

PubMed

Zhao, Huilin; Xu, Linlin; Rong, Qianyu; Xu, Zheng; Ding, Yunfei; Zhang, Ying; Wu, Yulong; Li, Boqing; Ji, Xiaofei

2018-05-23

Helicobacter pylori is an important gastrointestinal pathogen. Its strains possess different levels of powerful restriction modification systems, which are significant barriers to genetic tools used for studying the role of functional genes in its pathogenesis. Methylating vectors in vitro was reported as an alternative to overcome this barrier in several bacteria. In this study we used two H. pylori-E. coli shuttle plasmids and several single/double-crossover homologous recombination gene-targeting plasmids, to test the role of methylation in H. pylori transformation. According to our results, transformants could be obtained only after shuttle plasmids were methylated before transformation. It is helpful in gene complementation and over-expression although at a low frequency. The frequency of gene-targeting transformation was also increased after methylation, especially for the single-crossover recombination plasmids, the transformants of which could only be obtained after methylation. For the double-crossover recombination targeting plasmids, the initial yield of transformants was 0.3-0.8 × 10 2 CFUs per microgram plasmid DNA. With the help of methylation, the yield was increased to 0.4-1.3 × 10 2 CFUs per microgram plasmid DNA. These results suggest that in vitro methylation can improve H. pylori transformation by different plasmids, which will benefit the pathogenic mechanism research. Copyright © 2018. Published by Elsevier B.V.

Over 10,000 new maize mutants added to the uniformMu public resource: now 67,000 total Mu insertions with 42% genome coverage

USDA-ARS?s Scientific Manuscript database

Over 10,000 new mutants have been added to the UniformMu reverse genetics resource in release 7, bringing the total to over 67,000 germinal transposon insertions. These are available in 11,140 independent seed stocks. Close to half of the maize filtered gene set (42%) is represented by at least one ...

Pseudogap temperature and effects of a harmonic trap in the BCS-BEC crossover regime of an ultracold Fermi gas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsuchiya, Shunji; Research and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Kanagawa 223-8521; CREST

2011-10-15

We theoretically investigate excitation properties in the pseudogap regime of a trapped Fermi gas. Using a combined T-matrix theory with the local density approximation, we calculate strong-coupling corrections to single-particle local density of states (LDOS), as well as the single-particle local spectral weight (LSW). Starting from the superfluid phase transition temperature T{sub c}, we clarify how the pseudogap structures in these quantities disappear with increasing the temperature. As in the case of a uniform Fermi gas, LDOS and LSW give different pseudogap temperatures T{sup *} and T{sup **} at which the pseudogap structures in these quantities completely disappear. Determining T{supmore » *} and T{sup **} over the entire BCS (Bardeen-Cooper-Schrieffer)-BEC (Bose-Einstein condensation) crossover region, we identify the pseudogap regime in the phase diagram with respect to the temperature and the interaction strength. We also show that the so-called back-bending peak recently observed in the photoemission spectra by the JILA group may be explained as an effect of pseudogap phenomenon in the trap center. Since strong pairing fluctuations, spatial inhomogeneity, and finite temperatures are important keys in considering real cold Fermi gases, our results would be useful for clarifying normal-state properties of this strongly interacting Fermi system.« less

Effect of Short-Term Fasting on Systemic Cytochrome P450-Mediated Drug Metabolism in Healthy Subjects: A Randomized, Controlled, Crossover Study Using a Cocktail Approach.

PubMed

Lammers, Laureen A; Achterbergh, Roos; van Schaik, Ron H N; Romijn, Johannes A; Mathôt, Ron A A

2017-10-01

Short-term fasting can alter drug exposure but it is unknown whether this is an effect of altered oral bioavailability and/or systemic clearance. Therefore, the aim of our study was to assess the effect of short-term fasting on oral bioavailability and systemic clearance of different drugs. In a randomized, controlled, crossover trial, 12 healthy subjects received a single administration of a cytochrome P450 (CYP) probe cocktail, consisting of caffeine (CYP1A2), metoprolol (CYP2D6), midazolam (CYP3A4), omeprazole (CYP2C19) and warfarin (CYP2C9), on four occasions: an oral (1) and intravenous (2) administration after an overnight fast (control) and an oral (3) and intravenous (4) administration after 36 h of fasting. Pharmacokinetic parameters of the probe drugs were analyzed using the nonlinear mixed-effects modeling software NONMEM. Short-term fasting increased systemic caffeine clearance by 17% (p = 0.04) and metoprolol clearance by 13% (p < 0.01), whereas S-warfarin clearance decreased by 19% (p < 0.01). Fasting did not affect bioavailability. The study demonstrates that short-term fasting alters CYP-mediated drug metabolism in a non-uniform pattern without affecting oral bioavailability.

The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo

PubMed Central

Meerbrey, Kristen L.; Hu, Guang; Kessler, Jessica D.; Roarty, Kevin; Fang, Justin E.; Herschkowitz, Jason I.; Burrows, Anna E.; Ciccia, Alberto; Sun, Tingting; Schmitt, Earlene M.; Bernardi, Ronald J.; Fu, Xiaoyong; Bland, Christopher S.; Cooper, Thomas A.; Schiff, Rachel; Rosen, Jeffrey M.; Westbrook, Thomas F.; Elledge, Stephen J.

2011-01-01

The discovery of RNAi has revolutionized loss-of-function genetic studies in mammalian systems. However, significant challenges still remain to fully exploit RNAi for mammalian genetics. For instance, genetic screens and in vivo studies could be broadly improved by methods that allow inducible and uniform gene expression control. To achieve this, we built the lentiviral pINDUCER series of expression vehicles for inducible RNAi in vivo. Using a multicistronic design, pINDUCER vehicles enable tracking of viral transduction and shRNA or cDNA induction in a broad spectrum of mammalian cell types in vivo. They achieve this uniform temporal, dose-dependent, and reversible control of gene expression across heterogenous cell populations via fluorescence-based quantification of reverse tet-transactivator expression. This feature allows isolation of cell populations that exhibit a potent, inducible target knockdown in vitro and in vivo that can be used in human xenotransplantation models to examine cancer drug targets. PMID:21307310

Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius

PubMed Central

Wagner, Michaela; van Wolferen, Marleen; Wagner, Alexander; Lassak, Kerstin; Meyer, Benjamin H.; Reimann, Julia; Albers, Sonja-Verena

2012-01-01

For reverse genetic approaches inactivation or selective modification of genes are required to elucidate their putative function. Sulfolobus acidocaldarius is a thermoacidophilic Crenarchaeon which grows optimally at 76°C and pH 3. As many antibiotics do not withstand these conditions the development of a genetic system in this organism is dependent on auxotrophies. Therefore we constructed a pyrE deletion mutant of S. acidocaldarius wild type strain DSM639 missing 322 bp called MW001. Using this strain as the starting point, we describe here different methods using single as well as double crossover events to obtain markerless deletion mutants, tag genes genomically and ectopically integrate foreign DNA into MW001. These methods enable us to construct single, double, and triple deletions strains that can still be complemented with the pRN1 based expression vector. Taken together we have developed a versatile and robust genetic tool box for the crenarchaeote S. acidocaldarius that will promote the study of unknown gene functions in this organism and makes it a suitable host for synthetic biology approaches. PMID:22707949

New optimization model for routing and spectrum assignment with nodes insecurity

NASA Astrophysics Data System (ADS)

Xuan, Hejun; Wang, Yuping; Xu, Zhanqi; Hao, Shanshan; Wang, Xiaoli

2017-04-01

By adopting the orthogonal frequency division multiplexing technology, elastic optical networks can provide the flexible and variable bandwidth allocation to each connection request and get higher spectrum utilization. The routing and spectrum assignment problem in elastic optical network is a well-known NP-hard problem. In addition, information security has received worldwide attention. We combine these two problems to investigate the routing and spectrum assignment problem with the guaranteed security in elastic optical network, and establish a new optimization model to minimize the maximum index of the used frequency slots, which is used to determine an optimal routing and spectrum assignment schemes. To solve the model effectively, a hybrid genetic algorithm framework integrating a heuristic algorithm into a genetic algorithm is proposed. The heuristic algorithm is first used to sort the connection requests and then the genetic algorithm is designed to look for an optimal routing and spectrum assignment scheme. In the genetic algorithm, tailor-made crossover, mutation and local search operators are designed. Moreover, simulation experiments are conducted with three heuristic strategies, and the experimental results indicate that the effectiveness of the proposed model and algorithm framework.

Design of Genetic Algorithms for Topology Control of Unmanned Vehicles

DTIC Science & Technology

2010-01-01

decentralised topology control mechanism distributed among active running software agents to achieve a uniform spread of terrestrial unmanned vehicles...14. ABSTRACT We present genetic algorithms (GAs) as a decentralised topology control mechanism distributed among active running software agents to...inspired topology control algorithm. The topology control of UVs using a decentralised solution over an unknown geographical terrain is a challenging

Porous matrix structures for alkaline electrolyte fuel cells

NASA Technical Reports Server (NTRS)

Vine, R. W.; Narsavage, S. T.

1975-01-01

A number of advancements have been realized by a continuing research program to develop higher chemically stable porous matrix structures with high bubble pressure (crossover resistance) for use as separators in potassium hydroxide electrolyte fuel cells. More uniform, higher-bubble-pressure asbestos matrices were produced by reconstituting Johns-Manville asbestos paper; Fybex potassium titanate which was found compatible with 42% KOH at 250 F for up to 3000 hr; good agreement was found between bubble pressures predicted by an analytical study and those measured with filtered structures; Teflon-bonded Fybex matrices with bubble pressures greater than 30 psi were obtained by filtering a water slurry of the mixture directly onto fuel cell electrodes; and PBI fibers have satisfactory compatibility with 42% KOH at 250 F.

An Island Grouping Genetic Algorithm for Fuzzy Partitioning Problems

PubMed Central

Salcedo-Sanz, S.; Del Ser, J.; Geem, Z. W.

2014-01-01

This paper presents a novel fuzzy clustering technique based on grouping genetic algorithms (GGAs), which are a class of evolutionary algorithms especially modified to tackle grouping problems. Our approach hinges on a GGA devised for fuzzy clustering by means of a novel encoding of individuals (containing elements and clusters sections), a new fitness function (a superior modification of the Davies Bouldin index), specially tailored crossover and mutation operators, and the use of a scheme based on a local search and a parallelization process, inspired from an island-based model of evolution. The overall performance of our approach has been assessed over a number of synthetic and real fuzzy clustering problems with different objective functions and distance measures, from which it is concluded that the proposed approach shows excellent performance in all cases. PMID:24977235

The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen

PubMed Central

Croll, Daniel; Lendenmann, Mark H.; Stewart, Ethan; McDonald, Bruce A.

2015-01-01

Recombination has an impact on genome evolution by maintaining chromosomal integrity, affecting the efficacy of selection, and increasing genetic variability in populations. Recombination rates are a key determinant of the coevolutionary dynamics between hosts and their pathogens. Historic recombination events created devastating new pathogens, but the impact of ongoing recombination in sexual pathogens is poorly understood. Many fungal pathogens of plants undergo regular sexual cycles, and sex is considered to be a major factor contributing to virulence. We generated a recombination map at kilobase-scale resolution for the haploid plant pathogenic fungus Zymoseptoria tritici. To account for intraspecific variation in recombination rates, we constructed genetic maps from two independent crosses. We localized a total of 10,287 crossover events in 441 progeny and found that recombination rates were highly heterogeneous within and among chromosomes. Recombination rates on large chromosomes were inversely correlated with chromosome length. Short accessory chromosomes often lacked evidence for crossovers between parental chromosomes. Recombination was concentrated in narrow hotspots that were preferentially located close to telomeres. Hotspots were only partially conserved between the two crosses, suggesting that hotspots are short-lived and may vary according to genomic background. Genes located in hotspot regions were enriched in genes encoding secreted proteins. Population resequencing showed that chromosomal regions with high recombination rates were strongly correlated with regions of low linkage disequilibrium. Hence, genes in pathogen recombination hotspots are likely to evolve faster in natural populations and may represent a greater threat to the host. PMID:26392286

An improved self-adaptive ant colony algorithm based on genetic strategy for the traveling salesman problem

NASA Astrophysics Data System (ADS)

Wang, Pan; Zhang, Yi; Yan, Dong

2018-05-01

Ant Colony Algorithm (ACA) is a powerful and effective algorithm for solving the combination optimization problem. Moreover, it was successfully used in traveling salesman problem (TSP). But it is easy to prematurely converge to the non-global optimal solution and the calculation time is too long. To overcome those shortcomings, a new method is presented-An improved self-adaptive Ant Colony Algorithm based on genetic strategy. The proposed method adopts adaptive strategy to adjust the parameters dynamically. And new crossover operation and inversion operation in genetic strategy was used in this method. We also make an experiment using the well-known data in TSPLIB. The experiment results show that the performance of the proposed method is better than the basic Ant Colony Algorithm and some improved ACA in both the result and the convergence time. The numerical results obtained also show that the proposed optimization method can achieve results close to the theoretical best known solutions at present.

The genetic algorithm: A robust method for stress inversion

NASA Astrophysics Data System (ADS)

Thakur, Prithvi; Srivastava, Deepak C.; Gupta, Pravin K.

2017-01-01

The stress inversion of geological or geophysical observations is a nonlinear problem. In most existing methods, it is solved by linearization, under certain assumptions. These linear algorithms not only oversimplify the problem but also are vulnerable to entrapment of the solution in a local optimum. We propose the use of a nonlinear heuristic technique, the genetic algorithm, which searches the global optimum without making any linearizing assumption or simplification. The algorithm mimics the natural evolutionary processes of selection, crossover and mutation and, minimizes a composite misfit function for searching the global optimum, the fittest stress tensor. The validity and efficacy of the algorithm are demonstrated by a series of tests on synthetic and natural fault-slip observations in different tectonic settings and also in situations where the observations are noisy. It is shown that the genetic algorithm is superior to other commonly practised methods, in particular, in those tectonic settings where none of the principal stresses is directed vertically and/or the given data set is noisy.

Enhancing speech recognition using improved particle swarm optimization based hidden Markov model.

PubMed

Selvaraj, Lokesh; Ganesan, Balakrishnan

2014-01-01

Enhancing speech recognition is the primary intention of this work. In this paper a novel speech recognition method based on vector quantization and improved particle swarm optimization (IPSO) is suggested. The suggested methodology contains four stages, namely, (i) denoising, (ii) feature mining (iii), vector quantization, and (iv) IPSO based hidden Markov model (HMM) technique (IP-HMM). At first, the speech signals are denoised using median filter. Next, characteristics such as peak, pitch spectrum, Mel frequency Cepstral coefficients (MFCC), mean, standard deviation, and minimum and maximum of the signal are extorted from the denoised signal. Following that, to accomplish the training process, the extracted characteristics are given to genetic algorithm based codebook generation in vector quantization. The initial populations are created by selecting random code vectors from the training set for the codebooks for the genetic algorithm process and IP-HMM helps in doing the recognition. At this point the creativeness will be done in terms of one of the genetic operation crossovers. The proposed speech recognition technique offers 97.14% accuracy.

Self-consistent elastic continuum theory of degenerate, equilibrium aperiodic solids.

PubMed

Bevzenko, Dmytro; Lubchenko, Vassiliy

2014-11-07

We show that the vibrational response of a glassy liquid at finite frequencies can be described by continuum mechanics despite the vast degeneracy of the vibrational ground state; standard continuum elasticity assumes a unique ground state. The effective elastic constants are determined by the bare elastic constants of individual free energy minima of the liquid, the magnitude of built-in stress, and temperature, analogously to how the dielectric response of a polar liquid is determined by the dipole moment of the constituent molecules and temperature. In contrast with the dielectric constant--which is enhanced by adding polar molecules to the system--the elastic constants are down-renormalized by the relaxation of the built-in stress. The renormalization flow of the elastic constants has three fixed points, two of which are trivial and correspond to the uniform liquid state and an infinitely compressible solid, respectively. There is also a nontrivial fixed point at the Poisson ratio equal to 1/5, which corresponds to an isospin-like degeneracy between shear and uniform deformation. The present description predicts a discontinuous jump in the (finite frequency) shear modulus at the crossover from collisional to activated transport, consistent with the random first order transition theory.

The First National Student Conference: NASA University Research Centers at Minority Institutions

NASA Technical Reports Server (NTRS)

Daso, Endwell O. (Editor); Mebane, Stacie (Editor)

1997-01-01

The conference includes contributions from 13 minority universities with NASA University Research Centers. Topics discussed include: leadership, survival strategies, life support systems, food systems, simulated hypergravity, chromium diffusion doping, radiation effects on dc-dc converters, metal oxide glasses, crystal growth of Bil3, science and communication on wheels, semiconductor thin films, numerical solution of random algebraic equations, fuzzy logic control, spatial resolution of satellite images, programming language development, nitric oxide in the thermosphere and mesosphere, high performance polyimides, crossover control in genetic algorithms, hyperthermal ion scattering, etc.

Non-uniform cosine modulated filter banks using meta-heuristic algorithms in CSD space.

PubMed

Kalathil, Shaeen; Elias, Elizabeth

2015-11-01

This paper presents an efficient design of non-uniform cosine modulated filter banks (CMFB) using canonic signed digit (CSD) coefficients. CMFB has got an easy and efficient design approach. Non-uniform decomposition can be easily obtained by merging the appropriate filters of a uniform filter bank. Only the prototype filter needs to be designed and optimized. In this paper, the prototype filter is designed using window method, weighted Chebyshev approximation and weighted constrained least square approximation. The coefficients are quantized into CSD, using a look-up-table. The finite precision CSD rounding, deteriorates the filter bank performances. The performances of the filter bank are improved using suitably modified meta-heuristic algorithms. The different meta-heuristic algorithms which are modified and used in this paper are Artificial Bee Colony algorithm, Gravitational Search algorithm, Harmony Search algorithm and Genetic algorithm and they result in filter banks with less implementation complexity, power consumption and area requirements when compared with those of the conventional continuous coefficient non-uniform CMFB.

Non-uniform cosine modulated filter banks using meta-heuristic algorithms in CSD space

PubMed Central

Kalathil, Shaeen; Elias, Elizabeth

2014-01-01

This paper presents an efficient design of non-uniform cosine modulated filter banks (CMFB) using canonic signed digit (CSD) coefficients. CMFB has got an easy and efficient design approach. Non-uniform decomposition can be easily obtained by merging the appropriate filters of a uniform filter bank. Only the prototype filter needs to be designed and optimized. In this paper, the prototype filter is designed using window method, weighted Chebyshev approximation and weighted constrained least square approximation. The coefficients are quantized into CSD, using a look-up-table. The finite precision CSD rounding, deteriorates the filter bank performances. The performances of the filter bank are improved using suitably modified meta-heuristic algorithms. The different meta-heuristic algorithms which are modified and used in this paper are Artificial Bee Colony algorithm, Gravitational Search algorithm, Harmony Search algorithm and Genetic algorithm and they result in filter banks with less implementation complexity, power consumption and area requirements when compared with those of the conventional continuous coefficient non-uniform CMFB. PMID:26644921

Effects of the silvicultural intensity on the 4-years growth and leaf-level physiology of loblolly pine varieties

Treesearch

Marco Yanez; John Seiler; Thomas Fox

2015-01-01

The role that genetic improvement plays in the increase of productivity in loblolly pine (Pinus taeda L.) in the South has been recognized (McKeand and others 2003). Varietal forestry has the potential to improve the productivity and quality of loblolly pine stands, and higher genetic gains can be achieved in volume and stand uniformity (Zobel and Talbert 1984).

Pressure for Pattern-Specific Intertypic Recombination between Sabin Polioviruses: Evolutionary Implications.

PubMed

Korotkova, Ekaterina; Laassri, Majid; Zagorodnyaya, Tatiana; Petrovskaya, Svetlana; Rodionova, Elvira; Cherkasova, Elena; Gmyl, Anatoly; Ivanova, Olga E; Eremeeva, Tatyana P; Lipskaya, Galina Y; Agol, Vadim I; Chumakov, Konstantin

2017-11-22

Complete genomic sequences of a non-redundant set of 70 recombinants between three serotypes of attenuated Sabin polioviruses as well as location (based on partial sequencing) of crossover sites of 28 additional recombinants were determined and compared with the previously published data. It is demonstrated that the genomes of Sabin viruses contain distinct strain-specific segments that are eliminated by recombination. The presumed low fitness of these segments could be linked to mutations acquired upon derivation of the vaccine strains and/or may have been present in wild-type parents of Sabin viruses. These "weak" segments contribute to the propensity of these viruses to recombine with each other and with other enteroviruses as well as determine the choice of crossover sites. The knowledge of location of such segments opens additional possibilities for the design of more genetically stable and/or more attenuated variants, i.e., candidates for new oral polio vaccines. The results also suggest that the genome of wild polioviruses, and, by generalization, of other RNA viruses, may harbor hidden low-fitness segments that can be readily eliminated only by recombination.

Accelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural Network.

PubMed

Janet, Jon Paul; Chan, Lydia; Kulik, Heather J

2018-03-01

Machine learning (ML) has emerged as a powerful complement to simulation for materials discovery by reducing time for evaluation of energies and properties at accuracy competitive with first-principles methods. We use genetic algorithm (GA) optimization to discover unconventional spin-crossover complexes in combination with efficient scoring from an artificial neural network (ANN) that predicts spin-state splitting of inorganic complexes. We explore a compound space of over 5600 candidate materials derived from eight metal/oxidation state combinations and a 32-ligand pool. We introduce a strategy for error-aware ML-driven discovery by limiting how far the GA travels away from the nearest ANN training points while maximizing property (i.e., spin-splitting) fitness, leading to discovery of 80% of the leads from full chemical space enumeration. Over a 51-complex subset, average unsigned errors (4.5 kcal/mol) are close to the ANN's baseline 3 kcal/mol error. By obtaining leads from the trained ANN within seconds rather than days from a DFT-driven GA, this strategy demonstrates the power of ML for accelerating inorganic material discovery.

Efficiency Improvement of Action Acquisition in Two-Link Robot Arm Using Fuzzy ART with Genetic Algorithm

NASA Astrophysics Data System (ADS)

Kotani, Naoki; Taniguchi, Kenji

An efficient learning method using Fuzzy ART with Genetic Algorithm is proposed. The proposed method reduces the number of trials by using a policy acquired in other tasks because a reinforcement learning needs a lot of the number of trials until an agent acquires appropriate actions. Fuzzy ART is an incremental unsupervised learning algorithm in responce to arbitrary sequences of analog or binary input vectors. Our proposed method gives a policy by crossover or mutation when an agent observes unknown states. Selection controls the category proliferation problem of Fuzzy ART. The effectiveness of the proposed method was verified with the simulation of the reaching problem for the two-link robot arm. The proposed method achieves a reduction of both the number of trials and the number of states.

Effect of Crossover in Oncology Clinical Trials on Evidence Levels in Early Benefit Assessment in Germany.

PubMed

Isbary, Georg; Staab, Thomas R; Amelung, Volker E; Dintsios, Charalabos-Markos; Iking-Konert, Christof; Nesurini, Sonja Mariotti; Walter, Miriam; Ruof, Jörg

2018-06-01

In oncology clinical trials, crossover is used frequently but may lead to uncertainties regarding treatment effects. To investigate the handling of evidence from crossover trials by the European Medicines Agency (EMA) and the German Federal Joint Committee (G-BA). For oncology medicines with early benefit assessments before January 2015, presence of crossover, clinical data, EMA requests for additional data, and G-BA benefit ratings/evidence levels were analyzed from manufacturers' dossiers, G-BA appraisals, European Public Assessment Reports, and original publications. Eleven of 21 benefit assessments included crossover trials. Significant intergroup differences (P < 0.05) in overall survival (OS) were noted in 7 of 11 trials with and 7 of 10 without crossover. For 6 of 11 medicines with crossover, these were demonstrated before crossover. Treatment effects generally worsened with increasing proportions of crossover. The EMA requested additional data more frequently if crossover was performed, particularly if no OS data were available before crossover. The G-BA granted a considerable benefit to 73% of medicines with crossover and 40% of those without. Evidence levels were intermediate for 50% and 75%, respectively. None of the medicines received the highest evidence level. In G-BA appraisals, oncology medicines with crossover received better additional benefit ratings, but were assigned lower evidence levels, than those without. The five medicines with crossover after progression were assigned lower evidence levels than the six medicines with crossover after demonstration of superior OS, indicating that the way in which crossover is implemented may be one factor influencing the assignment of evidence levels by the G-BA. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

A fixed full-matrix method for determining ice sheet height change from satellite altimeter: an ENVISAT case study in East Antarctica with backscatter analysis

NASA Astrophysics Data System (ADS)

Yang, Yuande; Hwang, Cheinway; E, Dongchen

2014-09-01

A new method, called the fixed full-matrix method (FFM), is used to compute height changes at crossovers of satellite altimeter ground tracks. Using the ENVISAT data in East Antarctica, FFM results in crossovers of altimeter heights that are 1.9 and 79 times more than those from the fixed half method (FHM) and the one-row method (ORM). The mean standard error of height changes is about 14 cm from ORM, which is reduced to 7 cm by FHM and to 3 cm by FFM. Unlike FHM, FFM leads to uniform errors in the first-half and second-half height-change time series. FFM has the advantage in improving the accuracy of the change of height and backscattered power over ORM and FHM. Assisted by the ICESat-derived height changes, we determine the optimal threshold correlation coefficient (TCC) for a best correction for the backscatter effect on ENVISAT height changes. The TCC value of 0.92 yields an optimal result for FFM. With this value, FFM yields ENVISAT-derived height change rates in East Antarctica mostly falling between and 3 cm/year, and matching the ICESat result to 0.94 cm/year. The ENVISAT result will provide a constraint on the current mass balance result along the Chinese expedition route CHINARE.

The impact of a multidisciplinary self-care management program on quality of life, self-care, adherence to anti-hypertensive therapy, glycemic control, and renal function in diabetic kidney disease: A Cross-over Study Protocol.

PubMed

Helou, Nancy; Talhouedec, Dominique; Shaha, Maya; Zanchi, Anne

2016-07-19

Diabetic kidney disease, a global health issue, remains associated with high morbidity and mortality. Previous research has shown that multidisciplinary management of chronic disease can improve patient outcomes. The effect of multidisciplinary self-care management on quality of life and renal function of patients with diabetic kidney disease has not yet been well established. The aim of this study is to evaluate the impact of a multidisciplinary self-care management program on quality of life, self-care behavior, adherence to anti-hypertensive treatment, glycemic control, and renal function of adults with diabetic kidney disease. A uniform balanced cross-over design is used, with the objective to recruit 40 adult participants with diabetic kidney disease, from public and private out-patient settings in French speaking Switzerland. Participants are randomized in equal number into four study arms. Each participant receives usual care alternating with the multidisciplinary self- care management program. Each treatment period lasts three months and is repeated twice at different time intervals over 12 months depending on the cross-over arm. The multidisciplinary self-care management program is led by an advanced practice nurse and adds nursing and dietary consultations and follow-ups, to the habitual management provided by the general practitioner, the nephrologist and the diabetologist. Data is collected every three months for 12 months. Quality of life is measured using the Audit of Diabetes-Dependent Quality of Life scale, patient self-care behavior is assessed using the Revised Summary of Diabetes Self-Care Activities, and adherence to anti-hypertensive therapy is evaluated using the Medication Events Monitoring System. Blood glucose control is measured by the glycated hemoglobin levels and renal function by serum creatinine, estimated glomerular filtration rate and urinary albumin/creatinine ratio. Data will be analyzed using STATA version 14. The cross-over design will elucidate the responses of individual participant to each treatment, and will allow us to better evaluate the use of such a design in clinical settings and behavioral studies. This study also explores the impact of a theory-based nursing practice and its implementation into a multidisciplinary context. ClinicalTrials.gov identifier: NCT01967901 , registered on the 18th of October 2013.

A genetic analysis of Trichuris trichiura and Trichuris suis from Ecuador.

PubMed

Meekums, Hayley; Hawash, Mohamed B F; Sparks, Alexandra M; Oviedo, Yisela; Sandoval, Carlos; Chico, Martha E; Stothard, J Russell; Cooper, Philip J; Nejsum, Peter; Betson, Martha

2015-03-19

Since the nematodes Trichuris trichiura and T. suis are morphologically indistinguishable, genetic analysis is required to assess epidemiological cross-over between people and pigs. This study aimed to clarify the transmission biology of trichuriasis in Ecuador. Adult Trichuris worms were collected during a parasitological survey of 132 people and 46 pigs in Esmeraldas Province, Ecuador. Morphometric analysis of 49 pig worms and 64 human worms revealed significant variation. In discriminant analysis morphometric characteristics correctly classified male worms according to host species. In PCR-RFLP analysis of the ribosomal Internal Transcribed Spacer (ITS-2) and 18S DNA (59 pig worms and 82 human worms), nearly all Trichuris exhibited expected restriction patterns. However, two pig-derived worms showed a "heterozygous-type" ITS-2 pattern, with one also having a "heterozygous-type" 18S pattern. Phylogenetic analysis of the mitochondrial large ribosomal subunit partitioned worms by host species. Notably, some Ecuadorian T. suis clustered with porcine Trichuris from USA and Denmark and some with Chinese T. suis. This is the first study in Latin America to genetically analyse Trichuris parasites. Although T. trichiura does not appear to be zoonotic in Ecuador, there is evidence of genetic exchange between T. trichiura and T. suis warranting more detailed genetic sampling.

Clinical Significance of Epigenetic Alterations in Human Hepatocellular Carcinoma and Its Association with Genetic Mutations.

PubMed

Nishida, Naoshi; Kudo, Masatoshi

Accumulation of genetic and epigenetic alterations is a hallmark of cancer genomes, including those in hepatocellular carcinoma (HCC). Particularly, in human HCC, epigenetic changes are more frequently observed than genetic changes in a variety of cancer-related genes, suggesting a potential role for epigenetic alterations during hepatocarcinogenesis. Several environmental factors, such as inflammation, obesity, and steatosis, are reported to affect the epigenetic status in hepatocytes, which could play a role in HCC development. In addition, genetic mutations in histone modulators and chromatin regulators would be critical for the acceleration of epigenetic alteration. It is also possible that major genetic mutations of HCC, such as TP53 and CNTTB1 mutations, are associated with the disturbance of epigenetic integrity. For example, specific TP53 mutations frequently induced by aflatoxin B1 exposure might affect histone modifiers and nucleosome remodelers. Generally, epigenetic alteration is reversible, because of which dysregulation of transcription takes place, without affecting protein structure. Therefore, differentiation therapy is one of the potential approaches for HCC with advanced epigenetic alterations. On the other hand, a tumor carrying an accumulation of genetic mutations would result in many abnormal proteins that could be recognized as non-self and could be targets for immune reactions; thus, immune-checkpoint blockers should be effective for HCCs with genetic hypermutation. Although the emergence of genetic and epigenetic alterations could be linked to each other and there could be some crossover or convergence between these cancer pathways, characterization of the mutation spectrum of genetic and epigenetic alterations could influence future HCC treatment. © 2016 S. Karger AG, Basel.

Genetic control of residual variance of yearling weight in Nellore beef cattle.

PubMed

Iung, L H S; Neves, H H R; Mulder, H A; Carvalheiro, R

2017-04-01

There is evidence for genetic variability in residual variance of livestock traits, which offers the potential for selection for increased uniformity of production. Different statistical approaches have been employed to study this topic; however, little is known about the concordance between them. The aim of our study was to investigate the genetic heterogeneity of residual variance on yearling weight (YW; 291.15 ± 46.67) in a Nellore beef cattle population; to compare the results of the statistical approaches, the two-step approach and the double hierarchical generalized linear model (DHGLM); and to evaluate the effectiveness of power transformation to accommodate scale differences. The comparison was based on genetic parameters, accuracy of EBV for residual variance, and cross-validation to assess predictive performance of both approaches. A total of 194,628 yearling weight records from 625 sires were used in the analysis. The results supported the hypothesis of genetic heterogeneity of residual variance on YW in Nellore beef cattle and the opportunity of selection, measured through the genetic coefficient of variation of residual variance (0.10 to 0.12 for the two-step approach and 0.17 for DHGLM, using an untransformed data set). However, low estimates of genetic variance associated with positive genetic correlations between mean and residual variance (about 0.20 for two-step and 0.76 for DHGLM for an untransformed data set) limit the genetic response to selection for uniformity of production while simultaneously increasing YW itself. Moreover, large sire families are needed to obtain accurate estimates of genetic merit for residual variance, as indicated by the low heritability estimates (<0.007). Box-Cox transformation was able to decrease the dependence of the variance on the mean and decreased the estimates of genetic parameters for residual variance. The transformation reduced but did not eliminate all the genetic heterogeneity of residual variance, highlighting its presence beyond the scale effect. The DHGLM showed higher predictive ability of EBV for residual variance and therefore should be preferred over the two-step approach.

Distributed query plan generation using multiobjective genetic algorithm.

PubMed

Panicker, Shina; Kumar, T V Vijay

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability.

Distributed Query Plan Generation Using Multiobjective Genetic Algorithm

PubMed Central

Panicker, Shina; Vijay Kumar, T. V.

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability. PMID:24963513

Locating Critical Circular and Unconstrained Failure Surface in Slope Stability Analysis with Tailored Genetic Algorithm

NASA Astrophysics Data System (ADS)

Pasik, Tomasz; van der Meij, Raymond

2017-12-01

This article presents an efficient search method for representative circular and unconstrained slip surfaces with the use of the tailored genetic algorithm. Searches for unconstrained slip planes with rigid equilibrium methods are yet uncommon in engineering practice, and little publications regarding truly free slip planes exist. The proposed method presents an effective procedure being the result of the right combination of initial population type, selection, crossover and mutation method. The procedure needs little computational effort to find the optimum, unconstrained slip plane. The methodology described in this paper is implemented using Mathematica. The implementation, along with further explanations, is fully presented so the results can be reproduced. Sample slope stability calculations are performed for four cases, along with a detailed result interpretation. Two cases are compared with analyses described in earlier publications. The remaining two are practical cases of slope stability analyses of dikes in Netherlands. These four cases show the benefits of analyzing slope stability with a rigid equilibrium method combined with a genetic algorithm. The paper concludes by describing possibilities and limitations of using the genetic algorithm in the context of the slope stability problem.

Flexible Job-Shop Scheduling with Dual-Resource Constraints to Minimize Tardiness Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Paksi, A. B. N.; Ma'ruf, A.

2016-02-01

In general, both machines and human resources are needed for processing a job on production floor. However, most classical scheduling problems have ignored the possible constraint caused by availability of workers and have considered only machines as a limited resource. In addition, along with production technology development, routing flexibility appears as a consequence of high product variety and medium demand for each product. Routing flexibility is caused by capability of machines that offers more than one machining process. This paper presents a method to address scheduling problem constrained by both machines and workers, considering routing flexibility. Scheduling in a Dual-Resource Constrained shop is categorized as NP-hard problem that needs long computational time. Meta-heuristic approach, based on Genetic Algorithm, is used due to its practical implementation in industry. Developed Genetic Algorithm uses indirect chromosome representative and procedure to transform chromosome into Gantt chart. Genetic operators, namely selection, elitism, crossover, and mutation are developed to search the best fitness value until steady state condition is achieved. A case study in a manufacturing SME is used to minimize tardiness as objective function. The algorithm has shown 25.6% reduction of tardiness, equal to 43.5 hours.

Pseudosynapsis and Decreased Stringency of Meiotic Repair Pathway Choice on the Hemizygous Sex Chromosome of Caenorhabditis elegans Males

PubMed Central

Checchi, Paula M.; Lawrence, Katherine S.; Van, Mike V.; Larson, Braden J.; Engebrecht, JoAnne

2014-01-01

During meiosis, accurate chromosome segregation relies on homology to mediate chromosome pairing, synapsis, and crossover recombination. Crossovers are dependent upon formation and repair of double-strand breaks (DSBs) by homologous recombination (HR). In males of many species, sex chromosomes are largely hemizygous, yet DSBs are induced along nonhomologous regions. Here we analyzed the genetic requirements for meiotic DSB repair on the completely hemizygous X chromosome of Caenorhabditis elegans males. Our data reveal that the kinetics of DSB formation, chromosome pairing, and synapsis are tightly linked in the male germ line. Moreover, DSB induction on the X is concomitant with a brief period of pseudosynapsis that may allow X sister chromatids to masquerade as homologs. Consistent with this, neither meiotic kleisins nor the SMC-5/6 complex are essential for DSB repair on the X. Furthermore, early processing of X DSBs is dependent on the CtIP/Sae2 homolog COM-1, suggesting that as with paired chromosomes, HR is the preferred pathway. In contrast, the X chromosome is refractory to feedback mechanisms that ensure crossover formation on autosomes. Surprisingly, neither RAD-54 nor BRC-2 are essential for DSB repair on the X, suggesting that unlike autosomes, the X is competent for repair in the absence of HR. When both RAD-54 and the structure-specific nuclease XPF-1 are abrogated, X DSBs persist, suggesting that single-strand annealing is engaged in the absence of HR. Our findings indicate that alteration in sister chromatid interactions and flexibility in DSB repair pathway choice accommodate hemizygosity on sex chromosomes. PMID:24939994

A novel clinical decision support system using improved adaptive genetic algorithm for the assessment of fetal well-being.

PubMed

Ravindran, Sindhu; Jambek, Asral Bahari; Muthusamy, Hariharan; Neoh, Siew-Chin

2015-01-01

A novel clinical decision support system is proposed in this paper for evaluating the fetal well-being from the cardiotocogram (CTG) dataset through an Improved Adaptive Genetic Algorithm (IAGA) and Extreme Learning Machine (ELM). IAGA employs a new scaling technique (called sigma scaling) to avoid premature convergence and applies adaptive crossover and mutation techniques with masking concepts to enhance population diversity. Also, this search algorithm utilizes three different fitness functions (two single objective fitness functions and multi-objective fitness function) to assess its performance. The classification results unfold that promising classification accuracy of 94% is obtained with an optimal feature subset using IAGA. Also, the classification results are compared with those of other Feature Reduction techniques to substantiate its exhaustive search towards the global optimum. Besides, five other benchmark datasets are used to gauge the strength of the proposed IAGA algorithm.

The Ordered Clustered Travelling Salesman Problem: A Hybrid Genetic Algorithm

PubMed Central

Ahmed, Zakir Hussain

2014-01-01

The ordered clustered travelling salesman problem is a variation of the usual travelling salesman problem in which a set of vertices (except the starting vertex) of the network is divided into some prespecified clusters. The objective is to find the least cost Hamiltonian tour in which vertices of any cluster are visited contiguously and the clusters are visited in the prespecified order. The problem is NP-hard, and it arises in practical transportation and sequencing problems. This paper develops a hybrid genetic algorithm using sequential constructive crossover, 2-opt search, and a local search for obtaining heuristic solution to the problem. The efficiency of the algorithm has been examined against two existing algorithms for some asymmetric and symmetric TSPLIB instances of various sizes. The computational results show that the proposed algorithm is very effective in terms of solution quality and computational time. Finally, we present solution to some more symmetric TSPLIB instances. PMID:24701148

Evolutionary algorithm for optimization of nonimaging Fresnel lens geometry.

PubMed

Yamada, N; Nishikawa, T

2010-06-21

In this study, an evolutionary algorithm (EA), which consists of genetic and immune algorithms, is introduced to design the optical geometry of a nonimaging Fresnel lens; this lens generates the uniform flux concentration required for a photovoltaic cell. Herein, a design procedure that incorporates a ray-tracing technique in the EA is described, and the validity of the design is demonstrated. The results show that the EA automatically generated a unique geometry of the Fresnel lens; the use of this geometry resulted in better uniform flux concentration with high optical efficiency.

Automatic genetic optimization approach to two-dimensional blade profile design for steam turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trigg, M.A.; Tubby, G.R.; Sheard, A.G.

1999-01-01

In this paper a systematic approach to the optimization of two-dimensional blade profiles is presented. A genetic optimizer has been developed that modifies the blade profile and calculates its profile loss. This process is automatic, producing profile designs significantly faster and with significantly lower loss than has previously been possible. The optimizer developed uses a genetic algorithm to optimize a two-dimensional profile, defined using 17 parameters, for minimum loss with a given flow condition. The optimizer works with a population of two-dimensional profiles with varied parameters. A CFD mesh is generated for each profile, and the result is analyzed usingmore » a two-dimensional blade-to-blade solver, written for steady viscous compressible flow, to determine profile loss. The loss is used as the measure of a profile`s fitness. The optimizer uses this information to select the members of the next population, applying crossovers, mutations, and elitism in the process. Using this method, the optimizer tends toward the best values for the parameters defining the profile with minimum loss.« less

Modeling multilayer x-ray reflectivity using genetic algorithms

NASA Astrophysics Data System (ADS)

Sánchez del Río, M.; Pareschi, G.; Michetschläger, C.

2000-06-01

The x-ray reflectivity of a multilayer is a non-linear function of many parameters (materials, layer thickness, density, roughness). Non-linear fitting of experimental data with simulations requires the use of initial values sufficiently close to the optimum value. This is a difficult task when the topology of the space of the variables is highly structured. We apply global optimization methods to fit multilayer reflectivity. Genetic algorithms are stochastic methods based on the model of natural evolution: the improvement of a population along successive generations. A complete set of initial parameters constitutes an individual. The population is a collection of individuals. Each generation is built from the parent generation by applying some operators (selection, crossover, mutation, etc.) on the members of the parent generation. The pressure of selection drives the population to include "good" individuals. For large number of generations, the best individuals will approximate the optimum parameters. Some results on fitting experimental hard x-ray reflectivity data for Ni/C and W/Si multilayers using genetic algorithms are presented. This method can also be applied to design multilayers optimized for a target application.

Efficient and reproducible in vitro regeneration of Solanum lycopersicum and assessment genetic uniformity using flow cytometry and SPAR methods.

PubMed

Alatar, Abdulrahman A; Faisal, Mohammad; Abdel-Salam, Eslam M; Canto, Tomas; Saquib, Quaiser; Javed, Saad B; El-Sheikh, Mohamed A; Al-Khedhairy, Abdulaziz A

2017-09-01

In the present study, we develop an efficient and reproducible in vitro regeneration system for two cultivars viz. , Jamila and Tomaland of Solanum lycopersicum L., an economically important vegetable crop throughout the world. Sterilization of seeds with 2.5% (v/v) NaOCl was found to be most effective, about 97% of seeds germinated on cotton in magenta box moistened with sterile half strength (½)Murashige and Skoog (MS) medium. Regeneration efficiency of cotyledonary leaf (CL) and cotyledonary node (CN) explants derived from 08 days old aseptic seedling were assessed on MS medium supplemented with different concentrations of auxins and cytokinin. CL explants were found more responsive in comparison to CN in both the cultivars. Types of basal media were also assessed and found to have a significant effect on shoot regeneration. Highest regeneration frequency and maximum number of shoots were standardized from CL explants on MS medium supplied with 6-benzyl adenine (BA; 5.0 µM), indole-3-butyric acid (IBA; 2.5 µM) and Kinetin (Kin; 10.0 µM). In vitro regenerated microshoots were rooted on ½MS medium containing 0.5 µM indole-3-butyric acid (IBA). Regenerated plantlets with well-developed roots and shoot system were successfully acclimated to ex vitro condition. Genetic uniformity of tissue culture raised plantlets was first time evaluated using flow cytometry and single primer amplification reaction (SPAR) methods viz ., DAMD and ISSR. No significant changes in ploidy level and nuclear DNA content profile were observed between in vitro propagated plants and normal plants of both the cultivars. Similarly, the SPAR analysis also revealed monomorphic banding patterns in regenerated plantlets of S. lycopersicum verifying their genetic uniformity and clonal fidelity. This efficient regeneration system can be used as a fast and reproducible method for genetic transformation of this important vegetable crop.

Interactive genetic counseling role-play: a novel educational strategy for family physicians.

PubMed

Blaine, Sean M; Carroll, June C; Rideout, Andrea L; Glendon, Gord; Meschino, Wendy; Shuman, Cheryl; Telner, Deanna; Van Iderstine, Natasha; Permaul, Joanne

2008-04-01

Family physicians (FPs) are increasingly involved in delivering genetic services. Familiarization with aspects of genetic counseling may enable FPs to help patients make informed choices. Exploration of interactive role-play as a means to raise FPs' awareness of the process and content of genetic counseling. FPs attending two large Canadian family medicine conferences in 2005 were eligible -- 93 participated. FPs discussed a case during a one-on-one session with a genetic counselor. Evaluation involved pre and post intervention questionnaires FPs' baseline genetic knowledge was self-rated as uniformly poor. Baseline confidence was highest in eliciting family history and providing psychosocial support and lowest in discussing risks/benefits of genetic testing and counseling process. Post-intervention, 80% of FPs had better appreciation of family history and 97% indicated this was an effective learning experience. Role-play with FPs is effective in raising awareness of the process and content of genetic counseling and may be applied to other health disciplines.

Robustness of crossover trials against subject drop-out - Examples of perpetually connected designs.

PubMed

Godolphin, P J; Godolphin, E J

2017-01-01

When performing a repeated measures experiment, such as a clinical trial, there is a risk of subject drop-out during the experiment. If one or more subjects leave the study prematurely, a situation could arise where the eventual design is disconnected, implying that very few treatment contrasts for both direct effects and carryover effects are estimable. This paper aims to identify experimental conditions where this problem with the eventual design can be avoided. It is shown that in the class of uniformly balanced repeated measurement designs consisting of two or more Latin squares, there are planned designs with the following useful property. Provided that all subjects have completed the first two periods of study, such a design will not be replaced by a disconnected eventual design due to drop-out, irrespective of the type of drop-out behaviour that may occur. Designs with this property are referred to as perpetually connected. These experimental conditions are identified and examined in the paper and an example of at least one perpetually connected uniformly balanced repeated measurement design is given in each case. The results improve upon previous contributions in the literature that have been confined largely to cases in which drop-out occurs only in the final periods of study.

Threshold Levels of Infant and Under-Five Mortality for Crossover between Life Expectancies at Ages Zero, One and Five in India: A Decomposition Analysis.

PubMed

Dubey, Manisha; Ram, Usha; Ram, Faujdar

2015-01-01

Under the prevailing conditions of imbalanced life table and historic gender discrimination in India, our study examines crossover between life expectancies at ages zero, one and five years for India and quantifies the relative share of infant and under-five mortality towards this crossover. We estimate threshold levels of infant and under-five mortality required for crossover using age specific death rates during 1981-2009 for 16 Indian states by sex (comprising of India's 90% population in 2011). Kitagawa decomposition equations were used to analyse relative share of infant and under-five mortality towards crossover. India experienced crossover between life expectancies at ages zero and five in 2004 for menand in 2009 for women; eleven and nine Indian states have experienced this crossover for men and women, respectively. Men usually experienced crossover four years earlier than the women. Improvements in mortality below ages five have mostly contributed towards this crossover. Life expectancy at age one exceeds that at age zero for both men and women in India except for Kerala (the only state to experience this crossover in 2000 for men and 1999 for women). For India, using life expectancy at age zero and under-five mortality rate together may be more meaningful to measure overall health of its people until the crossover. Delayed crossover for women, despite higher life expectancy at birth than for men reiterates that Indian women are still disadvantaged and hence use of life expectancies at ages zero, one and five become important for India. Greater programmatic efforts to control leading causes of death during the first month and 1-59 months in high child mortality areas can help India to attain this crossover early.

Pediatric genetic disease of the cornea

PubMed Central

Fecarotta, Christopher M.; Huang, Wendy W.

2014-01-01

Our objective is to evaluate the literature regarding selected genetic diseases of the cornea, including megalocornea, keratoglobus, keratoconus, cystinosis, the mucopolysaccharidoses, sclerocornea, Peters' anomaly, familial dysautonomia, and various corneal dystrophies. The transparency of the cornea is a consequence of uniformity in both size and spacing of the collagen lamellae. The cornea's clarity depends on a delicate biochemical and structural balance; consequently, genetic disorders that disrupt either its metabolic or anatomic function can cause opacity and vision loss. Many childhood corneal diseases have a genetic etiology and are associated with known syndromes. Each disorder has unique associated set of possible complications. Prognosis often depends on the extent of opacity and disorganization of the anterior segment. Corneal transplantation has been performed for these disorders with variable success. PMID:27625877

Comparison of Genetic Algorithm and Hill Climbing for Shortest Path Optimization Mapping

NASA Astrophysics Data System (ADS)

Fronita, Mona; Gernowo, Rahmat; Gunawan, Vincencius

2018-02-01

Traveling Salesman Problem (TSP) is an optimization to find the shortest path to reach several destinations in one trip without passing through the same city and back again to the early departure city, the process is applied to the delivery systems. This comparison is done using two methods, namely optimization genetic algorithm and hill climbing. Hill Climbing works by directly selecting a new path that is exchanged with the neighbour's to get the track distance smaller than the previous track, without testing. Genetic algorithms depend on the input parameters, they are the number of population, the probability of crossover, mutation probability and the number of generations. To simplify the process of determining the shortest path supported by the development of software that uses the google map API. Tests carried out as much as 20 times with the number of city 8, 16, 24 and 32 to see which method is optimal in terms of distance and time computation. Based on experiments conducted with a number of cities 3, 4, 5 and 6 producing the same value and optimal distance for the genetic algorithm and hill climbing, the value of this distance begins to differ with the number of city 7. The overall results shows that these tests, hill climbing are more optimal to number of small cities and the number of cities over 30 optimized using genetic algorithms.

Control of Meiotic Crossovers: From Double-Strand Break Formation to Designation

PubMed Central

Gray, Stephen

2017-01-01

Meiosis, the mechanism of creating haploid gametes, is a complex cellular process observed across sexually reproducing organisms. Fundamental to meiosis is the process of homologous recombination, whereby DNA double-strand breaks are introduced into the genome and are subsequently repaired to generate either noncrossovers or crossovers. Although homologous recombination is essential for chromosome pairing during prophase I, the resulting crossovers are critical for maintaining homolog interactions and enabling accurate segregation at the first meiotic division. Thus, the placement, timing, and frequency of crossover formation must be exquisitely controlled. In this review, we discuss the proteins involved in crossover formation, the process of their formation and designation, and the rules governing crossovers, all within the context of the important landmarks of prophase I. We draw together crossover designation data across organisms, analyze their evolutionary divergence, and propose a universal model for crossover regulation. PMID:27648641

Necessity of Removing American Football Uniforms From Humans With Hyperthermia Before Cold-Water Immersion.

PubMed

Miller, Kevin C; Long, Blaine C; Edwards, Jeffrey

2015-12-01

The National Athletic Trainers' Association and the American College of Sports Medicine have recommended removing American football uniforms from athletes with exertional heat stroke before cold-water immersion (CWI) based on the assumption that the uniform impedes rectal temperature (T(rec)) cooling. Few experimental data exist to verify or disprove this assumption and the recommendations. To compare CWI durations, T(rec) cooling rates, thermal sensation, intensity of environmental symptoms, and onset of shivering when hyperthermic participants wore football uniforms during CWI or removed the uniforms immediately before CWI. Crossover study. Laboratory. Eighteen hydrated, physically active men (age = 22 ± 2 years, height = 182.5 ± 6.1 cm, mass = 85.4 ± 13.4 kg, body fat = 11% ± 5%, body surface area = 2.1 ± 0.2 m(2)) volunteered. On 2 days, participants exercised in the heat (approximately 40°C, approximately 40% relative humidity) while wearing a full American football uniform (shoes; crew socks; undergarments; shorts; game pants; undershirt; shoulder pads; jersey; helmet; and padding over the thighs, knees, hips, and tailbone [PADS]) until T(rec) reached 39.5°C. Next, participants immersed themselves in water that was approximately 10°C while wearing either undergarments, shorts, and crew socks (NOpads) or PADS without shoes until Trec reached 38°C. The CWI duration (minutes) and T(rec) cooling rates (°C/min). Participants had similar exercise times (NOpads = 40.8 ± 4.9 minutes, PADS = 43.2 ± 4.1 minutes; t(17) = 2.0, P = .10), hypohydration levels (NOpads = 1.5% ± 0.3%, PADS = 1.6% ± 0.4%; t(17) = 1.3, P = .22), and thermal-sensation ratings (NOpads = 7.2 ± 0.3, PADS = 7.1 ± 0.5; P > .05) before CWI. The CWI duration (median [interquartile range]; NOpads = 6.0 [5.4] minutes, PADS = 7.3 [9.8] minutes; z = 2.3, P = .01) and T(rec) cooling rates (NOpads = 0.28°C/min ± 0.14°C/min, PADS = 0.21°C/min ± 0.11°C/min; t(17) = 2.2, P = .02) differed between uniform conditions. Whereas participants cooled faster in NOpads, we still considered the PADS cooling rate to be acceptable (ie, >0.16°C/min). Therefore, if clinicians experience difficulty removing PADS or CWI treatment is delayed, they may immerse fully equipped hyperthermic football players in CWI and maintain acceptable T(rec) cooling rates. Otherwise, PADS should be removed preimmersion to ensure faster body core temperature cooling.

Effects of Temperature on the Meiotic Recombination Landscape of the Yeast Saccharomyces cerevisiae.

PubMed

Zhang, Ke; Wu, Xue-Chang; Zheng, Dao-Qiong; Petes, Thomas D

2017-12-19

Although meiosis in warm-blooded organisms takes place in a narrow temperature range, meiosis in many organisms occurs over a wide variety of temperatures. We analyzed the properties of meiosis in the yeast Saccharomyces cerevisiae in cells sporulated at 14°C, 30°C, or 37°C. Using comparative-genomic-hybridization microarrays, we examined the distribution of Spo11-generated meiosis-specific double-stranded DNA breaks throughout the genome. Although there were between 300 and 400 regions of the genome with high levels of recombination (hot spots) observed at each temperature, only about 20% of these hot spots were found to have occurred independently of the temperature. In S. cerevisiae , regions near the telomeres and centromeres tend to have low levels of meiotic recombination. This tendency was observed in cells sporulated at 14°C and 30°C, but not at 37°C. Thus, the temperature of sporulation in yeast affects some global property of chromosome structure relevant to meiotic recombination. Using single-nucleotide polymorphism (SNP)-specific whole-genome microarrays, we also examined crossovers and their associated gene conversion events as well as gene conversion events that were unassociated with crossovers in all four spores of tetrads obtained by sporulation of diploids at 14°C, 30°C, or 37°C. Although tetrads from cells sporulated at 30°C had slightly (20%) more crossovers than those derived from cells sporulated at the other two temperatures, spore viability was good at all three temperatures. Thus, despite temperature-induced variation in the genetic maps, yeast cells produce viable haploid products at a wide variety of sporulation temperatures. IMPORTANCE In the yeast Saccharomyces cerevisiae , recombination is usually studied in cells that undergo meiosis at 25°C or 30°C. In a genome-wide analysis, we showed that the locations of genomic regions with high and low levels of meiotic recombination (hot spots and cold spots, respectively) differed dramatically in cells sporulated at 14°C, 30°C, and 37°C. Thus, in yeast, and likely in other non-warm-blooded organisms, genetic maps are strongly affected by the environment. Copyright © 2017 Zhang et al.

Improved Evolutionary Programming with Various Crossover Techniques for Optimal Power Flow Problem

NASA Astrophysics Data System (ADS)

Tangpatiphan, Kritsana; Yokoyama, Akihiko

This paper presents an Improved Evolutionary Programming (IEP) for solving the Optimal Power Flow (OPF) problem, which is considered as a non-linear, non-smooth, and multimodal optimization problem in power system operation. The total generator fuel cost is regarded as an objective function to be minimized. The proposed method is an Evolutionary Programming (EP)-based algorithm with making use of various crossover techniques, normally applied in Real Coded Genetic Algorithm (RCGA). The effectiveness of the proposed approach is investigated on the IEEE 30-bus system with three different types of fuel cost functions; namely the quadratic cost curve, the piecewise quadratic cost curve, and the quadratic cost curve superimposed by sine component. These three cost curves represent the generator fuel cost functions with a simplified model and more accurate models of a combined-cycle generating unit and a thermal unit with value-point loading effect respectively. The OPF solutions by the proposed method and Pure Evolutionary Programming (PEP) are observed and compared. The simulation results indicate that IEP requires less computing time than PEP with better solutions in some cases. Moreover, the influences of important IEP parameters on the OPF solution are described in details.

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum

PubMed Central

Miles, Alistair; Iqbal, Zamin; Vauterin, Paul; Pearson, Richard; Campino, Susana; Theron, Michel; Gould, Kelda; Mead, Daniel; Drury, Eleanor; O'Brien, John; Ruano Rubio, Valentin; MacInnis, Bronwyn; Mwangi, Jonathan; Samarakoon, Upeka; Ranford-Cartwright, Lisa; Ferdig, Michael; Hayton, Karen; Su, Xin-zhuan; Wellems, Thomas; Rayner, Julian; McVean, Gil; Kwiatkowski, Dominic

2016-01-01

The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired. PMID:27531718

Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events in Drosophila melanogaster

PubMed Central

Miller, Danny E.; Cook, Kevin R.; Arvanitakis, Alexandra V.; Hawley, R. Scott

2016-01-01

Balancer chromosomes are multiply inverted chromosomes that suppress meiotic crossing over and prevent the recovery of crossover products. Balancers are commonly used in Drosophila melanogaster to maintain deleterious alleles and in stock construction. They exist for all three major chromosomes, yet the molecular location of the breakpoints and the exact nature of many of the mutations carried by the second and third chromosome balancers has not been available. Here, we precisely locate eight of 10 of the breakpoints on the third chromosome balancer TM3, six of eight on TM6, and nine of 11 breakpoints on TM6B. We find that one of the inversion breakpoints on TM3 bisects the highly conserved tumor suppressor gene p53—a finding that may have important consequences for a wide range of studies in Drosophila. We also identify evidence of single and double crossovers between several TM3 and TM6B balancers and their normal-sequence homologs that have created genetic diversity among these chromosomes. Overall, this work demonstrates the practical importance of precisely identifying the position of inversion breakpoints of balancer chromosomes and characterizing the mutant alleles carried by them. PMID:27172211

Arabidopsis thaliana FANCD2 Promotes Meiotic Crossover Formation[OPEN

PubMed Central

Kurzbauer, Marie-Therese; Kerzendorfer, Claudia; Sims, Jason; Oliver, Cecilia; Mosiolek, Magdalena; Schweizer, Dieter

2018-01-01

Fanconi anemia (FA) is a human autosomal recessive disorder characterized by chromosomal instability, developmental pathologies, predisposition to cancer, and reduced fertility. So far, 19 genes have been implicated in FA, most of them involved in DNA repair. Some are conserved across higher eukaryotes, including plants. The Arabidopsis thaliana genome encodes a homolog of the Fanconi anemia D2 gene (FANCD2) whose function in DNA repair is not yet fully understood. Here, we provide evidence that AtFANCD2 is required for meiotic homologous recombination. Meiosis is a specialized cell division that ensures reduction of genomic content by half and DNA exchange between homologous chromosomes via crossovers (COs) prior to gamete formation. In plants, a mutation in AtFANCD2 results in a 14% reduction of CO numbers. Genetic analysis demonstrated that AtFANCD2 acts in parallel to both MUTS HOMOLOG4 (AtMSH4), known for its role in promoting interfering COs and MMS AND UV SENSITIVE81 (AtMUS81), known for its role in the formation of noninterfering COs. AtFANCD2 promotes noninterfering COs in a MUS81-independent manner and is therefore part of an uncharted meiotic CO-promoting mechanism, in addition to those described previously. PMID:29352063

Berezinskii-Kosterlitz-Thouless crossover in a trapped atomic gas.

PubMed

Hadzibabic, Zoran; Krüger, Peter; Cheneau, Marc; Battelier, Baptiste; Dalibard, Jean

2006-06-29

Any state of matter is classified according to its order, and the type of order that a physical system can possess is profoundly affected by its dimensionality. Conventional long-range order, as in a ferromagnet or a crystal, is common in three-dimensional systems at low temperature. However, in two-dimensional systems with a continuous symmetry, true long-range order is destroyed by thermal fluctuations at any finite temperature. Consequently, for the case of identical bosons, a uniform two-dimensional fluid cannot undergo Bose-Einstein condensation, in contrast to the three-dimensional case. However, the two-dimensional system can form a 'quasi-condensate' and become superfluid below a finite critical temperature. The Berezinskii-Kosterlitz-Thouless (BKT) theory associates this phase transition with the emergence of a topological order, resulting from the pairing of vortices with opposite circulation. Above the critical temperature, proliferation of unbound vortices is expected. Here we report the observation of a BKT-type crossover in a trapped quantum degenerate gas of rubidium atoms. Using a matter wave heterodyning technique, we observe both the long-wavelength fluctuations of the quasi-condensate phase and the free vortices. At low temperatures, the gas is quasi-coherent on the length scale set by the system size. As the temperature is increased, the loss of long-range coherence coincides with the onset of proliferation of free vortices. Our results provide direct experimental evidence for the microscopic mechanism underlying the BKT theory, and raise new questions regarding coherence and superfluidity in mesoscopic systems.

Thermal transitions, pseudogap behavior, and BCS-BEC crossover in Fermi-Fermi mixtures

NASA Astrophysics Data System (ADS)

Karmakar, Madhuparna

2018-03-01

We study the mass imbalanced Fermi-Fermi mixture within the framework of a two-dimensional lattice fermion model. Based on the thermodynamic and species-dependent quasiparticle behavior, we map out the finite-temperature phase diagram of this system and show that unlike the balanced Fermi superfluid, there are now two different pseudogap regimes as PG-I and PG-II. While within the PG-I regime both the fermionic species are pseudogapped, PG-II corresponds to the regime where pseudogap feature survives only in the light species. We believe that the single-particle spectral features that we discuss in this paper are observable through the species-resolved radio-frequency spectroscopy and momentum-resolved photoemission spectroscopy measurements on systems such as 6Li-40K mixture. We further investigate the interplay between the population and mass imbalances and report that at a fixed population imbalance, the BCS-BEC crossover in a Fermi-Fermi mixture would require a critical interaction (Uc) for the realization of the uniform superfluid state. The effect of imbalance in mass on the exotic Fulde-Ferrell-Larkin-Ovchinnikov superfluid phase has been probed in detail in terms of the thermodynamic and quasiparticle behavior of this phase. It has been observed that in spite of the s -wave symmetry of the pairing field, a nodal superfluid gap is realized in the Larkin-Ovchinnikov regime. Our results on the various thermal scales and regimes are expected to serve as benchmarks for the experimental observations on 6Li-40K mixture.

Lack of association between allozyme heterozygosity and juvenile traits in Eucalyptus

USDA-ARS?s Scientific Manuscript database

Genetic variability for juvenile waits, which included basal diameter, height, biomass accumulation, and growth increment, was studied in eight provenances involving four species, Eucalyptus grandis, E. saligna, E. camaldulensis and E. urophylla, under uniform greenhouse conditions. The species diff...

Advertisement scheduling on commercial radio station using genetics algorithm

NASA Astrophysics Data System (ADS)

Purnamawati, S.; Nababan, E. B.; Tsani, B.; Taqyuddin, R.; Rahmat, R. F.

2018-03-01

On the commercial radio station, the advertising schedule is done manually, which resulted in ineffectiveness of ads schedule. Playback time consists of two types such as prime time and regular time. Radio Ads scheduling will be discussed in this research is based on ad playback schedule between 5am until 12am which rules every 15 minutes. It provides 3 slots ads with playback duration per ads maximum is 1 minute. If the radio broadcast time per day is 12 hours, then the maximum number of ads per day which can be aired is 76 ads. The other is the enactment of rules of prime time, namely the hours where the common people (listeners) have the greatest opportunity to listen to the radio, namely between the hours and hours of 4 am - 8 am, 6 pm - 10 pm. The number of screenings of the same ads on one day are limited to prime time ie 5 times, while for regular time is 8 times. Radio scheduling process is done using genetic algorithms which are composed of processes initialization chromosomes, selection, crossover and mutation. Study on chromosome 3 genes, each chromosome will be evaluated based on the value of fitness calculated based on the number of infractions that occurred on each individual chromosome. Where rule 1 is the number of screenings per ads must not be more than 5 times per day and rule 2 is there should never be two or more scheduling ads delivered on the same day and time. After fitness value of each chromosome is acquired, then the do the selection, crossover and mutation. From this research result, the optimal advertising schedule with schedule a whole day and ads data playback time ads with this level of accuracy: the average percentage was 83.79%.

Genetic Analysis of mlh3 Mutations Reveals Interactions Between Crossover Promoting Factors During Meiosis in Baker’s Yeast

PubMed Central

Brown, Megan Sonntag; Lim, Elisha; Chen, Cheng; Nishant, K. T.; Alani, Eric

2013-01-01

Crossing over between homologous chromosomes occurs during the prophase of meiosis I and is critical for chromosome segregation. In baker’s yeast, two heterodimeric complexes, Msh4-Msh5 and Mlh1-Mlh3, act in meiosis to promote interference-dependent crossing over. Mlh1-Mlh3 also plays a role in DNA mismatch repair (MMR) by interacting with Msh2-Msh3 to repair insertion and deletion mutations. Mlh3 contains an ATP-binding domain that is highly conserved among MLH proteins. To explore roles for Mlh3 in meiosis and MMR, we performed a structure−function analysis of eight mlh3 ATPase mutants. In contrast to previous work, our data suggest that ATP hydrolysis by both Mlh1 and Mlh3 is important for both meiotic and MMR functions. In meiotic assays, these mutants showed a roughly linear relationship between spore viability and genetic map distance. To further understand the relationship between crossing over and meiotic viability, we analyzed crossing over on four chromosomes of varying lengths in mlh3Δ mms4Δ strains and observed strong decreases (6- to 17-fold) in crossing over in all intervals. Curiously, mlh3Δ mms4Δ double mutants displayed spore viability levels that were greater than observed in mms4Δ strains that show modest defects in crossing over. The viability in double mutants also appeared greater than would be expected for strains that show such severe defects in crossing over. Together, these observations provide insights for how Mlh1-Mlh3 acts in crossover resolution and MMR and for how chromosome segregation in Meiosis I can occur in the absence of crossing over. PMID:23316435

Hybrid Sterility Locus on Chromosome X Controls Meiotic Recombination Rate in Mouse

PubMed Central

Balcova, Maria; Faltusova, Barbora; Gergelits, Vaclav; Bhattacharyya, Tanmoy; Mihola, Ondrej; Trachtulec, Zdenek; Knopf, Corinna; Fotopulosova, Vladana; Chvatalova, Irena; Gregorova, Sona; Forejt, Jiri

2016-01-01

Meiotic recombination safeguards proper segregation of homologous chromosomes into gametes, affects genetic variation within species, and contributes to meiotic chromosome recognition, pairing and synapsis. The Prdm9 gene has a dual role, it controls meiotic recombination by determining the genomic position of crossover hotspots and, in infertile hybrids of house mouse subspecies Mus m. musculus (Mmm) and Mus m. domesticus (Mmd), it further functions as the major hybrid sterility gene. In the latter role Prdm9 interacts with the hybrid sterility X 2 (Hstx2) genomic locus on Chromosome X (Chr X) by a still unknown mechanism. Here we investigated the meiotic recombination rate at the genome-wide level and its possible relation to hybrid sterility. Using immunofluorescence microscopy we quantified the foci of MLH1 DNA mismatch repair protein, the cytological counterparts of reciprocal crossovers, in a panel of inter-subspecific chromosome substitution strains. Two autosomes, Chr 7 and Chr 11, significantly modified the meiotic recombination rate, yet the strongest modifier, designated meiotic recombination 1, Meir1, emerged in the 4.7 Mb Hstx2 genomic locus on Chr X. The male-limited transgressive effect of Meir1 on recombination rate parallels the male-limited transgressive role of Hstx2 in hybrid male sterility. Thus, both genetic factors, the Prdm9 gene and the Hstx2/Meir1 genomic locus, indicate a link between meiotic recombination and hybrid sterility. A strong female-specific modifier of meiotic recombination rate with the effect opposite to Meir1 was localized on Chr X, distally to Meir1. Mapping Meir1 to a narrow candidate interval on Chr X is an important first step towards positional cloning of the respective gene(s) responsible for variation in the global recombination rate between closely related mouse subspecies. PMID:27104744

Hybrid Sterility Locus on Chromosome X Controls Meiotic Recombination Rate in Mouse.

PubMed

Balcova, Maria; Faltusova, Barbora; Gergelits, Vaclav; Bhattacharyya, Tanmoy; Mihola, Ondrej; Trachtulec, Zdenek; Knopf, Corinna; Fotopulosova, Vladana; Chvatalova, Irena; Gregorova, Sona; Forejt, Jiri

2016-04-01

Meiotic recombination safeguards proper segregation of homologous chromosomes into gametes, affects genetic variation within species, and contributes to meiotic chromosome recognition, pairing and synapsis. The Prdm9 gene has a dual role, it controls meiotic recombination by determining the genomic position of crossover hotspots and, in infertile hybrids of house mouse subspecies Mus m. musculus (Mmm) and Mus m. domesticus (Mmd), it further functions as the major hybrid sterility gene. In the latter role Prdm9 interacts with the hybrid sterility X 2 (Hstx2) genomic locus on Chromosome X (Chr X) by a still unknown mechanism. Here we investigated the meiotic recombination rate at the genome-wide level and its possible relation to hybrid sterility. Using immunofluorescence microscopy we quantified the foci of MLH1 DNA mismatch repair protein, the cytological counterparts of reciprocal crossovers, in a panel of inter-subspecific chromosome substitution strains. Two autosomes, Chr 7 and Chr 11, significantly modified the meiotic recombination rate, yet the strongest modifier, designated meiotic recombination 1, Meir1, emerged in the 4.7 Mb Hstx2 genomic locus on Chr X. The male-limited transgressive effect of Meir1 on recombination rate parallels the male-limited transgressive role of Hstx2 in hybrid male sterility. Thus, both genetic factors, the Prdm9 gene and the Hstx2/Meir1 genomic locus, indicate a link between meiotic recombination and hybrid sterility. A strong female-specific modifier of meiotic recombination rate with the effect opposite to Meir1 was localized on Chr X, distally to Meir1. Mapping Meir1 to a narrow candidate interval on Chr X is an important first step towards positional cloning of the respective gene(s) responsible for variation in the global recombination rate between closely related mouse subspecies.

Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas

PubMed Central

Falque, Matthieu; Trotoux, Gwenn; Eber, Frédérique; Nègre, Sylvie; Gilet, Marie; Huteau, Virginie; Lodé, Maryse; Jousseaume, Thibaut; Dechaumet, Sylvain; Morice, Jérôme; Coriton, Olivier; Rousseau-Gueutin, Mathieu

2017-01-01

Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs. PMID:28493942

Characterization of recombination features and the genetic basis in multiple cattle breeds.

PubMed

Shen, Botong; Jiang, Jicai; Seroussi, Eyal; Liu, George E; Ma, Li

2018-04-27

Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination. Based on large pedigrees of Jersey, Ayrshire and Brown Swiss cattle with genotype data, we identified over 3.4 million maternal and paternal crossover events from 161,309 three-generation families. We constructed six breed- and sex-specific genome-wide recombination maps using 58,982 autosomal SNPs for two sexes in the three dairy cattle breeds. A comparative analysis of the six recombination maps revealed similar global recombination patterns between cattle breeds but with significant differences between sexes. We confirmed that male recombination map is 10% longer than the female map in all three cattle breeds, consistent with previously reported results in Holstein cattle. When comparing recombination hotspot regions between cattle breeds, we found that 30% and 10% of the hotspots were shared between breeds in males and females, respectively, with each breed exhibiting some breed-specific hotspots. Finally, our multiple-breed GWAS found that SNPs in eight loci affected recombination rate and that the PRDM9 gene associated with hotspot usage in multiple cattle breeds, indicating a shared genetic basis for recombination across dairy cattle breeds. Collectively, our results generated breed- and sex-specific recombination maps for multiple cattle breeds, provided a comprehensive characterization and comparison of recombination patterns between breeds, and expanded our understanding of the breed-level variations in recombination features within an important livestock species.

Threshold Levels of Infant and Under-Five Mortality for Crossover between Life Expectancies at Ages Zero, One and Five in India: A Decomposition Analysis

PubMed Central

Dubey, Manisha

2015-01-01

Objectives Under the prevailing conditions of imbalanced life table and historic gender discrimination in India, our study examines crossover between life expectancies at ages zero, one and five years for India and quantifies the relative share of infant and under-five mortality towards this crossover. Methods We estimate threshold levels of infant and under-five mortality required for crossover using age specific death rates during 1981–2009 for 16 Indian states by sex (comprising of India’s 90% population in 2011). Kitagawa decomposition equations were used to analyse relative share of infant and under-five mortality towards crossover. Findings India experienced crossover between life expectancies at ages zero and five in 2004 for menand in 2009 for women; eleven and nine Indian states have experienced this crossover for men and women, respectively. Men usually experienced crossover four years earlier than the women. Improvements in mortality below ages five have mostly contributed towards this crossover. Life expectancy at age one exceeds that at age zero for both men and women in India except for Kerala (the only state to experience this crossover in 2000 for men and 1999 for women). Conclusions For India, using life expectancy at age zero and under-five mortality rate together may be more meaningful to measure overall health of its people until the crossover. Delayed crossover for women, despite higher life expectancy at birth than for men reiterates that Indian women are still disadvantaged and hence use of life expectancies at ages zero, one and five become important for India. Greater programmatic efforts to control leading causes of death during the first month and 1–59 months in high child mortality areas can help India to attain this crossover early. PMID:26683617

A compartmentalized signaling network mediates crossover control in meiosis

PubMed Central

Zhang, Liangyu; Köhler, Simone; Rillo-Bohn, Regina

2018-01-01

During meiosis, each pair of homologous chromosomes typically undergoes at least one crossover (crossover assurance), but these exchanges are strictly limited in number and widely spaced along chromosomes (crossover interference). The molecular basis for this chromosome-wide regulation remains mysterious. A family of meiotic RING finger proteins has been implicated in crossover regulation across eukaryotes. Caenorhabditis elegans expresses four such proteins, of which one (ZHP-3) is known to be required for crossovers. Here we investigate the functions of ZHP-1, ZHP-2, and ZHP-4. We find that all four ZHP proteins, like their homologs in other species, localize to the synaptonemal complex, an unusual, liquid crystalline compartment that assembles between paired homologs. Together they promote accumulation of pro-crossover factors, including ZHP-3 and ZHP-4, at a single recombination intermediate, thereby patterning exchanges along paired chromosomes. These proteins also act at the top of a hierarchical, symmetry-breaking process that enables crossovers to direct accurate chromosome segregation. PMID:29521627

An Integrated Optimization Design Method Based on Surrogate Modeling Applied to Diverging Duct Design

NASA Astrophysics Data System (ADS)

Hanan, Lu; Qiushi, Li; Shaobin, Li

2016-12-01

This paper presents an integrated optimization design method in which uniform design, response surface methodology and genetic algorithm are used in combination. In detail, uniform design is used to select the experimental sampling points in the experimental domain and the system performance is evaluated by means of computational fluid dynamics to construct a database. After that, response surface methodology is employed to generate a surrogate mathematical model relating the optimization objective and the design variables. Subsequently, genetic algorithm is adopted and applied to the surrogate model to acquire the optimal solution in the case of satisfying some constraints. The method has been applied to the optimization design of an axisymmetric diverging duct, dealing with three design variables including one qualitative variable and two quantitative variables. The method of modeling and optimization design performs well in improving the duct aerodynamic performance and can be also applied to wider fields of mechanical design and seen as a useful tool for engineering designers, by reducing the design time and computation consumption.

The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans

PubMed Central

Manhart, Carol M.; Ni, Xiaodan; White, Martin A.; Ortega, Joaquin; Surtees, Jennifer A.

2017-01-01

Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker’s yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I. Recent genetic, biochemical, and molecular studies in yeast are consistent with the hypothesis of Mlh1-Mlh3 DNA mismatch repair complex acting as the major endonuclease activity that resolves dHJs into crossovers. However, the mechanism by which the Mlh1-Mlh3 endonuclease is activated is unknown. Here, we provide evidence that Mlh1-Mlh3 does not behave like a structure-specific endonuclease but forms polymers required to generate nicks in DNA. This conclusion is supported by DNA binding studies performed with different-sized substrates that contain or lack polymerization barriers and endonuclease assays performed with varying ratios of endonuclease-deficient and endonuclease-proficient Mlh1-Mlh3. In addition, Mlh1-Mlh3 can generate religatable double-strand breaks and form an active nucleoprotein complex that can nick DNA substrates in trans. Together these observations argue that Mlh1-Mlh3 may not act like a canonical, RuvC-like Holliday junction resolvase and support a novel model in which Mlh1-Mlh3 is loaded onto DNA to form an activated polymer that cleaves DNA. PMID:28453523

The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans.

PubMed

Manhart, Carol M; Ni, Xiaodan; White, Martin A; Ortega, Joaquin; Surtees, Jennifer A; Alani, Eric

2017-04-01

Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker's yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I. Recent genetic, biochemical, and molecular studies in yeast are consistent with the hypothesis of Mlh1-Mlh3 DNA mismatch repair complex acting as the major endonuclease activity that resolves dHJs into crossovers. However, the mechanism by which the Mlh1-Mlh3 endonuclease is activated is unknown. Here, we provide evidence that Mlh1-Mlh3 does not behave like a structure-specific endonuclease but forms polymers required to generate nicks in DNA. This conclusion is supported by DNA binding studies performed with different-sized substrates that contain or lack polymerization barriers and endonuclease assays performed with varying ratios of endonuclease-deficient and endonuclease-proficient Mlh1-Mlh3. In addition, Mlh1-Mlh3 can generate religatable double-strand breaks and form an active nucleoprotein complex that can nick DNA substrates in trans. Together these observations argue that Mlh1-Mlh3 may not act like a canonical, RuvC-like Holliday junction resolvase and support a novel model in which Mlh1-Mlh3 is loaded onto DNA to form an activated polymer that cleaves DNA.

Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis

PubMed Central

Sutherland, Ben J.G.; Rico, Ciro; Audet, Céline; Bernatchez, Louis

2017-01-01

Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy), which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera). Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL) for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution. PMID:28626004

Characterization of susceptible chiasma configurations that increase the risk for maternal nondisjunction of chromosome 21.

PubMed

Lamb, N E; Feingold, E; Savage, A; Avramopoulos, D; Freeman, S; Gu, Y; Hallberg, A; Hersey, J; Karadima, G; Pettay, D; Saker, D; Shen, J; Taft, L; Mikkelsen, M; Petersen, M B; Hassold, T; Sherman, S L

1997-09-01

Recent studies of trisomy 21 have shown that altered levels of recombination are associated with maternal non-disjunction occurring at both meiosis I (MI) and meiosis II (MII). To comprehend better the association of recombination with nondisjunction, an understanding of the pattern of meiotic exchange, i.e. the exchange of genetic material at the four-strand stage during prophase, is required. We examined this underlying exchange pattern to determine if specific meiotic configurations are associated with a higher risk of non-disjunction than others. We examined the crossover frequencies of chromosome 21 for three populations: (i) normal female meiotic events; (ii) meiotic events leading to MI non-disjunction; and (iii) those leading to MII non-disjunction. From these crossover frequencies, we estimated the array of meiotic tetrads that produced the observed crossovers. Using this approach, we found that nearly one-half of MI errors were estimated to be achiasmate. The majority of the remaining MI bivalents had exchanges that clustered at the telomere. In contrast, exchanges occurring among MII cases clustered at the pericentromeric region of the chromosome. Unlike the single exchange distributions, double exchanges from the non-disjoined populations seemed to approximate the distribution in the normal population. These data suggest that the location of certain exchanges makes a tetrad susceptible to non-disjunction. Specifically, this susceptibility is associated with the distance between the centromere and closest exchange. This result challenges the widely held concept that events occurring at MII are largely independent of events occurring at MI, and suggests that all non-disjunction events may be initiated during MI and simply resolved at either of the two meiotic stages.

Effects of Temperature on the Meiotic Recombination Landscape of the Yeast Saccharomyces cerevisiae

PubMed Central

Zhang, Ke; Wu, Xue-Chang

2017-01-01

ABSTRACT Although meiosis in warm-blooded organisms takes place in a narrow temperature range, meiosis in many organisms occurs over a wide variety of temperatures. We analyzed the properties of meiosis in the yeast Saccharomyces cerevisiae in cells sporulated at 14°C, 30°C, or 37°C. Using comparative-genomic-hybridization microarrays, we examined the distribution of Spo11-generated meiosis-specific double-stranded DNA breaks throughout the genome. Although there were between 300 and 400 regions of the genome with high levels of recombination (hot spots) observed at each temperature, only about 20% of these hot spots were found to have occurred independently of the temperature. In S. cerevisiae, regions near the telomeres and centromeres tend to have low levels of meiotic recombination. This tendency was observed in cells sporulated at 14°C and 30°C, but not at 37°C. Thus, the temperature of sporulation in yeast affects some global property of chromosome structure relevant to meiotic recombination. Using single-nucleotide polymorphism (SNP)-specific whole-genome microarrays, we also examined crossovers and their associated gene conversion events as well as gene conversion events that were unassociated with crossovers in all four spores of tetrads obtained by sporulation of diploids at 14°C, 30°C, or 37°C. Although tetrads from cells sporulated at 30°C had slightly (20%) more crossovers than those derived from cells sporulated at the other two temperatures, spore viability was good at all three temperatures. Thus, despite temperature-induced variation in the genetic maps, yeast cells produce viable haploid products at a wide variety of sporulation temperatures. PMID:29259092

Individual and crossover effects of stress on adjustment in medical student marriages.

PubMed

Katz, J; Monnier, J; Libet, J; Shaw, D; Beach, S R

2000-07-01

High-stress individuals may benefit from social support, although their support providers may be adversely affected via stress crossover effects. Individual and crossover effects of perceived stress within medical student marriages (n = 30) were investigated. Perceived spousal support was positively associated with individuals' own marital and emotional adjustment, attenuating stress effects. With regard to crossover effects, medical students' perceived stress was significantly associated with their spouses' emotional adjustment. Further, medical students' own emotional adjustment fully mediated this crossover effect. Results suggest that the contagion of negative affect may serve as a key mechanism through which stress crossover effects operate in marriage.

Distinct DNA-binding surfaces in the ATPase and linker domains of MutLγ determine its substrate specificities and exert separable functions in meiotic recombination and mismatch repair

PubMed Central

2017-01-01

Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA-binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes. In vitro, MutLγ displayed separable DNA-binding activities toward Holliday junctions (HJ) and, surprisingly, single-stranded DNA (ssDNA), which was not predicted from current models. MutLγ bound DNA cooperatively, could bind multiple substrates simultaneously, and formed higher-order complexes. FeBABE hydroxyl radical footprinting indicated that the DNA-binding interfaces of MutLγ for ssDNA and HJ substrates only partially overlap. Most contacts with HJ substrates were located in the linker regions of MutLγ, whereas ssDNA contacts mapped within linker regions as well as the N-terminal ATPase domains. Using yeast genetic assays for mismatch repair and meiotic recombination, we found that mutations within different DNA-binding surfaces exert separable effects in vivo. For example, mutations within the Mlh1 linker conferred little or no meiotic phenotype but led to mismatch repair deficiency. Interestingly, mutations in the N-terminal domain of Mlh1 caused a stronger meiotic defect than mlh1Δ, suggesting that the mutant proteins retain an activity that interferes with alternative recombination pathways. Furthermore, mlh3Δ caused more chromosome missegregation than mlh1Δ, whereas mlh1Δ but not mlh3Δ partially alleviated meiotic defects of msh5Δ mutants. These findings illustrate functional differences between Mlh1 and Mlh3 during meiosis and suggest that their absence impinges on chromosome segregation not only via reduced formation of crossovers. Taken together, our results offer insights into the structure-function relationships of the MutLγ complex and reveal unanticipated genetic relationships between components of the meiotic recombination machinery. PMID:28505149

Designing a Unique Single Point Cross Over Method

NASA Technical Reports Server (NTRS)

Wilson, Richard Phillip

2002-01-01

The idea behind genetic algorithms is to extract optimization strategies nature uses successfully - known as Darwinian Evolution - and transform them for application in mathematical optimization theory to find the global optimum in a defined phase space. One could imagine a population of individual 'explorers' sent into the optimization phase-space. Each explorer is defined by its genes, what means, its position inside the phase-space is coded in his genes. Every explorer has the duty to find a value of the quality of his position in the phase space. (Consider the phase-space being a number of variables in some technological process, the value of quality of any position in the phase space - in other words: any set of the variables - can be expressed by the yield of the desired chemical product.) Then the struggle of 'life' begins. The three fundamental principles are selection, mating/crossover, and mutation. Only explorers (= genes) sitting on the best places will reproduce and create a new population. This is performed in the second step (mating/crossover). The 'hope' behind this part of the algorithm is, that 'good' sections of two parents will be recombined to yet better fitting children. In fact, many of the created children will not be successful (as in biological evolution), but a few children will indeed fulfill this hope. These good sections are named in some publications as building blocks. Now there appears a problem. Repeating these steps, no new area would be explored. The two former steps would only exploit the already known regions in the phase space, which could lead to premature convergence of the algorithm with the consequence of missing the global optimum by exploiting some local optimum. The third step, mutation, ensures the necessary accidental effects. One can imagine the new population being mixed up a little bit to bring some new information into this set of genes. Whereas in biology a gene is described as a macro-molecule with four different bases to code the genetic information, a gene in genetic algorithms is usually defined as a bitstring (a sequence of b 1's and 0's).

Modeling and Optimization of Multiple Unmanned Aerial Vehicles System Architecture Alternatives

PubMed Central

Wang, Weiping; He, Lei

2014-01-01

Unmanned aerial vehicle (UAV) systems have already been used in civilian activities, although very limitedly. Confronted different types of tasks, multi UAVs usually need to be coordinated. This can be extracted as a multi UAVs system architecture problem. Based on the general system architecture problem, a specific description of the multi UAVs system architecture problem is presented. Then the corresponding optimization problem and an efficient genetic algorithm with a refined crossover operator (GA-RX) is proposed to accomplish the architecting process iteratively in the rest of this paper. The availability and effectiveness of overall method is validated using 2 simulations based on 2 different scenarios. PMID:25140328

Spiromax, a New Dry Powder Inhaler: Dose Consistency under Simulated Real-World Conditions.

PubMed

Canonica, Giorgio Walter; Arp, Jan; Keegstra, Johan René; Chrystyn, Henry

2015-10-01

Spiromax(®) is a novel dry powder inhaler for patients with asthma or chronic obstructive pulmonary disease (COPD). The studies presented here provide further data on attributes (in vitro dosing consistency with budesonide-formoterol (DuoResp) Spiromax; flow rates through empty versions of the Spiromax and Turbuhaler inhaler) of importance to patients with asthma or COPD. Dose-delivery studies were performed using low-, middle-, and high-strength DuoResp Spiromax. Dose consistency was assessed over inhaler life. Total emitted doses (TEDs) were measured at various flow rates, after exposure to high and low temperature or humidity, at different inhaler orientations, and after dropping the inhaler. The criterion for evaluating dose uniformity was whether mean TEDs were within the product specification limits. In separate studies, flow rates were measured after training, using the patient information leaflets, and again after enhanced training as part of a randomized, open-label, cross-over study. Mean values for both budesonide and formoterol were within 85%-115% of the label claim for each strength of DuoResp Spiromax for initial dose uniformity and for the other investigated conditions (temperature, humidity, orientation, dropping, knocking), with the exception of approximately an 80% increase in first dose after dropping the inhaler (subsequent doses not affected). In the flow rate patient study, two patients' inhalations with Spiromax and six with Turbuhaler were <30 L/min. The majority of asthma patients [91% (Spiromax) versus 82% (Turbuhaler)] achieved the preferred flow rate of >60 L/min. DuoResp Spiromax consistently meets dose uniformity criteria, under controlled laboratory conditions and with variations intended to mimic real-world use. Following enhanced training, all patients in the flow study were able to achieve the minimal inspiratory flow rate of >30 L/min, which is required for effective treatment.

Spatial and temporal variability of microgeographic genetic structure in white-tailed deer

USGS Publications Warehouse

Scribner, Kim T.; Smith, Michael H.; Chesser, Ronald K.

1997-01-01

Techniques are described that define contiguous genetic subpopulations of white-tailed deer (Odocoileus virginianus) based on the spatial dispersion of 4,749 individuals that possessed discrete character values (alleles or genotypes) during each of 6 years (1974-1979). White-tailed deer were not uniformly distributed in space, but exhibited considerable spatial genetic structuring. Significant non-random clusters of individuals were documented during each year based on specific alleles and genotypes at the Sdh locus. Considerable temporal variation was observed in the position and genetic composition of specific clusters, which reflected changes in allele frequency in small geographic areas. The position of clusters did not consistently correspond with traditional management boundaries based on major discontinuities in habitat (swamp versus upland) and hunt compartments that were defined by roads and streams. Spatio-temporal stability of observed genetic contiguous clusters was interpreted relative to method and intensity of harvest, movements, and breeding ecology.

HetMappsS: Heterozygous mapping strategy for high resolution Genotyping-by-Sequencing Markers

USDA-ARS?s Scientific Manuscript database

Reduced representation genotyping approaches, such as genotyping-by-sequencing (GBS), provide opportunities to generate high-resolution genetic maps at a low per-sample cost. However, missing data and non-uniform sequence coverage can complicate map creation in highly heterozygous species. To facili...

Statistical analysis of strait time index and a simple model for trend and trend reversal

NASA Astrophysics Data System (ADS)

Chen, Kan; Jayaprakash, C.

2003-06-01

We analyze the daily closing prices of the Strait Time Index (STI) as well as the individual stocks traded in Singapore's stock market from 1988 to 2001. We find that the Hurst exponent is approximately 0.6 for both the STI and individual stocks, while the normal correlation functions show the random walk exponent of 0.5. We also investigate the conditional average of the price change in an interval of length T given the price change in the previous interval. We find strong correlations for price changes larger than a threshold value proportional to T; this indicates that there is no uniform crossover to Gaussian behavior. A simple model based on short-time trend and trend reversal is constructed. We show that the model exhibits statistical properties and market swings similar to those of the real market.

Exact solution of finite parabolic potential disc-like quantum dot with and without electric field R. Djelti, S. Bentata and Z. Aziz: Trimer barrier hight effect oh the nature of the electronic state of the superlatice GaAs/AlxGa1-xAs Bibhas K. Dutta and Prasanta K. Mahapatra: Study of velocity-dependent collision effects on Lamb dip and crossover resonances in three-level system

NASA Astrophysics Data System (ADS)

Hassanien, H. H.; Abdelmoly, S. S.; Elmeshad, N.

The exact series solutions of finite parabolic potential disc-like quantum dot are given in the absence and presence of uniform applied electric field. We define some normalized parameters. From the complex eigenenergy E=E0 - i G/2, due to the electric field, we calculate the resonance width G of a bounded state. The ground and the first excited state of the electron and the hole are obtained with and without the electric field. The corresponding envelope functions are presented as a function of the disc dimensionality, radius R and half-width L.

Dopant induced single electron tunneling within the sub-bands of single silicon NW tri-gate junctionless n-MOSFET

NASA Astrophysics Data System (ADS)

Uddin, Wasi; Georgiev, Yordan M.; Maity, Sarmistha; Das, Samaresh

2017-09-01

We report 1D electron transport of silicon junctionless tri-gate n-type transistor at 4.2 K. The step like curve observed in the current voltage characteristic suggests 1D transport. Besides the current steps for 1D transport, we found multiple spikes within individual steps, which we relate to inter-band single electron tunneling, mediated by the charged dopants available in the channel region. Clear Coulomb diamonds were observed in the stability diagram of the device. It is shown that a uniformly doped silicon nanowire can provide us the window for the single electron tunnelling. Back-gate versus front-gate color plot, where current is in a color scale, shows a crossover of the increased conduction region. This is a clear indication of the dopant-dopant interaction. It has been shown that back-gate biasing can be used to tune the coupling strength between the dopants.

50 CFR 660.320 - Open access fishery-crossover provisions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Open access fishery-crossover provisions... West Coast Groundfish-Open Access Fisheries § 660.320 Open access fishery—crossover provisions. The crossover provisions listed at § 660.60(h)(7), apply to vessels fishing in the open access fishery. [76 FR...

50 CFR 660.320 - Open access fishery-crossover provisions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Open access fishery-crossover provisions... West Coast Groundfish-Open Access Fisheries § 660.320 Open access fishery—crossover provisions. The crossover provisions listed at § 660.60(h)(7), apply to vessels fishing in the open access fishery. [76 FR...

50 CFR 660.320 - Open access fishery-crossover provisions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Open access fishery-crossover provisions... West Coast Groundfish-Open Access Fisheries § 660.320 Open access fishery—crossover provisions. The crossover provisions listed at § 660.60(h)(7), apply to vessels fishing in the open access fishery. [76 FR...

Using the Molecular Classification of Glioblastoma to Inform Personalized Treatment

PubMed Central

Olar, Adriana; Aldape, Kenneth D.

2014-01-01

Glioblastoma is the most common and most aggressive diffuse glioma, associated with short survival and uniformly fatal outcome irrespective of treatment. It is characterized by morphologic, genetic, and gene-expression heterogeneity. The current standard of treatment is maximal surgical resection, followed by radiation, with concurrent and adjuvant chemotherapy. Due to the heterogeneity most tumors develop resistance to treatment and shortly recur. Following recurrence glioblastoma is quickly fatal in the majority of cases. Recent genetic molecular advances have contributed to a better understanding of glioblastoma pathophysiology and disease stratification. In this paper we review the basic glioblastoma pathophysiology with emphasis on clinically relevant genetic molecular alterations and potential targets for further drug development. PMID:24114756

An approach to checking case-crossover analyses based on equivalence with time-series methods.

PubMed

Lu, Yun; Symons, James Morel; Geyh, Alison S; Zeger, Scott L

2008-03-01

The case-crossover design has been increasingly applied to epidemiologic investigations of acute adverse health effects associated with ambient air pollution. The correspondence of the design to that of matched case-control studies makes it inferentially appealing for epidemiologic studies. Case-crossover analyses generally use conditional logistic regression modeling. This technique is equivalent to time-series log-linear regression models when there is a common exposure across individuals, as in air pollution studies. Previous methods for obtaining unbiased estimates for case-crossover analyses have assumed that time-varying risk factors are constant within reference windows. In this paper, we rely on the connection between case-crossover and time-series methods to illustrate model-checking procedures from log-linear model diagnostics for time-stratified case-crossover analyses. Additionally, we compare the relative performance of the time-stratified case-crossover approach to time-series methods under 3 simulated scenarios representing different temporal patterns of daily mortality associated with air pollution in Chicago, Illinois, during 1995 and 1996. Whenever a model-be it time-series or case-crossover-fails to account appropriately for fluctuations in time that confound the exposure, the effect estimate will be biased. It is therefore important to perform model-checking in time-stratified case-crossover analyses rather than assume the estimator is unbiased.

Meiotic recombination protein Rec12: functional conservation, crossover homeostasis and early crossover/non-crossover decision

PubMed Central

Kan, Fengling; Davidson, Mari K.; Wahls, Wayne P.

2011-01-01

In fission yeast and other eukaryotes, Rec12 (Spo11) is thought to catalyze the formation of dsDNA breaks (DSBs) that initiate homologous recombination in meiosis. Rec12 is orthologous to the catalytic subunit of topoisomerase VI (Top6A). Guided by the crystal structure of Top6A, we engineered the rec12 locus to encode Rec12 proteins each with a single amino acid substitution in a conserved residue. Of 21 substitutions, 10 significantly reduced or abolished meiotic DSBs, gene conversion, crossover recombination and the faithful segregation of chromosomes. Critical residues map within the metal ion-binding pocket toprim (E179A, D229A, D231A), catalytic region 5Y-CAP (R94A, D95A, Y98F) and the DNA-binding interface (K201A, G202E, R209A, K242A). A subset of substitutions reduced DSBs but maintained crossovers, demonstrating crossover homeostasis. Furthermore, a strong separation of function mutation (R304A) suggests that the crossover/non-crossover decision is established early by a protein–protein interaction surface of Rec12. Fission yeast has multiple crossovers per bivalent, and chromosome segregation was robust above a threshold of about one crossover per bivalent, below which non-disjunction occurred. These results support structural and functional conservation among Rec12/Spo11/Top6A family members for the catalysis of DSBs, and they reveal how Rec12 regulates other features of meiotic chromosome dynamics. PMID:21030440

Improved adaptive genetic algorithm with sparsity constraint applied to thermal neutron CT reconstruction of two-phase flow

NASA Astrophysics Data System (ADS)

Yan, Mingfei; Hu, Huasi; Otake, Yoshie; Taketani, Atsushi; Wakabayashi, Yasuo; Yanagimachi, Shinzo; Wang, Sheng; Pan, Ziheng; Hu, Guang

2018-05-01

Thermal neutron computer tomography (CT) is a useful tool for visualizing two-phase flow due to its high imaging contrast and strong penetrability of neutrons for tube walls constructed with metallic material. A novel approach for two-phase flow CT reconstruction based on an improved adaptive genetic algorithm with sparsity constraint (IAGA-SC) is proposed in this paper. In the algorithm, the neighborhood mutation operator is used to ensure the continuity of the reconstructed object. The adaptive crossover probability P c and mutation probability P m are improved to help the adaptive genetic algorithm (AGA) achieve the global optimum. The reconstructed results for projection data, obtained from Monte Carlo simulation, indicate that the comprehensive performance of the IAGA-SC algorithm exceeds the adaptive steepest descent-projection onto convex sets (ASD-POCS) algorithm in restoring typical and complex flow regimes. It especially shows great advantages in restoring the simply connected flow regimes and the shape of object. In addition, the CT experiment for two-phase flow phantoms was conducted on the accelerator-driven neutron source to verify the performance of the developed IAGA-SC algorithm.

High performance genetic algorithm for VLSI circuit partitioning

NASA Astrophysics Data System (ADS)

Dinu, Simona

2016-12-01

Partitioning is one of the biggest challenges in computer-aided design for VLSI circuits (very large-scale integrated circuits). This work address the min-cut balanced circuit partitioning problem- dividing the graph that models the circuit into almost equal sized k sub-graphs while minimizing the number of edges cut i.e. minimizing the number of edges connecting the sub-graphs. The problem may be formulated as a combinatorial optimization problem. Experimental studies in the literature have shown the problem to be NP-hard and thus it is important to design an efficient heuristic algorithm to solve it. The approach proposed in this study is a parallel implementation of a genetic algorithm, namely an island model. The information exchange between the evolving subpopulations is modeled using a fuzzy controller, which determines an optimal balance between exploration and exploitation of the solution space. The results of simulations show that the proposed algorithm outperforms the standard sequential genetic algorithm both in terms of solution quality and convergence speed. As a direction for future study, this research can be further extended to incorporate local search operators which should include problem-specific knowledge. In addition, the adaptive configuration of mutation and crossover rates is another guidance for future research.

The genetic architecture of susceptibility to parasites.

PubMed

Wilfert, Lena; Schmid-Hempel, Paul

2008-06-30

The antagonistic co-evolution of hosts and their parasites is considered to be a potential driving force in maintaining host genetic variation including sexual reproduction and recombination. The examination of this hypothesis calls for information about the genetic basis of host-parasite interactions - such as how many genes are involved, how big an effect these genes have and whether there is epistasis between loci. We here examine the genetic architecture of quantitative resistance in animal and plant hosts by concatenating published studies that have identified quantitative trait loci (QTL) for host resistance in animals and plants. Collectively, these studies show that host resistance is affected by few loci. We particularly show that additional epistatic interactions, especially between loci on different chromosomes, explain a majority of the effects. Furthermore, we find that when experiments are repeated using different host or parasite genotypes under otherwise identical conditions, the underlying genetic architecture of host resistance can vary dramatically - that is, involves different QTLs and epistatic interactions. QTLs and epistatic loci vary much less when host and parasite types remain the same but experiments are repeated in different environments. This pattern of variability of the genetic architecture is predicted by strong interactions between genotypes and corroborates the prevalence of varying host-parasite combinations over varying environmental conditions. Moreover, epistasis is a major determinant of phenotypic variance for host resistance. Because epistasis seems to occur predominantly between, rather than within, chromosomes, segregation and chromosome number rather than recombination via cross-over should be the major elements affecting adaptive change in host resistance.

Genetic Network Programming with Reconstructed Individuals

NASA Astrophysics Data System (ADS)

Ye, Fengming; Mabu, Shingo; Wang, Lutao; Eto, Shinji; Hirasawa, Kotaro

A lot of research on evolutionary computation has been done and some significant classical methods such as Genetic Algorithm (GA), Genetic Programming (GP), Evolutionary Programming (EP), and Evolution Strategies (ES) have been studied. Recently, a new approach named Genetic Network Programming (GNP) has been proposed. GNP can evolve itself and find the optimal solution. It is based on the idea of Genetic Algorithm and uses the data structure of directed graphs. Many papers have demonstrated that GNP can deal with complex problems in the dynamic environments very efficiently and effectively. As a result, recently, GNP is getting more and more attentions and is used in many different areas such as data mining, extracting trading rules of stock markets, elevator supervised control systems, etc., and GNP has obtained some outstanding results. Focusing on the GNP's distinguished expression ability of the graph structure, this paper proposes a method named Genetic Network Programming with Reconstructed Individuals (GNP-RI). The aim of GNP-RI is to balance the exploitation and exploration of GNP, that is, to strengthen the exploitation ability by using the exploited information extensively during the evolution process of GNP and finally obtain better performances than that of GNP. In the proposed method, the worse individuals are reconstructed and enhanced by the elite information before undergoing genetic operations (mutation and crossover). The enhancement of worse individuals mimics the maturing phenomenon in nature, where bad individuals can become smarter after receiving a good education. In this paper, GNP-RI is applied to the tile-world problem which is an excellent bench mark for evaluating the proposed architecture. The performance of GNP-RI is compared with that of the conventional GNP. The simulation results show some advantages of GNP-RI demonstrating its superiority over the conventional GNPs.

What's Mine Is Yours: The Crossover of Day-Specific Self-Esteem

ERIC Educational Resources Information Center

Neff, Angela; Sonnentag, Sabine; Niessen, Cornelia; Unger, Dana

2012-01-01

This diary study examines the daily crossover of self-esteem within working couples. By integrating self-esteem research into the crossover framework, we hypothesized that the day-specific self-esteem experienced by one partner after work crosses over to the other partner. Furthermore, we proposed that this daily crossover process is moderated by…

The Crossover Time as an Evaluation of Ocean Models Against Persistence

NASA Astrophysics Data System (ADS)

Phillipson, L. M.; Toumi, R.

2018-01-01

A new ocean evaluation metric, the crossover time, is defined as the time it takes for a numerical model to equal the performance of persistence. As an example, the average crossover time calculated using the Lagrangian separation distance (the distance between simulated trajectories and observed drifters) for the global MERCATOR ocean model analysis is found to be about 6 days. Conversely, the model forecast has an average crossover time longer than 6 days, suggesting limited skill in Lagrangian predictability by the current generation of global ocean models. The crossover time of the velocity error is less than 3 days, which is similar to the average decorrelation time of the observed drifters. The crossover time is a useful measure to quantify future ocean model improvements.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm.

PubMed

Onyśk, Agnieszka; Boczkowska, Maja

2017-01-01

Simple Sequence Repeat (SSR) markers are one of the most frequently used molecular markers in studies of crop diversity and population structure. This is due to their uniform distribution in the genome, the high polymorphism, reproducibility, and codominant character. Additional advantages are the possibility of automatic analysis and simple interpretation of the results. The M13 tagged PCR reaction significantly reduces the costs of analysis by the automatic genetic analyzers. Here, we also disclose a short protocol of SSR data analysis.

Biochemical And Genetic Modification Of Polysaccharides

NASA Technical Reports Server (NTRS)

Kern, Roger G.; Petersen, Gene R.; Richards, Gil F.

1993-01-01

Bacteriophages producing endopolysaccharase-type enzymes used to produce, isolate, and purify high yields of modified polysaccharides from polysaccharides produced by, and incorporated into capsules of, certain bacteria. Bacteriophages used in conversion of native polysaccharide materials into polymers of nearly uniform high molecular weight or, alternatively, into highly pure oligosaccharides. Also used in genetic selection of families of polysaccharides structurally related to native polysaccharide materials, but having altered properties. Resulting new polysaccharides and oligosaccharides prove useful in variety of products, including pharmaceutical chemicals, coating materials, biologically active carbohydrates, and drag-reducing additives for fluids.

Application of genetic algorithms in nonlinear heat conduction problems.

PubMed

Kadri, Muhammad Bilal; Khan, Waqar A

2014-01-01

Genetic algorithms are employed to optimize dimensionless temperature in nonlinear heat conduction problems. Three common geometries are selected for the analysis and the concept of minimum entropy generation is used to determine the optimum temperatures under the same constraints. The thermal conductivity is assumed to vary linearly with temperature while internal heat generation is assumed to be uniform. The dimensionless governing equations are obtained for each selected geometry and the dimensionless temperature distributions are obtained using MATLAB. It is observed that GA gives the minimum dimensionless temperature in each selected geometry.

Temporospatial distribution of microglial activation in a murine model of scrapie

USDA-ARS?s Scientific Manuscript database

Mouse models of prion disease offer the advantages of genetic homogeneity and short incubation times while retaining the disease phenotype of natural mammalian hosts. Intracranial (IC) inoculation of C57BL/6 mice with a mouse-adapted scrapie strain (RML) yields uniform incubation periods with a rapi...

US-1136, US-1137, and US-1138 cowpea lines for cover crop use

USDA-ARS?s Scientific Manuscript database

Following five years of field evaluation, three cowpea populations were selected as best adapted for use as a cover crop. A pure line selection procedure was used to develop genetically uniform lines from the segregating populations. Field evaluations demonstrated that the lines grow rapidly for u...

How has agriculture influenced the geography and genetics of animal parasites?

PubMed

Rosenthal, Benjamin M

2009-02-01

Have farmers inadvertently promoted the distribution, and limited the diversity, of animal parasites? Abundant and broadly distributed livestock hosts evidently harbor exceptionally uniform populations of Trichinella, Taenia, Toxoplasma and Sarcocystis, indicating a fruitful avenue for future research on how we have influenced parasite evolutionary ecology.

Genetic difference in macro-element mineral concentrations among 52 historically important tomato varieties

USDA-ARS?s Scientific Manuscript database

Tomato (Solanum lycopersicum) fruit quality and yield are highly dependent on adequate uptake of nutrients. Potassium, magnesium and calcium are essential elements that influence fruit quality traits such as color, uniformity of ripening, hollow fruit, fruit shape, firmness, and acidity. Sodium is n...

Analyzing clonal fidelity of micropropagated Psidium guajava L. plants using simple sequence repeat markers

USDA-ARS?s Scientific Manuscript database

Micropropagation of Psidium guajava L. (guava) is a viable alternative to currently adopted techniques for large-scale plant propagation of commercial cultivars. Assessment of clonal fidelity in micropropagated plants is the first step towards ensuring genetic uniformity in mass production of planti...

Structure and Composition of the Grain

USDA-ARS?s Scientific Manuscript database

As a crop with a wide range of genetic diversity, sorghum grain composition and structure can vary widely. Such variability can be of great benefit in supplying a diversity of uses but can also be a negative when viewed from the standpoint of uniformity. Despite sharing similarities to other cereals...

The Austrian x red pine hybrid

Treesearch

W. B. Critchfield

1963-01-01

The genetic improvement of red pine (Pinus resinosa Ait.) presents tree breeders with one of their most difficult problems. Not only is this valuable species remarkably uniform, but until 1955 it resisted all attempts to cross it with other pines. In that year red pine and Austrian pine (P. nigra var. austriaca [...

Multi-objective optimization in spatial planning: Improving the effectiveness of multi-objective evolutionary algorithms (non-dominated sorting genetic algorithm II)

NASA Astrophysics Data System (ADS)

Karakostas, Spiros

2015-05-01

The multi-objective nature of most spatial planning initiatives and the numerous constraints that are introduced in the planning process by decision makers, stakeholders, etc., synthesize a complex spatial planning context in which the concept of solid and meaningful optimization is a unique challenge. This article investigates new approaches to enhance the effectiveness of multi-objective evolutionary algorithms (MOEAs) via the adoption of a well-known metaheuristic: the non-dominated sorting genetic algorithm II (NSGA-II). In particular, the contribution of a sophisticated crossover operator coupled with an enhanced initialization heuristic is evaluated against a series of metrics measuring the effectiveness of MOEAs. Encouraging results emerge for both the convergence rate of the evolutionary optimization process and the occupation of valuable regions of the objective space by non-dominated solutions, facilitating the work of spatial planners and decision makers. Based on the promising behaviour of both heuristics, topics for further research are proposed to improve their effectiveness.

Operating rules for multireservoir systems

NASA Astrophysics Data System (ADS)

Oliveira, Rodrigo; Loucks, Daniel P.

1997-04-01

Multireservoir operating policies are usually defined by rules that specify either individual reservoir desired (target) storage volumes or desired (target) releases based on the time of year and the existing total storage volume in all reservoirs. This paper focuses on the use of genetic search algorithms to derive these multireservoir operating policies. The genetic algorithms use real-valued vectors containing information needed to define both system release and individual reservoir storage volume targets as functions of total storage in each of multiple within-year periods. Elitism, arithmetic crossover, mutation, and "en bloc" replacement are used in the algorithms to generate successive sets of possible operating policies. Each policy is then evaluated using simulation to compute a performance index for a given flow series. The better performing policies are then used as a basis for generating new sets of possible policies. The process of improved policy generation and evaluation is repeated until no further improvement in performance is obtained. The proposed algorithm is applied to example reservoir systems used for water supply and hydropower.

Optimization of a Boiling Water Reactor Loading Pattern Using an Improved Genetic Algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobayashi, Yoko; Aiyoshi, Eitaro

2003-08-15

A search method based on genetic algorithms (GA) using deterministic operators has been developed to generate optimized boiling water reactor (BWR) loading patterns (LPs). The search method uses an Improved GA operator, that is, crossover, mutation, and selection. The handling of the encoding technique and constraint conditions is designed so that the GA reflects the peculiar characteristics of the BWR. In addition, some strategies such as elitism and self-reproduction are effectively used to improve the search speed. LP evaluations were performed with a three-dimensional diffusion code that coupled neutronic and thermal-hydraulic models. Strong axial heterogeneities and three-dimensional-dependent constraints have alwaysmore » necessitated the use of three-dimensional core simulators for BWRs, so that an optimization method is required for computational efficiency. The proposed algorithm is demonstrated by successfully generating LPs for an actual BWR plant applying the Haling technique. In test calculations, candidates that shuffled fresh and burned fuel assemblies within a reasonable computation time were obtained.« less

Rhombic-Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs.

PubMed

Ma, Zhipeng; Huang, Yunfei; Park, Seongsu; Kawai, Kentaro; Kim, Do-Nyun; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Yamada, Hirofumi; Tabata, Osamu

2018-01-01

DNA origami methods enable the fabrication of various nanostructures and nanodevices, but their effective use depends on an understanding of their structural and mechanical properties and the effects of basic structural features. Frequency-modulation atomic force microscopy is introduced to directly characterize, in aqueous solution, the crossover regions of sets of 2D DNA origami based on different crossover/nick designs. Rhombic-shaped nanostructures formed under the influence of flexible crossovers placed between DNA helices are observed in DNA origami incorporating crossovers every 3, 4, or 6 DNA turns. The bending rigidity of crossovers is determined to be only one-third of that of the DNA helix, based on interhelical electrostatic forces reported elsewhere, and the measured pitches of the 3-turn crossover design rhombic-shaped nanostructures undergoing negligible bending. To evaluate the robustness of their structural integrity, they are intentionally and simultaneously stressed using force-controlled atomic force microscopy. DNA crossovers are verified to have a stabilizing effect on the structural robustness, while the nicks have an opposite effect. The structural and mechanical properties of DNA origami and the effects of crossovers and nicks revealed in this paper can provide information essential for the design of versatile DNA origami structures that exhibit specified and desirable properties. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

49 CFR 213.353 - Turnouts, crossovers, and lift rail assemblies or other transition devices on moveable bridges.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Turnouts, crossovers, and lift rail assemblies or... SAFETY STANDARDS Train Operations at Track Classes 6 and Higher § 213.353 Turnouts, crossovers, and lift... shall be at least 11/2 inches wide. (d) For all turnouts and crossovers, and lift rail assemblies or...

49 CFR 213.353 - Turnouts, crossovers, and lift rail assemblies or other transition devices on moveable bridges.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Turnouts, crossovers, and lift rail assemblies or... SAFETY STANDARDS Train Operations at Track Classes 6 and Higher § 213.353 Turnouts, crossovers, and lift... shall be at least 11/2 inches wide. (d) For all turnouts and crossovers, and lift rail assemblies or...

The kinetochore prevents centromere-proximal crossover recombination during meiosis

PubMed Central

Vincenten, Nadine; Kuhl, Lisa-Marie; Lam, Isabel; Oke, Ashwini; Kerr, Alastair RW; Hochwagen, Andreas; Fung, Jennifer; Keeney, Scott; Vader, Gerben; Marston, Adèle L

2015-01-01

During meiosis, crossover recombination is essential to link homologous chromosomes and drive faithful chromosome segregation. Crossover recombination is non-random across the genome, and centromere-proximal crossovers are associated with an increased risk of aneuploidy, including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub-complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the Ctf19 complex, operating across distinct chromosomal distances. The Ctf19 complex prevents meiotic DNA break formation, the initiating event of recombination, proximal to the centromere. The Ctf19 complex independently drives the enrichment of cohesin throughout the broader pericentromere to suppress crossovers, but not DNA breaks. This non-canonical role of the kinetochore in defining a chromosome domain that is refractory to crossovers adds a new layer of functionality by which the kinetochore prevents the incidence of chromosome segregation errors that generate aneuploid gametes. DOI: http://dx.doi.org/10.7554/eLife.10850.001 PMID:26653857

Magnetization reversal dynamics in Co nanowires with competing magnetic anisotropies

NASA Astrophysics Data System (ADS)

Pal, Semanti; Saha, Susmita; Polley, Debanjan; Barman, Anjan

2011-12-01

We present the magnetization reversal dynamics of Co nanowires with competing magnetic anisotropies. The aspect ratio ( R) of the nanowires is varied between 2.5 and 60, and we observe a cross-over of the directions of the magnetic easy and hard axes at R=6.8. Micromagnetic simulations qualitatively reproduce the observed cross-over and give detailed insight into the reversal mechanisms associated with the cross-over. The reversal mechanism for a field applied along the long axis of the nanowire exhibits a quasi-coherent rotation mode and a corkscrew-like mode, respectively, above and below the cross-over, with the formation of a Bloch domain near the cross-over region. For a field applied along the short axis, the reversal occurs by nucleation and propagation of reversed domains from the two ends of the nanowires for very high values of the aspect ratio down to the cross-over region, but it transforms into quasi-coherent rotation mode for smaller aspect ratios (below the cross-over region).

Necessity of Removing American Football Uniforms From Humans With Hyperthermia Before Cold-Water Immersion

PubMed Central

Miller, Kevin C.; Long, Blaine C.; Edwards, Jeffrey

2015-01-01

Context  The National Athletic Trainers' Association and the American College of Sports Medicine have recommended removing American football uniforms from athletes with exertional heat stroke before cold-water immersion (CWI) based on the assumption that the uniform impedes rectal temperature (Trec) cooling. Few experimental data exist to verify or disprove this assumption and the recommendations. Objectives  To compare CWI durations, Trec cooling rates, thermal sensation, intensity of environmental symptoms, and onset of shivering when hyperthermic participants wore football uniforms during CWI or removed the uniforms immediately before CWI. Design  Crossover study. Setting  Laboratory. Patients or Other Participants  Eighteen hydrated, physically active men (age = 22 ± 2 years, height = 182.5 ± 6.1 cm, mass = 85.4 ± 13.4 kg, body fat = 11% ± 5%, body surface area = 2.1 ± 0.2 m2) volunteered. Intervention(s)  On 2 days, participants exercised in the heat (approximately 40°C, approximately 40% relative humidity) while wearing a full American football uniform (shoes; crew socks; undergarments; shorts; game pants; undershirt; shoulder pads; jersey; helmet; and padding over the thighs, knees, hips, and tailbone [PADS]) until Trec reached 39.5°C. Next, participants immersed themselves in water that was approximately 10°C while wearing either undergarments, shorts, and crew socks (NOpads) or PADS without shoes until Trec reached 38°C. Main Outcome Measure(s)  The CWI duration (minutes) and Trec cooling rates (°C/min). Results  Participants had similar exercise times (NOpads = 40.8 ± 4.9 minutes, PADS = 43.2 ± 4.1 minutes; t17 = 2.0, P = .10), hypohydration levels (NOpads = 1.5% ± 0.3%, PADS = 1.6% ± 0.4%; t17 = 1.3, P = .22), and thermal-sensation ratings (NOpads = 7.2 ± 0.3, PADS = 7.1 ± 0.5; P > .05) before CWI. The CWI duration (median [interquartile range]; NOpads = 6.0 [5.4] minutes, PADS = 7.3 [9.8] minutes; z = 2.3, P = .01) and Trec cooling rates (NOpads = 0.28°C/min ± 0.14°C/min, PADS = 0.21°C/min ± 0.11°C/min; t17 = 2.2, P = .02) differed between uniform conditions. Conclusions  Whereas participants cooled faster in NOpads, we still considered the PADS cooling rate to be acceptable (ie, >0.16°C/min). Therefore, if clinicians experience difficulty removing PADS or CWI treatment is delayed, they may immerse fully equipped hyperthermic football players in CWI and maintain acceptable Trec cooling rates. Otherwise, PADS should be removed preimmersion to ensure faster body core temperature cooling. PMID:26678288

Fuzzy Mixed Assembly Line Sequencing and Scheduling Optimization Model Using Multiobjective Dynamic Fuzzy GA

PubMed Central

Tahriri, Farzad; Dawal, Siti Zawiah Md; Taha, Zahari

2014-01-01

A new multiobjective dynamic fuzzy genetic algorithm is applied to solve a fuzzy mixed-model assembly line sequencing problem in which the primary goals are to minimize the total make-span and minimize the setup number simultaneously. Trapezoidal fuzzy numbers are implemented for variables such as operation and travelling time in order to generate results with higher accuracy and representative of real-case data. An improved genetic algorithm called fuzzy adaptive genetic algorithm (FAGA) is proposed in order to solve this optimization model. In establishing the FAGA, five dynamic fuzzy parameter controllers are devised in which fuzzy expert experience controller (FEEC) is integrated with automatic learning dynamic fuzzy controller (ALDFC) technique. The enhanced algorithm dynamically adjusts the population size, number of generations, tournament candidate, crossover rate, and mutation rate compared with using fixed control parameters. The main idea is to improve the performance and effectiveness of existing GAs by dynamic adjustment and control of the five parameters. Verification and validation of the dynamic fuzzy GA are carried out by developing test-beds and testing using a multiobjective fuzzy mixed production assembly line sequencing optimization problem. The simulation results highlight that the performance and efficacy of the proposed novel optimization algorithm are more efficient than the performance of the standard genetic algorithm in mixed assembly line sequencing model. PMID:24982962

A novel pipeline based FPGA implementation of a genetic algorithm

NASA Astrophysics Data System (ADS)

Thirer, Nonel

2014-05-01

To solve problems when an analytical solution is not available, more and more bio-inspired computation techniques have been applied in the last years. Thus, an efficient algorithm is the Genetic Algorithm (GA), which imitates the biological evolution process, finding the solution by the mechanism of "natural selection", where the strong has higher chances to survive. A genetic algorithm is an iterative procedure which operates on a population of individuals called "chromosomes" or "possible solutions" (usually represented by a binary code). GA performs several processes with the population individuals to produce a new population, like in the biological evolution. To provide a high speed solution, pipelined based FPGA hardware implementations are used, with a nstages pipeline for a n-phases genetic algorithm. The FPGA pipeline implementations are constraints by the different execution time of each stage and by the FPGA chip resources. To minimize these difficulties, we propose a bio-inspired technique to modify the crossover step by using non identical twins. Thus two of the chosen chromosomes (parents) will build up two new chromosomes (children) not only one as in classical GA. We analyze the contribution of this method to reduce the execution time in the asynchronous and synchronous pipelines and also the possibility to a cheaper FPGA implementation, by using smaller populations. The full hardware architecture for a FPGA implementation to our target ALTERA development card is presented and analyzed.

mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis.

PubMed

Zhang, Xiao-Zhou; Yan, Xin; Cui, Zhong-Li; Hong, Qing; Li, Shun-Peng

2006-05-19

Here, we present a novel method for the directed genetic manipulation of the Bacillus subtilis chromosome free of any selection marker. Our new approach employed the Escherichia coli toxin gene mazF as a counter-selectable marker. The mazF gene was placed under the control of an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible expression system and associated with a spectomycin-resistance gene to form the MazF cassette, which was flanked by two directly-repeated (DR) sequences. A double-crossover event between the linearized delivery vector and the chromosome integrated the MazF cassette into a target locus and yielded an IPTG-sensitive strain with spectomycin-resistance, in which the wild-type chromosome copy had been replaced by the modified copy at the targeted locus. Another single-crossover event between the two DR sequences led to the excision of the MazF cassette and generated a strain with IPTG resistance, thereby realizing the desired alteration to the chromosome without introducing any unwanted selection markers. We used this method repeatedly and successfully to inactivate a specific gene, to introduce a gene of interest and to realize the in-frame deletion of a target gene in the same strain. As there is no prerequisite strain for this method, it will be a powerful and universal tool.

Computer Analysis of 400 HZ Aircraft Electrical Generator Test Data.

DTIC Science & Technology

1980-06-01

Data Acquisition System. ............ 6 3 Voltage Waveform with Data Points. ....... 19 14 Zero Crossover Interpolation. ........ 20 5 Numerical...difference between successive positive-sloped zero crossovers of the waveform. However, the exact time of zero crossover is not known. This is because...data sampling and the generator output are not synchronized. This unsynchronization means that data points which correspond with an exact zero crossover

Mirror Neurons through the Lens of Epigenetics

PubMed Central

Ferrari, Pier F.; Tramacere, Antonella; Simpson, Elizabeth A.; Iriki, Atsushi

2013-01-01

The consensus view in mirror neuron research is that mirror neurons comprise a uniform, stable execution-observation matching system. In this article, we argue that, in light of recent evidence, this is, at best, an incomplete and oversimplified view of mirror neurons, whose activity is actually quite variable and more plastic than previously theorized. We propose an epigenetic account for understanding developmental changes in sensorimotor systems, including variations in mirror neuron activity. Although extant associative and genetic accounts fail to consider the complexity of genetic and non-genetic interactions, we propose a new Evo-Devo perspective, which predicts that environmental differences early in development, or through sensorimotor training, should produce variations in mirror neuron response patterns, tuning them to the social environment. PMID:23953747

Calorimetric indications of a cooperativity onset in the crossover region of dynamic glass transition for benzoin isobutylether

NASA Astrophysics Data System (ADS)

Kahle, S.; Schröter, K.; Hempel, E.; Donth, E.

1999-10-01

Heat capacity spectroscopy (HCS), dielectric spectroscopy, and shear viscosity data are reported for liquid benzoin isobutylether (BIBE). Dielectric and viscosity peculiarities indicate the crossover region of dynamic glass transition at T=(-8±8) °C where the extrapolated Johari Goldstein β relaxation intersects the main transition trace in an Arrhenius plot. Although HCS does not reach the crossover frequency of order ω=2×106 rad/s, the linear decrease of the square root of cooperativity as calculated from HCS data at lower frequencies indicates a cooperativity onset in the crossover temperature-frequency range. As BIBE belongs to another dielectric crossover scenario as the substances where such an onset could previously be observed, it seems that the cooperativity onset is a general property of the crossover region.

Crossover ensembles of random matrices and skew-orthogonal polynomials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Santosh, E-mail: skumar.physics@gmail.com; Pandey, Akhilesh, E-mail: ap0700@mail.jnu.ac.in

2011-08-15

Highlights: > We study crossover ensembles of Jacobi family of random matrices. > We consider correlations for orthogonal-unitary and symplectic-unitary crossovers. > We use the method of skew-orthogonal polynomials and quaternion determinants. > We prove universality of spectral correlations in crossover ensembles. > We discuss applications to quantum conductance and communication theory problems. - Abstract: In a recent paper (S. Kumar, A. Pandey, Phys. Rev. E, 79, 2009, p. 026211) we considered Jacobi family (including Laguerre and Gaussian cases) of random matrix ensembles and reported exact solutions of crossover problems involving time-reversal symmetry breaking. In the present paper we givemore » details of the work. We start with Dyson's Brownian motion description of random matrix ensembles and obtain universal hierarchic relations among the unfolded correlation functions. For arbitrary dimensions we derive the joint probability density (jpd) of eigenvalues for all transitions leading to unitary ensembles as equilibrium ensembles. We focus on the orthogonal-unitary and symplectic-unitary crossovers and give generic expressions for jpd of eigenvalues, two-point kernels and n-level correlation functions. This involves generalization of the theory of skew-orthogonal polynomials to crossover ensembles. We also consider crossovers in the circular ensembles to show the generality of our method. In the large dimensionality limit, correlations in spectra with arbitrary initial density are shown to be universal when expressed in terms of a rescaled symmetry breaking parameter. Applications of our crossover results to communication theory and quantum conductance problems are also briefly discussed.« less

Study on the optimization of the deposition rate of planetary GaN-MOCVD films based on CFD simulation and the corresponding surface model

PubMed Central

Fei, Ze-yuan; Xu, Yi-feng; Wang, Jie; Fan, Bing-feng; Ma, Xue-jin; Wang, Gang

2018-01-01

Metal-organic chemical vapour deposition (MOCVD) is a key technique for fabricating GaN thin film structures for light-emitting and semiconductor laser diodes. Film uniformity is an important index to measure equipment performance and chip processes. This paper introduces a method to improve the quality of thin films by optimizing the rotation speed of different substrates of a model consisting of a planetary with seven 6-inch wafers for the planetary GaN-MOCVD. A numerical solution to the transient state at low pressure is obtained using computational fluid dynamics. To evaluate the role of the different zone speeds on the growth uniformity, single factor analysis is introduced. The results show that the growth rate and uniformity are strongly related to the rotational speed. Next, a response surface model was constructed by using the variables and the corresponding simulation results. The optimized combination of the matching of different speeds is also proposed as a useful reference for applications in industry, obtained by a response surface model and genetic algorithm with a balance between the growth rate and the growth uniformity. This method can save time, and the optimization can obtain the most uniform and highest thin film quality. PMID:29515883

Study on the optimization of the deposition rate of planetary GaN-MOCVD films based on CFD simulation and the corresponding surface model.

PubMed

Li, Jian; Fei, Ze-Yuan; Xu, Yi-Feng; Wang, Jie; Fan, Bing-Feng; Ma, Xue-Jin; Wang, Gang

2018-02-01

Metal-organic chemical vapour deposition (MOCVD) is a key technique for fabricating GaN thin film structures for light-emitting and semiconductor laser diodes. Film uniformity is an important index to measure equipment performance and chip processes. This paper introduces a method to improve the quality of thin films by optimizing the rotation speed of different substrates of a model consisting of a planetary with seven 6-inch wafers for the planetary GaN-MOCVD. A numerical solution to the transient state at low pressure is obtained using computational fluid dynamics. To evaluate the role of the different zone speeds on the growth uniformity, single factor analysis is introduced. The results show that the growth rate and uniformity are strongly related to the rotational speed. Next, a response surface model was constructed by using the variables and the corresponding simulation results. The optimized combination of the matching of different speeds is also proposed as a useful reference for applications in industry, obtained by a response surface model and genetic algorithm with a balance between the growth rate and the growth uniformity. This method can save time, and the optimization can obtain the most uniform and highest thin film quality.

Study on the optimization of the deposition rate of planetary GaN-MOCVD films based on CFD simulation and the corresponding surface model

NASA Astrophysics Data System (ADS)

Li, Jian; Fei, Ze-yuan; Xu, Yi-feng; Wang, Jie; Fan, Bing-feng; Ma, Xue-jin; Wang, Gang

2018-02-01

Metal-organic chemical vapour deposition (MOCVD) is a key technique for fabricating GaN thin film structures for light-emitting and semiconductor laser diodes. Film uniformity is an important index to measure equipment performance and chip processes. This paper introduces a method to improve the quality of thin films by optimizing the rotation speed of different substrates of a model consisting of a planetary with seven 6-inch wafers for the planetary GaN-MOCVD. A numerical solution to the transient state at low pressure is obtained using computational fluid dynamics. To evaluate the role of the different zone speeds on the growth uniformity, single factor analysis is introduced. The results show that the growth rate and uniformity are strongly related to the rotational speed. Next, a response surface model was constructed by using the variables and the corresponding simulation results. The optimized combination of the matching of different speeds is also proposed as a useful reference for applications in industry, obtained by a response surface model and genetic algorithm with a balance between the growth rate and the growth uniformity. This method can save time, and the optimization can obtain the most uniform and highest thin film quality.

Design, Analysis, and Reporting of Crossover Trials for Inclusion in a Meta-Analysis.

PubMed

Li, Tianjing; Yu, Tsung; Hawkins, Barbara S; Dickersin, Kay

2015-01-01

To evaluate the characteristics of the design, analysis, and reporting of crossover trials for inclusion in a meta-analysis of treatment for primary open-angle glaucoma and to provide empirical evidence to inform the development of tools to assess the validity of the results from crossover trials and reporting guidelines. We searched MEDLINE, EMBASE, and Cochrane's CENTRAL register for randomized crossover trials for a systematic review and network meta-analysis we are conducting. Two individuals independently screened the search results for eligibility and abstracted data from each included report. We identified 83 crossover trials eligible for inclusion. Issues affecting the risk of bias in crossover trials, such as carryover, period effects and missing data, were often ignored. Some trials failed to accommodate the within-individual differences in the analysis. For a large proportion of the trials, the authors tabulated the results as if they arose from a parallel design. Precision estimates properly accounting for the paired nature of the design were often unavailable from the study reports; consequently, to include trial findings in a meta-analysis would require further manipulation and assumptions. The high proportion of poorly reported analyses and results has the potential to affect whether crossover data should or can be included in a meta-analysis. There is pressing need for reporting guidelines for crossover trials.

Time in Language, Language in Time

ERIC Educational Resources Information Center

Klein, Wolfgang

2008-01-01

Many millenia ago, a number of genetic changes endowed the human species with the remarkable capacity: (1) to construct highly complex systems of expressions--human languages; (2) to copy such systems, once created, from other members of the species; and (3) to use them for communicative and perhaps other purposes. This capacity is not uniform; it…

Contrasting insect attraction and herbivore-induced plant volatile production in maize

USDA-ARS?s Scientific Manuscript database

Maize inbred line W22 is an important resource for genetic studies due to the availability of the UniformMu mutant population and a complete genome sequence. In this study, we assessed the suitability of W22 as a model for tritrophic interactions between maize, Spodoptera frugiperda (fall armyworm) ...

Variance component and breeding value estimation for genetic heterogeneity of residual variance in Swedish Holstein dairy cattle.

PubMed

Rönnegård, L; Felleki, M; Fikse, W F; Mulder, H A; Strandberg, E

2013-04-01

Trait uniformity, or micro-environmental sensitivity, may be studied through individual differences in residual variance. These differences appear to be heritable, and the need exists, therefore, to fit models to predict breeding values explaining differences in residual variance. The aim of this paper is to estimate breeding values for micro-environmental sensitivity (vEBV) in milk yield and somatic cell score, and their associated variance components, on a large dairy cattle data set having more than 1.6 million records. Estimation of variance components, ordinary breeding values, and vEBV was performed using standard variance component estimation software (ASReml), applying the methodology for double hierarchical generalized linear models. Estimation using ASReml took less than 7 d on a Linux server. The genetic standard deviations for residual variance were 0.21 and 0.22 for somatic cell score and milk yield, respectively, which indicate moderate genetic variance for residual variance and imply that a standard deviation change in vEBV for one of these traits would alter the residual variance by 20%. This study shows that estimation of variance components, estimated breeding values and vEBV, is feasible for large dairy cattle data sets using standard variance component estimation software. The possibility to select for uniformity in Holstein dairy cattle based on these estimates is discussed. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval

PubMed Central

Wang, Yuan; Ding, Xiangdong; Tan, Zhen; Ning, Chao; Xing, Kai; Yang, Ting; Pan, Yongjie; Sun, Dongxiao; Wang, Chuduan

2017-01-01

Piglet uniformity (PU) and farrowing interval (FI) are important reproductive traits related to production and economic profits in the pig industry. However, the genetic architecture of the longitudinal trends of reproductive traits still remains elusive. Herein, we performed a genome-wide association study (GWAS) to detect potential genetic variation and candidate genes underlying the phenotypic records at different parities for PU and FI in a population of 884 Large White pigs. In total, 12 significant SNPs were detected on SSC1, 3, 4, 9, and 14, which collectively explained 1–1.79% of the phenotypic variance for PU from parity 1 to 4, and 2.58–4.11% for FI at different stages. Of these, seven SNPs were located within 16 QTL regions related to swine reproductive traits. One QTL region was associated with birth body weight (related to PU) and contained the peak SNP MARC0040730, and another was associated with plasma FSH concentration (related to FI) and contained the SNP MARC0031325. Finally, some positional candidate genes for PU and FI were identified because of their roles in prenatal skeletal muscle development, fetal energy substrate, pre-implantation, and the expression of mammary gland epithelium. Identification of novel variants and candidate genes will greatly advance our understanding of the genetic mechanisms of PU and FI, and suggest a specific opportunity for improving marker assisted selection or genomic selection in pigs. PMID:29234349

Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis.

PubMed

Medhi, Darpan; Goldman, Alastair Sh; Lichten, Michael

2016-11-18

The budding yeast genome contains regions where meiotic recombination initiates more frequently than in others. This pattern parallels enrichment for the meiotic chromosome axis proteins Hop1 and Red1. These proteins are important for Spo11-catalyzed double strand break formation; their contribution to crossover recombination remains undefined. Using the sequence-specific VMA1 -derived endonuclease (VDE) to initiate recombination in meiosis, we show that chromosome structure influences the choice of proteins that resolve recombination intermediates to form crossovers. At a Hop1-enriched locus, most VDE-initiated crossovers, like most Spo11-initiated crossovers, required the meiosis-specific MutLγ resolvase. In contrast, at a locus with lower Hop1 occupancy, most VDE-initiated crossovers were MutLγ-independent. In pch2 mutants, the two loci displayed similar Hop1 occupancy levels, and VDE-induced crossovers were similarly MutLγ-dependent. We suggest that meiotic and mitotic recombination pathways coexist within meiotic cells, and that features of meiotic chromosome structure determine whether one or the other predominates in different regions.

The joy of six: how to control your crossovers.

PubMed

Globus, Samuel T; Keeney, Scott

2012-03-30

Meiotic cells tightly regulate the number and distribution of crossovers to promote accurate chromosome segregation. Yokoo and colleagues uncover a metazoan-specific, cyclin-like protein that is crucial for crossover formation. They utilize this protein's unique properties to explore a remarkable example of biological numerology, whereby nearly every meiotic cell in C. elegans makes precisely six crossovers, one for each of its six chromosome pairs. Copyright © 2012 Elsevier Inc. All rights reserved.

Design of sparse Halbach magnet arrays for portable MRI using a genetic algorithm.

PubMed

Cooley, Clarissa Zimmerman; Haskell, Melissa W; Cauley, Stephen F; Sappo, Charlotte; Lapierre, Cristen D; Ha, Christopher G; Stockmann, Jason P; Wald, Lawrence L

2018-01-01

Permanent magnet arrays offer several attributes attractive for the development of a low-cost portable MRI scanner for brain imaging. They offer the potential for a relatively lightweight, low to mid-field system with no cryogenics, a small fringe field, and no electrical power requirements or heat dissipation needs. The cylindrical Halbach array, however, requires external shimming or mechanical adjustments to produce B 0 fields with standard MRI homogeneity levels (e.g., 0.1 ppm over FOV), particularly when constrained or truncated geometries are needed, such as a head-only magnet where the magnet length is constrained by the shoulders. For portable scanners using rotation of the magnet for spatial encoding with generalized projections, the spatial pattern of the field is important since it acts as the encoding field. In either a static or rotating magnet, it will be important to be able to optimize the field pattern of cylindrical Halbach arrays in a way that retains construction simplicity. To achieve this, we present a method for designing an optimized cylindrical Halbach magnet using the genetic algorithm to achieve either homogeneity (for standard MRI applications) or a favorable spatial encoding field pattern (for rotational spatial encoding applications). We compare the chosen designs against a standard, fully populated sparse Halbach design, and evaluate optimized spatial encoding fields using point-spread-function and image simulations. We validate the calculations by comparing to the measured field of a constructed magnet. The experimentally implemented design produced fields in good agreement with the predicted fields, and the genetic algorithm was successful in improving the chosen metrics. For the uniform target field, an order of magnitude homogeneity improvement was achieved compared to the un-optimized, fully populated design. For the rotational encoding design the resolution uniformity is improved by 95% compared to a uniformly populated design.

Population genetic structure of the melon fly, Bactrocera cucurbitae (Diptera: Tephritidae), from China and Southeast Asia.

PubMed

Hu, Jian; Zhang, Jun L; Nardi, Francesco; Zhang, Run J

2008-11-01

The melon fly, Bactrocera cucurbitae Coquillett, is a species of fruit flies of significant agricultural interest. Of supposed Indian origin, the melon fly is now widely distributed throughout South East Asia up to China, while it has been recently eradicated from Japan. The population structure of seven geographic populations from coastal China, as well as samples from other regions of South East Asia and Japan, including lab colonies, have been studied using a 782 bp fragment of mitochondrial cytochrome oxidase I (COI) gene sequence. The observed genetic diversity was exceedingly low, considering the geographic scale of the sampling, and one single haplotype was found to be predominant from Sri Lanka to China. We confirm that Bactrocera cucurbitae exists in South East Asia as a single phyletic lineage, that Chinese populations are genetically uniform, and that no apparent genetic differentiation exists between these and three available Japanese melon fly sequences.

Sensitivity Analysis of Genetic Algorithm Parameters for Optimal Groundwater Monitoring Network Design

NASA Astrophysics Data System (ADS)

Abdeh-Kolahchi, A.; Satish, M.; Datta, B.

2004-05-01

A state art groundwater monitoring network design is introduced. The method combines groundwater flow and transport results with optimization Genetic Algorithm (GA) to identify optimal monitoring well locations. Optimization theory uses different techniques to find a set of parameter values that minimize or maximize objective functions. The suggested groundwater optimal monitoring network design is based on the objective of maximizing the probability of tracking a transient contamination plume by determining sequential monitoring locations. The MODFLOW and MT3DMS models included as separate modules within the Groundwater Modeling System (GMS) are used to develop three dimensional groundwater flow and contamination transport simulation. The groundwater flow and contamination simulation results are introduced as input to the optimization model, using Genetic Algorithm (GA) to identify the groundwater optimal monitoring network design, based on several candidate monitoring locations. The groundwater monitoring network design model is used Genetic Algorithms with binary variables representing potential monitoring location. As the number of decision variables and constraints increase, the non-linearity of the objective function also increases which make difficulty to obtain optimal solutions. The genetic algorithm is an evolutionary global optimization technique, which is capable of finding the optimal solution for many complex problems. In this study, the GA approach capable of finding the global optimal solution to a groundwater monitoring network design problem involving 18.4X 1018 feasible solutions will be discussed. However, to ensure the efficiency of the solution process and global optimality of the solution obtained using GA, it is necessary that appropriate GA parameter values be specified. The sensitivity analysis of genetic algorithms parameters such as random number, crossover probability, mutation probability, and elitism are discussed for solution of monitoring network design.

apGA: An adaptive parallel genetic algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liepins, G.E.; Baluja, S.

1991-01-01

We develop apGA, a parallel variant of the standard generational GA, that combines aggressive search with perpetual novelty, yet is able to preserve enough genetic structure to optimally solve variably scaled, non-uniform block deceptive and hierarchical deceptive problems. apGA combines elitism, adaptive mutation, adaptive exponential scaling, and temporal memory. We present empirical results for six classes of problems, including the DeJong test suite. Although we have not investigated hybrids, we note that apGA could be incorporated into other recent GA variants such as GENITOR, CHC, and the recombination stage of mGA. 12 refs., 2 figs., 2 tabs.

Cross-over endocytosis of claudins is mediated by interactions via their extracellular loops.

PubMed

Gehne, Nora; Lamik, Agathe; Lehmann, Martin; Haseloff, Reiner F; Andjelkovic, Anuska V; Blasig, Ingolf E

2017-01-01

Claudins (Cldns) are transmembrane tight junction (TJ) proteins that paracellularly seal endo- and epithelial barriers by their interactions within the TJs. However, the mechanisms allowing TJ remodeling while maintaining barrier integrity are largely unknown. Cldns and occludin are heterophilically and homophilically cross-over endocytosed into neighboring cells in large, double membrane vesicles. Super-resolution microscopy confirmed the presence of Cldns in these vesicles and revealed a distinct separation of Cldns derived from opposing cells within cross-over endocytosed vesicles. Colocalization of cross-over endocytosed Cldn with the autophagosome markers as well as inhibition of autophagosome biogenesis verified involvement of the autophagosomal pathway. Accordingly, cross-over endocytosed Cldns underwent lysosomal degradation as indicated by lysosome markers. Cross-over endocytosis of Cldn5 depended on clathrin and caveolin pathways but not on dynamin. Cross-over endocytosis also depended on Cldn-Cldn-interactions. Amino acid substitutions in the second extracellular loop of Cldn5 (F147A, Q156E) caused impaired cis- and trans-interaction, as well as diminished cross-over endocytosis. Moreover, F147A exhibited an increased mobility in the membrane, while Q156E was not as mobile but enhanced the paracellular permeability. In conclusion, the endocytosis of TJ proteins depends on their ability to interact strongly with each other in cis and trans, and the mobility of Cldns in the membrane is not necessarily an indicator of barrier permeability. TJ-remodeling via cross-over endocytosis represents a general mechanism for the degradation of transmembrane proteins in cell-cell contacts and directly links junctional membrane turnover to autophagy.

The role of genetic diversity in nest cooling in a wild honey bee, Apis florea.

PubMed

Jones, Julia C; Nanork, Piyamas; Oldroyd, Benjamin P

2007-02-01

Simulation studies of the task threshold model for task allocation in social insect colonies suggest that nest temperature homeostasis is enhanced if workers have slightly different thresholds for engaging in tasks related to nest thermoregulation. Genetic variance in task thresholds is one way a distribution of task thresholds can be generated. Apis mellifera colonies with large genetic diversity are able to maintain more stable brood nest temperatures than colonies that are genetically uniform. If this phenomenon is generalizable to other species, we would predict that patrilines should vary in the threshold in which they engage in thermoregulatory tasks. We exposed A. florea colonies to different temperatures experimentally, and retrieved fanning workers at these different temperatures. In many cases we found statistically significant differences in the proportion of fanning workers of different patrilines at different experimental temperatures. This suggests that genetically different workers have different thresholds for performing the thermoregulatory task of fanning. We suggest, therefore, that genetically based variance in task threshold is a widespread phenomenon in the genus Apis.

Topoisomerase II Mediates Meiotic Crossover Interference

PubMed Central

Zhang, Liangran; Wang, Shunxin; Yin, Shen; Hong, Soogil; Kim, Keun P.; Kleckner, Nancy

2014-01-01

Summary Spatial patterning is a ubiquitous feature of biological systems. Meiotic crossovers provide an interesting example, defined by the classical phenomenon of crossover interference. Here, analysis of crossover patterns in budding yeast identifies a molecular pathway for interference. Topoisomerase II (Topo II) plays a central role, thus identifying a new function for this critical molecule. SUMOylation [of TopoII and axis component Red1] and ubiquitin-mediated removal of SUMOylated proteins are also required. These and other findings support the hypothesis that crossover interference involves accumulation, relief and redistribution of mechanical stress along the protein/DNA meshwork of meiotic chromosome axes, with TopoII required to adjust spatial relationships among DNA segments. PMID:25043020

Agarose droplet microfluidics for highly parallel and efficient single molecule emulsion PCR.

PubMed

Leng, Xuefei; Zhang, Wenhua; Wang, Chunming; Cui, Liang; Yang, Chaoyong James

2010-11-07

An agarose droplet method was developed for highly parallel and efficient single molecule emulsion PCR. The method capitalizes on the unique thermoresponsive sol-gel switching property of agarose for highly efficient DNA amplification and amplicon trapping. Uniform agarose solution droplets generated via a microfluidic chip serve as robust and inert nanolitre PCR reactors for single copy DNA molecule amplification. After PCR, agarose droplets are gelated to form agarose beads, trapping all amplicons in each reactor to maintain the monoclonality of each droplet. This method does not require cocapsulation of primer labeled microbeads, allows high throughput generation of uniform droplets and enables high PCR efficiency, making it a promising platform for many single copy genetic studies.

Sequence comparison in the crossover region of an oncogenic avian retrovirus recombinant and its nononcogenic parent: Genetic regions that control growth rate and oncogenic potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsichlis, P.N.; Donehower, L.; Hager, G.

1982-11-01

NTRE is an avian retrovirus recombinant of the endogeneous nononcogenic Rous-associated virus-0 (RAV-0) and the oncogenic, exogeneous, transformation-defective (td) Prague strain of Rous sarcoma virus B (td-PrRSV-B). Oligonucleotide mapping had shown that the recombinant virus is indistinguishable from its RAV-0 parent except for the 3'-end sequences, which were derived from td-PrRSV-B. However, the virus exhibits properties which are typical of an exogenous virus: it grows to high titers in tissue culture, and it is oncogenic in vivo. To accurately define the genetic region responsible for these properties, the authors determined the nucleotide sequences of the recombinant and its RAV-0 parentmore » by using molecular clones of their DNA. These were compared with sequences already available for PrRSV-C, a virus closely related to the exogenous parent td-PrRSV-B. The results suggested that the crossover event which generated NTRE 7 took place in a region -501 to -401 nucleotides from the 3' end of the td-PrRSV parental genome and that sequences to the right of the recombination region were responsible for its growth properties and oncogenic potential. Since the exogenous-virus-specific sequences are expected to be missing from transformation-defective mutants of the Schmidt-Ruppin strain of RSV, which, like other exogeneous viruses, grow to high tiers in tissue culture and are oncogenic in vivo, the authors concluded that the growth properties and oncogenic potential of the exogeneous viruses are determined by sequences in the U3 region of the long terminal repeat. However, the authors propose that the exogeneous-virus-specific region may play a role in determining the oncogenic spectrum of a given oncogenic virus.« less

Geosat crossover analysis in the tropical Pacific. Part 1: Constrained sinusoidal crossover adjustment

NASA Technical Reports Server (NTRS)

Tai, Chang-Kou

1988-01-01

A new method (constrained sinusoidal crossover adjustment) for removing the orbit error in satellite altimetry is tested (using crossovers accumulated in the first 91 days of the Geosat non-repeat era in the tropical Pacific) and found to have excellent qualities. Two features distinguish the new method from the conventional bias-and-tilt crossover adjustment. First, a sine wave (with wavelength equaling the circumference of the Earth) is used to represent the orbit error for each satellite revolution, instead of the bias-and-tilt (and curvature, if necessary) approach for each segment of the satellite ground track. Secondly, the indeterminacy of the adjustment process is removed by a simple constraint minimizing the amplitudes of the sine waves, rather than by fixing selected tracks. Overall the new method is more accurate, more efficient, and much less cumbersome than the old. The idea of restricting the crossover adjustment to crossovers between tracks that are less than certain days apart in order to preserve the large-scale long-term oceanic variability is also tested with inconclusive results because the orbit error was unusually nonstationary in the initial 91 days of the GEOSAT mission.

Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis

PubMed Central

Medhi, Darpan; Goldman, Alastair SH; Lichten, Michael

2016-01-01

The budding yeast genome contains regions where meiotic recombination initiates more frequently than in others. This pattern parallels enrichment for the meiotic chromosome axis proteins Hop1 and Red1. These proteins are important for Spo11-catalyzed double strand break formation; their contribution to crossover recombination remains undefined. Using the sequence-specific VMA1-derived endonuclease (VDE) to initiate recombination in meiosis, we show that chromosome structure influences the choice of proteins that resolve recombination intermediates to form crossovers. At a Hop1-enriched locus, most VDE-initiated crossovers, like most Spo11-initiated crossovers, required the meiosis-specific MutLγ resolvase. In contrast, at a locus with lower Hop1 occupancy, most VDE-initiated crossovers were MutLγ-independent. In pch2 mutants, the two loci displayed similar Hop1 occupancy levels, and VDE-induced crossovers were similarly MutLγ-dependent. We suggest that meiotic and mitotic recombination pathways coexist within meiotic cells, and that features of meiotic chromosome structure determine whether one or the other predominates in different regions. DOI: http://dx.doi.org/10.7554/eLife.19669.001 PMID:27855779

Genetic modulation of oxytocin sensitivity: a pharmacogenetic approach.

PubMed

Chen, F S; Kumsta, R; Dvorak, F; Domes, G; Yim, O S; Ebstein, R P; Heinrichs, M

2015-10-27

Intranasal administration of the neuropeptide oxytocin has been shown to influence a range of complex social cognitions and social behaviors, and it holds therapeutic potential for the treatment of mental disorders characterized by social functioning deficits such as autism, social phobia and borderline personality disorder. However, considerable variability exists in individual responses to oxytocin administration. Here, we undertook a study to investigate the role of genetic variation in sensitivity to exogenous oxytocin using a socioemotional task. In a randomized, double-blind, placebo-controlled experiment with a repeated-measures (crossover) design, we assessed the performance of 203 men on an emotion recognition task under oxytocin and placebo. We took a haplotype-based approach to investigate the association between oxytocin receptor gene variation and oxytocin sensitivity. We identified a six-marker haplotype block spanning the promoter region and intron 3 that was significantly associated with our measure of oxytocin sensitivity. Specifically, the TTCGGG haplotype comprising single-nucleotide polymorphisms rs237917-rs2268498-rs4564970-rs237897-rs2268495-rs53576 is associated with increased emotion recognition performance under oxytocin versus placebo, and the CCGAGA haplotype with the opposite pattern. These results on the genetic modulation of sensitivity to oxytocin document a significant source of individual differences with implications for personalized treatment approaches using oxytocin administration.

Genetic modulation of oxytocin sensitivity: a pharmacogenetic approach

PubMed Central

Chen, F S; Kumsta, R; Dvorak, F; Domes, G; Yim, O S; Ebstein, R P; Heinrichs, M

2015-01-01

Intranasal administration of the neuropeptide oxytocin has been shown to influence a range of complex social cognitions and social behaviors, and it holds therapeutic potential for the treatment of mental disorders characterized by social functioning deficits such as autism, social phobia and borderline personality disorder. However, considerable variability exists in individual responses to oxytocin administration. Here, we undertook a study to investigate the role of genetic variation in sensitivity to exogenous oxytocin using a socioemotional task. In a randomized, double-blind, placebo-controlled experiment with a repeated-measures (crossover) design, we assessed the performance of 203 men on an emotion recognition task under oxytocin and placebo. We took a haplotype-based approach to investigate the association between oxytocin receptor gene variation and oxytocin sensitivity. We identified a six-marker haplotype block spanning the promoter region and intron 3 that was significantly associated with our measure of oxytocin sensitivity. Specifically, the TTCGGG haplotype comprising single-nucleotide polymorphisms rs237917–rs2268498–rs4564970–rs237897–rs2268495–rs53576 is associated with increased emotion recognition performance under oxytocin versus placebo, and the CCGAGA haplotype with the opposite pattern. These results on the genetic modulation of sensitivity to oxytocin document a significant source of individual differences with implications for personalized treatment approaches using oxytocin administration. PMID:26506050

49 CFR 236.203 - Hand operated crossover between main tracks; protection.

Code of Federal Regulations, 2014 CFR

2014-10-01

...) Electric locking of the switches of the crossover. Signals governing movements over either switch shall... crossover is occupied by a train, locomotive or car in such a manner as to foul the main track. It shall not... electric locking releases. ...

49 CFR 236.203 - Hand operated crossover between main tracks; protection.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Electric locking of the switches of the crossover. Signals governing movements over either switch shall... crossover is occupied by a train, locomotive or car in such a manner as to foul the main track. It shall not... electric locking releases. ...

49 CFR 236.203 - Hand operated crossover between main tracks; protection.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Electric locking of the switches of the crossover. Signals governing movements over either switch shall... crossover is occupied by a train, locomotive or car in such a manner as to foul the main track. It shall not... electric locking releases. ...

24 CFR 3285.701 - Electrical crossovers.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 5 2011-04-01 2011-04-01 false Electrical crossovers. 3285.701... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Electrical Systems and Equipment § 3285.701 Electrical crossovers. Multi-section homes with electrical wiring in more than one section require...

24 CFR 3285.701 - Electrical crossovers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 24 Housing and Urban Development 5 2013-04-01 2013-04-01 false Electrical crossovers. 3285.701... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Electrical Systems and Equipment § 3285.701 Electrical crossovers. Multi-section homes with electrical wiring in more than one section require...

24 CFR 3285.701 - Electrical crossovers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 24 Housing and Urban Development 5 2014-04-01 2014-04-01 false Electrical crossovers. 3285.701... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Electrical Systems and Equipment § 3285.701 Electrical crossovers. Multi-section homes with electrical wiring in more than one section require...

24 CFR 3285.701 - Electrical crossovers.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 5 2012-04-01 2012-04-01 false Electrical crossovers. 3285.701... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Electrical Systems and Equipment § 3285.701 Electrical crossovers. Multi-section homes with electrical wiring in more than one section require...

49 CFR 236.203 - Hand operated crossover between main tracks; protection.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Electric locking of the switches of the crossover. Signals governing movements over either switch shall... crossover is occupied by a train, locomotive or car in such a manner as to foul the main track. It shall not... electric locking releases. ...

49 CFR 236.203 - Hand operated crossover between main tracks; protection.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Electric locking of the switches of the crossover. Signals governing movements over either switch shall... crossover is occupied by a train, locomotive or car in such a manner as to foul the main track. It shall not... electric locking releases. ...

Is Variability in Mate Choice Similar for Intelligence and Personality Traits? Testing a Hypothesis about the Evolutionary Genetics of Personality

ERIC Educational Resources Information Center

Stone, Emily A.; Shackelford, Todd K.; Buss, David M.

2012-01-01

This study tests the hypothesis presented by Penke, Denissen, and Miller (2007a) that condition-dependent traits, including intelligence, attractiveness, and health, are universally and uniformly preferred as characteristics in a mate relative to traits that are less indicative of condition, including personality traits. We analyzed…

Practical Disk Diffusion Test for Detecting Group B Streptococcus with Reduced Penicillin Susceptibility▿

PubMed Central

Kimura, Kouji; Wachino, Jun-ichi; Kurokawa, Hiroshi; Suzuki, Satowa; Yamane, Kunikazu; Shibata, Naohiro; Arakawa, Yoshichika

2009-01-01

Although group B streptococcus (GBS) has been considered to be uniformly susceptible to β-lactams, the presence of GBS with reduced penicillin susceptibility (PRGBS) was recently confirmed genetically. We developed a feasible and reliable method for screening PRGBS in clinical microbiology laboratories using a combination of ceftibuten, oxacillin, and ceftizoxime disks. PMID:19812274

Practical disk diffusion test for detecting group B streptococcus with reduced penicillin susceptibility.

PubMed

Kimura, Kouji; Wachino, Jun-Ichi; Kurokawa, Hiroshi; Suzuki, Satowa; Yamane, Kunikazu; Shibata, Naohiro; Arakawa, Yoshichika

2009-12-01

Although group B streptococcus (GBS) has been considered to be uniformly susceptible to beta-lactams, the presence of GBS with reduced penicillin susceptibility (PRGBS) was recently confirmed genetically. We developed a feasible and reliable method for screening PRGBS in clinical microbiology laboratories using a combination of ceftibuten, oxacillin, and ceftizoxime disks.

Increased uniformity by planting clones will likely have a minimal effect on inventory costs

Treesearch

Curtis L. VanderSchaaf; Dean W. Coble; David B. South

2012-01-01

When conducting inventories, reducing variability among tree diameters, heights, and ultimately volumes or biomass, can reduce the number of points/plots needed to obtain a desired level of precision. We present a simple analysis examining the potential reduction in discounted inventory costs when stand variability is decreased (via improved genetics and intensive...

Predictive Factors for Patients Undergoing ASD Device Occlusion Who "Crossover" to Surgery.

PubMed

Mulukutla, Venkatachalam; Qureshi, Athar M; Pignatelli, Ricardo; Ing, Frank F

2018-03-01

The aim of this study was to define characteristics of those patients who are referred for device closure of an Atrial septal defect (ASD), but identified to "crossover" surgery. All patients who underwent surgical and device (Amplatzer or Helex occluder) closures of secundum ASDs from 2001 to 2010 were reviewed and organized into three groups: surgical closure, device closure, and "crossover" group. 369 patients underwent ASD closure (265 device, 104 surgical). 42 of the 265 patients referred for device closure "crossed over" to the surgical group at various stages of the catheterization procedure. The device group had defect size measuring 14.2 mm (mean) and an ASD index (Defect Size (mm)/BSA) of 14.0 compared to the corresponding values in the surgical group (20.1 mm, ASD index 25.9) (P < 0.001) and in the "crossover" group (20.7 mm, 22.6 ASD index) (P < 0.001). 79 patients in the device group had a deficient rim, and 86% were located in the retroaortic region. 33 patients in the "crossover" group had deficient rims with 70% deficiency in the posterior/inferior rim. The device group with deficient rims had an ASD index of 14.7 compared with the crossover group ASD index of 23.8 (P < 0.001). Comparing the device and "crossover" groups, an ASD index greater than 23.7 had a 90% specificity in "crossing over" to surgery. The crossover and surgical groups had statistically larger ASD defect size indexes compared with the device group. Deficient rim in the posterior/inferior rim is associated with a large ASD size index which is a predictive factor for crossing over to surgery. Catheterization did not negatively impact surgical results in the "crossover" group.

Studies on Methanol Crossover in Liquid-Feed Direct Methanol Pem Fuel Cells

NASA Technical Reports Server (NTRS)

Narayanan, S. R.

1995-01-01

The performance of liquid feed direct methanol fuel cells using various types of Nafion membranes as the solid polymer electrolyte have been studied. The rate of fuel crossover and electrical performance has been measured for cells with Nafion membranes of various thicknesses and equivalent weights. The crossover rate is found to decrease with increasing thickness and applied current. The dependence of crossover rate on current density can be understood in terms of a simple linear diffusion model which suggests that the crossover rate can be influenced by the electrode structure in addition to the membrane. The studies suggest that Nafion EW 1500 is a very promising alternate to Nafion EW 1100 for direct methanol fuel cells.

Graded Maximal Exercise Testing to Assess Mouse Cardio-Metabolic Phenotypes

PubMed Central

Petrosino, Jennifer M.; Heiss, Valerie J.; Maurya, Santosh K.; Kalyanasundaram, Anuradha; Periasamy, Muthu; LaFountain, Richard A.; Wilson, Jacob M.; Simonetti, Orlando P.; Ziouzenkova, Ouliana

2016-01-01

Functional assessments of cardiovascular fitness (CVF) are needed to establish animal models of dysfunction, test the effects of novel therapeutics, and establish the cardio-metabolic phenotype of mice. In humans, the graded maximal exercise test (GXT) is a standardized diagnostic for assessing CVF and mortality risk. These tests, which consist of concurrent staged increases in running speed and inclination, provide diagnostic cardio-metabolic parameters, such as, VO2max, anaerobic threshold, and metabolic crossover. Unlike the human-GXT, published mouse treadmill tests have set, not staged, increases in inclination as speed progress until exhaustion (PXT). Additionally, they often lack multiple cardio-metabolic parameters. Here, we developed a mouse-GXT with the intent of improving mouse-exercise testing sensitivity and developing translatable parameters to assess CVF in healthy and dysfunctional mice. The mouse-GXT, like the human-GXT, incorporated staged increases in inclination, speed, and intensity; and, was designed by considering imitations of the PXT and differences between human and mouse physiology. The mouse-GXT and PXTs were both tested in healthy mice (C57BL/6J, FVBN/J) to determine their ability to identify cardio-metabolic parameters (anaerobic threshold, VO2max, metabolic crossover) observed in human-GXTs. Next, theses assays were tested on established diet-induced (obese-C57BL/6J) and genetic (cardiac isoform Casq2-/-) models of cardiovascular dysfunction. Results showed that both tests reported VO2max and provided reproducible data about performance. Only the mouse-GXT reproducibly identified anaerobic threshold, metabolic crossover, and detected impaired CVF in dysfunctional models. Our findings demonstrated that the mouse-GXT is a sensitive, non-invasive, and cost-effective method for assessing CVF in mice. This new test can be used as a functional assessment to determine the cardio-metabolic phenotype of various animal models or the effects of novel therapeutics. PMID:26859763

Graded Maximal Exercise Testing to Assess Mouse Cardio-Metabolic Phenotypes.

PubMed

Petrosino, Jennifer M; Heiss, Valerie J; Maurya, Santosh K; Kalyanasundaram, Anuradha; Periasamy, Muthu; LaFountain, Richard A; Wilson, Jacob M; Simonetti, Orlando P; Ziouzenkova, Ouliana

2016-01-01

Functional assessments of cardiovascular fitness (CVF) are needed to establish animal models of dysfunction, test the effects of novel therapeutics, and establish the cardio-metabolic phenotype of mice. In humans, the graded maximal exercise test (GXT) is a standardized diagnostic for assessing CVF and mortality risk. These tests, which consist of concurrent staged increases in running speed and inclination, provide diagnostic cardio-metabolic parameters, such as, VO2max, anaerobic threshold, and metabolic crossover. Unlike the human-GXT, published mouse treadmill tests have set, not staged, increases in inclination as speed progress until exhaustion (PXT). Additionally, they often lack multiple cardio-metabolic parameters. Here, we developed a mouse-GXT with the intent of improving mouse-exercise testing sensitivity and developing translatable parameters to assess CVF in healthy and dysfunctional mice. The mouse-GXT, like the human-GXT, incorporated staged increases in inclination, speed, and intensity; and, was designed by considering imitations of the PXT and differences between human and mouse physiology. The mouse-GXT and PXTs were both tested in healthy mice (C57BL/6J, FVBN/J) to determine their ability to identify cardio-metabolic parameters (anaerobic threshold, VO2max, metabolic crossover) observed in human-GXTs. Next, theses assays were tested on established diet-induced (obese-C57BL/6J) and genetic (cardiac isoform Casq2-/-) models of cardiovascular dysfunction. Results showed that both tests reported VO2max and provided reproducible data about performance. Only the mouse-GXT reproducibly identified anaerobic threshold, metabolic crossover, and detected impaired CVF in dysfunctional models. Our findings demonstrated that the mouse-GXT is a sensitive, non-invasive, and cost-effective method for assessing CVF in mice. This new test can be used as a functional assessment to determine the cardio-metabolic phenotype of various animal models or the effects of novel therapeutics.

Assortative mating and fragmentation within dog breeds.

PubMed

Björnerfeldt, Susanne; Hailer, Frank; Nord, Maria; Vilà, Carles

2008-01-28

There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds.

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae).

PubMed

da Silva, Marjorie; Noll, Fernando Barbosa; E Castro, Adriana C Morales-Corrêa

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks.

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae)

PubMed Central

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks. PMID:29538451

Assortative mating and fragmentation within dog breeds

PubMed Central

2008-01-01

Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds. PMID:18226210

A Case Study of Controlling Crossover in a Selection Hyper-heuristic Framework Using the Multidimensional Knapsack Problem.

PubMed

Drake, John H; Özcan, Ender; Burke, Edmund K

2016-01-01

Hyper-heuristics are high-level methodologies for solving complex problems that operate on a search space of heuristics. In a selection hyper-heuristic framework, a heuristic is chosen from an existing set of low-level heuristics and applied to the current solution to produce a new solution at each point in the search. The use of crossover low-level heuristics is possible in an increasing number of general-purpose hyper-heuristic tools such as HyFlex and Hyperion. However, little work has been undertaken to assess how best to utilise it. Since a single-point search hyper-heuristic operates on a single candidate solution, and two candidate solutions are required for crossover, a mechanism is required to control the choice of the other solution. The frameworks we propose maintain a list of potential solutions for use in crossover. We investigate the use of such lists at two conceptual levels. First, crossover is controlled at the hyper-heuristic level where no problem-specific information is required. Second, it is controlled at the problem domain level where problem-specific information is used to produce good-quality solutions to use in crossover. A number of selection hyper-heuristics are compared using these frameworks over three benchmark libraries with varying properties for an NP-hard optimisation problem: the multidimensional 0-1 knapsack problem. It is shown that allowing crossover to be managed at the domain level outperforms managing crossover at the hyper-heuristic level in this problem domain.

49 CFR 218.107 - Additional operational requirements for hand-operated crossover switches.

Code of Federal Regulations, 2011 CFR

2011-10-01

...-operated crossover switches. 218.107 Section 218.107 Transportation Other Regulations Relating to... PRACTICES Handling Equipment, Switches, and Fixed Derails § 218.107 Additional operational requirements for hand-operated crossover switches. (a) Each railroad shall adopt and comply with an operating rule which...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.107 - Additional operational requirements for hand-operated crossover switches.

Code of Federal Regulations, 2010 CFR

2010-10-01

...-operated crossover switches. 218.107 Section 218.107 Transportation Other Regulations Relating to... PRACTICES Handling Equipment, Switches, and Fixed Derails § 218.107 Additional operational requirements for hand-operated crossover switches. (a) Each railroad shall adopt and comply with an operating rule which...

49 CFR 218.107 - Additional operational requirements for hand-operated crossover switches.

Code of Federal Regulations, 2014 CFR

2014-10-01

...-operated crossover switches. 218.107 Section 218.107 Transportation Other Regulations Relating to... PRACTICES Handling Equipment, Switches, and Fixed Derails § 218.107 Additional operational requirements for hand-operated crossover switches. (a) Each railroad shall adopt and comply with an operating rule which...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.107 - Additional operational requirements for hand-operated crossover switches.

Code of Federal Regulations, 2012 CFR

2012-10-01

...-operated crossover switches. 218.107 Section 218.107 Transportation Other Regulations Relating to... PRACTICES Handling Equipment, Switches, and Fixed Derails § 218.107 Additional operational requirements for hand-operated crossover switches. (a) Each railroad shall adopt and comply with an operating rule which...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.107 - Additional operational requirements for hand-operated crossover switches.

Code of Federal Regulations, 2013 CFR

2013-10-01

...-operated crossover switches. 218.107 Section 218.107 Transportation Other Regulations Relating to... PRACTICES Handling Equipment, Switches, and Fixed Derails § 218.107 Additional operational requirements for hand-operated crossover switches. (a) Each railroad shall adopt and comply with an operating rule which...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

Heat strain evaluation of overt and covert body armour in a hot and humid environment.

PubMed

Pyke, Andrew J; Costello, Joseph T; Stewart, Ian B

2015-03-01

The aim of this study was to elucidate the thermophysiological effects of wearing lightweight non-military overt and covert personal body armour (PBA) in a hot and humid environment. Eight healthy males walked on a treadmill for 120 min at 22% of their heart rate reserve in a climate chamber simulating 31 °C (60%RH) wearing either no armour (control), overt or covert PBA in addition to a security guard uniform, in a randomised controlled crossover design. No significant difference between conditions at the end of each trial was observed in core temperature, heart rate or skin temperature (P > 0.05). Covert PBA produced a significantly greater amount of body mass change (-1.81 ± 0.44%) compared to control (-1.07 ± 0.38%, P = 0.009) and overt conditions (-1.27 ± 0.44%, P = 0.025). Although a greater change in body mass was observed after the covert PBA trial; based on the physiological outcome measures recorded, the heat strain encountered while wearing lightweight, non-military overt or covert PBA was negligible compared to no PBA. The wearing of bullet proof vests or body armour is a requirement of personnel engaged in a wide range of occupations including police, security, customs and even journalists in theatres of war. This randomised controlled crossover study is the first to examine the thermophysiological effects of wearing lightweight non-military overt and covert personal body armour (PBA) in a hot and humid environment. We conclude that the heat strain encountered while wearing both overt and covert lightweight, non-military PBA was negligible compared to no PBA. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Impact of non-uniform correlation structure on sample size and power in multiple-period cluster randomised trials.

PubMed

Kasza, J; Hemming, K; Hooper, R; Matthews, Jns; Forbes, A B

2017-01-01

Stepped wedge and cluster randomised crossover trials are examples of cluster randomised designs conducted over multiple time periods that are being used with increasing frequency in health research. Recent systematic reviews of both of these designs indicate that the within-cluster correlation is typically taken account of in the analysis of data using a random intercept mixed model, implying a constant correlation between any two individuals in the same cluster no matter how far apart in time they are measured: within-period and between-period intra-cluster correlations are assumed to be identical. Recently proposed extensions allow the within- and between-period intra-cluster correlations to differ, although these methods require that all between-period intra-cluster correlations are identical, which may not be appropriate in all situations. Motivated by a proposed intensive care cluster randomised trial, we propose an alternative correlation structure for repeated cross-sectional multiple-period cluster randomised trials in which the between-period intra-cluster correlation is allowed to decay depending on the distance between measurements. We present results for the variance of treatment effect estimators for varying amounts of decay, investigating the consequences of the variation in decay on sample size planning for stepped wedge, cluster crossover and multiple-period parallel-arm cluster randomised trials. We also investigate the impact of assuming constant between-period intra-cluster correlations instead of decaying between-period intra-cluster correlations. Our results indicate that in certain design configurations, including the one corresponding to the proposed trial, a correlation decay can have an important impact on variances of treatment effect estimators, and hence on sample size and power. An R Shiny app allows readers to interactively explore the impact of correlation decay.

Stress Crossover in Newlywed Marriage: A Longitudinal and Dyadic Perspective

ERIC Educational Resources Information Center

Neff, Lisa A.; Karney, Benjamin R.

2007-01-01

Studies of stress and marital quality often assess stress as an intrapersonal phenomenon, examining how spouses' stress may influence their own relationship well-being. Yet spouses' stress also may influence partners' relationship evaluations, a phenomenon referred to as stress crossover. This study examined stress crossover, and conditions that…

Electromagnetic pump stator frame having power crossover struts

DOEpatents

Fanning, Alan W.; Olich, Eugene E.

1995-01-01

A stator frame for an electromagnetic pump includes a casing joined to a hub by a plurality of circumferentially spaced apart struts. At least one electrically insulated power crossover lead extends through the hub, through a crossover one of the struts, and through the casing for carrying electrical current therethrough.

50 CFR 660.320 - Open access fishery-crossover provisions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Open access fishery-crossover provisions... West Coast Groundfish-Open Access Fisheries § 660.320 Open access fishery—crossover provisions. (a) Operating in both limited entry and open access fisheries. See provisions at § 660.60, subpart C. (b...

50 CFR 660.320 - Open access fishery-crossover provisions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Open access fishery-crossover provisions... West Coast Groundfish-Open Access Fisheries § 660.320 Open access fishery—crossover provisions. (a) Operating in both limited entry and open access fisheries. See provisions at § 660.60, subpart C. (b...

Determination of Effective Crossover Location and Dimensions for Branched Detonation in a Pulsed Detonation Engine

DTIC Science & Technology

2012-03-22

location is varied from the aft end of the detonation tube to the middle of the detonation tube while the crossover width is varied from 2.5 in to 0.5...the other end where the tube is connected to a source of fuel, oxidizer, and ignition .7 The engine cycle is divided into three equal phases: fill...location and width of the crossover duct for hydrogen, ethylene and an n-alkane. The crossover location is varied from the aft end of the

On the equivalence of case-crossover and time series methods in environmental epidemiology.

PubMed

Lu, Yun; Zeger, Scott L

2007-04-01

The case-crossover design was introduced in epidemiology 15 years ago as a method for studying the effects of a risk factor on a health event using only cases. The idea is to compare a case's exposure immediately prior to or during the case-defining event with that same person's exposure at otherwise similar "reference" times. An alternative approach to the analysis of daily exposure and case-only data is time series analysis. Here, log-linear regression models express the expected total number of events on each day as a function of the exposure level and potential confounding variables. In time series analyses of air pollution, smooth functions of time and weather are the main confounders. Time series and case-crossover methods are often viewed as competing methods. In this paper, we show that case-crossover using conditional logistic regression is a special case of time series analysis when there is a common exposure such as in air pollution studies. This equivalence provides computational convenience for case-crossover analyses and a better understanding of time series models. Time series log-linear regression accounts for overdispersion of the Poisson variance, while case-crossover analyses typically do not. This equivalence also permits model checking for case-crossover data using standard log-linear model diagnostics.

Effects of Subsensory Noise and Fatigue on Knee Landing and Cross-over Cutting Biomechanics in Male Athletes.

PubMed

Qu, Xingda; Jiang, Jianxin; Hu, Xinyao

2018-06-01

The objective of this study was to examine the effects of subsensory noise and fatigue on knee biomechanics during the athletic task of landing followed by cross-over cutting. A total of 32 healthy male athletes participated in the study. They were evenly divided into 2 groups: no fatigue group and fatigue group. Fatigue was induced to the lower extremity by a repetitive squatting exercise in the fatigue group. Subsensory noise was generated by linear miniature vibrators bilaterally placed around the knee joints. During data collection, the participants were instructed to perform landing followed by cross-over cutting in both the subsensory on and off conditions. Dependent variables were selected to assess knee biomechanics in the phases of landing and cross-over cutting, separately. Results showed that fatigue resulted in larger knee flexion during landing and larger knee internal rotation during cross-over cutting. Subsensory noise was found to reduce knee rotation impulse during cross-over cutting. These findings suggest that cross-over cutting is more dangerous than landing in the fatigue condition, and subsensory noise may lead to changes in knee biomechanics consistent with reduced risk of anterior cruciate ligament injuries, but the changes may be task-specific.

Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice

PubMed Central

de Boer, Esther; Jasin, Maria; Keeney, Scott

2015-01-01

Meiotic recombination initiated by programmed double-strand breaks (DSBs) yields two types of interhomolog recombination products, crossovers and noncrossovers, but what determines whether a DSB will yield a crossover or noncrossover is not understood. In this study, we analyzed the influence of sex and chromosomal location on mammalian recombination outcomes by constructing fine-scale recombination maps in both males and females at two mouse hot spots located in different regions of the same chromosome. These include the most comprehensive maps of recombination hot spots in oocytes to date. One hot spot, located centrally on chromosome 1, behaved similarly in male and female meiosis: Crossovers and noncrossovers formed at comparable levels and ratios in both sexes. In contrast, at a distal hot spot, crossovers were recovered only in males even though noncrossovers were obtained at similar frequencies in both sexes. These findings reveal an example of extreme sex-specific bias in recombination outcome. We further found that estimates of relative DSB levels are surprisingly poor predictors of relative crossover frequencies between hot spots in males. Our results demonstrate that the outcome of mammalian meiotic recombination can be biased, that this bias can vary depending on location and cellular context, and that DSB frequency is not the only determinant of crossover frequency. PMID:26251527

Confidence intervals for distinguishing ordinal and disordinal interactions in multiple regression.

PubMed

Lee, Sunbok; Lei, Man-Kit; Brody, Gene H

2015-06-01

Distinguishing between ordinal and disordinal interaction in multiple regression is useful in testing many interesting theoretical hypotheses. Because the distinction is made based on the location of a crossover point of 2 simple regression lines, confidence intervals of the crossover point can be used to distinguish ordinal and disordinal interactions. This study examined 2 factors that need to be considered in constructing confidence intervals of the crossover point: (a) the assumption about the sampling distribution of the crossover point, and (b) the possibility of abnormally wide confidence intervals for the crossover point. A Monte Carlo simulation study was conducted to compare 6 different methods for constructing confidence intervals of the crossover point in terms of the coverage rate, the proportion of true values that fall to the left or right of the confidence intervals, and the average width of the confidence intervals. The methods include the reparameterization, delta, Fieller, basic bootstrap, percentile bootstrap, and bias-corrected accelerated bootstrap methods. The results of our Monte Carlo simulation study suggest that statistical inference using confidence intervals to distinguish ordinal and disordinal interaction requires sample sizes more than 500 to be able to provide sufficiently narrow confidence intervals to identify the location of the crossover point. (c) 2015 APA, all rights reserved).

Spin crossover in (Mg,Fe3+)(Si,Fe3+)O3 bridgmanite: effects of disorder, iron concentration, and temperature

NASA Astrophysics Data System (ADS)

Shukla, Gaurav; Wentzcovitch, Renata

The spin crossover of iron in Fe3+-bearing bridgmanite, the most abundant mineral of the Earth's lower mantle, is by now a well-established phenomenon, though several aspects of this crossover remain unclear. Here we investigate effects of disorder, iron concentration, and temperature on this crossover using ab initio LDA + USC calculations. Disorder and concentration effects are addressed using complete statistical samplings of coupled substituted configurations up to 80 atoms supercells, while the vibrational effects using the quasiharmonic approximation. Our calculated compression curves for iron-free and iron-bearing bridgmanite compare well with the latest experimental measurements. The comparison also suggests that in a closed system, Fe2+ present in the sample may transform into Fe3+ by introduction of Mg and O vacancies with increasing pressure. As in the spin crossover in ferropericlase, this crossover in bridgmanite is accompanied by a clear volume reduction and an anomalous softening of the bulk modulus throughout the crossover pressure range. Though the concentration of [Fe3+]Si in bridgmanite may be small, related elastic anomalies may impact the interpretation of radial and lateral velocity structures of the Earth's lower mantle. This research was supported primarily by NSF Grant EAR 1348066. Computations are performed at the Minnesota Supercomputing Institute (MSI).

Acoustic Performance of a Real-Time Three-Dimensional Sound-Reproduction System

NASA Technical Reports Server (NTRS)

Faller, Kenneth J., II; Rizzi, Stephen A.; Aumann, Aric R.

2013-01-01

The Exterior Effects Room (EER) is a 39-seat auditorium at the NASA Langley Research Center and was built to support psychoacoustic studies of aircraft community noise. The EER has a real-time simulation environment which includes a three-dimensional sound-reproduction system. This system requires real-time application of equalization filters to compensate for spectral coloration of the sound reproduction due to installation and room effects. This paper describes the efforts taken to develop the equalization filters for use in the real-time sound-reproduction system and the subsequent analysis of the system s acoustic performance. The acoustic performance of the compensated and uncompensated sound-reproduction system is assessed for its crossover performance, its performance under stationary and dynamic conditions, the maximum spatialized sound pressure level it can produce from a single virtual source, and for the spatial uniformity of a generated sound field. Additionally, application examples are given to illustrate the compensated sound-reproduction system performance using recorded aircraft flyovers

Critical Slowing Down in Time-to-Extinction: An Example of Critical Phenomena in Ecology

NASA Technical Reports Server (NTRS)

Gandhi, Amar; Levin, Simon; Orszag, Steven

1998-01-01

We study a model for two competing species that explicitly accounts for effects due to discreteness, stochasticity and spatial extension of populations. The two species are equally preferred by the environment and do better when surrounded by others of the same species. We observe that the final outcome depends on the initial densities (uniformly distributed in space) of the two species. The observed phase transition is a continuous one and key macroscopic quantities like the correlation length of clusters and the time-to-extinction diverge at a critical point. Away from the critical point, the dynamics can be described by a mean-field approximation. Close to the critical point, however, there is a crossover to power-law behavior because of the gross mismatch between the largest and smallest scales in the system. We have developed a theory based on surface effects, which is in good agreement with the observed behavior. The course-grained reaction-diffusion system obtained from the mean-field dynamics agrees well with the particle system.

Structural and electronic transformation in low-angle twisted bilayer graphene

NASA Astrophysics Data System (ADS)

Gargiulo, Fernando; Yazyev, Oleg V.

2018-01-01

Experiments on bilayer graphene unveiled a fascinating realization of stacking disorder where triangular domains with well-defined Bernal stacking are delimited by a hexagonal network of strain solitons. Here we show by means of numerical simulations that this is a consequence of a structural transformation of the moiré pattern inherent to twisted bilayer graphene taking place at twist angles θ below a crossover angle θ\\star=1.2\\circ . The transformation is governed by the interplay between the interlayer van der Waals interaction and the in-plane strain field, and is revealed by a change in the functional form of the twist energy density. This transformation unveils an electronic regime characteristic of vanishing twist angles in which the charge density converges, though not uniformly, to that of ideal bilayer graphene with Bernal stacking. On the other hand, the stacking domain boundaries form a distinct charge density pattern that provides the STM signature of the hexagonal solitonic network.

Research reactor loading pattern optimization using estimation of distribution algorithms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, S.; Ziver, K.; AMCG Group, RM Consultants, Abingdon

2006-07-01

A new evolutionary search based approach for solving the nuclear reactor loading pattern optimization problems is presented based on the Estimation of Distribution Algorithms. The optimization technique developed is then applied to the maximization of the effective multiplication factor (K{sub eff}) of the Imperial College CONSORT research reactor (the last remaining civilian research reactor in the United Kingdom). A new elitism-guided searching strategy has been developed and applied to improve the local convergence together with some problem-dependent information based on the 'stand-alone K{sub eff} with fuel coupling calculations. A comparison study between the EDAs and a Genetic Algorithm with Heuristicmore » Tie Breaking Crossover operator has shown that the new algorithm is efficient and robust. (authors)« less

Combined Simulated Annealing and Genetic Algorithm Approach to Bus Network Design

NASA Astrophysics Data System (ADS)

Liu, Li; Olszewski, Piotr; Goh, Pong-Chai

A new method - combined simulated annealing (SA) and genetic algorithm (GA) approach is proposed to solve the problem of bus route design and frequency setting for a given road network with fixed bus stop locations and fixed travel demand. The method involves two steps: a set of candidate routes is generated first and then the best subset of these routes is selected by the combined SA and GA procedure. SA is the main process to search for a better solution to minimize the total system cost, comprising user and operator costs. GA is used as a sub-process to generate new solutions. Bus demand assignment on two alternative paths is performed at the solution evaluation stage. The method was implemented on four theoretical grid networks of different size and a benchmark network. Several GA operators (crossover and mutation) were utilized and tested for their effectiveness. The results show that the proposed method can efficiently converge to the optimal solution on a small network but computation time increases significantly with network size. The method can also be used for other transport operation management problems.

Biased random key genetic algorithm with insertion and gender selection for capacitated vehicle routing problem with time windows

NASA Astrophysics Data System (ADS)

Rochman, Auliya Noor; Prasetyo, Hari; Nugroho, Munajat Tri

2017-06-01

Vehicle Routing Problem (VRP) often occurs when the manufacturers need to distribute their product to some customers/outlets. The distribution process is typically restricted by the capacity of the vehicle and the working hours at the distributor. This type of VRP is also known as Capacitated Vehicle Routing Problem with Time Windows (CVRPTW). A Biased Random Key Genetic Algorithm (BRKGA) was designed and coded in MATLAB to solve the CVRPTW case of soft drink distribution. The standard BRKGA was then modified by applying chromosome insertion into the initial population and defining chromosome gender for parent undergoing crossover operation. The performance of the established algorithms was then compared to a heuristic procedure for solving a soft drink distribution. Some findings are revealed (1) the total distribution cost of BRKGA with insertion (BRKGA-I) results in a cost saving of 39% compared to the total cost of heuristic method, (2) BRKGA with the gender selection (BRKGA-GS) could further improve the performance of the heuristic method. However, the BRKGA-GS tends to yield worse results compared to that obtained from the standard BRKGA.

Online Learning of Genetic Network Programming and its Application to Prisoner’s Dilemma Game

NASA Astrophysics Data System (ADS)

Mabu, Shingo; Hirasawa, Kotaro; Hu, Jinglu; Murata, Junichi

A new evolutionary model with the network structure named Genetic Network Programming (GNP) has been proposed recently. GNP, that is, an expansion of GA and GP, represents solutions as a network structure and evolves it by using “offline learning (selection, mutation, crossover)”. GNP can memorize the past action sequences in the network flow, so it can deal with Partially Observable Markov Decision Process (POMDP) well. In this paper, in order to improve the ability of GNP, Q learning (an off-policy TD control algorithm) that is one of the famous online methods is introduced for online learning of GNP. Q learning is suitable for GNP because (1) in reinforcement learning, the rewards an agent will get in the future can be estimated, (2) TD control doesn’t need much memory and can learn quickly, and (3) off-policy is suitable in order to search for an optimal solution independently of the policy. Finally, in the simulations, online learning of GNP is applied to a player for “Prisoner’s dilemma game” and its ability for online adaptation is confirmed.

A genetically optimized kinetic model for ethanol electro-oxidation on Pt-based binary catalysts used in direct ethanol fuel cells

NASA Astrophysics Data System (ADS)

Sánchez-Monreal, Juan; García-Salaberri, Pablo A.; Vera, Marcos

2017-09-01

A one-dimensional model is proposed for the anode of a liquid-feed direct ethanol fuel cell. The complex kinetics of the ethanol electro-oxidation reaction is described using a multi-step reaction mechanism that considers free and adsorbed intermediate species on Pt-based binary catalysts. The adsorbed species are modeled using coverage factors to account for the blockage of the active reaction sites on the catalyst surface. The reaction rates are described by Butler-Volmer equations that are coupled to a one-dimensional mass transport model, which incorporates the effect of ethanol and acetaldehyde crossover. The proposed kinetic model circumvents the acetaldehyde bottleneck effect observed in previous studies by incorporating CH3CHOHads among the adsorbed intermediates. A multi-objetive genetic algorithm is used to determine the reaction constants using anode polarization and product selectivity data obtained from the literature. By adjusting the reaction constants using the methodology developed here, different catalyst layers could be modeled and their selectivities could be successfully reproduced.

An incremental approach to genetic-algorithms-based classification.

PubMed

Guan, Sheng-Uei; Zhu, Fangming

2005-04-01

Incremental learning has been widely addressed in the machine learning literature to cope with learning tasks where the learning environment is ever changing or training samples become available over time. However, most research work explores incremental learning with statistical algorithms or neural networks, rather than evolutionary algorithms. The work in this paper employs genetic algorithms (GAs) as basic learning algorithms for incremental learning within one or more classifier agents in a multiagent environment. Four new approaches with different initialization schemes are proposed. They keep the old solutions and use an "integration" operation to integrate them with new elements to accommodate new attributes, while biased mutation and crossover operations are adopted to further evolve a reinforced solution. The simulation results on benchmark classification data sets show that the proposed approaches can deal with the arrival of new input attributes and integrate them with the original input space. It is also shown that the proposed approaches can be successfully used for incremental learning and improve classification rates as compared to the retraining GA. Possible applications for continuous incremental training and feature selection are also discussed.

Meiosis.

PubMed

Hillers, Kenneth J; Jantsch, Verena; Martinez-Perez, Enrique; Yanowitz, Judith L

2017-05-04

Sexual reproduction requires the production of haploid gametes (sperm and egg) with only one copy of each chromosome; fertilization then restores the diploid chromosome content in the next generation. This reduction in genetic content is accomplished during a specialized cell division called meiosis, in which two rounds of chromosome segregation follow a single round of DNA replication. In preparation for the first meiotic division, homologous chromosomes pair and synapse, creating a context that promotes formation of crossover recombination events. These crossovers, in conjunction with sister chromatid cohesion, serve to connect the two homologs and facilitate their segregation to opposite poles during the first meiotic division. During the second meiotic division, which is similar to mitosis, sister chromatids separate; the resultant products are haploid cells that become gametes. In Caenorhabditis elegans (and most other eukaryotes) homologous pairing and recombination are required for proper chromosome inheritance during meiosis; accordingly, the events of meiosis are tightly coordinated to ensure the proper execution of these events. In this chapter, we review the seminal events of meiosis: pairing of homologous chromosomes, the changes in chromosome structure that chromosomes undergo during meiosis, the events of meiotic recombination, the differentiation of homologous chromosome pairs into structures optimized for proper chromosome segregation at Meiosis I, and the ultimate segregation of chromosomes during the meiotic divisions. We also review the regulatory processes that ensure the coordinated execution of these meiotic events during prophase I.

High Resolution Analysis of Meiotic Chromosome Structure and Behaviour in Barley (Hordeum vulgare L.)

PubMed Central

Phillips, Dylan; Nibau, Candida; Wnetrzak, Joanna; Jenkins, Glyn

2012-01-01

Reciprocal crossing over and independent assortment of chromosomes during meiosis generate most of the genetic variation in sexually reproducing organisms. In barley, crossovers are confined primarily to distal regions of the chromosomes, which means that a substantial proportion of the genes of this crop rarely, if ever, engage in recombination events. There is potentially much to be gained by redistributing crossovers to more proximal regions, but our ability to achieve this is dependent upon a far better understanding of meiosis in this species. This study explores the meiotic process by describing with unprecedented resolution the early behaviour of chromosomal domains, the progression of synapsis and the structure of the synaptonemal complex (SC). Using a combination of molecular cytogenetics and advanced fluorescence imaging, we show for the first time in this species that non-homologous centromeres are coupled prior to synapsis. We demonstrate that at early meiotic prophase the loading of the SC-associated structural protein ASY1, the cluster of telomeres, and distal synaptic initiation sites occupy the same polarised region of the nucleus. Through the use of advanced 3D image analysis, we show that synapsis is driven predominantly from the telomeres, and that new synaptic initiation sites arise during zygotene. In addition, we identified two different SC configurations through the use of super-resolution 3D structured illumination microscopy (3D-SIM). PMID:22761818

Parallel targeted next generation sequencing of childhood and adult acute myeloid leukemia patients reveals uniform genomic profile of the disease.

PubMed

Marjanovic, Irena; Kostic, Jelena; Stanic, Bojana; Pejanovic, Nadja; Lucic, Bojana; Karan-Djurasevic, Teodora; Janic, Dragana; Dokmanovic, Lidija; Jankovic, Srdja; Vukovic, Nada Suvajdzic; Tomin, Dragica; Perisic, Ognjen; Rakocevic, Goran; Popovic, Milos; Pavlovic, Sonja; Tosic, Natasa

2016-10-01

The age-specific differences in the genetic mechanisms of myeloid leukemogenesis have been observed and studied previously. However, NGS technology has provided a possibility to obtain a large amount of mutation data. We analyzed DNA samples from 20 childhood (cAML) and 20 adult AML (aAML) patients, using NGS targeted sequencing. The average coverage of high-quality sequences was 2981 × per amplicon. A total of 412 (207 cAML, 205 aAML) variants in the coding regions were detected; out of which, only 122 (62 cAML and 60 aAML) were potentially protein-changing. Our results confirmed that AML contains small number of genetic alterations (median 3 mutations/patient in both groups). The prevalence of the most frequent single gene AML associated mutations differed in cAML and aAML patient cohorts: IDH1 (0 % cAML, 5 % aAML), IDH2 (0 % cAML, 10 % aAML), NPM1 (10 % cAML, 35 % aAML). Additionally, potentially protein-changing variants were found in tyrosine kinase genes or genes encoding tyrosine kinase associated proteins (JAK3, ABL1, GNAQ, and EGFR) in cAML, while among aAML, the prevalence is directed towards variants in the methylation and histone modifying genes (IDH1, IDH2, and SMARCB1). Besides uniform genomic profile of AML, specific genetic characteristic was exclusively detected in cAML and aAML.

Dental implant customization using numerical optimization design and 3-dimensional printing fabrication of zirconia ceramic.

PubMed

Cheng, Yung-Chang; Lin, Deng-Huei; Jiang, Cho-Pei; Lin, Yuan-Min

2017-05-01

This study proposes a new methodology for dental implant customization consisting of numerical geometric optimization and 3-dimensional printing fabrication of zirconia ceramic. In the numerical modeling, exogenous factors for implant shape include the thread pitch, thread depth, maximal diameter of implant neck, and body size. Endogenous factors are bone density, cortical bone thickness, and non-osseointegration. An integration procedure, including uniform design method, Kriging interpolation and genetic algorithm, is applied to optimize the geometry of dental implants. The threshold of minimal micromotion for optimization evaluation was 100 μm. The optimized model is imported to the 3-dimensional slurry printer to fabricate the zirconia green body (powder is bonded by polymer weakly) of the implant. The sintered implant is obtained using a 2-stage sintering process. Twelve models are constructed according to uniform design method and simulated the micromotion behavior using finite element modeling. The result of uniform design models yields a set of exogenous factors that can provide the minimal micromotion (30.61 μm), as a suitable model. Kriging interpolation and genetic algorithm modified the exogenous factor of the suitable model, resulting in 27.11 μm as an optimization model. Experimental results show that the 3-dimensional slurry printer successfully fabricated the green body of the optimization model, but the accuracy of sintered part still needs to be improved. In addition, the scanning electron microscopy morphology is a stabilized t-phase microstructure, and the average compressive strength of the sintered part is 632.1 MPa. Copyright © 2016 John Wiley & Sons, Ltd.

Expected Number of Fixed Points in Boolean Networks with Arbitrary Topology.

PubMed

Mori, Fumito; Mochizuki, Atsushi

2017-07-14

Boolean network models describe genetic, neural, and social dynamics in complex networks, where the dynamics depend generally on network topology. Fixed points in a genetic regulatory network are typically considered to correspond to cell types in an organism. We prove that the expected number of fixed points in a Boolean network, with Boolean functions drawn from probability distributions that are not required to be uniform or identical, is one, and is independent of network topology if only a feedback arc set satisfies a stochastic neutrality condition. We also demonstrate that the expected number is increased by the predominance of positive feedback in a cycle.

The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podsiadlowski, L.; Carapelli, A.; Nardi, F.

2005-12-01

Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions.

Adoptive therapy with chimeric antigen receptor-modified T cells of defined subset composition.

PubMed

Riddell, Stanley R; Sommermeyer, Daniel; Berger, Carolina; Liu, Lingfeng Steven; Balakrishnan, Ashwini; Salter, Alex; Hudecek, Michael; Maloney, David G; Turtle, Cameron J

2014-01-01

The ability to engineer T cells to recognize tumor cells through genetic modification with a synthetic chimeric antigen receptor has ushered in a new era in cancer immunotherapy. The most advanced clinical applications are in targeting CD19 on B-cell malignancies. The clinical trials of CD19 chimeric antigen receptor therapy have thus far not attempted to select defined subsets before transduction or imposed uniformity of the CD4 and CD8 cell composition of the cell products. This review will discuss the rationale for and challenges to using adoptive therapy with genetically modified T cells of defined subset and phenotypic composition.

Spiromax, a New Dry Powder Inhaler: Dose Consistency under Simulated Real-World Conditions

PubMed Central

Canonica, Giorgio Walter; Arp, Jan; Keegstra, Johan René

2015-01-01

Abstract Background: Spiromax® is a novel dry powder inhaler for patients with asthma or chronic obstructive pulmonary disease (COPD). The studies presented here provide further data on attributes (in vitro dosing consistency with budesonide–formoterol (DuoResp) Spiromax; flow rates through empty versions of the Spiromax and Turbuhaler inhaler) of importance to patients with asthma or COPD. Methods: Dose-delivery studies were performed using low-, middle-, and high-strength DuoResp Spiromax. Dose consistency was assessed over inhaler life. Total emitted doses (TEDs) were measured at various flow rates, after exposure to high and low temperature or humidity, at different inhaler orientations, and after dropping the inhaler. The criterion for evaluating dose uniformity was whether mean TEDs were within the product specification limits. In separate studies, flow rates were measured after training, using the patient information leaflets, and again after enhanced training as part of a randomized, open-label, cross-over study. Results: Mean values for both budesonide and formoterol were within 85%–115% of the label claim for each strength of DuoResp Spiromax for initial dose uniformity and for the other investigated conditions (temperature, humidity, orientation, dropping, knocking), with the exception of approximately an 80% increase in first dose after dropping the inhaler (subsequent doses not affected). In the flow rate patient study, two patients' inhalations with Spiromax and six with Turbuhaler were <30 L/min. The majority of asthma patients [91% (Spiromax) versus 82% (Turbuhaler)] achieved the preferred flow rate of >60 L/min. Conclusions: DuoResp Spiromax consistently meets dose uniformity criteria, under controlled laboratory conditions and with variations intended to mimic real-world use. Following enhanced training, all patients in the flow study were able to achieve the minimal inspiratory flow rate of >30 L/min, which is required for effective treatment. PMID:26352860

Lattice and compact family block designs in forest genetics

Treesearch

E. Bayne Snyder

1966-01-01

One of the principles of experimental design is that replicates be relatively homogeneous. Thus, in forest research a replicate is often assigned to a single crew for planting in a single day on a uniform site. When treatments are numerous, a large area is required per replication, and homogeneity of site is difficult to achieve. In this situation, crop scientists (...

Genetic variation and seed transfer guidelines for lodgepole pine in central Oregon.

Treesearch

Frank C. Sorensen

1992-01-01

Cones were collected from 272 trees at 189 locations uniformly distributed over the east slopes of the Oregon Cascade Range and Warner Mountains. Variation in seed and seedling traits was related to (1) seed source latitude, distance from the Cascade crest, elevation, slope, and aspect in multiple regression analyses; and (2) seed zone and elevation band in...

A novel hybrid algorithm for the design of the phase diffractive optical elements for beam shaping

NASA Astrophysics Data System (ADS)

Jiang, Wenbo; Wang, Jun; Dong, Xiucheng

2013-02-01

In this paper, a novel hybrid algorithm for the design of a phase diffractive optical elements (PDOE) is proposed. It combines the genetic algorithm (GA) with the transformable scale BFGS (Broyden, Fletcher, Goldfarb, Shanno) algorithm, the penalty function was used in the cost function definition. The novel hybrid algorithm has the global merits of the genetic algorithm as well as the local improvement capabilities of the transformable scale BFGS algorithm. We designed the PDOE using the conventional simulated annealing algorithm and the novel hybrid algorithm. To compare the performance of two algorithms, three indexes of the diffractive efficiency, uniformity error and the signal-to-noise ratio are considered in numerical simulation. The results show that the novel hybrid algorithm has good convergence property and good stability. As an application example, the PDOE was used for the Gaussian beam shaping; high diffractive efficiency, low uniformity error and high signal-to-noise were obtained. The PDOE can be used for high quality beam shaping such as inertial confinement fusion (ICF), excimer laser lithography, fiber coupling laser diode array, laser welding, etc. It shows wide application value.

Spin state switching in iron coordination compounds

PubMed Central

Gaspar, Ana B; Garcia, Yann

2013-01-01

Summary The article deals with coordination compounds of iron(II) that may exhibit thermally induced spin transition, known as spin crossover, depending on the nature of the coordinating ligand sphere. Spin transition in such compounds also occurs under pressure and irradiation with light. The spin states involved have different magnetic and optical properties suitable for their detection and characterization. Spin crossover compounds, though known for more than eight decades, have become most attractive in recent years and are extensively studied by chemists and physicists. The switching properties make such materials potential candidates for practical applications in thermal and pressure sensors as well as optical devices. The article begins with a brief description of the principle of molecular spin state switching using simple concepts of ligand field theory. Conditions to be fulfilled in order to observe spin crossover will be explained and general remarks regarding the chemical nature that is important for the occurrence of spin crossover will be made. A subsequent section describes the molecular consequences of spin crossover and the variety of physical techniques usually applied for their characterization. The effects of light irradiation (LIESST) and application of pressure are subjects of two separate sections. The major part of this account concentrates on selected spin crossover compounds of iron(II), with particular emphasis on the chemical and physical influences on the spin crossover behavior. The vast variety of compounds exhibiting this fascinating switching phenomenon encompasses mono-, oligo- and polynuclear iron(II) complexes and cages, polymeric 1D, 2D and 3D systems, nanomaterials, and polyfunctional materials that combine spin crossover with another physical or chemical property. PMID:23504535

Common Genetic Variant Risk Score Is Associated With Drug-Induced QT Prolongation and Torsade de Pointes Risk: A Pilot Study.

PubMed

Strauss, David G; Vicente, Jose; Johannesen, Lars; Blinova, Ksenia; Mason, Jay W; Weeke, Peter; Behr, Elijah R; Roden, Dan M; Woosley, Ray; Kosova, Gulum; Rosenberg, Michael A; Newton-Cheh, Christopher

2017-04-04

Drug-induced QT interval prolongation, a risk factor for life-threatening ventricular arrhythmias, is a potential side effect of many marketed and withdrawn medications. The contribution of common genetic variants previously associated with baseline QT interval to drug-induced QT prolongation and arrhythmias is not known. We tested the hypothesis that a weighted combination of common genetic variants contributing to QT interval at baseline, identified through genome-wide association studies, can predict individual response to multiple QT-prolonging drugs. Genetic analysis of 22 subjects was performed in a secondary analysis of a randomized, double-blind, placebo-controlled, crossover trial of 3 QT-prolonging drugs with 15 time-matched QT and plasma drug concentration measurements. Subjects received single doses of dofetilide, quinidine, ranolazine, and placebo. The outcome was the correlation between a genetic QT score comprising 61 common genetic variants and the slope of an individual subject's drug-induced increase in heart rate-corrected QT (QTc) versus drug concentration. The genetic QT score was correlated with drug-induced QTc prolongation. Among white subjects, genetic QT score explained 30% of the variability in response to dofetilide ( r =0.55; 95% confidence interval, 0.09-0.81; P =0.02), 23% in response to quinidine ( r =0.48; 95% confidence interval, -0.03 to 0.79; P =0.06), and 27% in response to ranolazine ( r =0.52; 95% confidence interval, 0.05-0.80; P =0.03). Furthermore, the genetic QT score was a significant predictor of drug-induced torsade de pointes in an independent sample of 216 cases compared with 771 controls ( r 2 =12%, P =1×10 -7 ). We demonstrate that a genetic QT score comprising 61 common genetic variants explains a significant proportion of the variability in drug-induced QT prolongation and is a significant predictor of drug-induced torsade de pointes. These findings highlight an opportunity for recent genetic discoveries to improve individualized risk-benefit assessment for pharmacological therapies. Replication of these findings in larger samples is needed to more precisely estimate variance explained and to establish the individual variants that drive these effects. URL: http://www.clinicaltrials.gov. Unique identifier: NCT01873950. © 2017 American Heart Association, Inc.

Two measures of bilingualism in the memories of immigrants and indigenous minorities: crossover memories and codeswitching.

PubMed

Altman, Carmit

2015-04-01

Two indices of bilingualism, crossover memories and codeswitching (CS), were explored in five groups of immigrant (English-Hebrew, Georgian-Hebrew Russian-Hebrew) and indigenous bilinguals (Arabic-Hebrew, Hebrew-English). Participants recalled memories in response to cue words and then were asked to report the language of retrieval and provide a more elaborate narrative. More memories were 'same language' memories, recalled in the language of the experimental session/cue word, but as many as 48 % of the memories were crossovers, i.e. memories reported in a language other than the language of the session/cue word. In an effort to examine the ecological validity of the self-reported language of the memories, the frequency of CS in the elaborated narratives was investigated. For the entire sample, more CS was found for self-reported crossover memories in L2 sessions. In a further analysis of CS in crossover memories, collapsed across L1 and L2 sessions, significant differences emerged between immigrants and indigenous bilinguals. Differences between immigrant and non-immigrant bilinguals are discussed in terms of the role of activation in crossover memories.

Interference-mediated synaptonemal complex formation with embedded crossover designation

PubMed Central

Zhang, Liangran; Espagne, Eric; de Muyt, Arnaud; Zickler, Denise; Kleckner, Nancy E.

2014-01-01

Biological systems exhibit complex patterns at length scales ranging from the molecular to the organismic. Along chromosomes, events often occur stochastically at different positions in different nuclei but nonetheless tend to be relatively evenly spaced. Examples include replication origin firings, formation of chromatin loops along chromosome axes and, during meiosis, localization of crossover recombination sites (“crossover interference”). We present evidence in the fungus Sordaria macrospora that crossover interference is part of a broader pattern that includes synaptonemal complex (SC) nucleation. This pattern comprises relatively evenly spaced SC nucleation sites, among which a subset are crossover sites that show a classical interference distribution. This pattern ensures that SC forms regularly along the entire length of the chromosome as required for the maintenance of homolog pairing while concomitantly having crossover interactions locally embedded within the SC structure as required for both DNA recombination and structural events of chiasma formation. This pattern can be explained by a threshold-based designation and spreading interference process. This model can be generalized to give diverse types of related and/or partially overlapping patterns, in two or more dimensions, for any type of object. PMID:25380597

Source Identification of Human Biological Materials and Its Prospect in Forensic Science.

PubMed

Zou, K N; Gui, C; Gao, Y; Yang, F; Zhou, H G

2016-06-01

Source identification of human biological materials in crime scene plays an important role in reconstructing the crime process. Searching specific genetic markers to identify the source of different human biological materials is the emphasis and difficulty of the research work of legal medical experts in recent years. This paper reviews the genetic markers which are used for identifying the source of human biological materials and studied widely, such as DNA methylation, mRNA, microRNA, microflora and protein, etc. By comparing the principles and methods of source identification of human biological materials using different kinds of genetic markers, different source of human biological material owns suitable marker types and can be identified by detecting single genetic marker or combined multiple genetic markers. Though there is no uniform standard and method for identifying the source of human biological materials in forensic laboratories at present, the research and development of a series of mature and reliable methods for distinguishing different human biological materials play the role as forensic evidence which will be the future development direction. Copyright© by the Editorial Department of Journal of Forensic Medicine.

Energy expenditure in people with transtibial amputation walking with crossover and energy storing prosthetic feet: A randomized within-subject study.

PubMed

McDonald, Cody L; Kramer, Patricia A; Morgan, Sara J; Halsne, Elizabeth G; Cheever, Sarah M; Hafner, Brian J

2018-05-01

Energy storing feet are unable to reduce the energy required for normal locomotion among people with transtibial amputation. Crossover feet, which incorporate aspects of energy storing and running specific feet, are designed to maximize energy return while providing stability for everyday activities. Do crossover prosthetic feet reduce the energy expenditure of walking across a range of speeds, when compared with energy storing feet among people with transtibial amputation due to non-dysvascular causes? A randomized within-subject study was conducted with a volunteer sample of twenty-seven adults with unilateral transtibial amputation due to non-dysvascular causes. Participants were fit with two prostheses. One had an energy storing foot (Össur Variflex) and the other a crossover foot (Össur Cheetah Xplore). Other components, including sockets, suspension, and interface were standardized. Energy expenditure was measured with a portable respirometer (Cosmed K4b2) while participants walked on a treadmill at self-selected slow, comfortable, and fast speeds with each prosthesis. Gross oxygen consumption rates (VO 2  ml/min) were compared between foot conditions. Energy storing feet were used as the baseline condition because they are used by most people with a lower limb prosthesis. Analyses were performed to identify people who may benefit from transition to crossover feet. On average, participants had lower oxygen consumption in the crossover foot condition compared to the energy storing foot condition at each self-selected walking speed, but this difference was not statistically significant. Participants with farther six-minute walk test distances, higher daily step counts, and higher Medicare Functional Classification Levels at baseline were more likely to use less energy in the crossover foot. Crossover feet may be most beneficial for people with higher activity levels and physical fitness. Further research is needed to examine the effect of crossover feet on energy expenditure during high-level activities. Copyright © 2018 Elsevier B.V. All rights reserved.

Diversity and uniformity in genetic responsibility: moral attitudes of patients, relatives and lay people in Germany and Israel.

PubMed

Raz, Aviad E; Schicktanz, Silke

2009-11-01

The professional and institutional responsibility for handling genetic knowledge is well discussed; less attention has been paid to how lay people and particularly people who are affected by genetic diseases perceive and frame such responsibilities. In this exploratory study we qualitatively examine the attitudes of lay people, patients and relatives of patients in Germany and Israel towards genetic testing. These attitudes are further examined in the national context of Germany and Israel, which represent opposite regulatory approaches and bioethical debates concerning genetic testing. Three major themes of responsibility emerged from the inter-group and cross-cultural comparison: self-responsibility, responsibility for kin, and responsibility of society towards its members. National contrast was apparent in the moral reasoning of lay respondents concerning, for example, the right not to know versus the duty to know (self-responsibility) and the moral conflict concerning informing kin versus the moral duty to inform (responsibility for kin). Attitudes of respondents affected by genetic diseases were, however, rather similar in both countries. We conclude by discussing how moral discourses of responsibility are embedded within cultural (national, religious) as well as phenomenological (being affected) narratives, and the role of public engagement in bioethical discourse.

Optimal sensor placement for spatial lattice structure based on genetic algorithms

NASA Astrophysics Data System (ADS)

Liu, Wei; Gao, Wei-cheng; Sun, Yi; Xu, Min-jian

2008-10-01

Optimal sensor placement technique plays a key role in structural health monitoring of spatial lattice structures. This paper considers the problem of locating sensors on a spatial lattice structure with the aim of maximizing the data information so that structural dynamic behavior can be fully characterized. Based on the criterion of optimal sensor placement for modal test, an improved genetic algorithm is introduced to find the optimal placement of sensors. The modal strain energy (MSE) and the modal assurance criterion (MAC) have been taken as the fitness function, respectively, so that three placement designs were produced. The decimal two-dimension array coding method instead of binary coding method is proposed to code the solution. Forced mutation operator is introduced when the identical genes appear via the crossover procedure. A computational simulation of a 12-bay plain truss model has been implemented to demonstrate the feasibility of the three optimal algorithms above. The obtained optimal sensor placements using the improved genetic algorithm are compared with those gained by exiting genetic algorithm using the binary coding method. Further the comparison criterion based on the mean square error between the finite element method (FEM) mode shapes and the Guyan expansion mode shapes identified by data-driven stochastic subspace identification (SSI-DATA) method are employed to demonstrate the advantage of the different fitness function. The results showed that some innovations in genetic algorithm proposed in this paper can enlarge the genes storage and improve the convergence of the algorithm. More importantly, the three optimal sensor placement methods can all provide the reliable results and identify the vibration characteristics of the 12-bay plain truss model accurately.

Pressure and Temperature Sensors Using Two Spin Crossover Materials.

PubMed

Jureschi, Catalin-Maricel; Linares, Jorge; Boulmaali, Ayoub; Dahoo, Pierre Richard; Rotaru, Aurelian; Garcia, Yann

2016-02-02

The possibility of a new design concept for dual spin crossover based sensors for concomitant detection of both temperature and pressure is presented. It is conjectured from numerical results obtained by mean field approximation applied to a Ising-like model that using two different spin crossover compounds containing switching molecules with weak elastic interactions it is possible to simultaneously measure P and T. When the interaction parameters are optimized, the spin transition is gradual and for each spin crossover compounds, both temperature and pressure values being identified from their optical densities. This concept offers great perspectives for smart sensing devices.

A powerful and robust test in genetic association studies.

PubMed

Cheng, Kuang-Fu; Lee, Jen-Yu

2014-01-01

There are several well-known single SNP tests presented in the literature for detecting gene-disease association signals. Having in place an efficient and robust testing process across all genetic models would allow a more comprehensive approach to analysis. Although some studies have shown that it is possible to construct such a test when the variants are common and the genetic model satisfies certain conditions, the model conditions are too restrictive and in general difficult to verify. In this paper, we propose a powerful and robust test without assuming any model restrictions. Our test is based on the selected 2 × 2 tables derived from the usual 2 × 3 table. By signals from these tables, we show through simulations across a wide range of allele frequencies and genetic models that this approach may produce a test which is almost uniformly most powerful in the analysis of low- and high-frequency variants. Two cancer studies are used to demonstrate applications of the proposed test. © 2014 S. Karger AG, Basel.

Application of genetic algorithms to focal mechanism determination

NASA Astrophysics Data System (ADS)

Kobayashi, Reiji; Nakanishi, Ichiro

1994-04-01

Genetic algorithms are a new class of methods for global optimization. They resemble Monte Carlo techniques, but search for solutions more efficiently than uniform Monte Carlo sampling. In the field of geophysics, genetic algorithms have recently been used to solve some non-linear inverse problems (e.g., earthquake location, waveform inversion, migration velocity estimation). We present an application of genetic algorithms to focal mechanism determination from first-motion polarities of P-waves and apply our method to two recent large events, the Kushiro-oki earthquake of January 15, 1993 and the SW Hokkaido (Japan Sea) earthquake of July 12, 1993. Initial solution and curvature information of the objective function that gradient methods need are not required in our approach. Moreover globally optimal solutions can be efficiently obtained. Calculation of polarities based on double-couple models is the most time-consuming part of the source mechanism determination. The amount of calculations required by the method designed in this study is much less than that of previous grid search methods.

Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice.

PubMed

de Boer, Esther; Jasin, Maria; Keeney, Scott

2015-08-15

Meiotic recombination initiated by programmed double-strand breaks (DSBs) yields two types of interhomolog recombination products, crossovers and noncrossovers, but what determines whether a DSB will yield a crossover or noncrossover is not understood. In this study, we analyzed the influence of sex and chromosomal location on mammalian recombination outcomes by constructing fine-scale recombination maps in both males and females at two mouse hot spots located in different regions of the same chromosome. These include the most comprehensive maps of recombination hot spots in oocytes to date. One hot spot, located centrally on chromosome 1, behaved similarly in male and female meiosis: Crossovers and noncrossovers formed at comparable levels and ratios in both sexes. In contrast, at a distal hot spot, crossovers were recovered only in males even though noncrossovers were obtained at similar frequencies in both sexes. These findings reveal an example of extreme sex-specific bias in recombination outcome. We further found that estimates of relative DSB levels are surprisingly poor predictors of relative crossover frequencies between hot spots in males. Our results demonstrate that the outcome of mammalian meiotic recombination can be biased, that this bias can vary depending on location and cellular context, and that DSB frequency is not the only determinant of crossover frequency. © 2015 de Boer et al.; Published by Cold Spring Harbor Laboratory Press.

Spillover and Crossover of Exhaustion and Life Satisfaction among Dual-Earner Parents

ERIC Educational Resources Information Center

Demerouti, Evangelia; Bakker, Arnold B.; Schaufeli, Wilmar B.

2005-01-01

This study integrates spillover research of stress transferring from work to home and crossover research of strains transferring from one spouse to another. A spillover and crossover model was tested among 191 (couples of) dual-earner parents. For both males and females, it was hypothesized that (self-reported and partners' rating of)…

Detection of crossover time scales in multifractal detrended fluctuation analysis

NASA Astrophysics Data System (ADS)

Ge, Erjia; Leung, Yee

2013-04-01

Fractal is employed in this paper as a scale-based method for the identification of the scaling behavior of time series. Many spatial and temporal processes exhibiting complex multi(mono)-scaling behaviors are fractals. One of the important concepts in fractals is crossover time scale(s) that separates distinct regimes having different fractal scaling behaviors. A common method is multifractal detrended fluctuation analysis (MF-DFA). The detection of crossover time scale(s) is, however, relatively subjective since it has been made without rigorous statistical procedures and has generally been determined by eye balling or subjective observation. Crossover time scales such determined may be spurious and problematic. It may not reflect the genuine underlying scaling behavior of a time series. The purpose of this paper is to propose a statistical procedure to model complex fractal scaling behaviors and reliably identify the crossover time scales under MF-DFA. The scaling-identification regression model, grounded on a solid statistical foundation, is first proposed to describe multi-scaling behaviors of fractals. Through the regression analysis and statistical inference, we can (1) identify the crossover time scales that cannot be detected by eye-balling observation, (2) determine the number and locations of the genuine crossover time scales, (3) give confidence intervals for the crossover time scales, and (4) establish the statistically significant regression model depicting the underlying scaling behavior of a time series. To substantive our argument, the regression model is applied to analyze the multi-scaling behaviors of avian-influenza outbreaks, water consumption, daily mean temperature, and rainfall of Hong Kong. Through the proposed model, we can have a deeper understanding of fractals in general and a statistical approach to identify multi-scaling behavior under MF-DFA in particular.

Protocol for production of a genetic cross of the rodent malaria parasites.

PubMed

Pattaradilokrat, Sittiporn; Li, Jian; Su, Xin-zhuan

2011-01-03

Variation in response to antimalarial drugs and in pathogenicity of malaria parasites is of biologic and medical importance. Linkage mapping has led to successful identification of genes or loci underlying various traits in malaria parasites of rodents and humans. The malaria parasite Plasmodium yoelii is one of many malaria species isolated from wild African rodents and has been adapted to grow in laboratories. This species reproduces many of the biologic characteristics of the human malaria parasites; genetic markers such as microsatellite and amplified fragment length polymorphism (AFLP) markers have also been developed for the parasite. Thus, genetic studies in rodent malaria parasites can be performed to complement research on Plasmodium falciparum. Here, we demonstrate the techniques for producing a genetic cross in P. yoelii that were first pioneered by Drs. David Walliker, Richard Carter, and colleagues at the University of Edinburgh. Genetic crosses in P. yoelii and other rodent malaria parasites are conducted by infecting mice Mus musculus with an inoculum containing gametocytes of two genetically distinct clones that differ in phenotypes of interest and by allowing mosquitoes to feed on the infected mice 4 days after infection. The presence of male and female gametocytes in the mouse blood is microscopically confirmed before feeding. Within 48 hrs after feeding, in the midgut of the mosquito, the haploid gametocytes differentiate into male and female gametes, fertilize, and form a diploid zygote (Fig. 1). During development of a zygote into an ookinete, meiosis appears to occur. If the zygote is derived through cross-fertilization between gametes of the two genetically distinct parasites, genetic exchanges (chromosomal reassortment and cross-overs between the non-sister chromatids of a pair of homologous chromosomes; Fig. 2) may occur, resulting in recombination of genetic material at homologous loci. Each zygote undergoes two successive nuclear divisions, leading to four haploid nuclei. An ookinete further develops into an oocyst. Once the oocyst matures, thousands of sporozoites (the progeny of the cross) are formed and released into mosquito hemoceal. Sporozoites are harvested from the salivary glands and injected into a new murine host, where pre-erythrocytic and erythrocytic stage development takes place. Erythrocytic forms are cloned and classified with regard to the characters distinguishing the parental lines prior to genetic linkage mapping. Control infections of individual parental clones are performed in the same way as the production of a genetic cross.

What is in a cause? Exploring the relationship between genetic cause and felt stigma

PubMed Central

Sankar, Pamela; Cho, Mildred K.; Wolpe, Paul Root; Schairer, Cynthia

2008-01-01

Purpose Concern over stigma as a consequence of genetic testing has grown in response to the recent increase in genetic research and testing resulting from the Human Genome Project. However, whether a genetic or hereditary basis necessarily confers a stigma to a condition remains unexamined. Methods We performed a qualitative interview study with 86 individuals with one of four conditions: deafness or hearing loss, breast cancer, sickle cell disease, and cystic fibrosis. The first two groups were divided approximately between people who ascribed their conditions to a genetic or hereditary cause and those who did not. Results Respondents interpreted genetic or hereditary causes and nongenetic causes in a variety of ways. Subjects with breast cancer reported the most consistently negative interpretation of genetic cause. This response concerned future ill health, not an enduring sense of stigma. Deaf and hard of hearing subjects provided the most consistently positive comments about a genetic or hereditary basis to their condition, casting familial hearing loss as a vital component of group and individual identity. Respondents with sickle cell disease and cystic fibrosis offered similar and positive interpretations of the genetic cause of their condition insofar as it meant their conditions were not contagious. Conclusions Although some subjects report feeling stigmatized as a result of their condition, this stigmatization is not uniformly associated with the condition’s cause, genetic or otherwise. Instead, stigma emerges from a variety of sources in the context of the lived experience of a particular condition. PMID:16418597

Diffusion MRI and the Detection of Alterations Following Traumatic Brain Injury

DTIC Science & Technology

2017-06-13

Bioengineering, National Institutes of Health , Bethesda, Maryland 2Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National...Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 3Henry M. Jackson Foundation for the Advancement of...Military Medicine, Inc, Bethesda, Maryland 4Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda

Basic Course Deskbook, Volume 2: General Administrative Law

DTIC Science & Technology

2002-03-01

jurisdictions can result in a void marriage. 5. Impotence: usually must render the party physically incapable of normal sexual relations and must...ground for annulment in itself, but may constitute fraud if the party never intended to have sexual relations. IX. UNIFORMED SERVICES FORMER SPOUSES...must submit a sworn statement articulating reasonable facts supporting the existence or nonexistence of requisite sexual contact before genetic

Genetic effects on stand-level uniformity, and above- and belowground dry mass production in juvenile loblolly pine

Treesearch

Michael J. Aspinwall; John S. King; Steven E. McKeand; Bronson P. Bullock

2012-01-01

Several decades of tree improvement operations have drastically increased loblolly pine plantation productivity in the southern U.S. (McKeand et al., 2003). This work has lead to the availability of a number of highly productive open-pollinated and full-sib families (McKeand et al., 2006). In addition, vegetative propagation (somatic embryogenesis) has also made it...

Social Justice for Crossover Youth: The Intersection of the Child Welfare and Juvenile Justice Systems.

PubMed

Kolivoski, Karen M; Goodkind, Sara; Shook, Jeffrey J

2017-10-01

Social workers are critical to promoting racial and social justice. "Crossover youth," a term used to describe youths who have contact with both the child welfare and juvenile justice systems, are an especially vulnerable but often overlooked population with whom social workers engage. A disproportionate number of crossover youth are African American. Empirical research on crossover youth is growing, but such scholarship rarely engages with a human rights and social justice perspective. African American children and youths have a distinct place within the history and current context of the child welfare and juvenile justice systems. These systems have historically excluded them or treated them differently; now, African American youths are overrepresented in each of them, and evidence suggests they are more likely to cross over. The purpose of this article is to describe the historical and current context of crossover youth, with a particular focus on African American youths, to provide the foundation for a discussion of what social workers can do to promote racial and social justice for crossover youth, including specific implications for practice and policy, as well as broader implications for human and civil rights. © 2017 National Association of Social Workers.

Six different roles for crossover inhibition in the retina: correcting the nonlinearities of synaptic transmission.

PubMed

Werblin, Frank S

2010-03-01

Early retinal studies categorized ganglion cell behavior as either linear or nonlinear and rectifying as represented by the familiar X- and Y-type ganglion cells in cat. Nonlinear behavior is in large part a consequence of the rectifying nonlinearities inherent in synaptic transmission. These nonlinear signals underlie many special functions in retinal processing, including motion detection, motion in motion, and local edge detection. But linear behavior is also required for some visual processing tasks. For these tasks, the inherently nonlinear signals are "linearized" by "crossover inhibition." Linearization utilizes a circuitry whereby nonlinear ON inhibition adds with nonlinear OFF excitation or ON excitation adds with OFF inhibition to generate a more linear postsynaptic voltage response. Crossover inhibition has now been measured in most bipolar, amacrine, and ganglion cells. Functionally crossover inhibition enhances edge detection, allows ganglion cells to recognize luminance-neutral patterns with their receptive fields, permits ganglion cells to distinguish contrast from luminance, and maintains a more constant conductance during the light response. In some cases, crossover extends the operating range of cone-driven OFF ganglion cells into the scotopic levels. Crossover inhibition is also found in neurons of the lateral geniculate nucleus and V1.

Buckling and weight optimization for non-coupled antisymmetric laminates

NASA Astrophysics Data System (ADS)

Bhatnagar, Aditi

This research work describes the application of genetic algorithms to weight minimization and buckling load maximization of the non-coupled antisymmetric composite laminated plates. Previous studies of composite tailoring were limited to symmetric and balanced laminates. With the availability of many methodologies for composite tailoring, genetic algorithm is preferably used because of its ability to handle discrete design variable and attain multiple near optimum design solutions. A comparative study is made between optimum symmetric-balanced laminate designs and optimum non-coupled antisymmetric laminate designs, both of which are subjected to biaxial in-plane compressive loads. With the implementation of various genetic algorithm operators such as selection, crossover and mutation, critical buckling load factors are obtained for the optimum stacking sequence for both types of laminates. The mechanical properties for non-coupled antisymmetric laminates is independent of all types of coupling effects such as bending-twisting coupling, bending-extension coupling, and shear-extension coupling, thus giving the laminate a non-coupling behavior. This is in contrast to that of symmetric-balanced laminates where finite bending-twisting coupling terms are present. Optimized laminate layups satisfying the constraints of balance, buckling and adjoining were obtained for two types of graphite epoxy rectangular composite laminated plates. The current research augments the laminate thickness minimization designs with both odd and even number of layers, and the optimum buckling load maximization designs by the introduction of non-coupled antisymmetric laminates.

Interpretation of magnetic anomalies using a genetic algorithm

NASA Astrophysics Data System (ADS)

Kaftan, İlknur

2017-08-01

A genetic algorithm (GA) is an artificial intelligence method used for optimization. We applied a GA to the inversion of magnetic anomalies over a thick dike. Inversion of nonlinear geophysical problems using a GA has advantages because it does not require model gradients or well-defined initial model parameters. The evolution process consists of selection, crossover, and mutation genetic operators that look for the best fit to the observed data and a solution consisting of plausible compact sources. The efficiency of a GA on both synthetic and real magnetic anomalies of dikes by estimating model parameters, such as depth to the top of the dike ( H), the half-width of the dike ( B), the distance from the origin to the reference point ( D), the dip of the thick dike ( δ), and the susceptibility contrast ( k), has been shown. For the synthetic anomaly case, it has been considered for both noise-free and noisy magnetic data. In the real case, the vertical magnetic anomaly from the Pima copper mine in Arizona, USA, and the vertical magnetic anomaly in the Bayburt-Sarıhan skarn zone in northeastern Turkey have been inverted and interpreted. We compared the estimated parameters with the results of conventional inversion methods used in previous studies. We can conclude that the GA method used in this study is a useful tool for evaluating magnetic anomalies for dike models.

A Genetic Algorithm Method for Direct estimation of paleostress states from heterogeneous fault-slip observations

NASA Astrophysics Data System (ADS)

Srivastava, D. C.

2016-12-01

A Genetic Algorithm Method for Direct estimation of paleostress states from heterogeneous fault-slip observationsDeepak C. Srivastava, Prithvi Thakur and Pravin K. GuptaDepartment of Earth Sciences, Indian Institute of Technology Roorkee, Roorkee 247667, India. Abstract Paleostress estimation from a group of heterogeneous fault-slip observations entails first the classification of the observations into homogeneous fault sets and then a separate inversion of each homogeneous set. This study combines these two issues into a nonlinear inverse problem and proposes a heuristic search method that inverts the heterogeneous fault-slip observations. The method estimates different paleostress states in a group of heterogeneous fault-slip observations and classifies it into homogeneous sets as a byproduct. It uses the genetic algorithm operators, elitism, selection, encoding, crossover and mutation. These processes translate into a guided search that finds successively fitter solutions and operate iteratively until the termination criteria is met and the globally fittest stress tensors are obtained. We explain the basic steps of the algorithm on a working example and demonstrate validity of the method on several synthetic and a natural group of heterogeneous fault-slip observations. The method is independent of any user-defined bias or any entrapment of solution in a local optimum. It succeeds even in the difficult situations where other classification methods are found to fail.

Road screening and distribution route multi-objective robust optimization for hazardous materials based on neural network and genetic algorithm.

PubMed

Ma, Changxi; Hao, Wei; Pan, Fuquan; Xiang, Wang

2018-01-01

Route optimization of hazardous materials transportation is one of the basic steps in ensuring the safety of hazardous materials transportation. The optimization scheme may be a security risk if road screening is not completed before the distribution route is optimized. For road screening issues of hazardous materials transportation, a road screening algorithm of hazardous materials transportation is built based on genetic algorithm and Levenberg-Marquardt neural network (GA-LM-NN) by analyzing 15 attributes data of each road network section. A multi-objective robust optimization model with adjustable robustness is constructed for the hazardous materials transportation problem of single distribution center to minimize transportation risk and time. A multi-objective genetic algorithm is designed to solve the problem according to the characteristics of the model. The algorithm uses an improved strategy to complete the selection operation, applies partial matching cross shift and single ortho swap methods to complete the crossover and mutation operation, and employs an exclusive method to construct Pareto optimal solutions. Studies show that the sets of hazardous materials transportation road can be found quickly through the proposed road screening algorithm based on GA-LM-NN, whereas the distribution route Pareto solutions with different levels of robustness can be found rapidly through the proposed multi-objective robust optimization model and algorithm.

Recombination in diverse maize is stable, predictable, and associated with genetic load.

PubMed

Rodgers-Melnick, Eli; Bradbury, Peter J; Elshire, Robert J; Glaubitz, Jeffrey C; Acharya, Charlotte B; Mitchell, Sharon E; Li, Chunhui; Li, Yongxiang; Buckler, Edward S

2015-03-24

Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.

The genetics of green thorax, a new larval colour mutant, non-linked with ruby - eye locus in the malaria mosquito, Anopheles stephensi.

PubMed

Sanil, D; Shetty, N J

2009-06-01

Anopheles stephensi, an important vector of malaria continues to be distributed widely in the Indian subcontinent. The natural vigour of the species combined with its new tolerance, indeed resistance to insecticides has made it obligatory that we look for control methods involving genetic manipulation. Hence, there is an immediate need for greater understanding of the genetics of this vector species. One of the requirements for such genetic studies is the establishment of naturally occurring mutants, establishment of the genetic basis for the same and use of such mutants in the genetic transformation studies and other genetic control programme(s). This paper describes the isolation and genetic studies of a larval colour mutant, green thorax (gt), and linkage studies involving another autosomal recessive mutant ruby- eye (ru) in An. stephensi. After the initial discovery, the mutant green thorax was crossed inter se and pure homozygous stock of the mutant was established. The stock of the mutant ruby- eye, which has been maintained as a pure stock in the laboratory. Crosses were made between the wild type and mutant, green thorax to determine the mode of inheritance of green thorax. For linkage studies, crosses were made between the mutant green thorax and another autosomal recessive mutant ruby-eye. The percentage cross-over was calculated for the genes linkage relationship for gt and gt ru. Results of crosses between mutant and wild type showed that the inheritance of green thorax (gt) in An. stephensi is monofactorial in nature. The gt allele is recessive to wild type and is autosomal. The linkage studies showed no linkage between ru and gt. The mutant gt represents an excellent marker for An. stephensi as it is expressed in late III instar stage of larvae and is prominent in IV instar and pupal stages with complete penetrance and high viability. The said mutant could be easily identified without the aid of a microscope. This mutant can be used extensively to conduct basic and applied research. The mutant has been maintained in two large cages in our laboratory.

Precise orbit determination using the batch filter based on particle filtering with genetic resampling approach

NASA Astrophysics Data System (ADS)

Kim, Young-Rok; Park, Eunseo; Choi, Eun-Jung; Park, Sang-Young; Park, Chandeok; Lim, Hyung-Chul

2014-09-01

In this study, genetic resampling (GRS) approach is utilized for precise orbit determination (POD) using the batch filter based on particle filtering (PF). Two genetic operations, which are arithmetic crossover and residual mutation, are used for GRS of the batch filter based on PF (PF batch filter). For POD, Laser-ranging Precise Orbit Determination System (LPODS) and satellite laser ranging (SLR) observations of the CHAMP satellite are used. Monte Carlo trials for POD are performed by one hundred times. The characteristics of the POD results by PF batch filter with GRS are compared with those of a PF batch filter with minimum residual resampling (MRRS). The post-fit residual, 3D error by external orbit comparison, and POD repeatability are analyzed for orbit quality assessments. The POD results are externally checked by NASA JPL’s orbits using totally different software, measurements, and techniques. For post-fit residuals and 3D errors, both MRRS and GRS give accurate estimation results whose mean root mean square (RMS) values are at a level of 5 cm and 10-13 cm, respectively. The mean radial orbit errors of both methods are at a level of 5 cm. For POD repeatability represented as the standard deviations of post-fit residuals and 3D errors by repetitive PODs, however, GRS yields 25% and 13% more robust estimation results than MRRS for post-fit residual and 3D error, respectively. This study shows that PF batch filter with GRS approach using genetic operations is superior to PF batch filter with MRRS in terms of robustness in POD with SLR observations.

Impact of prosocial neuropeptides on human brain function.

PubMed

Meyer-Lindenberg, Andreas

2008-01-01

Oxytocin and vasopressin are key effectors of social behaviour (Insel, T. R. and Fernald, R. D. (2004). Annu. Rev. Neurosci., 27: 697-722). Oxytocin effects in humans were recently demonstrated by a behavioural study showing selectively increased trust after hormone administration (Kosfeld, M., et al. (2005). Nature, 435: 673-676). Since this suggested involvement of the amygdala, which is linked to trust (Winston, J. S., et al. (2002). Nat. Neurosci., 5: 277-283) - presumably because of its role in danger monitoring - and highly expresses oxytocin receptors (Huber, D., et al. (2005). Science, 308: 245-248), we studied amygdala circuitry after double-blind crossover intranasal application of placebo or oxytocin (Kirsch, P., et al. (2005). J. Neurosci., 25: 11489-11493). Oxytocin potently reduced amygdala activation and decreased coupling to brainstem regions implicated in autonomic and behavioural manifestations of fear, indicating a neural mechanism for the effects of oxytocin in social cognition in humans and providing a potential therapeutic approach to social anxiety currently being tested in social phobia and autism. Furthermore, these data suggested a translational genetic approach. Preliminary findings (data not presented) from our laboratory using imaging genetics indeed implicate genetic variants for both AVPR1A, encoding the primary receptor of vasopressin in brain, and the oxytocin receptor, OXTR, in amygdala regulation and activation. Taken together, our results indicate neural mechanisms for human social behaviour mediating genetic risk for autism through an impact on amygdala signalling and provide a rationale for exploring therapeutic strategies aimed at abnormal amygdala function in this disorder and in social dysfunction in general.

A Genetic System for Clostridium ljungdahlii: a Chassis for Autotrophic Production of Biocommodities and a Model Homoacetogen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leang, C; Ueki, T; Nevin, KP

Methods for genetic manipulation of Clostridium ljungdahlii are of interest because of the potential for production of fuels and other biocommodities from carbon dioxide via microbial electrosynthesis or more traditional modes of autotrophy with hydrogen or carbon monoxide as the electron donor. Furthermore, acetogenesis plays an important role in the global carbon cycle. Gene deletion strategies required for physiological studies of C. ljungdahlii have not previously been demonstrated. An electroporation procedure for introducing plasmids was optimized, and four different replicative origins for plasmid propagation in C. ljungdahlii were identified. Chromosomal gene deletion via double-crossover homologous recombination with a suicide vectormore » was demonstrated initially with deletion of the gene for FliA, a putative sigma factor involved in flagellar biogenesis and motility in C. ljungdahlii. Deletion of fliA yielded a strain that lacked flagella and was not motile. To evaluate the potential utility of gene deletions for functional genomic studies and to redirect carbon and electron flow, the genes for the putative bifunctional aldehyde/alcohol dehydrogenases, adhE1 and adhE2, were deleted individually or together. Deletion of adhE1, but not adhE2, diminished ethanol production with a corresponding carbon recovery in acetate. The double deletion mutant had a phenotype similar to that of the adhE1-deficient strain. Expression of adhE1 in trans partially restored the capacity for ethanol production. These results demonstrate the feasibility of genetic investigations of acetogen physiology and the potential for genetic manipulation of C. ljungdahlii to optimize autotrophic biocommodity production.« less

Thermoregulatory and Perceptual Effects of a Percooling Garment Worn Underneath an American Football Uniform.

PubMed

Keen, Megan L; Miller, Kevin C; Zuhl, Micah N

2017-11-01

Keen, ML, Miller, KC, and Zuhl, MN. Thermoregulatory and perceptual effects of a percooling garment worn underneath an American football uniform. J Strength Cond Res 31(11): 2983-2991, 2017-American football athletes are at the highest risk of developing exertional heat illness (EHI). We investigated whether percooling (i.e., cooling during exercise) garments affected perceptual or physiological variables in individuals exercising in the heat while wearing football uniforms. Twelve male participants (age = 24 ± 4 year, mass = 80.1 ± 8.5 kg, height = 182.5 ± 10.4 cm) completed this cross-over, counterbalanced study. On day 1, we measured peak oxygen consumption (V[Combining Dot Above]O2). On days 2 and 3, participants wore percooling garments with (ICE) or without (CON) ice packs over the femoral and brachial arteries. They donned a football uniform and completed 3, 20-minute bouts of treadmill exercise at ∼50% of peak V[Combining Dot Above]O2 (∼33° C, ∼42% relative humidity) followed by a 10-minute rest period. Ice packs were replaced every 20 minutes. Rating of perceived exertion (RPE), thermal sensation, and thirst sensation were measured before and after each exercise bout. Environmental symptoms questionnaire (ESQ) responses and urine specific gravity (Usg) were measured pretesting and after the last exercise bout. V[Combining Dot Above]O2, change in heart rate (ΔHR), and change in rectal temperature (ΔTrec) were measured every 5 minutes. Sweat rate, sweat volume, and percent hypohydration were calculated. No interactions (F17,187 ≤ 1.6, p ≥ 0.1) or main effect of cooling condition (F1,11 ≤ 1.4, p ≥ 0.26) occurred for ΔTrec, ΔHR, thermal sensation, thirst, RPE, ESQ, or Usg. No differences between conditions occurred for sweat volume, sweat rate, or percent hypohydration (t11 ≤ 0.7, p ≥ 0.25). V[Combining Dot Above]O2 differed between conditions over time (F15,165 = 3.3, p < 0.001); ICE was lower than CON at 30, 55, and 70 minutes (p ≤ 0.05). It is unlikely that these garments would prevent EHI or minimize dehydration in football athletes.

Evolving molecular era of childhood medulloblastoma: time to revisit therapy.

PubMed

Khatua, Soumen

2016-01-01

Currently medulloblastoma is treated with a uniform therapeutic approach based on histopathology and clinico-radiological risk stratification, resulting in unpredictable treatment failure and relapses. Improved understanding of the biological, molecular and genetic make-up of these tumors now clearly identifies it as a compendium of four distinct subtypes (WNT, SHH, group 3 and 4). Advances in utilization of the genomic and epigenomic machinery have now delineated genetic aberrations and epigenetic perturbations in each subgroup as potential druggable targets. This has resulted in endeavors to profile targeted therapy. The challenge and future of medulloblastoma therapeutics will be to keep pace with the evolving novel biological insights and translating them into optimal targeted treatment regimens.

Brief Report: Initial Trial of Alpha7-Nicotinic Receptor Stimulation in Two Adult Patients with Autism Spectrum Disorder.

PubMed

Olincy, Ann; Blakeley-Smith, Audrey; Johnson, Lynn; Kem, William R; Freedman, Robert

2016-12-01

Abnormalities in CHRNA7, the alpha7-nicotinic receptor gene, have been reported in autism spectrum disorder. These genetic abnormalities potentially decrease the receptor's expression and diminish its functional role. This double-blind, placebo-controlled crossover study in two adult patients investigated whether an investigational receptor-specific partial agonist drug would increase the inhibitory functions of the gene and thereby increase patients' attention. An electrophysiological biomarker, P50 inhibition, verified the intended neurobiological effect of the agonist, and neuropsychological testing verified a primary cognitive effect. Both patients perceived increased attention in their self-ratings. Alpha7-nicotinic receptor agonists, currently the target of drug development in schizophrenia and Alzheimer Disease, may also have positive clinical effects in autism spectrum disorder.

Structural Variation Shapes the Landscape of Recombination in Mouse.

PubMed

Morgan, Andrew P; Gatti, Daniel M; Najarian, Maya L; Keane, Thomas M; Galante, Raymond J; Pack, Allan I; Mott, Richard; Churchill, Gary A; de Villena, Fernando Pardo-Manuel

2017-06-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from [Formula: see text] DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as [Formula: see text] of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or [Formula: see text] of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. Copyright © 2017 by the Genetics Society of America.

A Genetically Engineered Mouse Model of Sporadic Colorectal Cancer.

PubMed

Betzler, Alexander M; Kochall, Susan; Blickensdörfer, Linda; Garcia, Sebastian A; Thepkaysone, May-Linn; Nanduri, Lahiri K; Muders, Michael H; Weitz, Jürgen; Reissfelder, Christoph; Schölch, Sebastian

2017-07-06

Despite the advantages of easy applicability and cost-effectiveness, colorectal cancer mouse models based on tumor cell injection have severe limitations and do not accurately simulate tumor biology and tumor cell dissemination. Genetically engineered mouse models have been introduced to overcome these limitations; however, such models are technically demanding, especially in large organs such as the colon in which only a single tumor is desired. As a result, an immunocompetent, genetically engineered mouse model of colorectal cancer was developed which develops highly uniform tumors and can be used for tumor biology studies as well as therapeutic trials. Tumor development is initiated by surgical, segmental infection of the distal colon with adeno-cre virus in compound conditionally mutant mice. The tumors can be easily detected and monitored via colonoscopy. We here describe the surgical technique of segmental adeno-cre infection of the colon, the surveillance of the tumor via high-resolution colonoscopy and present the resulting colorectal tumors.

Design of a DNA chip for detection of unknown genetically modified organisms (GMOs).

PubMed

Nesvold, Håvard; Kristoffersen, Anja Bråthen; Holst-Jensen, Arne; Berdal, Knut G

2005-05-01

Unknown genetically modified organisms (GMOs) have not undergone a risk evaluation, and hence might pose a danger to health and environment. There are, today, no methods for detecting unknown GMOs. In this paper we propose a novel method intended as a first step in an approach for detecting unknown genetically modified (GM) material in a single plant. A model is designed where biological and combinatorial reduction rules are applied to a set of DNA chip probes containing all possible sequences of uniform length n, creating probes capable of detecting unknown GMOs. The model is theoretically tested for Arabidopsis thaliana Columbia, and the probabilities for detecting inserts and receiving false positives are assessed for various parameters for this organism. From a theoretical standpoint, the model looks very promising but should be tested further in the laboratory. The model and algorithms will be available upon request to the corresponding author.

Progress in Developing a New Field-theoretical Crossover Equation-of-State

NASA Technical Reports Server (NTRS)

Rudnick, Joseph; Barmatz, M.; Zhong, Fang

2003-01-01

A new field-theoretical crossover equation-of-state model is being developed. This model of a liquid-gas critical point provides a bridge between the asymptotic equation-of-state behavior close to the transition, obtained by the Guida and Zinn-Justin parametric model [J. Phys. A: Math. Gen. 31, 8103 (1998)], and the expected mean field behavior farther away. The crossover is based on the beta function for the renormalized fourth-order coupling constant and incorporates the correct crossover exponents and critical amplitude ratios in both regimes. A crossover model is now being developed that is consistent with predictions along the critical isochore and along the coexistence curve of the minimal subtraction renormalization approach developed by Dohm and co-workers and recently applied to the O(1) universality class [Phys. Rev. E, 67, 021106 (2003)]. Experimental measurements of the heat capacity at constant volume, isothermal susceptibility, and coexistence curve near the He-3 critical point are being compared to the predictions of this model. The results of these comparisons will be presented.

A ghrelin gene variant may predict crossover rate from restricting-type anorexia nervosa to other phenotypes of eating disorders: a retrospective survival analysis.

PubMed

Ando, Tetsuya; Komaki, Gen; Nishimura, Hiroki; Naruo, Tetsuro; Okabe, Kenjiro; Kawai, Keisuke; Takii, Masato; Oka, Takakazu; Kodama, Naoki; Nakamoto, Chiemi; Ishikawa, Toshio; Suzuki-Hotta, Mari; Minatozaki, Kazunori; Yamaguchi, Chikara; Nishizono-Maher, Aya; Kono, Masaki; Kajiwara, Sohei; Suematsu, Hiroyuki; Tomita, Yuichiro; Ebana, Shoichi; Okamoto, Yuri; Nagata, Katsutaro; Nakai, Yoshikatsu; Koide, Masanori; Kobayashi, Nobuyuki; Kurokawa, Nobuo; Nagata, Toshihiko; Kiriike, Nobuo; Takenaka, Yoshito; Nagamine, Kiyohide; Ookuma, Kazuyoshi; Murata, Shiho

2010-08-01

Patients with anorexia nervosa restricting type (AN-R) often develop bulimic symptoms and crossover to AN-binge eating/purging type (AN-BP), or to bulimia nervosa (BN). We have reported earlier that genetic variants of an orexigenic peptide ghrelin are associated with BN. Here, the relationship between a ghrelin gene variant and the rate of change from AN-R to other phenotypes of eating disorders (EDs) was investigated. Participants were 165 patients with ED, initially diagnosed as AN-R. The dates of their AN-R onset and changes in diagnosis to other subtypes of ED were investigated retrospectively. Ghrelin gene 3056 T-->C SNP (single nucleotide polymorphism) was genotyped. Probability and hazard ratios were analyzed using life table analysis and Cox's proportional hazard regression model, in which the starting point was the time of AN-R onset and the outcome events were the time of (i) onset of binge eating, that is, when patients changed to binge eating AN and BN and (ii) recovery of normal weight, that is, when patients changed to BN or remission. Patients with the TT genotype at 3056 T-->C had a higher probability and hazard ratio for recovery of normal weight. The ghrelin SNP was not related with the onset of binge eating. The 3056 T-->C SNP of the ghrelin gene is related to the probability and the rate of recovery of normal body weight from restricting-type AN.

Directed mutagenesis of the Rickettsia prowazekii pld gene encoding phospholipase D.

PubMed

Driskell, Lonnie O; Yu, Xue-jie; Zhang, Lihong; Liu, Yan; Popov, Vsevolod L; Walker, David H; Tucker, Aimee M; Wood, David O

2009-08-01

Rickettsia prowazekii, the causative agent of epidemic typhus, is an obligately intracytoplasmic bacterium, a lifestyle that imposes significant barriers to genetic manipulation. The key to understanding how this unique bacterium evades host immunity is the mutagenesis of selected genes hypothesized to be involved in virulence. The R. prowazekii pld gene, encoding a protein with phospholipase D activity, has been associated with phagosomal escape. To demonstrate the feasibility of site-directed knockout mutagenesis of rickettsial genes and to generate a nonrevertible vaccine strain, we utilized homologous recombination to generate a pld mutant of the virulent R. prowazekii strain Madrid Evir. Using linear DNA for transformation, a double-crossover event resulted in the replacement of the rickettsial wild-type gene with a partially deleted pld gene. Linear DNA was used to prevent potentially revertible single-crossover events resulting in plasmid insertion. Southern blot and PCR analyses were used to confirm the presence of the desired mutation and to demonstrate clonality. While no phenotypic differences were observed between the mutant and wild-type strains when grown in tissue culture, the pld mutant exhibited attenuated virulence in the guinea pig model. In addition, animals immunized with the mutant strain were protected against subsequent challenge with the virulent Breinl strain, suggesting that this transformant could serve as a nonrevertible, attenuated vaccine strain. This study demonstrates the feasibility of generating site-directed rickettsial gene mutants, providing a new tool for understanding rickettsial biology and furthering advances in the prevention of epidemic typhus.

Defining the proximal border of the Huntington disease candidate region by multipoint recombination analyses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skraastad, M.I.; De Rooij, K.E.; De Koning Gans, P.A.M.

1993-06-01

The candidate region for the Huntington disease (HD) gene has been narrowed down to a 2.2-Mb region between D4S10 and D4S98 on the short arm of chromosome 4. To map the HD gene within this candidate region 65 Dutch HD families were studied. In total 338 informative meioses were analyzed and 11 multiple informative crossovers were detected. Assuming a minimum number of recombinations and no double recombinations, the multiple informative crossovers are consistent with one specific genetic order for 12 loci: D4S10-(D4S81,D4S126)-D4S125-(D4S127,D4S95)-D4S43-(D4S115, D4S96, D4S111, D4S90, D4S141).This is in agreement with the known data derived from similar and other methods. Themore » loci between brackets could not be mapped relative to each other. In the family material, two informative three-point marker recombination events were detected in the proximal HD candidate region, which are also informative for HD. Both recombination events map the HD gene distal to D4S81 and most likely distal to D4S125, narrowing down the HD candidate region to a 1.7-Mb region between D4S125 and D4S98. 39 refs., 3 figs., 2 tabs.« less

Effects of chemical and physical agents on recombination events in cells of the germ line of male and female Drosophila melanogaster.

PubMed

Würgler, F E

1991-01-01

Genotoxic agents can induce mutations as well as recombination in the genetic material. The fruit fly Drosophila melanogaster was one of the first assay systems to test physical and chemical agents for recombinogenic effects. Such effects can be observed in cells of the germ line as well as in somatic cells. At present information is available on 54 agents, among them 48 chemicals that have been tested in cells of the germ line of males and/or females. Effects on meiotic recombination in female germ cells cannot simply be classified as positive or negative since for a number of agents, depending on the chromosome region studied, recombination frequencies may be increased, unaffected or decreased. The male germ line of D. melanogaster represents a unique situation because meiotic recombination does not occur. Among 25 agents tested in male germ cells 24 did induce male recombination, among them alkylating, intercalating and cross-linking agents, direct-acting ones as well as compounds needing metabolic activation. With several compounds the frequency of induced recombination is highest in the heterochromatic regions near the centromeres. In brood pattern analyses, e.g., after exposure of adult males to ionizing radiation, the first appearance of crossover progeny is indicative of the sampling of exposed spermatocytes. In premeiotic cells of the male and the female germ line mitotic recombination can occur. Upon clonal expansion of the recombinant cells, clusters of identical crossovers can be observed.

No correlation between germline mutation at repeat DNA and meiotic crossover in male mice exposed to X-rays or cisplatin.

PubMed

Barber, R; Plumb, M; Smith, A G; Cesar, C E; Boulton, E; Jeffreys, A J; Dubrova, Y E

2000-12-20

To test the hypothesis that mouse germline expanded simple tandem repeat (ESTR) mutations are associated with recombination events during spermatogenesis, crossover frequencies were compared with germline mutation rates at ESTR loci in male mice acutely exposed to 1Gy of X-rays or to 10mg/kg of the anticancer drug cisplatin. Ionising radiation resulted in a highly significant 2.7-3.6-fold increase in ESTR mutation rate in males mated 4, 5 and 6 weeks after exposure, but not 3 weeks after exposure. In contrast, irradiation had no effect on meiotic crossover frequencies assayed on six chromosomes using 25 polymorphic microsatellite loci spaced at approximately 20cM intervals and covering 421cM of the mouse genome. Paternal exposure to cisplatin did not affect either ESTR mutation rates or crossover frequencies, despite a report that cisplatin can increase crossover frequency in mice. Correlation analysis did not reveal any associations between the paternal ESTR mutation rate and crossover frequency in unexposed males and in those exposed to X-rays or cisplatin. This study does not, therefore, support the hypothesis that mutation induction at mouse ESTR loci results from a general genome-wide increase in meiotic recombination rate.

East African cheetahs: evidence for two population bottlenecks?

PubMed Central

O'Brien, S J; Wildt, D E; Bush, M; Caro, T M; FitzGibbon, C; Aggundey, I; Leakey, R E

1987-01-01

A combined population genetic and reproductive analysis was undertaken to compare free-ranging cheetahs from east Africa (Acinonyx jubatus raineyi) with the genetically impoverished and reproductively impaired south African subspecies (Acinonyx jubatus jubatus). Like that of their south African counterparts, the quality of semen specimens from east African cheetahs was poor, with a low concentration of spermatozoa (25.3 X 10(6) per ejaculate) and a high incidence of morphological abnormalities (79%). From an electrophoretic survey of the products of 49 genetic loci in A. jubatus raineyi, two allozyme polymorphisms were detected; one of these, for a nonspecific esterase, shows an allele that is rare (less than 1% incidence) in south African specimens. Estimates of polymorphism (2-4%) and average heterozygosity (0.0004-0.014) affirm the cheetah as the least genetically variable felid species. The genetic distance between south and east African cheetahs was low (0.004), suggesting that the development of genetic uniformity preceded the recent geographic isolation of the subspecies. We propose that at least two population bottlenecks followed by inbreeding produced the modern cheetah species. The first and most extreme was ancient, possibly late Pleistocene (circa 10,000 years ago); the second was more recent (within the last century) and led to the south African populations. PMID:3467370

Microsatellite diversity among the primitive tribes of India

PubMed Central

Mukherjee, Malay B.; Tripathy, V.; Colah, R. B.; Solanki, P. K.; Ghosh, K.; Reddy, B. M.; Mohanty, D.

2009-01-01

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall GST value was high (GST = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines. PMID:21088716

Modifier genes in Mendelian disorders: the example of cystic fibrosis

PubMed Central

Cutting, Garry R.

2011-01-01

In the past three decades, scientists have had immense success in identifying genes and their variants that contribute to an array of diseases. While the identification of such genetic variants has informed our knowledge of the etiologic bases of diseases, there continues to be a substantial gap in our understanding of the factors that modify disease severity. Monogenic diseases provide an opportunity to identify modifiers as they have uniform etiology, detailed phenotyping of affected individuals, and familial clustering. Cystic fibrosis (CF) is among the more common life-shortening recessive disorders that displays wide variability in clinical features and survival. Considerable progress has been made in elucidating the contribution of genetic and nongenetic factors to CF. Allelic variation in CFTR, the gene responsible for CF, correlates with some aspects of the disease. However, lung function, neonatal intestinal obstruction, diabetes, and anthropometry display strong genetic control independent of CFTR, and candidate gene studies have revealed genetic modifiers underlying these traits. The application of genome-wide techniques holds great promise for the identification of novel genetic variants responsible for the heritable features and complications of CF. Since the genetic modifiers are known to alter the course of disease, their protein products become immediate targets for therapeutic intervention. PMID:21175684

Lack of genetic variation in tree ring delta13C suggests a uniform, stomatally-driven response to drought stress across Pinus radiata genotypes.

PubMed

Rowell, Douglas M; Ades, Peter K; Tausz, Michael; Arndt, Stefan K; Adams, Mark A

2009-02-01

We assessed the variation in delta(13)C signatures of Pinus radiata D. Don stemwood taken from three genetic trials in southern Australia. We sought to determine the potential of using delta(13)C signatures as selection criteria for drought tolerance. Increment cores were taken from P. radiata and were used to determine the basal area increment and the delta(13)C signature of extracted cellulose. Both growth increment and cellulose delta(13)C were affected by water availability. Growth increment and delta(13)C were negatively correlated suggesting that growth was water-limited. While there was significant genetic variation in growth, there was no significant genetic variation in cellulose delta(13)C of tree rings. This suggests that different genotypes of P. radiata display significant differences in growth and yet respond similarly to drought stress. The delta(13)C response to drought stress was more due to changes in stomatal conductance than to the variation in photosynthetic capacity, and this may explain the lack of genetic variation in delta(13)C. The lack of genetic variation in cellulose delta(13)C of tree rings precludes its use as a selection criterion for drought tolerance among P. radiata genotypes.

Identification of DSB-1, a Protein Required for Initiation of Meiotic Recombination in Caenorhabditis elegans, Illuminates a Crossover Assurance Checkpoint

PubMed Central

Stamper, Ericca L.; Rodenbusch, Stacia E.; Rosu, Simona; Ahringer, Julie; Villeneuve, Anne M.; Dernburg, Abby F.

2013-01-01

Meiotic recombination, an essential aspect of sexual reproduction, is initiated by programmed DNA double-strand breaks (DSBs). DSBs are catalyzed by the widely-conserved Spo11 enzyme; however, the activity of Spo11 is regulated by additional factors that are poorly conserved through evolution. To expand our understanding of meiotic regulation, we have characterized a novel gene, dsb-1, that is specifically required for meiotic DSB formation in the nematode Caenorhabditis elegans. DSB-1 localizes to chromosomes during early meiotic prophase, coincident with the timing of DSB formation. DSB-1 also promotes normal protein levels and chromosome localization of DSB-2, a paralogous protein that plays a related role in initiating recombination. Mutations that disrupt crossover formation result in prolonged DSB-1 association with chromosomes, suggesting that nuclei may remain in a DSB-permissive state. Extended DSB-1 localization is seen even in mutants with defects in early recombination steps, including spo-11, suggesting that the absence of crossover precursors triggers the extension. Strikingly, failure to form a crossover precursor on a single chromosome pair is sufficient to extend the localization of DSB-1 on all chromosomes in the same nucleus. Based on these observations we propose a model for crossover assurance that acts through DSB-1 to maintain a DSB-permissive state until all chromosome pairs acquire crossover precursors. This work identifies a novel component of the DSB machinery in C. elegans, and sheds light on an important pathway that regulates DSB formation for crossover assurance. PMID:23990794

Crossover from capillary fingering to viscous fingering in a rough fracture

NASA Astrophysics Data System (ADS)

Hu, R.; Chen, Y.; Wu, D. S.

2017-12-01

Controlled by the competition between capillary and viscous forces, the displacement patterns of one fluid displacing another more viscous one exhibit capillary fingering, viscous fingering, and the crossover between the two. Although extensive studies have investigated viscous and capillary fingerings in porous and fractured media, a few studies focused on the crossover in rough fractures, and how viscous and capillary forces affect the crossover remains unclear. Using a transparent fracture visualization system, we studied how the competition impacts the crossover in a horizontal rough fracture. Drainage experiments of water displacing oil were conducted at seven flow rates (capillary number log10Ca ranging from -7.07 to -3.07) and four viscosity ratios (M = 1/1000, 1/500, 1/100 and 1/50). We consistently observed lower invading fluid saturations in the crossover zone. In addition, we proposed a phase diagram for the displacement patterns in a rough fracture that is consistent with similar studies in porous media. Based on real-time imaging and statistical analysis of the invasion morphology, we showed that the competition between the capillary and viscous forces is responsible for the saturation reduction in the crossover zone. In this zone, finger propagation toward the outlet (characteristic of viscous fingering) as well as void-filling in the transverse and backward directions (characteristic of capillary fingering), are both suppressed. Therefore, the invading fluid tends to occupy larger apertures with higher characteristic front velocity, promoting void-filling toward the outlet with thinner finger growth and resulting in a larger volume of defending fluid left behind.

MS-HRM assay identifies high levels of epigenetic heterogeneity in human immortalized cell lines.

PubMed

Putnik, Milica; Wojdacz, Tomasz K; Pournara, Angeliki; Vahter, Marie; Wallberg, Annika E

2015-04-15

Immortalized cell lines are widely used in genetic and epigenetic studies, from exploration of basic molecular pathways to evaluation of disease-specific cellular properties. They are also used in biotechnology, e.g., in drug toxicity tests and vaccine production. Cellular and genetic uniformity is the main feature of immortalized cell lines and it has been particularly advantageous in functional genomic research, which has in recent years been expanded to include epigenetic mechanisms of gene expression regulation. Using the MS-HRM technique, we demonstrated heterogeneity in locus-specific methylation patterns in different cell cultures of four human cell lines: HEK293, HEK293T, LCL and DU145. Our results show that some human immortalized cell lines consist of cells that differ in the methylation status of specific loci, i.e., that they are epigenetically heterogeneous. We show that even two cultures of the same cell line obtained from different laboratories can differ in the methylation status of the specific loci. The results indicated that epigenetic uniformity of the cell lines cannot be assumed in experiments which utilize cell cultures and that the methylation status of the specific loci in the immortalized cell lines should be re-characterized and carefully profiled before epigenetic studies are performed. Copyright © 2015 Elsevier B.V. All rights reserved.

Symbiont survival and host-symbiont disequilibria under differential vertical transmission.

PubMed Central

Sánchez, M S; Arnold, J; Asmussen, M A

2000-01-01

Interspecific genetic interactions in host-symbiont systems raise intriguing coevolutionary questions and may influence the effectiveness of public health and management policies. Here we present an analytical and numerical investigation of the effects of host genetic heterogeneity in the rate of vertical transmission of a symbiont. We consider the baseline case with a monomorphic symbiont and a single diallelic locus in its diploid host, where vertical transmission is the sole force. Our analysis introduces interspecific disequilibria to quantify nonrandom associations between host genotypes and alleles and symbiont presence/absence. The transient and equilibrium behavior is examined in simulations with randomly generated initial conditions and transmission parameters. Compared to the case where vertical transmission rates are uniform across host genotypes, differential transmission (i) increases average symbiont survival from 50% to almost 60%, (ii) dramatically reduces the minimum average transmission rate for symbiont survival from 0.5 to 0.008, and (iii) readily creates permanent host-symbiont disequilibria de novo, whereas uniform transmission can neither create nor maintain such associations. On average, heterozygotes are slightly more likely to carry and maintain the symbiont in the population and are more randomly associated with the symbiont. Results show that simple evolutionary forces can create substantial nonrandom associations between two species. PMID:10757775

Relaxation of selection, niche construction, and the Baldwin effect in language evolution.

PubMed

Yamauchi, Hajime; Hashimoto, Takashi

2010-01-01

Deacon has suggested that one of the key factors of language evolution is not characterized by an increase in genetic contribution, often known as the Baldwin effect, but rather by a decrease. This process effectively increases linguistic learning capability by organizing a novel synergy of multiple lower-order functions previously irrelevant to the process of language acquisition. Deacon posits that this transition is not caused by natural selection. Rather, it is due to the relaxation of natural selection. While there are some cases in which relaxation caused by some external factors indeed induces the transition, we do not know what kind of relaxation has worked in language evolution. In this article, a genetic-algorithm-based computer simulation is used to investigate how the niche-constructing aspect of linguistic behavior may trigger the degradation of genetic predisposition related to language learning. The results show that agents initially increase their genetic predisposition for language learning—the Baldwin effect. They create a highly uniform sociolinguistic environment—a linguistic niche construction. This means that later generations constantly receive very similar inputs from adult agents, and subsequently the selective pressure to retain the genetic predisposition is relaxed.

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

PubMed Central

2010-01-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. PMID:20650823

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

PubMed

van Baal, Sjozef; Zlotogora, Joël; Lagoumintzis, George; Gkantouna, Vassiliki; Tzimas, Ioannis; Poulas, Konstantinos; Tsakalidis, Athanassios; Romeo, Giovanni; Patrinos, George P

2010-06-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.

Risk factors for amyotrophic lateral sclerosis

PubMed Central

Ingre, Caroline; Roos, Per M; Piehl, Fredrik; Kamel, Freya; Fang, Fang

2015-01-01

Amyotrophic lateral sclerosis (ALS) is the most common motor neuron disease. It is typically fatal within 2–5 years of symptom onset. The incidence of ALS is largely uniform across most parts of the world, but an increasing ALS incidence during the last decades has been suggested. Although recent genetic studies have substantially improved our understanding of the causes of ALS, especially familial ALS, an important role of non-genetic factors in ALS is recognized and needs further study. In this review, we briefly discuss several major genetic contributors to ALS identified to date, followed by a more focused discussion on the most commonly examined non-genetic risk factors for ALS. We first review factors related to lifestyle choices, including smoking, intake of antioxidants, physical fitness, body mass index, and physical exercise, followed by factors related to occupational and environmental exposures, including electromagnetic fields, metals, pesticides, β-methylamino-L-alanine, and viral infection. Potential links between ALS and other medical conditions, including head trauma, metabolic diseases, cancer, and inflammatory diseases, are also discussed. Finally, we outline several future directions aiming to more efficiently examine the role of non-genetic risk factors in ALS. PMID:25709501

An overview of STRUCTURE: applications, parameter settings, and supporting software

PubMed Central

Porras-Hurtado, Liliana; Ruiz, Yarimar; Santos, Carla; Phillips, Christopher; Carracedo, Ángel; Lareu, Maria V.

2013-01-01

Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data. PMID:23755071

Impact of treatment crossovers on clinical outcomes in the rate and rhythm control strategies for atrial fibrillation: Insights from the AFFIRM (Atrial Fibrillation Follow-up Investigation of Rhythm Management) trial.

PubMed

Maan, Abhishek; Zhang, Zheng; Qin, Ziling; Wang, Yanbing; Dudley, Samuel; Dabhadakar, Kaustubh; Refaat, Marwan; Mansour, Moussa; Ruskin, Jeremy N; Heist, E Kevin

2017-07-01

We investigated the rates and reasons for crossover to alternative treatment strategies and its impact on mortality in patients who were enrolled in the Atrial Fibrillation Follow-up Investigation of Rhythm Management (AFFIRM) trial. Over a mean follow-up period of 3.5 years, 842 patients underwent crossover to the alternative treatment arms in AFFIRM. The rate of crossover from rhythm to rate control (594/2,033, 29.2%) was more frequent than the rate of crossover from rate to rhythm control (248/2,027, 12.2%, P < 0.0001). The leading reasons for crossover from rhythm to rate control were failure to achieve or maintain sinus rhythm (272/594, 45.8%) and intolerable adverse effects (122/594, 20.5%). In comparison, the major reasons for crossover from rate to rhythm control were failure to control atrial fibrillation symptoms (159/248, 64.1%) and intolerable adverse effects (9/248, 3.6%). This difference in crossover pattern was statistically significant (P < 0.0001). There was a significantly decreased risk of all-cause mortality (adjusted HR: 0.61, 95% CI: 0.48-0.78, P < 0.0001) and cardiac mortality (adjusted hazard ratio [HR]: 0.61, 95% confidence interval [CI]: 0.43-0.88, P = 0.008) in the subgroup of patients who crossed over from rhythm to rate control as compared to those who continued in rhythm control. There was a nonsignificant trend toward decreased all-cause (adjusted HR: 0.76, 95% CI: 0.53-1.10, P = 0.14) and cardiac mortality (adjusted HR: 0.70, 95% CI: 0.42-1.18, P = 0.18) in patients who crossed over from rate to rhythm control as compared to those who continued rate control. © 2017 Wiley Periodicals, Inc.

Genetic architecture of differences between populations of cowpea weevil (Callosobruchus maculatus) evolved in the same environment.

PubMed

Bieri, Jonas; Kawecki, Tadeusz J

2003-02-01

We investigated the genetic architecture underlying differentiation in fitness-related traits between two pairs of populations of the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae). These populations had geographically distant (> 2000 km) origins but evolved in a uniform laboratory environment for 120 generations. For each pair of populations (Nigeria x Yemen and Cameroon x Uganda) we estimated the means of five fitness-related characters and a measure of fitness (net reproductive rate R0) in each of the parental populations and 12 types of hybrids (two F1 and two F2 lines and eight backcrosses). Models containing up to nine composite genetic parameters were fitted to the means of the 14 lines. The patterns of line means for all traits in the Nigeria x Yemen cross and for four traits (larval survival, developmental rate, female body weight, and fecundity) in the Cameroon x Uganda cross were best explained by models including additive, dominance, and maternal effects, but excluding epistasis. We did not find any evidence for outbreeding depression for any trait. An epistatic component of divergence was detected for egg hatching success and R0 in the Cameroon x Uganda cross, but its sign was opposite to that expected under outbreeding depression, that is, additive x additive epistasis had a positive effect on the performance of F2 hybrids. All traits except fecundity showed a pattern of heterosis. A large difference of egg-hatching success between the two reciprocal F1 lines in that cross was best explained as fertilization incompatibility between Cameroon females and sperm carrying Uganda genes. The results suggest that these populations have not converged to the same life-history phenotype and genetic architecture, despite 120 generations of uniform natural selection. However, the absence of outbreeding depression implies that they did not evolve toward different adaptive peaks.

White Matter Hyperintensities Are Under Strong Genetic Influence.

PubMed

Sachdev, Perminder S; Thalamuthu, Anbupalam; Mather, Karen A; Ames, David; Wright, Margaret J; Wen, Wei

2016-06-01

The genetic basis of white matter hyperintensities (WMH) is still unknown. This study examines the heritability of WMH in both sexes and in different brain regions, and the influence of age. Participants from the Older Australian Twins Study were recruited (n=320; 92 monozygotic and 68 dizygotic pairs) who volunteered for magnetic resonance imaging scans and medical assessments. Heritability, that is, the ratio of the additive genetic variance to the total phenotypic variance, was estimated using the twin design. Heritability was high for total WMH volume (0.76), and for periventricular WMH (0.64) and deep WMH (0.77), and varied from 0.18 for the cerebellum to 0.76 for the occipital lobe. The genetic correlation between deep and periventricular WMH regions was 0.85, with one additive genetics factor accounting for most of the shared variance. Heritability was consistently higher in women in the cerebral regions. Heritability in deep but not periventricular WMH declined with age, in particular after the age of 75. WMH have a strong genetic influence but this is not uniform through the brain, being higher for deep than periventricular WMH and in the cerebral regions. The genetic influence is higher in women, and there is an age-related decline, most markedly for deep WMH. The data suggest some heterogeneity in the pathogenesis of WMH for different brain regions and for men and women. © 2016 American Heart Association, Inc.

A Double-Deck Elevator Group Supervisory Control System with Destination Floor Guidance System Using Genetic Network Programming

NASA Astrophysics Data System (ADS)

Yu, Lu; Zhou, Jin; Mabu, Shingo; Hirasawa, Kotaro; Hu, Jinglu; Markon, Sandor

The Elevator Group Supervisory Control Systems (EGSCS) are the control systems that systematically manage three or more elevators in order to efficiently transport the passengers in buildings. Double-deck elevators, where two elevators are connected with each other, serve passengers at two consecutive floors simultaneously. Double-deck Elevator systems (DDES) become more complex in their behavior than conventional single-deck elevator systems (SDES). Recently, Artificial Intelligence (AI) technology has been used in such complex systems. Genetic Network Programming (GNP), a graph-based evolutionary method, has been applied to EGSCS and its advantages are shown in some papers. GNP can obtain the strategy of a new hall call assignment to the optimal elevator when it performs crossover and mutation operations to judgment nodes and processing nodes. Meanwhile, Destination Floor Guidance System (DFGS) is installed in DDES, so that passengers can also input their destinations at elevator halls. In this paper, we have applied GNP to DDES and compared DFGS with normal systems. The waiting time and traveling time of DFGS are all improved because of getting more information from DFGS. The simulations showed the effectiveness of the double-deck elevators with DFGS in different building traffics.

Locating hazardous gas leaks in the atmosphere via modified genetic, MCMC and particle swarm optimization algorithms

NASA Astrophysics Data System (ADS)

Wang, Ji; Zhang, Ru; Yan, Yuting; Dong, Xiaoqiang; Li, Jun Ming

2017-05-01

Hazardous gas leaks in the atmosphere can cause significant economic losses in addition to environmental hazards, such as fires and explosions. A three-stage hazardous gas leak source localization method was developed that uses movable and stationary gas concentration sensors. The method calculates a preliminary source inversion with a modified genetic algorithm (MGA) and has the potential to crossover with eliminated individuals from the population, following the selection of the best candidate. The method then determines a search zone using Markov Chain Monte Carlo (MCMC) sampling, utilizing a partial evaluation strategy. The leak source is then accurately localized using a modified guaranteed convergence particle swarm optimization algorithm with several bad-performing individuals, following selection of the most successful individual with dynamic updates. The first two stages are based on data collected by motionless sensors, and the last stage is based on data from movable robots with sensors. The measurement error adaptability and the effect of the leak source location were analyzed. The test results showed that this three-stage localization process can localize a leak source within 1.0 m of the source for different leak source locations, with measurement error standard deviation smaller than 2.0.

A Comparison of Hybrid Approaches for Turbofan Engine Gas Path Fault Diagnosis

NASA Astrophysics Data System (ADS)

Lu, Feng; Wang, Yafan; Huang, Jinquan; Wang, Qihang

2016-09-01

A hybrid diagnostic method utilizing Extended Kalman Filter (EKF) and Adaptive Genetic Algorithm (AGA) is presented for performance degradation estimation and sensor anomaly detection of turbofan engine. The EKF is used to estimate engine component performance degradation for gas path fault diagnosis. The AGA is introduced in the integrated architecture and applied for sensor bias detection. The contributions of this work are the comparisons of Kalman Filters (KF)-AGA algorithms and Neural Networks (NN)-AGA algorithms with a unified framework for gas path fault diagnosis. The NN needs to be trained off-line with a large number of prior fault mode data. When new fault mode occurs, estimation accuracy by the NN evidently decreases. However, the application of the Linearized Kalman Filter (LKF) and EKF will not be restricted in such case. The crossover factor and the mutation factor are adapted to the fitness function at each generation in the AGA, and it consumes less time to search for the optimal sensor bias value compared to the Genetic Algorithm (GA). In a word, we conclude that the hybrid EKF-AGA algorithm is the best choice for gas path fault diagnosis of turbofan engine among the algorithms discussed.

An improved genetic algorithm for increasing the addressing accuracy of encoding fiber Bragg grating sensor network

NASA Astrophysics Data System (ADS)

Liu, Huanlin; Wang, Chujun; Chen, Yong

2018-01-01

Large-capacity encoding fiber Bragg grating (FBG) sensor network is widely used in modern long-term health monitoring system. Encoding FBG sensors have greatly improved the capacity of distributed FBG sensor network. However, the error of addressing increases correspondingly with the enlarging of capacity. To address the issue, an improved algorithm called genetic tracking algorithm (GTA) is proposed in the paper. In the GTA, for improving the success rate of matching and reducing the large number of redundant matching operations generated by sequential matching, the individuals are designed based on the feasible matching. Then, two kinds of self-crossover ways and a dynamic variation during mutation process are designed to increase the diversity of individuals and to avoid falling into local optimum. Meanwhile, an assistant decision is proposed to handle the issue that the GTA cannot solve when the variation of sensor information is highly overlapped. The simulation results indicate that the proposed GTA has higher accuracy compared with the traditional tracking algorithm and the enhanced tracking algorithm. In order to address the problems of spectrum fragmentation and low sharing degree of spectrum resources in survivable.

The Hawk-Dove game in phenotypically homogeneous and heterogeneous populations of finite dimension

NASA Astrophysics Data System (ADS)

Laruelle, Annick; da Silva Rocha, André Barreira; Escobedo, Ramón

2018-02-01

The Hawk-Dove game played between individuals in populations of finite dimension is analyzed by means of a stochastic model. We take into account both cases when all individuals in the population are either phenotypically homogeneous or heterogeneous. A strategy in the model is a gene representing the probability of playing the Hawk strategy. Individual interactions at the microscopic level are described by a genetic algorithm where evolution results from the interplay among selection, mutation, drift and cross-over of genes. We show that the behavioral patterns observed at the macroscopic level can be reproduced as the emergent result of individual interactions governed by the rules of the Hawk-Dove game at the microscopic level. We study how the results of the genetic algorithm compare with those obtained in evolutionary game theory, finding that, although genes continuously change both their presence and frequency in the population over time, the population average behavior always achieves stationarity and, when this happens, the final average strategy played in the population oscillates around the evolutionarily stable strategy in the homogeneous population case or the neutrally stable set in the heterogeneous population case.

An improved genetic algorithm for multidimensional optimization of precedence-constrained production planning and scheduling

NASA Astrophysics Data System (ADS)

Dao, Son Duy; Abhary, Kazem; Marian, Romeo

2017-06-01

Integration of production planning and scheduling is a class of problems commonly found in manufacturing industry. This class of problems associated with precedence constraint has been previously modeled and optimized by the authors, in which, it requires a multidimensional optimization at the same time: what to make, how many to make, where to make and the order to make. It is a combinatorial, NP-hard problem, for which no polynomial time algorithm is known to produce an optimal result on a random graph. In this paper, the further development of Genetic Algorithm (GA) for this integrated optimization is presented. Because of the dynamic nature of the problem, the size of its solution is variable. To deal with this variability and find an optimal solution to the problem, GA with new features in chromosome encoding, crossover, mutation, selection as well as algorithm structure is developed herein. With the proposed structure, the proposed GA is able to "learn" from its experience. Robustness of the proposed GA is demonstrated by a complex numerical example in which performance of the proposed GA is compared with those of three commercial optimization solvers.

1/f Noise in the Simple Genetic Algorithm Applied to a Traveling Salesman Problem

NASA Astrophysics Data System (ADS)

Yamada, Mitsuhiro

Complex dynamical systems are observed in physics, biology, and even economics. Such systems in balance are considered to be in a critical state, and 1/f noise is considered to be a footprint. Complex dynamical systems have also been investigated in the field of evolutionary algorithms inspired by biological evolution. The genetic algorithm (GA) is a well-known evolutionary algorithm in which many individuals interact, and the simplest GA is referred to as the simple GA (SGA). However, the GA has not been examined from the viewpoint of the emergence of 1/f noise. In the present paper, the SGA is applied to a traveling salesman problem in order to investigate the SGA from such a viewpoint. The timecourses of the fitness of the candidate solution were examined. As a result, when the mutation and crossover probabilities were optimal, the system evolved toward a critical state in which the average maximum fitness over all trial runs was maximum. In this situation, the fluctuation of the fitness of the candidate solution resulted in the 1/f power spectrum, and the dynamics of the system had no intrinsic time or length scale.

On the Crossover from Classical to Fermi Liquid Behavior in Dense Plasmas

NASA Astrophysics Data System (ADS)

Daligault, Jerome

2017-10-01

We explore the crossover from classical plasma to quantum Fermi liquid behavior of electrons in dense plasmas. To this end, we analyze the evolution with density and temperature of the momentum lifetime of a test electron introduced in a dense electron gas. This allows us 1) to determine the boundaries of the crossover region in the temperature-density plane and to shed light on the evolution of scattering properties across it, 2) to quantify the role of the fermionic nature of electrons on electronic collisions across the crossover region, and 3) to explain how the concept of Coulomb logarithm emerges at high enough temperature but disappears at low enough temperature. Work supported by LDRD Grant No. 20170490ER.

Magnesium Increases Homoeologous Crossover Frequency During Meiosis in ZIP4 (Ph1 Gene) Mutant Wheat-Wild Relative Hybrids.

PubMed

Rey, María-Dolores; Martín, Azahara C; Smedley, Mark; Hayta, Sadiye; Harwood, Wendy; Shaw, Peter; Moore, Graham

2018-01-01

Wild relatives provide an important source of useful traits in wheat breeding. Wheat and wild relative hybrids have been widely used in breeding programs to introduce such traits into wheat. However, successful introgression is limited by the low frequency of homoeologous crossover (CO) between wheat and wild relative chromosomes. Hybrids between wheat carrying a 70 Mb deletion on chromosome 5B ( ph1b ) and wild relatives, have been exploited to increase the level of homoeologous CO, allowing chromosome exchange between their chromosomes. In ph1b -rye hybrids, CO number increases from a mean of 1 CO to 7 COs per cell. CO number can be further increased up to a mean of 12 COs per cell in these ph1b hybrids by treating the plants with Hoagland solution. More recently, it was shown that the major meiotic crossover gene ZIP4 on chromosome 5B ( TaZIP4-B2 ) within the 70 Mb deletion, was responsible for the restriction of homoeologous COs in wheat-wild relative hybrids, confirming the ph1b phenotype as a complete Tazip4-B2 deletion mutant ( Tazip4-B2 ph1b) . In this study, we have identified the particular Hoagland solution constituent responsible for the increased chiasma frequency in Tazip4-B2 ph1b mutant-rye hybrids and extended the analysis to Tazip4-B2 TILLING and CRISPR mutant- Ae variabilis hybrids. Chiasma frequency at meiotic metaphase I, in the absence of each Hoagland solution macronutrient (NH 4 H 2 PO 4 , KNO 3 , Ca (NO 3 )2·4H 2 O or Mg SO 4 ·7H 2 O) was analyzed. A significant decrease in homoeologous CO frequency was observed when the Mg 2+ ion was absent. A significant increase of homoeologous CO frequency was observed in all analyzed hybrids, when plants were irrigated with a 1 mM Mg 2+ solution. These observations suggest a role for magnesium supplementation in improving the success of genetic material introgression from wild relatives into wheat.

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine

PubMed Central

Wang, Minghui; Londo, Jason P.; Acharya, Charlotte B.; Mitchell, Sharon E.; Sun, Qi; Reisch, Bruce; Cadle-Davidson, Lance

2015-01-01

Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications. PMID:26244767

Fanconi anemia: causes and consequences of genetic instability.

PubMed

Kalb, R; Neveling, K; Nanda, I; Schindler, D; Hoehn, H

2006-01-01

Fanconi anemia (FA) is a rare recessive disease that reflects the cellular and phenotypic consequences of genetic instability: growth retardation, congenital malformations, bone marrow failure, high risk of neoplasia, and premature aging. At the cellular level, manifestations of genetic instability include chromosomal breakage, cell cycle disturbance, and increased somatic mutation rates. FA cells are exquisitely sensitive towards oxygen and alkylating drugs such as mitomycin C or diepoxybutane, pointing to a function of FA genes in the defense against reactive oxygen species and other DNA damaging agents. FA is caused by biallelic mutations in at least 12 different genes which appear to function in the maintenance of genomic stability. Eight of the FA proteins form a nuclear core complex with a catalytic function involving ubiquitination of the central FANCD2 protein. The posttranslational modification of FANCD2 promotes its accumulation in nuclear foci, together with known DNA maintenance proteins such as BRCA1, BRCA2, and the RAD51 recombinase. Biallelic mutations in BRCA2 cause a severe FA-like phenotype, as do biallelic mutations in FANCD2. In fact, only leaky or hypomorphic mutations in this central group of FA genes appear to be compatible with life birth and survival. The newly discovered FANCJ (= BRIP1) and FANCM (= Hef ) genes correspond to known DNA-maintenance genes (helicase resp. helicase-associated endonuclease for fork-structured DNA). These genes provide the most convincing evidence to date of a direct involvement of FA genes in DNA repair functions associated with the resolution of DNA crosslinks and stalled replication forks. Even though genetic instability caused by mutational inactivation of the FANC genes has detrimental effects for the majority of FA patients, around 20% of patients appear to benefit from genetic instability since genetic instability also increases the chance of somatic reversion of their constitutional mutations. Intragenic crossover, gene conversion, back mutation and compensating mutations in cis have all been observed in revertant, and, consequently, mosaic FA-patients, leading to improved bone marrow function. There probably is no other experiment of nature in our species in which causes and consequences of genetic instability, including the role of reactive oxygen species, can be better documented and explored than in FA.

Investigation of Sustained Detonation Devices: the Pulse Detonation Engine-Crossover System and the Rotating Detonation Engine System

NASA Astrophysics Data System (ADS)

Driscoll, Robert B.

An experimental study is conducted on a Pulse Detonation Engine-Crossover System to investigate the feasibility of repeated, shock-initiated combustion and characterize the initiation performance. A PDE-crossover system can decrease deflagration-to-detonation transition length while employing a single spark source to initiate a multi-PDE system. Visualization of a transferred shock wave propagating through a clear channel reveals a complex shock train behind the leading shock. Shock wave Mach number and decay rate remains constant for varying crossover tube geometries and operational frequencies. A temperature gradient forms within the crossover tube due to forward flow of high temperature ionized gas into the crossover tube from the driver PDE and backward flow of ionized gas into the crossover tube from the driven PDE, which can cause intermittent auto-ignition of the driver PDE. Initiation performance in the driven PDE is strongly dependent on initial driven PDE skin temperature in the shock wave reflection region. An array of detonation tubes connected with crossover tubes is developed using optimized parameters and successful operation utilizing shock-initiated combustion through shock wave reflection is achieved and sustained. Finally, an air-breathing, PDE-Crossover System is developed to characterize the feasibility of shock-initiated combustion within an air-breathing pulse detonation engine. The initiation effectiveness of shock-initiated combustion is compared to spark discharge and detonation injection through a pre-detonator. In all cases, shock-initiated combustion produces improved initiation performance over spark discharge and comparable detonation transition run-up lengths relative to pre-detonator initiation. A computational study characterizes the mixing processes and injection flow field within a rotating detonation engine. Injection parameters including reactant flow rate, reactant injection area, placement of the fuel injection, and fuel injection distribution are varied to assess the impact on mixing. Decreasing reactant injection areas improves fuel penetration into the cross-flowing air stream, enhances turbulent diffusion of the fuel within the annulus, and increases local equivalence ratio and fluid mixedness. Staggering fuel injection holes produces a decrease in mixing when compared to collinear fuel injection. Finally, emulating nozzle integration by increasing annulus back-pressure increases local equivalence ratio in the injection region due to increased convection residence time.

Virus-mimetic nanovesicles as a versatile antigen-delivery system

PubMed Central

Zhang, Pengfei; Chen, Yixin; Zeng, Yun; Shen, Chenguang; Li, Rui; Guo, Zhide; Li, Shaowei; Zheng, Qingbing; Chu, Chengchao; Wang, Zhantong; Zheng, Zizheng; Tian, Rui; Ge, Shengxiang; Zhang, Xianzhong; Xia, Ning-Shao; Liu, Gang; Chen, Xiaoyuan

2015-01-01

It is a critically important challenge to rapidly design effective vaccines to reduce the morbidity and mortality of unexpected pandemics. Inspired from the way that most enveloped viruses hijack a host cell membrane and subsequently release by a budding process that requires cell membrane scission, we genetically engineered viral antigen to harbor into cell membrane, then form uniform spherical virus-mimetic nanovesicles (VMVs) that resemble natural virus in size, shape, and specific immunogenicity with the help of surfactants. Incubation of major cell membrane vesicles with surfactants generates a large amount of nano-sized uniform VMVs displaying the native conformational epitopes. With the diverse display of epitopes and viral envelope glycoproteins that can be functionally anchored onto VMVs, we demonstrate VMVs to be straightforward, robust and tunable nanobiotechnology platforms for fabricating antigen delivery systems against a wide range of enveloped viruses. PMID:26504197

In vitro and in vivo evaluation of a sublingual fentanyl wafer formulation

PubMed Central

Lim, Stephen CB; Paech, Michael J; Sunderland, Bruce; Liu, Yandi

2013-01-01

Background The objective of this study was to prepare a novel fentanyl wafer formulation by a freeze-drying method, and to evaluate its in vitro and in vivo release characteristics, including its bioavailability via the sublingual route. Methods The wafer formulation was prepared by freeze-drying an aqueous dispersion of fentanyl containing sodium carboxymethylcellulose and amylogum as matrix formers. Uniformity of weight, friability, and dissolution testing of the fentanyl wafer was achieved using standard methods, and the residual moisture content was measured. The fentanyl wafer was also examined using scanning electron microscopy and x-ray diffraction. The absolute bioavailability of the fentanyl wafer was evaluated in 11 opioid-naïve adult female patients using a randomized crossover design. Results In vitro release showed that almost 90% of the fentanyl dissolved in one minute. In vivo, the first detectable plasma fentanyl concentration was observed after 3.5 minutes and the peak plasma concentration between 61.5 and 67 minutes. The median absolute bioavailability was 53.0%. Conclusion These results indicate that this wafer has potential as an alternative sublingual fentanyl formulation. PMID:23596347

Melt Electrowriting of Thermoplastic Elastomers.

PubMed

Hochleitner, Gernot; Fürsattel, Eva; Giesa, Reiner; Groll, Jürgen; Schmidt, Hans-Werner; Dalton, Paul D

2018-04-14

Melt electrowriting (MEW), an additive manufacturing process, is established using polycaprolactone as the benchmark material. In this study, a thermoplastic elastomer, namely, poly(urea-siloxane), is synthesized and characterized to identify how different classes of polymers are compatible with MEW. This polyaddition polymer has reversible hydrogen bonding from the melt upon heating/cooling and highly resolved structures are achieved by MEW. The influence of applied voltage, temperature, and feeding pressure on printing outcomes behavior is optimized. Balancing these parameters, highly uniform and smooth-surfaced fibers with diameters ranging from 10 to 20 µm result. The quality of the 3D MEW scaffolds is excellent, with very accurate fiber stacking capacity-up to 50 layers with minimal defects and good fiber fusion between the layers. There is also minimal fiber sagging between the crossover points, which is a characteristic of thicker MEW scaffolds previously reported with other polymers. In summary, poly(urea-siloxane) demonstrates outstanding compatibility with the MEW process and represents a class of polymer-thermoplastic elastomers-that are, until now, untested with this approach. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Redox Active Colloids as Discrete Energy Storage Carriers.

PubMed

Montoto, Elena C; Nagarjuna, Gavvalapalli; Hui, Jingshu; Burgess, Mark; Sekerak, Nina M; Hernández-Burgos, Kenneth; Wei, Teng-Sing; Kneer, Marissa; Grolman, Joshua; Cheng, Kevin J; Lewis, Jennifer A; Moore, Jeffrey S; Rodríguez-López, Joaquín

2016-10-12

Versatile and readily available battery materials compatible with a range of electrode configurations and cell designs are desirable for renewable energy storage. Here we report a promising class of materials based on redox active colloids (RACs) that are inherently modular in their design and overcome challenges faced by small-molecule organic materials for battery applications, such as crossover and chemical/morphological stability. RACs are cross-linked polymer spheres, synthesized with uniform diameters between 80 and 800 nm, and exhibit reversible redox activity as single particles, as monolayer films, and in the form of flowable dispersions. Viologen-based RACs display reversible cycling, accessing up to 99% of their capacity and 99 ± 1% Coulombic efficiency over 50 cycles by bulk electrolysis owing to efficient, long-distance intraparticle charge transfer. Ferrocene-based RACs paired with viologen-based RACs cycled efficiently in a nonaqueous redox flow battery employing a simple size-selective separator, thus demonstrating a possible application that benefits from their colloidal dimensions. The unprecedented versatility in RAC synthetic and electrochemical design opens new avenues for energy storage.

Visualizing and quantifying the crossover from capillary fingering to viscous fingering in a rough fracture

NASA Astrophysics Data System (ADS)

Chen, Yi-Feng; Fang, Shu; Wu, Dong-Sheng; Hu, Ran

2017-09-01

Immiscible fluid-fluid displacement in permeable media is important in many subsurface processes, including enhanced oil recovery and geological CO2 sequestration. Controlled by capillary and viscous forces, displacement patterns of one fluid displacing another more viscous one exhibit capillary and viscous fingering, and crossover between the two. Although extensive studies investigated viscous and capillary fingering in porous media, a few studies focused on the crossover in rough fractures, and how viscous and capillary forces affect the crossover remains unclear. Using a transparent fracture-visualization system, we studied how the two forces impact the crossover in a horizontal rough fracture. Drainage experiments of water displacing oil were conducted at seven flow rates (capillary number log10Ca ranging from -7.07 to -3.07) and four viscosity ratios (M=1/1000,1/500,1/100 and 1/50). We consistently observed lower invading fluid saturations in the crossover zone. We also proposed a phase diagram for the displacement patterns in a rough fracture that is consistent with similar studies in porous media. Based on real-time imaging and statistical analysis of the invasion morphology, we showed that the competition between capillary and viscous forces is responsible for the saturation reduction in the crossover zone. In this zone, finger propagation toward the outlet (characteristic of viscous fingering) as well as void-filling in the transverse/backward directions (characteristic of capillary fingering), are both suppressed. Therefore, the invading fluid tends to occupy larger apertures with higher characteristic front velocity, promoting void-filling toward the outlet with thinner finger growth and resulting in a larger volume of defending fluid left behind.

Spin crossover in ferropericlase and velocity heterogeneities in the lower mantle

NASA Astrophysics Data System (ADS)

Wu, Z.; Wentzcovitch, R. M.

2014-12-01

Ferropericlase (Fp) is believed to be the second most abundant phase in the lower mantle. Since the discovery of the high spin (HS) to low spin (LS) crossover in iron in Fp [1], this phenomenon has been investigated extensively experimentally and theoretically. This is a broad and smooth crossover that takes place throughout most of the lower mantle and does not produce an obvious signature in radial velocity or density profiles [2]. Therefore, the spin transition has been generally considered to be invisible to seismic waves. This study, however, shows that it can produce a peculiar effect on lateral velocity heterogeneities at certain depths[3]. Deciphering the origin of seismic velocity heterogeneities in the mantle is crucial to understanding internal structures and processes at work in the Earth. The spin crossover in iron introduces unfamiliar effects on seismic velocities. First principles calculations indicate that anti-correlation between shear velocity (VS) and bulk sound velocity (Vφ) in the mantle, usually interpreted as compositional heterogeneity, can also be produced in homogeneous aggregates containing Fp. The spin crossover also suppresses thermally induced heterogeneity in VP but not in VS. This effect is observed in tomographic models at conditions where the spin crossover in Fp is expected in the lower mantle. In addition, the one-of-a-kind signature of this spin crossover in the RS/P () heterogeneity ratio might be a useful "fingerprint" to detect the presence of Fp in the lower mantle. [1] Badro J, et al. (2003) Science 300(5620):789-791. [2] Wu Z, Justo J. F., and Wentzcovitch R. M., (2013). Phys. Rev. Lett. 110. 228501-5 [3]Wu Z., and Wentzcovitch R. M., (2014) Proc Natl Acad Sci USA. www.pnas.org/cgi/doi/10.1073/pnas.1322427111

Problem formulation in the environmental risk assessment for genetically modified plants

PubMed Central

Wolt, Jeffrey D.; Keese, Paul; Raybould, Alan; Burachik, Moisés; Gray, Alan; Olin, Stephen S.; Schiemann, Joachim; Sears, Mark; Wu, Felicia

2009-01-01

Problem formulation is the first step in environmental risk assessment (ERA) where policy goals, scope, assessment endpoints, and methodology are distilled to an explicitly stated problem and approach for analysis. The consistency and utility of ERAs for genetically modified (GM) plants can be improved through rigorous problem formulation (PF), producing an analysis plan that describes relevant exposure scenarios and the potential consequences of these scenarios. A properly executed PF assures the relevance of ERA outcomes for decision-making. Adopting a harmonized approach to problem formulation should bring about greater uniformity in the ERA process for GM plants among regulatory regimes globally. This paper is the product of an international expert group convened by the International Life Sciences Institute (ILSI) Research Foundation. PMID:19757133

The short-term effects of air pollutants on respiratory disease mortality in Wuhan, China: comparison of time-series and case-crossover analyses

PubMed Central

Ren, Meng; Li, Na; Wang, Zhan; Liu, Yisi; Chen, Xi; Chu, Yuanyuan; Li, Xiangyu; Zhu, Zhongmin; Tian, Liqiao; Xiang, Hao

2017-01-01

Few studies have compared different methods when exploring the short-term effects of air pollutants on respiratory disease mortality in Wuhan, China. This study assesses the association between air pollutants and respiratory disease mortality with both time-series and time-stratified–case-crossover designs. The generalized additive model (GAM) and the conditional logistic regression model were used to assess the short-term effects of air pollutants on respiratory disease mortality. Stratified analyses were performed by age, sex, and diseases. A 10 μg/m3 increment in SO2 level was associated with an increase in relative risk for all respiratory disease mortality of 2.4% and 1.9% in the case-crossover and time-series analyses in single pollutant models, respectively. Strong evidence of an association between NO2 and daily respiratory disease mortality among men or people older than 65 years was found in the case-crossover study. There was a positive association between air pollutants and respiratory disease mortality in Wuhan, China. Both time-series and case-crossover analyses consistently reveal the association between three air pollutants and respiratory disease mortality. The estimates of association between air pollution and respiratory disease mortality from the case–crossover analysis displayed greater variation than that from the time-series analysis. PMID:28084399

The short-term effects of air pollutants on respiratory disease mortality in Wuhan, China: comparison of time-series and case-crossover analyses.

PubMed

Ren, Meng; Li, Na; Wang, Zhan; Liu, Yisi; Chen, Xi; Chu, Yuanyuan; Li, Xiangyu; Zhu, Zhongmin; Tian, Liqiao; Xiang, Hao

2017-01-13

Few studies have compared different methods when exploring the short-term effects of air pollutants on respiratory disease mortality in Wuhan, China. This study assesses the association between air pollutants and respiratory disease mortality with both time-series and time-stratified-case-crossover designs. The generalized additive model (GAM) and the conditional logistic regression model were used to assess the short-term effects of air pollutants on respiratory disease mortality. Stratified analyses were performed by age, sex, and diseases. A 10 μg/m 3 increment in SO 2 level was associated with an increase in relative risk for all respiratory disease mortality of 2.4% and 1.9% in the case-crossover and time-series analyses in single pollutant models, respectively. Strong evidence of an association between NO 2 and daily respiratory disease mortality among men or people older than 65 years was found in the case-crossover study. There was a positive association between air pollutants and respiratory disease mortality in Wuhan, China. Both time-series and case-crossover analyses consistently reveal the association between three air pollutants and respiratory disease mortality. The estimates of association between air pollution and respiratory disease mortality from the case-crossover analysis displayed greater variation than that from the time-series analysis.

The short-term effects of air pollutants on respiratory disease mortality in Wuhan, China: comparison of time-series and case-crossover analyses

NASA Astrophysics Data System (ADS)

Ren, Meng; Li, Na; Wang, Zhan; Liu, Yisi; Chen, Xi; Chu, Yuanyuan; Li, Xiangyu; Zhu, Zhongmin; Tian, Liqiao; Xiang, Hao

2017-01-01

Few studies have compared different methods when exploring the short-term effects of air pollutants on respiratory disease mortality in Wuhan, China. This study assesses the association between air pollutants and respiratory disease mortality with both time-series and time-stratified-case-crossover designs. The generalized additive model (GAM) and the conditional logistic regression model were used to assess the short-term effects of air pollutants on respiratory disease mortality. Stratified analyses were performed by age, sex, and diseases. A 10 μg/m3 increment in SO2 level was associated with an increase in relative risk for all respiratory disease mortality of 2.4% and 1.9% in the case-crossover and time-series analyses in single pollutant models, respectively. Strong evidence of an association between NO2 and daily respiratory disease mortality among men or people older than 65 years was found in the case-crossover study. There was a positive association between air pollutants and respiratory disease mortality in Wuhan, China. Both time-series and case-crossover analyses consistently reveal the association between three air pollutants and respiratory disease mortality. The estimates of association between air pollution and respiratory disease mortality from the case-crossover analysis displayed greater variation than that from the time-series analysis.

Looking forwards and backwards: The real-time processing of Strong and Weak Crossover

PubMed Central

Lidz, Jeffrey; Phillips, Colin

2017-01-01

We investigated the processing of pronouns in Strong and Weak Crossover constructions as a means of probing the extent to which the incremental parser can use syntactic information to guide antecedent retrieval. In Experiment 1 we show that the parser accesses a displaced wh-phrase as an antecedent for a pronoun when no grammatical constraints prohibit binding, but the parser ignores the same wh-phrase when it stands in a Strong Crossover relation to the pronoun. These results are consistent with two possibilities. First, the parser could apply Principle C at antecedent retrieval to exclude the wh-phrase on the basis of the c-command relation between its gap and the pronoun. Alternatively, retrieval might ignore any phrases that do not occupy an Argument position. Experiment 2 distinguished between these two possibilities by testing antecedent retrieval under Weak Crossover. In Weak Crossover binding of the pronoun is ruled out by the argument condition, but not Principle C. The results of Experiment 2 indicate that antecedent retrieval accesses matching wh-phrases in Weak Crossover configurations. On the basis of these findings we conclude that the parser can make rapid use of Principle C and c-command information to constrain retrieval. We discuss how our results support a view of antecedent retrieval that integrates inferences made over unseen syntactic structure into constraints on backward-looking processes like memory retrieval. PMID:28936483

Crossover between the Gaussian orthogonal ensemble, the Gaussian unitary ensemble, and Poissonian statistics.

PubMed

Schweiner, Frank; Laturner, Jeanine; Main, Jörg; Wunner, Günter

2017-11-01

Until now only for specific crossovers between Poissonian statistics (P), the statistics of a Gaussian orthogonal ensemble (GOE), or the statistics of a Gaussian unitary ensemble (GUE) have analytical formulas for the level spacing distribution function been derived within random matrix theory. We investigate arbitrary crossovers in the triangle between all three statistics. To this aim we propose an according formula for the level spacing distribution function depending on two parameters. Comparing the behavior of our formula for the special cases of P→GUE, P→GOE, and GOE→GUE with the results from random matrix theory, we prove that these crossovers are described reasonably. Recent investigations by F. Schweiner et al. [Phys. Rev. E 95, 062205 (2017)2470-004510.1103/PhysRevE.95.062205] have shown that the Hamiltonian of magnetoexcitons in cubic semiconductors can exhibit all three statistics in dependence on the system parameters. Evaluating the numerical results for magnetoexcitons in dependence on the excitation energy and on a parameter connected with the cubic valence band structure and comparing the results with the formula proposed allows us to distinguish between regular and chaotic behavior as well as between existent or broken antiunitary symmetries. Increasing one of the two parameters, transitions between different crossovers, e.g., from the P→GOE to the P→GUE crossover, are observed and discussed.

Spin crossover in liquid (Mg,Fe)O at extreme conditions

NASA Astrophysics Data System (ADS)

Holmström, E.; Stixrude, L.

2016-05-01

We use first-principles free-energy calculations to predict a pressure-induced spin crossover in the liquid planetary material (Mg,Fe)O, whereby the magnetic moments of Fe ions vanish gradually over a range of hundreds of GPa. Because electronic entropy strongly favors the nonmagnetic low-spin state of Fe, the crossover has a negative effective Clapeyron slope, in stark contrast to the crystalline counterpart of this transition-metal oxide. Diffusivity of liquid (Mg,Fe)O is similar to that of MgO, displaying a weak dependence on element and spin state. Fe-O and Mg-O coordination increases from approximately 4 to 7 as pressure goes from 0 to 200 GPa. We find partitioning of Fe to induce a density inversion between the crystal and melt, implying separation of a basal magma ocean from a surficial one in the early Earth. The spin crossover induces an anomaly into the density contrast, and the oppositely signed Clapeyron slopes for the crossover in the liquid and crystalline phases imply that the solid-liquid transition induces a spin transition in (Mg,Fe)O.

Correlation between Fragility and the Arrhenius Crossover Phenomenon in Metallic, Molecular, and Network Liquids.

PubMed

Jaiswal, Abhishek; Egami, Takeshi; Kelton, K F; Schweizer, Kenneth S; Zhang, Yang

2016-11-11

We report the observation of a distinct correlation between the kinetic fragility index m and the reduced Arrhenius crossover temperature θ_{A}=T_{A}/T_{g} in various glass-forming liquids, identifying three distinguishable groups. In particular, for 11 glass-forming metallic liquids, we universally observe a crossover in the mean diffusion coefficient from high-temperature Arrhenius to low-temperature super-Arrhenius behavior at approximately θ_{A}≈2 which is in the stable liquid phases. In contrast, for fragile molecular liquids, this crossover occurs at much lower θ_{A}≈1.4 and usually in their supercooled states. The θ_{A} values for strong network liquids spans a wide range higher than 2. Intriguingly, the high-temperature activation barrier E_{∞} is universally found to be ∼11k_{B}T_{g} and uncorrelated with the fragility or the reduced crossover temperature θ_{A} for metallic and molecular liquids. These observations provide a way to estimate the low-temperature glassy characteristics (T_{g} and m) from the high-temperature liquid quantities (E_{∞} and θ_{A}).

Correlation between Fragility and the Arrhenius Crossover Phenomenon in Metallic, Molecular, and Network Liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jaiswal, Abhishek; Egami, Takeshi; Kelton, K. F.

2016-11-10

In this paper, we report the observation of a distinct correlation between the kinetic fragility index m and the reduced Arrhenius crossover temperature θ A = T A/T g in various glass-forming liquids, identifying three distinguishable groups. In particular, for 11 glass-forming metallic liquids, we universally observe a crossover in the mean diffusion coefficient from high-temperature Arrhenius to low-temperature super-Arrhenius behavior at approximately θ A ≈ 2 which is in the stable liquid phases. In contrast, for fragile molecular liquids, this crossover occurs at much lower θ A ≈ 1.4 and usually in their supercooled states. The θ A valuesmore » for strong network liquids spans a wide range higher than 2. Intriguingly, the high-temperature activation barrier E ∞ is universally found to be ~11k BT g and uncorrelated with the fragility or the reduced crossover temperature θ A for metallic and molecular liquids. Finally, these observations provide a way to estimate the low-temperature glassy characteristics (T g and m) from the high-temperature liquid quantities (E ∞ and θ A).« less

Are fractal dimensions of the spatial distribution of mineral deposits meaningful?

USGS Publications Warehouse

Raines, G.L.

2008-01-01

It has been proposed that the spatial distribution of mineral deposits is bifractal. An implication of this property is that the number of deposits in a permissive area is a function of the shape of the area. This is because the fractal density functions of deposits are dependent on the distance from known deposits. A long thin permissive area with most of the deposits in one end, such as the Alaskan porphyry permissive area, has a major portion of the area far from known deposits and consequently a low density of deposits associated with most of the permissive area. On the other hand, a more equi-dimensioned permissive area, such as the Arizona porphyry permissive area, has a more uniform density of deposits. Another implication of the fractal distribution is that the Poisson assumption typically used for estimating deposit numbers is invalid. Based on datasets of mineral deposits classified by type as inputs, the distributions of many different deposit types are found to have characteristically two fractal dimensions over separate non-overlapping spatial scales in the range of 5-1000 km. In particular, one typically observes a local dimension at spatial scales less than 30-60 km, and a regional dimension at larger spatial scales. The deposit type, geologic setting, and sample size influence the fractal dimensions. The consequence of the geologic setting can be diminished by using deposits classified by type. The crossover point between the two fractal domains is proportional to the median size of the deposit type. A plot of the crossover points for porphyry copper deposits from different geologic domains against median deposit sizes defines linear relationships and identifies regions that are significantly underexplored. Plots of the fractal dimension can also be used to define density functions from which the number of undiscovered deposits can be estimated. This density function is only dependent on the distribution of deposits and is independent of the definition of the permissive area. Density functions for porphyry copper deposits appear to be significantly different for regions in the Andes, Mexico, United States, and western Canada. Consequently, depending on which regional density function is used, quite different estimates of numbers of undiscovered deposits can be obtained. These fractal properties suggest that geologic studies based on mapping at scales of 1:24,000 to 1:100,000 may not recognize processes that are important in the formation of mineral deposits at scales larger than the crossover points at 30-60 km. ?? 2008 International Association for Mathematical Geology.

24 CFR 3285.701 - Electrical crossovers.

Code of Federal Regulations, 2010 CFR

2010-04-01

... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Electrical Systems and Equipment § 3285.701 Electrical crossovers. Multi-section homes with electrical wiring in more than one section require... installation instructions. ...

Optimization and Simulation of Plastic Injection Process using Genetic Algorithm and Moldflow

NASA Astrophysics Data System (ADS)

Martowibowo, Sigit Yoewono; Kaswadi, Agung

2017-03-01

The use of plastic-based products is continuously increasing. The increasing demands for thinner products, lower production costs, yet higher product quality has triggered an increase in the number of research projects on plastic molding processes. An important branch of such research is focused on mold cooling system. Conventional cooling systems are most widely used because they are easy to make by using conventional machining processes. However, the non-uniform cooling processes are considered as one of their weaknesses. Apart from the conventional systems, there are also conformal cooling systems that are designed for faster and more uniform plastic mold cooling. In this study, the conformal cooling system is applied for the production of bowl-shaped product made of PP AZ564. Optimization is conducted to initiate machine setup parameters, namely, the melting temperature, injection pressure, holding pressure and holding time. The genetic algorithm method and Moldflow were used to optimize the injection process parameters at a minimum cycle time. It is found that, an optimum injection molding processes could be obtained by setting the parameters to the following values: T M = 180 °C; P inj = 20 MPa; P hold = 16 MPa and t hold = 8 s, with a cycle time of 14.11 s. Experiments using the conformal cooling system yielded an average cycle time of 14.19 s. The studied conformal cooling system yielded a volumetric shrinkage of 5.61% and the wall shear stress was found at 0.17 MPa. The difference between the cycle time obtained through simulations and experiments using the conformal cooling system was insignificant (below 1%). Thus, combining process parameters optimization and simulations by using genetic algorithm method with Moldflow can be considered as valid.

A rapid and efficient protocol for in vitro multiplication of genetically uniform Stevia rebaudiana (Bertoni).

PubMed

Khan, A; Jayanthi, M; Gantasala, Nagavara Prasad; Bhooshan, N; Rao, Uma

2016-07-01

Stevia rebaudiana (Bertoni), commonly called candy leaf or sweet leaf, endemic to South America, is an important medicinal plant. As a source of low calorie natural sweetener 'stevoside', it is used in obesity, diabetes, treatment of heartburn and tooth decay, and also serves as a food supplement. Large scale commercial propagation of S. rebaudiana demands a suitable protocol. Here, we propose an improved protocol for in vitro multiplication of S. rebaudiana from nodal explants. In this protocol, the effect of laboratory grade urea on multiple shoot induction from nodal explants was studied. The nodal explants were initially cultured on Murashige and Skoog (MS) basal media for 2 weeks which facilitated the axillary bud break. Further, culturing of these explants on MS medium fortified with 6 benzyl amninopurine (BAP) (2 mg/L) and Naphthalene acetic acid (NAA) (1 mg/L) with and .without urea (5 mg/L) for a period of 40 days revealed maximum shoot production of 44.56 from a single nodal explant in media supplemented with urea as compared to 22.44 without urea. The differences in the number of shoots produced were significant and these shoots readily rooted in MS media with NAA (4 mg/L). Primary and secondary hardening was successful in these plants. There were no visible morphological abnormalities observed in the micropropagated plantlets. Genetic analysis from random samples also revealed that these plants are genetically uniform. The advantage of the present protocol is that the complete process of multiple shoot induction, rooting and hardening could be completed within a period of 6 months as compared to the existing protocols.

Increase in the rate of recombinants in tomato (Lycopersicon esculentum L.) after in vitro regeneration.

PubMed

Sibi, M; Biglary, M; Demarly, Y

1984-07-01

Modification to the cross-over (C. O.) rate of tomato (Lycopersicon esculentum) was attempted by using in vitro plant regeneration. F1 hybrids with the same genetical homozygous background were compared at two loci: "bs-ms32" on chromosome I, and "aa-d" on chromosome II. For each, the genetic distance separating the two markers was about 20 to 30 map units. One cotyledon of each F2 hybrid seedling was used as in vitro tissue culture material, while the rest of the plantlet was grown as a control. Recombination rates of the selfed progenies from each regenerated and matched control couple were compared. For the first set of markers 59,000 seeds were analysed (5 controls' and 7 regenerated progenies), and for the second, 11,000 (5 controls' and 8 regenerated progenies). There were significant increases in the genetic distance between markers in about half the regenerated individuals. For the first set the increases ranged from 6.07 to 6.91 units out of a control distance of the 19.84 to 25.65, corresponding to lengthenings of 30.59 to 35.29%. For the second set they ranged from 4.92 to 6.04 out of a control distance of 25.05 to 26.57, representing increases of 19.64 to 22.75%. Such a phenomenon can be important either from a fundamental or practical viewpoint, regarding selection efficiency in plants, and potential for gene reassortment.

Effects of a common variant in the CD38 gene on social processing in an oxytocin challenge study: possible links to autism.

PubMed

Sauer, Carina; Montag, Christian; Wörner, Christiane; Kirsch, Peter; Reuter, Martin

2012-05-01

The intranasal application of oxytocin (OT) has been shown to influence behavioral and neural correlates of social processing. These effects are probably mediated by genetic variations within the OT system. One potential candidate could be the CD38 gene, which codes for a transmembrane protein engaged in OT secretion processes. A common variation in this gene (rs3796863) was recently found to be associated with autism spectrum disorders (ASD). Using an imaging genetics approach, we studied differential effects of an intranasal OT application on neural processing of social stimuli in 55 healthy young men depending on their CD38 gene variant in a double-blind placebo-controlled crossover design. Genotype had a significant influence on both behavioral and neuronal measures of social processing. Homozygotic risk allele carriers showed slower reaction times (RT) and higher activation of left fusiform gyrus during visual processing of social stimuli. Under OT activation differences between genotypes were more evident (though not statistically significantly increased) and RT were accelerated in homozygotic risk allele carriers. According to our data, rs3796863 mainly influences fusiform gyrus activation, an area which has been widely discussed in ASD research. OT seems to modulate this effect by enhancing activation differences between allele groups, which suggests an interaction between genetic makeup and OT availability on fusiform gyrus activation. These results support recent approaches to apply OT as a pharmacological treatment of ASD symptoms.

Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes

PubMed Central

Anderson, Lorinda K.; Lai, Ann; Stack, Stephen M.; Rizzon, Carene; Gaut, Brandon S.

2006-01-01

Examining the relationships among DNA sequence, meiotic recombination, and chromosome structure at a genome-wide scale has been difficult because only a few markers connect genetic linkage maps with physical maps. Here, we have positioned 1195 genetically mapped expressed sequence tag (EST) markers onto the 10 pachytene chromosomes of maize by using a newly developed resource, the RN-cM map. The RN-cM map charts the distribution of crossing over in the form of recombination nodules (RNs) along synaptonemal complexes (SCs, pachytene chromosomes) and allows genetic cM distances to be converted into physical micrometer distances on chromosomes. When this conversion is made, most of the EST markers used in the study are located distally on the chromosomes in euchromatin. ESTs are significantly clustered on chromosomes, even when only euchromatic chromosomal segments are considered. Gene density and recombination rate (as measured by EST and RN frequencies, respectively) are strongly correlated. However, crossover frequencies for telomeric intervals are much higher than was expected from their EST frequencies. For pachytene chromosomes, EST density is about fourfold higher in euchromatin compared with heterochromatin, while DNA density is 1.4 times higher in heterochromatin than in euchromatin. Based on DNA density values and the fraction of pachytene chromosome length that is euchromatic, we estimate that ∼1500 Mbp of the maize genome is in euchromatin. This overview of the organization of the maize genome will be useful in examining genome and chromosome evolution in plants. PMID:16339046

Microelectronic superconducting crossover and coil

DOEpatents

Wellstood, F.C.; Kingston, J.J.; Clarke, J.

1994-03-01

A microelectronic component comprising a crossover is provided comprising a substrate, a first high T[sub c] superconductor thin film, a second insulating thin film comprising SrTiO[sub 3]; and a third high T[sub c] superconducting film which has strips which crossover one or more areas of the first superconductor film. An in situ method for depositing all three films on a substrate is provided which does not require annealing steps and which can be opened to the atmosphere between depositions. 13 figures.

Analysis of genetic diversity of Chinese dairy goats via microsatellite markers.

PubMed

Wang, G Z; Chen, S S; Chao, T L; Ji, Z B; Hou, L; Qin, Z J; Wang, J M

2017-05-01

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

Assessing pharmacokinetic interactions between the sodium glucose cotransporter 2 inhibitor empagliflozin and hydrochlorothiazide or torasemide in patients with type 2 diabetes mellitus: a randomized, open-label, crossover study.

PubMed

Heise, Tim; Mattheus, Michaela; Woerle, Hans J; Broedl, Uli C; Macha, Sreeraj

2015-04-01

Empagliflozin is a potent, selective sodium glucose cotransporter 2 inhibitor approved for the treatment of type 2 diabetes mellitus. Thiazide or loop diuretics are commonly prescribed in patients with type 2 diabetes mellitus. This study investigated potential pharmacokinetic drug-drug interactions between empagliflozin and hydrochlorothiazide (HCTZ) or torasemide (TOR). This was an open-label, crossover study. Patients with type 2 diabetes mellitus were randomized to receive empagliflozin 25 mg once daily for 5 days and either HCTZ 25 mg once daily for 4 days followed by HCTZ 25 mg once daily plus empagliflozin 25 mg once daily for 5 days or TOR 5 mg once daily for 4 days followed by TOR 5 mg once daily plus empagliflozin once daily for 5 days in 1 of 4 sequences, with at least a 7-day washout period between treatments. Pharmacokinetic parameters of empagliflozin, HCTZ, and TOR were assessed and standard bioequivalence criteria (80%-125%) were applied. Tolerability assessments included the frequency of adverse events and an investigator assessment of global tolerability. Mean (SD) age of the 22 patients treated was 54.0 (8.1) years and body mass index was 27.1 (3.7) kg/m(2). Coadministration of empagliflozin with HCTZ or TOR had no effect on exposure to empagliflozin, HCTZ, or TOR. Geometric mean ratios (90% CIs) for empagliflozin AUC over a uniform dosing interval and Cmax at steady state were 107.1% (90% CI, 97.1-118.1) and 102.8% (90% CI, 88.6-119.3), respectively, when coadministered with HCTZ versus administration alone, and 107.8% (90% CI, 100.1-116.1) and 107.5% (90% CI, 97.9-118.0), respectively, when coadministered with TOR versus administration alone. For HCTZ, the geometric mean ratios for AUC over a uniform dosing interval and Cmax at steady state were 96.3% (90% CI, 89.1-104.0) and 101.8% (90% CI, 88.6-116.9), respectively, and for TOR were 101.4% (90% CI, 99.1-103.9) and 104.4% (90% CI, 93.8-116.3), respectively, for combined treatment versus administration alone. The pharmacokinetic profiles of empagliflozin, HCTZ, and TOR were similar after administration alone and in combination. Global tolerability was good for all patients after each treatment, and no severe or serious adverse events were reported. No pharmacokinetic drug-drug interaction was observed between empagliflozin and HCTZ or TOR. ClinicalTrials.gov identifier: NCT01276288. Copyright © 2015 Elsevier HS Journals, Inc. All rights reserved.

Cyclic and Coherent States in Flocks with Topological Distance

NASA Astrophysics Data System (ADS)

Bhattacherjee, Biplab; Bhattacharya, Kunal; Manna, Subhrangshu

2014-01-01

A simple model of the two dimensional collective motion of a group of mobile agents have been studied. Like birds, these agents travel in open free space where each of them interacts with the first n neighbors determined by the topological distance with a free boundary condition. Using the same prescription for interactions used in the Vicsek model with scalar noise it has been observed that the flock, in absence of the noise, arrives at a number of interesting stationary states. One of the two most prominent states is the `single sink state' where the entire flock travels along the same direction maintaining perfect cohesion and coherence. The other state is the `cyclic state' where every individual agent executes a uniform circular motion, and the correlation among the agents guarantees that the entire flock executes a pulsating dynamics i.e., expands and contracts periodically between a minimum and a maximum size of the flock. We have studied another limiting situation when refreshing rate of the interaction zone is the fastest. In this case the entire flock gets fragmented into smaller clusters of different sizes. On introduction of scalar noise a crossover is observed when the agents cross over from a ballistic motion to a diffusive motion. Expectedly the crossover time is dependent on the strength of the noise η and diverges as η → 0. An even more simpler version of this model has been studied by suppressing the translational degrees of freedom of the agents but retaining their angular motion. Here agents are the spins, placed at the sites of a square lattice with periodic boundary condition. Every spin interacts with its n = 2, 3 or 4 nearest neighbors. In the stationary state the entire spin pattern moves as a whole when interactions are anisotropic with n = 2 and 3; but it is completely frozen when the interaction is isotropic with n=4$. These spin configu

Structural Variation Shapes the Landscape of Recombination in Mouse

PubMed Central

Morgan, Andrew P.; Gatti, Daniel M.; Najarian, Maya L.; Keane, Thomas M.; Galante, Raymond J.; Pack, Allan I.; Mott, Richard; Churchill, Gary A.; de Villena, Fernando Pardo-Manuel

2017-01-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from 6886 DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as 26% of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or 12% of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. PMID:28592499

Four new species of coral gobies (Teleostei: Gobiidae: Gobiodon), with comments on their relationships within the genus

PubMed Central

Bogorodsky, Sergey V.; Suzuki, Toshiyuki

2013-01-01

Four new species of the coral-associated gobiid genus Gobiodon were discovered in the Red Sea. Although several of these species are common not only in the Red Sea but also in the Indian and western Pacific Ocean, they have not been described before. Detailed descriptions of the four species are based on morphological and molecular genetic (mitochondrial 12s and 16s rRNA) investigations. The new species, like most species of the genus, lack scales and have species-specific life colouration. Gobiodon bilineatus sp. nov. is the closest relative to G. quinquestrigatus (Valenciennes) and of G. sp. D (Munday et al.), and has five distinct, blue lines on the head as juveniles and subadults, which disappear in adults, and which are often uniformly orange-red with two distinct, vertical blue lines through each eye. Gobiodon irregularis sp. nov. has been confused with the former new species in the past, and is closely related to G. oculolineatus Wu, but is unmistakable in live colouration. Juveniles are characterised by a transparent body, red bars on the head with bluish to greyish interspaces, and irregular red lines and dots on the nape and dorsally on the body. Adults are usually uniformly brown or green-brown, with only remnants of the bars through the eye and below the orbit. Gobiodon ater sp. nov. is a small, entirely black species and can be easily confused with other black species, although it is genetically clearly distinct from G. ceramensis Bleeker and its black relatives. Gobiodon fuscoruber sp. nov. is likely to be the closest relative of G. ater sp. nov., but is uniformly reddish-brown or brown, has bright median fin margins (at least in the Red Sea), and grows considerably larger than G. ater. It has been genetically determined that G. fuscoruber sp. nov. is identical with an Indian Ocean/western Pacific species that has been called G. unicolor Castelnau by several authors. However, examination of the holotype of G. unicolor, including the original description, revealed that the type species and original description are clearly different from the species frequently called G. unicolor. The holotype resembles G. histrio (Valenciennes) and the name G. unicolor must therefore be considered a junior synonym of G. histrio. As a consequence, a new name for this species is provided. PMID:24511221

Three-cable median barrier final report.

DOT National Transportation Integrated Search

1998-07-01

Oregon public interest peaked regarding crossover highway safety following three fatalities from a crossover accident in August of 1996. The Oregon Department of Transportation (ODOT) conducted a review of possible barrier solutions for the interstat...

Flexible chain molecules in the marginal and concentrated regimes: universal static scaling laws and cross-over predictions.

PubMed

Laso, Manuel; Karayiannis, Nikos Ch

2008-05-07

We present predictions for the static scaling exponents and for the cross-over polymer volumetric fractions in the marginal and concentrated solution regimes. Corrections for finite chain length are made. Predictions are based on an analysis of correlated fluctuations in density and chain length, in a semigrand ensemble in which mers and solvent sites exchange identities. Cross-over volumetric fractions are found to be chain length independent to first order, although reciprocal-N corrections are also estimated. Predicted scaling exponents and cross-over regimes are compared with available data from extensive off-lattice Monte Carlo simulations [Karayiannis and Laso, Phys. Rev. Lett. 100, 050602 (2008)] on freely jointed, hard-sphere chains of average lengths from N=12-500 and at packing densities from dilute ones up to the maximally random jammed state.

Randomized crossover clinical trial of real and sham peripheral prism glasses for hemianopia

PubMed Central

Bowers, Alex R.; Keeney, Karen; Peli, Eli

2013-01-01

Objective To evaluate the efficacy of real relative to sham peripheral prism glasses for patients with complete homonymous hemianopia and without visual neglect. Methods Patients recruited at 13 clinics were allocated by minimization into a double-masked, crossover trial with two groups. One group received real (57Δ) oblique and sham (≤ 5Δ) horizontal prisms; the other received real horizontal and sham oblique, in counterbalanced order. A masked data collector at each clinic administered questionnaires after each 4-week crossover period. Main outcome measure The primary outcome was the overall difference, across the two periods of the crossover, between the proportion of participants who wanted to continue with (said “yes” to) real prisms and the proportion who said yes to sham prisms. The secondary outcome was the difference in perceived mobility improvement between real and sham prisms. Results Of 73 patients randomized, 61 completed the crossover. A significantly higher proportion said yes to real than sham prisms (64% vs. 36%; odds ratio 5.3, 95% CI 1.8 to 21.0). Participants who continued wear after 6 months reported greater improvement in mobility with real than sham prisms at crossover end (p=0.002); participants who discontinued wear reported no difference. Conclusion Real peripheral prism glasses were more helpful for obstacle avoidance when walking than sham glasses, with no differences between the horizontal and oblique designs. Applications to clinical practice Peripheral prism glasses provide a simple and inexpensive mobility rehabilitation intervention for hemianopia. PMID:24201760

Bayesian analysis of time-series data under case-crossover designs: posterior equivalence and inference.

PubMed

Li, Shi; Mukherjee, Bhramar; Batterman, Stuart; Ghosh, Malay

2013-12-01

Case-crossover designs are widely used to study short-term exposure effects on the risk of acute adverse health events. While the frequentist literature on this topic is vast, there is no Bayesian work in this general area. The contribution of this paper is twofold. First, the paper establishes Bayesian equivalence results that require characterization of the set of priors under which the posterior distributions of the risk ratio parameters based on a case-crossover and time-series analysis are identical. Second, the paper studies inferential issues under case-crossover designs in a Bayesian framework. Traditionally, a conditional logistic regression is used for inference on risk-ratio parameters in case-crossover studies. We consider instead a more general full likelihood-based approach which makes less restrictive assumptions on the risk functions. Formulation of a full likelihood leads to growth in the number of parameters proportional to the sample size. We propose a semi-parametric Bayesian approach using a Dirichlet process prior to handle the random nuisance parameters that appear in a full likelihood formulation. We carry out a simulation study to compare the Bayesian methods based on full and conditional likelihood with the standard frequentist approaches for case-crossover and time-series analysis. The proposed methods are illustrated through the Detroit Asthma Morbidity, Air Quality and Traffic study, which examines the association between acute asthma risk and ambient air pollutant concentrations. © 2013, The International Biometric Society.

Experimental observation and simulation of unusual microwave response for the superconducting microstrip resonator at small dc magnetic field

NASA Astrophysics Data System (ADS)

Ong, C. K.; Rao, X. S.; Jin, B. B.

1999-11-01

An unusual microwave response of the surface impedance Zs of high-Tc thin films at an applied small dc magnetic field (Bdc) at 77 K, namely a decrease of Zs, is observed with the microstrip resonator technique. The resonant frequency is 1.107 GHz. The direction of Bdc is parallel or perpendicular to the a-b plane. Bdc ranges from 0 to 200 G. It is found that the surface resistance (Rs) at Bdc parallel to the a-b plane first decreases with Bdc and then increases above a crossover field. The Rs behaviour for Bdc perpendicular to the a-b plane is the same but with a different crossover field. The two behaviours can be collapsed to one curve by scaling the crossover fields. The changes of surface reactance Xs correlated linearly with the changes of Rs in the ranges of Bdc. The ratios rH of changes of Rs and Xs (rH = icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Rs/icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Xs) are 0.5 at Bdc less than the crossover field and 0.1 at Bdc greater than the crossover field. The measurements also show that the crossover field is independent of rf input power. A phenomenological model is also proposed to explain this unusual behaviour. By adjusting fitting parameters the computed results agree with the experimental results qualitatively.

Comparative expression analysis reveals lineage relationships between human and murine gliomas and a dominance of glial signatures during tumor propagation in vitro.

PubMed

Henriquez, Nico V; Forshew, Tim; Tatevossian, Ruth; Ellis, Matthew; Richard-Loendt, Angela; Rogers, Hazel; Jacques, Thomas S; Reitboeck, Pablo Garcia; Pearce, Kerra; Sheer, Denise; Grundy, Richard G; Brandner, Sebastian

2013-09-15

Brain tumors are thought to originate from stem/progenitor cell populations that acquire specific genetic mutations. Although current preclinical models have relevance to human pathogenesis, most do not recapitulate the histogenesis of the human disease. Recently, a large series of human gliomas and medulloblastomas were analyzed for genetic signatures of prognosis and therapeutic response. Using a mouse model system that generates three distinct types of intrinsic brain tumors, we correlated RNA and protein expression levels with human brain tumors. A combination of genetic mutations and cellular environment during tumor propagation defined the incidence and phenotype of intrinsic murine tumors. Importantly, in vitro passage of cancer stem cells uniformly promoted a glial expression profile in culture and in brain tumors. Gene expression profiling revealed that experimental gliomas corresponded to distinct subclasses of human glioblastoma, whereas experimental supratentorial primitive neuroectodermal tumors (sPNET) correspond to atypical teratoid/rhabdoid tumor (AT/RT), a rare childhood tumor. ©2013 AACR.

Electrospun fiber membranes enable proliferation of genetically modified cells

PubMed Central

Borjigin, Mandula; Eskridge, Chris; Niamat, Rohina; Strouse, Bryan; Bialk, Pawel; Kmiec, Eric B

2013-01-01

Polycaprolactone (PCL) and its blended composites (chitosan, gelatin, and lecithin) are well-established biomaterials that can enrich cell growth and enable tissue engineering. However, their application in the recovery and proliferation of genetically modified cells has not been studied. In the study reported here, we fabricated PCL-biomaterial blended fiber membranes, characterized them using physicochemical techniques, and used them as templates for the growth of genetically modified HCT116-19 colon cancer cells. Our data show that the blended polymers are highly miscible and form homogenous electrospun fiber membranes of uniform texture. The aligned PCL nanofibers support robust cell growth, yielding a 2.5-fold higher proliferation rate than cells plated on standard plastic plate surfaces. PCL-lecithin fiber membranes yielded a 2.7-fold higher rate of proliferation, while PCL-chitosan supported a more modest growth rate (1.5-fold higher). Surprisingly, PCL-gelatin did not enhance cell proliferation when compared to the rate of cell growth on plastic surfaces. PMID:23467983

A non-genetic approach to labelling acute myeloid leukemia and bone marrow cells with quantum dots.

PubMed

Zheng, Yanwen; Tan, Dongming; Chen, Zheng; Hu, Chenxi; Mao, Zhengwei J; Singleton, Timothy P; Zeng, Yan; Shao, Xuejun; Yin, Bin

2014-06-01

The difficulty in manipulation of leukemia cells has long hindered the dissection of leukemia pathogenesis. We have introduced a non-genetic approach of marking blood cells, using quantum dots. We compared quantum dots complexed with different vehicles, including a peptide Tat, cationic polymer Turbofect and liposome. Quantum dots-Tat showed the highest efficiency of marking hematopoietic cells among the three vehicles. Quantum dots-Tat could also label a panel of leukemia cell lines at varied efficiencies. More uniform intracellular distributions of quantum dots in mouse bone marrow and leukemia cells were obtained with quantum dots-Tat, compared with the granule-like formation obtained with quantum dots-liposome. Our results suggest that quantum dots have provided a photostable and non-genetic approach that labels normal and malignant hematopoietic cells, in a cell type-, vehicle-, and quantum dot concentration-dependent manner. We expect for potential applications of quantum dots as an easy and fast marking tool assisting investigations of various types of blood cells in the future.

Additive genetic contribution to symptom dimensions in major depressive disorder.

PubMed

Pearson, Rahel; Palmer, Rohan H C; Brick, Leslie A; McGeary, John E; Knopik, Valerie S; Beevers, Christopher G

2016-05-01

Major depressive disorder (MDD) is a phenotypically heterogeneous disorder with a complex genetic architecture. In this study, genomic-relatedness-matrix restricted maximum-likelihood analysis (GREML) was used to investigate the extent to which variance in depression symptoms/symptom dimensions can be explained by variation in common single nucleotide polymorphisms (SNPs) in a sample of individuals with MDD (N = 1,558) who participated in the National Institute of Mental Health Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. A principal components analysis of items from the Hamilton Rating Scale for Depression (HRSD) obtained prior to treatment revealed 4 depression symptom components: (a) appetite, (b) core depression symptoms (e.g., depressed mood, anhedonia), (c) insomnia, and (d) anxiety. These symptom dimensions were associated with SNP-based heritability (hSNP2) estimates of 30%, 14%, 30%, and 5%, respectively. Results indicated that the genetic contribution of common SNPs to depression symptom dimensions were not uniform. Appetite and insomnia symptoms in MDD had a relatively strong genetic contribution whereas the genetic contribution was relatively small for core depression and anxiety symptoms. While in need of replication, these results suggest that future gene discovery efforts may strongly benefit from parsing depression into its constituent parts. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

PREPARATION, IN VITRO AND IN VIVO CHARACTERIZATION OF HYDROPHOBIC PATCHES OF A HIGHLY WATER SOLUBLE DRUG FOR PROLONGED PLASMA HALF LIFE: EFFECT OF PERMEATION ENHANCERS.

PubMed

Yaqoob, Ayesha; Ahmad, Mahmood; Mahmood, Asif; Sarfraz, Rai Muhammad

2016-11-01

Aim of present study was to develop metoprolol matrix patches using different enhancers. Combination of two hydrophobic polymers, ethyl cellulose and eudragit RL 100 (8 : 2) were used for preparation of unilaminated matrix patch. 10% w/w of isopropyl myristate (IPM), dimethyl sulfoxide (DMSO), span (20 (S20), Tween 20 (T20) and eucalyptus oil as enhancers and 40% of dibutyl phthalate as plasticizer were used. Prepared patches were evaluated for physical appearance, weight uniformity and thickness. FTIR studies were performed to assess compatibility among ingredients and developed formulation. Dissolution and permeation studies were performed to compare effects of enhancers. Surface morphology after release was examined by scanning electron microscopy. Selected formulation was subjected to in vivo studies by randomized crossover design in rabbits (n = 6) for pharmacokinetic comparison with oral solution administration. Physical evaluation revealed that translucent, flexible, non brittle patches of uniform weight and thickness were prepared. Release from patches followed Higuchi model. Mechanism of release was Fickian. Formulation containing IPM showed that release was by anomalous transport. Highest permeation flux was observed for formulation containing IPM with 2-fold enhancement in permeation. Permeation flux for patches was in order of formulation with no enhancer > IPM > T20 > S20 > DMSO = eucalyptus oil. Plasma concentration from in vivo studies exhibited sustained plasma levels of metoprolol after transdermal patch application in comparison to oral solution administration. Pharmacokinetic analysis of in vivo data elucidated that half life was increased 8 times when compared to oral administration, due to controlled release of drug for longer period of time. These findings suggested that hydrophobic transdermal patches of highly water soluble drug metoprolol were successfully prepared with 10% of IPM for sustained systemic delivery for prolonged half life.

Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

PubMed

Pissard, Audrey; Arbizu, Carlos; Ghislain, Marc; Faux, Anne-Michèle; Paulet, Sébastien; Bertin, Pierre

2008-01-01

Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.

Combination of uniform design with artificial neural network coupling genetic algorithm: an effective way to obtain high yield of biomass and algicidal compound of a novel HABs control actinomycete

PubMed Central

2014-01-01

Controlling harmful algae blooms (HABs) using microbial algicides is cheap, efficient and environmental-friendly. However, obtaining high yield of algicidal microbes to meet the need of field test is still a big challenge since qualitative and quantitative analysis of algicidal compounds is difficult. In this study, we developed a protocol to increase the yield of both biomass and algicidal compound present in a novel algicidal actinomycete Streptomyces alboflavus RPS, which kills Phaeocystis globosa. To overcome the problem in algicidal compound quantification, we chose algicidal ratio as the index and used artificial neural network to fit the data, which was appropriate for this nonlinear situation. In this protocol, we firstly determined five main influencing factors through single factor experiments and generated the multifactorial experimental groups with a U15(155) uniform-design-table. Then, we used the traditional quadratic polynomial stepwise regression model and an accurate, fully optimized BP-neural network to simulate the fermentation. Optimized with genetic algorithm and verified using experiments, we successfully increased the algicidal ratio of the fermentation broth by 16.90% and the dry mycelial weight by 69.27%. These results suggested that this newly developed approach is a viable and easy way to optimize the fermentation conditions for algicidal microorganisms. PMID:24886410

Combination of uniform design with artificial neural network coupling genetic algorithm: an effective way to obtain high yield of biomass and algicidal compound of a novel HABs control actinomycete.

PubMed

Cai, Guanjing; Zheng, Wei; Yang, Xujun; Zhang, Bangzhou; Zheng, Tianling

2014-05-24

Controlling harmful algae blooms (HABs) using microbial algicides is cheap, efficient and environmental-friendly. However, obtaining high yield of algicidal microbes to meet the need of field test is still a big challenge since qualitative and quantitative analysis of algicidal compounds is difficult. In this study, we developed a protocol to increase the yield of both biomass and algicidal compound present in a novel algicidal actinomycete Streptomyces alboflavus RPS, which kills Phaeocystis globosa. To overcome the problem in algicidal compound quantification, we chose algicidal ratio as the index and used artificial neural network to fit the data, which was appropriate for this nonlinear situation. In this protocol, we firstly determined five main influencing factors through single factor experiments and generated the multifactorial experimental groups with a U15(155) uniform-design-table. Then, we used the traditional quadratic polynomial stepwise regression model and an accurate, fully optimized BP-neural network to simulate the fermentation. Optimized with genetic algorithm and verified using experiments, we successfully increased the algicidal ratio of the fermentation broth by 16.90% and the dry mycelial weight by 69.27%. These results suggested that this newly developed approach is a viable and easy way to optimize the fermentation conditions for algicidal microorganisms.

Tuning porosity and radial mechanical properties of DNA origami nanotubes via crossover design

NASA Astrophysics Data System (ADS)

Ma, Zhipeng; Kawai, Kentaro; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

2017-06-01

DNA origami nanotubes are utilized as structural platforms for the fabrication of various micro/nanosystems for drug delivery, optical or biological sensing, and even nanoscale robots. Their radial structural and mechanical properties, which play a crucial role in the effective use of micro/nanosystems, have not been fully studied. In particular, the effects of crossovers, which are basic structures for rationally assembling double-stranded DNA (dsDNA) helices into a nanotube configuration, have not yet been characterized experimentally. To investigate the effects of crossovers on the porosity and the radial mechanical properties of DNA origami nanotubes, we fabricated a DNA origami nanotube with varied crossover designs along the nanotube axis. The radial geometry of the DNA origami nanotube is experimentally characterized by both atomic force microscopy (AFM) and electron cryomicroscopy (cryo-EM). Moreover, the radial mechanical properties of the DNA origami nanotube including the radial modulus are directly measured by force-distance-based AFM. These measurements reveal that the porosity and the radial modulus of DNA origami nanotubes can be tuned by adjusting the crossover design, which enables the optimal design and construction of DNA origami nanostructures for various applications.

The Saccharomyces cerevisiae Mlh1-Mlh3 Heterodimer Is an Endonuclease That Preferentially Binds to Holliday Junctions*

PubMed Central

Ranjha, Lepakshi; Anand, Roopesh; Cejka, Petr

2014-01-01

MutLγ, a heterodimer of the MutL homologues Mlh1 and Mlh3, plays a critical role during meiotic homologous recombination. The meiotic function of Mlh3 is fully dependent on the integrity of a putative nuclease motif DQHAX2EX4E, inferring that the anticipated nuclease activity of Mlh1-Mlh3 is involved in the processing of joint molecules to generate crossover recombination products. Although a vast body of genetic and cell biological data regarding Mlh1-Mlh3 is available, mechanistic insights into its function have been lacking due to the unavailability of the recombinant protein complex. Here we expressed the yeast Mlh1-Mlh3 heterodimer and purified it into near homogeneity. We show that recombinant MutLγ is a nuclease that nicks double-stranded DNA. We demonstrate that MutLγ binds DNA with a high affinity and shows a marked preference for Holliday junctions. We also expressed the human MLH1-MLH3 complex and show that preferential binding to Holliday junctions is a conserved capacity of eukaryotic MutLγ complexes. Specific DNA recognition has never been observed with any other eukaryotic MutL homologue. MutLγ thus represents a new paradigm for the function of the eukaryotic MutL protein family. We provide insights into the mode of Holliday junction recognition and show that Mlh1-Mlh3 prefers to bind the open unstacked Holliday junction form. This further supports the model where MutLγ is part of a complex acting on joint molecules to generate crossovers in meiosis. PMID:24443562

The Saccharomyces cerevisiae Mlh1-Mlh3 heterodimer is an endonuclease that preferentially binds to Holliday junctions.

PubMed

Ranjha, Lepakshi; Anand, Roopesh; Cejka, Petr

2014-02-28

MutLγ, a heterodimer of the MutL homologues Mlh1 and Mlh3, plays a critical role during meiotic homologous recombination. The meiotic function of Mlh3 is fully dependent on the integrity of a putative nuclease motif DQHAX2EX4E, inferring that the anticipated nuclease activity of Mlh1-Mlh3 is involved in the processing of joint molecules to generate crossover recombination products. Although a vast body of genetic and cell biological data regarding Mlh1-Mlh3 is available, mechanistic insights into its function have been lacking due to the unavailability of the recombinant protein complex. Here we expressed the yeast Mlh1-Mlh3 heterodimer and purified it into near homogeneity. We show that recombinant MutLγ is a nuclease that nicks double-stranded DNA. We demonstrate that MutLγ binds DNA with a high affinity and shows a marked preference for Holliday junctions. We also expressed the human MLH1-MLH3 complex and show that preferential binding to Holliday junctions is a conserved capacity of eukaryotic MutLγ complexes. Specific DNA recognition has never been observed with any other eukaryotic MutL homologue. MutLγ thus represents a new paradigm for the function of the eukaryotic MutL protein family. We provide insights into the mode of Holliday junction recognition and show that Mlh1-Mlh3 prefers to bind the open unstacked Holliday junction form. This further supports the model where MutLγ is part of a complex acting on joint molecules to generate crossovers in meiosis.

Mitochondrial Haplotype Diversity in Zambian Lions: Bridging a Gap in the Biogeography of an Iconic Species

PubMed Central

Curry, Caitlin J.; White, Paula A.; Derr, James N.

2015-01-01

Analysis of DNA sequence diversity at the 12S to 16S mitochondrial genes of 165 African lions (Panthera leo) from five main areas in Zambia has uncovered haplotypes which link Southern Africa with East Africa. Phylogenetic analysis suggests Zambia may serve as a bridge connecting the lion populations in southern Africa to eastern Africa, supporting earlier hypotheses that eastern-southern Africa may represent the evolutionary cradle for the species. Overall gene diversity throughout the Zambian lion population was 0.7319 +/- 0.0174 with eight haplotypes found; three haplotypes previously described and the remaining five novel. The addition of these five novel haplotypes, so far only found within Zambia, nearly doubles the number of haplotypes previously reported for any given geographic location of wild lions. However, based on an AMOVA analysis of these haplotypes, there is little to no matrilineal gene flow (Fst = 0.47) when the eastern and western regions of Zambia are considered as two regional sub-populations. Crossover haplotypes (H9, H11, and Z1) appear in both populations as rare in one but common in the other. This pattern is a possible result of the lion mating system in which predominately males disperse, as all individuals with crossover haplotypes were male. The determination and characterization of lion sub-populations, such as done in this study for Zambia, represent a higher-resolution of knowledge regarding both the genetic health and connectivity of lion populations, which can serve to inform conservation and management of this iconic species. PMID:26674533

Mitochondrial Haplotype Diversity in Zambian Lions: Bridging a Gap in the Biogeography of an Iconic Species.

PubMed

Curry, Caitlin J; White, Paula A; Derr, James N

2015-01-01

Analysis of DNA sequence diversity at the 12S to 16S mitochondrial genes of 165 African lions (Panthera leo) from five main areas in Zambia has uncovered haplotypes which link Southern Africa with East Africa. Phylogenetic analysis suggests Zambia may serve as a bridge connecting the lion populations in southern Africa to eastern Africa, supporting earlier hypotheses that eastern-southern Africa may represent the evolutionary cradle for the species. Overall gene diversity throughout the Zambian lion population was 0.7319 +/- 0.0174 with eight haplotypes found; three haplotypes previously described and the remaining five novel. The addition of these five novel haplotypes, so far only found within Zambia, nearly doubles the number of haplotypes previously reported for any given geographic location of wild lions. However, based on an AMOVA analysis of these haplotypes, there is little to no matrilineal gene flow (Fst = 0.47) when the eastern and western regions of Zambia are considered as two regional sub-populations. Crossover haplotypes (H9, H11, and Z1) appear in both populations as rare in one but common in the other. This pattern is a possible result of the lion mating system in which predominately males disperse, as all individuals with crossover haplotypes were male. The determination and characterization of lion sub-populations, such as done in this study for Zambia, represent a higher-resolution of knowledge regarding both the genetic health and connectivity of lion populations, which can serve to inform conservation and management of this iconic species.

Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize.

PubMed

He, Yan; Wang, Minghui; Dukowic-Schulze, Stefanie; Zhou, Adele; Tiang, Choon-Lin; Shilo, Shay; Sidhu, Gaganpreet K; Eichten, Steven; Bradbury, Peter; Springer, Nathan M; Buckler, Edward S; Levy, Avraham A; Sun, Qi; Pillardy, Jaroslaw; Kianian, Penny M A; Kianian, Shahryar F; Chen, Changbin; Pawlowski, Wojciech P

2017-11-14

Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.

Increasing spin crossover cooperativity in 2D Hofmann-type materials with guest molecule removal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zenere, Katrina A.; Duyker, Samuel G.; Trzop, Elzbieta

Ambient temperature spin crossover with wide hysteresis has been achieved in 2D Hofmann-type materials, where removal of guest molecules optimises ligand–ligand interactions, resulting in increased cooperativity.

Increasing spin crossover cooperativity in 2D Hofmann-type materials with guest molecule removal

DOE PAGES

Zenere, Katrina A.; Duyker, Samuel G.; Trzop, Elzbieta; ...

2018-01-01

Ambient temperature spin crossover with wide hysteresis has been achieved in 2D Hofmann-type materials, where removal of guest molecules optimises ligand–ligand interactions, resulting in increased cooperativity.

30 CFR 56.19023 - Examinations.

Code of Federal Regulations, 2010 CFR

2010-07-01

... drum, at drum crossovers, and at change-of-layer regions. When any visible condition that results in a... leaves the drum at regular stopping points; and (4) At drum crossover and change-of-layer regions. (d) At...

30 CFR 75.827 - Guarding of trailing cables.

Code of Federal Regulations, 2012 CFR

2012-07-01

... grounded metal. (b) Suspended cables and cable crossovers. When equipment must cross any portion of the cable, the cable must be either: (1) Suspended from the mine roof; or (2) Protected by a cable crossover...

30 CFR 75.827 - Guarding of trailing cables.

Code of Federal Regulations, 2014 CFR

2014-07-01

... grounded metal. (b) Suspended cables and cable crossovers. When equipment must cross any portion of the cable, the cable must be either: (1) Suspended from the mine roof; or (2) Protected by a cable crossover...

30 CFR 75.827 - Guarding of trailing cables.

Code of Federal Regulations, 2011 CFR

2011-07-01

... grounded metal. (b) Suspended cables and cable crossovers. When equipment must cross any portion of the cable, the cable must be either: (1) Suspended from the mine roof; or (2) Protected by a cable crossover...