A method to assign failure rates for piping reliability assessments

International Nuclear Information System (INIS)

Gamble, R.M.; Tagart, S.W. Jr.

1991-01-01

This paper reports on a simplified method that has been developed to assign failure rates that can be used in reliability and risk studies of piping. The method can be applied on a line-by-line basis by identifying line and location specific attributes that can lead to piping unreliability from in-service degradation mechanisms and random events. A survey of service experience for nuclear piping reliability also was performed. The data from this survey provides a basis for identifying in-service failure attributes and assigning failure rates for risk and reliability studies

A Review on Eigenstructure Assignment Methods and Orthogonal Eigenstructure Control of Structural Vibrations

Directory of Open Access Journals (Sweden)

Mohammad Rastgaar

2009-01-01

Full Text Available This paper provides a state-of-the-art review of eigenstructure assignment methods for vibration cancellation. Eigenstructure assignment techniques have been widely used during the past three decades for vibration suppression in structures, especially in large space structures. These methods work similar to mode localization in which global vibrations are managed such that they remain localized within the structure. Such localization would help reducing vibrations more effectively than other methods of vibration cancellation, by virtue of confining the vibrations close to the source of disturbance. The common objective of different methods of eigenstructure assignment is to provide controller design freedom beyond pole placement, and define appropriate shapes for the eigenvectors of the systems. These methods; however, offer a large and complex design space of options that can often overwhelm the control designer. Recent developments in orthogonal eigenstructure control offers a significant simplification of the design task while allowing some experience-based design freedom. The majority of the papers from the past three decades in structural vibration cancellation using eigenstructure assignment methods are reviewed, along with recent studies that introduce new developments in eigenstructure assignment techniques.

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

Directory of Open Access Journals (Sweden)

Sarah L. Westcott

2015-12-01

Full Text Available Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important.Methods. Our analysis implemented six de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew’s Correlation Coefficient (MCC to assess the stability and quality of OTU assignments.Results. The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and

The phase-resolved photoacoustic method to indicate chemical assignments of paracetamol

Science.gov (United States)

Camilotti, J. G.; Somer, A.; Costa, G. F.; Ribeiro, M. A.; Bonardi, C.; Cruz, G. K.; Gómez, S. L.; Beltrame, F. L.; Medina, A. N.; Sato, F.; Astrath, N. G. C.; Novatski, A.

2014-03-01

In this work, the phase-resolved photoacoustic method was applied to provide specific information on the chemical assignments of paracetamol in the near-infrared region. Two broad bands, centered at 1370 and 1130 nm, were well-resolved using this method, making it possible to assign the peaks centered at 1398, 1355 and 1295 nm to a C-H combination from a CH3 structure and the peak at 1305 nm to a C-H combination from the aromatic ring. This information represents a new finding in chemical studies regarding this medicament.

Mathematical programming models for solving in equal-sized facilities layout problems. A genetic search method

International Nuclear Information System (INIS)

Tavakkoli-Moghaddam, R.

1999-01-01

This paper present unequal-sized facilities layout solutions generated by a genetic search program. named Layout Design using a Genetic Algorithm) 9. The generalized quadratic assignment problem requiring pre-determined distance and material flow matrices as the input data and the continuous plane model employing a dynamic distance measure and a material flow matrix are discussed. Computational results on test problems are reported as compared with layout solutions generated by the branch - and bound algorithm a hybrid method merging simulated annealing and local search techniques, and an optimization process of an enveloped block

An Optimization Method of Passenger Assignment for Customized Bus

OpenAIRE

Yang Cao; Jian Wang

2017-01-01

This study proposes an optimization method of passenger assignment on customized buses (CB). Our proposed method guarantees benefits to passengers by balancing the elements of travel time, waiting time, delay, and economic cost. The optimization problem was solved using a Branch and Bound (B&B) algorithm based on the shortest path for the selected stations. A simulation-based evaluation of the proposed optimization method was conducted. We find that a CB service can save 38.33% in average tra...

AN EVOLUTIONARY ALGORITHM FOR CHANNEL ASSIGNMENT PROBLEM IN WIRELESS MOBILE NETWORKS

Directory of Open Access Journals (Sweden)

Yee Shin Chia

2012-12-01

Full Text Available The channel assignment problem in wireless mobile network is the assignment of appropriate frequency spectrum to incoming calls while maintaining a satisfactory level of electromagnetic compatibility (EMC constraints. An effective channel assignment strategy is important due to the limited capacity of frequency spectrum in wireless mobile network. Most of the existing channel assignment strategies are based on deterministic methods. In this paper, an adaptive genetic algorithm (GA based channel assignment strategy is introduced for resource management and to reduce the effect of EMC interferences. The most significant advantage of the proposed optimization method is its capability to handle both the reassignment of channels for existing calls as well as the allocation of channel to a new incoming call in an adaptive process to maximize the utility of the limited resources. It is capable to adapt the population size to the number of eligible channels for a particular cell upon new call arrivals to achieve reasonable convergence speed. The MATLAB simulation on a 49-cells network model for both uniform and nonuniform call traffic distributions showed that the proposed channel optimization method can always achieve a lower average new incoming call blocking probability compared to the deterministic based channel assignment strategy.

A method for simultaneously counterbalancing condition order and assignment of stimulus materials to conditions.

Science.gov (United States)

Zeelenberg, René; Pecher, Diane

2015-03-01

Counterbalanced designs are frequently used in the behavioral sciences. Studies often counterbalance either the order in which conditions are presented in the experiment or the assignment of stimulus materials to conditions. Occasionally, researchers need to simultaneously counterbalance both condition order and stimulus assignment to conditions. Lewis (1989; Behavior Research Methods, Instruments, & Computers 25:414-415, 1993) presented a method for constructing Latin squares that fulfill these requirements. The resulting Latin squares counterbalance immediate sequential effects, but not remote sequential effects. Here, we present a new method for generating Latin squares that simultaneously counterbalance both immediate and remote sequential effects and assignment of stimuli to conditions. An Appendix is provided to facilitate implementation of these Latin square designs.

Method for assigning sites to projected generic nuclear power plants

Energy Technology Data Exchange (ETDEWEB)

Holter, G.M.; Purcell, W.L.; Shutz, M.E.; Young, J.R.

1986-07-01

Pacific Northwest Laboratory developed a method for forecasting potential locations and startup sequences of nuclear power plants that will be required in the future but have not yet been specifically identified by electric utilities. Use of the method results in numerical ratings for potential nuclear power plant sites located in each of the 10 federal energy regions. The rating for each potential site is obtained from numerical factors assigned to each of 5 primary siting characteristics: (1) cooling water availability, (2) site land area, (3) power transmission land area, (4) proximity to metropolitan areas, and (5) utility plans for the site. The sequence of plant startups in each federal energy region is obtained by use of the numerical ratings and the forecasts of generic nuclear power plant startups obtained from the EIA Middle Case electricity forecast. Sites are assigned to generic plants in chronological order according to startup date.

Method for assigning sites to projected generic nuclear power plants

International Nuclear Information System (INIS)

Holter, G.M.; Purcell, W.L.; Shutz, M.E.; Young, J.R.

1986-07-01

Pacific Northwest Laboratory developed a method for forecasting potential locations and startup sequences of nuclear power plants that will be required in the future but have not yet been specifically identified by electric utilities. Use of the method results in numerical ratings for potential nuclear power plant sites located in each of the 10 federal energy regions. The rating for each potential site is obtained from numerical factors assigned to each of 5 primary siting characteristics: (1) cooling water availability, (2) site land area, (3) power transmission land area, (4) proximity to metropolitan areas, and (5) utility plans for the site. The sequence of plant startups in each federal energy region is obtained by use of the numerical ratings and the forecasts of generic nuclear power plant startups obtained from the EIA Middle Case electricity forecast. Sites are assigned to generic plants in chronological order according to startup date

Accuracy of administratively-assigned ancestry for diverse populations in an electronic medical record-linked biobank.

Directory of Open Access Journals (Sweden)

Jacob B Hall

Full Text Available Recently, the development of biobanks linked to electronic medical records has presented new opportunities for genetic and epidemiological research. Studies based on these resources, however, present unique challenges, including the accurate assignment of individual-level population ancestry. In this work we examine the accuracy of administratively-assigned race in diverse populations by comparing assigned races to genetically-defined ancestry estimates. Using 220 ancestry informative markers, we generated principal components for patients in our dataset, which were used to cluster patients into groups based on genetic ancestry. Consistent with other studies, we find a strong overall agreement (Kappa  = 0.872 between genetic ancestry and assigned race, with higher rates of agreement for African-descent and European-descent assignments, and reduced agreement for Hispanic, East Asian-descent, and South Asian-descent assignments. These results suggest caution when selecting study samples of non-African and non-European backgrounds when administratively-assigned race from biobanks is used.

Automation of block assignment planning using a diagram-based scenario modeling method

Directory of Open Access Journals (Sweden)

In Hyuck Hwang

2014-03-01

Full Text Available Most shipbuilding scheduling research so far has focused on the load level on the dock plan. This is because the dock is the least extendable resource in shipyards, and its overloading is difficult to resolve. However, once dock scheduling is completed, making a plan that makes the best use of the rest of the resources in the shipyard to minimize any additional cost is also important. Block assignment planning is one of the midterm planning tasks; it assigns a block to the facility (factory/shop or surface plate that will actually manufacture the block according to the block characteristics and current situation of the facility. It is one of the most heavily loaded midterm planning tasks and is carried out manually by experienced workers. In this study, a method of representing the block assignment rules using a diagram was suggested through analysis of the existing manual process. A block allocation program was developed which automated the block assignment process according to the rules represented by the diagram. The planning scenario was validated through a case study that compared the manual assignment and two automated block assignment results.

Automation of block assignment planning using a diagram-based scenario modeling method

Directory of Open Access Journals (Sweden)

Hwang In Hyuck

2014-03-01

Full Text Available Most shipbuilding scheduling research so far has focused on the load level on the dock plan. This is be¬cause the dock is the least extendable resource in shipyards, and its overloading is difficult to resolve. However, once dock scheduling is completed, making a plan that makes the best use of the rest of the resources in the shipyard to minimize any additional cost is also important. Block assignment planning is one of the midterm planning tasks; it assigns a block to the facility (factory/shop or surface plate that will actually manufacture the block according to the block characteristics and current situation of the facility. It is one of the most heavily loaded midterm planning tasks and is carried out manu¬ally by experienced workers. In this study, a method of representing the block assignment rules using a diagram was su¬ggested through analysis of the existing manual process. A block allocation program was developed which automated the block assignment process according to the rules represented by the diagram. The planning scenario was validated through a case study that compared the manual assignment and two automated block assignment results.

On minimizing assignment errors and the trade-off between false positives and negatives in parentage analysis

KAUST Repository

Harrison, Hugo B.

2013-11-04

Genetic parentage analyses provide a practical means with which to identify parent-offspring relationships in the wild. In Harrison et al.\\'s study (2013a), we compare three methods of parentage analysis and showed that the number and diversity of microsatellite loci were the most important factors defining the accuracy of assignments. Our simulations revealed that an exclusion-Bayes theorem method was more susceptible to false-positive and false-negative assignments than other methods tested. Here, we analyse and discuss the trade-off between type I and type II errors in parentage analyses. We show that controlling for false-positive assignments, without reporting type II errors, can be misleading. Our findings illustrate the need to estimate and report both the rate of false-positive and false-negative assignments in parentage analyses. © 2013 John Wiley & Sons Ltd.

On minimizing assignment errors and the trade-off between false positives and negatives in parentage analysis

KAUST Repository

Harrison, Hugo B.; Saenz Agudelo, Pablo; Planes, Serge; Jones, Geoffrey P.; Berumen, Michael L.

2013-01-01

Genetic parentage analyses provide a practical means with which to identify parent-offspring relationships in the wild. In Harrison et al.'s study (2013a), we compare three methods of parentage analysis and showed that the number and diversity of microsatellite loci were the most important factors defining the accuracy of assignments. Our simulations revealed that an exclusion-Bayes theorem method was more susceptible to false-positive and false-negative assignments than other methods tested. Here, we analyse and discuss the trade-off between type I and type II errors in parentage analyses. We show that controlling for false-positive assignments, without reporting type II errors, can be misleading. Our findings illustrate the need to estimate and report both the rate of false-positive and false-negative assignments in parentage analyses. © 2013 John Wiley & Sons Ltd.

The Empirical Verification of an Assignment of Items to Subtests : The Oblique Multiple Group Method Versus the Confirmatory Common Factor Method

NARCIS (Netherlands)

Stuive, Ilse; Kiers, Henk A.L.; Timmerman, Marieke E.; ten Berge, Jos M.F.

2008-01-01

This study compares two confirmatory factor analysis methods on their ability to verify whether correct assignments of items to subtests are supported by the data. The confirmatory common factor (CCF) method is used most often and defines nonzero loadings so that they correspond to the assignment of

Methods to estimate the genetic risk

International Nuclear Information System (INIS)

Ehling, U.H.

1989-01-01

The estimation of the radiation-induced genetic risk to human populations is based on the extrapolation of results from animal experiments. Radiation-induced mutations are stochastic events. The probability of the event depends on the dose; the degree of the damage dose not. There are two main approaches in making genetic risk estimates. One of these, termed the direct method, expresses risk in terms of expected frequencies of genetic changes induced per unit dose. The other, referred to as the doubling dose method or the indirect method, expresses risk in relation to the observed incidence of genetic disorders now present in man. The advantage of the indirect method is that not only can Mendelian mutations be quantified, but also other types of genetic disorders. The disadvantages of the method are the uncertainties in determining the current incidence of genetic disorders in human and, in addition, the estimasion of the genetic component of congenital anomalies, anomalies expressed later and constitutional and degenerative diseases. Using the direct method we estimated that 20-50 dominant radiation-induced mutations would be expected in 19 000 offspring born to parents exposed in Hiroshima and Nagasaki, but only a small proportion of these mutants would have been detected with the techniques used for the population study. These methods were used to predict the genetic damage from the fallout of the reactor accident at Chernobyl in the vicinity of Southern Germany. The lack of knowledge for the interaction of chemicals with ionizing radiation and the discrepancy between the high safety standards for radiation protection and the low level of knowledge for the toxicological evaluation of chemical mutagens will be emphasized. (author)

ANALYSIS AND PERFORMANCE MEASUREMENT OF EXISTING SOLUTION METHODS OF QUADRATIC ASSIGNMENT PROBLEM

Directory of Open Access Journals (Sweden)

Morteza KARAMI

2014-01-01

Full Text Available Quadratic Assignment Problem (QAP is known as one of the most difficult combinatorial optimization problems that is classified in the category of NP-hard problems. Quadratic Assignment Problem Library (QAPLIB is a full database of QAPs which contains several problems from different authors and different sizes. Many exact and meta-heuristic solution methods have been introduced to solve QAP. In this study we focus on previously introduced solution methods of QAP e.g. Branch and Bound (B&B, Simulated Annealing (SA Algorithm, Greedy Randomized Adaptive Search Procedure (GRASP for dense and sparse QAPs. The codes of FORTRAN for these methods were downloaded from QAPLIB. All problems of QAPLIB were solved by the abovementioned methods. Several results were obtained from the computational experiments part. The Results show that the Branch and Bound method is able to introduce a feasible solution for all problems while Simulated Annealing Algorithm and GRASP methods are not able to find any solution for some problems. On the other hand, Simulated Annealing and GRASP methods have shorter run time comparing to the Branch and Bound method. In addition, the performance of the methods on the objective function value is discussed.

Parentage assignment of progeny in mixed milt fertilization of ...

African Journals Online (AJOL)

Administrator

2011-06-13

Jun 13, 2011 ... individuals. Overall, 98.8% of progeny were assigned to their parents using Family Assignment. Program (FAP). Selection of hyper-variable microsatellites in Caspian brown trout to identify unique alleles was effective for unambiguous parentage determination and estimation of genetic diversity in this study.

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

KAUST Repository

Abbas, Ahmed

2014-04-19

Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on \\'slices\\', which are one-dimensional vectors in three-dimensional spectra that correspond to certain (N, H) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2014 Springer Science+Business Media.

Statistical methods in spatial genetics

DEFF Research Database (Denmark)

Guillot, Gilles; Leblois, Raphael; Coulon, Aurelie

2009-01-01

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult...... to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only...

Comparison of genetic algorithms with conjugate gradient methods

Science.gov (United States)

Bosworth, J. L.; Foo, N. Y.; Zeigler, B. P.

1972-01-01

Genetic algorithms for mathematical function optimization are modeled on search strategies employed in natural adaptation. Comparisons of genetic algorithms with conjugate gradient methods, which were made on an IBM 1800 digital computer, show that genetic algorithms display superior performance over gradient methods for functions which are poorly behaved mathematically, for multimodal functions, and for functions obscured by additive random noise. Genetic methods offer performance comparable to gradient methods for many of the standard functions.

From Genetics to Genetic Algorithms

Indian Academy of Sciences (India)

artificial genetic system) string feature or ... called the genotype whereas it is called a structure in artificial genetic ... assigned a fitness value based on the cost function. Better ..... way it has produced complex, intelligent living organisms capable of ...

Rationalization of some genetic anticodonic assignments

Science.gov (United States)

Lacey, J. C., Jr.; Hall, L. M.; Mullins, D. W., Jr.

1985-01-01

The hydrophobicity of most amino acids correlates well with that of their anticodon nucleotides, with Trp, Tyr, Ile, and Ser being the exceptions to this rule. Using previous data on hydrophobicity and binding constants, and new data on rates of esterification of polyadenylic acid with several N-acetylaminoacyl imidazolides, several of the anticodon assignments are rationalized. Chemical reasons are shown supporting the idea of the inclusion of the Ile in the catalog of biological amino acids late in the evolution, through a mutation of the existing tRNA and its aminoacyl-tRNA-synthetase. It was found that an addition of hexane increases the incorporation of hydrophobic Ac-Phe into poly-A, in support of the Fox (1965) and Oparin (1965) emphasis on the biogenetic importance of phase-separated systems.

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

Directory of Open Access Journals (Sweden)

Shannon M Clarke

Full Text Available Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development--firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage are assigned. An 84 "parentage SNP panel" was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams was absent, highlighting the SNP test's suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.

Characterizing dispersal patterns in a threatened seabird with limited genetic structure

NARCIS (Netherlands)

Hall, Laurie A.; Palsboll, Per J.; Beissinger, Steven R.; Harvey, James T.; Berube, Martine; Raphael, Martin G.; Nelson, S. Kim; Golightly, Richard T.; Mcfarlane-Tranquilla, Laura; Newman, Scott H.; Peery, M. Zachariah

2009-01-01

Genetic assignment methods provide an appealing approach for characterizing dispersal patterns on ecological time scales, but require sufficient genetic differentiation to accurately identify migrants and a large enough sample size of migrants to, for example, compare dispersal between sexes or age

Statistical methods and challenges in connectome genetics

KAUST Repository

Pluta, Dustin; Yu, Zhaoxia; Shen, Tong; Chen, Chuansheng; Xue, Gui; Ombao, Hernando

2018-01-01

The study of genetic influences on brain connectivity, known as connectome genetics, is an exciting new direction of research in imaging genetics. We here review recent results and current statistical methods in this area, and discuss some

Consumers' Kansei Needs Clustering Method for Product Emotional Design Based on Numerical Design Structure Matrix and Genetic Algorithms.

Science.gov (United States)

Yang, Yan-Pu; Chen, Deng-Kai; Gu, Rong; Gu, Yu-Feng; Yu, Sui-Huai

2016-01-01

Consumers' Kansei needs reflect their perception about a product and always consist of a large number of adjectives. Reducing the dimension complexity of these needs to extract primary words not only enables the target product to be explicitly positioned, but also provides a convenient design basis for designers engaging in design work. Accordingly, this study employs a numerical design structure matrix (NDSM) by parameterizing a conventional DSM and integrating genetic algorithms to find optimum Kansei clusters. A four-point scale method is applied to assign link weights of every two Kansei adjectives as values of cells when constructing an NDSM. Genetic algorithms are used to cluster the Kansei NDSM and find optimum clusters. Furthermore, the process of the proposed method is presented. The details of the proposed approach are illustrated using an example of electronic scooter for Kansei needs clustering. The case study reveals that the proposed method is promising for clustering Kansei needs adjectives in product emotional design.

COMPUTER METHODS OF GENETIC ANALYSIS.

Directory of Open Access Journals (Sweden)

A. L. Osipov

2017-02-01

Full Text Available The basic statistical methods used in conducting the genetic analysis of human traits. We studied by segregation analysis, linkage analysis and allelic associations. Developed software for the implementation of these methods support.

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations.

Directory of Open Access Journals (Sweden)

Paul Moran

Full Text Available Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

Science.gov (United States)

Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

FLEET ASSIGNMENT MODELLING

Directory of Open Access Journals (Sweden)

2016-01-01

Full Text Available The article is devoted to the airline scheduling process and methods of its modeling. This article describes the main stages of airline scheduling process (scheduling, fleet assignment, revenue management, operations, their features and interactions. The main part of scheduling process is fleet assignment. The optimal solution of the fleet assignment problem enables airlines to increase their incomes up to 3 % due to quality improving of connections and execution of the planned number of flights operated by less number of aircraft than usual or planned earlier. Fleet assignment of scheduling process is examined and Conventional Leg-Based Fleet Assignment Model is analyzed. Finally strong and weak aspects of the model (SWOT are released and applied. The article gives a critical analysis of FAM model, with the purpose of identi- fying possible options and constraints of its use (for example, in cases of short-term and long-term planning, changing the schedule or replacing the aircraft, as well as possible ways to improve the model.

Statistical methods and challenges in connectome genetics

KAUST Repository

Pluta, Dustin

2018-03-12

The study of genetic influences on brain connectivity, known as connectome genetics, is an exciting new direction of research in imaging genetics. We here review recent results and current statistical methods in this area, and discuss some of the persistent challenges and possible directions for future work.

A Capacity-Restraint Transit Assignment Model When a Predetermination Method Indicates the Invalidity of Time Independence

Directory of Open Access Journals (Sweden)

Haoyang Ding

2015-01-01

Full Text Available The statistical independence of time of every two adjacent bus links plays a crucial role in deciding the feasibility of using many mathematical models to analyze urban transit networks. Traditional research generally ignores the time independence that acts as the ground of their models. Assumption is usually made that time independence of every two adjacent links is sound. This is, however, actually groundless and probably causes problematic conclusions reached by corresponding models. Many transit assignment models such as multinomial probit-based models lose their effects when the time independence is not valid. In this paper, a simple method to predetermine the time independence is proposed. Based on the predetermination method, a modified capacity-restraint transit assignment method aimed at engineering practice is put forward and tested through a small contrived network and a case study in Nanjing city, China, respectively. It is found that the slope of regression equation between the mean and standard deviation of normal distribution acts as the indicator of time independence at the same time. Besides, our modified assignment method performs better than the traditional one with more reasonable results while keeping the property of simplicity well.

Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

Directory of Open Access Journals (Sweden)

Y. H. Li

2014-05-01

Full Text Available The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates

Multiobjective Order Assignment Optimization in a Global Multiple-Factory Environment

Directory of Open Access Journals (Sweden)

Rong-Chang Chen

2014-01-01

Full Text Available In response to radically increasing competition, many manufacturers who produce time-sensitive products have expanded their production plants to worldwide sites. Given this environment, how to aggregate customer orders from around the globe and assign them quickly to the most appropriate plants is currently a crucial issue. This study proposes an effective method to solve the order assignment problem of companies with multiple plants distributed worldwide. A multiobjective genetic algorithm (MOGA is used to find solutions. To validate the effectiveness of the proposed approach, this study employs some real data, provided by a famous garment company in Taiwan, as a base to perform some experiments. In addition, the influences of orders with a wide range of quantities demanded are discussed. The results show that feasible solutions can be obtained effectively and efficiently. Moreover, if managers aim at lower total costs, they can divide a big customer order into more small manufacturing ones.

A Post-Final Assignment for the Methods Course: Providing an Incentive to Professional Growth for Future Teachers.

Science.gov (United States)

Bentley, Michael L.

This paper describes J. Rosengren's post-final assignment and M. Harmin's truth signs activity that were incorporated into a secondary science methods course for preservice teachers. The strength of the post-final assignment is that it is a strategy for extending student learning past the end of a course and even beyond the initial teaching…

Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

Directory of Open Access Journals (Sweden)

Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

2011-12-01

Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

Identifying the source of farmed escaped Atlantic salmon (Salmo salar): Bayesian clustering analysis increases accuracy of assignment

DEFF Research Database (Denmark)

Glover, Kevin A.; Hansen, Michael Møller; Skaala, Oystein

2009-01-01

44 cages located on 26 farms in the Hardangerfjord, western Norway. This fjord represents one of the major salmon farming areas in Norway, with a production of 57,000 t in 2007. Based upon genetic data from 17 microsatellite markers, significant but highly variable differentiation was observed among....... Accuracy of assignment varied greatly among the individual samples. For the Bayesian clustered data set consisting of five genetic groups, overall accuracy of self-assignment was 99%, demonstrating the effectiveness of this strategy to significantly increase accuracy of assignment, albeit at the expense...

HEURISTIC METHOD FOR LOW POWER RACE-FREE STATE-ASSIGNMENT OF AN ASYNGHRONOUS AUTOMATON

Directory of Open Access Journals (Sweden)

Yu. V. Pottosin

2016-01-01

Full Text Available The problem of race free state-assignment of an asynchronous automaton minimizing the switching activity of memory elements in an implementing circuit is considered. A heuristic method to solve this problem for an asynchronous automaton is suggested where the critical races between memory elements of the implementing circuit are eliminated.

Methods for genetic transformation of filamentous fungi.

Science.gov (United States)

Li, Dandan; Tang, Yu; Lin, Jun; Cai, Weiwen

2017-10-03

Filamentous fungi have been of great interest because of their excellent ability as cell factories to manufacture useful products for human beings. The development of genetic transformation techniques is a precondition that enables scientists to target and modify genes efficiently and may reveal the function of target genes. The method to deliver foreign nucleic acid into cells is the sticking point for fungal genome modification. Up to date, there are some general methods of genetic transformation for fungi, including protoplast-mediated transformation, Agrobacterium-mediated transformation, electroporation, biolistic method and shock-wave-mediated transformation. This article reviews basic protocols and principles of these transformation methods, as well as their advantages and disadvantages.

A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins

International Nuclear Information System (INIS)

Plevin, Michael J.; Hamelin, Olivier; Boisbouvier, Jérôme; Gans, Pierre

2011-01-01

A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[ 13 C]glucose and subsaturating amounts of 2-[ 13 C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1 H- 13 C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NMR assignments of prochiral methyl groups.

Method and system for assigning a confidence metric for automated determination of optic disc location

Science.gov (United States)

Karnowski, Thomas P [Knoxville, TN; Tobin, Jr., Kenneth W.; Muthusamy Govindasamy, Vijaya Priya [Knoxville, TN; Chaum, Edward [Memphis, TN

2012-07-10

A method for assigning a confidence metric for automated determination of optic disc location that includes analyzing a retinal image and determining at least two sets of coordinates locating an optic disc in the retinal image. The sets of coordinates can be determined using first and second image analysis techniques that are different from one another. An accuracy parameter can be calculated and compared to a primary risk cut-off value. A high confidence level can be assigned to the retinal image if the accuracy parameter is less than the primary risk cut-off value and a low confidence level can be assigned to the retinal image if the accuracy parameter is greater than the primary risk cut-off value. The primary risk cut-off value being selected to represent an acceptable risk of misdiagnosis of a disease having retinal manifestations by the automated technique.

Comparison of Methods for Adjusting Incorrect Assignments of Items to Subtests Oblique Multiple Group Method Versus Confirmatory Common Factor Method

NARCIS (Netherlands)

Stuive, Ilse; Kiers, Henk A.L.; Timmerman, Marieke E.

2009-01-01

A common question in test evaluation is whether an a priori assignment of items to subtests is supported by empirical data. If the analysis results indicate the assignment of items to subtests under study is not supported by data, the assignment is often adjusted. In this study the authors compare

Optimization of the test intervals of a nuclear safety system by genetic algorithms, solution clustering and fuzzy preference assignment

International Nuclear Information System (INIS)

Zio, E.; Bazzo, R.

2010-01-01

In this paper, a procedure is developed for identifying a number of representative solutions manageable for decision-making in a multiobjective optimization problem concerning the test intervals of the components of a safety system of a nuclear power plant. Pareto Front solutions are identified by a genetic algorithm and then clustered by subtractive clustering into 'families'. On the basis of the decision maker's preferences, each family is then synthetically represented by a 'head of the family' solution. This is done by introducing a scoring system that ranks the solutions with respect to the different objectives: a fuzzy preference assignment is employed to this purpose. Level Diagrams are then used to represent, analyze and interpret the Pareto Fronts reduced to the head-of-the-family solutions

A robust algorithm to solve the signal setting problem considering different traffic assignment approaches

Directory of Open Access Journals (Sweden)

Adacher Ludovica

2017-12-01

Full Text Available In this paper we extend a stochastic discrete optimization algorithm so as to tackle the signal setting problem. Signalized junctions represent critical points of an urban transportation network, and the efficiency of their traffic signal setting influences the overall network performance. Since road congestion usually takes place at or close to junction areas, an improvement in signal settings contributes to improving travel times, drivers’ comfort, fuel consumption efficiency, pollution and safety. In a traffic network, the signal control strategy affects the travel time on the roads and influences drivers’ route choice behavior. The paper presents an algorithm for signal setting optimization of signalized junctions in a congested road network. The objective function used in this work is a weighted sum of delays caused by the signalized intersections. We propose an iterative procedure to solve the problem by alternately updating signal settings based on fixed flows and traffic assignment based on fixed signal settings. To show the robustness of our method, we consider two different assignment methods: one based on user equilibrium assignment, well established in the literature as well as in practice, and the other based on a platoon simulation model with vehicular flow propagation and spill-back. Our optimization algorithm is also compared with others well known in the literature for this problem. The surrogate method (SM, particle swarm optimization (PSO and the genetic algorithm (GA are compared for a combined problem of global optimization of signal settings and traffic assignment (GOSSTA. Numerical experiments on a real test network are reported.

Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

Science.gov (United States)

Dale, Julia; Price, Erin P; Hornstra, Heidie; Busch, Joseph D; Mayo, Mark; Godoy, Daniel; Wuthiekanun, Vanaporn; Baker, Anthony; Foster, Jeffrey T; Wagner, David M; Tuanyok, Apichai; Warner, Jeffrey; Spratt, Brian G; Peacock, Sharon J; Currie, Bart J; Keim, Paul; Pearson, Talima

2011-12-01

Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics

Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

Directory of Open Access Journals (Sweden)

Julia Dale

2011-12-01

Full Text Available Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST. These populations correlate with the major foci of endemicity (Australia and Southeast Asia. Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs. Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic

Methods for Analyzing Multivariate Phenotypes in Genetic Association Studies

Directory of Open Access Journals (Sweden)

Qiong Yang

2012-01-01

Full Text Available Multivariate phenotypes are frequently encountered in genetic association studies. The purpose of analyzing multivariate phenotypes usually includes discovery of novel genetic variants of pleiotropy effects, that is, affecting multiple phenotypes, and the ultimate goal of uncovering the underlying genetic mechanism. In recent years, there have been new method development and application of existing statistical methods to such phenotypes. In this paper, we provide a review of the available methods for analyzing association between a single marker and a multivariate phenotype consisting of the same type of components (e.g., all continuous or all categorical or different types of components (e.g., some are continuous and others are categorical. We also reviewed causal inference methods designed to test whether the detected association with the multivariate phenotype is truly pleiotropy or the genetic marker exerts its effects on some phenotypes through affecting the others.

Interactive visual exploration and refinement of cluster assignments.

Science.gov (United States)

Kern, Michael; Lex, Alexander; Gehlenborg, Nils; Johnson, Chris R

2017-09-12

With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data. In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes. Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.

Computational Aspects of Assigning Agents to a Line

DEFF Research Database (Denmark)

Aziz, Haris; Hougaard, Jens Leth; Moreno-Ternero, Juan D.

2017-01-01

-egalitarian assignments. The approach relies on an algorithm which is shown to be faster than general purpose algorithms for the assignment problem. We also extend the approach to probabilistic assignments and explore the computational features of existing, as well as new, methods for this setting....

Computational aspects of assigning agents to a line

DEFF Research Database (Denmark)

Aziz, Haris; Hougaard, Jens Leth; Moreno-Ternero, Juan D.

2017-01-01

-egalitarian assignments. The approach relies on an algorithm which is shown to be faster than general purpose algorithms for the assignment problem. We also extend the approach to probabilistic assignments and explore the computational features of existing, as well as new, methods for this setting....

[Application of case-based method in genetics and eugenics teaching].

Science.gov (United States)

Li, Ya-Xuan; Zhao, Xin; Zhang, Fei-Xiong; Hu, Ying-Kao; Yan, Yue-Ming; Cai, Min-Hua; Li, Xiao-Hui

2012-05-01

Genetics and Eugenics is a cross-discipline between genetics and eugenics. It is a common curriculum in many Chinese universities. In order to increase the learning interest, we introduced case teaching method and got a better teaching effect. Based on our teaching practices, we summarized some experiences about this subject. In this article, the main problem of case-based method applied in Genetics and Eugenics teaching was discussed.

A Computerized Approach to Trickle-Process, Random Assignment.

Science.gov (United States)

Braucht, G. Nicholas; Reichardt, Charles S.

1993-01-01

Procedures for implementing random assignment with trickle processing and ways they can be corrupted are described. A computerized method for implementing random assignment with trickle processing is presented as a desirable alternative in many situations and a way of protecting against threats to assignment validity. (SLD)

Method of detecting genetic deletions identified with chromosomal abnormalities

Energy Technology Data Exchange (ETDEWEB)

Gray, Joe W; Pinkel, Daniel; Tkachuk, Douglas

2013-11-26

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acids probes are typically of a complexity greater tha 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particlularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar ut genetically different diseases, and for many prognostic and diagnostic applications.

Assigning breed origin to alleles in crossbred animals.

Science.gov (United States)

Vandenplas, Jérémie; Calus, Mario P L; Sevillano, Claudia A; Windig, Jack J; Bastiaansen, John W M

2016-08-22

For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions. Thus, SNP effects may be breed-specific, which has led to the development of genomic evaluations for crossbred performance that take such effects into account. However, to estimate breed-specific effects, it is necessary to know breed origin of alleles in crossbred animals. Therefore, our aim was to develop an approach for assigning breed origin to alleles of crossbred animals (termed BOA) without information on pedigree and to study its accuracy by considering various factors, including distance between breeds. The BOA approach consists of: (1) phasing genotypes of purebred and crossbred animals; (2) assigning breed origin to phased haplotypes; and (3) assigning breed origin to alleles of crossbred animals based on a library of assigned haplotypes, the breed composition of crossbred animals, and their SNP genotypes. The accuracy of allele assignments was determined for simulated datasets that include crosses between closely-related, distantly-related and unrelated breeds. Across these scenarios, the percentage of alleles of a crossbred animal that were correctly assigned to their breed origin was greater than 90 %, and increased with increasing distance between breeds, while the percentage of incorrectly assigned alleles was always less than 2 %. For the remaining alleles, i.e. 0 to 10 % of all alleles of a crossbred animal, breed origin could not be assigned. The BOA approach accurately assigns

Methods in Molecular Biology Mouse Genetics: Methods and Protocols | Center for Cancer Research

Science.gov (United States)

Mouse Genetics: Methods and Protocols provides selected mouse genetic techniques and their application in modeling varieties of human diseases. The chapters are mainly focused on the generation of different transgenic mice to accomplish the manipulation of genes of interest, tracing cell lineages, and modeling human diseases.

Assessing population genetic structure via the maximisation of genetic distance

Directory of Open Access Journals (Sweden)

Toro Miguel A

2009-11-01

Full Text Available Abstract Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy

Flexible taxonomic assignment of ambiguous sequencing reads

Directory of Open Access Journals (Sweden)

Jansson Jesper

2011-01-01

Full Text Available Abstract Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

Multivariate Methods for Meta-Analysis of Genetic Association Studies.

Science.gov (United States)

Dimou, Niki L; Pantavou, Katerina G; Braliou, Georgia G; Bagos, Pantelis G

2018-01-01

Multivariate meta-analysis of genetic association studies and genome-wide association studies has received a remarkable attention as it improves the precision of the analysis. Here, we review, summarize and present in a unified framework methods for multivariate meta-analysis of genetic association studies and genome-wide association studies. Starting with the statistical methods used for robust analysis and genetic model selection, we present in brief univariate methods for meta-analysis and we then scrutinize multivariate methodologies. Multivariate models of meta-analysis for a single gene-disease association studies, including models for haplotype association studies, multiple linked polymorphisms and multiple outcomes are discussed. The popular Mendelian randomization approach and special cases of meta-analysis addressing issues such as the assumption of the mode of inheritance, deviation from Hardy-Weinberg Equilibrium and gene-environment interactions are also presented. All available methods are enriched with practical applications and methodologies that could be developed in the future are discussed. Links for all available software implementing multivariate meta-analysis methods are also provided.

Multivariate analysis method for energy calibration and improved mass assignment in recoil spectrometry

International Nuclear Information System (INIS)

El Bouanani, Mohamed; Hult, Mikael; Persson, Leif; Swietlicki, Erik; Andersson, Margaretha; Oestling, Mikael; Lundberg, Nils; Zaring, Carina; Cohen, D.D.; Dytlewski, Nick; Johnston, P.N.; Walker, S.R.; Bubb, I.F.; Whitlow, H.J.

1994-01-01

Heavy ion recoil spectrometry is rapidly becoming a well established analysis method, but the associated data analysis processing is still not well developed. The pronounced nonlinear response of silicon detectors for heavy ions leads to serious limitation and complication in mass gating, which is the principal factor in obtaining energy spectra with minimal cross talk between elements. To overcome the above limitation, a simple empirical formula with an associated multiple regression method is proposed for the absolute energy calibration of the time of flight-energy dispersive detector telescope used in recoil spectrometry. A radical improvement in mass assignment was realized, which allows a more accurate and improved depth profiling with the important feature of making the data processing much easier. ((orig.))

Artificial intelligence applied to assigned merchandise location in retail sales systems

Directory of Open Access Journals (Sweden)

Cruz-Domínguez, O.

2016-05-01

Full Text Available This paper presents an option for improving the process of assigning storage locations for merchandise in a warehouse. A disadvantage of policies in the literature is that the merchandise is assigned allocation only according to the volume of sales and the rotation it presents. However, in some cases it is necessary to deal with other aspects such as family group membership, the physical characteristics of the products, and their sales pattern to design an integral policy. This paper presents an alternative to the afore- mentioned process using Flexsim®, artificial neural networks, and genetic algorithms.

A proposed impact assessment method for genetically modified plants (AS-GMP Method)

International Nuclear Information System (INIS)

Jesus-Hitzschky, Katia Regina Evaristo de; Silveira, Jose Maria F.J. da

2009-01-01

An essential step in the development of products based on biotechnology is an assessment of their potential economic impacts and safety, including an evaluation of the potential impact of transgenic crops and practices related to their cultivation on the environment and human or animal health. The purpose of this paper is to provide an assessment method to evaluate the impact of biotechnologies that uses quantifiable parameters and allows a comparative analysis between conventional technology and technologies using GMOs. This paper introduces a method to perform an impact analysis associated with the commercial release and use of genetically modified plants, the Assessment System GMP Method. The assessment is performed through indicators that are arranged according to their dimension criterion likewise: environmental, economic, social, capability and institutional approach. To perform an accurate evaluation of the GMP specific indicators related to genetic modification are grouped in common fields: genetic insert features, GM plant features, gene flow, food/feed field, introduction of the GMP, unexpected occurrences and specific indicators. The novelty is the possibility to include specific parameters to the biotechnology under assessment. In this case by case analysis the factors of moderation and the indexes are parameterized to perform an available assessment.

Interactive Level Design for iOS Assignment Delivery: A Case Study

Directory of Open Access Journals (Sweden)

Anson Brown

2014-02-01

Full Text Available This paper presents an application of an iOS-based online gaming assignment in a real classroom. The core concept of the project is a gameplay environment involving two players that have full control over creation and modification of levels. This level design mechanism was implemented in an iOS-based game in the area of genetics and based on an existing written assignment. The game includes support for both instructors, who have the ability to create and post assignments and students, who can take the assignments. Two trials of the iOS application consisted of in-class testing of twenty- one students. Students first took the original paper assignment, followed by the iOS version. Start times, end times, and grades were recorded for both versions. A comprehensive study of the grades and times for the iOS version of the assignment versus the paper version was conducted and is presented in this paper. Our Study showed that the iOS version was completed much faster in nearly every case while a strong delivery mechanism is needed to ensure student grades and completion of the assignment will not be affected. These results are not unexpected due to some major difference between the two formats. Future updates and additions will address any currently existing issues.

Dynamics and genetic structure of Argentine ant supercolonies in their native range

DEFF Research Database (Denmark)

Vogel, Valérie; Pedersen, Jes S; d'Ettorre, Patrizia

2009-01-01

analyses revealed the presence of 11 supercolonies (width 1 to 515 m) over a 3-km transect. As in the introduced range, there was always strong aggression between but never within supercolonies. The genetic data were in perfect agreement with the behavioral tests, all nests being assigned to identical...... supercolonies with the different methods. There was strong genetic differentiation between supercolonies but no genetic differentiation among nests within supercolonies. We never found more than a single mitochondrial haplotype per supercolony, further supporting the view that supercolonies are closed breeding...

Methods for genetic modification of megakaryocytes and platelets.

Science.gov (United States)

Pendaries, Caroline; Watson, Stephen P; Spalton, Jennifer C

2007-09-01

During recent decades there have been major advances in the fields of thrombosis and haemostasis, in part through development of powerful molecular and genetic technologies. Nevertheless, genetic modification of megakaryocytes and generation of mutant platelets in vitro remains a highly specialized area of research. Developments are hampered by the low frequency of megakaryocytes and their progenitors, a poor efficiency of transfection and a lack of understanding with regard to the mechanism by which megakaryocytes release platelets. Current methods used in the generation of genetically modified megakaryocytes and platelets include mutant mouse models, cell line studies and use of viruses to transform primary megakaryocytes or haematopoietic precursor cells. This review summarizes the advantages, limitations and technical challenges of such methods, with a particular focus on recent successes and advances in this rapidly progressing field including the potential for use in gene therapy for treatment of patients with platelet disorders.

Application of computational methods in genetic study of inflammatory bowel disease.

Science.gov (United States)

Li, Jin; Wei, Zhi; Hakonarson, Hakon

2016-01-21

Genetic factors play an important role in the etiology of inflammatory bowel disease (IBD). The launch of genome-wide association study (GWAS) represents a landmark in the genetic study of human complex disease. Concurrently, computational methods have undergone rapid development during the past a few years, which led to the identification of numerous disease susceptibility loci. IBD is one of the successful examples of GWAS and related analyses. A total of 163 genetic loci and multiple signaling pathways have been identified to be associated with IBD. Pleiotropic effects were found for many of these loci; and risk prediction models were built based on a broad spectrum of genetic variants. Important gene-gene, gene-environment interactions and key contributions of gut microbiome are being discovered. Here we will review the different types of analyses that have been applied to IBD genetic study, discuss the computational methods for each type of analysis, and summarize the discoveries made in IBD research with the application of these methods.

Evaluation of Genetic Pattern of Non-Tuberculosis Mycobacterium Using VNTR Method

Directory of Open Access Journals (Sweden)

Noorozi J

2011-06-01

Full Text Available Background and Objectives: Epidemiological studies of Non-tuberculosis Mycobacterium is important because of the drug resistance pattern and worldwide dissemination of these organisms. One of genetic fingerprinting methods for epidemiological studies is VNTR (Variable Number Tandem Repeat. In this study genetic pattern of atypical Mycobacterium was evaluated by VNTR method for epidemiologic studies. Methods: 48 pulmonary and non pulmonary specimens separated from patients with the symptoms of pulmonary tuberculosis (PTB and identified as Non-tuberculosis Mycobacteriumby phenotypic and PCR-RFLP methods were selected for this study. Clinical samples and their standard strains were evaluated according to VNTR pattern using the 7 genetic loci including ETR-B. ETR-F. ETR-C. MPTR-A. ETR-A. ETR-E. ETR-D.Results: The results of VNTR method showed that none of the 7 loci had any polymorphism in the standard strains of atypical mycobacterium. Some of these variable number tandem repeat in 42 clinical samples of non-tuberculosis Mycobacterium were polymorphic while the PCR product (for any loci was not found in the remaining 6 specimens. Conclusion: Although the used genetic loci of this study were suitable for epidemiological studies of Mycobacterium tuberculosis, these loci were not able to determine the diversity of genetics of non-tuberculosis Mycobacterium Therefore, it seems necessary that other loci be studied using VNTR method.

Assignment of Colletotrichum coccodes isolates into vegetative compatibility groups using infrared spectroscopy: a step towards practical application.

Science.gov (United States)

Salman, A; Shufan, E; Lapidot, I; Tsror, L; Moreh, R; Mordechai, S; Huleihel, M

2015-05-07

Colletotrichum coccodes (C. coccodes) is a pathogenic fungus that causes anthracnose on tomatoes and black dot disease in potatoes. It is considered as a seed tuber and soil-borne pathogen that is difficult to control. C. coccodes isolates are classified into Vegetative Compatibility Groups (VCGs). Early classification of isolates into VCGs is of great importance for a better understanding of the epidemiology of the disease and improving its control. Moreover, the differentiation among these isolates and the assignment of newly-discovered isolates enable control of the disease at its early stages. Distinguishing between isolates using microbiological or genetic methods is time-consuming and not readily available. Our results show that it is possible to assign the isolates into their VCGs and to classify them at the isolate level with a high success rate using Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA).

A Simple Method for Solving Fully Intuitionistic Fuzzy Real Life Assignment Problem

OpenAIRE

Senthil Kumar, P.; Jahir Hussain, R.

2016-01-01

In solving real life assignment problem we often face the state of uncertainty as well as hesitation due to various uncontrollable factors. To deal with uncertainty and hesitation many authors have suggested the intuitionistic fuzzy representations for the data. So, in this paper, the authors consider the assignment problem having uncertainty and hesitation in cost/time/profit. They formulate the problem and utilize triangular intuitionistic fuzzy numbers (TIFNs) to deal with uncertainty and ...

Assignment tests for variety identification compared to genetic similarity-based methods using experimental datasets from different marker systems in sugar beet

NARCIS (Netherlands)

Riek, de J.; Everaert, I.; Esselink, D.; Calsyn, E.; Smulders, M.J.M.; Vosman, B.

2007-01-01

High genetic variation within sugar beet (Beta vulgaris L.) varieties hampers reliable classification procedures independent of the type of marker technique applied. Datasets on amplified fragment length polymorphisms, sequence tagged microsatellite sites, and cleaved amplified polymorphic sites

The Presentation Assignment: Creating Learning Opportunities for Diverse Student Populations.

Science.gov (United States)

Spencer, Brenda H.; Bartle-Angus, Kathryn

2000-01-01

Finds the presentation assignment to be an effective method of providing students with the opportunity to apply the literacy skills they are learning in ways that are personally meaningful. Describes the presentation assignment framework and provides an example of an assignment that required students to analyze and interpret works of literature…

A probabilistic approach for validating protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Wang Bowei; Wang, Yunjun; Wishart, David S.

2010-01-01

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

Optimal assignment methods in three-form planned missing data designs for longitudinal panel studies

NARCIS (Netherlands)

Jorgensen, T.D.; Rhemtulla, M.; Schoemann, A.; McPherson, B.; Wu, W.; Little, T.D.

2014-01-01

Planned missing designs are becoming increasingly popular, but because there is no consensus on how to implement them in longitudinal research, we simulated longitudinal data to distinguish between strategies of assigning items to forms and of assigning forms to participants across measurement

Assessment of combating-desertification strategies using the linear assignment method

Science.gov (United States)

Hassan Sadeghravesh, Mohammad; Khosravi, Hassan; Ghasemian, Soudeh

2016-04-01

Nowadays desertification, as a global problem, affects many countries in the world, especially developing countries like Iran. With respect to increasing importance of desertification and its complexity, the necessity of attention to the optimal combating-desertification alternatives is essential. Selecting appropriate strategies according to all effective criteria to combat the desertification process can be useful in rehabilitating degraded lands and avoiding degradation in vulnerable fields. This study provides systematic and optimal strategies of combating desertification by use of a group decision-making model. To this end, the preferences of indexes were obtained through using the Delphi model, within the framework of multi-attribute decision making (MADM). Then, priorities of strategies were evaluated by using linear assignment (LA) method. According to the results, the strategies to prevent improper change of land use (A18), development and reclamation of plant cover (A23), and control overcharging of groundwater resources (A31) were identified as the most important strategies for combating desertification in this study area. Therefore, it is suggested that the aforementioned ranking results be considered in projects which control and reduce the effects of desertification and rehabilitate degraded lands.

Assigning agents to a line

DEFF Research Database (Denmark)

Hougaard, Jens Leth; Moreno-Ternero, Juan D.; Østerdal, Lars Peter Raahave

2014-01-01

minimizing modification of the classic random priority method to solve this class of problems. We also provide some logical relations in our setting among standard axioms in the literature on assignment problems, and explore the robustness of our results to several extensions of our setting....

Methods for sequential resonance assignment in solid, uniformly 13C, 15N labelled peptides: Quantification and application to antamanide

International Nuclear Information System (INIS)

Detken, Andreas; Hardy, Edme H.; Ernst, Matthias; Kainosho, Masatsune; Kawakami, Toru; Aimoto, Saburo; Meier, Beat H.

2001-01-01

The application of adiabatic polarization-transfer experiments to resonance assignment in solid, uniformly 13 C- 15 N-labelled polypeptides is demonstrated for the cyclic decapeptide antamanide. A homonuclear correlation experiment employing the DREAM sequence for adiabatic dipolar transfer yields a complete assignment of the C α and aliphatic side-chain 13 C resonances to amino acid types. The same information can be obtained from a TOBSY experiment using the recently introduced P9 1 12 TOBSY sequence, which employs the J couplings as a transfer mechanism. A comparison of the two methods is presented. Except for some aromatic phenylalanine resonances, a complete sequence-specific assignment of the 13 C and 15 N resonances in antamanide is achieved by a series of selective or broadband adiabatic triple-resonance experiments. Heteronuclear transfer by adiabatic-passage Hartmann-Hahn cross polarization is combined with adiabatic homonuclear transfer by the DREAM and rotational-resonance tickling sequences into two- and three-dimensional experiments. The performance of these experiments is evaluated quantitatively

A genetic algorithm for finding good balanced sequences in a customer assignment problem with no state information

NARCIS (Netherlands)

Hordijk, W.; Hordijk, A.; Heidergott, B.F.

2015-01-01

In this paper, we study the control problem of optimal assignment of tasks to servers in a multi-server queue with inhomogeneous servers. In order to improve the performance of the system, we use a periodic deterministic sequence of job assignments to servers called a billiard sequence. We then use

Tales from the front lines: the creative essay as a tool for teaching genetics.

Science.gov (United States)

Koehler, K E; Hawley, R S

1999-07-01

In contrast to the more typical mock grant proposals or literature reviews, we describe the use of the creative essay as a novel tool for teaching human genetics at the college level. This method has worked well for both nonmajor and advanced courses for biology majors. The 10- to 15-page essay is written in storylike form and represents a student's response to the choice of 6-8 scenarios describing human beings coping with various genetic dilemmas. We have found this tool to be invaluable both in developing students' ability to express genetic concepts in lay terms and in promoting student awareness of genetic issues outside of the classroom. Examples from student essays are presented to illustrate these points, and guidelines are suggested regarding instructor expectations of student creativity and scientific accuracy. Methods of grading this assignment are also discussed.

MOLECULAR GENETIC MARKERS AND METHODS OF THEIR IDENTIFICATION IN MODERN FISH-FARMING

Directory of Open Access Journals (Sweden)

I. Hrytsyniak

2014-03-01

Full Text Available Purpose. The application of molecular genetic markers has been widely used in modern experimental fish-farming in recent years. This methodology is currently presented by a differentiated approach with individual mechanisms and clearly defined possibilities. Numerous publications in the scientific literature that are dedicated to molecular genetic markers for the most part offer purely practical data. Thus, the synthesis and analysis of existing information on the general principles of action and the limits of the main methods of using molecular genetic markers is an actual problem. In particular, such a description will make it possible to plan more effectively the experiment and to obtain the desired results with high reliability. Findings. The main types of variable parts of DNA that can be used as molecular genetic markers in determining the level of stock hybridization, conducting genetic inventory of population and solving other problems in modern fish-farming are described in this paper. Also, the article provides an overview of principal modern methods that can be used to identify molecular genetic markers. Originality. This work is a generalization of modern ideas about the mechanisms of experiments with molecular genetic markers in fish-farming. Information is provided in the form of consistent presentation of the principles and purpose of each method, as well as significant advances during their practical application. Practical value. The proposed review of classic and modern literature data on molecular genetic markers can be used for planning, modernization and correction of research activity in modern fish-farming.

Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers

Science.gov (United States)

Gilbey, John; Cauwelier, Eef; Coulson, Mark W.; Stradmeyer, Lee; Sampayo, James N.; Armstrong, Anja; Verspoor, Eric; Corrigan, Laura; Shelley, Jonathan; Middlemas, Stuart

2016-01-01

Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations. PMID:27723810

NONLINEAR ASSIGNMENT-BASED METHODS FOR INTERVAL-VALUED INTUITIONISTIC FUZZY MULTI-CRITERIA DECISION ANALYSIS WITH INCOMPLETE PREFERENCE INFORMATION

OpenAIRE

TING-YU CHEN

2012-01-01

In the context of interval-valued intuitionistic fuzzy sets, this paper develops nonlinear assignment-based methods to manage imprecise and uncertain subjective ratings under incomplete preference structures and thereby determines the optimal ranking order of the alternatives for multiple criteria decision analysis. By comparing each interval-valued intuitionistic fuzzy number's score function, accuracy function, membership uncertainty index, and hesitation uncertainty index, a ranking proced...

Grouping puts figure-ground assignment in context by constraining propagation of edge assignment.

Science.gov (United States)

Brooks, Joseph L; Brook, Joseph L; Driver, Jon

2010-05-01

Figure-ground organization involves the assignment of edges to a figural shape on one or the other side of each dividing edge. Established visual cues for edge assignment primarily concern relatively local rather than contextual factors. In the present article, we show that an assignment for a locally unbiased edge can be affected by an assignment of a remote contextual edge that has its own locally biased assignment. We find that such propagation of edge assignment from the biased remote context occurs only when the biased and unbiased edges are grouped. This new principle, whereby grouping constrains the propagation of figural edge assignment, emerges from both subjective reports and an objective short-term edge-matching task. It generalizes from moving displays involving grouping by common fate and collinearity, to static displays with grouping by similarity of edge-contrast polarity, or apparent occlusion. Our results identify a new contextual influence on edge assignment. They also identify a new mechanistic relation between grouping and figure-ground processes, whereby grouping between remote elements can constrain the propagation of edge assignment between those elements. Supplemental materials for this article may be downloaded from http://app.psychonomic-journals.org/content/supplemental.

ActionMap: A web-based software that automates loci assignments to framework maps.

Science.gov (United States)

Albini, Guillaume; Falque, Matthieu; Joets, Johann

2003-07-01

Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

A Tomographic method based on genetic algorithms

International Nuclear Information System (INIS)

Turcanu, C.; Alecu, L.; Craciunescu, T.; Niculae, C.

1997-01-01

Computerized tomography being a non-destructive and non-evasive technique is frequently used in medical application to generate three dimensional images of objects. Genetic algorithms are efficient, domain independent for a large variety of problems. The proposed method produces good quality reconstructions even in case of very small number of projection angles. It requests no a priori knowledge about the solution and takes into account the statistical uncertainties. The main drawback of the method is the amount of computer memory and time needed. (author)

Yeast genetics. A manual of methods

Energy Technology Data Exchange (ETDEWEB)

Spencer, J.F.T.; Spencer, D.M.; Bruce, I.J.

1989-01-01

This is a bench-top manual of methods needed both for classical genetics as related to yeasts, such as mating, sporulation, isolation of hybrids, microdissection of asci for the isolation of single-spore clones, as well as for mapping of genes and the construction of new strains by protoplast fusion. Special emphasis is on mutations in general, and on methods of isolating a number of important classes of mutants in particular. Basic techniques for the separation of chromosomes by electrophoresis, such as OFAGE, FIGE, and CHEF, are discussed, with detailed protocols for the first two. Furthermore, new methods, e.g. for the isolation of high molecular weight DNA from yeast, isolation of RNA, and techniques for transformation of yeasts, are also described in detail. (orig.) With 10 figs.

First Trimester Fetal Gender Assignment by Ultrasound

Directory of Open Access Journals (Sweden)

Sabahattin Altunyurt

2010-03-01

Full Text Available Objective: To investigate the efficiency of genital tubercule angle on detecting fetal gender in first trimester by ultrasonography. Material-Method: Fetal sex assignment by ultrasound was carried out in 172 pregnancies at 11-13+6 weeks between 2007 June and 2007 December. Gestational age was determined by the measurement of crown-rump length (CRL. The ultrasound predictions were compared with actual sex at birth. Mid-sagittal planes of a section of the fetal genital tubercle were performed to identify the gender. Results: 155 of 172 patients’ data were achieved. The overall success rate was 92.3 % in sonographic assignment of fetal sex. The correct assignment rate in female fetuses was significantly higher than males (95.9 % - 88.8 % [p=0,001]. The correct identification of fetal sex improved with advancing gestational age from 89.3 % between 11-11+6 weeks, 92.5 % between 12-12+6 weeks and 93.4 % between 13-13+6 weeks (p=0,96. Conclusion: The fetal sex assignment by ultrasonography between 11-13+6 weeks had high success rate. The sensitivity of fetal sex assignment was not affected with fetus position and gestational age.

A game theoretic approach to assignment problems

NARCIS (Netherlands)

Klijn, F.

2000-01-01

Game theory deals with the mathematical modeling and analysis of conflict and cooperation in the interaction of multiple decision makers. This thesis adopts two game theoretic methods to analyze a range of assignment problems that arise in various economic situations. The first method has as

Integer Linear Programming for Constrained Multi-Aspect Committee Review Assignment

Science.gov (United States)

Karimzadehgan, Maryam; Zhai, ChengXiang

2011-01-01

Automatic review assignment can significantly improve the productivity of many people such as conference organizers, journal editors and grant administrators. A general setup of the review assignment problem involves assigning a set of reviewers on a committee to a set of documents to be reviewed under the constraint of review quota so that the reviewers assigned to a document can collectively cover multiple topic aspects of the document. No previous work has addressed such a setup of committee review assignments while also considering matching multiple aspects of topics and expertise. In this paper, we tackle the problem of committee review assignment with multi-aspect expertise matching by casting it as an integer linear programming problem. The proposed algorithm can naturally accommodate any probabilistic or deterministic method for modeling multiple aspects to automate committee review assignments. Evaluation using a multi-aspect review assignment test set constructed using ACM SIGIR publications shows that the proposed algorithm is effective and efficient for committee review assignments based on multi-aspect expertise matching. PMID:22711970

Bag-of-features based medical image retrieval via multiple assignment and visual words weighting

KAUST Repository

Wang, Jingyan

2011-11-01

Bag-of-features based approaches have become prominent for image retrieval and image classification tasks in the past decade. Such methods represent an image as a collection of local features, such as image patches and key points with scale invariant feature transform (SIFT) descriptors. To improve the bag-of-features methods, we first model the assignments of local descriptors as contribution functions, and then propose a novel multiple assignment strategy. Assuming the local features can be reconstructed by their neighboring visual words in a vocabulary, reconstruction weights can be solved by quadratic programming. The weights are then used to build contribution functions, resulting in a novel assignment method, called quadratic programming (QP) assignment. We further propose a novel visual word weighting method. The discriminative power of each visual word is analyzed by the sub-similarity function in the bin that corresponds to the visual word. Each sub-similarity function is then treated as a weak classifier. A strong classifier is learned by boosting methods that combine those weak classifiers. The weighting factors of the visual words are learned accordingly. We evaluate the proposed methods on medical image retrieval tasks. The methods are tested on three well-known data sets, i.e., the ImageCLEFmed data set, the 304 CT Set, and the basal-cell carcinoma image set. Experimental results demonstrate that the proposed QP assignment outperforms the traditional nearest neighbor assignment, the multiple assignment, and the soft assignment, whereas the proposed boosting based weighting strategy outperforms the state-of-the-art weighting methods, such as the term frequency weights and the term frequency-inverse document frequency weights. © 2011 IEEE.

Bag-of-features based medical image retrieval via multiple assignment and visual words weighting

KAUST Repository

Wang, Jingyan; Li, Yongping; Zhang, Ying; Wang, Chao; Xie, Honglan; Chen, Guoling; Gao, Xin

2011-01-01

Bag-of-features based approaches have become prominent for image retrieval and image classification tasks in the past decade. Such methods represent an image as a collection of local features, such as image patches and key points with scale invariant feature transform (SIFT) descriptors. To improve the bag-of-features methods, we first model the assignments of local descriptors as contribution functions, and then propose a novel multiple assignment strategy. Assuming the local features can be reconstructed by their neighboring visual words in a vocabulary, reconstruction weights can be solved by quadratic programming. The weights are then used to build contribution functions, resulting in a novel assignment method, called quadratic programming (QP) assignment. We further propose a novel visual word weighting method. The discriminative power of each visual word is analyzed by the sub-similarity function in the bin that corresponds to the visual word. Each sub-similarity function is then treated as a weak classifier. A strong classifier is learned by boosting methods that combine those weak classifiers. The weighting factors of the visual words are learned accordingly. We evaluate the proposed methods on medical image retrieval tasks. The methods are tested on three well-known data sets, i.e., the ImageCLEFmed data set, the 304 CT Set, and the basal-cell carcinoma image set. Experimental results demonstrate that the proposed QP assignment outperforms the traditional nearest neighbor assignment, the multiple assignment, and the soft assignment, whereas the proposed boosting based weighting strategy outperforms the state-of-the-art weighting methods, such as the term frequency weights and the term frequency-inverse document frequency weights. © 2011 IEEE.

[An Efficient Method for Genetic Certification of Bacillus subtilis strains, Prospective Producers of Biopreparations].

Science.gov (United States)

Terletskiy, V P; Tyshenko, V I; Novikova, I I; Boikova, I V; Tyulebaev, S D; Shakhtamirov, I Ya

2016-01-01

Genetic certification of commercial strains of bacteria antagonistic to phytopathogenic microorganisms guarantees their unequivocal identification and confirmation of safety. In Russia, unlike EU countries, genetic certification of Bacillus subtilis strains is not used. Based on the previously proposed double digestion selective label (DDSL) fingerprinting, a method for genetic identification and certification of B. subtilis strains was proposed. The method was tested on several strains differing in their physiological and biochemical properties and in the composition of secondary metabolites responsible for the spectrum of antibiotic activity. High resolving power of this approach was shown. Optimal restriction endonucleases (SgsI and Eco32I) were determined and validated. A detailed protocol for genetic certification of this bacterial species was developed. DDSL is a universal method, which may be adapted for genetic identification and certification of other bacterial species.

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

International Nuclear Information System (INIS)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

2012-01-01

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

Energy Technology Data Exchange (ETDEWEB)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

2012-04-15

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

Genetic stock identification of Russian honey bees.

Science.gov (United States)

Bourgeois, Lelania; Sheppard, Walter S; Sylvester, H Allen; Rinderer, Thomas E

2010-06-01

A genetic stock certification assay was developed to distinguish Russian honey bees from other European (Apis mellifera L.) stocks that are commercially produced in the United States. In total, 11 microsatellite and five single-nucleotide polymorphism loci were used. Loci were selected for relatively high levels of homogeneity within each group and for differences in allele frequencies between groups. A baseline sample consisted of the 18 lines of Russian honey bees released to the Russian Bee Breeders Association and bees from 34 queen breeders representing commercially produced European honey bee stocks. Suitability tests of the baseline sample pool showed high levels of accuracy. The probability of correct assignment was 94.2% for non-Russian bees and 93.3% for Russian bees. A neighbor-joining phenogram representing genetic distance data showed clear distinction of Russian and non-Russian honey bee stocks. Furthermore, a test of appropriate sample size showed a sample of eight bees per colony maximizes accuracy and consistency of the results. An additional 34 samples were tested as blind samples (origin unknown to those collecting data) to determine accuracy of individual assignment tests. Only one of these samples was incorrectly assigned. The 18 current breeding lines were represented among the 2009 blind sampling, demonstrating temporal stability of the genetic stock identification assay. The certification assay will be used through services provided by a service laboratory, by the Russian Bee Breeders Association to genetically certify their stock. The genetic certification will be used in conjunction with continued selection for favorable traits, such as honey production and varroa and tracheal mite resistance.

Kinetics of cancer: a method to test hypotheses of genetic causation

Directory of Open Access Journals (Sweden)

Lipkin Steven M

2005-12-01

Full Text Available Abstract Background Mouse studies have recently compared the age-onset patterns of cancer between different genotypes. Genes associated with earlier onset are tentatively assigned a causal role in carcinogenesis. These standard analyses ignore the great amount of information about kinetics contained in age-onset curves. We present a method for analyzing kinetics that measures quantitatively the causal role of candidate genes in cancer progression. We use our method to demonstrate a clear association between somatic mutation rates of different DNA mismatch repair (MMR genotypes and the kinetics of cancer progression. Methods Most experimental studies report age-onset curves as the fraction diagnosed with tumors at each age for each group. We use such data to estimate smoothed survival curves, then measure incidence rates at each age by the slope of the fitted curve divided by the fraction of mice that remain undiagnosed for tumors at that age. With the estimated incidence curves, we compare between different genotypes the median age of cancer onset and the acceleration of cancer, which is the rate of increase in incidence with age. Results The direction of change in somatic mutation rate between MMR genotypes predicts the direction of change in the acceleration of cancer onset in all 7 cases (p ˜ 0.008, with the same result for the association between mutation rate and the median age of onset. Conclusion Many animal experiments compare qualitatively the onset curves for different genotypes. If such experiments were designed to analyze kinetics, the research could move to the next stage in which the mechanistic consequences of particular genetic pathways are related to the dynamics of carcinogenesis. The data we analyzed here were not collected to test mechanistic and quantitative hypotheses about kinetics. Even so, a simple reanalysis revealed significant insights about how DNA repair genotypes affect separately the age of onset and the

DMPD: The Toll-like receptors: analysis by forward genetic methods. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 16001129 The Toll-like receptors: analysis by forward genetic methods. Beutler B. I...mmunogenetics. 2005 Jul;57(6):385-92. (.png) (.svg) (.html) (.csml) Show The Toll-like receptors: analysis by forwar...d genetic methods. PubmedID 16001129 Title The Toll-like receptors: analysis by forward genetic meth

Danish Public Construction Counselling Selection and Assignment Criteria in European Tendering

DEFF Research Database (Denmark)

Larsen, Jesper Kranker; Ussing, Lene Faber; Brunø, Thomas Ditlev

2014-01-01

One of the largest customers in the Danish construction industry is public agencies that own and develop projects. For some of the counselling services, they recur to be put out in European tendering. The aim is to find which selection and assignment criteria are used most in public tendering. How...... projects use selection and assignment criteria for counselling services and finally if there is significant use of selection and assignment methods in public counselling. The method is based on 74 public counselling tenders from the European Tenders Electronic Daily database from January 2010 to March 2013...

Determination of Selection Method in Genetic Algorithm for Land Suitability

Directory of Open Access Journals (Sweden)

Irfianti Asti Dwi

2016-01-01

Full Text Available Genetic Algoirthm is one alternative solution in the field of modeling optimization, automatic programming and machine learning. The purpose of the study was to compare some type of selection methods in Genetic Algorithm for land suitability. Contribution of this research applies the best method to develop region based horticultural commodities. This testing is done by comparing the three methods on the method of selection, the Roulette Wheel, Tournament Selection and Stochastic Universal Sampling. Parameters of the locations used in the test scenarios include Temperature = 27°C, Rainfall = 1200 mm, hummidity = 30%, Cluster fruit = 4, Crossover Probabiitiy (Pc = 0.6, Mutation Probabilty (Pm = 0.2 and Epoch = 10. The second test epoch incluides location parameters consist of Temperature = 30°C, Rainfall = 2000 mm, Humidity = 35%, Cluster fruit = 5, Crossover Probability (Pc = 0.7, Mutation Probability (Pm = 0.3 and Epoch 10. The conclusion of this study shows that the Roulette Wheel is the best method because it produces more stable and fitness value than the other two methods.

Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus Phrynocephalus

Directory of Open Access Journals (Sweden)

Fu Jinzhong

2010-06-01

Full Text Available Abstract Background Species are fundamental units in biology, yet much debate exists surrounding how we should delineate species in nature. Species discovery now requires the use of separate, corroborating datasets to quantify independently evolving lineages and test species criteria. However, the complexity of the speciation process has ushered in a need to infuse studies with new tools capable of aiding in species delineation. We suggest that model-based assignment tests are one such tool. This method circumvents constraints with traditional population genetic analyses and provides a novel means of describing cryptic and complex diversity in natural systems. Using toad-headed agamas of the Phrynocephalus vlangalii complex as a case study, we apply model-based assignment tests to microsatellite DNA data to test whether P. putjatia, a controversial species that closely resembles P. vlangalii morphologically, represents a valid species. Mitochondrial DNA and geographic data are also included to corroborate the assignment test results. Results Assignment tests revealed two distinct nuclear DNA clusters with 95% (230/243 of the individuals being assigned to one of the clusters with > 90% probability. The nuclear genomes of the two clusters remained distinct in sympatry, particularly at three syntopic sites, suggesting the existence of reproductive isolation between the identified clusters. In addition, a mitochondrial ND2 gene tree revealed two deeply diverged clades, which were largely congruent with the two nuclear DNA clusters, with a few exceptions. Historical mitochondrial introgression events between the two groups might explain the disagreement between the mitochondrial and nuclear DNA data. The nuclear DNA clusters and mitochondrial clades corresponded nicely to the hypothesized distributions of P. vlangalii and P. putjatia. Conclusions These results demonstrate that assignment tests based on microsatellite DNA data can be powerful tools

Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals

Science.gov (United States)

Brown, Robert; Pasaniuc, Bogdan

2014-01-01

Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g., Latino Americans) plays a major role in medical and population genetic inferences, ranging from finding disease-risk loci, to inferring recombination rates, to mapping missing contigs in the human genome. Although many methods for local ancestry inference have been proposed, most are designed for use with genotyping arrays and fail to make use of the full spectrum of data available from sequencing. In addition, current haplotype-based approaches are very computationally demanding, requiring large computational time for moderately large sample sizes. Here we present new methods for local ancestry inference that leverage continent-specific variants (CSVs) to attain increased performance over existing approaches in sequenced admixed genomes. A key feature of our approach is that it incorporates the admixed genomes themselves jointly with public datasets, such as 1000 Genomes, to improve the accuracy of CSV calling. We use simulations to show that our approach attains accuracy similar to widely used computationally intensive haplotype-based approaches with large decreases in runtime. Most importantly, we show that our method recovers comparable local ancestries, as the 1000 Genomes consensus local ancestry calls in the real admixed individuals from the 1000 Genomes Project. We extend our approach to account for low-coverage sequencing and show that accurate local ancestry inference can be attained at low sequencing coverage. Finally, we generalize CSVs to sub-continental population-specific variants (sCSVs) and show that in some cases it is possible to determine the sub-continental ancestry for short chromosomal segments on the basis of sCSVs. PMID:24743331

Quality Control Test for Sequence-Phenotype Assignments

Science.gov (United States)

Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

2015-01-01

Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

Modeling multiple visual words assignment for bag-of-features based medical image retrieval

KAUST Repository

Wang, Jim Jing-Yan

2012-01-01

In this paper, we investigate the bag-of-features based medical image retrieval methods, which represent an image as a collection of local features, such as image patch and key points with SIFT descriptor. To improve the bag-of-features method, we first model the assignment of local descriptor as contribution functions, and then propose a new multiple assignment strategy. By assuming the local feature can be reconstructed by its neighboring visual words in vocabulary, we solve the reconstruction weights as a QP problem and then use the solved weights as contribution functions, which results in a new assignment method called the QP assignment. We carry our experiments on ImageCLEFmed datasets. Experiments\\' results show that our proposed method exceeds the performances of traditional solutions and works well for the bag-of-features based medical image retrieval tasks.

Modeling multiple visual words assignment for bag-of-features based medical image retrieval

KAUST Repository

Wang, Jim Jing-Yan; Almasri, Islam

2012-01-01

In this paper, we investigate the bag-of-features based medical image retrieval methods, which represent an image as a collection of local features, such as image patch and key points with SIFT descriptor. To improve the bag-of-features method, we first model the assignment of local descriptor as contribution functions, and then propose a new multiple assignment strategy. By assuming the local feature can be reconstructed by its neighboring visual words in vocabulary, we solve the reconstruction weights as a QP problem and then use the solved weights as contribution functions, which results in a new assignment method called the QP assignment. We carry our experiments on ImageCLEFmed datasets. Experiments' results show that our proposed method exceeds the performances of traditional solutions and works well for the bag-of-features based medical image retrieval tasks.

LOW POWER RACE-FREE STATE ASSIGNMENT OF AN ASYNGHRONOUS AUTOMATON

Directory of Open Access Journals (Sweden)

Yu. V. Pottosin

2015-01-01

Full Text Available The problem of a race free state assignment of an asynchronous automaton is considered. A method for the state assignment is suggested that provides the minimization of the number and theswitching activity of the memory elements along with the elimination of the critical races betweenthem.

UOP LDR 300 All Assignments New

OpenAIRE

ADMIN

2018-01-01

UOP LDR 300 All Assignments New Check this A+ tutorial guideline at http://www.ldr300assignment.com/ldr-300-uop/ldr-300-all-assignments-latest For more classes visit http://www.ldr300assignment.com LDR 300 Week 1 Assignment Leadership Assessment (2 Papers) LDR 300 Week 2 Assignment Leadership Theories Matrix (2 Set) LDR 300 Week 2 Assignment Formulating Leadership Part I (2 Papers) LDR 300 Week 3 Assignment Interaction and Influence Amo...

Current perspectives on genetically modified crops and detection methods.

Science.gov (United States)

Kamle, Madhu; Kumar, Pradeep; Patra, Jayanta Kumar; Bajpai, Vivek K

2017-07-01

Genetically modified (GM) crops are the fastest adopted commodities in the agribiotech industry. This market penetration should provide a sustainable basis for ensuring food supply for growing global populations. The successful completion of two decades of commercial GM crop production (1996-2015) is underscored by the increasing rate of adoption of genetic engineering technology by farmers worldwide. With the advent of introduction of multiple traits stacked together in GM crops for combined herbicide tolerance, insect resistance, drought tolerance or disease resistance, the requirement of reliable and sensitive detection methods for tracing and labeling genetically modified organisms in the food/feed chain has become increasingly important. In addition, several countries have established threshold levels for GM content which trigger legally binding labeling schemes. The labeling of GM crops is mandatory in many countries (such as China, EU, Russia, Australia, New Zealand, Brazil, Israel, Saudi Arabia, Korea, Chile, Philippines, Indonesia, Thailand), whereas in Canada, Hong Kong, USA, South Africa, and Argentina voluntary labeling schemes operate. The rapid adoption of GM crops has increased controversies, and mitigating these issues pertaining to the implementation of effective regulatory measures for the detection of GM crops is essential. DNA-based detection methods have been successfully employed, while the whole genome sequencing using next-generation sequencing (NGS) technologies provides an advanced means for detecting genetically modified organisms and foods/feeds in GM crops. This review article describes the current status of GM crop commercialization and discusses the benefits and shortcomings of common and advanced detection systems for GMs in foods and animal feeds.

A parametric visualization software for the assignment problem

Directory of Open Access Journals (Sweden)

Papamanthou Charalampos

2005-01-01

Full Text Available In this paper we present a parametric visualization software used to assist the teaching of the Network Primal Simplex Algorithm for the assignment problem (AP. The assignment problem is a special case of the balanced transportation problem. The main functions of the algorithm and design techniques are also presented. Through this process, we aim to underline the importance and necessity of using such educational methods in order to improve the teaching of Computer Algorithms.

Genetic Algorithms Principles Towards Hidden Markov Model

Directory of Open Access Journals (Sweden)

Nabil M. Hewahi

2011-10-01

Full Text Available In this paper we propose a general approach based on Genetic Algorithms (GAs to evolve Hidden Markov Models (HMM. The problem appears when experts assign probability values for HMM, they use only some limited inputs. The assigned probability values might not be accurate to serve in other cases related to the same domain. We introduce an approach based on GAs to find
out the suitable probability values for the HMM to be mostly correct in more cases than what have been used to assign the probability values.

Organic Chemistry YouTube Writing Assignment for Large Lecture Classes

Science.gov (United States)

Franz, Annaliese K.

2012-01-01

This work describes efforts to incorporate and evaluate the use of a YouTube writing assignment in large lecture classes to personalize learning and improve conceptual understanding of chemistry through peer- and self-explanation strategies. Although writing assignments can be a method to incorporate peer- and self-explanation strategies, this…

Fair Package Assignment

Science.gov (United States)

Lahaie, Sébastien; Parkes, David C.

We consider the problem of fair allocation in the package assignment model, where a set of indivisible items, held by single seller, must be efficiently allocated to agents with quasi-linear utilities. A fair assignment is one that is efficient and envy-free. We consider a model where bidders have superadditive valuations, meaning that items are pure complements. Our central result is that core outcomes are fair and even coalition-fair over this domain, while fair distributions may not even exist for general valuations. Of relevance to auction design, we also establish that the core is equivalent to the set of anonymous-price competitive equilibria, and that superadditive valuations are a maximal domain that guarantees the existence of anonymous-price competitive equilibrium. Our results are analogs of core equivalence results for linear prices in the standard assignment model, and for nonlinear, non-anonymous prices in the package assignment model with general valuations.

Effectiveness of author-assigned keywords to INIS indexing

International Nuclear Information System (INIS)

Yokoo, Hiroshi; Takahashi, Satoko; Habara, Tadashi

1977-01-01

A test was carried out on the quality of indexing data which is based only upon author-assigned keywords in order to appreciate effectiveness of the keywords. As measures of the quality, the retrievability and the consistency of the indexing data were evaluated by comparison with the case of the conventional indexing method under the circumstances of the INIS descriptor assignment to the journal articles of the Atomic Energy Society of Japan. The indexing consistency obtained was approximately 0.61 on an average (or 0.66 when the narrower-broader hierarchical relations were regarded as consistent ones). Of the hit, noise, or total documents retrieved with the conventional indexing data, 0.86, 0.27, or 0.71, respectively, were retrievable with the keywords-based indexing data. From the results the recall ratio for the keywords-based indexing is estimated to be no less than 0.86 of that for the conventional indexing method, and the consistency of the hit documents are to be 0.75 at least. Consequently, the author-assigned keywords proved to be very effective to the document indexing. (auth.)

Molecular Darwinism: The Contingency of Spontaneous Genetic Variation

OpenAIRE

Arber, Werner

2011-01-01

The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign...

The Tourette International Collaborative Genetics (TIC Genetics) study, finding the genes causing Tourette syndrome: objectives and methods.

Science.gov (United States)

Dietrich, Andrea; Fernandez, Thomas V; King, Robert A; State, Matthew W; Tischfield, Jay A; Hoekstra, Pieter J; Heiman, Gary A

2015-02-01

Tourette syndrome (TS) is a neuropsychiatric disorder characterized by recurrent motor and vocal tics, often accompanied by obsessive-compulsive disorder and/or attention-deficit/hyperactivity disorder. While the evidence for a genetic contribution is strong, its exact nature has yet to be clarified fully. There is now mounting evidence that the genetic risks for TS include both common and rare variants and may involve complex multigenic inheritance or, in rare cases, a single major gene. Based on recent progress in many other common disorders with apparently similar genetic architectures, it is clear that large patient cohorts and open-access repositories will be essential to further advance the field. To that end, the large multicenter Tourette International Collaborative Genetics (TIC Genetics) study was established. The goal of the TIC Genetics study is to undertake a comprehensive gene discovery effort, focusing both on familial genetic variants with large effects within multiply affected pedigrees and on de novo mutations ascertained through the analysis of apparently simplex parent-child trios with non-familial tics. The clinical data and biomaterials (DNA, transformed cell lines, RNA) are part of a sharing repository located within the National Institute for Mental Health Center for Collaborative Genomics Research on Mental Disorders, USA, and will be made available to the broad scientific community. This resource will ultimately facilitate better understanding of the pathophysiology of TS and related disorders and the development of novel therapies. Here, we describe the objectives and methods of the TIC Genetics study as a reference for future studies from our group and to facilitate collaboration between genetics consortia in the field of TS.

Forensic Science in Support of Wildlife Conservation Efforts - Genetic Approaches (Global Trends).

Science.gov (United States)

Linacre, A

2011-01-01

Wildlife forensic science is a relatively recent development to meet the increasing need of the criminal justice system where there are investigations in alleged transgressions of either international or national legislation. This application of science draws on conservation genetics and forensic geneticists from mainstream forensic science. This review is a broad overview of the history of forensic wildlife science and some of the recent developments in forensic wildlife genetics with the application of DNA developments to nonhuman samples encountered in a forensic science investigation. The review will move from methods to look at the entire genome, when there is no previous knowledge of the species studied, through methods of species identification, using DNA to determine a possible geographic origin, through to assigning samples to a particular individual or a close genetic relative of this individual. The transfer of research methods into the criminal justice system for the investigation of wildlife crimes has been largely successful as is illustrated in the review. The review concludes with comments on the need for standardization and regulation in wildlife forensic science. Copyright © 2011 Central Police University.

The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency.

Science.gov (United States)

Rubinstein, Wendy S; Maglott, Donna R; Lee, Jennifer M; Kattman, Brandi L; Malheiro, Adriana J; Ovetsky, Michael; Hem, Vichet; Gorelenkov, Viatcheslav; Song, Guangfeng; Wallin, Craig; Husain, Nora; Chitipiralla, Shanmuga; Katz, Kenneth S; Hoffman, Douglas; Jang, Wonhee; Johnson, Mark; Karmanov, Fedor; Ukrainchik, Alexander; Denisenko, Mikhail; Fomous, Cathy; Hudson, Kathy; Ostell, James M

2013-01-01

The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information's databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html).

Plagiarism-Proofing Assignments

Science.gov (United States)

Johnson, Doug

2004-01-01

Mr. Johnson has discovered that the higher the level of student engagement and creativity, the lower the probability of plagiarism. For teachers who would like to see such desirable results, he describes the characteristics of assignments that are most likely to produce them. Two scenarios of types of assignments that avoid plagiarism are…

Report of the Advisory Group Meeting on Genetic Methods of Insect Control

International Nuclear Information System (INIS)

1987-01-01

Despite the availability of a range of modern pest control techniques, insects remain a major cause of production losses in agriculture and contribute significantly to diseases of man and livestock. The increasing incidence of pesticide resistance, and concerns over the environmental impact of residues, have highlighted the need for improved technologies. As a result, genetic methods of pest control, including the use of irradiation sterilized insects, have become of increasing importance. It is therefore essential that the Joint FAO/IAEA Division continues to promote the development and application of this method of pest control. The advisory group concluded that the opportunities for genetic control might be widened by the application of new techniques, particularly recombinant DNA technology. The scope for integration of genetic control methods with other control measures, and ist use as a temporary suppressive measure on an area-wide basis was also recognized. Examples are given from representative groups of insect pests to illustrate how these concepts can be applied. The advisory group regarded the Seibersdorf laboratory as a unique facility for the conduct of tactical research related to mass-rearing and release procedures for major pests such as medfly and tsetse spp. Associated research on genetic sexing of medfly, diet recycling and the development of more environmentally acceptable alternatives for pre-release suppression of medfly were considered to be important research projects. The advisory group concluded that the laboratory should continue to remain a centre of excellence for mass-rearing technologies for medfly and tsetse spp., and for training scientists and technicians from developing countries. The Joint FAO/IAEA Division currently plays a major co-ordinating and supportive role for those areas of international research which impinge on genetic control. The advisory group believes that the Joint FAO/IAEA Division should maintain its initiative

Report of the Advisory Group Meeting on Genetic Methods of Insect Control

Energy Technology Data Exchange (ETDEWEB)

NONE

1987-07-01

Despite the availability of a range of modern pest control techniques, insects remain a major cause of production losses in agriculture and contribute significantly to diseases of man and livestock. The increasing incidence of pesticide resistance, and concerns over the environmental impact of residues, have highlighted the need for improved technologies. As a result, genetic methods of pest control, including the use of irradiation sterilized insects, have become of increasing importance. It is therefore essential that the Joint FAO/IAEA Division continues to promote the development and application of this method of pest control. The advisory group concluded that the opportunities for genetic control might be widened by the application of new techniques, particularly recombinant DNA technology. The scope for integration of genetic control methods with other control measures, and ist use as a temporary suppressive measure on an area-wide basis was also recognized. Examples are given from representative groups of insect pests to illustrate how these concepts can be applied. The advisory group regarded the Seibersdorf laboratory as a unique facility for the conduct of tactical research related to mass-rearing and release procedures for major pests such as medfly and tsetse spp. Associated research on genetic sexing of medfly, diet recycling and the development of more environmentally acceptable alternatives for pre-release suppression of medfly were considered to be important research projects. The advisory group concluded that the laboratory should continue to remain a centre of excellence for mass-rearing technologies for medfly and tsetse spp., and for training scientists and technicians from developing countries. The Joint FAO/IAEA Division currently plays a major co-ordinating and supportive role for those areas of international research which impinge on genetic control. The advisory group believes that the Joint FAO/IAEA Division should maintain its initiative

Influence of crossover methods used by genetic algorithm-based ...

Indian Academy of Sciences (India)

numerical methods like Newton–Raphson, sequential homotopy calculation, Walsh ... But the paper does not touch upon the elements of crossover operators. ... if SHE problems are solved with optimization tools like GA (Schutten ..... Goldberg D E 1989 Genetic algorithms in search, optimization and machine learning.

Optimisation of timetable-based, stochastic transit assignment models based on MSA

DEFF Research Database (Denmark)

Nielsen, Otto Anker; Frederiksen, Rasmus Dyhr

2006-01-01

(CRM), such a large-scale transit assignment model was developed and estimated. The Stochastic User Equilibrium problem was solved by the Method of Successive Averages (MSA). However, the model suffered from very large calculation times. The paper focuses on how to optimise transit assignment models...

METHOD OF CONSTRUCTION OF GENETIC DATA CLUSTERS

Directory of Open Access Journals (Sweden)

N. A. Novoselova

2016-01-01

Full Text Available The paper presents a method of construction of genetic data clusters (functional modules using the randomized matrices. To build the functional modules the selection and analysis of the eigenvalues of the gene profiles correlation matrix is performed. The principal components, corresponding to the eigenvalues, which are significantly different from those obtained for the randomly generated correlation matrix, are used for the analysis. Each selected principal component forms gene cluster. In a comparative experiment with the analogs the proposed method shows the advantage in allocating statistically significant different-sized clusters, the ability to filter non- informative genes and to extract the biologically interpretable functional modules matching the real data structure.

Methods for genetic linkage analysis using trisomies.

OpenAIRE

Feingold, E; Lamb, N E; Sherman, S L

1995-01-01

Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of "susceptibility" ...

Columbia River Stock Identification Study; Validation of Genetic Method, 1980-1981 Final Report.

Energy Technology Data Exchange (ETDEWEB)

Milner, George B.; Teel, David J.; Utter, Fred M. (Northwest and Alaska Fisheries Science Center, Coastal Zone and Estuarine Studies Division, Seattle, WA)

1981-06-01

The reliability of a method for obtaining maximum likelihood estimate of component stocks in mixed populations of salmonids through the frequency of genetic variants in a mixed population and in potentially contributing stocks was tested in 1980. A data base of 10 polymorphic loci from 14 hatchery stocks of spring chinook salmon of the Columbia River was used to estimate proportions of these stocks in four different blind'' mixtures whose true composition was only revealed subsequent to obtaining estimates. The accuracy and precision of these blind tests have validated the genetic method as a valuable means for identifying components of stock mixtures. Properties of the genetic method were further examined by simulation studies using the pooled data of the four blind tests as a mixed fishery. Replicated tests with samples sizes between 100 and 1,000 indicated that actual standard deviations on estimated contributions were consistently lower than calculated standard deviations; this difference diminished as sample size increased. It is recommended that future applications of the method be preceded by simulation studies that will identify appropriate levels of sampling required for acceptable levels of accuracy and precision. Variables in such studies include the stocks involved, the loci used, and the genetic differentiation among stocks. 8 refs., 6 figs., 4 tabs.

Advances in the application of genetic manipulation methods to apicomplexan parasites.

Science.gov (United States)

Suarez, C E; Bishop, R P; Alzan, H F; Poole, W A; Cooke, B M

2017-10-01

Apicomplexan parasites such as Babesia, Theileria, Eimeria, Cryptosporidium and Toxoplasma greatly impact animal health globally, and improved, cost-effective measures to control them are urgently required. These parasites have complex multi-stage life cycles including obligate intracellular stages. Major gaps in our understanding of the biology of these relatively poorly characterised parasites and the diseases they cause severely limit options for designing novel control methods. Here we review potentially important shared aspects of the biology of these parasites, such as cell invasion, host cell modification, and asexual and sexual reproduction, and explore the potential of the application of relatively well-established or newly emerging genetic manipulation methods, such as classical transfection or gene editing, respectively, for closing important gaps in our knowledge of the function of specific genes and proteins, and the biology of these parasites. In addition, genetic manipulation methods impact the development of novel methods of control of the diseases caused by these economically important parasites. Transient and stable transfection methods, in conjunction with whole and deep genome sequencing, were initially instrumental in improving our understanding of the molecular biology of apicomplexan parasites and paved the way for the application of the more recently developed gene editing methods. The increasingly efficient and more recently developed gene editing methods, in particular those based on the CRISPR/Cas9 system and previous conceptually similar techniques, are already contributing to additional gene function discovery using reverse genetics and related approaches. However, gene editing methods are only possible due to the increasing availability of in vitro culture, transfection, and genome sequencing and analysis techniques. We envisage that rapid progress in the development of novel gene editing techniques applied to apicomplexan parasites of

[Personal identification with biometric and genetic methods].

Science.gov (United States)

Cabanis, Emmanuel-Alain; Le Gall, Jean-Yves; Ardaillou, Raymond

2007-11-01

The need for personal identification is growing in many avenues of society. To "identify" a person is to establish a link between his or her observed characteristics and those previously stored in a database. To "authenticate" is to decide whether or not someone is the person he or she claims to be. These two objectives can now be achieved by analysing biometric data and genetic prints. All biometric techniques proceed in several stages: acquisition of an image or physical parameters, encoding them with a mathematical model, comparing the results of this model with those contained in the database, and calculating the error risk. These techniques must be usable worldwide and must examine specific and permanent personal data. The most widely used are facial recognition, digital prints (flexion folds and dermatoglyphs, that offer the advantage of leaving marks), and the surface and texture of the iris. Other biometric techniques analyse behaviours such as walking, signing, typing, or speaking. Implanted radio-transmitters are another means of identification. All these systems are evaluated on the basis of the same parameters, namely the false rejection rate, the false acceptance rate, and the failure-to-enrol rate. The uses of biometrics are increasing and diversifying, and now include national and international identification systems, control of access to protected sites, criminal and victim identification, and transaction security. Genetic methods can identify individuals almost infallibly, based on short tandem repeats of 2-5 nucleotides, or microsatellites. The most recent kits analyze 11-16 independent autosomal markers. Mitochondrial DNA and Y chromosome DNA can also be analyzed. These genetic tests are currently used to identify suspected criminals or their victims from biological samples, and to establish paternity. Personal identification raises many ethical questions, however, such as when to create and how to use a database while preserving personal freedom

An integrated multi-population genetic algorithm for multi-vehicle task assignment in a drift field

NARCIS (Netherlands)

Bai, Xiaoshan; Yan, Weisheng; Ge, Shuzhi Sam; Cao, Ming

This paper investigates the task assignment problem for a team of autonomous aerial/marine vehicles driven by constant thrust and maneuvering in a planar lateral drift field. The aim is to minimize the total traveling time in order to guide the vehicles to deliver a number of customized sensors to a

Bayesian inference on genetic merit under uncertain paternity

Directory of Open Access Journals (Sweden)

Tempelman Robert J

2003-09-01

Full Text Available Abstract A hierarchical animal model was developed for inference on genetic merit of livestock with uncertain paternity. Fully conditional posterior distributions for fixed and genetic effects, variance components, sire assignments and their probabilities are derived to facilitate a Bayesian inference strategy using MCMC methods. We compared this model to a model based on the Henderson average numerator relationship (ANRM in a simulation study with 10 replicated datasets generated for each of two traits. Trait 1 had a medium heritability (h2 for each of direct and maternal genetic effects whereas Trait 2 had a high h2 attributable only to direct effects. The average posterior probabilities inferred on the true sire were between 1 and 10% larger than the corresponding priors (the inverse of the number of candidate sires in a mating pasture for Trait 1 and between 4 and 13% larger than the corresponding priors for Trait 2. The predicted additive and maternal genetic effects were very similar using both models; however, model choice criteria (Pseudo Bayes Factor and Deviance Information Criterion decisively favored the proposed hierarchical model over the ANRM model.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

International Nuclear Information System (INIS)

Swain, Monalisa; Atreya, Hanudatta S.

2009-01-01

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

A generic method for assignment of reliability scores applied to solvent accessibility predictions

Directory of Open Access Journals (Sweden)

Nielsen Morten

2009-07-01

Full Text Available Abstract Background Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best methods associate a prediction with a reliability score or index. For discrete qualitative predictions, the reliability is conventionally estimated as the difference between output scores of selected classes. Such an approach is not feasible for methods that predict a biological feature as a single real value rather than a classification. As a solution to this challenge, we have implemented a method that predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score. Results An ensemble of artificial neural networks has been trained on a set of experimentally solved protein structures to predict the relative exposure of the amino acids. The method assigns a reliability score to each surface accessibility prediction as an inherent part of the training process. This is in contrast to the most commonly used procedures where reliabilities are obtained by post-processing the output. Conclusion The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when comparing the Pearson's correlation coefficient for the upper 20% of predictions sorted according to reliability. For this subset, values of 0

General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models.

Science.gov (United States)

de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael

2016-11-01

Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population. Copyright © 2016 de Villemereuil et al.

Coherent spectroscopic methods for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution

International Nuclear Information System (INIS)

Moguilnaya, T.; Suminov, Y.; Botikov, A.; Ignatov, S.; Kononenko, A.; Agibalov, A.

2017-01-01

We developed the new automatic method that combines the method of forced luminescence and stimulated Brillouin scattering. This method is used for monitoring pathogens, genetically modified products and nanostructured materials in colloidal solution. We carried out the statistical spectral analysis of pathogens, genetically modified soy and nano-particles of silver in water from different regions in order to determine the statistical errors of the method. We studied spectral characteristics of these objects in water to perform the initial identification with 95% probability. These results were used for creation of the model of the device for monitor of pathogenic organisms and working model of the device to determine the genetically modified soy in meat.

Incorporating breeding abundance into spatial assignments on continuous surfaces.

Science.gov (United States)

Rushing, Clark S; Marra, Peter P; Studds, Colin E

2017-06-01

Determining the geographic connections between breeding and nonbreeding populations, termed migratory connectivity, is critical to advancing our understanding of the ecology and conservation of migratory species. Assignment models based on stable isotopes historically have been an important tool for studying migratory connectivity of small-bodied species, but the low resolution of these assignments has generated interest into combining isotopes with other sources in information. Abundance is one of the most appealing data sources to include in isotope-based assignments, but there are currently no statistical methods or guidelines for optimizing the contribution of stable isotopes and abundance for inferring migratory connectivity. Using known-origin stable-hydrogen isotope samples of six Neotropical migratory bird species, we rigorously assessed the performance of assignment models that differentially weight the contribution of the isotope and abundance data. For two species with adequate sample sizes, we used Pareto optimality to determine the set of models that simultaneously minimized both assignment error rate and assignment area. We then assessed the ability of the top models from these two species to improve assignments of the remaining four species compared to assignments based on isotopes alone. We show that the increased precision of models that include abundance is often offset by a large increase in assignment error. However, models that optimally weigh the abundance data relative to the isotope data can result in higher precision and, in some cases, lower error than models based on isotopes alone. The top models, however, depended on the distribution of relative breeding abundance, with patchier distributions requiring stronger downweighting of abundance, and we present general guidelines for future studies. These results confirm that breeding abundance can be an important source of information for studies investigating broad-scale movements of

Natural transformation of Vibrio parahaemolyticus: A rapid method to create genetic deletions.

Science.gov (United States)

Chimalapati, Suneeta; de Souza Santos, Marcela; Servage, Kelly; De Nisco, Nicole J; Dalia, Ankur B; Orth, Kim

2018-03-19

The Gram-negative bacterium Vibrio parahaemolyticus is an opportunistic human pathogen and the leading cause of seafood borne acute gastroenteritis worldwide. Recently, this bacterium was implicated as the etiologic agent of a severe shrimp disease with consequent devastating outcomes to shrimp farming. In both cases, acquisition of genetic material via horizontal transfer provided V. parahaemolyticus with new virulence tools to cause disease. Dissecting the molecular mechanisms of V. parahaemolyticus pathogenesis often requires manipulating its genome. Classically, genetic deletions in V. parahaemolyticus are performed using a laborious, lengthy, multi-step process. Herein, we describe a fast and efficient method to edit this bacterium's genome based on V. parahaemolyticus natural competence. Although this method is similar to one previously described, V. parahaemolyticus requires counter selection for curing of acquired plasmids due to its recalcitrant nature of retaining extrachromosomal DNA. We believe this approach will be of use to the Vibrio community. Importance Spreading of Vibrios throughout the world correlates with increased global temperatures. As they spread, they find new niches to survive, proliferate and invade. Therefore, genetic manipulation of Vibrios is of utmost importance for studying these species. Herein, we have delineated and validated a rapid method to create genetic deletions in Vibrio parahaemolyticus This study provides insightful methodology for studies with other Vibrio species. Copyright © 2018 American Society for Microbiology.

Using optimal combination of teaching-learning methods (open book assignment and group tutorials) as revision exercises to improve learning outcome in low achievers in biochemistry.

Science.gov (United States)

Rajappa, Medha; Bobby, Zachariah; Nandeesha, H; Suryapriya, R; Ragul, Anithasri; Yuvaraj, B; Revathy, G; Priyadarssini, M

2016-07-08

Graduate medical students of India are taught Biochemistry by didactic lectures and they hardly get any opportunity to clarify their doubts and reinforce the concepts which they learn in these lectures. We used a combination of teaching-learning (T-L) methods (open book assignment followed by group tutorials) to study their efficacy in improving the learning outcome. About 143 graduate medical students were classified into low (75%: group 3, n = 46) achievers, based on their internal assessment marks. After the regular teaching module on the topics "Vitamins and Enzymology", all the students attempted an open book assignment without peer consultation. Then all the students participated in group tutorials. The effects on the groups were evaluated by pre and posttests at the end of each phase, with the same set of MCQs. Gain from group tutorials and overall gain was significantly higher in the low achievers, compared to other groups. High and medium achievers obtained more gain from open book assignment, than group tutorials. The overall gain was significantly higher than the gain obtained from open book assignment or group tutorials, in all three groups. All the three groups retained the gain even after 1 week of the exercise. Hence, optimal use of novel T-L methods (open book assignment followed by group tutorials) as revision exercises help in strengthening concepts in Biochemistry in this oft neglected group of low achievers in graduate medical education. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):321-325, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Comparisons of likelihood and machine learning methods of individual classification

Science.gov (United States)

Guinand, B.; Topchy, A.; Page, K.S.; Burnham-Curtis, M. K.; Punch, W.F.; Scribner, K.T.

2002-01-01

Classification methods used in machine learning (e.g., artificial neural networks, decision trees, and k-nearest neighbor clustering) are rarely used with population genetic data. We compare different nonparametric machine learning techniques with parametric likelihood estimations commonly employed in population genetics for purposes of assigning individuals to their population of origin (“assignment tests”). Classifier accuracy was compared across simulated data sets representing different levels of population differentiation (low and high FST), number of loci surveyed (5 and 10), and allelic diversity (average of three or eight alleles per locus). Empirical data for the lake trout (Salvelinus namaycush) exhibiting levels of population differentiation comparable to those used in simulations were examined to further evaluate and compare classification methods. Classification error rates associated with artificial neural networks and likelihood estimators were lower for simulated data sets compared to k-nearest neighbor and decision tree classifiers over the entire range of parameters considered. Artificial neural networks only marginally outperformed the likelihood method for simulated data (0–2.8% lower error rates). The relative performance of each machine learning classifier improved relative likelihood estimators for empirical data sets, suggesting an ability to “learn” and utilize properties of empirical genotypic arrays intrinsic to each population. Likelihood-based estimation methods provide a more accessible option for reliable assignment of individuals to the population of origin due to the intricacies in development and evaluation of artificial neural networks. In recent years, characterization of highly polymorphic molecular markers such as mini- and microsatellites and development of novel methods of analysis have enabled researchers to extend investigations of ecological and evolutionary processes below the population level to the level of

Dynamic Sequence Assignment.

Science.gov (United States)

1983-12-01

D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

Visual words assignment via information-theoretic manifold embedding.

Science.gov (United States)

Deng, Yue; Li, Yipeng; Qian, Yanjun; Ji, Xiangyang; Dai, Qionghai

2014-10-01

Codebook-based learning provides a flexible way to extract the contents of an image in a data-driven manner for visual recognition. One central task in such frameworks is codeword assignment, which allocates local image descriptors to the most similar codewords in the dictionary to generate histogram for categorization. Nevertheless, existing assignment approaches, e.g., nearest neighbors strategy (hard assignment) and Gaussian similarity (soft assignment), suffer from two problems: 1) too strong Euclidean assumption and 2) neglecting the label information of the local descriptors. To address the aforementioned two challenges, we propose a graph assignment method with maximal mutual information (GAMI) regularization. GAMI takes the power of manifold structure to better reveal the relationship of massive number of local features by nonlinear graph metric. Meanwhile, the mutual information of descriptor-label pairs is ultimately optimized in the embedding space for the sake of enhancing the discriminant property of the selected codewords. According to such objective, two optimization models, i.e., inexact-GAMI and exact-GAMI, are respectively proposed in this paper. The inexact model can be efficiently solved with a closed-from solution. The stricter exact-GAMI nonparametrically estimates the entropy of descriptor-label pairs in the embedding space and thus leads to a relatively complicated but still trackable optimization. The effectiveness of GAMI models are verified on both the public and our own datasets.

DNA extraction methods for detecting genetically modified foods: A comparative study.

Science.gov (United States)

Elsanhoty, Rafaat M; Ramadan, Mohamed Fawzy; Jany, Klaus Dieter

2011-06-15

The work presented in this manuscript was achieved to compare six different methods for extracting DNA from raw maize and its derived products. The methods that gave higher yield and quality of DNA were chosen to detect the genetic modification in the samples collected from the Egyptian market. The different methods used were evaluated for extracting DNA from maize kernels (without treatment), maize flour (mechanical treatment), canned maize (sweet corn), frozen maize (sweet corn), maize starch, extruded maize, popcorn, corn flacks, maize snacks, and bread made from corn flour (mechanical and thermal treatments). The quality and quantity of the DNA extracted from the standards, containing known percentages of GMO material and from the different food products were evaluated. For qualitative detection of the GMO varieties in foods, the GMOScreen 35S/NOS test kit was used, to screen the genetic modification in the samples. The positive samples for the 35S promoter and/or the NOS terminator were identified by the standard methods adopted by EU. All of the used methods extracted yielded good DNA quality. However, we noted that the purest DNA extract were obtained using the DNA extraction kit (Roche) and this generally was the best method for extracting DNA from most of the maize-derived foods. We have noted that the yield of DNA extracted from maize-derived foods was generally lower in the processed products. The results indicated that 17 samples were positive for the presence of 35S promoter, while 34% from the samples were positive for the genetically modified maize line Bt-176. Copyright © 2010 Elsevier Ltd. All rights reserved.

Microsatellite markers reveal low genetic differentiation among ...

African Journals Online (AJOL)

Ben

Assignment. 1* Khai Apple Game Reserve, Kathu, Northern Cape ... Previous genetic studies on Camelidae in Dubai, Germany, Australia, Kenya and Ethiopia mainly reporting the ... All the biological samples were deposited in the Bio-Bank at.

Teaching genetics using hands-on models, problem solving, and inquiry-based methods

Science.gov (United States)

Hoppe, Stephanie Ann

Teaching genetics can be challenging because of the difficulty of the content and misconceptions students might hold. This thesis focused on using hands-on model activities, problem solving, and inquiry-based teaching/learning methods in order to increase student understanding in an introductory biology class in the area of genetics. Various activities using these three methods were implemented into the classes to address any misconceptions and increase student learning of the difficult concepts. The activities that were implemented were shown to be successful based on pre-post assessment score comparison. The students were assessed on the subjects of inheritance patterns, meiosis, and protein synthesis and demonstrated growth in all of the areas. It was found that hands-on models, problem solving, and inquiry-based activities were more successful in learning concepts in genetics and the students were more engaged than tradition styles of lecture.

Probabilistic validation of protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Dashti, Hesam; Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel; Ulrich, Eldon L.; Markley, John L.

2016-01-01

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/

Probabilistic validation of protein NMR chemical shift assignments

Energy Technology Data Exchange (ETDEWEB)

Dashti, Hesam [University of Wisconsin-Madison, Graduate Program in Biophysics, Biochemistry Department (United States); Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States); Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Biochemistry Department (United States); Markley, John L., E-mail: markley@nmrfam.wisc.edu, E-mail: jmarkley@wisc.edu [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States)

2016-01-15

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/.

Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS

Directory of Open Access Journals (Sweden)

Kim Nora

2012-07-01

Full Text Available Abstract Background It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic associations aggregate in specific functional groups as defined by the Gene Ontology (GO. Results We first estimated all pairwise additive and nonadditive genetic effects using the multifactor dimensionality reduction (MDR method that makes few assumptions about the underlying genetic model. Statistical significance was evaluated using permutation testing in two genome-wide association studies of ALS. The detection data consisted of 276 subjects with ALS and 271 healthy controls while the replication data consisted of 221 subjects with ALS and 211 healthy controls. Both studies included genotypes from approximately 550,000 single-nucleotide polymorphisms (SNPs. Each SNP was mapped to a gene if it was within 500 kb of the start or end. Each SNP was assigned a p-value based on its strongest joint effect with the other SNPs. We then used the Exploratory Visual Analysis (EVA method and software to assign a p-value to each gene based on the overabundance of significant SNPs at the α = 0.05 level in the gene. We also used EVA to assign p-values to each GO group based on the overabundance of significant genes at the α = 0.05 level. A GO category was determined to replicate if that category was significant at the α = 0.05 level in both studies. We found two GO categories that replicated in both studies. The first, ‘Regulation of Cellular Component Organization and Biogenesis’, a GO Biological Process, had p-values of 0.010 and 0.014 in the detection and replication studies, respectively. The second, ‘Actin Cytoskeleton’, a GO Cellular Component, had p-values of 0.040 and 0.046 in the detection and replication studies, respectively. Conclusions Pathway

A review of statistical methods for testing genetic anticipation: looking for an answer in Lynch syndrome

DEFF Research Database (Denmark)

Boonstra, Philip S; Gruber, Stephen B; Raymond, Victoria M

2010-01-01

Anticipation, manifested through decreasing age of onset or increased severity in successive generations, has been noted in several genetic diseases. Statistical methods for genetic anticipation range from a simple use of the paired t-test for age of onset restricted to affected parent-child pairs......, and this right truncation effect is more pronounced in children than in parents. In this study, we first review different statistical methods for testing genetic anticipation in affected parent-child pairs that address the issue of bias due to right truncation. Using affected parent-child pair data, we compare...... the issue of multiplex ascertainment and its effect on the different methods. We then focus on exploring genetic anticipation in Lynch syndrome and analyze new data on the age of onset in affected parent-child pairs from families seen at the University of Michigan Cancer Genetics clinic with a mutation...

A map of directional genetic interactions in a metazoan cell.

Science.gov (United States)

Fischer, Bernd; Sandmann, Thomas; Horn, Thomas; Billmann, Maximilian; Chaudhary, Varun; Huber, Wolfgang; Boutros, Michael

2015-03-06

Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

Monitoring Species of Concern Using Noninvasive Genetic Sampling and Capture-Recapture Methods

Science.gov (United States)

2016-11-01

RC-201205) Monitoring Species of Concern Using Noninvasive Genetic Sampling and Capture- Recapture Methods November 2016 This document has been...From - To) Apr 25 2012-Jan 31 2016 4. TITLE AND SUBTITLE Monitoring Species of Concern Using Noninvasive Genetic Sampling and Capture- Recapture...NGS-CR) modeling to evaluate the status of species of conservation concern . A secondary objective was to demonstrate the combination of NGS with

Utilization of niching methods of genetic algorithms in nuclear reactor problems optimization

International Nuclear Information System (INIS)

Sacco, Wagner Figueiredo; Schirru, Roberto

2000-01-01

Genetic Algorithms (GAs) are biologically motivated adaptive systems which have been used, with good results, in function optimization. However, traditional GAs rapidly push an artificial population toward convergence. That is, all individuals in the population soon become nearly identical. Niching Methods allow genetic algorithms to maintain a population of diverse individuals. GAs that incorporate these methods are capable of locating multiple, optimal solutions within a single population. The purpose of this study is to test existing niching techniques and two methods introduced herein, bearing in mind their eventual application in nuclear reactor related problems, specially the nuclear reactor core reload one, which has multiple solutions. Tests are performed using widely known test functions and their results show that the new methods are quite promising, specially in real world problems like the nuclear reactor core reload. (author)

Heuristic for Task-Worker Assignment with Varying Learning Slopes

Directory of Open Access Journals (Sweden)

Wipawee Tharmmaphornphilas

2010-04-01

Full Text Available Fashion industry has variety products, so the multi-skilled workers are required to improve flexibility in production and assignment. Generally the supervisor will assign task to the workers based on skill and skill levels of worker. Since in fashion industry new product styles are launched more frequently and the order size tends to be smaller, the workers always learn when the raw material and the production process changes. Consequently they require less time to produce the succeeding units of a task based on their learning ability. Since the workers have both experience and inexperience workers, so each worker has different skill level and learning ability. Consequently, the assignment which assumed constant skill level is not proper to use. This paper proposes a task-worker assignment considering worker skill levels and learning abilities. Processing time of each worker changes along production period due to a worker learning ability. We focus on a task-worker assignment in a fashion industry where tasks are ordered in series; the number of tasks is greater than the number of workers. Therefore, workers can perform multiple assignments followed the precedence restriction as an assembly line balancing problem. The problem is formulated in an integer linear programming model with objective to minimize makespan. A heuristic is proposed to determine the lower bound (LB and the upper bound (UB of the problem and the best assignment is determined. The performance of the heuristic method is tested by comparing quality of solution and computational time to optimal solutions.

Fragment assignment in the cloud with eXpress-D

Science.gov (United States)

2013-01-01

Background Probabilistic assignment of ambiguously mapped fragments produced by high-throughput sequencing experiments has been demonstrated to greatly improve accuracy in the analysis of RNA-Seq and ChIP-Seq, and is an essential step in many other sequence census experiments. A maximum likelihood method using the expectation-maximization (EM) algorithm for optimization is commonly used to solve this problem. However, batch EM-based approaches do not scale well with the size of sequencing datasets, which have been increasing dramatically over the past few years. Thus, current approaches to fragment assignment rely on heuristics or approximations for tractability. Results We present an implementation of a distributed EM solution to the fragment assignment problem using Spark, a data analytics framework that can scale by leveraging compute clusters within datacenters–“the cloud”. We demonstrate that our implementation easily scales to billions of sequenced fragments, while providing the exact maximum likelihood assignment of ambiguous fragments. The accuracy of the method is shown to be an improvement over the most widely used tools available and can be run in a constant amount of time when cluster resources are scaled linearly with the amount of input data. Conclusions The cloud offers one solution for the difficulties faced in the analysis of massive high-thoughput sequencing data, which continue to grow rapidly. Researchers in bioinformatics must follow developments in distributed systems–such as new frameworks like Spark–for ways to port existing methods to the cloud and help them scale to the datasets of the future. Our software, eXpress-D, is freely available at: http://github.com/adarob/express-d. PMID:24314033

[Rapid assessment of critical quality attributes of Chinese materia medica (II): strategy of NIR assignment].

Science.gov (United States)

Pei, Yan-Ling; Wu, Zhi-Sheng; Shi, Xin-Yuan; Zhou, Lu-Wei; Qiao, Yan-Jiang

2014-09-01

The present paper firstly reviewed the research progress and main methods of NIR spectral assignment coupled with our research results. Principal component analysis was focused on characteristic signal extraction to reflect spectral differences. Partial least squares method was concerned with variable selection to discover characteristic absorption band. Two-dimensional correlation spectroscopy was mainly adopted for spectral assignment. Autocorrelation peaks were obtained from spectral changes, which were disturbed by external factors, such as concentration, temperature and pressure. Density functional theory was used to calculate energy from substance structure to establish the relationship between molecular energy and spectra change. Based on the above reviewed method, taking a NIR spectral assignment of chlorogenic acid as example, a reliable spectral assignment for critical quality attributes of Chinese materia medica (CMM) was established using deuterium technology and spectral variable selection. The result demonstrated the assignment consistency according to spectral features of different concentrations of chlorogenic acid and variable selection region of online NIR model in extract process. Although spectral assignment was initial using an active pharmaceutical ingredient, it is meaningful to look forward to the futurity of the complex components in CMM. Therefore, it provided methodology for NIR spectral assignment of critical quality attributes in CMM.

基于业务预测的时隙分配算法%Timeslot Assign Method Based on Business Predicts

Institute of Scientific and Technical Information of China (English)

徐达; 张有志; 郝学坤

2016-01-01

The resource of MF⁃TDMA satellite systems is very precious,how efficiently assign and make use of channel resources of satellite communication system,it is necessary to design an algoritm which can reduce satellite communication delay.This paper puts forward a timeslot assign method based on business predicts in MF⁃TDMA satellite communication system. This method performs the business predict of next moment based on the queue size and business arrival rate and the master station performs in advance channel resource allocation of next moment according to the business predict value. The simulation results show that the timeslot assign method can effectively reduce the transmission delay and improve the channel resource utilization.%多频－时分多址（ MF⁃TDMA）卫星通信系统中信道资源十分宝贵，如何高效地分配和利用卫星通信系统信道资源，研究出一种可以降低卫星通信时延的算法很有必要。提出了一种MF⁃TDMA卫星通信系统中基于业务预测的时隙分配方法，通过终端缓存区域的队列长度和业务到达率来进行下一时刻的业务预测，中心站根据业务预测值来提前进行下一时刻信道资源的分配。仿真结果表明，通过基于业务预测的时隙分配算法可以有效降低传输时延，提高信道资源的利用率。

Statistical methods to detect novel genetic variants using publicly available GWAS summary data.

Science.gov (United States)

Guo, Bin; Wu, Baolin

2018-03-01

We propose statistical methods to detect novel genetic variants using only genome-wide association studies (GWAS) summary data without access to raw genotype and phenotype data. With more and more summary data being posted for public access in the post GWAS era, the proposed methods are practically very useful to identify additional interesting genetic variants and shed lights on the underlying disease mechanism. We illustrate the utility of our proposed methods with application to GWAS meta-analysis results of fasting glucose from the international MAGIC consortium. We found several novel genome-wide significant loci that are worth further study. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genetic similarity of soybean genotypes revealed by seed protein

Directory of Open Access Journals (Sweden)

Nikolić Ana

2005-01-01

Full Text Available More accurate and complete descriptions of genotypes could help determinate future breeding strategies and facilitate introgression of new genotypes in current soybean genetic pool. The objective of this study was to characterize 20 soybean genotypes from the Maize Research Institute "Zemun Polje" collection, which have good agronomic performances, high yield, lodging and drought resistance, and low shuttering by seed proteins as biochemical markers. Seed proteins were isolated and separated by PAA electrophoresis. On the basis of the presence/absence of protein fractions coefficients of similarity were calculated as Dice and Roger and Tanamoto coefficient between pairs of genotypes. The similarity matrix was submitted for hierarchical cluster analysis of un weighted pair group using arithmetic average (UPGMA method and necessary computation were performed using NTSYS-pc program. Protein seed analysis confirmed low level of genetic diversity in soybean. The highest genetic similarity was between genotypes P9272 and Kador. According to obtained results, soybean genotypes were assigned in two larger groups and coefficients of similarity showed similar results. Because of the lack of pedigree data for analyzed genotypes, correspondence with marker data could not be determined. In plant with a narrow genetic base in their gene pool, such as soybean, protein markers may not be sufficient for characterization and study of genetic diversity.

Distributed Schemes for Crowdsourcing-Based Sensing Task Assignment in Cognitive Radio Networks

Directory of Open Access Journals (Sweden)

Linbo Zhai

2017-01-01

Full Text Available Spectrum sensing is an important issue in cognitive radio networks. The unlicensed users can access the licensed wireless spectrum only when the licensed wireless spectrum is sensed to be idle. Since mobile terminals such as smartphones and tablets are popular among people, spectrum sensing can be assigned to these mobile intelligent terminals, which is called crowdsourcing method. Based on the crowdsourcing method, this paper studies the distributed scheme to assign spectrum sensing task to mobile terminals such as smartphones and tablets. Considering the fact that mobile terminals’ positions may influence the sensing results, a precise sensing effect function is designed for the crowdsourcing-based sensing task assignment. We aim to maximize the sensing effect function and cast this optimization problem to address crowdsensing task assignment in cognitive radio networks. This problem is difficult to be solved because the complexity of this problem increases exponentially with the growth in mobile terminals. To assign crowdsensing task, we propose four distributed algorithms with different transition probabilities and use a Markov chain to analyze the approximation gap of our proposed schemes. Simulation results evaluate the average performance of our proposed algorithms and validate the algorithm’s convergence.

Optimization of Personnel Assignment Problem Based on Traveling Time by Using Hungarian Methods: Case Study on the Central Post Office Bandung

Science.gov (United States)

Supian, Sudradjat; Wahyuni, Sri; Nahar, Julita; Subiyanto

2018-01-01

In this paper, traveling time workers from the central post office Bandung in delivering the package to the destination location was optimized by using Hungarian method. Sensitivity analysis against data changes that may occur was also conducted. The sampled data in this study are 10 workers who will be assigned to deliver mail package to 10 post office delivery centers in Bandung that is Cikutra, Padalarang, Ujung Berung, Dayeuh Kolot, Asia- Africa, Soreang, Situ Saeur, Cimahi, Cipedes and Cikeruh. The result of this research is optimal traveling time from 10 workers to 10 destination locations. The optimal traveling time required by the workers is 387 minutes to reach the destination. Based on this result, manager of the central post office Bandung can make optimal decisions to assign tasks to their workers.

Genetic Algorithm Optimizes Q-LAW Control Parameters

Science.gov (United States)

Lee, Seungwon; von Allmen, Paul; Petropoulos, Anastassios; Terrile, Richard

2008-01-01

A document discusses a multi-objective, genetic algorithm designed to optimize Lyapunov feedback control law (Q-law) parameters in order to efficiently find Pareto-optimal solutions for low-thrust trajectories for electronic propulsion systems. These would be propellant-optimal solutions for a given flight time, or flight time optimal solutions for a given propellant requirement. The approximate solutions are used as good initial solutions for high-fidelity optimization tools. When the good initial solutions are used, the high-fidelity optimization tools quickly converge to a locally optimal solution near the initial solution. Q-law control parameters are represented as real-valued genes in the genetic algorithm. The performances of the Q-law control parameters are evaluated in the multi-objective space (flight time vs. propellant mass) and sorted by the non-dominated sorting method that assigns a better fitness value to the solutions that are dominated by a fewer number of other solutions. With the ranking result, the genetic algorithm encourages the solutions with higher fitness values to participate in the reproduction process, improving the solutions in the evolution process. The population of solutions converges to the Pareto front that is permitted within the Q-law control parameter space.

Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment

International Nuclear Information System (INIS)

Schedlbauer, Andreas; Auer, Renate; Ledolter, Karin; Tollinger, Martin; Kloiber, Karin; Lichtenecker, Roman; Ruedisser, Simon; Hommel, Ulrich; Schmid, Walther; Konrat, Robert; Kontaxis, Georg

2008-01-01

Direct methods in NMR based structure determination start from an unassigned ensemble of unconnected gaseous hydrogen atoms. Under favorable conditions they can produce low resolution structures of proteins. Usually a prohibitively large number of NOEs is required, to solve a protein structure ab-initio, but even with a much smaller set of distance restraints low resolution models can be obtained which resemble a protein fold. One problem is that at such low resolution and in the absence of a force field it is impossible to distinguish the correct protein fold from its mirror image. In a hybrid approach these ambiguous models have the potential to aid in the process of sequential backbone chemical shift assignment when 13 C β and 13 C' shifts are not available for sensitivity reasons. Regardless of the overall fold they enhance the information content of the NOE spectra. These, combined with residue specific labeling and minimal triple-resonance data using 13 C α connectivity can provide almost complete sequential assignment. Strategies for residue type specific labeling with customized isotope labeling patterns are of great advantage in this context. Furthermore, this approach is to some extent error-tolerant with respect to data incompleteness, limited precision of the peak picking, and structural errors caused by misassignment of NOEs

DNA barcode data accurately assign higher spider taxa

Directory of Open Access Journals (Sweden)

Jonathan A. Coddington

2016-07-01

Full Text Available The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%. Accurate assignment of higher taxa (PIdent above which errors totaled less than 5% occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However

Exergetic optimization of turbofan engine with genetic algorithm method

Energy Technology Data Exchange (ETDEWEB)

Turan, Onder [Anadolu University, School of Civil Aviation (Turkey)], e-mail: onderturan@anadolu.edu.tr

2011-07-01

With the growth of passenger numbers, emissions from the aeronautics sector are increasing and the industry is now working on improving engine efficiency to reduce fuel consumption. The aim of this study is to present the use of genetic algorithms, an optimization method based on biological principles, to optimize the exergetic performance of turbofan engines. The optimization was carried out using exergy efficiency, overall efficiency and specific thrust of the engine as evaluation criteria and playing on pressure and bypass ratio, turbine inlet temperature and flight altitude. Results showed exergy efficiency can be maximized with higher altitudes, fan pressure ratio and turbine inlet temperature; the turbine inlet temperature is the most important parameter for increased exergy efficiency. This study demonstrated that genetic algorithms are effective in optimizing complex systems in a short time.

On the Solution of the Eigenvalue Assignment Problem for Discrete-Time Systems

Directory of Open Access Journals (Sweden)

El-Sayed M. E. Mostafa

2017-01-01

Full Text Available The output feedback eigenvalue assignment problem for discrete-time systems is considered. The problem is formulated first as an unconstrained minimization problem, where a three-term nonlinear conjugate gradient method is proposed to find a local solution. In addition, a cut to the objective function is included, yielding an inequality constrained minimization problem, where a logarithmic barrier method is proposed for finding the local solution. The conjugate gradient method is further extended to tackle the eigenvalue assignment problem for the two cases of decentralized control systems and control systems with time delay. The performance of the methods is illustrated through various test examples.

Assignment of releves to pre-defined classes by supervised clustering of plant communities using a new composite index

NARCIS (Netherlands)

Tongeren, O.; Gremmen, N.; Hennekens, S.M.

2008-01-01

Question: How does a newly designed method of supervised clustering perform in the assignment of releve ( species composition) data to a previously established classification. How do the results compare to the assignment by experts and to the assignment using a completely different numerical method?

P-wave assignment of 232Th neutron resonances

International Nuclear Information System (INIS)

Corvi, F.; Pasquariello, G.; Veen, T. van der

1978-01-01

A method of p-wave assignment which exploits the parity dependence of the primary capture γ-ray spectrum was applied to the 232 Th resonance. The yield of capture γ-rays above 4.4 MeV from a 6 mm thick metallic thorium disk was measured in the neutron energy range 20-2200 eV and compared to a similar run with γ-rays in the range 3.7 - 4.4 MeV. A total of 58 resonances showing an enhancement of the high energy γ-ray yield were assigned as p-waves. Assuming that their reduced neutron widths follow a Porter-Thomas distribution, their average value and then the p-wave strength function S 1 were estimated with a maximum likelihood method. The results are: average neutron width=3.4(+0.8 or -0.6)meV; S 1 = 2.0 (+0.5 or -0.4).10 -4

A multi-objective approach to the assignment of stock keeping units to unidirectional picking lines

Directory of Open Access Journals (Sweden)

Le Roux, G. J.

2017-05-01

Full Text Available An order picking system in a distribution centre consisting of parallel unidirectional picking lines is considered. The objectives are to minimise the walking distance of the pickers, the largest volume of stock on a picking line over all picking lines, the number of small packages, and the total penalty incurred for late distributions. The problem is formulated as a multi-objective multiple knapsack problem that is not solvable in a realistic time. Population-based algorithms, including the artificial bee colony algorithm and the genetic algorithm, are also implemented. The results obtained from all algorithms indicate a substantial improvement on all objectives relative to historical assignments. The genetic algorithm delivers the best performance.

Using HL7 in hospital staff assignments.

Science.gov (United States)

Unluturk, Mehmet S

2014-02-01

Hospital staff assignments are the instructions that allocate the hospital staff members to the hospital beds. Currently, hospital administrators make the assignments without accessing the information regarding the occupancy of the hospital beds and the acuity of the patient. As a result, administrators cannot distinguish between occupied and unoccupied beds, and may therefore assign staff to unoccupied beds. This gives rise to uneven and inefficient staff assignments. In this paper, the hospital admission-discharge-transfer (ADT) system is employed both as a data source and an assignment device to create staff assignments. When the patient data is newly added or modified, the ADT system updates the assignment software client with the relevant data. Based on the relevant data, the assignment software client is able to construct staff assignments in a more efficient way. © 2013 Elsevier Ltd. All rights reserved.

Synthetical analysis of the spin assignment for the superdeformed bands in A≅190 region

International Nuclear Information System (INIS)

Di Yaomin

2002-01-01

The spin assignment for the superdeformed bands of even-even nuclei in A ≅190 region is given by means of using the method of synthetical analysis. The I( I + 1) expression is used to fit the experimental data of the transition γ energies. In contrast to other procedure, the convergence process of the series expansions is put stress upon, whereas taking how many terms exactly in the expression does not emphasized. Moreover as well as the method of fitting the physical quantity, by use of these series expansions the moment of inertia of band heads is also calculated and then the systematics is used for the spin assignments. In practice, when the experimental data is abundant the systematics of the moment of inertia of band heads is more efficient than the method of fitting the physical quantity in the spin assignment. As for a few bands which spin assignment is difficult, the deviation from the typical rotational bands must be considered, which may be judged easily from the second class of moment of inertia of the bands. Finally the results of the spin assignment and the comparison with other literature are presented. These results should be more reliable

Improvement in PWR automatic optimization reloading methods using genetic algorithm

International Nuclear Information System (INIS)

Levine, S.H.; Ivanov, K.; Feltus, M.

1996-01-01

The objective of using automatic optimized reloading methods is to provide the Nuclear Engineer with an efficient method for reloading a nuclear reactor which results in superior core configurations that minimize fuel costs. Previous methods developed by Levine et al required a large effort to develop the initial core loading using a priority loading scheme. Subsequent modifications to this core configuration were made using expert rules to produce the final core design. Improvements in this technique have been made by using a genetic algorithm to produce improved core reload designs for PWRs more efficiently (authors)

Improvement in PWR automatic optimization reloading methods using genetic algorithm

Energy Technology Data Exchange (ETDEWEB)

Levine, S H; Ivanov, K; Feltus, M [Pennsylvania State Univ., University Park, PA (United States)

1996-12-01

The objective of using automatic optimized reloading methods is to provide the Nuclear Engineer with an efficient method for reloading a nuclear reactor which results in superior core configurations that minimize fuel costs. Previous methods developed by Levine et al required a large effort to develop the initial core loading using a priority loading scheme. Subsequent modifications to this core configuration were made using expert rules to produce the final core design. Improvements in this technique have been made by using a genetic algorithm to produce improved core reload designs for PWRs more efficiently (authors).

Mining Staff Assignment Rules from Event-Based Data

NARCIS (Netherlands)

Ly, Linh Thao; Rinderle, Stefanie; Dadam, Peter; Reichert, Manfred; Bussler, Christoph J.; Haller, Armin

2006-01-01

Process mining offers methods and techniques for capturing process behaviour from log data of past process executions. Although many promising approaches on mining the control flow have been published, no attempt has been made to mine the staff assignment situation of business processes. In this

A Stone Resource Assignment Model under the Fuzzy Environment

Directory of Open Access Journals (Sweden)

Liming Yao

2012-01-01

to tackle a stone resource assignment problem with the aim of decreasing dust and waste water emissions. On the upper level, the local government wants to assign a reasonable exploitation amount to each stone plant so as to minimize total emissions and maximize employment and economic profit. On the lower level, stone plants must reasonably assign stone resources to produce different stone products under the exploitation constraint. To deal with inherent uncertainties, the object functions and constraints are defuzzified using a possibility measure. A fuzzy simulation-based improved simulated annealing algorithm (FS-ISA is designed to search for the Pareto optimal solutions. Finally, a case study is presented to demonstrate the practicality and efficiency of the model. Results and a comparison analysis are presented to highlight the performance of the optimization method, which proves to be very efficient compared with other algorithms.

Application of Neutrosophic Set Theory in Generalized Assignment Problem

Directory of Open Access Journals (Sweden)

Supriya Kar

2015-09-01

Full Text Available This paper presents the application of Neutrosophic Set Theory (NST in solving Generalized Assignment Problem (GAP. GAP has been solved earlier under fuzzy environment. NST is a generalization of the concept of classical set, fuzzy set, interval-valued fuzzy set, intuitionistic fuzzy set. Elements of Neutrosophic set are characterized by a truth-membership function, falsity and also indeterminacy which is a more realistic way of expressing the parameters in real life problem. Here the elements of the cost matrix for the GAP are considered as neutrosophic elements which have not been considered earlier by any other author. The problem has been solved by evaluating score function matrix and then solving it by Extremum Difference Method (EDM [1] to get the optimal assignment. The method has been demonstrated by a suitable numerical example.

Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures.

Science.gov (United States)

Bastiaansen, John W M; Coster, Albart; Calus, Mario P L; van Arendonk, Johan A M; Bovenhuis, Henk

2012-01-24

Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects. Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations. Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure. The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was

Assigning Main Orientation to an EOH Descriptor on Multispectral Images.

Science.gov (United States)

Li, Yong; Shi, Xiang; Wei, Lijun; Zou, Junwei; Chen, Fang

2015-07-01

This paper proposes an approach to compute an EOH (edge-oriented histogram) descriptor with main orientation. EOH has a better matching ability than SIFT (scale-invariant feature transform) on multispectral images, but does not assign a main orientation to keypoints. Alternatively, it tends to assign the same main orientation to every keypoint, e.g., zero degrees. This limits EOH to matching keypoints between images of translation misalignment only. Observing this limitation, we propose assigning to keypoints the main orientation that is computed with PIIFD (partial intensity invariant feature descriptor). In the proposed method, SIFT keypoints are detected from images as the extrema of difference of Gaussians, and every keypoint is assigned to the main orientation computed with PIIFD. Then, EOH is computed for every keypoint with respect to its main orientation. In addition, an implementation variant is proposed for fast computation of the EOH descriptor. Experimental results show that the proposed approach performs more robustly than the original EOH on image pairs that have a rotation misalignment.

A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.

Science.gov (United States)

Lu, George J; Son, Woo Sung; Opella, Stanley J

2011-04-01

A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly ¹⁵N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly ¹⁵N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

Revealing barriers and facilitators to use a new genetic test: comparison of three user involvement methods.

Science.gov (United States)

Rhebergen, Martijn D F; Visser, Maaike J; Verberk, Maarten M; Lenderink, Annet F; van Dijk, Frank J H; Kezic, Sanja; Hulshof, Carel T J

2012-10-01

We compared three common user involvement methods in revealing barriers and facilitators from intended users that might influence their use of a new genetic test. The study was part of the development of a new genetic test on the susceptibility to hand eczema for nurses. Eighty student nurses participated in five focus groups (n = 33), 15 interviews (n = 15) or questionnaires (n = 32). For each method, data were collected until saturation. We compared the mean number of items and relevant remarks that could influence the use of the genetic test obtained per method, divided by the number of participants in that method. Thematic content analysis was performed using MAXQDA software. The focus groups revealed 30 unique items compared to 29 in the interviews and 21 in the questionnaires. The interviews produced more items and relevant remarks per participant (1.9 and 8.4 pp) than focus groups (0.9 and 4.8 pp) or questionnaires (0.7 and 2.3 pp). All three involvement methods revealed relevant barriers and facilitators to use a new genetic test. Focus groups and interviews revealed substantially more items than questionnaires. Furthermore, this study suggests a preference for the use of interviews because the number of items per participant was higher than for focus groups and questionnaires. This conclusion may be valid for other genetic tests as well.

Genetic Risk by Experience Interaction for Childhood Internalizing Problems: Converging Evidence across Multiple Methods

Science.gov (United States)

Vendlinski, Matthew K.; Lemery-Chalfant, Kathryn; Essex, Marilyn J.; Goldsmith, H. Hill

2011-01-01

Background: Identifying how genetic risk interacts with experience to predict psychopathology is an important step toward understanding the etiology of mental health problems. Few studies have examined genetic risk by experience interaction (GxE) in the development of childhood psychopathology. Methods: We used both co-twin and parent mental…

Colloquium paper: three ambitious (and rather unorthodox) assignments for the field of biodiversity genetics.

Science.gov (United States)

Avise, John C

2008-08-12

The field of molecular genetics has many roles in biodiversity assessment and conservation. I summarize three of those standard roles and propose logical extensions of each. First, many biologists suppose that a comprehensive picture of the Tree of Life will soon emerge from multilocus DNA sequence data interpreted in concert with fossils and other evidence. If nonreticulate trees are indeed valid metaphors for life's history, then a well dated global phylogeny will offer an opportunity to erect a universally standardized scheme of biological classification. If life's history proves to be somewhat reticulate, a web-like phylogenetic pattern should become evident and will offer opportunities to reevaluate the fundamental nature of evolutionary processes. Second, extensive networks of wildlife sanctuaries offer some hope for shepherding appreciable biodiversity through the ongoing extinction crisis, and molecular genetics can assist in park design by helping to identify key species, historically important biotic areas, and biodiversity hotspots. An opportunity centers on the concept of Pleistocene Parks that could protect "legacy biotas" in much the same way that traditional national parks preserve special geological features and historical landmarks honor legacy events in human affairs. Third, genetic perspectives have become an integral part of many focused conservation efforts by unveiling ecological, behavioral, or evolutionary phenomena relevant to population management. They also can open opportunities to educate the public about the many intellectual gifts and aesthetic marvels of the natural world.

Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

Science.gov (United States)

Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S.

2011-01-01

Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. ?? 2011 by the authors; licensee MDPI, Basel, Switzerland.

The use of different clustering methods in the evaluation of genetic diversity in upland cotton

Directory of Open Access Journals (Sweden)

Laíse Ferreira de Araújo

Full Text Available The continuous development and evaluation of new genotypes through crop breeding is essential in order to obtain new cultivars. The objective of this work was to evaluate the genetic divergences between cultivars of upland cotton (Gossypium hirsutum L. using the agronomic and technological characteristics of the fibre, in order to select superior parent plants. The experiment was set up during 2010 at the Federal University of Ceará in Fortaleza, Ceará, Brazil. Eleven cultivars of upland cotton were used in an experimental design of randomised blocks with three replications. In order to evaluate the genetic diversity among cultivars, the generalised Mahalanobis distance matrix was calculated, with cluster analysis then being applied, employing various methods: single linkage, Ward, complete linkage, median, average linkage within a cluster and average linkage between clusters. Genetic variability exists among the evaluated genotypes. The most consistant clustering method was that employing average linkage between clusters. Among the characteristics assessed, mean boll weight presented the highest contribution to genetic diversity, followed by elongation at rupture. Employing the method of mean linkage between clusters, the cultivars with greater genetic divergence were BRS Acacia and LD Frego; those of greater similarity were BRS Itaúba and BRS Araripe.

Stereospecific assignments of glycine in proteins by stereospecific deuteration and {sup 15}N labeling

Energy Technology Data Exchange (ETDEWEB)

Hansen, A.P.; Curley, R.W. Jr.; Panigot, M.J.; Fesik, S.W. [Ohio State Univ., Columbus, OH (United States)

1994-12-01

Stereospecific assignments are important for accurately determining the three-dimensional structures of proteins through the use of multidimensional NMR techniques. It is especially important to stereospecifically assign the glycine {alpha}-protons in proteins because of the potential for different backbone conformations of this residue. These stereospecific assignments are critical for interpreting the {sup 3}J{sub NH,{alpha}H} coupling constants and NOEs involving the glycine {alpha}-protons that determine the conformation of this part of the protein. However, it is often difficult to unambiguously obtain the stereospecific assignments for glycine residues by using only NOE data. In this poster, we present a method for unambiguous, stereospecific assignment of the {alpha}-protons of glycine residues. This method involves synthesis of stereo-specifically deuterated and {sup 15}N-labeled Gly using a slightly modified procedure originally described by Woodard and coworkers for the stereoselective deuteration of glycine. The stereospecifically deuterated and {sup 15}N-labeled Gy has been incorporated into recombinant proteins expressed in both bacterial systems (FKBP) and mammalian cells (u-PA). Two- and three-dimensional isotope-filtered and isotope-edited NMR experiments were used to obtain the stereospecific assignments of the glycine {alpha}-protons for these proteins.

Genetic methods for area-wide management of Lepidopterous pests with emphasis on F1 sterility

International Nuclear Information System (INIS)

Ocampo, V.R.

1996-01-01

Enormous losses in the production and marketing of food and fiber are caused by larvae of Lepidoptera. Currently, large quantities of insecticides are used to combat these pests. Insecticide resistance, increasing concern over pesticide pollution, and the desire to effectively manage lepidopteran pests on an area-wide basis have motivated scientists to identify and develop new pest management tactics that are compatible with current IPM. Genetic methods have emerged as a promising control strategy for lepidopteran pests. Genetic control as a practical means of pest management was first successfully implemented by Knipling and colleagues in the USA during the 1960's with the sterile insect technique (SIT) program for the screwworm fly. SIT is not a readily adapted for use against Lepidoptera as against Diptera. Radiation-induced inherited sterility (or F 1 sterility) is generally considered the most promising genetic methods for large-scale suppression of lepidopteran populations. This papers discusses four genetic control methods that have been developed and the progress that has been made in integrating sterility with other IPM tactics. (author)

Chemical Genetics — A Versatile Method to Combine Science and Higher Level Teaching in Molecular Genetics

Directory of Open Access Journals (Sweden)

Björn Sandrock

2012-10-01

Full Text Available Phosphorylation is a key event in many cellular processes like cell cycle, transformation of environmental signals to transcriptional activation or polar growth. The chemical genetics approach can be used to analyse the effect of highly specific inhibition in vivo and is a promising method to screen for kinase targets. We have used this approach to study the role of the germinal centre kinase Don3 during the cell division in the phytopathogenic fungus Ustilago maydis. Due to the easy determination of the don3 phenotype we have chosen this approach for a genetic course for M.Sc. students and for IMPRS (International Max-Planck research school students. According to the principle of “problem-based learning” the aim of this two-week course is to transfer knowledge about the broad spectrum of kinases to the students and that the students acquire the ability to design their own analog-sensitive kinase of interest. In addition to these training goals, we benefit from these annual courses the synthesis of basic constructs for genetic modification of several kinases in our model system U. maydis.

A systematic analysis of backbone amide assignments achieved via combinatorial selective labelling of amino acids

Energy Technology Data Exchange (ETDEWEB)

Jeremy Craven, C. [University of Sheffield, Department of Biotechnology and Molecular Biology (United Kingdom); Al-Owais, Moza; Parker, Martin J. [University of Leeds, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology (United Kingdom)], E-mail: m.j.parker@leeds.ac.uk

2007-06-15

With the advent of high-yield cell-free expressions systems, many researchers are exploiting selective isotope labelling of amino acids to increase the efficiency and accuracy of the NMR assignment process. We developed recently a combinatorial selective labelling (CSL) method capable of yielding large numbers of residue-type and sequence-specific backbone amide assignments, which involves comparing cross-peak intensities in {sup 1}H-{sup 15}N HSQC and 2D {sup 1}H-{sup 15}N HNCO spectra collected for five samples containing different combinations of {sup 13}C- and {sup 15}N-labelled amino acids [Parker MJ, Aulton-Jones M, Hounslow A, Craven C J (2004) J Am Chem Soc 126:5020-5021]. In this paper we develop a robust method for establishing the reliability of these assignments. We have performed a detailed statistical analysis of the CSL data collected for a model system (the B1 domain of protein G from Streptococcus), developing a scoring method which allows the confidence in assignments to be assessed, and which enables the effects of overlap on assignment fidelity to be predicted. To further test the scoring method and also to assess the performance of CSL in relation to sample quality, we have applied the method to the CSL data collected for GFP in our previous study.

A note on ranking assignments using reoptimization

DEFF Research Database (Denmark)

Pedersen, Christian Roed; Nielsen, L.R.; Andersen, K.A.

2005-01-01

We consider the problem of ranking assignments according to cost in the classical linear assignment problem. An algorithm partitioning the set of possible assignments, as suggested by Murty, is presented where, for each partition, the optimal assignment is calculated using a new reoptimization...

A simple method for combining genetic mapping data from multiple crosses and experimental designs.

Directory of Open Access Journals (Sweden)

Jeremy L Peirce

Full Text Available BACKGROUND: Over the past decade many linkage studies have defined chromosomal intervals containing polymorphisms that modulate a variety of traits. Many phenotypes are now associated with enough mapping data that meta-analysis could help refine locations of known QTLs and detect many novel QTLs. METHODOLOGY/PRINCIPAL FINDINGS: We describe a simple approach to combining QTL mapping results for multiple studies and demonstrate its utility using two hippocampus weight loci. Using data taken from two populations, a recombinant inbred strain set and an advanced intercross population we demonstrate considerable improvements in significance and resolution for both loci. 1-LOD support intervals were improved 51% for Hipp1a and 37% for Hipp9a. We first generate locus-wise permuted P-values for association with the phenotype from multiple maps, which can be done using a permutation method appropriate to each population. These results are then assigned to defined physical positions by interpolation between markers with known physical and genetic positions. We then use Fisher's combination test to combine position-by-position probabilities among experiments. Finally, we calculate genome-wide combined P-values by generating locus-specific P-values for each permuted map for each experiment. These permuted maps are then sampled with replacement and combined. The distribution of best locus-specific P-values for each combined map is the null distribution of genome-wide adjusted P-values. CONCLUSIONS/SIGNIFICANCE: Our approach is applicable to a wide variety of segregating and non-segregating mapping populations, facilitates rapid refinement of physical QTL position, is complementary to other QTL fine mapping methods, and provides an appropriate genome-wide criterion of significance for combined mapping results.

The use of genetic algorithms with niching methods in nuclear reactor related problems

International Nuclear Information System (INIS)

Sacco, Wagner Figueiredo

2000-03-01

Genetic Algorithms (GAs) are biologically motivated adaptive systems which have been used, with good results, in function optimization. However, traditional GAs rapidly push an artificial population toward convergence. That is, all individuals in the population soon become nearly identical. Niching Methods allow genetic algorithms to maintain a population of diverse individuals. GAs that incorporate these methods are capable of locating multiple, optimal solutions within a single population. The purpose of this study is to test existing niching techniques and two methods introduced herein, bearing in mind their eventual application in nuclear reactor related problems, specially the nuclear reactor core reload one, which has multiple solutions. Tests are performed using widely known test functions and their results show that the new methods are quite promising, specially in real world problems like the nuclear reactor core reload. (author)

Competitive Traffic Assignment in Road Networks

Directory of Open Access Journals (Sweden)

Krylatov Alexander Y.

2016-09-01

Full Text Available Recently in-vehicle route guidance and information systems are rapidly developing. Such systems are expected to reduce congestion in an urban traffic area. This social benefit is believed to be reached by imposing the route choices on the network users that lead to the system optimum traffic assignment. However, guidance service could be offered by different competitive business companies. Then route choices of different mutually independent groups of users may reject traffic assignment from the system optimum state. In this paper, a game theoretic approach is shown to be very efficient to formalize competitive traffic assignment problem with various groups of users in the form of non-cooperative network game with the Nash equilibrium search. The relationships between the Wardrop’s system optimum associated with the traffic assignment problem and the Nash equilibrium associated with the competitive traffic assignment problem are investigated. Moreover, some related aspects of the Nash equilibrium and the Wardrop’s user equilibrium assignments are also discussed.

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Energy Technology Data Exchange (ETDEWEB)

Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

2007-01-15

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

Science.gov (United States)

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

Real life working shift assignment problem

Science.gov (United States)

Sze, San-Nah; Kwek, Yeek-Ling; Tiong, Wei-King; Chiew, Kang-Leng

2017-07-01

This study concerns about the working shift assignment in an outlet of Supermarket X in Eastern Mall, Kuching. The working shift assignment needs to be solved at least once in every month. Current approval process of working shifts is too troublesome and time-consuming. Furthermore, the management staff cannot have an overview of manpower and working shift schedule. Thus, the aim of this study is to develop working shift assignment simulation and propose a working shift assignment solution. The main objective for this study is to fulfill manpower demand at minimum operation cost. Besides, the day off and meal break policy should be fulfilled accordingly. Demand based heuristic is proposed to assign working shift and the quality of the solution is evaluated by using the real data.

A compensation controller based on a regional pole-assignment method for AMD control systems with a time-varying delay

Science.gov (United States)

Li, Zuohua; Chen, Chaojun; Teng, Jun; Wang, Ying

2018-04-01

Active mass damper/driver (AMD) control system has been proposed as an effective tool for high-rise buildings to resist strong dynamic loads. However, such disadvantage as time-varying delay in AMD control systems impedes their application in practices. Time-varying delay, which has an effect on the performance and stability of single-degree-of-freedom (SDOF) and multi-degree-of-freedom (MDOF) systems, is considered in the paper. In addition, a new time-delay compensation controller based on regional pole-assignment method is presented. To verify its effectiveness, the proposed method is applied to a numerical example of a ten-storey frame and an experiment of a single span four-storey steel frame. Both numerical and experimental results demonstrate that the proposed method can enhance the performances of an AMD control system with time-varying delays.

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

Science.gov (United States)

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

24 CFR 221.770 - Assignment option.

Science.gov (United States)

2010-04-01

... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.770 Section... § 221.770 Assignment option. A mortgagee holding a conditional or firm commitment issued on or before... mortgagee's approved underwriter on or before November 30, 1983) has the option to assign, transfer and...

State Generation Method for Humanoid Motion Planning Based on Genetic Algorithm

Directory of Open Access Journals (Sweden)

Xuyang Wang

2012-05-01

Full Text Available A new approach to generate the original motion data for humanoid motion planning is presented in this paper. And a state generator is developed based on the genetic algorithm, which enables users to generate various motion states without using any reference motion data. By specifying various types of constraints such as configuration constraints and contact constraints, the state generator can generate stable states that satisfy the constraint conditions for humanoid robots. To deal with the multiple constraints and inverse kinematics, the state generation is finally simplified as a problem of optimizing and searching. In our method, we introduce a convenient mathematic representation for the constraints involved in the state generator, and solve the optimization problem with the genetic algorithm to acquire a desired state. To demonstrate the effectiveness and advantage of the method, a number of motion states are generated according to the requirements of the motion.

State Generation Method for Humanoid Motion Planning Based on Genetic Algorithm

Directory of Open Access Journals (Sweden)

Xuyang Wang

2008-11-01

Full Text Available A new approach to generate the original motion data for humanoid motion planning is presented in this paper. And a state generator is developed based on the genetic algorithm, which enables users to generate various motion states without using any reference motion data. By specifying various types of constraints such as configuration constraints and contact constraints, the state generator can generate stable states that satisfy the constraint conditions for humanoid robots.To deal with the multiple constraints and inverse kinematics, the state generation is finally simplified as a problem of optimizing and searching. In our method, we introduce a convenient mathematic representation for the constraints involved in the state generator, and solve the optimization problem with the genetic algorithm to acquire a desired state. To demonstrate the effectiveness and advantage of the method, a number of motion states are generated according to the requirements of the motion.

Job Assignments under Moral Hazard

DEFF Research Database (Denmark)

Koch, Alexander; Nafziger, Julia

Inefficient job assignments are usually explained with incomplete information about employees' abilities or contractual imperfections. We show that inefficient assignments arise even without uncertainty about the employee's ability and with complete contracts. Building on this result we provide...

EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

Energy Technology Data Exchange (ETDEWEB)

Zuiderweg, Erik R. P., E-mail: zuiderwe@umich.edu; Bagai, Ireena [The University of Michigan Medical School, Department of Biological Chemistry (United States); Rossi, Paolo [Rutgers University, Center for Integrative Proteomics Research (United States); Bertelsen, Eric B. [Arbor Communications, Inc. (United States)

2013-10-15

For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 Multiplication-Sign 10{sup 260} possible assignments. In 'EZ-ASSIGN', the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281-298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592-610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335-344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested.

24 CFR 221.255 - Assignment option.

Science.gov (United States)

2010-04-01

... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.255 Section... Assignment option. (a) A mortgagee holding a mortgage insured pursuant to a conditional or firm commitment issued on or before November 30, 1983 has the option to assign, transfer and deliver to the Commissioner...

Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

NARCIS (Netherlands)

Simko, I.; Eujayl, I.; Hintum, van T.J.L.

2012-01-01

Dominant and co-dominant molecular markers are routinely used in plant genetic research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected population. A

Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

Science.gov (United States)

Dominant and co-dominant molecular markers are routinely used in plant genetic diversity research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected pop...

PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts

Energy Technology Data Exchange (ETDEWEB)

Skinner, Simon P., E-mail: skinnersp@chem.leidenuniv.nl [Leiden University, Gorlaeus Laboratories, Leiden Institute of Chemistry (Netherlands); Moshev, Mois, E-mail: mois@monomon.me [Leiden University, Leiden Institute of Advanced Computer Science (Netherlands); Hass, Mathias A. S., E-mail: hassmas@chem.leidenuniv.nl; Ubbink, Marcellus, E-mail: m.ubbink@chem.leidenuniv.nl [Leiden University, Gorlaeus Laboratories, Leiden Institute of Chemistry (Netherlands)

2013-04-15

The use of paramagnetic NMR data for the refinement of structures of proteins and protein complexes is widespread. However, the power of paramagnetism for protein assignment has not yet been fully exploited. PARAssign is software that uses pseudocontact shift data derived from several paramagnetic centers attached to the protein to obtain amide and methyl assignments. The ability of PARAssign to perform assignment when the positions of the paramagnetic centers are known and unknown is demonstrated. PARAssign has been tested using synthetic data for methyl assignment of a 47 kDa protein, and using both synthetic and experimental data for amide assignment of a 14 kDa protein. The complex fitting space involved in such an assignment procedure necessitates that good starting conditions are found, both regarding placement and strength of paramagnetic centers. These starting conditions are obtained through automated tensor placement and user-defined tensor parameters. The results presented herein demonstrate that PARAssign is able to successfully perform resonance assignment in large systems with a high degree of reliability. This software provides a method for obtaining the assignments of large systems, which may previously have been unassignable, by using 2D NMR spectral data and a known protein structure.

An algorithm for ranking assignments using reoptimization

DEFF Research Database (Denmark)

Pedersen, Christian Roed; Nielsen, Lars Relund; Andersen, Kim Allan

2008-01-01

We consider the problem of ranking assignments according to cost in the classical linear assignment problem. An algorithm partitioning the set of possible assignments, as suggested by Murty, is presented where, for each partition, the optimal assignment is calculated using a new reoptimization...... technique. Computational results for the new algorithm are presented...

48 CFR 42.602 - Assignment and location.

Science.gov (United States)

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Assignment and location... Assignment and location. (a) A CACO may be assigned only when (1) the contractor has at least two locations..., or a full-time CACO may be assigned. In determining the location of the CACO, the responsible agency...

Genetic diversity measures of local European beef cattle breeds for conservation purposes

Directory of Open Access Journals (Sweden)

Pereira Albano

2001-05-01

Full Text Available Abstract This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean Fst = 0.07; P

Assignment methodology for larger RNA oligonucleotides: Application to an ATP-binding RNA aptamer

International Nuclear Information System (INIS)

Dieckmann, Thorsten; Feigon, Juli

1997-01-01

The use of uniform 13C, 15N labeling in the NMR spectroscopic study of RNA structures has greatly facilitated the assignment process in small RNA oligonucleotides. For ribose spinsystem assignments, exploitation of these labels has followed previously developed methods for the study of proteins. However, for sequential assignment of the exchangeable and nonexchangeable protons of the nucleotides, it has been necessary to develop a variety of new NMR experiments. Even these are of limited utility in the unambiguous assignment of larger RNAs due to the short carbon relaxation times and extensive spectral overlap for all nuclei.These problems can largely be overcome by the additional use of base-type selectively 13C, 15N-labeled RNA in combination with a judicious use of related RNAs with base substitutions. We report the application of this approach to a 36-nucleotide ATP-binding RNA aptamer in complex with AMP. Complete sequential 1H assignments, as well as the majority of 13C and 15N assignments, were obtained

Assigning Main Orientation to an EOH Descriptor on Multispectral Images

Directory of Open Access Journals (Sweden)

Yong Li

2015-07-01

Full Text Available This paper proposes an approach to compute an EOH (edge-oriented histogram descriptor with main orientation. EOH has a better matching ability than SIFT (scale-invariant feature transform on multispectral images, but does not assign a main orientation to keypoints. Alternatively, it tends to assign the same main orientation to every keypoint, e.g., zero degrees. This limits EOH to matching keypoints between images of translation misalignment only. Observing this limitation, we propose assigning to keypoints the main orientation that is computed with PIIFD (partial intensity invariant feature descriptor. In the proposed method, SIFT keypoints are detected from images as the extrema of difference of Gaussians, and every keypoint is assigned to the main orientation computed with PIIFD. Then, EOH is computed for every keypoint with respect to its main orientation. In addition, an implementation variant is proposed for fast computation of the EOH descriptor. Experimental results show that the proposed approach performs more robustly than the original EOH on image pairs that have a rotation misalignment.

The double pedigree: a method for studying culturally and genetically inherited behavior in tandem.

Directory of Open Access Journals (Sweden)

Etienne Danchin

Full Text Available Transgenerational sources of biological variation have been at the center of evolutionary studies ever since Darwin and Wallace identified natural selection. This is because evolution can only operate on traits whose variation is transmitted, i.e. traits that are heritable. The discovery of genetic inheritance has led to a semantic shift, resulting in the tendency to consider that only genes are inherited across generations. Today, however, concepts of heredity are being broadened again to integrate the accruing evidence of non-genetic inheritance, and many evolutionary biologists are calling for the inclusion of non-genetic inheritance into an inclusive evolutionary synthesis. Here, we focus on social heredity and its role in the inheritance of behavioral traits. We discuss quantitative genetics methods that might allow us to disentangle genetic and non-genetic transmission in natural populations with known pedigrees. We then propose an experimental design based on cross-fostering among animal cultures, environments and families that has the potential to partition inherited phenotypic variation into socially (i.e. culturally and genetically inherited components. This approach builds towards a new conceptual framework based on the use of an extended version of the animal model of quantitative genetics to integrate genetic and cultural components of behavioral inheritance.

A new method to estimate genetic gain in annual crops

Directory of Open Access Journals (Sweden)

Flávio Breseghello

1998-12-01

Full Text Available The genetic gain obtained by breeding programs to improve quantitative traits may be estimated by using data from regional trials. A new statistical method for this estimate is proposed and includes four steps: a joint analysis of regional trial data using a generalized linear model to obtain adjusted genotype means and covariance matrix of these means for the whole studied period; b calculation of the arithmetic mean of the adjusted genotype means, exclusively for the group of genotypes evaluated each year; c direct year comparison of the arithmetic means calculated, and d estimation of mean genetic gain by regression. Using the generalized least squares method, a weighted estimate of mean genetic gain during the period is calculated. This method permits a better cancellation of genotype x year and genotype x trial/year interactions, thus resulting in more precise estimates. This method can be applied to unbalanced data, allowing the estimation of genetic gain in series of multilocational trials.Os ganhos genéticos obtidos pelo melhoramento de caracteres quantitativos podem ser estimados utilizando resultados de ensaios regionais de avaliação de linhagens e cultivares. Um novo método estatístico para esta estimativa é proposto, o qual consiste em quatro passos: a análise conjunta da série de dados dos ensaios regionais através de um modelo linear generalizado de forma a obter as médias ajustadas dos genótipos e a matriz de covariâncias destas médias; b para o grupo de genótipos avaliados em cada ano, cálculo da média aritmética das médias ajustadas obtidas na análise conjunta; c comparação direta dos anos, conforme as médias aritméticas obtidas, e d estimativa de um ganho genético médio, por regressão. Aplicando-se o método de quadrados mínimos generalizado, é calculada uma estimativa ponderada do ganho genético médio no período. Este método permite um melhor cancelamento das interações genótipo x ano e gen

Study on the Method of Association Rules Mining Based on Genetic Algorithm and Application in Analysis of Seawater Samples

Directory of Open Access Journals (Sweden)

Qiuhong Sun

2014-04-01

Full Text Available Based on the data mining research, the data mining based on genetic algorithm method, the genetic algorithm is briefly introduced, while the genetic algorithm based on two important theories and theoretical templates principle implicit parallelism is also discussed. Focuses on the application of genetic algorithms for association rule mining method based on association rule mining, this paper proposes a genetic algorithm fitness function structure, data encoding, such as the title of the improvement program, in particular through the early issues study, proposed the improved adaptive Pc, Pm algorithm is applied to the genetic algorithm, thereby improving efficiency of the algorithm. Finally, a genetic algorithm based association rule mining algorithm, and be applied in sea water samples database in data mining and prove its effective.

EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

International Nuclear Information System (INIS)

Zuiderweg, Erik R. P.; Bagai, Ireena; Rossi, Paolo; Bertelsen, Eric B.

2013-01-01

For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 × 10 260 possible assignments. In “EZ-ASSIGN”, the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281–298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592–610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335–344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested

Waste-aware fluid volume assignment for flow-based microfluidic biochips

DEFF Research Database (Denmark)

Schneider, Alexander Rüdiger; Pop, Paul; Madsen, Jan

2017-01-01

complex Fluidic Units (FUs) such as switches, micropumps, mixers and separators can be constructed. When running a biochemical application on a FBMB, fluid volumes are dispensed from input reservoirs and used by the FUs. Given a biochemical application and a biochip, we are interested in determining...... the fluid volume assignment for each operation of the application, such that the FUs volume requirements are satisfied, while over- and underflow are avoided and the total volume of fluid used is minimized. We propose an algorithm for this fluid assignment problem. Compared to previous work, our method...

Rapid identification of Enterobacter hormaechei and Enterobacter cloacae genetic cluster III.

Science.gov (United States)

Ohad, S; Block, C; Kravitz, V; Farber, A; Pilo, S; Breuer, R; Rorman, E

2014-05-01

Enterobacter cloacae complex bacteria are of both clinical and environmental importance. Phenotypic methods are unable to distinguish between some of the species in this complex, which often renders their identification incomplete. The goal of this study was to develop molecular assays to identify Enterobacter hormaechei and Ent. cloacae genetic cluster III which are relatively frequently encountered in clinical material. The molecular assays developed in this study are qPCR technology based and served to identify both Ent. hormaechei and Ent. cloacae genetic cluster III. qPCR results were compared to hsp60 sequence analysis. Most clinical isolates were assigned to Ent. hormaechei subsp. steigerwaltii and Ent. cloacae genetic cluster III. The latter was proportionately more frequently isolated from bloodstream infections than from other material (P < 0·05). The qPCR assays detecting Ent. hormaechei and Ent. cloacae genetic cluster III demonstrated high sensitivity and specificity. The presented qPCR assays allow accurate and rapid identification of clinical isolates of the Ent. cloacae complex. The improved identifications obtained can specifically assist analysis of Ent. hormaechei and Ent. cloacae genetic cluster III in nosocomial outbreaks and can promote rapid environmental monitoring. An association was observed between Ent. cloacae cluster III and systemic infection that deserves further attention. © 2014 The Society for Applied Microbiology.

Evaluation of Dynamic Channel and Power Assignment for Cognitive Networks

Energy Technology Data Exchange (ETDEWEB)

Syed A. Ahmad; Umesh Shukla; Ryan E. Irwin; Luiz A. DaSilva; Allen B. MacKenzie

2011-03-01

In this paper, we develop a unifying optimization formulation to describe the Dynamic Channel and Power Assignment (DCPA) problem and evaluation method for comparing DCPA algorithms. DCPA refers to the allocation of transmit power and frequency channels to links in a cognitive network so as to maximize the total number of feasible links while minimizing the aggregate transmit power. We apply our evaluation method to five algorithms representative of DCPA used in literature. This comparison illustrates the tradeoffs between control modes (centralized versus distributed) and channel/power assignment techniques. We estimate the complexity of each algorithm. Through simulations, we evaluate the effectiveness of the algorithms in achieving feasible link allocations in the network, as well as their power efficiency. Our results indicate that, when few channels are available, the effectiveness of all algorithms is comparable and thus the one with smallest complexity should be selected. The Least Interfering Channel and Iterative Power Assignment (LICIPA) algorithm does not require cross-link gain information, has the overall lowest run time, and highest feasibility ratio of all the distributed algorithms; however, this comes at a cost of higher average power per link.

Method for the production of l-serine using genetically engineered microorganisms deficient in serine degradation pathways

DEFF Research Database (Denmark)

2016-01-01

The present invention generally relates to the microbiological industry, and specifically to the production of L-serine using genetically modified bacteria. The present invention provides genetically modified microorganisms, such as bacteria, wherein the expression of genes encoding for enzymes...... concentrations of serine. The present invention also provides methods for the production of L-serine or L-serine derivative using such genetically modified microorganisms....

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Assignment of human sprouty 4 gene to chromosome segment 5q32∼33 and analysis of its pattern of expression ... State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China; United Gene Holdings, Ltd., Shanghai 200092, People's Republic of ...

Exogenous spatial attention influences figure-ground assignment.

Science.gov (United States)

Vecera, Shaun P; Flevaris, Anastasia V; Filapek, Joseph C

2004-01-01

In a hierarchical stage account of vision, figure-ground assignment is thought to be completed before the operation of focal spatial attention. Results of previous studies have supported this account by showing that unpredictive, exogenous spatial precues do not influence figure-ground assignment, although voluntary attention can influence figure-ground assignment. However, in these studies, attention was not summoned directly to a region in a figure-ground display. In three experiments, we addressed the relationship between figure-ground assignment and visuospatial attention. In Experiment 1, we replicated the finding that exogenous precues do not influence figure-ground assignment when they direct attention outside of a figure-ground stimulus. In Experiment 2, we demonstrated that exogenous attention can influence figure-ground assignment if it is directed to one of the regions in a figure-ground stimulus. In Experiment 3, we demonstrated that exogenous attention can influence figure-ground assignment in displays that contain a Gestalt figure-ground cue; this result suggests that figure-ground processes are not entirely completed prior to the operation of focal spatial attention. Exogenous spatial attention acts as a cue for figure-ground assignment and can affect the outcome of figure-ground processes.

Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations.

Science.gov (United States)

Martin, Michael D; Jay, Flora; Castellano, Sergi; Slatkin, Montgomery

2017-08-01

We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available. © 2017 John Wiley & Sons Ltd.

Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping

Directory of Open Access Journals (Sweden)

Trognitz Friederike

2007-02-01

Full Text Available Abstract Background The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels of genetic variation within the S. caripense genome it proved impossible to generate a dense genetic map and to assign individual Solanum chromosomes through the use of conventional chromosome-specific SSR, RFLP, AFLP, as well as gene- or locus-specific markers. The ease of detection of DNA polymorphisms depends on both frequency and form of sequence variation. The narrow genetic background of close relatives and inbreds complicates the detection of persisting, reduced polymorphism and is a challenge to the development of reliable molecular markers. Nonetheless, monomorphic DNA fragments representing not directly usable conventional markers can contain considerable variation at the level of single nucleotide polymorphisms (SNPs. This can be used for the design of allele-specific molecular markers. The reproducible detection of allele-specific markers based on SNPs has been a technical challenge. Results We present a fast and cost-effective protocol for the detection of allele-specific SNPs by applying Sequence Polymorphism-Derived (SPD markers. These markers proved highly efficient for fingerprinting of individuals possessing a homogeneous genetic background. SPD markers are obtained from within non-informative, conventional molecular marker fragments that are screened for SNPs to design allele-specific PCR primers. The method makes use of primers containing a single, 3'-terminal Locked Nucleic Acid (LNA base. We demonstrate the applicability of the technique by successful genetic mapping of allele-specific SNP markers derived from monomorphic Conserved Ortholog Set II (COSII markers mapped to Solanum chromosomes, in S. caripense. By using SPD markers it was possible for the first time to map the S. caripense alleles

Creating IRT-Based Parallel Test Forms Using the Genetic Algorithm Method

Science.gov (United States)

Sun, Koun-Tem; Chen, Yu-Jen; Tsai, Shu-Yen; Cheng, Chien-Fen

2008-01-01

In educational measurement, the construction of parallel test forms is often a combinatorial optimization problem that involves the time-consuming selection of items to construct tests having approximately the same test information functions (TIFs) and constraints. This article proposes a novel method, genetic algorithm (GA), to construct parallel…

Forecasting nonlinear chaotic time series with function expression method based on an improved genetic-simulated annealing algorithm.

Science.gov (United States)

Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

2015-01-01

The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior.

Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

KAUST Repository

Jang, Richard; Gao, Xin; Li, Ming

2011-01-01

In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg's contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

KAUST Repository

Jang, Richard

2011-03-01

In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg\\'s contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

KAUST Repository

Abbas, Ahmed; Guo, Xianrong; Jing, Bingyi; Gao, Xin

2014-01-01

positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas

The various aspects of genetic and epigenetic toxicology: testing methods and clinical applications.

Science.gov (United States)

Ren, Ning; Atyah, Manar; Chen, Wan-Yong; Zhou, Chen-Hao

2017-05-22

Genotoxicity refers to the ability of harmful substances to damage genetic information in cells. Being exposed to chemical and biological agents can result in genomic instabilities and/or epigenetic alterations, which translate into a variety of diseases, cancer included. This concise review discusses, from both a genetic and epigenetic point of view, the current detection methods of different agents' genotoxicity, along with their basic and clinical relation to human cancer, chemotherapy, germ cells and stem cells.

Synchronization and Arrest of the Budding Yeast Cell Cycle Using Chemical and Genetic Methods.

Science.gov (United States)

Rosebrock, Adam P

2017-01-03

The cell cycle of budding yeast can be arrested at specific positions by different genetic and chemical methods. These arrests enable study of cell cycle phase-specific phenotypes that would be missed during examination of asynchronous cultures. Some methods for arrest are reversible, with kinetics that enable release of cells back into a synchronous cycling state. Benefits of chemical and genetic methods include scalability across a large range of culture sizes from a few milliliters to many liters, ease of execution, the absence of specific equipment requirements, and synchronization and release of the entire culture. Of note, cell growth and division are decoupled during arrest and block-release experiments. Cells will continue transcription, translation, and accumulation of protein while arrested. If allowed to reenter the cell cycle, cells will do so as a population of mixed, larger-than-normal cells. Despite this important caveat, many aspects of budding yeast physiology are accessible using these simple chemical and genetic tools. Described here are methods for the block and release of cells in G 1 phase and at the M/G 1 transition using α-factor mating pheromone and the temperature-sensitive cdc15-2 allele, respectively, in addition to methods for arresting the cell cycle in early S phase and at G 2 /M by using hydroxyurea and nocodazole, respectively. © 2017 Cold Spring Harbor Laboratory Press.

Genetic improvement of olive (Olea europaea L.) by conventional and in vitro biotechnology methods.

Science.gov (United States)

Rugini, E; Cristofori, V; Silvestri, C

2016-01-01

In olive (Olea europaea L.) traditional methods of genetic improvement have up to now produced limited results. Intensification of olive growing requires appropriate new cultivars for fully mechanized groves, but among the large number of the traditional varieties very few are suitable. High-density and super high-density hedge row orchards require genotypes with reduced size, reduced apical dominance, a semi-erect growth habit, easy to propagate, resistant to abiotic and biotic stresses, with reliably high productivity and quality of both fruits and oil. Innovative strategies supported by molecular and biotechnological techniques are required to speed up novel hybridisation methods. Among traditional approaches the Gene Pool Method seems a reasonable option, but it requires availability of widely diverse germplasm from both cultivated and wild genotypes, supported by a detailed knowledge of their genetic relationships. The practice of "gene therapy" for the most important existing cultivars, combined with conventional methods, could accelerate achievement of the main goals, but efforts to overcome some technical and ideological obstacles are needed. The present review describes the benefits that olive and its products may obtain from genetic improvement using state of the art of conventional and unconventional methods, and includes progress made in the field of in vitro techniques. The uses of both traditional and modern technologies are discussed with recommendations. Copyright © 2016 Elsevier Inc. All rights reserved.

WebAssign: Assessing Your Students' Understanding Continuously

Science.gov (United States)

Risley, John S.

1999-11-01

Motivating students to learn is a constant challenge for faculty. Technology can play a significant role. One such solution is WebAssign — a web-based homework system that offers new teaching and learning opportunities for educators and their students. WebAssign delivers, collects, grades, and records customized homework assignments over the Internet. Students get immediate feedback with credit and instructors can implement "Just-in-Time" teaching. In this talk, I will describe how assignments can be generated with different numerical values for each question, giving each student a unique problem to solve. This feature encourages independent thinking with the benefit of collaborative learning. Example assignments taken from textbook questions and intellectually engaging Java applet simulations will be shown. Studies and first-hand experience on the educational impact of using WebAssign will also be discussed.

Relabeling exchange method (REM) for learning in neural networks

Science.gov (United States)

Wu, Wen; Mammone, Richard J.

1994-02-01

The supervised training of neural networks require the use of output labels which are usually arbitrarily assigned. In this paper it is shown that there is a significant difference in the rms error of learning when `optimal' label assignment schemes are used. We have investigated two efficient random search algorithms to solve the relabeling problem: the simulated annealing and the genetic algorithm. However, we found them to be computationally expensive. Therefore we shall introduce a new heuristic algorithm called the Relabeling Exchange Method (REM) which is computationally more attractive and produces optimal performance. REM has been used to organize the optimal structure for multi-layered perceptrons and neural tree networks. The method is a general one and can be implemented as a modification to standard training algorithms. The motivation of the new relabeling strategy is based on the present interpretation of dyslexia as an encoding problem.

Optimizing and accelerating the assignation of lineages in Mycobacterium tuberculosis using novel alternative single-tube assays.

Directory of Open Access Journals (Sweden)

María Carcelén

Full Text Available The assignation of lineages in Mycobacterium tuberculosis (MTB provides valuable information for evolutionary and phylogeographic studies and makes for more accurate knowledge of the distribution of this pathogen worldwide. Differences in virulence have also been found for certain lineages. MTB isolates were initially assigned to lineages based on data obtained from genotyping techniques, such as spoligotyping or MIRU-VNTR analysis, some of which are more suitable for molecular epidemiology studies. However, since these methods are subject to a certain degree of homoplasy, other criteria have been chosen to assign lineages. These are based on targeting robust and specific SNPs for each lineage. Here, we propose two newly designed multiplex targeting methods-both of which are single-tube tests-to optimize the assignation of the six main lineages in MTB. The first method is based on ASO-PCR and offers an inexpensive and easy-to-implement assay for laboratories with limited resources. The other, which is based on SNaPshot, enables more refined standardized assignation of lineages for laboratories with better resources. Both methods performed well when assigning lineages from cultured isolates from a control panel, a test panel, and a problem panel from an unrelated population, Mexico, which included isolates in which standard genotyping was not able to classify lineages. Both tests were also able to assign lineages from stored isolates, without the need for subculture or purification of DNA, and even directly from clinical specimens with a medium-high bacilli burden. Our assays could broaden the contexts where information on lineages can be acquired, thus enabling us to quickly update data from retrospective collections and to merge data with those obtained at the time of diagnosis of a new TB case.

Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.

Science.gov (United States)

Mondol, Samrat; Sridhar, Vanjulavalli; Yadav, Prasanjeet; Gubbi, Sanjay; Ramakrishnan, Uma

2015-04-01

Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond. © 2014 Society for Conservation Biology.

Assignment about providing of substitute haptic interface for visually disabled persons

OpenAIRE

浅川, 貴史

2013-01-01

[Abstract] This paper is described about an assignment of haptic interface. We have made a proposal for a music baton system for visually disabled persons. The system is constituted by an acceleration sensor, a radio module, and a haptic interface device. We have carried out an experiment of comparing the visual and the haptic interface. The assignments are declared by the results that are rise-time of a motor and pre-motion. In the paper, we make a proposal for new method of the voltage cont...

Genetic algorithm for the optimization of the loading pattern for reactor core fuel management

International Nuclear Information System (INIS)

Zhou Sheng; Hu Yongming; zheng Wenxiang

2000-01-01

The paper discusses the application of a genetic algorithm to the optimization of the loading pattern for in-core fuel management with the NP characteristics. The algorithm develops a matrix model for the fuel assembly loading pattern. The burnable poisons matrix was assigned randomly considering the distributed nature of the poisons. A method based on the traveling salesman problem was used to solve the problem. A integrated code for in-core fuel management was formed by combining this code with a reactor physics code

The Kinetics of Chirality Assignment in Catalytic Single Walled Carbon Nanotube Growth

OpenAIRE

Xu, Ziwei; Yan, Tianying; Ding, Feng

2014-01-01

Chirality-selected single-walled carbon nanotubes (SWCNTs) ensure a great potential of building ~1 nm sized electronics. However, the reliable method for chirality-selected SWCNT is still pending. Here we present a theoretical study on the SWCNT's chirality assignment and control during the catalytic growth. This study reveals that the chirality of a SWCNT is determined by the kinetic incorporation of the pentagon formation during SWCNT nucleation. Therefore, chirality is randomly assigned on...

A method of genetically engineering acidophilic, heterotrophic, bacteria by electroporation and conjugation

Energy Technology Data Exchange (ETDEWEB)

Roberto, F.F.; Glenn, A.W.; Ward, T.E.

1990-08-07

A method of genetically manipulating an acidophilic bacteria is provided by two different procedures. Using electroporation, chimeric and broad-host range plasmids are introduced into Acidiphilium. Conjugation is also employed to introduce broad-host range plasmids into Acidiphilium at neutral pH.

Solving the rectangular assignment problem and applications

NARCIS (Netherlands)

Bijsterbosch, J.; Volgenant, A.

2010-01-01

The rectangular assignment problem is a generalization of the linear assignment problem (LAP): one wants to assign a number of persons to a smaller number of jobs, minimizing the total corresponding costs. Applications are, e.g., in the fields of object recognition and scheduling. Further, we show

7 CFR 900.106 - Assignment of mediator.

Science.gov (United States)

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Assignment of mediator. 900.106 Section 900.106 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing... Assignment of mediator. The Director of the Division shall assign a mediator, from the group designated by...

DNA barcoding for species assignment: the case of Mediterranean marine fishes.

Directory of Open Access Journals (Sweden)

Monica Landi

Full Text Available DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity.A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1 a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2 the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS and 72% (GenBank of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%, most of them of high commercial relevance, suggesting possible cryptic species.We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several

Multi-objective genetic algorithm based innovative wind farm layout optimization method

International Nuclear Information System (INIS)

Chen, Ying; Li, Hua; He, Bang; Wang, Pengcheng; Jin, Kai

2015-01-01

Highlights: • Innovative optimization procedures for both regular and irregular shape wind farm. • Using real wind condition and commercial wind turbine parameters. • Using multiple-objective genetic algorithm optimization method. • Optimize the selection of different wind turbine types and their hub heights. - Abstract: Layout optimization has become one of the critical approaches to increase power output and decrease total cost of a wind farm. Previous researches have applied intelligent algorithms to optimizing the wind farm layout. However, those wind conditions used in most of previous research are simplified and not accurate enough to match the real world wind conditions. In this paper, the authors propose an innovative optimization method based on multi-objective genetic algorithm, and test it with real wind condition and commercial wind turbine parameters. Four case studies are conducted to investigate the number of wind turbines needed in the given wind farm. Different cost models are also considered in the case studies. The results clearly demonstrate that the new method is able to optimize the layout of a given wind farm with real commercial data and wind conditions in both regular and irregular shapes, and achieve a better result by selecting different type and hub height wind turbines.

My Favorite Assignment.

Science.gov (United States)

ABCA Bulletin, 1983

1983-01-01

Describes three assignments for enticing business communication students to undertake library research: an analysis of a Fortune 500 company, a career choice report, and a report on an organization that offers potential employment. (AEA)

Genetic characterisation of farmed rainbow trout in Norway: intra- and inter-strain variation reveals potential for identification of escapees

Directory of Open Access Journals (Sweden)

Glover Kevin A

2008-12-01

Full Text Available Abstract Background The rainbow trout (Oncorhynchus mykiss is one of the most important aquaculture species in the world, and Norway is one of the largest producers. The present study was initiated in response to a request from the Norwegian police authority to identify the farm of origin for 35 escaped rainbow trout captured in a fjord. Eleven samples, each consisting of approximately 47 fish, were collected from the three farms operating in the fjord where the escapees were captured. In order to gain a better general understanding of the genetic structure of rainbow trout strains used in Norwegian aquaculture, seven samples (47 fish per sample were collected from six farms located outside the region where the escapees were captured. All samples, including the escapees, were genotyped with 12 microsatellite loci. Results All samples displayed considerable genetic variability at all loci (mean number of alleles per locus per sample ranged from 5.4–8.6. Variable degrees of genetic differentiation were observed among the samples, with pair-wise FST values ranging from 0–0.127. Self-assignment tests conducted among the samples collected from farms outside the fjord where the escapees were observed gave an overall correct assignment of 82.5%, demonstrating potential for genetic identification of escapees. In the "real life" assignment of the 35 captured escapees, all were excluded from two of the samples included as controls in the analysis, and 26 were excluded from the third control sample. In contrast, only 1 of the escapees was excluded from the 11 pooled samples collected on the 3 farms operating in the fjord. Conclusion Considerable genetic variation exists within and among rainbow trout strains farmed in Norway. Together with modern statistical methods, this will provide commercial operators with a tool to monitor breeding and fish movements, and management authorities with the ability to identify the source of escapees. The data

Generation of Compliant Mechanisms using Hybrid Genetic Algorithm

Science.gov (United States)

Sharma, D.; Deb, K.

2014-10-01

Compliant mechanism is a single piece elastic structure which can deform to perform the assigned task. In this work, compliant mechanisms are evolved using a constraint based bi-objective optimization formulation which requires one user defined parameter ( η). This user defined parameter limits a gap between a desired path and an actual path traced by the compliant mechanism. The non-linear and discrete optimization problems are solved using the hybrid Genetic Algorithm (GA) wherein domain specific initialization, two-dimensional crossover operator and repairing techniques are adopted. A bit-wise local search method is used with elitist non-dominated sorting genetic algorithm to further refine the compliant mechanisms. Parallel computations are performed on the master-slave architecture to reduce the computation time. A parametric study is carried out for η value which suggests a range to evolve topologically different compliant mechanisms. The applied and boundary conditions to the compliant mechanisms are considered the variables that are evolved by the hybrid GA. The post-analysis of results unveils that the complaint mechanisms are always supported at unique location that can evolve the non-dominated solutions.

Gene Flow Results in High Genetic Similarity Between Sibiraea (Rosaceae species in the Qinghai-Tibetan Plateau

Directory of Open Access Journals (Sweden)

Peng-Cheng Fu

2016-10-01

Full Text Available Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of S. laevigata and S. angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45% rather than between species (4.39%. We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of these 2 species resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures between the species occurred.

Assessment of Random Assignment in Training and Test Sets using Generalized Cluster Analysis Technique

Directory of Open Access Journals (Sweden)

Sorana D. BOLBOACĂ

2011-06-01

Full Text Available Aim: The properness of random assignment of compounds in training and validation sets was assessed using the generalized cluster technique. Material and Method: A quantitative Structure-Activity Relationship model using Molecular Descriptors Family on Vertices was evaluated in terms of assignment of carboquinone derivatives in training and test sets during the leave-many-out analysis. Assignment of compounds was investigated using five variables: observed anticancer activity and four structure descriptors. Generalized cluster analysis with K-means algorithm was applied in order to investigate if the assignment of compounds was or not proper. The Euclidian distance and maximization of the initial distance using a cross-validation with a v-fold of 10 was applied. Results: All five variables included in analysis proved to have statistically significant contribution in identification of clusters. Three clusters were identified, each of them containing both carboquinone derivatives belonging to training as well as to test sets. The observed activity of carboquinone derivatives proved to be normal distributed on every. The presence of training and test sets in all clusters identified using generalized cluster analysis with K-means algorithm and the distribution of observed activity within clusters sustain a proper assignment of compounds in training and test set. Conclusion: Generalized cluster analysis using the K-means algorithm proved to be a valid method in assessment of random assignment of carboquinone derivatives in training and test sets.

Task Assignment and Path Planning for Multiple Autonomous Underwater Vehicles Using 3D Dubins Curves †.

Science.gov (United States)

Cai, Wenyu; Zhang, Meiyan; Zheng, Yahong Rosa

2017-07-11

This paper investigates the task assignment and path planning problem for multiple AUVs in three dimensional (3D) underwater wireless sensor networks where nonholonomic motion constraints of underwater AUVs in 3D space are considered. The multi-target task assignment and path planning problem is modeled by the Multiple Traveling Sales Person (MTSP) problem and the Genetic Algorithm (GA) is used to solve the MTSP problem with Euclidean distance as the cost function and the Tour Hop Balance (THB) or Tour Length Balance (TLB) constraints as the stop criterion. The resulting tour sequences are mapped to 2D Dubins curves in the X - Y plane, and then interpolated linearly to obtain the Z coordinates. We demonstrate that the linear interpolation fails to achieve G 1 continuity in the 3D Dubins path for multiple targets. Therefore, the interpolated 3D Dubins curves are checked against the AUV dynamics constraint and the ones satisfying the constraint are accepted to finalize the 3D Dubins curve selection. Simulation results demonstrate that the integration of the 3D Dubins curve with the MTSP model is successful and effective for solving the 3D target assignment and path planning problem.

Oral infection of Aedes aegypti with yellow fever virus: geographic variation and genetic considerations.

Science.gov (United States)

Tabachnick, W J; Wallis, G P; Aitken, T H; Miller, B R; Amato, G D; Lorenz, L; Powell, J R; Beaty, B J

1985-11-01

Twenty-eight populations representing a worldwide distribution of Aedes aegypti were tested for their ability to become orally infected with yellow fever virus (YFV). Populations had been analyzed for genetic variations at 11 isozyme loci and assigned to one of 8 genetic geographic groups of Ae. aegypti. Infection rates suggest that populations showing isozyme genetic relatedness also demonstrate similarity to oral infection rates with YFV. The findings support the hypothesis that genetic variation exists for oral susceptibility to YFV in Ae. aegypti.

Gene variation and genetic differentiation among populations of the solitary mud dauber wasp Trypoxylon (Trypargilum albitarse Fabricius 1804 (Hymenoptera, Crabronidae

Directory of Open Access Journals (Sweden)

Antonio C.B. Bergamaschi

2015-01-01

Full Text Available Abstract Trypoxylon is a genus of solitary crabronid wasps whose population genetics is poorly known. The purpose of the present study was to investigate the genetic variation and differentiation among five populations of Trypoxylon albitarse, a species widely distributed throughout the Neotropics, with records from Panama to northern Argentina. Eight species-specific microsatellite loci were used for genotyping 96 adult wasps (one female per nest sampled at five sites in Brazil. The analysis of allelic richness and private alleles indicated high genetic diversity in the populations sampled. Pairwise comparisons using the Fst and Dest indices revealed significant differentiation for all, but one pair of populations. Fst, Dest, AMOVA and assignment test values pointed to inter-population differentiation. Additionally, the analysis of population structure using Bayesian and PCA methods characterized two alternative genetic groups. The Mantel test indicated no correlation between genetic and geographic distances. Despite evidence of considerable dispersal capacity for T. albitarse, the data indicate low to moderate population structuring in this species.

Exact route-length formulas and a storage location assignment heuristic for picker-to-parts warehouses

NARCIS (Netherlands)

Dijkstra, Arjan; Roodbergen, Kees Jan

2017-01-01

Order picking is one of the most time-critical processes in warehouses. We focus on the combined effects of routing methods and storage location assignment on process performance. We present exact formulas for the average route length under any storage location assignment for four common routing

Alteration of Box-Jenkins methodology by implementing genetic algorithm method

Science.gov (United States)

Ismail, Zuhaimy; Maarof, Mohd Zulariffin Md; Fadzli, Mohammad

2015-02-01

A time series is a set of values sequentially observed through time. The Box-Jenkins methodology is a systematic method of identifying, fitting, checking and using integrated autoregressive moving average time series model for forecasting. Box-Jenkins method is an appropriate for a medium to a long length (at least 50) time series data observation. When modeling a medium to a long length (at least 50), the difficulty arose in choosing the accurate order of model identification level and to discover the right parameter estimation. This presents the development of Genetic Algorithm heuristic method in solving the identification and estimation models problems in Box-Jenkins. Data on International Tourist arrivals to Malaysia were used to illustrate the effectiveness of this proposed method. The forecast results that generated from this proposed model outperformed single traditional Box-Jenkins model.

Evoked Feelings, Assigned Meanings and Constructed Knowledge Based on Mistakes

Directory of Open Access Journals (Sweden)

Luciane Guimarães Batistella Bianchini

2017-09-01

Full Text Available By means of Piaget's critical clinical method, the study investigated the meanings assigned to mistakes by four students in different activities and interactive situations. The research also analyzed the results of using self-regulatory situations in understanding mistakes initially committed by the students. Data collection instruments consisted of games, video recordings, diaries and interviews. Following intervention, the students were able to recognize their competence, establish positive interactions within the group, and avoid viewing mistakes as obstacles to learning. We concluded that the meanings assigned to mistakes depend on certain variables, among them feelings nurtured by the individuals about themselves, the other, and the object of knowledge.

CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

International Nuclear Information System (INIS)

Wang Jianyong; Wang Tianzhi; Zuiderweg, Erik R. P.; Crippen, Gordon M.

2005-01-01

Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations

Managing voluntary turnover through challenging assignments

NARCIS (Netherlands)

Preenen, P.T.Y.; de Pater, I.E.; van Vianen, A.E.M.; Keijzer, L.

2011-01-01

This study examines employees’ challenging assignments as manageable means to reduce turnover intentions, job search behaviors, and voluntary turnover. Results indicate that challenging assignments are negatively related to turnover intentions and job search behaviors and that these relationships

Managing voluntary turnover through challenging assignments

NARCIS (Netherlands)

Preenen, P.T.Y.; Pater, I.E. de; Vianen, A.E.M. van; Keijzer, L.

2011-01-01

This study examines employees' challenging assignments as manageable means to reduce turnover intentions, job search behaviors, and voluntary turnover. Results indicate that challenging assignments are negatively related to turnover intentions and job search behaviors and that these relationships

Methods for genetic transformation in Dendrobium.

Science.gov (United States)

da Silva, Jaime A Teixeira; Dobránszki, Judit; Cardoso, Jean Carlos; Chandler, Stephen F; Zeng, Songjun

2016-03-01

The genetic transformation of Dendrobium orchids will allow for the introduction of novel colours, altered architecture and valuable traits such as abiotic and biotic stress tolerance. The orchid genus Dendrobium contains species that have both ornamental value and medicinal importance. There is thus interest in producing cultivars that have increased resistance to pests, novel horticultural characteristics such as novel flower colours, improved productivity, longer flower spikes, or longer post-harvest shelf-life. Tissue culture is used to establish clonal plants while in vitro flowering allows for the production of flowers or floral parts within a sterile environment, expanding the selection of explants that can be used for tissue culture or genetic transformation. The latter is potentially the most effective, rapid and practical way to introduce new agronomic traits into Dendrobium. Most (69.4 %) Dendrobium genetic transformation studies have used particle bombardment (biolistics) while 64 % have employed some form of Agrobacterium-mediated transformation. A singe study has explored ovary injection, but no studies exist on floral dip transformation. While most of these studies have involved the use of selector or reporter genes, there are now a handful of studies that have introduced genes for horticulturally important traits.

Determinism and mass-media portrayals of genetics.

Science.gov (United States)

Condit, C M; Ofulue, N; Sheedy, K M

1998-01-01

Scholars have expressed concern that the introduction of substantial coverage of "medical genetics" in the mass media during the past 2 decades represents an increase in biological determinism in public discourse. To test this contention, we analyzed the contents of a randomly selected, structured sample of American public newspapers (n=250) and magazines (n=722) published during 1919-95. Three coders, using three measures, all with intercoder reliability >85%, were employed. Results indicate that the introduction of the discourse of medical genetics is correlated with both a statistically significant decrease in the degree to which articles attribute human characteristics to genetic causes (P<.001) and a statistically significant increase in the differentiation of attributions to genetic and other causes among various conditions or outcomes (P<. 016). There has been no statistically significant change in the relative proportions of physical phenomena attributed to genetic causes, but there has been a statistically significant decrease in the number of articles assigning genetic causes to mental (P<.002) and behavioral (P<.000) characteristics. These results suggest that the current discourse of medical genetics is not accurately described as more biologically deterministic than its antecedents. PMID:9529342

An optimization method of relativistic backward wave oscillator using particle simulation and genetic algorithms

Energy Technology Data Exchange (ETDEWEB)

Chen, Zaigao; Wang, Jianguo [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi' an, Shaanxi 710049 (China); Northwest Institute of Nuclear Technology, P.O. Box 69-12, Xi' an, Shaanxi 710024 (China); Wang, Yue; Qiao, Hailiang; Zhang, Dianhui [Northwest Institute of Nuclear Technology, P.O. Box 69-12, Xi' an, Shaanxi 710024 (China); Guo, Weijie [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi' an, Shaanxi 710049 (China)

2013-11-15

Optimal design method of high-power microwave source using particle simulation and parallel genetic algorithms is presented in this paper. The output power, simulated by the fully electromagnetic particle simulation code UNIPIC, of the high-power microwave device is given as the fitness function, and the float-encoding genetic algorithms are used to optimize the high-power microwave devices. Using this method, we encode the heights of non-uniform slow wave structure in the relativistic backward wave oscillators (RBWO), and optimize the parameters on massively parallel processors. Simulation results demonstrate that we can obtain the optimal parameters of non-uniform slow wave structure in the RBWO, and the output microwave power enhances 52.6% after the device is optimized.

A search for symmetries in the genetic code

International Nuclear Information System (INIS)

Hornos, J.E.M.; Hornos, Y.M.M.

1991-01-01

A search for symmetries based on the classification theorem of Cartan for the compact simple Lie algebras is performed to verify to what extent the genetic code is a manifestation of some underlying symmetry. An exact continuous symmetry group cannot be found to reproduce the present, universal code. However a unique approximate symmetry group is compatible with codon assignment for the fundamental amino acids and the termination codon. In order to obtain the actual genetic code, the symmetry must be slightly broken. (author). 27 refs, 3 figs, 6 tabs

A novel method to design S-box based on chaotic map and genetic algorithm

International Nuclear Information System (INIS)

Wang, Yong; Wong, Kwok-Wo; Li, Changbing; Li, Yang

2012-01-01

The substitution box (S-box) is an important component in block encryption algorithms. In this Letter, the problem of constructing S-box is transformed to a Traveling Salesman Problem and a method for designing S-box based on chaos and genetic algorithm is proposed. Since the proposed method makes full use of the traits of chaotic map and evolution process, stronger S-box is obtained. The results of performance test show that the presented S-box has good cryptographic properties, which justify that the proposed algorithm is effective in generating strong S-boxes. -- Highlights: ► The problem of constructing S-box is transformed to a Traveling Salesman Problem. ► We present a new method for designing S-box based on chaos and genetic algorithm. ► The proposed algorithm is effective in generating strong S-boxes.

A novel method to design S-box based on chaotic map and genetic algorithm

Energy Technology Data Exchange (ETDEWEB)

Wang, Yong, E-mail: wangyong_cqupt@163.com [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China); Key Laboratory of Electronic Commerce and Logistics, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Wong, Kwok-Wo [Department of Electronic Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong (Hong Kong); Li, Changbing [Key Laboratory of Electronic Commerce and Logistics, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Li, Yang [Department of Automatic Control and Systems Engineering, The University of Sheffield, Mapping Street, S1 3DJ (United Kingdom)

2012-01-30

The substitution box (S-box) is an important component in block encryption algorithms. In this Letter, the problem of constructing S-box is transformed to a Traveling Salesman Problem and a method for designing S-box based on chaos and genetic algorithm is proposed. Since the proposed method makes full use of the traits of chaotic map and evolution process, stronger S-box is obtained. The results of performance test show that the presented S-box has good cryptographic properties, which justify that the proposed algorithm is effective in generating strong S-boxes. -- Highlights: ► The problem of constructing S-box is transformed to a Traveling Salesman Problem. ► We present a new method for designing S-box based on chaos and genetic algorithm. ► The proposed algorithm is effective in generating strong S-boxes.

Recent advances in ratio primary reference measurement procedures (definitive methods) and their use in certification of reference materials and controlling assigned values in proficiency testing

International Nuclear Information System (INIS)

Dybczynski, R.S.; Polkowska-Motrenko, H.; Chajduk, E.; Danko, B.; Pyszynska, M.

2014-01-01

Three very accurate (definitive) methods by RNAA for the determination of Se, As and Fe respectively, which were recently elaborated in our laboratory, are reviewed and their use in certification of reference materials and in checking the assigned values in proficiency tests is demonstrated on several examples. According to VIM 3 nomenclature these methods may be called: ratio primary reference measurement procedures (RPRMPs). RPRMPs with their expanded uncertainties of 2.7-3.6 % are comparable to ID-MS methods and are the only methods of such high metrological quality which can be used for the determination of trace amounts of monoisotopic elements. (author)

Scaffolding students’ assignments

DEFF Research Database (Denmark)

Slot, Marie Falkesgaard

2013-01-01

This article discusses scaffolding in typical student assignments in mother tongue learning materials in upper secondary education in Denmark and the United Kingdom. It has been determined that assignments do not have sufficient scaffolding end features to help pupils understand concepts and build...... objects. The article presents the results of empirical research on tasks given in Danish and British learning materials. This work is based on a further development of my PhD thesis: “Learning materials in the subject of Danish” (Slot 2010). The main focus is how cognitive models (and subsidiary explicit...... learning goals) can help students structure their argumentative and communica-tive learning processes, and how various multimodal representations can give more open-ended learning possibilities for collaboration. The article presents a short introduction of the skills for 21st century learning and defines...

Gamification for Non-Majors Mathematics: An Innovative Assignment Model

Science.gov (United States)

Leong, Siow Hoo; Tang, Howe Eng

2017-01-01

The most important ingredient of the pedagogy for teaching non-majors is getting their engagement. This paper proposes to use gamification to engage non-majors. An innovative game termed as Cover the Hungarian's Zeros is designed to tackle the common weakness of non-majors mathematics in solving the assignment problem using the Hungarian Method.…

Mars - robust automatic backbone assignment of proteins

International Nuclear Information System (INIS)

Jung, Young-Sang; Zweckstetter, Markus

2004-01-01

MARS a program for robust automatic backbone assignment of 13 C/ 15 N labeled proteins is presented. MARS does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds and it can work with a wide variety of NMR experiments. Using only 13 C α / 13 C β connectivity information, MARS allows automatic, error-free assignment of 96% of the 370-residue maltose-binding protein. MARS can successfully be used when data are missing for a substantial portion of residues or for proteins with very high chemical shift degeneracy such as partially or fully unfolded proteins. Other sources of information, such as residue specific information or known assignments from a homologues protein, can be included into the assignment process. MARS exports its result in SPARKY format. This allows visual validation and integration of automated and manual assignment

Genetic algorithms

Science.gov (United States)

Wang, Lui; Bayer, Steven E.

1991-01-01

Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

Assignment of element and isotope factors

International Nuclear Information System (INIS)

Schneider, R.A.

1984-01-01

Element and isotope factors are assigned in the NICS internal accounting system at the Exxon Fuel Fabrication Facility on the basis of coded information included on the material transfer documents. This paper explains more fully the manner in which NICS assigns these factors

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods.

Science.gov (United States)

Austerlitz, Frederic; David, Olivier; Schaeffer, Brigitte; Bleakley, Kevin; Olteanu, Madalina; Leblois, Raphael; Veuille, Michel; Laredo, Catherine

2009-11-10

DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to deal with within-species genetic variability and potential transpecific polymorphism. In this context, we examine several assignation methods belonging to two main categories: (i) phylogenetic methods (neighbour-joining and PhyML) that attempt to account for the genealogical framework of DNA evolution and (ii) supervised classification methods (k-nearest neighbour, CART, random forest and kernel methods). These methods range from basic to elaborate. We investigated the ability of each method to correctly classify query sequences drawn from samples of related species using both simulated and real data. Simulated data sets were generated using coalescent simulations in which we varied the genealogical history, mutation parameter, sample size and number of species. No method was found to be the best in all cases. The simplest method of all, "one nearest neighbour", was found to be the most reliable with respect to changes in the parameters of the data sets. The parameter most influencing the performance of the various methods was molecular diversity of the data. Addition of genetically independent loci--nuclear genes--improved the predictive performance of most methods. The study implies that taxonomists can influence the quality of their analyses either by choosing a method best-adapted to the configuration of their sample, or, given a certain method, increasing the sample size or altering the amount of molecular diversity. This can be achieved either by sequencing more mtDNA or by sequencing additional nuclear genes. In the latter case, they may also have to modify their data analysis method.

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

Directory of Open Access Journals (Sweden)

Leblois Raphael

2009-11-01

Full Text Available Abstract Background DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to deal with within-species genetic variability and potential transpecific polymorphism. In this context, we examine several assignation methods belonging to two main categories: (i phylogenetic methods (neighbour-joining and PhyML that attempt to account for the genealogical framework of DNA evolution and (ii supervised classification methods (k-nearest neighbour, CART, random forest and kernel methods. These methods range from basic to elaborate. We investigated the ability of each method to correctly classify query sequences drawn from samples of related species using both simulated and real data. Simulated data sets were generated using coalescent simulations in which we varied the genealogical history, mutation parameter, sample size and number of species. Results No method was found to be the best in all cases. The simplest method of all, "one nearest neighbour", was found to be the most reliable with respect to changes in the parameters of the data sets. The parameter most influencing the performance of the various methods was molecular diversity of the data. Addition of genetically independent loci - nuclear genes - improved the predictive performance of most methods. Conclusion The study implies that taxonomists can influence the quality of their analyses either by choosing a method best-adapted to the configuration of their sample, or, given a certain method, increasing the sample size or altering the amount of molecular diversity. This can be achieved either by sequencing more mtDNA or by sequencing additional nuclear genes. In the latter case, they may also have to modify their data analysis method.

Inferential backbone assignment for sparse data

International Nuclear Information System (INIS)

Vitek, Olga; Bailey-Kellogg, Chris; Craig, Bruce; Vitek, Jan

2006-01-01

This paper develops an approach to protein backbone NMR assignment that effectively assigns large proteins while using limited sets of triple-resonance experiments. Our approach handles proteins with large fractions of missing data and many ambiguous pairs of pseudoresidues, and provides a statistical assessment of confidence in global and position-specific assignments. The approach is tested on an extensive set of experimental and synthetic data of up to 723 residues, with match tolerances of up to 0.5 ppm for C α and C β resonance types. The tests show that the approach is particularly helpful when data contain experimental noise and require large match tolerances. The keys to the approach are an empirical Bayesian probability model that rigorously accounts for uncertainty in the data at all stages in the analysis, and a hybrid stochastic tree-based search algorithm that effectively explores the large space of possible assignments

Temporal changes in genetic variation of boll weevil (Coleoptera: Curculionidae) populations, and implications for population assignment in eradication zones

Science.gov (United States)

Genetic differentiation among 10 populations of boll weevil, Anthonomus grandis grandis, sampled in 2009, in Texas and Mexico, was determined using ten microsatellite loci. In addition, temporal changes in genetic composition were examined in the eight populations for which samples were available fr...

Analyzing the multiple-target-multiple-agent scenario using optimal assignment algorithms

Science.gov (United States)

Kwok, Kwan S.; Driessen, Brian J.; Phillips, Cynthia A.; Tovey, Craig A.

1997-09-01

This work considers the problem of maximum utilization of a set of mobile robots with limited sensor-range capabilities and limited travel distances. The robots are initially in random positions. A set of robots properly guards or covers a region if every point within the region is within the effective sensor range of at least one vehicle. We wish to move the vehicles into surveillance positions so as to guard or cover a region, while minimizing the maximum distance traveled by any vehicle. This problem can be formulated as an assignment problem, in which we must optimally decide which robot to assign to which slot of a desired matrix of grid points. The cost function is the maximum distance traveled by any robot. Assignment problems can be solved very efficiently. Solution times for one hundred robots took only seconds on a silicon graphics crimson workstation. The initial positions of all the robots can be sampled by a central base station and their newly assigned positions communicated back to the robots. Alternatively, the robots can establish their own coordinate system with the origin fixed at one of the robots and orientation determined by the compass bearing of another robot relative to this robot. This paper presents example solutions to the multiple-target-multiple-agent scenario using a matching algorithm. Two separate cases with one hundred agents in each were analyzed using this method. We have found these mobile robot problems to be a very interesting application of network optimization methods, and we expect this to be a fruitful area for future research.

Analyzing the multiple-target-multiple-agent scenario using optimal assignment algorithms

International Nuclear Information System (INIS)

Kwok, K.S.; Driessen, B.J.; Phillips, C.A.; Tovey, C.A.

1997-01-01

This work considers the problem of maximum utilization of a set of mobile robots with limited sensor-range capabilities and limited travel distances. The robots are initially in random positions. A set of robots properly guards or covers a region if every point within the region is within the effective sensor range of at least one vehicle. The authors wish to move the vehicles into surveillance positions so as to guard or cover a region, while minimizing the maximum distance traveled by any vehicle. This problem can be formulated as an assignment problem, in which they must optimally decide which robot to assign to which slot of a desired matrix of grid points. The cost function is the maximum distance traveled by any robot. Assignment problems can be solved very efficiently. Solutions times for one hundred robots took only seconds on a Silicon Graphics Crimson workstation. The initial positions of all the robots can be sampled by a central base station and their newly assigned positions communicated back to the robots. Alternatively, the robots can establish their own coordinate system with the origin fixed at one of the robots and orientation determined by the compass bearing of another robot relative to this robot. This paper presents example solutions to the multiple-target-multiple-agent scenario using a matching algorithm. Two separate cases with one hundred agents in each were analyzed using this method. They have found these mobile robot problems to be a very interesting application of network optimization methods, and they expect this to be a fruitful area for future research

Reporting the national antimicrobial consumption in Danish pigs: influence of assigned daily dosage values and population measurement

DEFF Research Database (Denmark)

Dupont, Nana Hee; Fertner, Mette Ely; Kristensen, Charlotte Sonne

2016-01-01

Transparent calculation methods are crucial when investigating trends in antimicrobial consumption over time and between populations. Until 2011, one single standardized method was applied when quantifying the Danish pig antimicrobial consumption with the unit "Animal Daily Dose" (ADD). However...... assignment methods, Denmark has also experienced a shift in the production pattern, towards a larger export of live pigs. The aims of this paper were to (1) describe previous and current ADD assignment methods used by the major Danish institutions and (2) to illustrate how ADD assignment method and choice...... DANMAP and DVFA were only identical for 48 % of antimicrobial products approved for use in pigs. From 2007 to 2013, the total number of ADDs per year increased by 9 % when using the new DVFA ADD-values, but decreased by 2 and 7 % when using the new DANMAP ADD-values or the old VetStat ADD...

Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

Directory of Open Access Journals (Sweden)

Rangel-Figueiredo Teresa

2010-06-01

Full Text Available Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95. With breed information, 30 cows and three bulls were identified (q > 0.95 that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10 relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P st = 0.028, P > 0.05. Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50 to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that

Genetic Stratification in Myeloid Diseases: From Risk Assessment to Clinical Decision Support Tool

Directory of Open Access Journals (Sweden)

Yishai Ofran

2014-10-01

Full Text Available Genetic aberrations have become a dominant factor in the stratification of myeloid malignancies. Cytogenetic and a few mutation studies are the backbone of risk assessment models of myeloid malignancies which are a major consideration in clinical decisions, especially patient assignment for allogeneic stem cell transplantation. Progress in our understanding of the genetic basis of the pathogenesis of myeloid malignancies and the growing capabilities of mass sequencing may add new roles for the clinical usage of genetic data. A few recently identified mutations recognized to be associated with specific diseases or clinical scenarios may soon become part of the diagnostic criteria of such conditions. Mutational studies may also advance our capabilities for a more efficient patient selection process, assigning the most effective therapy at the best timing for each patient. The clinical utility of genetic data is anticipated to advance further with the adoption of deep sequencing and next-generation sequencing techniques. We herein suggest some future potential applications of sequential genetic data to identify pending deteriorations at time points which are the best for aggressive interventions such as allogeneic stem cell transplantation. Genetics is moving from being mostly a prognostic factor to becoming a multitasking decision support tool for hematologists. Physicians must pay attention to advances in molecular hematology as it will soon be accessible and influential for most of our patients.

Modelling the Preferences of Students for Alternative Assignment Designs Using the Discrete Choice Experiment Methodology

Directory of Open Access Journals (Sweden)

Brendan Kennelly

2014-11-01

Full Text Available This paper outlines how a discrete choice experiment (DCE can be used to learn more about how students are willing to trade off various features of assignments such as the nature and timing of feedback and the method used to submit assignments. A DCE identifies plausible levels of the key attributes of a good or service and then presents the respondent with alternative bundles of these attributes and their levels and asks the respondent to choose between particular bundles. We report results from a DCE we conducted with undergraduate business students regarding their preferences for assignment systems. We find that the most important features of assignments are how relevant the assignments are for exam preparation and the nature of the feedback that students receive. We also find that students generally prefer online to paper assignments. We argue that the DCE approach has a lot of potential in education research.

Analysis of conditional genetic effects and variance components in developmental genetics.

Science.gov (United States)

Zhu, J

1995-12-01

A genetic model with additive-dominance effects and genotype x environment interactions is presented for quantitative traits with time-dependent measures. The genetic model for phenotypic means at time t conditional on phenotypic means measured at previous time (t-1) is defined. Statistical methods are proposed for analyzing conditional genetic effects and conditional genetic variance components. Conditional variances can be estimated by minimum norm quadratic unbiased estimation (MINQUE) method. An adjusted unbiased prediction (AUP) procedure is suggested for predicting conditional genetic effects. A worked example from cotton fruiting data is given for comparison of unconditional and conditional genetic variances and additive effects.

Using Optimal Combination of Teaching-Learning Methods (Open Book Assignment and Group Tutorials) as Revision Exercises to Improve Learning Outcome in Low Achievers in Biochemistry

Science.gov (United States)

Rajappa, Medha; Bobby, Zachariah; Nandeesha, H.; Suryapriya, R.; Ragul, Anithasri; Yuvaraj, B.; Revathy, G.; Priyadarssini, M.

2016-01-01

Graduate medical students of India are taught Biochemistry by didactic lectures and they hardly get any opportunity to clarify their doubts and reinforce the concepts which they learn in these lectures. We used a combination of teaching-learning (T-L) methods (open book assignment followed by group tutorials) to study their efficacy in improving…

Molecular Darwinism: the contingency of spontaneous genetic variation.

Science.gov (United States)

Arber, Werner

2011-01-01

The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.

Unified method to integrate and blend several, potentially related, sources of information for genetic evaluation.

Science.gov (United States)

Vandenplas, Jérémie; Colinet, Frederic G; Gengler, Nicolas

2014-09-30

A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For example, in dairy cattle, internal (i.e. local) populations lead to evaluations based only on internal records while widely used foreign sires have been selected using internally unavailable external records. In such cases, internal genetic evaluations may be less accurate and biased. Because external records are unavailable, methods were developed to combine external information that summarizes these records, i.e. external estimated breeding values and associated reliabilities, with internal records to improve accuracy of internal genetic evaluations. Two issues of these methods concern double-counting of contributions due to relationships and due to records. These issues could be worse if external information came from several evaluations, at least partially based on the same records, and combined into a single internal evaluation. Based on a Bayesian approach, the aim of this research was to develop a unified method to integrate and blend simultaneously several sources of information into an internal genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. This research resulted in equations that integrate and blend simultaneously several sources of information and avoid double-counting of contributions due to relationships and due to records. The performance of the developed equations was evaluated using simulated and real datasets. The results showed that the developed equations integrated and blended several sources of information well into a genetic evaluation. The developed equations also avoided double-counting of contributions due to relationships and due to records. Furthermore, because all available external sources of information were correctly propagated, relatives of external animals benefited from the integrated

Proposed method for assigning metric tons of heavy metal values to defense high-level waste forms to be disposed of in a geologic repository

International Nuclear Information System (INIS)

1987-08-01

A proposed method is described for assigning an equivalent metric ton heavy metal (eMTHM) value to defense high-level waste forms to be disposed of in a geologic repository. This method for establishing a curie equivalency between defense high-level waste and irradiated commercial fuel is based on the ratio of defense fuel exposure to the typical commercial fuel exposure, MWd/MTHM. application of this technique to defense high-level wastes is described. Additionally, this proposed technique is compared to several alternate calculations for eMTHM. 15 refs., 2 figs., 10 tabs

Safety assessment and detection methods of genetically modified organisms.

Science.gov (United States)

Xu, Rong; Zheng, Zhe; Jiao, Guanglian

2014-01-01

Genetically modified organisms (GMOs), are gaining importance in agriculture as well as the production of food and feed. Along with the development of GMOs, health and food safety concerns have been raised. These concerns for these new GMOs make it necessary to set up strict system on food safety assessment of GMOs. The food safety assessment of GMOs, current development status of safety and precise transgenic technologies and GMOs detection have been discussed in this review. The recent patents about GMOs and their detection methods are also reviewed. This review can provide elementary introduction on how to assess and detect GMOs.

Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis.

Science.gov (United States)

Cui, Licong; Xu, Rong; Luo, Zhihui; Wentz, Susan; Scarberry, Kyle; Zhang, Guo-Qiang

2014-08-03

Finding quality consumer health information online can effectively bring important public health benefits to the general population. It can empower people with timely and current knowledge for managing their health and promoting wellbeing. Despite a popular belief that search engines such as Google can solve all information access problems, recent studies show that using search engines and simple search terms is not sufficient. Our objective is to provide an approach to organizing consumer health information for navigational exploration, complementing keyword-based direct search. Multi-topic assignment to health information, such as online questions, is a fundamental step for navigational exploration. We introduce a new multi-topic assignment method combining semantic annotation using UMLS concepts (CUIs) and Formal Concept Analysis (FCA). Each question was tagged with CUIs identified by MetaMap. The CUIs were filtered with term-frequency and a new term-strength index to construct a CUI-question context. The CUI-question context and a topic-subject context were used for multi-topic assignment, resulting in a topic-question context. The topic-question context was then directly used for constructing a prototype navigational exploration interface. Experimental evaluation was performed on the task of automatic multi-topic assignment of 99 predefined topics for about 60,000 consumer health questions from NetWellness. Using example-based metrics, suitable for multi-topic assignment problems, our method achieved a precision of 0.849, recall of 0.774, and F₁ measure of 0.782, using a reference standard of 278 questions with manually assigned topics. Compared to NetWellness' original topic assignment, a 36.5% increase in recall is achieved with virtually no sacrifice in precision. Enhancing the recall of multi-topic assignment without sacrificing precision is a prerequisite for achieving the benefits of navigational exploration. Our new multi-topic assignment method

Genetic structure of three Croatian horse breeds: implications for their conservation strategy

Directory of Open Access Journals (Sweden)

Miljenko Konjačić

2010-01-01

Full Text Available The genetic variability for a sample of 107 animals from three autochthonous Croatian horse breeds was estimated using 20 microsatellites. The average number of alleles per locus (6.3 and proportion of heterozygosity (0.732 indicated a moderate variability. The expected heterozygosity was similar among all breeds and ranged between 0.724 in the Posavina horse, and 0.737 in the Croatian Coldblood and Murinsulaner horse. The inbreeding coefficient FIS was low and non-significant over the three populations. The genetic differentiation among the three populations was low (FST=0.026, suggesting that only 2.6% of the total genetic variability was due to differences between the breeds, and 97% to individual differences. The results of pairwise genetic differentiation suggest that the Posavina horse and the Croatian Coldblood were the most closely related populations (FST=0.016. These results are confirmed by Nei’s genetic distances with the highest value observed between the Posavina horse and the Murinsulaner (0.082 and the lowest between the Posavina horse and the Croatian Coldblood (0.044. An assignment test correctly assigned 82% of individuals to the correct breed. Strategies for preserving the original native genes in the Croatian native horse breeds should be considered in order to prevent these breeds from becoming extinct and include them in the future breeding programmes.

De novo protein structure generation from incomplete chemical shift assignments

Energy Technology Data Exchange (ETDEWEB)

Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-02-15

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

Genetic characterization of the Bardigiano horse using microsatellite markers

Directory of Open Access Journals (Sweden)

Claudio Lisa

2010-01-01

Full Text Available The study was aimed at investigating the genetic structure of the Bardigiano horse and its relationships with the Haflinger, Maremmano and Arabian breeds using 11 microsatellite markers. A total of 94 alleles were detected across the breeds, with a mean of 8.5 alleles per locus and a mean observed heterozygosity of 0.69. Compared to the other breeds, the Bardigiano horse showed quite a high genetic variability, as indicated by the mean number of alleles (7.0 vs 6.1÷7.6 and by the observed heterozygosity (0.72 vs 0.66÷0.71. Moreover, the genotype distributions in the Bardigiano groups of different sex and age were not significantly different. The overall FST value showed that the genetic differences among breeds accounted for 7.8% (P=0.001 of the total variation, and the pairwise FST values were all significant. The assignment test allocated between 96.8 and 98.9% of the individuals to the population they were collected from, with a mean probability of assignment of about 97% for all breeds, except for the Arabian, where it approached 100%. The results have highlighted that the Bardigiano breed has a high within and between breed variability, which is considerably more than could be expected by looking at its evolution history. This justifies the need for the development of additional breeding strategies to preserve the existing genetic variability.

32 CFR 884.2 - Assigned responsibilities.

Science.gov (United States)

2010-07-01

... OF PERSONNEL TO UNITED STATES CIVILIAN AUTHORITIES FOR TRIAL § 884.2 Assigned responsibilities. (a... 32 National Defense 6 2010-07-01 2010-07-01 false Assigned responsibilities. 884.2 Section 884.2... requests for return of members to the United States for delivery to civilian authorities when the request...

Multi-Path OD-Matrix Estimation (MPME) based on Stochastic User Equilibrium Traffic Assignment

DEFF Research Database (Denmark)

Nielsen, Otto Anker

1997-01-01

Most conventional methods for estimating trip matrices from traffic counts assume either that the counts are error-free, determin-istic variables or they use a simplified traffic assignment model. Without these assumptions, the methods often demand prohibitive calculation times. The paper present...

Statistical assignment of DNA sequences using Bayesian phylogenetics

DEFF Research Database (Denmark)

Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P.

2008-01-01

We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data...... that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re......-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA....

Personnel dose assignment practices

International Nuclear Information System (INIS)

Fix, J.J.

1993-04-01

Implementation of DOE N 5480.6 Radiological Control Manual Article 511(3) requirements, to minimize the assignment of personnel dosimeters, should be done only under a broader context ensuring that capabilities are in place to monitor and record personnel exposure both for compliance and for potential litigation. As noted in NCRP Report No. 114, personnel dosimetry programs are conducted to meet four major objectives: radiation safety program control and evaluation; regulatory compliance; epidemiological research; and litigation. A change to Article 511(3) is proposed that would require that minimizing the assignment of personnel dosimeters take place only following full evaluation of overall capabilities (e.g., access control, area dosimetry, etc.) to meet the NCRP objectives

Task Assignment and Path Planning for Multiple Autonomous Underwater Vehicles Using 3D Dubins Curves †

Directory of Open Access Journals (Sweden)

Wenyu Cai

2017-07-01

Full Text Available This paper investigates the task assignment and path planning problem for multiple AUVs in three dimensional (3D underwater wireless sensor networks where nonholonomic motion constraints of underwater AUVs in 3D space are considered. The multi-target task assignment and path planning problem is modeled by the Multiple Traveling Sales Person (MTSP problem and the Genetic Algorithm (GA is used to solve the MTSP problem with Euclidean distance as the cost function and the Tour Hop Balance (THB or Tour Length Balance (TLB constraints as the stop criterion. The resulting tour sequences are mapped to 2D Dubins curves in the X − Y plane, and then interpolated linearly to obtain the Z coordinates. We demonstrate that the linear interpolation fails to achieve G 1 continuity in the 3D Dubins path for multiple targets. Therefore, the interpolated 3D Dubins curves are checked against the AUV dynamics constraint and the ones satisfying the constraint are accepted to finalize the 3D Dubins curve selection. Simulation results demonstrate that the integration of the 3D Dubins curve with the MTSP model is successful and effective for solving the 3D target assignment and path planning problem.

A Competitive and Experiential Assignment in Search Engine Optimization Strategy

Science.gov (United States)

Clarke, Theresa B.; Clarke, Irvine, III

2014-01-01

Despite an increase in ad spending and demand for employees with expertise in search engine optimization (SEO), methods for teaching this important marketing strategy have received little coverage in the literature. Using Bloom's cognitive goals hierarchy as a framework, this experiential assignment provides a process for educators who may be new…

Common genetic variants associated with cognitive performance identified using the proxy-phenotype method

NARCIS (Netherlands)

C.A. Rietveld (Niels); T. Esko (Tõnu); G. Davies (Gail); T.H. Pers (Tune); P. Turley (Patrick); B. Benyamin (Beben); C.F. Chabris (Christopher F.); V. Emilsson (Valur); A.D. Johnson (Andrew); J.J. Lee (James J.); C. de Leeuw (Christiaan); R.E. Marioni (Riccardo); S.E. Medland (Sarah Elizabeth); M. Miller (Mike); O. Rostapshova (Olga); S.J. van der Lee (Sven); A.A.E. Vinkhuyzen (Anna A.); N. Amin (Najaf); D. Conley (Dalton); J. Derringer; C.M. van Duijn (Cornelia); R.S.N. Fehrmann (Rudolf); L. Franke (Lude); E.L. Glaeser (Edward L.); N.K. Hansell (Narelle); C. Hayward (Caroline); W.G. Iacono (William); C.A. Ibrahim-Verbaas (Carla); V.W.V. Jaddoe (Vincent); J. Karjalainen (Juha); D. Laibson (David); P. Lichtenstein (Paul); D.C. Liewald (David C.); P.K. Magnusson (Patrik); N.G. Martin (Nicholas); M. McGue (Matt); G. Mcmahon (George); N.L. Pedersen (Nancy); S. Pinker (Steven); D.J. Porteous (David J.); D. Posthuma (Danielle); F. Rivadeneira Ramirez (Fernando); B.H. Smithk (Blair H.); J.M. Starr (John); H.W. Tiemeier (Henning); N.J. Timpsonm (Nicholas J.); M. Trzaskowskin (Maciej); A.G. Uitterlinden (André); F.C. Verhulst (Frank); M.E. Ward (Mary); M.J. Wright (Margaret); G.D. Smith; I.J. Deary (Ian J.); M. Johannesson (Magnus); R. Plomin (Robert); P.M. Visscher (Peter); D.J. Benjamin (Daniel J.); D. Cesarini (David); Ph.D. Koellinger (Philipp)

2014-01-01

textabstractWe identify common genetic variants associated with cognitive performance using a two-stage approach, which we call the proxyphenotype method. First, we conduct a genome-wide association study of educational attainment in a large sample (n = 106,736), which produces a set of 69

Writing Assignments that Promote Active Learning

Science.gov (United States)

Narayanan, M.

2014-12-01

Encourage students to write a detailed, analytical report correlating classroom discussions to an important historical event or a current event. Motivate students interview an expert from industry on a topic that was discussed in class. Ask the students to submit a report with supporting sketches, drawings, circuit diagrams and graphs. Propose that the students generate a complete a set of reading responses pertaining to an assigned topic. Require each student to bring in one comment or one question about an assigned reading. The assignment should be a recent publication in an appropriate journal. Have the students conduct a web search on an assigned topic. Ask them to generate a set of ideas that can relate to classroom discussions. Provide the students with a study guide. The study guide should provide about 10 or 15 short topics. Quiz the students on one or two of the topics. Encourage the students to design or develop some creative real-world examples based on a chapter discussed or a topic of interest. Require that students originate, develop, support and defend a viewpoint using a specifically assigned material. Make the students practice using or utilizing a set of new technical terms they have encountered in an assigned chapter. Have students develop original examples explaining the different terms. Ask the students to select one important terminology from the previous classroom discussions. Encourage the students to explain why they selected that particular word. Ask them to talk about the importance of the terminology from the point of view of their educational objectives and future career. Angelo, T. A. (1991). Ten easy pieces: Assessing higher learning in four dimensions. In T. A. Angelo (Ed.), Classroom research: Early lessons from success (pp. 17-31). New Directions for Teaching and Learning, No. 46. San Francisco: Jossey-Bass.

DNA degradation in genetically modified rice with Cry1Ab by food processing methods: implications for the quantification of genetically modified organisms.

Science.gov (United States)

Xing, Fuguo; Zhang, Wei; Selvaraj, Jonathan Nimal; Liu, Yang

2015-05-01

Food processing methods contribute to DNA degradation, thereby affecting genetically modified organism detection and quantification. This study evaluated the effect of food processing methods on the relative transgenic content of genetically modified rice with Cry1Ab. In steamed rice and rice noodles, the levels of Cry1Ab were ⩾ 100% and <83%, respectively. Frying and baking in rice crackers contributed to a reduction in Pubi and Cry1Ab, while microwaving caused a decrease in Pubi and an increase in Cry1Ab. The processing methods of sweet rice wine had the most severe degradation effects on Pubi and Cry1Ab. In steamed rice and rice noodles, Cry1Ab was the most stable, followed by SPS and Pubi. However, in rice crackers and sweet rice wine, SPS was the most stable, followed by Cry1Ab and Pubi. Therefore, Cry1Ab is a better representative of transgenic components than is Pubi because the levels of Cry1Ab were less affected compared to Pubi. Copyright © 2014 Elsevier Ltd. All rights reserved.

Peer Influence, Genetic Propensity, and Binge Drinking: A Natural Experiment and a Replication.

Science.gov (United States)

Guo, Guang; Li, Yi; Wang, Hongyu; Cai, Tianji; Duncan, Greg J

2015-11-01

The authors draw data from the College Roommate Study (ROOM) and the National Longitudinal Study of Adolescent Health to investigate gene-environment interaction effects on youth binge drinking. In ROOM, the environmental influence was measured by the precollege drinking behavior of randomly assigned roommates. Random assignment safeguards against friend selection and removes the threat of gene-environment correlation that makes gene-environment interaction effects difficult to interpret. On average, being randomly assigned a drinking peer as opposed to a nondrinking peer increased college binge drinking by 0.5-1.0 episodes per month, or 20%-40% the average amount of binge drinking. However, this peer influence was found only among youths with a medium level of genetic propensity for alcohol use; those with either a low or high genetic propensity were not influenced by peer drinking. A replication of the findings is provided in data drawn from Add Health. The study shows that gene-environment interaction analysis can uncover social-contextual effects likely to be missed by traditional sociological approaches.

[Current options of preimplantion genetic screening and preimplantation genetic diagnostics].

Science.gov (United States)

Šimečková, V

The aim of this work is to summarize the current knowledge about preimplantation genetic screening and diagnostics. A review article. Department of Gynecology and Obstetrics, District Hospital Šternberk, IVF Clinic, Olomouc. Preimplantation genetic testing is a complex of genetic and molecular cytogenetic examinations, which can help to detect abnormalities in embryos before transfer into the uterus of the mother. These specialized examinations are based on the latest findings in genetics and assisted reproduction. The preimplantation genetic testing is necessarily associated with a method of in vitro fertilization. It is performed on isolated blastomeres on the third day of embryo cultivation. Nowadays, it is preferred trophectoderm examination of cells from the five-day blastocysts. Generally speaking, after preimplantation genetic testing, we can select only embryos without genetic load to transfer into uterus. Preimplantation genetic testing is an important part of treatment of infertility. Complex diagnostics and treatment of infertile couples are increasingly influenced by the development and use of advanced genomic technologies. Further development and application of these modern methods require close cooperation between the field of assisted reproduction and clinical genetics.

Genetic Engineering and the Amelioration of Genetic Defect

Science.gov (United States)

Lederberg, Joshua

1970-01-01

Discusses the claims for a brave new world of genetic manipulation" and concludes that if we could agree upon applying genetic (or any other effective) remedies to global problems we probably would need no rescourse to them. Suggests that effective methods of preventing genetic disease are prevention of mutations and detection and…

Detecting Plagiarism in MS Access Assignments

Science.gov (United States)

Singh, Anil

2013-01-01

Assurance of individual effort from students in computer-based assignments is a challenge. Due to digitization, students can easily use a copy of their friend's work and submit it as their own. Plagiarism in assignments puts students who cheat at par with those who work honestly and this compromises the learning evaluation process. Using a…

Development and Evaluation of Event-Specific Quantitative PCR Method for Genetically Modified Soybean MON87701.

Science.gov (United States)

Tsukahara, Keita; Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Nishimaki-Mogami, Tomoko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi

2016-01-01

A real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) soybean event, MON87701. First, a standard plasmid for MON87701 quantification was constructed. The conversion factor (C f ) required to calculate the amount of genetically modified organism (GMO) was experimentally determined for a real-time PCR instrument. The determined C f for the real-time PCR instrument was 1.24. For the evaluation of the developed method, a blind test was carried out in an inter-laboratory trial. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDr), respectively. The determined biases and the RSDr values were less than 30 and 13%, respectively, at all evaluated concentrations. The limit of quantitation of the method was 0.5%, and the developed method would thus be applicable for practical analyses for the detection and quantification of MON87701.

Complete sequence-specific 1H NMR assignments for human insulin

International Nuclear Information System (INIS)

Kline, A.D.; Justice, R.M. Jr.

1990-01-01

Solvent conditions where human insulin could be studied by high-resolution NMR were determined. Both low pH and addition of acetonitrile were required to overcome the protein's self-association and to obtain useful spectra. Two hundred eighty-six 1 H resonances were located and assigned to specific sites on the protein by using two-dimensional NMR methods. The presence and position of numerous d NN sequential NOE's indicate that the insulin conformation seen in crystallographic studies is largely retained under these solution conditions. Slowly exchanging protons were observed for seven backbone amide protons and were assigned to positions A15 and A16 and to positions B15-B19. These amides all occur within helical regions of the protein

Disease-Concordant Twins Empower Genetic Association Studies

DEFF Research Database (Denmark)

Tan, Qihua; Li, Weilong; Vandin, Fabio

2017-01-01

and ordinary healthy samples as controls. We examined the power gain of the twin-based design for various scenarios (i.e., cases from monozygotic and dizygotic twin pairs concordant for a disease) and compared the power with the ordinary case-control design with cases collected from the unrelated patient...... concordant for a disease, should confer increased power in genetic association analysis because of their genetic relatedness. We conducted a computer simulation study to explore the power advantage of the disease-concordant twin design, which uses singletons from disease-concordant twin pairs as cases...... population. Simulation was done by assigning various allele frequencies and allelic relative risks for different mode of genetic inheritance. In general, for achieving a power estimate of 80%, the sample sizes needed for dizygotic and monozygotic twin cases were one half and one fourth of the sample size...

A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.

Science.gov (United States)

Rishishwar, Lavanya; Conley, Andrew B; Vidakovic, Brani; Jordan, I King

2015-12-15

Uniparental genetic markers, mitochondrial DNA (mtDNA) and Y chromosomal DNA, are widely used for the inference of human ancestry. However, the resolution of ancestral origins based on mtDNA haplotypes is limited by the fact that such haplotypes are often found to be distributed across wide geographical regions. We have addressed this issue here by combining two sources of ancestry information that have typically been considered separately: historical records regarding population origins and genetic information on mtDNA haplotypes. To combine these distinct data sources, we applied a Bayesian approach that considers historical records, in the form of prior probabilities, together with data on the geographical distribution of mtDNA haplotypes, formulated as likelihoods, to yield ancestry assignments from posterior probabilities. This combined evidence Bayesian approach to ancestry assignment was evaluated for its ability to accurately assign sub-continental African ancestral origins to Afro-Colombians based on their mtDNA haplotypes. We demonstrate that the incorporation of historical prior probabilities via this analytical framework can provide for substantially increased resolution in sub-continental African ancestry assignment for members of this population. In addition, a personalized approach to ancestry assignment that involves the tuning of priors to individual mtDNA haplotypes yields even greater resolution for individual ancestry assignment. Despite the fact that Colombia has a large population of Afro-descendants, the ancestry of this community has been understudied relative to populations with primarily European and Native American ancestry. Thus, the application of the kind of combined evidence approach developed here to the study of ancestry in the Afro-Colombian population has the potential to be impactful. The formal Bayesian analytical framework we propose for combining historical and genetic information also has the potential to be widely applied

Population genetics without intraspecific data

DEFF Research Database (Denmark)

Thorne, Jeffrey L; Choi, Sang Chul; Yu, Jiaye

2007-01-01

A central goal of computational biology is the prediction of phenotype from DNA and protein sequence data. Recent models of sequence change use in silico prediction systems to incorporate the effects of phenotype on evolutionary rates. These models have been designed for analyzing sequence data...... populations, and parameters of interspecific models should have population genetic interpretations. We show, with two examples, how population genetic interpretations can be assigned to evolutionary models. The first example considers the impact of RNA secondary structure on sequence change, and the second...... reflects the tendency for protein tertiary structure to influence nonsynonymous substitution rates. We argue that statistical fit to data should not be the sole criterion for assessing models of sequence change. A good interspecific model should also yield a clear and biologically plausible population...

Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers.

Science.gov (United States)

Streitberger, K; Schweizer, M; Kropatsch, R; Dekomien, G; Distl, O; Fischer, M S; Epplen, J T; Hertwig, S T

2012-10-01

As a result of strong artificial selection, the domesticated dog has arguably become one of the most morphologically diverse vertebrate species, which is mirrored in the classification of around 400 different breeds. To test the influence of breeding history on the genetic structure and variability of today's dog breeds, we investigated 12 dog breeds using a set of 19 microsatellite markers from a total of 597 individuals with about 50 individuals analysed per breed. High genetic diversity was noted over all breeds, with the ancient Asian breeds (Akita, Chow Chow, Shar Pei) exhibiting the highest variability, as was indicated chiefly by an extraordinarily high number of rare and private alleles. Using a Bayesian clustering method, we detected significant genetic stratification within the closely related Schnauzer breeds. The individuals of these three recently differentiated breeds (Miniature, Standard and Giant Schnauzer) could not be assigned to a single cluster each. This hidden genetic structure was probably caused by assortative mating owing to breeders' preferences regarding coat colour types and the underlying practice of breeding in separate lineages. Such processes of strong artificial disruptive selection for different morphological traits in isolated and relatively small lineages can result in the rapid creation of new dog types and potentially new breeds and represent a unique opportunity to study the evolution of genetic and morphological differences in recently diverged populations. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables

DEFF Research Database (Denmark)

Burgess, Stephen; Thompson, Simon G; Thompson, Grahame

2010-01-01

Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context o...

A review of statistical methods for testing genetic anticipation: looking for an answer in Lynch syndrome

DEFF Research Database (Denmark)

Boonstra, Philip S; Gruber, Stephen B; Raymond, Victoria M

2010-01-01

the issue of multiplex ascertainment and its effect on the different methods. We then focus on exploring genetic anticipation in Lynch syndrome and analyze new data on the age of onset in affected parent-child pairs from families seen at the University of Michigan Cancer Genetics clinic with a mutation...... in one of the three main mismatch repair (MMR) genes. In contrast to the clinic-based population, we re-analyze data on a population-based Lynch syndrome cohort, derived from the Danish HNPCC-register. Both datasets indicate evidence of genetic anticipation in Lynch syndrome. We then expand our review...

Structural characterization of homogalacturonan by NMR spectroscopy - assignment of reference compounds

DEFF Research Database (Denmark)

Petersen, Bent O.; Meier, Sebastian; Duus, Jens Øllgaard

2008-01-01

Complete assignment of 1H and 13C NMR of six hexagalactopyranuronic acids with varying degree and pattern of methyl esterification is reported. The NMR experiments were run at room temperature using approximately 2 mg of sample making this method convenient for studying the structure...

Recent advances in ratio primary reference measurement procedures (definitive methods) and their use in certification of reference materials and controlling assigned values in proficiency testing

International Nuclear Information System (INIS)

Dybczyñski, R.S.; Polkowska-Motrenko, H.; Chajduk, E.; Danko, B.; Pyszynska, M.

2014-01-01

The idea of definitive methods based on radiochemical neutron activation analysis (RNAA), consists in combination of neutron activation with the highly selective and quantitative post-irradiation isolation of the desired radionuclide by column chromatography followed by γ-ray spectrometric measurement. The principles of construction of such methods, which were devised in the Institute of Nuclear Chemistry and Technology, are reminded and the significance of these methods for analytical quality assurance is emphasized. According to VIM 3 nomenclature these methods may be called: ratio primary reference measurement procedures (RPRMPs). RPRMP for the determination of Se is briefly presented and its use for checking the accuracy of 'assigned values' established by expert laboratories in some proficiency tests, is demonstrated

Loop-mediated isothermal amplification (LAMP) method for detection of genetically modified maize T25.

Science.gov (United States)

Xu, Junyi; Zheng, Qiuyue; Yu, Ling; Liu, Ran; Zhao, Xin; Wang, Gang; Wang, Qinghua; Cao, Jijuan

2013-11-01

The loop-mediated isothermal amplification (LAMP) assay indicates a potential and valuable means for genetically modified organism (GMO) detection especially for its rapidity, simplicity, and low cost. We developed and evaluated the specificity and sensitivity of the LAMP method for rapid detection of the genetically modified (GM) maize T25. A set of six specific primers was successfully designed to recognize six distinct sequences on the target gene, including a pair of inner primers, a pair of outer primers, and a pair of loop primers. The optimum reaction temperature and time were verified to be 65°C and 45 min, respectively. The detection limit of this LAMP assay was 5 g kg(-1) GMO component. Comparative experiments showed that the LAMP assay was a simple, rapid, accurate, and specific method for detecting the GM maize T25.

Insights to genetic characterization tools for epidemiological tracking of Francisella tularensis in Sweden.

Directory of Open Access Journals (Sweden)

Tara Wahab

Full Text Available Tularaemia, caused by the bacterium Francisella tularensis, is endemic in Sweden and is poorly understood. The aim of this study was to evaluate the effectiveness of three different genetic typing systems to link a genetic type to the source and place of tularemia infection in Sweden. Canonical single nucleotide polymorphisms (canSNPs, MLVA including five variable number of tandem repeat loci and PmeI-PFGE were tested on 127 F. tularensis positive specimens collected from Swedish case-patients. All three typing methods identified two major genetic groups with near-perfect agreement. Higher genetic resolution was obtained with canSNP and MLVA compared to PFGE; F. tularensis samples were first assigned into ten phylogroups based on canSNPs followed by 33 unique MLVA types. Phylogroups were geographically analysed to reveal complex phylogeographic patterns in Sweden. The extensive phylogenetic diversity found within individual counties posed a challenge to linking specific genetic types with specific geographic locations. Despite this, a single phylogroup (B.22, defined by a SNP marker specific to a lone Swedish sequenced strain, did link genetic type with a likely geographic place. This result suggests that SNP markers, highly specific to a particular reference genome, may be found most frequently among samples recovered from the same location where the reference genome originated. This insight compels us to consider whole-genome sequencing (WGS as the appropriate tool for effectively linking specific genetic type to geography. Comparing the WGS of an unknown sample to WGS databases of archived Swedish strains maximizes the likelihood of revealing those rare geographically informative SNPs.

Hybrid Genetic Algorithm - Local Search Method for Ground-Water Management

Science.gov (United States)

Chiu, Y.; Nishikawa, T.; Martin, P.

2008-12-01

Ground-water management problems commonly are formulated as a mixed-integer, non-linear programming problem (MINLP). Relying only on conventional gradient-search methods to solve the management problem is computationally fast; however, the methods may become trapped in a local optimum. Global-optimization schemes can identify the global optimum, but the convergence is very slow when the optimal solution approaches the global optimum. In this study, we developed a hybrid optimization scheme, which includes a genetic algorithm and a gradient-search method, to solve the MINLP. The genetic algorithm identifies a near- optimal solution, and the gradient search uses the near optimum to identify the global optimum. Our methodology is applied to a conjunctive-use project in the Warren ground-water basin, California. Hi- Desert Water District (HDWD), the primary water-manager in the basin, plans to construct a wastewater treatment plant to reduce future septic-tank effluent from reaching the ground-water system. The treated wastewater instead will recharge the ground-water basin via percolation ponds as part of a larger conjunctive-use strategy, subject to State regulations (e.g. minimum distances and travel times). HDWD wishes to identify the least-cost conjunctive-use strategies that control ground-water levels, meet regulations, and identify new production-well locations. As formulated, the MINLP objective is to minimize water-delivery costs subject to constraints including pump capacities, available recharge water, water-supply demand, water-level constraints, and potential new-well locations. The methodology was demonstrated by an enumerative search of the entire feasible solution and comparing the optimum solution with results from the branch-and-bound algorithm. The results also indicate that the hybrid method identifies the global optimum within an affordable computation time. Sensitivity analyses, which include testing different recharge-rate scenarios, pond

Do natural methods for fertility regulation increase the risks of genetic errors?

Science.gov (United States)

Serra, A

1981-09-01

Genetic errors of many kinds are connected with the reproductive processes and are favored by a nunber of largely uncontrollable, endogenous, and/or exogenous factors. For a long time human beings have taken into their own hands the control of this process. The regulation of fertility is clearly a forceful request to any family, to any community, were it only to lower the level of the consequences of genetic errors. In connection with this request, and in the context of the Congress for the Family of Africa and Europe (Catholic University, January 1981), 1 question must still be raised and possibly answered. The question is: do or can the so called "natural methods" for the regulation of fertility increase the risks of genetic errors with their generally dramatic effects on families and on communities. It is important to try to give as far as possible a scientifically based answer to this question. Fr. Haring, a moral theologian, citing scientific evidence finds it shocking that the rhythm method, so strongly and recently endorsed again by Church authorities, should be classified among the means of "birth control" by way of spontaneous abortion or at least by spontaneous loss of a large number of zygotes which, due to the concrete application of the rhythm method, lack of necessary vitality for survival. He goes on to state that the scientific research provides overwhelming evidence that the rhythm method in its traditional form is responsible for a disproportionate waste of zygotes and a disproportionate frequency of spontaneous abortions and a defective childern. Professor Hilgers, a reproductive physiologist, takes on opposite view, maintaining that the hypotheses are arbitrary and the alarm false. The strongest evidence upon which Fr. Haring bases his moral principles about the use of the natural methods of fertility regulation is a paper by Guerrero and Rojos (1975). These authors examined, retrospectively, the success of 965 pregnancies which occurred in

Historical WBAN ID Assignments

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — 4"x6" index cards represent the first written assignments of Weather Bureau Army Navy (WBAN) station identifier numbers by the National Climatic Data Center....

Development of a qualitative real-time PCR method to detect 19 targets for identification of genetically modified organisms.

Science.gov (United States)

Peng, Cheng; Wang, Pengfei; Xu, Xiaoli; Wang, Xiaofu; Wei, Wei; Chen, Xiaoyun; Xu, Junfeng

2016-01-01

As the amount of commercially available genetically modified organisms (GMOs) grows recent years, the diversity of target sequences for molecular detection techniques are eagerly needed. Considered as the gold standard for GMO analysis, the real-time PCR technology was optimized to produce a high-throughput GMO screening method. With this method we can detect 19 transgenic targets. The specificity of the assays was demonstrated to be 100 % by the specific amplification of DNA derived from reference material from 20 genetically modified crops and 4 non modified crops. Furthermore, most assays showed a very sensitive detection, reaching the limit of ten copies. The 19 assays are the most frequently used genetic elements present in GM crops and theoretically enable the screening of the known GMO described in Chinese markets. Easy to use, fast and cost efficient, this method approach fits the purpose of GMO testing laboratories.

A modeling of dynamic storage assignment for order picking in beverage warehousing with Drive-in Rack system

Science.gov (United States)

Hadi, M. Z.; Djatna, T.; Sugiarto

2018-04-01

This paper develops a dynamic storage assignment model to solve storage assignment problem (SAP) for beverages order picking in a drive-in rack warehousing system to determine the appropriate storage location and space for each beverage products dynamically so that the performance of the system can be improved. This study constructs a graph model to represent drive-in rack storage position then combine association rules mining, class-based storage policies and an arrangement rule algorithm to determine an appropriate storage location and arrangement of the product according to dynamic orders from customers. The performance of the proposed model is measured as rule adjacency accuracy, travel distance (for picking process) and probability a product become expiry using Last Come First Serve (LCFS) queue approach. Finally, the proposed model is implemented through computer simulation and compare the performance for different storage assignment methods as well. The result indicates that the proposed model outperforms other storage assignment methods.

Paternity assignment in the polyploid Acipenser dabryanus based on a novel microsatellite marker system.

Directory of Open Access Journals (Sweden)

Ya Liu

Full Text Available Acipenser dabryanus is listed as a Critical Endangered species in the IUCN Red List and the first class protected animals in China. Fortunately, A. dabryanus specimens are being successfully bred in captivity for conservation. However, for effective ex situ conservation, we should be aware of the genetic diversity and the degree of relatedness of the individuals selected for breeding. In this study, we aimed at the development of novel and reliable microsatellites used for the genetic study of A. dabryanus. A total of 14,321 simple sequence repeats (SSRs were detected by transcriptome sequencing and screening. We selected 20 novel and polymorphic microsatellites (non-dinucleotide with good repeatability from the 100 tested loci for a subsequent genetic and paternity study. A set of captive broodstock (F1 stock, n = 43 and their offspring (F2 stock, n = 96 were used to examine the efficiency of the 20 SSRs for assigning parentage to offspring, with an allocation success of 91.7%. We also found that only a few families predominantly contributed to the progeny produced by the 43 breeders. In addition, mitochondrial DNA data showed that the captive broodstock (F1 individuals had an excellent probability of the same lineage, implying that a high level of inbreeding may have occurred in these individuals. Our research provides useful information on genetic diversity and reproductive pattern of A. dabryanus, and the 20 SSRs developed in this study can be applied to the future breeding program to avoid inbreeding for this stock or other related species of Acipenseriformes.

Reducing health risk assigned to organic emissions from a chemical weapons incinerator.

Science.gov (United States)

Laman, David M; Weiler, B Douglas; Skeen, Rodney S

2013-03-01

Organic emissions from a chemical weapons incinerator have been characterized with an improved set of analytical methods to reduce the human health risk assigned to operations of the facility. A gas chromatography/mass selective detection method with substantially reduced detection limits has been used in conjunction with scanning electron microscopy/energy dispersive X-ray spectrometry and Fourier transform infrared microscopy to improve the speciation of semi-volatile and non-volatile organics emitted from the incinerator. The reduced detection limits have allowed a significant reduction in the assumed polycyclic aromatic hydrocarbon (PAH) and aminobiphenyl (ABP) emission rates used as inputs to the human health risk assessment for the incinerator. A mean factor of 17 decrease in assigned human health risk is realized for six common local exposure scenarios as a result of the reduced PAH and ABP detection limits.

SCRAED - Simple and Complex Random Assignment in Experimental Designs

OpenAIRE

Alferes, Valentim R.

2009-01-01

SCRAED is a package of 37 self-contained SPSS syntax files that performs simple and complex random assignment in experimental designs. For between-subjects designs, SCRAED includes simple random assignment (no restrictions, forced equal sizes, forced unequal sizes, and unequal probabilities), block random assignment (simple and generalized blocks), and stratified random assignment (no restrictions, forced equal sizes, forced unequal sizes, and unequal probabilities). For within-subject...

SERS-based detection methods for screening of genetically modified bacterial strains

DEFF Research Database (Denmark)

Morelli, Lidia

factories vary largely, including industrial production of valuable compounds for biofuels, polymer synthesis and food, cosmetic and pharmaceutical industry. The improvement of computational and biochemical tools has revolutionized the synthesis of novel modified microbial strains, opening up new......The importance of metabolic engineering has been growing over the last decades, establishing the use of genetically modified microbial strains for overproduction of metabolites at industrial scale as an innovative, convenient and biosustainable method. Nowadays, application areas of microbial...

Automated grading of homework assignments and tests in introductory and intermediate statistics courses using active server pages.

Science.gov (United States)

Stockburger, D W

1999-05-01

Active server pages permit a software developer to customize the Web experience for users by inserting server-side script and database access into Web pages. This paper describes applications of these techniques and provides a primer on the use of these methods. Applications include a system that generates and grades individualized homework assignments and tests for statistics students. The student accesses the system as a Web page, prints out the assignment, does the assignment, and enters the answers on the Web page. The server, running on NT Server 4.0, grades the assignment, updates the grade book (on a database), and returns the answer key to the student.

Class Schedule Assignment Based on Students Learning Rhythms Using A Genetic Algorithm Asignación de horarios de clase basado en los ritmos de aprendizaje de los estudiantes usando un algoritmo genético

Directory of Open Access Journals (Sweden)

Victor F. Suarez Chilma

2013-03-01

Full Text Available The objective of this proposal is to implement a school day agenda focused on the learning rhythms of students of elementary and secondary schools using a genetic algorithm. The methodology of this proposal takes into account legal requirements and constraints on the assignment of teachers and classrooms in public educational institutions in Colombia. In addition, this proposal provides a set of constraints focused on cognitive rhythms and subjects are scheduled at the most convenient times according to the area of knowledge. The genetic algorithm evolves through a process of mutation and selection and builds a total solution based on the best solutions for each group. Sixteen groups in a school are tested and the results of class schedule assignments are presented. The quality of the solution obtained through the established approach is validated by comparing the results to the solutions obtained using another algorithm.El objetivo de esta propuesta es implementar un horario escolar que tenga en cuenta los ritmos de aprendizaje en los estudiantes de educación primaria y secundaria, utilizando un algoritmo genético. La metodología considera los requerimientos legales y las restricciones necesarias para la asignación de maestros y aulas en instituciones educativas públicas de Colombia. Adicionalmente, se establecen un conjunto de restricciones relacionadas con el enfoque en los ritmos cognitivos, determinando las horas de la jornada en las que es más conveniente la ubicación de ciertas materias de acuerdo al área del conocimiento al que pertenecen. El algoritmo genético evoluciona mediante un proceso de mutación y selección, a través del cual se construye una solución completa a partir de la búsqueda de las mejores soluciones por grupo. Se presentan los resultados de las pruebas realizadas para la asignación de una institución con 16 grupos. La calidad de las soluciones obtenidas de acuerdo al enfoque establecido es validada

A fuzzy-based particle swarm optimisation approach for task assignment in home healthcare

Directory of Open Access Journals (Sweden)

Mutingi, Michael

2014-11-01

Full Text Available Home healthcare (HHC organisations provide coordinated healthcare services to patients at their homes. Motivated by the ever-increasing need for home-based care, the assignment of tasks to available healthcare staff is a common and complex problem in homecare organisations. Designing high quality task schedules is critical for improving worker morale, job satisfaction, service efficiency, service quality, and competitiveness over the long term. The desire is to provide high quality task assignment schedules that satisfy the patient, the care worker, and the management. This translates to maximising schedule fairness in terms of workload assignments, avoiding task time window violation, and meeting management goals as much as possible. However, in practice, these desires are often subjective as they involve imprecise human perceptions. This paper develops a fuzzy multi-criteria particle swarm optimisation (FPSO approach for task assignment in a home healthcare setting in a fuzzy environment. The proposed approach uses a fuzzy evaluation method from a multi-criteria point of view. Results from illustrative computational experiments show that the approach is promising.

GENERAL ISSUES CONCERNING THE ASSIGNMENT OF SOCIAL PARTS

Directory of Open Access Journals (Sweden)

Stela Mihăilescu

2012-11-01

Full Text Available By means of the present study, we try to offer a thorough image and an analysis concerning the assignment mode of social parts within a company having limited liability. The assignment of social parts is free and unrestricted except for the cases provided by article 202, paragraph 2 from Law no. 31/ 1990- the law of commercial companies with further modifications and completions and the ones provided in OUG no. 54/ 2010 concerning some measures for fighting fiscal evasion. By means of the assignment operation a transmission is made up by an assignment of social parts contract towards one or more already associated persons in the company or towards other individual or legal persons who are going to obtain the associate quality. The principle governing any assignment is the one of goods circulation freedom, a freedom restricted only by the public order and imperative judicial norms.

An Airway Network Flow Assignment Approach Based on an Efficient Multiobjective Optimization Framework

Directory of Open Access Journals (Sweden)

Xiangmin Guan

2015-01-01

Full Text Available Considering reducing the airspace congestion and the flight delay simultaneously, this paper formulates the airway network flow assignment (ANFA problem as a multiobjective optimization model and presents a new multiobjective optimization framework to solve it. Firstly, an effective multi-island parallel evolution algorithm with multiple evolution populations is employed to improve the optimization capability. Secondly, the nondominated sorting genetic algorithm II is applied for each population. In addition, a cooperative coevolution algorithm is adapted to divide the ANFA problem into several low-dimensional biobjective optimization problems which are easier to deal with. Finally, in order to maintain the diversity of solutions and to avoid prematurity, a dynamic adjustment operator based on solution congestion degree is specifically designed for the ANFA problem. Simulation results using the real traffic data from China air route network and daily flight plans demonstrate that the proposed approach can improve the solution quality effectively, showing superiority to the existing approaches such as the multiobjective genetic algorithm, the well-known multiobjective evolutionary algorithm based on decomposition, and a cooperative coevolution multiobjective algorithm as well as other parallel evolution algorithms with different migration topology.

Stress Assignment in Reading Italian Polysyllabic Pseudowords

Science.gov (United States)

Sulpizio, Simone; Arduino, Lisa S.; Paizi, Despina; Burani, Cristina

2013-01-01

In 4 naming experiments we investigated how Italian readers assign stress to pseudowords. We assessed whether participants assign stress following distributional information such as stress neighborhood (the proportion and number of existent words sharing orthographic ending and stress pattern) and whether such distributional information affects…

The concept of symptomatic epilepsy and the complexities of assigning cause in epilepsy.

Science.gov (United States)

Shorvon, Simon

2014-03-01

The concept of symptomatic epilepsy and the difficulties in assigning cause in epilepsy are described. A historical review is given, emphasizing aspects of the history which are relevant today. The historical review is divided into three approximately semicentenial periods (1860-1910, 1910-1960, 1960-present). A definition of symptomatic epilepsy and this is followed by listing of causes of symptomatic epilepsy. The fact that not all the causes of idiopathic epilepsy are genetic is discussed. A category of provoked epilepsy is proposed. The complexities in assigning cause include the following: the multifactorial nature of epilepsy, the distinction between remote and proximate causes, the role of nongenetic factors in idiopathic epilepsy, the role of investigation in determining the range of causes, the fact that not all symptomatic epilepsy is acquired, the nosological position of provoked epilepsy and the view of epilepsy as a process, and the differentiation of new-onset and established epilepsy. The newly proposed ILAE classification of epilepsy and its changes in terminologies and the difficulties in the concept of acute symptomatic epilepsy are discussed, including the inconsistencies and gray areas and the distinction between idiopathic, symptomatic, and provoked epilepsies. Points to be considered in future work are listed. Copyright © 2013 Elsevier Inc. All rights reserved.

Gender identity, gender assignment and reassignment in individuals with disorders of sex development: a major of dilemma.

Science.gov (United States)

Fisher, A D; Ristori, J; Fanni, E; Castellini, G; Forti, G; Maggi, M

2016-11-01

Disorders of Sex Development (DSD) are a wide range of congenital conditions characterized by an incongruence of components involved in sexual differentiation, including gender psychosexual development. The management of such disorders is complex, and one of the most crucial decision is represented by gender assignment. In fact, the primary goal in DSD is to have a gender assignment consistent with the underlying gender identity in order to prevent the distress related to a forthcoming Gender Dysphoria. Historically, gender assignment was based essentially on surgical outcomes, assuming the neutrality of gender identity at birth. This policy has been challenged in the past decade refocusing on the importance of prenatal and postnatal hormonal and genetic influences on psychosexual development. (1) to update the main psychological and medical issues that surround DSD, in particular regarding gender identity and gender assignment; (2) to report specific clinical recommendations according to the different diagnosis. A systematic search of published evidence was performed using Medline (from 1972 to March 2016). Review of the relevant literature and recommendations was based on authors' expertise. A review of gender identity and assignment in DSD is provided as well as clinical recommendations for the management of individuals with DSD. Given the complexity of this management, DSD individuals and their families need to be supported by a specialized multidisciplinary team, which has been universally recognized as the best practice for intersexual conditions. In case of juvenile GD in DSD, the prescription of gonadotropin-releasing hormone analogues, following the World Professional Association for Transgender Health and the Endocrine Society guidelines, should be considered. It should always be taken into account that every DSD person is unique and has to be treated with individualized care. In this perspective, international registries are crucial to improve the

Evaluative Indices Assigned to Contraceptive Methods by University Undergraduates

Science.gov (United States)

McDermott, Robert J.; Malo, Teri L.; Dodd, Virginia J.; Daley, Ellen M.; Mayer, Alyssa B.

2011-01-01

Background: Preordinate attitudes and beliefs about contraception may influence acceptance or rejection of a particular method. Purpose: We examined the attitudes about contraception methods held by undergraduate students (N=792) at two large southeastern universities in the United States. Methods: Twelve methods were rated on 40 semantic…

Approximate k-NN delta test minimization method using genetic algorithms: Application to time series

CERN Document Server

Mateo, F; Gadea, Rafael; Sovilj, Dusan

2010-01-01

In many real world problems, the existence of irrelevant input variables (features) hinders the predictive quality of the models used to estimate the output variables. In particular, time series prediction often involves building large regressors of artificial variables that can contain irrelevant or misleading information. Many techniques have arisen to confront the problem of accurate variable selection, including both local and global search strategies. This paper presents a method based on genetic algorithms that intends to find a global optimum set of input variables that minimize the Delta Test criterion. The execution speed has been enhanced by substituting the exact nearest neighbor computation by its approximate version. The problems of scaling and projection of variables have been addressed. The developed method works in conjunction with MATLAB's Genetic Algorithm and Direct Search Toolbox. The goodness of the proposed methodology has been evaluated on several popular time series examples, and also ...

Image acquisition, transmission and assignment in 60Co container inspection system

International Nuclear Information System (INIS)

Wu Zhifang; Zhou Liye; Liu Ximing; Wang Liqiang

1999-01-01

The author describes the data acquisition mode and image reconstruction method in 60 Co container inspection system, analyzes the relationship between line pick period and geometry distortion, makes clear the demand to data transmitting rate. It discusses several data communication methods, draws up a plan for network, realizes automatic direction and reasonable assignment of data in the system, cooperation of multi-computer and parallel processing, thus greatly improves the systems inspection efficiency

SimPhospho: a software tool enabling confident phosphosite assignment.

Science.gov (United States)

Suni, Veronika; Suomi, Tomi; Tsubosaka, Tomoya; Imanishi, Susumu Y; Elo, Laura L; Corthals, Garry L

2018-03-27

Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. SimPhospho is available for Windows, Linux and Mac operating systems at https://sourceforge.net/projects/simphospho/. It is open source and implemented in C ++. A user's manual with detailed description of data analysis using SimPhospho as well as test data can be found as supplementary material of this article. Supplementary data are available at https://www.btk.fi/research/ computational-biomedicine/software/.

Algorithms for selecting informative marker panels for population assignment.

Science.gov (United States)

Rosenberg, Noah A

2005-11-01

Given a set of potential source populations, genotypes of an individual of unknown origin at a collection of markers can be used to predict the correct source population of the individual. For improved efficiency, informative markers can be chosen from a larger set of markers to maximize the accuracy of this prediction. However, selecting the loci that are individually most informative does not necessarily produce the optimal panel. Here, using genotypes from eight species--carp, cat, chicken, dog, fly, grayling, human, and maize--this univariate accumulation procedure is compared to new multivariate "greedy" and "maximin" algorithms for choosing marker panels. The procedures generally suggest similar panels, although the greedy method often recommends inclusion of loci that are not chosen by the other algorithms. In seven of the eight species, when applied to five or more markers, all methods achieve at least 94% assignment accuracy on simulated individuals, with one species--dog--producing this level of accuracy with only three markers, and the eighth species--human--requiring approximately 13-16 markers. The new algorithms produce substantial improvements over use of randomly selected markers; where differences among the methods are noticeable, the greedy algorithm leads to slightly higher probabilities of correct assignment. Although none of the approaches necessarily chooses the panel with optimal performance, the algorithms all likely select panels with performance near enough to the maximum that they all are suitable for practical use.

Big Data on a Smaller Scale: A Social Media Analytics Assignment

Science.gov (United States)

Fischbach, Sarah; Zarzosa, Jennifer

2018-01-01

It is truly important for students to understand how to monitor online marketing buzz. This assignment, social media analytics, utilizes the content analysis research method to build student's in-depth understanding on how to evaluate and interpret user-generated content (UGC) to create social media campaigns. The authors adapted Resnik and…

Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.

Science.gov (United States)

Leo, Sarah S T; Gonzalez, Andrew; Millien, Virginie

2016-05-01

Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies.

Combined Simulated Annealing and Genetic Algorithm Approach to Bus Network Design

Science.gov (United States)

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.

Assignment and Correspondence Tracking System - Tactical / Operational Reporting

Data.gov (United States)

Social Security Administration — Reporting data store for the Assignment and Correspondence Tracking System (ACT). ACT automates the assignment and tracking of correspondence processing within the...

Statistical aspects of optimal treatment assignment

OpenAIRE

van der Linden, Willem J.

1980-01-01

The issues of treatment assignment is ordinarily dealt with within the framework of testing aptitude treatment interaction (ATI) hypothesis. ATI research mostly uses linear regression techniques, and an ATI exists when the aptitude treatment (AT) regression lines cross each other within the relevant interval of the aptitude variable. Consistent with this approach is the use of the points of interaction of AT regression lines as treatment-assignment rule. The replacement of such rules by monot...

One of My Favorite Assignments: Automated Teller Machine Simulation.

Science.gov (United States)

Oberman, Paul S.

2001-01-01

Describes an assignment for an introductory computer science class that requires the student to write a software program that simulates an automated teller machine. Highlights include an algorithm for the assignment; sample file contents; language features used; assignment variations; and discussion points. (LRW)

Phase modulated 2D HSQC-TOCSY for unambiguous assignment of overlapping spin systems

Science.gov (United States)

Singh, Amrinder; Dubey, Abhinav; Adiga, Satish K.; Atreya, Hanudatta S.

2018-01-01

We present a new method that allows one to unambiguously resolve overlapping spin systems often encountered in biomolecular systems such as peptides and proteins or in samples containing a mixture of different molecules such as in metabolomics. We address this problem using the recently proposed phase modulation approach. By evolving the 1H chemical shifts in a conventional two dimensional (2D) HSQC-TOCSY experiment for a fixed delay period, the phase/intensity of set of cross peaks belonging to one spin system are modulated differentially relative to those of its overlapping counterpart, resulting in their discrimination and recognition. The method thus accelerates the process of identification and resonance assignment of individual compounds in complex mixtures. This approach facilitated the assignment of molecules in the embryo culture medium used in human assisted reproductive technology.

7 CFR 1900.5 - Assignment of cases.

Science.gov (United States)

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Assignment of cases. 1900.5 Section 1900.5 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS... REGULATIONS GENERAL Delegations of Authority § 1900.5 Assignment of cases. The State Director may, in writing...

Development and validation of an event-specific quantitative PCR method for genetically modified maize MIR162.

Science.gov (United States)

Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi

2014-01-01

A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) maize event, MIR162. We first prepared a standard plasmid for MIR162 quantification. The conversion factor (Cf) required to calculate the genetically modified organism (GMO) amount was empirically determined for two real-time PCR instruments, the Applied Biosystems 7900HT (ABI7900) and the Applied Biosystems 7500 (ABI7500) for which the determined Cf values were 0.697 and 0.635, respectively. To validate the developed method, a blind test was carried out in an interlaboratory study. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDr). The determined biases were less than 25% and the RSDr values were less than 20% at all evaluated concentrations. These results suggested that the limit of quantitation of the method was 0.5%, and that the developed method would thus be suitable for practical analyses for the detection and quantification of MIR162.

Roads, interrupted dispersal, and genetic diversity in timber rattlesnakes.

Science.gov (United States)

Clark, Rulon W; Brown, William S; Stechert, Randy; Zamudio, Kelly R

2010-08-01

Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads.

Detection of Genetically Modified Food: Has Your Food Been Genetically Modified?

Science.gov (United States)

Brandner, Diana L.

2002-01-01

Explains the benefits and risks of genetically-modified foods and describes methods for genetically modifying food. Presents a laboratory experiment using a polymerase chain reaction (PCR) test to detect foreign DNA in genetically-modified food. (Contains 18 references.) (YDS)

Statistical Methods for Studying Genetic Variation in Populations

Science.gov (United States)

2012-08-01

iteration will converge to a local optimum, similar to what happens in an EM algorithm. Empirically, a near global optimal can be obtained by multiple...and E Matthysen. Genetic variability and gene flow 131 in the globally , critically-endangered Taita thrush. Conservation Genetics, 1:45–55, 2000. 4.5.2...Libioulle, Edouard Louis, Sarah Hansoul, Cynthia Sandor, Frédéric Farnir, Denis Franchi - mont, Séverine Vermeire, Olivier Dewit, Martine de Vos, Anna

Is preimplantation genetic diagnosis the ideal embryo selection method in aneuploidy screening?

Directory of Open Access Journals (Sweden)

Levent Sahin

2014-10-01

Full Text Available To select cytogenetically normal embryos, preimplantation genetic diagnosis (PGD aneuploidy screening (AS is used in numerous centers around the world. Chromosomal abnormalities lead to developmental problems, implantation failure, and early abortion of embryos. The usefulness of PGD in identifying single-gene diseases, human leukocyte antigen typing, X-linked diseases, and specific genetic diseases is well-known. In this review, preimplantation embryo genetics, PGD research studies, and the European Society of Human Reproduction and Embryology PGD Consortium studies and reports are examined. In addition, criteria for embryo selection, technical aspects of PGD-AS, and potential noninvasive embryo selection methods are described. Indications for PGD and possible causes of discordant PGD results between the centers are discussed. The limitations of fluorescence in situ hybridization, and the advantages of the array comparative genomic hybridization are included in this review. Although PGD-AS for patients of advanced maternal age has been shown to improve in vitro fertilization outcomes in some studies, to our knowledge, there is not sufficient evidence to use advanced maternal age as the sole indication for PGD-AS. PGD-AS might be harmful and may not increase the success rates of in vitro fertilization. At the same time PGD, is not recommended for recurrent implantation failure and unexplained recurrent pregnancy loss.

Plant Genetic Resources: Selected Issues from Genetic Erosion to Genetic Engineering

Directory of Open Access Journals (Sweden)

Karl Hammer

2008-04-01

Full Text Available Plant Genetic Resources (PGR continue to play an important role in the development of agriculture. The following aspects receive a special consideration:1. Definition. The term was coined in 1970. The genepool concept served as an important tool in the further development. Different approaches are discussed.2. Values of Genetic Resources. A short introduction is highlighting this problem and stressing the economic usfulness of PGR.3. Genetic Erosion. Already observed by E. Baur in 1914, this is now a key issue within PGR. The case studies cited include Ethiopia, Italy, China, S Korea, Greece and S. Africa. Modern approaches concentrate on allelic changes in varieties over time but neglect the landraces. The causes and consequences of genetic erosion are discussed.4. Genetic Resources Conservation. Because of genetic erosion there is a need for conservation. PGR should be consigned to the appropriate method of conservation (ex situ, in situ, on-farm according to the scientific basis of biodiversity (genetic diversity, species diversity, ecosystem diversity and the evolutionary status of plants (cultivated plants, weeds, related wild plants (crop wild relatives.5. GMO. The impact of genetically engineered plants on genetic diversity is discussed.6. The Conclusions and Recommendations stress the importance of PGR. Their conservation and use are urgent necessities for the present development and future survival of mankind.

Genetic transformation of Eucalyptus camaldulensis by agrobalistic method

Directory of Open Access Journals (Sweden)

Evânia Galvão Mendonça

2013-06-01

Full Text Available Eucalyptus stands in the setting of worldwide forestry due to its adaptability, rapid growth, production of high-quality and low cost of wood pulp fibers. The eucalyptus convetional breeding is impaired mainlly by the long life cycle making the genetic transformation systems an important tool for this purpose. However, this system requires in vitro eficient protocols for plant induction, regeneration and seletion, that allow to obtain transgenic plants from the transformed cell groups. The aim of this work was to evaluate the callus formation and to optimize the leaves and callus genetic transformation protocol by using the Agrobacterium tumefaciens system. Concerning callus formation, two different culture media were evaluated: MS medium supplemented with auxin, cytokinin (M1 and the MS medium with reduced nitrogen concentration and supplemented with auxin, cytokinin coconut water (M2. To establish the leave genetic transformation, those were exposed to agrobiolistics technique (gene gun, to tissue injury, and A. tumesfasciens EHA 105 contening the vetor pCambia 3301 (35S::GUS::NOS, for gene transference and to establish the callus transformation thoses were exposed only to A. tumefasciens. For both experiments, the influence of different infection periods was evaluated. The M2 medium provided the best values for callus sizea and fresh and dry weight. The leaves genetic transformation using the agrobiolistics technique was effective, the gus gene transient expression could be observed. No significant differences were obtained in the infection periods (4, 6 and 8 minutes. The callus genetic transformation with A. tumefaciens also promotend the gus gene transient expression on the callus co-cultiveted for 15 e 30 minutes. The transformed callus was transfered to a regeneration and selection medium and transformed plants were obtained.

Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

Energy Technology Data Exchange (ETDEWEB)

Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus, E-mail: rali@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department for NMR-Based Structural Biology (Germany)

2015-07-15

Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common {sup 13}C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

International Nuclear Information System (INIS)

Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus

2015-01-01

Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common 13 C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR

Genetic improvement of vegetables

International Nuclear Information System (INIS)

Jaramillo Vasquez, J.G.

2001-01-01

Some genetic bases of the improvement of vegetables are given. The objectives of the genetic improvement and the fundamental stages of this process are done. The sources of genetic variation are indicated and they are related the reproduction systems of the main horticultural species. It is analyzed the concept of genetic inheritance like base to determine the procedures more appropriate of improvement. The approaches are discussed, has more than enough phenotypic value, genetic action and genotypic variance; Equally the heredability concepts and value of improvement. The conventional methods of improvement are described, like they are: the introduction of species or varieties, the selection, the pure line, the pedigree method, the selection for families, the recurrent selection, the selection for unique seed, the haploids method, the selection for heterosis and the synthetic varieties

Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method.

Science.gov (United States)

Du, Lei; Huang, Heng; Yan, Jingwen; Kim, Sungeun; Risacher, Shannon L; Inlow, Mark; Moore, Jason H; Saykin, Andrew J; Shen, Li

2016-05-15

Structured sparse canonical correlation analysis (SCCA) models have been used to identify imaging genetic associations. These models either use group lasso or graph-guided fused lasso to conduct feature selection and feature grouping simultaneously. The group lasso based methods require prior knowledge to define the groups, which limits the capability when prior knowledge is incomplete or unavailable. The graph-guided methods overcome this drawback by using the sample correlation to define the constraint. However, they are sensitive to the sign of the sample correlation, which could introduce undesirable bias if the sign is wrongly estimated. We introduce a novel SCCA model with a new penalty, and develop an efficient optimization algorithm. Our method has a strong upper bound for the grouping effect for both positively and negatively correlated features. We show that our method performs better than or equally to three competing SCCA models on both synthetic and real data. In particular, our method identifies stronger canonical correlations and better canonical loading patterns, showing its promise for revealing interesting imaging genetic associations. The Matlab code and sample data are freely available at http://www.iu.edu/∼shenlab/tools/angscca/ shenli@iu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A genetic-algorithm-based method to find unitary transformations for any desired quantum computation and application to a one-bit oracle decision problem

Energy Technology Data Exchange (ETDEWEB)

Bang, Jeongho [Seoul National University, Seoul (Korea, Republic of); Hanyang University, Seoul (Korea, Republic of); Yoo, Seokwon [Hanyang University, Seoul (Korea, Republic of)

2014-12-15

We propose a genetic-algorithm-based method to find the unitary transformations for any desired quantum computation. We formulate a simple genetic algorithm by introducing the 'genetic parameter vector' of the unitary transformations to be found. In the genetic algorithm process, all components of the genetic parameter vectors are supposed to evolve to the solution parameters of the unitary transformations. We apply our method to find the optimal unitary transformations and to generalize the corresponding quantum algorithms for a realistic problem, the one-bit oracle decision problem, or the often-called Deutsch problem. By numerical simulations, we can faithfully find the appropriate unitary transformations to solve the problem by using our method. We analyze the quantum algorithms identified by the found unitary transformations and generalize the variant models of the original Deutsch's algorithm.

Testing the Effectiveness of Online Assignments in Theory of Finance

Science.gov (United States)

Batu, Michael; Bower, Nancy; Lun, Esmond; Sadanand, Asha

2018-01-01

The authors investigated the effectiveness of online versus paper assignments using final examination scores in three cohorts of theory of finance. In particular, two cohorts were exposed to online assignments while another cohort was exposed to traditional assignments. The central result is that exposure to online assignments robustly leads to…

Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

Science.gov (United States)

Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Schaeffer, Jeff; Roseman, Edward F.; Harford, William J.; Johnson, James E.; Fietsch, Cherie-Lee

2012-01-01

Genetic analysis of spawning lake whitefish (Coregonus clupeaformis) from six sites in the main basin of Lake Huron was conducted to determine population structure. Samples from fisheryindependent assessment surveys in the northwest main basin were analyzed to determine the relative contributions of lake whitefish genetic populations. Genetic population structure was identified using data from seven microsatellite DNA loci. One population was identified at Manitoulin Island, one to two were observed in the east-central main basin (Fishing Island and Douglas Point), and one to two populations were found in the northwest (Thunder Bay and Duncan Bay). The genetic identity of collections from Duncan Bay and Thunder Bay was not consistent among methods used to analyze population structure. Low genetic distances suggested that they comprised one population, but genic differences indicated that they may constitute separate populations. Simulated data indicated that the genetic origins of samples from a mixed-fishery could be accurately identified, but accuracy could be improved by incorporating additional microsatellite loci. Mixture analysis and individual assignment tests performed on mixed-stock samples collected from the western main basin suggested that genetic populations from the east-central main basin contributed less than those from the western main basin and that the proportional contribution of each baseline population was similar in each assessment sample. Analysis of additional microsatellite DNA loci may be useful to help improve the precision of the estimates, thus increasing our ability to manage and protect this valuable resource.

A 100-Year Review: Methods and impact of genetic selection in dairy cattle-From daughter-dam comparisons to deep learning algorithms.

Science.gov (United States)

Weigel, K A; VanRaden, P M; Norman, H D; Grosu, H

2017-12-01

In the early 1900s, breed society herdbooks had been established and milk-recording programs were in their infancy. Farmers wanted to improve the productivity of their cattle, but the foundations of population genetics, quantitative genetics, and animal breeding had not been laid. Early animal breeders struggled to identify genetically superior families using performance records that were influenced by local environmental conditions and herd-specific management practices. Daughter-dam comparisons were used for more than 30 yr and, although genetic progress was minimal, the attention given to performance recording, genetic theory, and statistical methods paid off in future years. Contemporary (herdmate) comparison methods allowed more accurate accounting for environmental factors and genetic progress began to accelerate when these methods were coupled with artificial insemination and progeny testing. Advances in computing facilitated the implementation of mixed linear models that used pedigree and performance data optimally and enabled accurate selection decisions. Sequencing of the bovine genome led to a revolution in dairy cattle breeding, and the pace of scientific discovery and genetic progress accelerated rapidly. Pedigree-based models have given way to whole-genome prediction, and Bayesian regression models and machine learning algorithms have joined mixed linear models in the toolbox of modern animal breeders. Future developments will likely include elucidation of the mechanisms of genetic inheritance and epigenetic modification in key biological pathways, and genomic data will be used with data from on-farm sensors to facilitate precision management on modern dairy farms. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Evaluation of Penalized and Nonpenalized Methods for Disease Prediction with Large-Scale Genetic Data

Directory of Open Access Journals (Sweden)

Sungho Won

2015-01-01

Full Text Available Owing to recent improvement of genotyping technology, large-scale genetic data can be utilized to identify disease susceptibility loci and this successful finding has substantially improved our understanding of complex diseases. However, in spite of these successes, most of the genetic effects for many complex diseases were found to be very small, which have been a big hurdle to build disease prediction model. Recently, many statistical methods based on penalized regressions have been proposed to tackle the so-called “large P and small N” problem. Penalized regressions including least absolute selection and shrinkage operator (LASSO and ridge regression limit the space of parameters, and this constraint enables the estimation of effects for very large number of SNPs. Various extensions have been suggested, and, in this report, we compare their accuracy by applying them to several complex diseases. Our results show that penalized regressions are usually robust and provide better accuracy than the existing methods for at least diseases under consideration.

Establishment and application of a multiplex genetic mutation-detection method of lung cancer based on MassARRAY platform

International Nuclear Information System (INIS)

Tian, Hong-Xia; Zhang, Xu-Chao; Wang, Zhen; Chen, Jian-Guang; Chen, Shi-Liang; Guo, Wei-Bang; Wu, Yi-Long

2016-01-01

Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena iPLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on MassARRAY mass spectrometry platform. Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of 99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a LungCarta TM kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases. Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with LungCarta TM kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively. Conclusions: The proposed MassARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues

Genetic Algorithm (GA Method for Optimization of Multi-Reservoir Systems Operation

Directory of Open Access Journals (Sweden)

Shervin Momtahen

2006-01-01

Full Text Available A Genetic Algorithm (GA method for optimization of multi-reservoir systems operation is proposed in this paper. In this method, the parameters of operating policies are optimized using system simulation results. Hence, any operating problem with any sort of objective function, constraints and structure of operating policy can be optimized by GA. The method is applied to a 3-reservoir system and is compared with two traditional methods of Stochastic Dynamic Programming and Dynamic Programming and Regression. The results show that GA is superior both in objective function value and in computational speed. The proposed method is further improved using a mutation power updating rule and a varying period simulation method. The later is a novel procedure proposed in this paper that is believed to help in solving computational time problem in large systems. These revisions are evaluated and proved to be very useful in converging to better solutions in much less time. The final GA method is eventually evaluated as a very efficient procedure that is able to solve problems of large multi-reservoir system which is usually impossible by traditional methods. In fact, the real performance of the GA method starts where others fail to function.

12 CFR 563e.28 - Assigned ratings.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Assigned ratings. 563e.28 Section 563e.28 Banks... for Assessing Performance § 563e.28 Assigned ratings. (a) Ratings in general. Subject to paragraphs (b... performance under the lending, investment and service tests, the community development test, the small savings...

Using probability modelling and genetic parentage assignment to test the role of local mate availability in mating system variation.

Science.gov (United States)

Blyton, Michaela D J; Banks, Sam C; Peakall, Rod; Lindenmayer, David B

2012-02-01

The formal testing of mating system theories with empirical data is important for evaluating the relative importance of different processes in shaping mating systems in wild populations. Here, we present a generally applicable probability modelling framework to test the role of local mate availability in determining a population's level of genetic monogamy. We provide a significance test for detecting departures in observed mating patterns from model expectations based on mate availability alone, allowing the presence and direction of behavioural effects to be inferred. The assessment of mate availability can be flexible and in this study it was based on population density, sex ratio and spatial arrangement. This approach provides a useful tool for (1) isolating the effect of mate availability in variable mating systems and (2) in combination with genetic parentage analyses, gaining insights into the nature of mating behaviours in elusive species. To illustrate this modelling approach, we have applied it to investigate the variable mating system of the mountain brushtail possum (Trichosurus cunninghami) and compared the model expectations with the outcomes of genetic parentage analysis over an 18-year study. The observed level of monogamy was higher than predicted under the model. Thus, behavioural traits, such as mate guarding or selective mate choice, may increase the population level of monogamy. We show that combining genetic parentage data with probability modelling can facilitate an improved understanding of the complex interactions between behavioural adaptations and demographic dynamics in driving mating system variation. © 2011 Blackwell Publishing Ltd.

A Comparative Study of Fuzzy Logic, Genetic Algorithm, and Gradient-Genetic Algorithm Optimization Methods for Solving the Unit Commitment Problem

Directory of Open Access Journals (Sweden)

Sahbi Marrouchi

2014-01-01

Full Text Available Due to the continuous increase of the population and the perpetual progress of industry, the energy management presents nowadays a relevant topic that concerns researchers in electrical engineering. Indeed, in order to establish a good exploitation of the electrical grid, it is necessary to solve technical and economic problems. This can only be done through the resolution of the Unit Commitment Problem. Unit Commitment Problem allows optimizing the combination of the production units’ states and determining their production planning, in order to satisfy the expected consumption with minimal cost during a specified period which varies usually from 24 hours to one week. However, each production unit has some constraints that make this problem complex, combinatorial, and nonlinear. This paper presents a comparative study between a strategy based on hybrid gradient-genetic algorithm method and two strategies based on metaheuristic methods, fuzzy logic, and genetic algorithm, in order to predict the combinations and the unit commitment scheduling of each production unit in one side and to minimize the total production cost in the other side. To test the performance of the optimization proposed strategies, strategies have been applied to the IEEE electrical network 14 busses and the obtained results are very promising.

Privacy-Preserving Task Assignment in Spatial Crowdsourcing

KAUST Repository

Liu, An

2017-09-20

With the progress of mobile devices and wireless networks, spatial crowdsourcing (SC) is emerging as a promising approach for problem solving. In SC, spatial tasks are assigned to and performed by a set of human workers. To enable effective task assignment, however, both workers and task requesters are required to disclose their locations to untrusted SC systems. In this paper, we study the problem of assigning workers to tasks in a way that location privacy for both workers and task requesters is preserved. We first combine the Paillier cryptosystem with Yao’s garbled circuits to construct a secure protocol that assigns the nearest worker to a task. Considering that this protocol cannot scale to a large number of workers, we then make use of Geohash, a hierarchical spatial index to design a more efficient protocol that can securely find approximate nearest workers. We theoretically show that these two protocols are secure against semi-honest adversaries. Through extensive experiments on two real-world datasets, we demonstrate the efficiency and effectiveness of our protocols.

Valuing the benefits of genetic testing for retinitis pigmentosa: a pilot application of the contingent valuation method.

Science.gov (United States)

Eden, Martin; Payne, Katherine; Combs, Ryan M; Hall, Georgina; McAllister, Marion; Black, Graeme C M

2013-08-01

Technological advances present an opportunity for more people with, or at risk of, developing retinitis pigmentosa (RP) to be offered genetic testing. Valuation of these tests using current evaluative frameworks is problematic since benefits may be derived from diagnostic information rather than improvements in health. This pilot study aimed to explore if contingent valuation method (CVM) can be used to value the benefits of genetic testing for RP. CVM was used to elicit willingness-to-pay (WTP) values for (1) genetic counselling and (2) genetic counselling with genetic testing. Telephone and face-to-face interviews with a purposive sample of individuals with (n=25), and without (n=27), prior experience of RP were used to explore the feasibility and validity of CVM in this context. Faced with a hypothetical scenario, the majority of participants stated that they would seek genetic counselling and testing in the context of RP. Between participant groups, respondents offered similar justifications for stated WTP values. Overall stated WTP was higher for genetic counselling plus testing (median=£524.00) compared with counselling alone (median=£224.50). Between-group differences in stated WTP were statistically significant; participants with prior knowledge of the condition were willing to pay more for genetic ophthalmology services. Participants were able to attach a monetary value to the perceived potential benefit that genetic testing offered regardless of prior experience of the condition. This exploratory work represents an important step towards evaluating these services using formal cost-benefit analysis.

Genetics education for non-genetic health care professionals in the Netherlands

NARCIS (Netherlands)

Plass, Anne Marie C.; Baars, Marieke J. H.; Beemer, Frits A.; ten Kate, Leo P.

2006-01-01

OBJECTIVE: The aim of the present study was to investigate whether medical care providers in the Netherlands are adequately educated in genetics by collecting information about the current state of genetics education of non-genetics health care professionals. METHOD: The curricula of the 8

A second generation genetic map for rainbow trout (Oncorhynchus mykiss

Directory of Open Access Journals (Sweden)

Gahr Scott A

2008-11-01

Full Text Available Abstract Background Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species. Results A genetic map ordering 1124 microsatellite loci spanning a sex-averaged distance of 2927.10 cM (Kosambi and having 2.6 cM resolution was constructed by genotyping 10 parents and 150 offspring from the National Center for Cool and Cold Water Aquaculture (NCCCWA reference family mapping panel. Microsatellite markers, representing pairs of loci resulting from an evolutionarily recent whole genome duplication event, identified 180 duplicated regions within the rainbow trout genome. Microsatellites associated with genes through expressed sequence tags or bacterial artificial chromosomes produced comparative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology for 199 loci. Conclusion The second generation NCCCWA genetic map provides an increased microsatellite marker density and quantifies differences in recombination rate between the sexes in outbred populations. It has the potential to integrate with cytogenetic and other physical maps, identifying paralogous regions of the rainbow trout genome arising from the evolutionarily recent genome duplication event, and

Establishment of an efficient genetic transformation method in Dunaliella tertiolecta mediated by Agrobacterium tumefaciens.

Science.gov (United States)

Norzagaray-Valenzuela, Claudia D; Germán-Báez, Lourdes J; Valdez-Flores, Marco A; Hernández-Verdugo, Sergio; Shelton, Luke M; Valdez-Ortiz, Angel

2018-05-16

Microalgae are photosynthetic microorganisms widely used for the production of highly valued compounds, and recently they have been shown to be promising as a system for the heterologous expression of proteins. Several transformation methods have been successfully developed, from which the Agrobacterium tumefaciens-mediated method remains the most promising. However, microalgae transformation efficiency by A. tumefaciens is shown to vary depending on several transformation conditions. The present study aimed to establish an efficient genetic transformation system in the green microalgae Dunaliella tertiolecta using the A. tumefaciens method. The parameters assessed were the infection medium, the concentration of the A. tumefaciens and co-culture time. As a preliminary screening, the expression of the gusA gene and the viability of transformed cells were evaluated and used to calculate a novel parameter called Transformation Efficiency Index (TEI). The statistical analysis of TEI values showed five treatments with the highest gusA gene expression. To ensure stable transformation, transformed colonies were cultured on selective medium using hygromycin B and the DNA of resistant colonies were extracted after five subcultures and molecularly analyzed by PCR. Results revealed that treatments which use solid infection medium, A. tumefaciens OD 600  = 0.5 and co-culture times of 72 h exhibited the highest percentage of stable gusA expression. Overall, this study established an efficient, optimized A. tumefaciens-mediated genetic transformation of D. tertiolecta, which represents a relatively easy procedure with no expensive equipment required. This simple and efficient protocol opens the possibility for further genetic manipulation of this commercially-important microalgae for biotechnological applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Generalized characteristic ratios assignment for commensurate fractional order systems with one zero.

Science.gov (United States)

Tabatabaei, Mohammad

2017-07-01

In this paper, a new method for determination of the desired characteristic equation and zero location of commensurate fractional order systems is presented. The concept of the characteristic ratio is extended for zero-including commensurate fractional order systems. The generalized version of characteristic ratios is defined such that the time-scaling property of characteristic ratios is also preserved. The monotonicity of the magnitude frequency response is employed to assign the generalized characteristic ratios for commensurate fractional order transfer functions with one zero. A simple pattern for characteristic ratios is proposed to reach a non-overshooting step response. Then, the proposed pattern is revisited to reach a low overshoot (say for example 2%) step response. Finally, zero-including controllers such as fractional order PI or lag (lead) controllers are designed using generalized characteristic ratios assignment method. Numerical simulations are provided to show the efficiency of the so designed controllers. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Molecular marker systems for Oenothera genetics.

Science.gov (United States)

Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

2008-11-01

The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

Consistent assignment of nursing staff to residents in nursing homes: a critical review of conceptual and methodological issues.

Science.gov (United States)

Roberts, Tonya; Nolet, Kimberly; Bowers, Barbara

2015-06-01

Consistent assignment of nursing staff to residents is promoted by a number of national organizations as a strategy for improving nursing home quality and is included in pay for performance schedules in several states. However, research has shown inconsistent effects of consistent assignment on quality outcomes. In order to advance the state of the science of research on consistent assignment and inform current practice and policy, a literature review was conducted to critique conceptual and methodological understandings of consistent assignment. Twenty original research reports of consistent assignment in nursing homes were found through a variety of search strategies. Consistent assignment was conceptualized and operationalized in multiple ways with little overlap from study to study. There was a lack of established methods to measure consistent assignment. Methodological limitations included a lack of control and statistical analyses of group differences in experimental-level studies, small sample sizes, lack of attention to confounds in multicomponent interventions, and outcomes that were not theoretically linked. Future research should focus on developing a conceptual understanding of consistent assignment focused on definition, measurement, and links to outcomes. To inform current policies, testing consistent assignment should include attention to contexts within and levels at which it is most effective. Published by Oxford University Press on behalf of the Gerontological Society of America 2013.

Development and interlaboratory validation of quantitative polymerase chain reaction method for screening analysis of genetically modified soybeans.

Science.gov (United States)

Takabatake, Reona; Onishi, Mari; Koiwa, Tomohiro; Futo, Satoshi; Minegishi, Yasutaka; Akiyama, Hiroshi; Teshima, Reiko; Kurashima, Takeyo; Mano, Junichi; Furui, Satoshi; Kitta, Kazumi

2013-01-01

A novel real-time polymerase chain reaction (PCR)-based quantitative screening method was developed for three genetically modified soybeans: RRS, A2704-12, and MON89788. The 35S promoter (P35S) of cauliflower mosaic virus is introduced into RRS and A2704-12 but not MON89788. We then designed a screening method comprised of the combination of the quantification of P35S and the event-specific quantification of MON89788. The conversion factor (Cf) required to convert the amount of a genetically modified organism (GMO) from a copy number ratio to a weight ratio was determined experimentally. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDR), respectively. The determined RSDR values for the method were less than 25% for both targets. We consider that the developed method would be suitable for the simple detection and approximate quantification of GMO.

Statistical Methods for Population Genetic Inference Based on Low-Depth Sequencing Data from Modern and Ancient DNA

DEFF Research Database (Denmark)

Korneliussen, Thorfinn Sand

Due to the recent advances in DNA sequencing technology genomic data are being generated at an unprecedented rate and we are gaining access to entire genomes at population level. The technology does, however, not give direct access to the genetic variation and the many levels of preprocessing...... that is required before being able to make inferences from the data introduces multiple levels of uncertainty, especially for low-depth data. Therefore methods that take into account the inherent uncertainty are needed for being able to make robust inferences in the downstream analysis of such data. This poses...... a problem for a range of key summary statistics within populations genetics where existing methods are based on the assumption that the true genotypes are known. Motivated by this I present: 1) a new method for the estimation of relatedness between pairs of individuals, 2) a new method for estimating...

A novel strategy for NMR resonance assignment and protein structure determination

International Nuclear Information System (INIS)

Lemak, Alexander; Gutmanas, Aleksandras; Chitayat, Seth; Karra, Murthy; Farès, Christophe; Sunnerhagen, Maria; Arrowsmith, Cheryl H.

2011-01-01

The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

Insect chromosomes preparing methods for genetic researches

African Journals Online (AJOL)

STORAGESEVER

2009-01-05

Jan 5, 2009 ... Ankara University Faculty of Science Department of Biology Tandogan Ankara Turkey. Accepted 21 ... intraspecific level; and the genetics evolution of the groups of .... Animal cytology and evolution Cambridge University. Press.

Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods

Energy Technology Data Exchange (ETDEWEB)

Penzel, Susanne; Smith, Albert A.; Agarwal, Vipin; Hunkeler, Andreas [ETH Zürich, Physical Chemistry (Switzerland); Org, Mai-Liis; Samoson, Ago, E-mail: ago.samoson@ttu.ee [Tallinn University of Technology, NMR Instituut, Tartu Teadus, Tehnomeedikum (Estonia); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Université de Lyon 1, Institut de Biologie et Chimie des Protéines (France); Ernst, Matthias, E-mail: maer@ethz.ch; Meier, Beat H., E-mail: beme@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

2015-10-15

We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T{sub 2}′ times and a site-specific comparison of T{sub 2}′ at 93 kHz versus 60 kHz MAS frequency. A quantitative analysis of transfer efficiencies of building blocks, as they are used for typical 3D experiments, was performed. To do this, we compared dipolar-coupling and J-coupling based transfer steps. The building blocks were then combined into 3D experiments for sequential resonance assignment, where we evaluated signal-to-noise ratio and information content of the different 3D spectra in order to identify the best assignment strategy. Based on this comparison, six experiments were selected to optimally assign the model protein ubiquitin, solely using spectra acquired at 93 kHz MAS. Within 3 days of instrument time, the required spectra were recorded from which the backbone resonances have been assigned to over 96 %.

Dual earners’ willingness to accept an international assignment.

NARCIS (Netherlands)

van der Velde, E.G.; Bossink, C.J.H.; Jansen, P.G.W.

2005-01-01

Multinational organisations experience difficulties in finding managers willing to accept international assignments. This study has therefore focused on factors that can predict males' and females' willingness to accept international assignments, or to follow their partners on international

Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens

DEFF Research Database (Denmark)

Timms, Richard T.; Menzies, Sam A.; Tchasovnikarova, Iva A.

2016-01-01

The application of forward genetic screens to cultured human cells represents a powerful method to study gene function. The repurposing of the bacterial CRISPR/Cas9 system provides an effective method to disrupt gene function in mammalian cells, and has been applied to genome-wide screens. Here, we...... compare the efficacy of genome-wide CRISPR/Cas9-mediated forward genetic screens versus gene-trap mutagenesis screens in haploid human cells, which represent the existing ‘gold standard’ method. This head-to-head comparison aimed to identify genes required for the endoplasmic reticulum....../3-associated disulphide reductase. Genome-wide CRISPR/Cas9-mediated screens together with haploid genetic screens provide a powerful addition to the forward genetic toolbox....

Fixed channel assignment in cellular communication systems considering the whole set of packed patterns

DEFF Research Database (Denmark)

Borges, Pedro Manuel F. C.; Vidal, Rene Victor Valqui

2000-01-01

This paper addresses the problem of fixed channel assignment in cellular communication systems with nonuniform traffic distribution. The objective of the channel assignment is to minimise the average blocking probability. Methods for finding a good allocation can be based on first building a number...... of flexibility when dealing with extensions to the problem. A neighbouring structure was used, that facilitated the calculations while still allowing for the search in the entire solution space. A summary of extensive numerical experiments is presented. The outcome is an improvement over previous results...

Current PCR Methods for the Detection, Identification and Quantification of Genetically Modified Organisms(GMOs: a Brief Review

Directory of Open Access Journals (Sweden)

Gadani F

2014-12-01

Full Text Available Analytical methods based on the polymerase chain reaction (PCR technology are increasingly used for the detection of deoxyribonucleic acid (DNA sequences associated with genetically modified organisms (GMOs. In the European Union and Switzerland, mandatory labeling of novel foods and food ingredients consisting of, or containing GMOs is required according to food regulations and is triggered by the presence of newly introduced foreign DNA sequences, or newly expressed proteins. In order to meet regulatory and consumer demand, numerous PCR-based methods have been developed which can detect, identify and quantify GMOs in agricultural crops, food and feed. Moreover, the determination of genetic identity allows for segregation and traceability (identity preservation throughout the supply chain of GM crops that have been enhanced with value-added quality traits. Prerequisites for GMO detection include a minimum amount of the target gene and prior knowledge of the type of genetic modification, such as virus or insect resistance traits, including controlling elements (promoters and terminators. Moreover, DNA extraction and purification is a critical step for the preparation of PCR-quality samples, particularly for processed agricultural crops such as tobacco. This paper reviews the state-of-the-art of PCR-based method development for the qualitative and quantitative determination and identification of GMOs, and includes a short summary of official and validated GMO detection methods.

Mitigating the impact of the DESI fiber assignment on galaxy clustering

Energy Technology Data Exchange (ETDEWEB)

Burden, Angela; Padmanabhan, Nikhil [Department of Physics, Yale University, New Haven, CT 06511 (United States); Cahn, Robert N.; White, Martin J. [Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Samushia, Lado, E-mail: angela.burden@yale.edu, E-mail: nikhil.padmanabhan@yale.edu, E-mail: rncahn@lbl.gov, E-mail: mwhite@berkeley.edu, E-mail: lado@phys.ksu.edu [Physics Department, Kansas State University, 116 Cardwell Hall, 1228 N. 17th St. Manhattan, KS 66506 (United States)

2017-03-01

We present a simple strategy to mitigate the impact of an incomplete spectroscopic redshift galaxy sample as a result of fiber assignment and survey tiling. The method has been designed for the Dark Energy Spectroscopic Instrument (DESI) galaxy survey but may have applications beyond this. We propose a modification to the usual correlation function that nulls the almost purely angular modes affected by survey incompleteness due to fiber assignment. Predictions of this modified statistic can be calculated given a model of the two point correlation function. The new statistic can be computed with a slight modification to the data catalogues input to the standard correlation function code and does not incur any additional computational time. Finally we show that the spherically averaged baryon acoustic oscillation signal is not biased by the new statistic.

Developing a Novel Multi-objective Programming Model for Personnel Assignment Problem

Directory of Open Access Journals (Sweden)

Mehdi Seifbarghy

2014-05-01

Full Text Available The assignment of personnel to the right positions in order to increase organization's performance is one of the most crucial tasks in human resource management. In this paper, personnel assignment problem is formulated as a multi-objective binary integer programming model in which skills, level of satisfaction and training cost of personnel are considered simultaneously in productive company. The purpose of this model is to obtain the best matching between candidates and positions. In this model, a set of methods such as a group analytic hierarchy process (GAHP, Shannon entropy, coefficient of variation (CV and fuzzy logic are used to calculate the weights of evaluation criteria, weights of position and coefficient of objective functions. This proposed model can rationalize the subjective judgments of decision makers with mathematic models.

Task assignment and coaching

NARCIS (Netherlands)

Dominguez-Martinez, S.

2009-01-01

An important task of a manager is to motivate her subordinates. One way in which a manager can give incentives to junior employees is through the assignment of tasks. How a manager allocates tasks in an organization, provides information to the junior employees about his ability. Without coaching

Toward efficient task assignment and motion planning for large-scale underwater missions

Directory of Open Access Journals (Sweden)

Somaiyeh MahmoudZadeh

2016-10-01

Full Text Available An autonomous underwater vehicle needs to possess a certain degree of autonomy for any particular underwater mission to fulfil the mission objectives successfully and ensure its safety in all stages of the mission in a large-scale operating field. In this article, a novel combinatorial conflict-free task assignment strategy, consisting of an interactive engagement of a local path planner and an adaptive global route planner, is introduced. The method takes advantage of the heuristic search potency of the particle swarm optimization algorithm to address the discrete nature of routing-task assignment approach and the complexity of nondeterministic polynomial-time-hard path planning problem. The proposed hybrid method is highly efficient as a consequence of its reactive guidance framework that guarantees successful completion of missions particularly in cluttered environments. To examine the performance of the method in a context of mission productivity, mission time management, and vehicle safety, a series of simulation studies are undertaken. The results of simulations declare that the proposed method is reliable and robust, particularly in dealing with uncertainties, and it can significantly enhance the level of a vehicle’s autonomy by relying on its reactive nature and capability of providing fast feasible solutions.

Genetically Modified GMDH Method with Cloning

Czech Academy of Sciences Publication Activity Database

Jiřina, Marcel; Jiřina jr., M.

2007-01-01

Roč. 28, - (2007), s. 29-37 ISSN 1870-4069. [NNAM 2007. International Conference on Neural Networks and Associative Memories /2./. Mexico City, 04.11.2007-09.11.2007] R&D Projects: GA MŠk(CZ) 1M0567 Institutional research plan: CEZ:AV0Z10300504 Keywords : GMDH neural network * genetic selection * cloning * Machine Learning Repository Subject RIV: BA - General Mathematics

Tracking the Genetic Stability of a Honey Bee (Hymenoptera: Apidae) Breeding Program With Genetic Markers.

Science.gov (United States)

Bourgeois, Lelania; Beaman, Lorraine

2017-08-01

A genetic stock identification (GSI) assay was developed in 2008 to distinguish Russian honey bees from other honey bee stocks that are commercially produced in the United States. Probability of assignment (POA) values have been collected and maintained since the stock release in 2008 to the Russian Honey Bee Breeders Association. These data were used to assess stability of the breeding program and the diversity levels of the contemporary breeding stock through comparison of POA values and genetic diversity parameters from the initial release to current values. POA values fluctuated throughout 2010-2016, but have recovered to statistically similar levels in 2016 (POA(2010) = 0.82, POA(2016) = 0.74; P = 0.33). Genetic diversity parameters (i.e., allelic richness and gene diversity) in 2016 also remained at similar levels when compared to those in 2010. Estimates of genetic structure revealed stability (FST(2009/2016) = 0.0058) with a small increase in the estimate of the inbreeding coefficient (FIS(2010) = 0.078, FIS(2016) = 0.149). The relationship among breeding lines, based on genetic distance measurement, was similar in 2008 and 2016 populations, but with increased homogeneity among lines (i.e., decreased genetic distance). This was expected based on the closed breeding system used for Russian honey bees. The successful application of the GSI assay in a commercial breeding program demonstrates the utility and stability of such technology to contribute to and monitor the genetic integrity of a breeding stock of an insect species. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by US Government employees and is in the public domain in the US.

The Matrix Method of Representation, Analysis and Classification of Long Genetic Sequences

Directory of Open Access Journals (Sweden)

Ivan V. Stepanyan

2017-01-01

Full Text Available The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of presenting each sequence in the form of three digital binary sequences. This method uses a set of symmetries of biochemical attributes of nucleotides. It also uses the possibility of presentation of every whole set of N-mers as one of the members of a Kronecker family of genetic matrices. With this method, a long nucleotide sequence can be visually represented as an individual fractal-like mosaic or another regular mosaic of binary type. In contrast to natural nucleotide sequences, artificial random sequences give non-regular patterns. Examples of binary mosaics of long nucleotide sequences are shown, including cases of human chromosomes and penicillins. The obtained results are then discussed.

"The Theory was Beautiful Indeed": Rise, Fall and Circulation of Maximizing Methods in Population Genetics (1930-1980).

Science.gov (United States)

Grodwohl, Jean-Baptiste

2017-08-01

Describing the theoretical population geneticists of the 1960s, Joseph Felsenstein reminisced: "our central obsession was finding out what function evolution would try to maximize. Population geneticists used to think, following Sewall Wright, that mean relative fitness, W, would be maximized by natural selection" (Felsenstein 2000). The present paper describes the genesis, diffusion and fall of this "obsession", by giving a biography of the mean fitness function in population genetics. This modeling method devised by Sewall Wright in the 1930s found its heyday in the late 1950s and early 1960s, in the wake of Motoo Kimura's and Richard Lewontin's works. It seemed a reliable guide in the mathematical study of deterministic effects (the study of natural selection in populations of infinite size, with no drift), leading to powerful generalizations presenting law-like properties. Progress in population genetics theory, it then seemed, would come from the application of this method to the study of systems with several genes. This ambition came to a halt in the context of the influential objections made by the Australian mathematician Patrick Moran in 1963. These objections triggered a controversy between mathematically- and biologically-inclined geneticists, with affected both the formal standards and the aims of population genetics as a science. Over the course of the 1960s, the mean fitness method withered with the ambition of developing the deterministic theory. The mathematical theory became increasingly complex. Kimura re-focused his modeling work on the theory of random processes; as a result of his computer simulations, Lewontin became the staunchest critic of maximizing principles in evolutionary biology. The mean fitness method then migrated to other research areas, being refashioned and used in evolutionary quantitative genetics and behavioral ecology.

Investigating the Correlation Between Pharmacy Student Performance on the Health Science Reasoning Test and a Critical Thinking Assignment.

Science.gov (United States)

Nornoo, Adwoa O; Jackson, Jonathan; Axtell, Samantha

2017-03-25

Objective. To determine whether there is a correlation between pharmacy students' scores on the Health Science Reasoning Test (HSRT) and their grade on a package insert assignment designed to assess critical thinking. Methods. The HSRT was administered to first-year pharmacy students during a critical-thinking course in the spring semester. In the same semester, a required package insert assignment was completed in a pharmacokinetics course. To determine whether there was a relationship between HSRT scores and grades on the assignment, a Spearman's rho correlation test was performed. Results. A very weak but significant positive correlation was found between students' grades on the assignment and their overall HSRT score (r=0.19, p critical-thinking skills in pharmacy students.

A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis.

Science.gov (United States)

Mimee, Benjamin; Duceppe, Marc-Olivier; Véronneau, Pierre-Yves; Lafond-Lapalme, Joël; Jean, Martine; Belzile, François; Bélair, Guy

2015-11-01

Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species. © 2015 Her Majesty the Queen in Right of Canada Molecular Ecology Resources © 2015 John Wiley & Sons Ltd Reproduced with the permission of the Minister of Agriculture and Agri-food.

Consequences of population topology for studying gene flow using link-based landscape genetic methods.

Science.gov (United States)

van Strien, Maarten J

2017-07-01

Many landscape genetic studies aim to determine the effect of landscape on gene flow between populations. These studies frequently employ link-based methods that relate pairwise measures of historical gene flow to measures of the landscape and the geographical distance between populations. However, apart from landscape and distance, there is a third important factor that can influence historical gene flow, that is, population topology (i.e., the arrangement of populations throughout a landscape). As the population topology is determined in part by the landscape configuration, I argue that it should play a more prominent role in landscape genetics. Making use of existing literature and theoretical examples, I discuss how population topology can influence results in landscape genetic studies and how it can be taken into account to improve the accuracy of these results. In support of my arguments, I have performed a literature review of landscape genetic studies published during the first half of 2015 as well as several computer simulations of gene flow between populations. First, I argue why one should carefully consider which population pairs should be included in link-based analyses. Second, I discuss several ways in which the population topology can be incorporated in response and explanatory variables. Third, I outline why it is important to sample populations in such a way that a good representation of the population topology is obtained. Fourth, I discuss how statistical testing for link-based approaches could be influenced by the population topology. I conclude the article with six recommendations geared toward better incorporating population topology in link-based landscape genetic studies.

A Novel Technique for Steganography Method Based on Improved Genetic Algorithm Optimization in Spatial Domain

Directory of Open Access Journals (Sweden)

M. Soleimanpour-moghadam

2013-06-01

Full Text Available This paper devotes itself to the study of secret message delivery using cover image and introduces a novel steganographic technique based on genetic algorithm to find a near-optimum structure for the pair-wise least-significant-bit (LSB matching scheme. A survey of the related literatures shows that the LSB matching method developed by Mielikainen, employs a binary function to reduce the number of changes of LSB values. This method verifiably reduces the probability of detection and also improves the visual quality of stego images. So, our proposal draws on the Mielikainen's technique to present an enhanced dual-state scoring model, structured upon genetic algorithm which assesses the performance of different orders for LSB matching and searches for a near-optimum solution among all the permutation orders. Experimental results confirm superiority of the new approach compared to the Mielikainen’s pair-wise LSB matching scheme.

TMTI Task 1.6 Genetic Engineering Methods and Detection

Energy Technology Data Exchange (ETDEWEB)

Slezak, T; Lenhoff, R; Allen, J; Borucki, M; Vitalis, E; Gardner, S

2009-12-04

A large number of GE techniques can be adapted from other microorganisms to biothreat bacteria and viruses. Detection of GE in a microorganism increases in difficulty as the size of the genetic change decreases. In addition to the size of the engineered change, the consensus genomic sequence of the microorganism can impact the difficulty of detecting an engineered change in genomes that are highly variable from strain to strain. This problem will require comprehensive databases of whole genome sequences for more genetically variable biothreat bacteria and viruses. Preliminary work with microarrays for detecting synthetic elements or virulence genes and analytic bioinformatic approaches for whole genome sequence comparison to detect genetic engineering show promise for attacking this difficult problem but a large amount of future work remains.

Replacement method and enhanced replacement method versus the genetic algorithm approach for the selection of molecular descriptors in QSPR/QSAR theories.

Science.gov (United States)

Mercader, Andrew G; Duchowicz, Pablo R; Fernández, Francisco M; Castro, Eduardo A

2010-09-27

We compare three methods for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. On the one hand is our enhanced replacement method (ERM) and on the other is the simpler replacement method (RM) and the genetic algorithm (GA). These methods avoid the impracticable full search for optimal variables in large sets of molecular descriptors. Present results for 10 different experimental databases suggest that the ERM is clearly preferable to the GA that is slightly better than the RM. However, the latter approach requires the smallest amount of linear regressions and, consequently, the lowest computation time.

The effect of reading assignments in guided inquiry learning on students’ critical thinking skills

Science.gov (United States)

Syarkowi, A.

2018-05-01

The purpose of this study was to determine the effect of reading assignment in guided inquiry learning on senior high school students’ critical thinking skills. The research method which was used in this research was quasi-experiment research method with reading task as the treatment. Topic of inquiry process was Kirchhoff law. The instrument was used for this research was 25 multiple choice interpretive exercises with justification. The multiple choice test was divided on 3 categories such as involve basic clarification, the bases for a decision and inference skills. The result of significance test proved the improvement of students’ critical thinking skills of experiment class was significantly higher when compared with the control class, so it could be concluded that reading assignment can improve students’ critical thinking skills.

Conformational Stability, Structural Parameters And Vibrational Assignments of Allantoin

International Nuclear Information System (INIS)

Haman, S.

2008-01-01

Allantoin 2,5-Dioxo-4-imidazolinyl) urea , the diureide of glyoxylic acid, is a crystallisable oxidation product of uric acid found in allantoic and amniotic fluids, in fetal urine and in many plants. It is a healing, moisturizing, soothing and anti-irritating, keratolytic and non-toxic agent useful in dermatological, cosmetic and veterinary preparation. The optimized geometries and energies of the low-energy conformers of allantoin have been calculated using density functional theory (Daft) method. The calculations were performed with Beck's nonlocal three-parameter hybrid functional in combination with the Lee, Yang, and Parr correlation functional (By-play) using the 6-311++G(d,p) basis set. We calculated the infrared frequencies and intensities of the most stable conformers in order to assist in the assignment of the vibrational bands in the experimental spectrum. The B3LYP/6-311+G(d,p) harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported

Effortless assignment with 4D covariance sequential correlation maps.

Science.gov (United States)

Harden, Bradley J; Mishra, Subrata H; Frueh, Dominique P

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase. Copyright © 2015 Elsevier Inc. All rights reserved.

Justifying the Use of Internet Sources in School Assignments on Controversial Issues

Science.gov (United States)

Mikkonen, Teemu

2018-01-01

Introduction: This study concerns students' criteria in the evaluation of Internet sources for a school assignment requiring reflections on a controversial issue. The findings are elaborated by analysing students' discursive accounts in justifying the use or non-use of sources. Method: The interview data was collected in a Finnish upper secondary…

Accurate continuous geographic assignment from low- to high-density SNP data

DEFF Research Database (Denmark)

Guillot, Gilles; Jónsson, Hákon; Hinge, Antoine

2016-01-01

of georeferenced genotypes. Statistical inference under this model can be implemented within the theoretical framework of Integrated Nested Laplace Approximation (INLA), which represents one of the major recent breakthroughs in statistics, devoid of Monte Carlo simulations. We compare the performance of our method...... and SPA in a simulation framework. We highlight the accuracy and limits of continuous spatial assignment methods at various scales by analyzing genotype datasets from a diversity of species, including Florida scrub jay birds Aphelocoma coerulescens, Arabidopsis thaliana and humans, representing 41 to 197...

Development and validation of a 48-target analytical method for high-throughput monitoring of genetically modified organisms.

Science.gov (United States)

Li, Xiaofei; Wu, Yuhua; Li, Jun; Li, Yunjing; Long, Likun; Li, Feiwu; Wu, Gang

2015-01-05

The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection.

Regional Genetic Structuring and Evolutionary History of the Impala Aepyceros melampus

DEFF Research Database (Denmark)

Lorenzen, Eline Deirdre; Arctander, Peter; Siegismund, Hans Redlef

2006-01-01

Samples of 162 impala antelope (Aepyceros melampus) from throughout its distribution range in sub-Saharan Africa were surveyed using eight polymorphic microsatellite loci. Furthermore, 155 previously published mitochondrial DNA (mtDNA) sequences from the same localities were reanalyzed. Two...... subspecies of impala are presently recognized-the isolated black-faced impala (Aepyceros melampus petersi) in southwest Africa and the common impala (Aepyceros melampus melampus) abundant in southern and east Africa. All tests performed indicated significant genetic differentiation at the subspecific level....... Furthermore, individual-based analyses split the common impala subspecies into two distinct genetic groups, conforming with regional geographic affiliation to southern or east Africa. This was supported by assignment tests, genetic distance measures, pairwise values, and analysis of molecular variance. We...

How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?

Science.gov (United States)

Veturi, Yogasudha; Ritchie, Marylyn D

2018-01-01

Transcriptome-wide association studies (TWAS) have recently been employed as an approach that can draw upon the advantages of genome-wide association studies (GWAS) and gene expression studies to identify genes associated with complex traits. Unlike standard GWAS, summary level data suffices for TWAS and offers improved statistical power. Two popular TWAS methods include either (a) imputing the cis genetic component of gene expression from smaller sized studies (using multi-SNP prediction or MP) into much larger effective sample sizes afforded by GWAS - TWAS-MP or (b) using summary-based Mendelian randomization - TWAS-SMR. Although these methods have been effective at detecting functional variants, it remains unclear how extensive variability in the genetic architecture of complex traits and diseases impacts TWAS results. Our goal was to investigate the different scenarios under which these methods yielded enough power to detect significant expression-trait associations. In this study, we conducted extensive simulations based on 6000 randomly chosen, unrelated Caucasian males from Geisinger's MyCode population to compare the power to detect cis expression-trait associations (within 500 kb of a gene) using the above-described approaches. To test TWAS across varying genetic backgrounds we simulated gene expression and phenotype using different quantitative trait loci per gene and cis-expression /trait heritability under genetic models that differentiate the effect of causality from that of pleiotropy. For each gene, on a training set ranging from 100 to 1000 individuals, we either (a) estimated regression coefficients with gene expression as the response using five different methods: LASSO, elastic net, Bayesian LASSO, Bayesian spike-slab, and Bayesian ridge regression or (b) performed eQTL analysis. We then sampled with replacement 50,000, 150,000, and 300,000 individuals respectively from the testing set of the remaining 5000 individuals and conducted GWAS on each

MEB 2013, Regulation for Administrator Assignment and Relocation Based On the Opinions of Administrators

Directory of Open Access Journals (Sweden)

Soner DOĞAN

2014-04-01

Full Text Available In this study; it is aimed to determine the opinions of the institution managers concerning the Regulation for Administrator Assignment and Relocation dated February 28, 2013, the scoring criteria in the regulation and the disturbances experienced in the application process of the regulation. The study is carried out in accordance with the phenomenological pattern through qualitative research methods. The participants were determined with the criterion sampling method which is one of the purposeful sampling methods. The study group of the research is composed of the eight managers serving in a province. In the study, a semi-structured interview form was used as data collection tool. In the interpretation process of the interviews, the inductive descriptive analysis, the content analysis and the constant comparison technique were used. Three main themes have come out regarding the result of the data analysis process of assigning the administrators, the combining of the different types of institutions and the application of the forced relocation.

Calibrated peer review assignments for the earth sciences

Science.gov (United States)

Rudd, J.A.; Wang, V.Z.; Cervato, C.; Ridky, R.W.

2009-01-01

Calibrated Peer Review ??? (CPR), a web-based instructional tool developed as part of the National Science Foundation reform initiatives in undergraduate science education, allows instructors to incorporate multiple writing assignments in large courses without overwhelming the instructor. This study reports successful implementation of CPR in a large, introductory geology course and student learning of geoscience content. For each CPR assignment in this study, students studied web-based and paper resources, wrote an essay, and reviewed seven essays (three from the instructor, three from peers, and their own) on the topic. Although many students expressed negative attitudes and concerns, particularly about the peer review process of this innovative instructional approach, they also recognized the learning potential of completing CPR assignments. Comparing instruction on earthquakes and plate boundaries using a CPR assignment vs. an instructional video lecture and homework essay with extensive instructor feedback, students mastered more content via CPR instruction.

Subcarrier Group Assignment for MC-CDMA Wireless Networks

Directory of Open Access Journals (Sweden)

Le-Ngoc Tho

2007-01-01

Full Text Available Two interference-based subcarrier group assignment strategies in dynamic resource allocation are proposed for MC-CDMA wireless systems to achieve high throughput in a multicell environment. Least interfered group assignment (LIGA selects for each session the subcarrier group on which the user receives the minimum interference, while best channel ratio group assignment (BCRGA chooses the subcarrier group with the largest channel response-to-interference ratio. Both analytical framework and simulation model are developed for evaluation of throughput distribution of the proposed schemes. An iterative approach is devised to handle the complex interdependency between multicell interference profiles in the throughput analysis. Illustrative results show significant throughput improvement offered by the interference-based assignment schemes for MC-CDMA multicell wireless systems. In particular, under low loading conditions, LIGA renders the best performance. However, as the load increases BCRGA tends to offer superior performance.

Subcarrier Group Assignment for MC-CDMA Wireless Networks

Directory of Open Access Journals (Sweden)

Tho Le-Ngoc

2007-12-01

Full Text Available Two interference-based subcarrier group assignment strategies in dynamic resource allocation are proposed for MC-CDMA wireless systems to achieve high throughput in a multicell environment. Least interfered group assignment (LIGA selects for each session the subcarrier group on which the user receives the minimum interference, while best channel ratio group assignment (BCRGA chooses the subcarrier group with the largest channel response-to-interference ratio. Both analytical framework and simulation model are developed for evaluation of throughput distribution of the proposed schemes. An iterative approach is devised to handle the complex interdependency between multicell interference profiles in the throughput analysis. Illustrative results show significant throughput improvement offered by the interference-based assignment schemes for MC-CDMA multicell wireless systems. In particular, under low loading conditions, LIGA renders the best performance. However, as the load increases BCRGA tends to offer superior performance.

A New Waveform Signal Processing Method Based on Adaptive Clustering-Genetic Algorithms

International Nuclear Information System (INIS)

Noha Shaaban; Fukuzo Masuda; Hidetsugu Morota

2006-01-01

We present a fast digital signal processing method for numerical analysis of individual pulses from CdZnTe compound semiconductor detectors. Using Maxi-Mini Distance Algorithm and Genetic Algorithms based discrimination technique. A parametric approach has been used for classifying the discriminated waveforms into a set of clusters each has a similar signal shape with a corresponding pulse height spectrum. A corrected total pulse height spectrum was obtained by applying a normalization factor for the full energy peak for each cluster with a highly improvements in the energy spectrum characteristics. This method applied successfully for both simulated and real measured data, it can be applied to any detector suffers from signal shape variation. (authors)

Using a digital storytelling assignment to teach public health advocacy.

Science.gov (United States)

de Castro, A B; Levesque, Salem

2018-03-01

The need and expectation for advocacy is central to public health nursing practice. Advocacy efforts that effectively call attention to population health threats and promote the well-being of communities rely on strategies that deliver influential messaging. The digital story is a lay method to capture meaningful, impactful stories that can be used to advocate for public health concerns. Readily available, user-friendly digital technologies allow engagement in digital media production to create digital stories. This paper describes how digital story making can be utilized as an academic assignment to teach public health advocacy within an undergraduate nursing curriculum. Providing nursing students this artistic outlet can facilitate meeting academic learning goals, while also equipping them with creative skills that can be applied in future professional practice. Nursing educators can take advantage of institutional resources and campus culture to support the use of novel digital media assignments that facilitate application of advocacy concepts. © 2017 Wiley Periodicals, Inc.

Student generated assignments about electrical circuits in a computer simulation

NARCIS (Netherlands)

Vreman-de Olde, Cornelise; de Jong, Anthonius J.M.

2004-01-01

In this study we investigated the design of assignments by students as a knowledge-generating activity. Students were required to design assignments for 'other students' in a computer simulation environment about electrical circuits. Assignments consisted of a question, alternatives, and feedback on

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update.

Science.gov (United States)

Peakall, Rod; Smouse, Peter E

2012-10-01

GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'(ST), G''(ST), Jost's D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. rod.peakall@anu.edu.au.

Optimizing Properties of Aluminum-Based Nanocomposites by Genetic Algorithm Method

Directory of Open Access Journals (Sweden)

M.R. Dashtbayazi

2015-07-01

Full Text Available Based on molecular dynamics simulation results, a model was developed for determining elastic properties of aluminum nanocomposites reinforced with silicon carbide particles. Also, two models for prediction of density and price of nanocomposites were suggested. Then, optimal volume fraction of reinforcement was obtained by genetic algorithm method for the least density and price, and the highest elastic properties. Based on optimization results, the optimum volume fraction of reinforcement was obtained equal to 0.44. For this optimum volume fraction, optimum Young’s modulus, shear modulus, the price and the density of the nanocomposite were obtained 165.89 GPa, 111.37 GPa, 8.75 $/lb and 2.92 gr/cm3, respectively.

Patient Electronic Health Records as a Means to Approach Genetic Research in Gastroenterology.

Science.gov (United States)

Ananthakrishnan, Ashwin N; Lieberman, David

2015-10-01

Electronic health records (EHRs) are being increasingly utilized and form a unique source of extensive data gathered during routine clinical care. Through use of codified and free text concepts identified using clinical informatics tools, disease labels can be assigned with a high degree of accuracy. Analysis linking such EHR-assigned disease labels to a biospecimen repository has demonstrated that genetic associations identified in prospective cohorts can be replicated with adequate statistical power and novel phenotypic associations identified. In addition, genetic discovery research can be performed utilizing clinical, laboratory, and procedure data obtained during care. Challenges with such research include the need to tackle variability in quality and quantity of EHR data and importance of maintaining patient privacy and data security. With appropriate safeguards, this novel and emerging field of research offers considerable promise and potential to further scientific research in gastroenterology efficiently, cost-effectively, and with engagement of patients and communities. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

On pole structure assignment in linear systems

Czech Academy of Sciences Publication Activity Database

Loiseau, J.-J.; Zagalak, Petr

2009-01-01

Roč. 82, č. 7 (2009), s. 1179-1192 ISSN 0020-7179 R&D Projects: GA ČR(CZ) GA102/07/1596 Institutional research plan: CEZ:AV0Z10750506 Keywords : linear systems * linear state feedback * pole structure assignment Subject RIV: BC - Control Systems Theory Impact factor: 1.124, year: 2009 http://library.utia.cas.cz/separaty/2009/AS/zagalak-on pole structure assignment in linear systems.pdf

Jet-parton assignment in t t-bar H events using deep learning

International Nuclear Information System (INIS)

Erdmann, M.; Fischer, B.; Rieger, M.

2017-01-01

The direct measurement of the top quark-Higgs coupling is one of the important questions in understanding the Higgs boson. The coupling can be obtained through measurement of the top quark pair-associated Higgs boson production cross-section. Of the multiple challenges arising in this cross-section measurement, we investigate the reconstruction of the partons originating from the hard scattering process using the measured jets in simulated t t-bar H events. The task corresponds to an assignment challenge of m objects (jets) to n other objects (partons), where m ≥ n . We compare several methods with emphasis on a concept based on deep learning techniques which yields the best results with more than 50% of correct jet-parton assignments.

A comparison of fitness-case sampling methods for genetic programming

Science.gov (United States)

Martínez, Yuliana; Naredo, Enrique; Trujillo, Leonardo; Legrand, Pierrick; López, Uriel

2017-11-01

Genetic programming (GP) is an evolutionary computation paradigm for automatic program induction. GP has produced impressive results but it still needs to overcome some practical limitations, particularly its high computational cost, overfitting and excessive code growth. Recently, many researchers have proposed fitness-case sampling methods to overcome some of these problems, with mixed results in several limited tests. This paper presents an extensive comparative study of four fitness-case sampling methods, namely: Interleaved Sampling, Random Interleaved Sampling, Lexicase Selection and Keep-Worst Interleaved Sampling. The algorithms are compared on 11 symbolic regression problems and 11 supervised classification problems, using 10 synthetic benchmarks and 12 real-world data-sets. They are evaluated based on test performance, overfitting and average program size, comparing them with a standard GP search. Comparisons are carried out using non-parametric multigroup tests and post hoc pairwise statistical tests. The experimental results suggest that fitness-case sampling methods are particularly useful for difficult real-world symbolic regression problems, improving performance, reducing overfitting and limiting code growth. On the other hand, it seems that fitness-case sampling cannot improve upon GP performance when considering supervised binary classification.

Genetic structure in the coral, Montastraea cavernosa: assessing genetic differentiation among and within Mesophotic reefs.

Directory of Open Access Journals (Sweden)

Daniel A Brazeau

Full Text Available Mesophotic coral reefs (30-150 m have recently received increased attention as a potential source of larvae (e.g., the refugia hypothesis to repopulate a select subset of the shallow water (<30 m coral fauna. To test the refugia hypothesis we used highly polymorphic Amplified Fragment Length Polymorphism (AFLP markers as a means to assess small-scale genetic heterogeneity between geographic locations and across depth clines in the Caribbean coral, Montastraea cavernosa. Zooxanthellae-free DNA extracts of coral samples (N = 105 were analyzed from four depths, shallow (3-10 m, medium (15-25 m, deep (30-50 m and very deep (60-90 m from Little Cayman Island (LCI, Lee Stocking Island (LSI, Bahamas and San Salvador (SS, Bahamas which range in distance from 170 to 1,600 km apart. Using AMOVA analysis there were significant differences in ΦST values in pair wise comparisons between LCI and LSI. Among depths at LCI, there was significant genetic differentiation between shallow and medium versus deep and very deep depths in contrast there were no significant differences in ΦST values among depths at LSI. The assignment program AFLPOP, however, correctly assigned 95.7% of the LCI and LSI samples to the depths from which they were collected, differentiating among populations as little as 10 to 20 m in depth from one another. Discriminant function analysis of the data showed significant differentiation among samples when categorized by collection site as well as collection depth. FST outlier analyses identified 2 loci under positive selection and 3 under balancing selection at LCI. At LSI 2 loci were identified, both showing balancing selection. This data shows that adult populations of M. cavernosa separated by depths of tens of meters exhibits significant genetic structure, indicative of low population connectivity among and within sites and are not supplying successful recruits to adjacent coral reefs less than 30 m in depth.

Personnel shift assignment: Existence conditions and network models

NARCIS (Netherlands)

van den Berg, Jeroen P.; van den Berg, J.P.; Panton, David M.

1994-01-01

The personnel scheduling problem is known to be a five-stage process in which the final stage involves the assignment of shifts to the days worked in the schedule. This paper discusses the existence conditions for both continuous and forward rotating shift assignments and heuristic network

75 FR 55355 - Delegation of Authority and Assignment of Responsibility

Science.gov (United States)

2010-09-10

... DEPARTMENT OF LABOR Office of the Secretary Delegation of Authority and Assignment of Responsibility Secretary's Order 4-2010 Subject: Delegation of Authority and Assignment of Responsibility to the... delegations and assignments in full force and effect, except as expressly modified herein. 4. Delegation of...

Diallel Analysis using Hayman Method to Study Genetic Parameters of Yield Components in Pepper(Capsicum annuum L.

Directory of Open Access Journals (Sweden)

MUHAMAD SYUKUR

2010-12-01

Full Text Available One method to obtain genetic information is the diallel cross analysis. The objective of this study was to eavluate the genetic parameters of six inbred pepper (Capsicum annuum L. using full diallel crosses. The experiment was conducted at IPB Experiment Field, Cikabayan, Darmaga. The design was randomized complete block design (RCBD using three replications as blocks. Data from generation F1 and parents were analyzed using the Hayman Method. Results indicated that no epistatic effects were significant for all the traits assessed. Additive genetic effects were larger than the dominant effects for yield per plant, fruit length, and diameter fruit traits. Dominant genetic effects were larger than the additive effects for fruit weight traits. Narrow-sense and broad-sense heritability were high for all the traits assessed. The character of the yield per plant, fruit weight and fruit diameter shows that there were more dominant genes in the parents. There were more recessive genes in parents for the fruit length character. IPB C7 parent was the most recessive genes containing control characters in the yield per plant. In the new improved varieties of high yielding, IPB C7 could be crossed with IPB C9. Employing individual or mass selection breeding should be successful in developing high-productivity lines in this population.

Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation

NARCIS (Netherlands)

Botta, Filippo; Eriksen, Casper; Fontaine, Michael Christophe; Guillot, Gilles

2015-01-01

In a recent paper, Bradburd et al. (2013) proposed a model to quantify the relative effect ofgeographic and environmental distance on genetic differentiation. Here, we enhance this method in several ways. 1. We modify the covariance model so as to fit better with mainstream geostatistical models and

Staff assignment practices in nursing homes: review of the literature.

Science.gov (United States)

Rahman, Anna; Straker, Jane K; Manning, Lydia

2009-01-01

Consistent assignment, whereby nursing home staff members, particularly certified nurse aides, are assigned to the same residents on most shifts, is increasingly viewed as a cornerstone of culture change in nursing homes. It has been advocated as a best-care model that increases residents' quality of life while contributing to a more stable frontline staff. Given these potential benefits, consistent assignment is now widely viewed as superior to rotating assignment, an alternative staffing model that aims to distribute care burden more fairly among staff and ensure that workers are familiar with most residents. Despite favorable anecdotal reports about the benefits of consistent assignment, the research literature reports mixed and sometimes contradictory findings for this staffing practice. This article reviews the research pertaining to staff assignment practices in nursing homes. Reviewed here are 13 reports on experimental trials (6 reports), evaluation research (4 reports), and nursing home surveys (3 reports). The review reveals broad diversity in staffing practices and raises questions that challenge popular assumptions about consistent assignment. The article closes with a discussion of the research, policy, and practice implications of the research findings.

75 FR 55354 - Delegation of Authority and Assignment of Responsibilities

Science.gov (United States)

2010-09-10

... DEPARTMENT OF LABOR Office of the Secretary Delegation of Authority and Assignment of Responsibilities Secretary's Order 3-2010 Subject: Delegation of Authority and Assignment of Responsibilities to... Secretary to enforce sections 18A and 18B of the FLSA. 4. Delegation of Authority and Assignment of...

25 CFR 225.33 - Assignment of minerals agreements.

Science.gov (United States)

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false Assignment of minerals agreements. 225.33 Section 225.33 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS OIL AND GAS, GEOTHERMAL, AND SOLID MINERALS AGREEMENTS Minerals Agreements § 225.33 Assignment of minerals agreements. An...

Automating Formative and Summative Feedback for Individualised Assignments

Science.gov (United States)

Hamilton, Ian Robert

2009-01-01

Purpose: The purpose of this paper is to report on the rationale behind the use of a unique paper-based individualised accounting assignment, which automated the provision to students of immediate formative and timely summative feedback. Design/methodology/approach: As students worked towards completing their assignment, the package provided…

submission of art studio-based assignments: students experience

African Journals Online (AJOL)