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Sample records for detecting evolutionary selection

  1. JCoDA: a tool for detecting evolutionary selection

    PubMed Central

    2010-01-01

    Background The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. Results JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. Conclusions JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary

  2. Evolutionary Theories of Detection

    SciTech Connect

    Fitch, J P

    2005-04-29

    Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

  3. Molecular selection in a unified evolutionary sequence

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1986-01-01

    With guidance from experiments and observations that indicate internally limited phenomena, an outline of unified evolutionary sequence is inferred. Such unification is not visible for a context of random matrix and random mutation. The sequence proceeds from Big Bang through prebiotic matter, protocells, through the evolving cell via molecular and natural selection, to mind, behavior, and society.

  4. Extrapolating Weak Selection in Evolutionary Games

    PubMed Central

    Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

    2013-01-01

    In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

  5. Product Mix Selection Using AN Evolutionary Technique

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Vasant, Pandian

    2009-08-01

    This paper proposes an evolutionary technique for the solution of a real—life industrial problem and particular for the product mix selection problem. The evolutionary technique is a combination of a genetic algorithm that preserves the feasibility of the trial solutions with penalties and some local optimization method. The goal of this paper has been achieved in finding the best near optimal solution for the profit fitness function respect to vagueness factor and level of satisfaction. The findings of the profit values will be very useful for the decision makers in the industrial engineering sector for the implementation purpose. It's possible to improve the solutions obtained in this study by employing other meta-heuristic methods such as simulated annealing, tabu Search, ant colony optimization, particle swarm optimization and artificial immune systems.

  6. Selective evolutionary generation systems: Theory and applications

    NASA Astrophysics Data System (ADS)

    Menezes, Amor A.

    This dissertation is devoted to the problem of behavior design, which is a generalization of the standard global optimization problem: instead of generating the optimizer, the generalization produces, on the space of candidate optimizers, a probability density function referred to as the behavior. The generalization depends on a parameter, the level of selectivity, such that as this parameter tends to infinity, the behavior becomes a delta function at the location of the global optimizer. The motivation for this generalization is that traditional off-line global optimization is non-resilient and non-opportunistic. That is, traditional global optimization is unresponsive to perturbations of the objective function. On-line optimization methods that are more resilient and opportunistic than their off-line counterparts typically consist of the computationally expensive sequential repetition of off-line techniques. A novel approach to inexpensive resilience and opportunism is to utilize the theory of Selective Evolutionary Generation Systems (SECS), which sequentially and probabilistically selects a candidate optimizer based on the ratio of the fitness values of two candidates and the level of selectivity. Using time-homogeneous, irreducible, ergodic Markov chains to model a sequence of local, and hence inexpensive, dynamic transitions, this dissertation proves that such transitions result in behavior that is called rational; such behavior is desirable because it can lead to both efficient search for an optimizer as well as resilient and opportunistic behavior. The dissertation also identifies system-theoretic properties of the proposed scheme, including equilibria, their stability and their optimality. Moreover, this dissertation demonstrates that the canonical genetic algorithm with fitness proportional selection and the (1+1) evolutionary strategy are particular cases of the scheme. Applications in three areas illustrate the versatility of the SECS theory: flight

  7. Human evolutionary history and contemporary evolutionary theory provide insight when assessing cultural group selection.

    PubMed

    Fuentes, Agustin; Kissel, Marc

    2016-01-01

    Richerson et al. provide a much needed roadmap for assessing cultural group selection (CGS) theory and for applying it to understanding variation between contemporary human groups. However, the current proposal lacks connection to relevant evidence from the human evolutionary record and requires a better integration with contemporary evolutionary theory. The article also misapplies the F st statistic. PMID:27562510

  8. An Evolutionary Perspective of Friendship Selection

    ERIC Educational Resources Information Center

    Coutinho, Savia A.

    2007-01-01

    The research reported in this article investigates whether promiscuity plays a role in same-sex and opposite-sex friend selection. Since same-sex friends share strong similarity and spend time with their friends' mates or potential mates, it becomes important to select same-sex friends who will not be sexual rivals. One way to determine rivalry in…

  9. Evolutionary Design of a Robotic Material Defect Detection System

    NASA Technical Reports Server (NTRS)

    Ballard, Gary; Howsman, Tom; Craft, Mike; ONeil, Daniel; Steincamp, Jim; Howell, Joe T. (Technical Monitor)

    2002-01-01

    During the post-flight inspection of SSME engines, several inaccessible regions must be disassembled to inspect for defects such as cracks, scratches, gouges, etc. An improvement to the inspection process would be the design and development of very small robots capable of penetrating these inaccessible regions and detecting the defects. The goal of this research was to utilize an evolutionary design approach for the robotic detection of these types of defects. A simulation and visualization tool was developed prior to receiving the hardware as a development test bed. A small, commercial off-the-shelf (COTS) robot was selected from several candidates as the proof of concept robot. The basic approach to detect the defects was to utilize Cadmium Sulfide (CdS) sensors to detect changes in contrast of an illuminated surface. A neural network, optimally designed utilizing a genetic algorithm, was employed to detect the presence of the defects (cracks). By utilization of the COTS robot and US sensors, the research successfully demonstrated that an evolutionarily designed neural network can detect the presence of surface defects.

  10. Neuro-evolutionary event detection technique for downhole microseismic surveys

    NASA Astrophysics Data System (ADS)

    Maity, Debotyam; Salehi, Iraj

    2016-01-01

    Recent years have seen a significant increase in borehole microseismic data acquisition programs associated with unconventional reservoir developments such as hydraulic fracturing programs for shale oil and gas. The data so acquired is used for hydraulic fracture monitoring and diagnostics and therefore, the quality of the data in terms of resolution and accuracy has a significant impact on its value to the industry. Borehole microseismic data acquired in such environments typically suffer from propagation effects due to the presence of thin interbedded shale layers as well as noise and interference effects. Moreover, acquisition geometry has significant impact on detectability across portions of the sensor array. Our work focuses on developing robust first arrival detection and pick selection workflow for both P and S waves specifically designed for such environments. We introduce a novel workflow for refinement of picks with immunity towards significant noise artifacts and applicability over data with very low signal-to-noise ratio provided some accurate picks have already been made. This workflow utilizes multi-step hybrid detection and classification routine which makes use of a neural network based autopicker for initial picking and an evolutionary algorithm for pick refinement. We highlight the results from an actual field case study including multiple examples demonstrating immunity towards noise and compare the effectiveness of the workflow with two contemporary autopicking routines without the application of the shared detection/refinement procedure. Finally, we use a windowed waveform cross-correlation based uncertainty estimation method for potential quality control purposes. While the workflow was developed to work with the neural network based autopicker, it can be used with any other traditional autopicker and provides significant improvements in pick detection across seismic gathers.

  11. Threat-detection in child development: an evolutionary perspective.

    PubMed

    Boyer, Pascal; Bergstrom, Brian

    2011-03-01

    Evidence for developmental aspects of fear-targets and anxiety suggests a complex but stable pattern whereby specific kinds of fears emerge at different periods of development. This developmental schedule seems appropriate to dangers encountered repeatedly during human evolution. Also consistent with evolutionary perspective, the threat-detection systems are domain-specific, comprising different kinds of cues to do with predation, intraspecific violence, contamination-contagion and status loss. Proper evolutionary models may also be relevant to outstanding issues in the domain, notably the connections between typical development and pathology. PMID:20832423

  12. Evolutionary response when selection and genetic variation covary across environments.

    PubMed

    Wood, Corlett W; Brodie, Edmund D

    2016-10-01

    Although models of evolution usually assume that the strength of selection on a trait and the expression of genetic variation in that trait are independent, whenever the same ecological factor impacts both parameters, a correlation between the two may arise that accelerates trait evolution in some environments and slows it in others. Here, we address the evolutionary consequences and ecological causes of a correlation between selection and expressed genetic variation. Using a simple analytical model, we show that the correlation has a modest effect on the mean evolutionary response and a large effect on its variance, increasing among-population or among-generation variation in the response when positive, and diminishing variation when negative. We performed a literature review to identify the ecological factors that influence selection and expressed genetic variation across traits. We found that some factors - temperature and competition - are unlikely to generate the correlation because they affected one parameter more than the other, and identified others - most notably, environmental novelty - that merit further investigation because little is known about their impact on one of the two parameters. We argue that the correlation between selection and genetic variation deserves attention alongside other factors that promote or constrain evolution in heterogeneous landscapes. PMID:27531600

  13. Evolutionary stasis in pollen morphogenesis due to natural selection.

    PubMed

    Matamoro-Vidal, Alexis; Prieu, Charlotte; Furness, Carol A; Albert, Béatrice; Gouyon, Pierre-Henri

    2016-01-01

    The contribution of developmental constraints and selective forces to the determination of evolutionary patterns is an important and unsolved question. We test whether the long-term evolutionary stasis observed for pollen morphogenesis (microsporogenesis) in eudicots is due to developmental constraints or to selection on a morphological trait shaped by microsporogenesis: the equatorial aperture pattern. Most eudicots have three equatorial apertures but several taxa have independently lost the equatorial pattern and have microsporogenesis decoupled from aperture pattern determination. If selection on the equatorial pattern limits variation, we expect to see increased variation in microsporogenesis in the nonequatorial clades. Variation of microsporogenesis was studied using phylogenetic comparative analyses in 83 species dispersed throughout eudicots including species with and without equatorial apertures. The species that have lost the equatorial pattern have highly variable microsporogenesis at the intra-individual and inter-specific levels regardless of their pollen morphology, whereas microsporogenesis remains stable in species with the equatorial pattern. The observed burst of variation upon loss of equatorial apertures shows that there are no strong developmental constraints precluding variation in microsporogenesis, and that the stasis is likely to be due principally to selective pressure acting on pollen morphogenesis because of its implication in the determination of the equatorial aperture pattern. PMID:26248868

  14. Pairwise comparison and selection temperature in evolutionary game dynamics

    PubMed Central

    Traulsen, Arne; Pacheco, Jorge M.; Nowak, Martin A.

    2007-01-01

    Recently, the frequency dependent Moran process has been introduced in order to describe evolutionary game dynamics in finite populations. Here, an alternative to this process is investigated that is based on pairwise comparison between two individuals. We follow a long tradition in the physics community and introduce a temperature (of selection) to account for stochastic effects. We calculate the fixation probabilities and fixation times for any symmetric 2 × 2 game, for any intensity of selection and any initial number of mutants. The temperature can be used to gauge continuously from neutral drift to the extreme selection intensity known as imitation dynamics. For some payoff matrices the distribution of fixation times can become so broad that the average value is no longer very meaningful. PMID:17292423

  15. Multiobjective Evolutionary Path Planning via Sugeno-Based Tournament Selection

    NASA Technical Reports Server (NTRS)

    Dozier, Gerry; McCullough, Shaun; Homaifar, Abdollah; Esterline, Albert

    1998-01-01

    This paper introduces a new tournament selection algorithm that can be used for evolutionary path planning systems. The fuzzy (Sugeno) tournament selection algorithm (STSA) described in this paper selects candidate paths (CPs) to be parents and undergo reproduction based on: (1) path feasibility, (2) the euclidean distance of a path from the origin to its destination, and (3) the average change in the slope of a path. In this paper, we provide a detailed description of the fuzzy inference system used in the STSA as well as some examples of its usefulness. We then use 12 instances of our STSA to rank a population of CPs based on the above criteria. We also show how the STSA can obviate the need for the development of an explicit (lexicographic multiobjective) evaluation function and use it to develop multiobjective motion paths.

  16. Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions.

    PubMed

    Goz, Eli; Tuller, Tamir

    2016-08-01

    A large number of studies demonstrated the importance of different HIV RNA structural elements at all stages of the viral life cycle. Nevertheless, the significance of many of these structures is unknown, and plausibly new regions containing RNA structure-mediated regulatory signals remain to be identified. An important characteristic of genomic regions carrying functionally significant secondary structures is their mutational robustness, that is, the extent to which a sequence remains constant in spite of despite mutations in terms of its underlying secondary structure. Structural robustness to mutations is expected to be important in the case of functional RNA structures in viruses with high mutation rate; it may prevent fitness loss due to disruption of possibly functional conformations, pointing to the specific significance of the corresponding genomic region. In the current work, we perform a genome-wide computational analysis to detect signals of a direct evolutionary selection for strong folding and RNA structure-based mutational robustness within HIV coding sequences. We provide evidence that specific regions of HIV structural genes undergo an evolutionary selection for strong folding; in addition, we demonstrate that HIV Rev responsive element seems to undergo a direct evolutionary selection for increased secondary structure robustness to point mutations. We believe that our analysis may enable a better understanding of viral evolutionary dynamics at the RNA structural level and may benefit to practical efforts of engineering antiviral vaccines and novel therapeutic approaches. PMID:27347769

  17. Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements

    PubMed Central

    Brunet, Tyler D.P.; Doolittle, W. Ford

    2015-01-01

    One of several issues at play in the renewed debate over “junk DNA” is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to “speed evolution” or as an “evolutionary repository” could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness—or are instead junk— is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. PMID:26253318

  18. Evolutionary feature selection to estimate forest stand variables using LiDAR

    NASA Astrophysics Data System (ADS)

    Garcia-Gutierrez, Jorge; Gonzalez-Ferreiro, Eduardo; Riquelme-Santos, Jose C.; Miranda, David; Dieguez-Aranda, Ulises; Navarro-Cerrillo, Rafael M.

    2014-02-01

    Light detection and ranging (LiDAR) has become an important tool in forestry. LiDAR-derived models are mostly developed by means of multiple linear regression (MLR) after stepwise selection of predictors. An increasing interest in machine learning and evolutionary computation has recently arisen to improve regression use in LiDAR data processing. Although evolutionary machine learning has already proven to be suitable for regression, evolutionary computation may also be applied to improve parametric models such as MLR. This paper provides a hybrid approach based on joint use of MLR and a novel genetic algorithm for the estimation of the main forest stand variables. We show a comparison between our genetic approach and other common methods of selecting predictors. The results obtained from several LiDAR datasets with different pulse densities in two areas of the Iberian Peninsula indicate that genetic algorithms perform better than the other methods statistically. Preliminary studies suggest that a lack of parametric conditions in field data and possible misuse of parametric tests may be the main reasons for the better performance of the genetic algorithm. This research confirms the findings of previous studies that outline the importance of evolutionary computation in the context of LiDAR analisys of forest data, especially when the size of fieldwork datatasets is reduced.

  19. Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

    PubMed

    Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

    2016-02-10

    Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses. PMID:26867176

  20. Evolutionary selection of enzymatically synthesized semiconductors from biomimetic mineralization vesicles

    SciTech Connect

    Bawazer, Lukmaan A.; Izumi, Michi; Kolodin, Dmitriy; Neilson, James R.; Schwenzer, Birgit; Morse, Daniel E.

    2012-10-29

    The way nature evolves and sculpts materials using proteins inspires new approaches to materials engineering but is still not completely understood. Here, we present a cell-free synthetic biological platform to advance studies of biologically synthesized solid-state materials. This platform is capable of simultaneously exerting many of the hierarchical levels of control found in natural biomineralization, including genetic, chemical, spatial, structural, and morphological control, while supporting the evolutionary selection of new mineralizing proteins and the corresponding genetically encoded materials that they produce. DNA-directed protein expression and enzymatic mineralization occur on polystyrene microbeads in water-in-oil emulsions, yielding synthetic surrogates of biomineralizing cells that are then screened by flow sorting, with light-scattering signals used to sort the resulting mineralized composites differentially. We demonstrate the utility of this platform by evolutionarily selecting newly identified silicateins, biomineralizing enzymes previously identified from the silica skeleton of a marine sponge, for enzyme variants capable of synthesizing silicon dioxide (silica) or titanium dioxide (titania) composites. Mineral composites of intermediate strength are preferentially selected to remain intact for identification during cell sorting, and then to collapse postsorting to expose the encoding genes for enzymatic DNA amplification. Some of the newly selected silicatein variants catalyze the formation of crystalline silicates, whereas the parent silicateins lack this ability. The demonstrated bioengineered route to previously undescribed materials introduces in vitro enzyme selection as a viable strategy for mimicking genetic evolution of materials as it occurs in nature.

  1. Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme

    PubMed Central

    Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

    2015-01-01

    Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton–Jacobi inequality – constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer

  2. Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme.

    PubMed

    Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

    2015-01-01

    Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton-Jacobi inequality - constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer

  3. Detection and evolutionary analysis of picobirnaviruses in treated wastewater

    PubMed Central

    Zhang, Shiwei; Bai, Ru; Feng, Run; Zhang, Hongxun; Liu, Lixin

    2015-01-01

    Wastewater contains numerous viruses. In this study, picobirnaviruses (PBVs) were detected in the stream of a wastewater treatment plant in Changsha, Hunan province, China, and evolutionary analysis of the isolated PBVs was performed. The phylogenetic tree revealed that the PBVs were highly divergent and could be classified into six distinct groups according to their hosts. Among these groups, pairwise comparison of the six groups revealed that the nucleotide distance of group 4 (bootstrap value = 0.92; nucleotide identity = 94%) was the largest. Thus, group 4 might represent a new division of PBVs. Comprehensive analysis of the obtained PBV sequences to investigate their evolutionary history and phylodynamics revealed that group 5 (PBVs from monkey) exhibited maximum polymorphism (K = 30.582, S = 74, η = 98, Pa = 47) and lowest nucleotide substitutions per site per year (6.54E-3 subs per site per year), except group 4. Maximum clade credibility tree indicated that group 5 appeared earlier than the other groups. In conclusion, this study detected PBVs in treated wastewater in China, and identified a new PBV group. Furthermore, among these PBVs, group 5 was found to survive longer and present a balance between PBVs and their monkey host. PMID:25546400

  4. Design of an Evolutionary Approach for Intrusion Detection

    PubMed Central

    2013-01-01

    A novel evolutionary approach is proposed for effective intrusion detection based on benchmark datasets. The proposed approach can generate a pool of noninferior individual solutions and ensemble solutions thereof. The generated ensembles can be used to detect the intrusions accurately. For intrusion detection problem, the proposed approach could consider conflicting objectives simultaneously like detection rate of each attack class, error rate, accuracy, diversity, and so forth. The proposed approach can generate a pool of noninferior solutions and ensembles thereof having optimized trade-offs values of multiple conflicting objectives. In this paper, a three-phase, approach is proposed to generate solutions to a simple chromosome design in the first phase. In the first phase, a Pareto front of noninferior individual solutions is approximated. In the second phase of the proposed approach, the entire solution set is further refined to determine effective ensemble solutions considering solution interaction. In this phase, another improved Pareto front of ensemble solutions over that of individual solutions is approximated. The ensemble solutions in improved Pareto front reported improved detection results based on benchmark datasets for intrusion detection. In the third phase, a combination method like majority voting method is used to fuse the predictions of individual solutions for determining prediction of ensemble solution. Benchmark datasets, namely, KDD cup 1999 and ISCX 2012 dataset, are used to demonstrate and validate the performance of the proposed approach for intrusion detection. The proposed approach can discover individual solutions and ensemble solutions thereof with a good support and a detection rate from benchmark datasets (in comparison with well-known ensemble methods like bagging and boosting). In addition, the proposed approach is a generalized classification approach that is applicable to the problem of any field having multiple conflicting

  5. Detecting selection in immunoglobulin sequences.

    PubMed

    Uduman, Mohamed; Yaari, Gur; Hershberg, Uri; Stern, Jacob A; Shlomchik, Mark J; Kleinstein, Steven H

    2011-07-01

    The ability to detect selection by analyzing mutation patterns in experimentally derived immunoglobulin (Ig) sequences is a critical part of many studies. Such techniques are useful not only for understanding the response to pathogens, but also to determine the role of antigen-driven selection in autoimmunity, B cell cancers and the diversification of pre-immune repertoires in certain species. Despite its importance, quantifying selection in experimentally derived sequences is fraught with difficulties. The necessary parameters for statistical tests (such as the expected frequency of replacement mutations in the absence of selection) are non-trivial to calculate, and results are not easily interpretable when analyzing more than a handful of sequences. We have developed a web server that implements our previously proposed Focused binomial test for detecting selection. Several features are integrated into the web site in order to facilitate analysis, including V(D)J germline segment identification with IMGT alignment, batch submission of sequences and integration of additional test statistics proposed by other groups. We also implement a Z-score-based statistic that increases the power of detecting selection while maintaining specificity, and further allows for the combined analysis of sequences from different germlines. The tool is freely available at http://clip.med.yale.edu/selection. PMID:21665923

  6. Model selection for anomaly detection

    NASA Astrophysics Data System (ADS)

    Burnaev, E.; Erofeev, P.; Smolyakov, D.

    2015-12-01

    Anomaly detection based on one-class classification algorithms is broadly used in many applied domains like image processing (e.g. detection of whether a patient is "cancerous" or "healthy" from mammography image), network intrusion detection, etc. Performance of an anomaly detection algorithm crucially depends on a kernel, used to measure similarity in a feature space. The standard approaches (e.g. cross-validation) for kernel selection, used in two-class classification problems, can not be used directly due to the specific nature of a data (absence of a second, abnormal, class data). In this paper we generalize several kernel selection methods from binary-class case to the case of one-class classification and perform extensive comparison of these approaches using both synthetic and real-world data.

  7. Evolutionary Psychology: A Natural Selection for Music Education?

    ERIC Educational Resources Information Center

    Graham, Rodger

    2006-01-01

    In this viewpoint it is suggested that recent research and authorship in the evolutionary psychology (EP) of music can provide musicians and educators with an enriched understanding of the adaptive role of music in human life. Within a climate of continual educational reform in which music is often marginalised from other mainstream curricular…

  8. Testing hypotheses in evolutionary ecology with imperfect detection: capture-recapture structural equation modeling.

    PubMed

    Cubaynes, Sarah; Doutrelant, Claire; Grégoire, Arnaud; Perret, Philippe; Faivre, Bruno; Gimenez, Olivier

    2012-02-01

    Studying evolutionary mechanisms in natural populations often requires testing multifactorial scenarios of causality involving direct and indirect relationships among individual and environmental variables. It is also essential to account for the imperfect detection of individuals to provide unbiased demographic parameter estimates. To cope with these issues, we developed a new approach combining structural equation models with capture-recapture models (CR-SEM) that allows the investigation of competing hypotheses about individual and environmental variability observed in demographic parameters. We employ Markov chain Monte Carlo sampling in a Bayesian framework to (1) estimate model parameters, (2) implement a model selection procedure to evaluate competing hypotheses about causal mechanisms, and (3) assess the fit of models to data using posterior predictive checks. We illustrate the value of our approach using two case studies on wild bird populations. We first show that CR-SEM can be useful to quantify the action of selection on a set of phenotypic traits with an analysis of selection gradients on morphological traits in Common Blackbirds (Turdus merula). In a second case study on Blue Tits (Cyanistes caeruleus), we illustrate the use of CR-SEM to study evolutionary trade-offs in the wild, while accounting for varying environmental conditions. PMID:22624306

  9. Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission

    PubMed Central

    Zhang, Zhao; Shen, Libing; Gu, Xun

    2016-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) belongs to beta group of coronavirus and was first discovered in 2012. MERS-CoV can infect multiple host species and cause severe diseases in human. We conducted a series of phylogenetic and bioinformatic analyses to study the evolution dynamics of MERS-CoV among different host species with genomic data. Our analyses show: 1) 28 potential recombinant sequences were detected and they can be classified into seven potential recombinant types; 2) The spike (S) protein of MERS-CoV was under strong positive selection when MERS-CoV transmitted from their natural host to human; 3) Six out of nine positive selection sites detected in spike (S) protein are located in its receptor-binding domain which is in direct contact with host cells; 4) MERS-CoV frequently transmitted back and forth between human and camel after it had acquired the human-camel infection capability. Together, these results suggest that potential recombination events might have happened frequently during MERS-CoV’s evolutionary history and the positive selection sites in MERS-CoV’s S protein might enable it to infect human. PMID:27142087

  10. Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission.

    PubMed

    Zhang, Zhao; Shen, Libing; Gu, Xun

    2016-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) belongs to beta group of coronavirus and was first discovered in 2012. MERS-CoV can infect multiple host species and cause severe diseases in human. We conducted a series of phylogenetic and bioinformatic analyses to study the evolution dynamics of MERS-CoV among different host species with genomic data. Our analyses show: 1) 28 potential recombinant sequences were detected and they can be classified into seven potential recombinant types; 2) The spike (S) protein of MERS-CoV was under strong positive selection when MERS-CoV transmitted from their natural host to human; 3) Six out of nine positive selection sites detected in spike (S) protein are located in its receptor-binding domain which is in direct contact with host cells; 4) MERS-CoV frequently transmitted back and forth between human and camel after it had acquired the human-camel infection capability. Together, these results suggest that potential recombination events might have happened frequently during MERS-CoV's evolutionary history and the positive selection sites in MERS-CoV's S protein might enable it to infect human. PMID:27142087

  11. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

    PubMed Central

    2009-01-01

    Background The bacterium Salmonella enterica includes a diversity of serotypes that cause disease in humans and different animal species. Some Salmonella serotypes show a broad host range, some are host restricted and exclusively associated with one particular host, and some are associated with one particular host species, but able to cause disease in other host species and are thus considered "host adapted". Five Salmonella genome sequences, representing a broad host range serotype (Typhimurium), two host restricted serotypes (Typhi [two genomes] and Paratyphi) and one host adapted serotype (Choleraesuis) were used to identify core genome genes that show evidence for recombination and positive selection. Results Overall, 3323 orthologous genes were identified in all 5 Salmonella genomes analyzed. Use of four different methods to assess homologous recombination identified 270 genes that showed evidence for recombination with at least one of these methods (false discovery rate [FDR] <10%). After exclusion of genes with evidence for recombination, site and branch specific models identified 41 genes as showing evidence for positive selection (FDR <20%), including a number of genes with confirmed or likely roles in virulence and ompC, a gene encoding an outer membrane protein, which has also been found to be under positive selection in other bacteria. A total of 8, 16, 7, and 5 genes showed evidence for positive selection in Choleraesuis, Typhi, Typhimurium, and Paratyphi branch analyses, respectively. Sequencing and evolutionary analyses of four genes in an additional 42 isolates representing 23 serotypes confirmed branch specific positive selection and recombination patterns. Conclusion Our data show that, among the four serotypes analyzed, (i) less than 10% of Salmonella genes in the core genome show evidence for homologous recombination, (ii) a number of Salmonella genes are under positive selection, including genes that appear to contribute to virulence, and (iii

  12. Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

    PubMed Central

    Huang, Lei; Liao, Li; Wu, Cathy H.

    2016-01-01

    Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

  13. Natural or internal selection? The case of canalization in complex evolutionary systems.

    PubMed

    Riegler, Alexander

    2008-01-01

    Using biological examples and theoretical arguments, the case is presented for extending the notion of natural selection to include internal selection in order to account for the evolution of complex systems. It is suggested that we take into consideration internal factors that arise from the hierarchical dynamics of complex systems. In addition to environmental selection, it is argued, decisive constraints are created by the system itself. Canalization is shown to be an indispensable ingredient for evolutionary processes in both biological and artificial complex systems. In artificial life systems canalization is not only an instrument for controlling complexity, it also increases the speed and stability of evolutionary processes. PMID:18489255

  14. The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

    PubMed Central

    Chen, Bor-Sen; Ho, Shih-Ju

    2014-01-01

    In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to

  15. Evolutionary stasis despite selection on a heritable trait in an invasive zooplankton.

    PubMed

    Miehls, A L J; Peacor, S D; Valliant, L; McAdam, A G

    2015-05-01

    Invasive species are one of the greatest threats to ecosystems, and there is evidence that evolution plays an important role in the success or failure of invasions. Yet, few studies have measured natural selection and evolutionary responses to selection in invasive species, particularly invasive animals. We quantified the strength of natural selection on the defensive morphology (distal spine) of an invasive zooplankton, Bythotrephes longimanus, in Lake Michigan across multiple months during three growing seasons. We used multiple lines of evidence, including historic and contemporary wild-captured individuals and palaeoecology of retrieved spines, to assess phenotypic change in distal spine length since invasion. We found evidence of temporally variable selection, with selection for decreased distal spine length early in the growing season and selection for increased distal spine length later in the season. This trend in natural selection is consistent with seasonal changes in the relative strength of non-gape-limited and gape-limited fish predation. Yet, despite net selection for increased distal spine length and a known genetic basis for distal spine length, we observed little evidence of an evolutionary response to selection. Multiple factors likely limit an evolutionary response to selection, including genetic correlations, trade-offs between components of fitness, and phenotypic plasticity. PMID:25833682

  16. Kinetic evolutionary behavior of catalysis-select migration

    NASA Astrophysics Data System (ADS)

    Wu, Yuan-Gang; Lin, Zhen-Quan; Ke, Jian-Hong

    2012-06-01

    We propose a catalysis-select migration driven evolution model of two-species (A- and B-species) aggregates, where one unit of species A migrates to species B under the catalysts of species C, while under the catalysts of species D the reaction will become one unit of species B migrating to species A. Meanwhile the catalyst aggregates of species C perform self-coagulation, as do the species D aggregates. We study this catalysis-select migration driven kinetic aggregation phenomena using the generalized Smoluchowski rate equation approach with C species catalysis-select migration rate kernel K(k;i,j) = Kkij and D species catalysis-select migration rate kernel J(k;i,j)= Jkij. The kinetic evolution behaviour is found to be dominated by the competition between the catalysis-select immigration and emigration, in which the competition is between JD0 and KC0 (D0 and C0 are the initial numbers of the monomers of species D and C, respectively). When JD0 -KC0 > 0, the aggregate size distribution of species A satisfies the conventional scaling form and that of species B satisfies a modified scaling form. And in the case of JD0-KC0 < 0, species A and B exchange their aggregate size distributions as in the above JD0-KC0 > 0 case.

  17. Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure

    PubMed Central

    Webber, Mark A.; Whitehead, Rebekah N.; Mount, Manuella; Loman, Nick J.; Pallen, Mark J.; Piddock, Laura J. V.

    2015-01-01

    Objectives Biocides are widely used to prevent infection. We aimed to determine whether exposure of Salmonella to various biocides could act as a driver of antibiotic resistance. Methods Salmonella enterica serovar Typhimurium was exposed to four biocides with differing modes of action. Antibiotic-resistant mutants were selected during exposure to all biocides and characterized phenotypically and genotypically to identify mechanisms of resistance. Results All biocides tested selected MDR mutants with decreased antibiotic susceptibility; these occurred randomly throughout the experiments. Mutations that resulted in de-repression of the multidrug efflux pump AcrAB-TolC were seen in MDR mutants. A novel mutation in rpoA was also selected and contributed to the MDR phenotype. Other mutants were highly resistant to both quinolone antibiotics and the biocide triclosan. Conclusions This study shows that exposure of bacteria to biocides can select for antibiotic-resistant mutants and this is mediated by clinically relevant mechanisms of resistance prevalent in human pathogens. PMID:25953808

  18. Genotype–phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate

    PubMed Central

    O'Connor, Timothy D.; Mundy, Nicholas I.

    2009-01-01

    Motivation: Mapping between genotype and phenotype is one of the primary goals of evolutionary genetics but one that has received little attention at the interspecies level. Recent developments in phylogenetics and statistical modelling have typically been used to examine molecular and phenotypic evolution separately. We have used this background to develop phylogenetic substitution models to test for associations between evolutionary rate of genotype and phenotype. We do this by creating hybrid rate matrices between genotype and phenotype. Results: Simulation results show our models to be accurate in detecting genotype–phenotype associations and robust for various factors that typically affect maximum likelihood methods, such as number of taxa, level of relevant signal, proportion of sites affected and length of evolutionary divergence. Further, simulations show that our method is robust to homogeneity assumptions. We apply the models to datasets of male reproductive system genes in relation to mating systems of primates. We show that evolution of semenogelin II is significantly associated with mating systems whereas two negative control genes (cytochrome b and peptidase inhibitor 3) show no significant association. This provides the first hybrid substitution model of which we are aware to directly test the association between genotype and phenotype using a phylogenetic framework. Availability: Perl and HYPHY scripts are available upon request from the authors. Contact: to252@cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19478022

  19. Evolutionary rates for multivariate traits: the role of selection and genetic variation

    PubMed Central

    Pitchers, William; Wolf, Jason B.; Tregenza, Tom; Hunt, John; Dworkin, Ian

    2014-01-01

    A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (), which predicts evolutionary change for a suite of phenotypic traits () as a product of directional selection acting on them (β) and the genetic variance–covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates. PMID:25002697

  20. Photobiont selectivity leads to ecological tolerance and evolutionary divergence in a polymorphic complex of lichenized fungi

    PubMed Central

    Muggia, Lucia; Pérez-Ortega, Sergio; Kopun, Theodora; Zellnig, Günther; Grube, Martin

    2014-01-01

    Background and Aims The integrity and evolution of lichen symbioses depend on a fine-tuned combination of algal and fungal genotypes. Geographically widespread species complexes of lichenized fungi can occur in habitats with slightly varying ecological conditions, and it remains unclear how this variation correlates with symbiont selectivity patterns in lichens. In an attempt to address this question, >300 samples were taken of the globally distributed and ecologically variable lichen-forming species complex Tephromela atra, together with closely allied species, in order to study genetic diversity and the selectivity patterns of their photobionts. Methods Lichen thalli of T. atra and of closely related species T. grumosa, T. nashii and T. atrocaesia were collected from six continents, across 24 countries and 62 localities representing a wide range of habitats. Analyses of genetic diversity and phylogenetic relationships were carried out both for photobionts amplified directly from the lichen thalli and from those isolated in axenic cultures. Morphological and anatomical traits were studied with light and transmission electron microscopy in the isolated algal strains. Key Results Tephromela fungal species were found to associate with 12 lineages of Trebouxia. Five new clades demonstrate the still-unrecognized genetic diversity of lichen algae. Culturable, undescribed lineages were also characterized by phenotypic traits. Strong selectivity of the mycobionts for the photobionts was observed in six monophyletic Tephromela clades. Seven Trebouxia lineages were detected in the poorly resolved lineage T. atra sensu lato, where co-occurrence of multiple photobiont lineages in single thalli was repeatedly observed. Conclusions Low selectivity apparently allows widespread lichen-forming fungi to establish successful symbioses with locally adapted photobionts in a broader range of habitats. This flexibility might correlate with both lower phylogenetic resolution and

  1. Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations.

    PubMed

    Haafke, Julia; Abou Chakra, Maria; Becks, Lutz

    2016-03-01

    Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here, we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated. PMID:26899793

  2. Selection and evolutionary potential of spring arrival phenology in males and females of a migratory songbird.

    PubMed

    Tarka, M; Hansson, B; Hasselquist, D

    2015-05-01

    The timing of annual life-history events affects survival and reproduction of all organisms. A changing environment can perturb phenological adaptations and an important question is if populations can evolve fast enough to track the environmental changes. Yet, little is known about selection and evolutionary potential of traits determining the timing of crucial annual events. Migratory species, which travel between different climatic regions, are particularly affected by global environmental changes. To increase our understanding of evolutionary potential and selection of timing traits, we investigated the quantitative genetics of arrival date at the breeding ground using a multigenerational pedigree of a natural great reed warbler (Acrocephalus arundinaceus) population. We found significant heritability of 16.4% for arrival date and directional selection for earlier arrival in both sexes acting through reproductive success, but not through lifespan. Mean arrival date advanced with 6 days over 20 years, which is in exact accordance with our predicted evolutionary response based on the breeder's equation. However, this phenotypic change is unlikely to be caused by microevolution, because selection seems mainly to act on the nongenetic component of the trait. Furthermore, demographical changes could also not account for the advancing arrival date. Instead, a strong correlation between spring temperatures and population mean arrival date suggests that phenotypic plasticity best explains the advancement of arrival date in our study population. Our study dissects the evolutionary and environmental forces that shape timing traits and thereby increases knowledge of how populations cope with rapidly changing environments. PMID:25847825

  3. RELAX: detecting relaxed selection in a phylogenetic framework.

    PubMed

    Wertheim, Joel O; Murrell, Ben; Smith, Martin D; Kosakovsky Pond, Sergei L; Scheffler, Konrad

    2015-03-01

    Relaxation of selective strength, manifested as a reduction in the efficiency or intensity of natural selection, can drive evolutionary innovation and presage lineage extinction or loss of function. Mechanisms through which selection can be relaxed range from the removal of an existing selective constraint to a reduction in effective population size. Standard methods for estimating the strength and extent of purifying or positive selection from molecular sequence data are not suitable for detecting relaxed selection, because they lack power and can mistake an increase in the intensity of positive selection for relaxation of both purifying and positive selection. Here, we present a general hypothesis testing framework (RELAX) for detecting relaxed selection in a codon-based phylogenetic framework. Given two subsets of branches in a phylogeny, RELAX can determine whether selective strength was relaxed or intensified in one of these subsets relative to the other. We establish the validity of our test via simulations and show that it can distinguish between increased positive selection and a relaxation of selective strength. We also demonstrate the power of RELAX in a variety of biological scenarios where relaxation of selection has been hypothesized or demonstrated previously. We find that obligate and facultative γ-proteobacteria endosymbionts of insects are under relaxed selection compared with their free-living relatives and obligate endosymbionts are under relaxed selection compared with facultative endosymbionts. Selective strength is also relaxed in asexual Daphnia pulex lineages, compared with sexual lineages. Endogenous, nonfunctional, bornavirus-like elements are found to be under relaxed selection compared with exogenous Borna viruses. Finally, selection on the short-wavelength sensitive, SWS1, opsin genes in echolocating and nonecholocating bats is relaxed only in lineages in which this gene underwent pseudogenization; however, selection on the functional

  4. Miiuy croaker transferrin gene and evidence for positive selection events reveal different evolutionary patterns.

    PubMed

    Sun, Yueyan; Zhu, Zhihuang; Wang, Rixin; Sun, Yuena; Xu, Tianjun

    2012-01-01

    Transferrin (TF) is a protein that plays a central role in iron metabolism. This protein is associated with the innate immune system, which is responsible for disease defense responses after bacterial infection. The clear link between TF and the immune defense mechanism has led researchers to consider TF as a candidate gene for disease resistance. In this study, the Miichthys miiuy (miiuy croaker) TF gene (MIMI-TF) was cloned and characterized. The gene structure consisted of a coding region of 2070 nucleotides divided into 17 exons, as well as a non-coding region that included 16 introns and spans 6757 nucleotides. The deduced MIMI-TF protein consisted of 689 amino acids that comprised a signal peptide and two lobes (N- and C-lobes). MIMI-TF expression was significantly up-regulated after infection with Vibrio anguillarum. A series of model tests implemented in the CODEML program showed that TF underwent a complex evolutionary process. Branch-site models revealed that vertebrate TF was vastly different from that of invertebrates, and that the TF of the ancestors of aquatic and terrestrial organisms underwent different selection pressures. The site models detected 10 positively selected sites in extant TF genes. One site was located in the cleft between the N1 and N2 domains and was expected to affect the capability of TF to bind to or release iron indirectly. In addition, eight sites were found near the TF exterior. Two of these sites, which could have evolved from the competition for iron between pathogenic bacteria and TF, were located in potential pathogen-binding domains. Our results could be used to further investigate the function of TF and the selective mechanisms involved. PMID:22957037

  5. Evolutionary optimization of transcription factor binding motif detection.

    PubMed

    Zhang, Zhao; Wang, Ze; Mai, Guoqin; Luo, Youxi; Zhao, Miaomiao; Zhou, Fengfeng

    2015-01-01

    All the cell types are under strict control of how their genes are transcribed into expressed transcripts by the temporally dynamic orchestration of the transcription factor binding activities. Given a set of known binding sites (BSs) of a given transcription factor (TF), computational TFBS screening technique represents a cost efficient and large scale strategy to complement the experimental ones. There are two major classes of computational TFBS prediction algorithms based on the tertiary and primary structures, respectively. A tertiary structure based algorithm tries to calculate the binding affinity between a query DNA fragment and the tertiary structure of the given TF. Due to the limited number of available TF tertiary structures, primary structure based TFBS prediction algorithm is a necessary complementary technique for large scale TFBS screening. This study proposes a novel evolutionary algorithm to randomly mutate the weights of different positions in the binding motif of a TF, so that the overall TFBS prediction accuracy is optimized. The comparison with the most widely used algorithm, Position Weight Matrix (PWM), suggests that our algorithm performs better or the same level in all the performance measurements, including sensitivity, specificity, accuracy and Matthews correlation coefficient. Our data also suggests that it is necessary to remove the widely used assumption of independence between motif positions. The supplementary material may be found at: http://www.healthinformaticslab.org/supp/ . PMID:25387969

  6. An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection.

    PubMed

    Forni, Diego; Cagliani, Rachele; Tresoldi, Claudia; Pozzoli, Uberto; De Gioia, Luca; Filippi, Giulia; Riva, Stefania; Menozzi, Giorgia; Colleoni, Marta; Biasin, Mara; Lo Caputo, Sergio; Mazzotta, Francesco; Comi, Giacomo P; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2014-03-01

    The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes

  7. Using evolutionary computation to optimize an SVM used in detecting buried objects in FLIR imagery

    NASA Astrophysics Data System (ADS)

    Paino, Alex; Popescu, Mihail; Keller, James M.; Stone, Kevin

    2013-06-01

    In this paper we describe an approach for optimizing the parameters of a Support Vector Machine (SVM) as part of an algorithm used to detect buried objects in forward looking infrared (FLIR) imagery captured by a camera installed on a moving vehicle. The overall algorithm consists of a spot-finding procedure (to look for potential targets) followed by the extraction of several features from the neighborhood of each spot. The features include local binary pattern (LBP) and histogram of oriented gradients (HOG) as these are good at detecting texture classes. Finally, we project and sum each hit into UTM space along with its confidence value (obtained from the SVM), producing a confidence map for ROC analysis. In this work, we use an Evolutionary Computation Algorithm (ECA) to optimize various parameters involved in the system, such as the combination of features used, parameters on the Canny edge detector, the SVM kernel, and various HOG and LBP parameters. To validate our approach, we compare results obtained from an SVM using parameters obtained through our ECA technique with those previously selected by hand through several iterations of "guess and check".

  8. The evolutionary legacy of size-selective harvesting extends from genes to populations.

    PubMed

    Uusi-Heikkilä, Silva; Whiteley, Andrew R; Kuparinen, Anna; Matsumura, Shuichi; Venturelli, Paul A; Wolter, Christian; Slate, Jon; Primmer, Craig R; Meinelt, Thomas; Killen, Shaun S; Bierbach, David; Polverino, Giovanni; Ludwig, Arne; Arlinghaus, Robert

    2015-07-01

    Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size. PMID:26136825

  9. The evolutionary legacy of size-selective harvesting extends from genes to populations

    PubMed Central

    Uusi-Heikkilä, Silva; Whiteley, Andrew R; Kuparinen, Anna; Matsumura, Shuichi; Venturelli, Paul A; Wolter, Christian; Slate, Jon; Primmer, Craig R; Meinelt, Thomas; Killen, Shaun S; Bierbach, David; Polverino, Giovanni; Ludwig, Arne; Arlinghaus, Robert

    2015-01-01

    Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size. PMID:26136825

  10. Conserved evolutionary history for quick detection of threatening faces.

    PubMed

    Kawai, Nobuyuki; Kubo, Kenta; Masataka, Nobuo; Hayakawa, Sachiko

    2016-05-01

    Humans quickly recognize threats such as snakes and threatening faces, suggesting that human ancestors evolved specialized visual systems to detect biologically relevant threat stimuli. Although non-human primates also detect snakes quickly, it is unclear whether primates share the efficient visual systems to process the threatening faces of their conspecifics. Primates may not necessarily process conspecific threats by facial expressions, because threats from conspecifics in natural situations are often accompanied by other cues such as threatening actions (or attacks) and vocal calls. Here, we show a similar threat superiority effect in both humans and macaque Japanese monkeys. In visual search tasks, monkeys and humans both responded to pictures of a threatening face of an unfamiliar adult male monkey among neutral faces faster than to pictures of a neutral face among threatening faces. However, the monkeys' response times to detect deviant pictures of a non-face stimulus were not slower when it was shown among threat faces than when it was shown among neutral faces. These results provide the first evidence that monkeys have an attentional bias toward the threatening faces of conspecifics and suggest that threatening faces are evolutionarily relevant fear stimuli. The subcortical visual systems in primates likely process not only snakes, but also more general biological threat-relevant stimuli, including threatening conspecific faces. PMID:26714818

  11. Dynamic selective environments and evolutionary traps in human-dominated landscapes.

    PubMed

    Rodewald, Amanda D; Shustack, Daniel P; Jones, Todd M

    2011-09-01

    Human activities can alter selective environments in ways that can reduce the usefulness of certain ornamental traits as honest signals of individual quality and, in some cases, may create evolutionary traps, where rapid changes in selective environments result in maladaptive behavioral decisions. Using the sexually dichromatic, socially monogamous Northern Cardinal (Cardinalis cardinalis) as a model, we hypothesized that urbanization would erode the relationship between plumage coloration and reproductive success. Because the exotic Amur honeysuckle (Lonicera maackii) provides carotenoids, is a preferred habitat attribute, and increases vulnerability to nest predation, we predicted the presence of an evolutionary trap, whereby the brightest males would achieve the lowest reproductive success. Working at 14 forests in Ohio, USA, 2006-2008, we measured plumage color, monitored reproduction, and quantified habitat within territories. In rural landscapes, the brightest males bred earliest in the season and secured more preferred territories; however, annual reproduction declined with plumage brightness. Coloration of urban males was not associated with territory attributes or reproduction. Female redness across all landscapes was negatively related to reproduction. Poor reproductive performance of otherwise higher-quality males probably resulted from preferences for honeysuckle, which reduces annual reproduction when used as a nesting substrate early in the season. In this way, exotic shrubs prompted an evolutionary trap that was avoided in urban forests where anthropogenic resources disassociated male color and reproductive phenology and success. Our study illustrates how modified selective environments in human-dominated landscapes might shape microevolutionary processes in wild bird populations. PMID:21939074

  12. How quickly do brains catch up with bodies? A comparative method for detecting evolutionary lag.

    PubMed Central

    Deaner, R O; Nunn, C L

    1999-01-01

    A trait may be at odds with theoretical expectation because it is still in the process of responding to a recent selective force. Such a situation can be termed evolutionary lag. Although many cases of evolutionary lag have been suggested, almost all of the arguments have focused on trait fitness. An alternative approach is to examine the prediction that trait expression is a function of the time over which the trait could evolve. Here we present a phylogenetic comparative method for using this 'time' approach and we apply the method to a long-standing lag hypothesis: evolutionary changes in brain size lag behind evolutionary changes in body size. We tested the prediction in primates that brain mass contrast residuals, calculated from a regression of pairwise brain mass contrasts on positive pairwise body mass contrasts, are correlated with the time since the paired species diverged. Contrary to the brain size lag hypothesis, time since divergence was not significantly correlated with brain mass contrast residuals. We found the same result when we accounted for socioecology, used alternative body mass estimates and used male rather than female values. These tests do not support the brain size lag hypothesis. Therefore, body mass need not be viewed as a suspect variable in comparative neuroanatomical studies and relative brain size should not be used to infer recent evolutionary changes in body size. PMID:10331289

  13. Evolutionary signals of selection on cognition from the great tit genome and methylome.

    PubMed

    Laine, Veronika N; Gossmann, Toni I; Schachtschneider, Kyle M; Garroway, Colin J; Madsen, Ole; Verhoeven, Koen J F; de Jager, Victor; Megens, Hendrik-Jan; Warren, Wesley C; Minx, Patrick; Crooijmans, Richard P M A; Corcoran, Pádraic; Sheldon, Ben C; Slate, Jon; Zeng, Kai; van Oers, Kees; Visser, Marcel E; Groenen, Martien A M

    2016-01-01

    For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species. PMID:26805030

  14. Evolutionary signals of selection on cognition from the great tit genome and methylome

    PubMed Central

    Laine, Veronika N.; Gossmann, Toni I.; Schachtschneider, Kyle M.; Garroway, Colin J.; Madsen, Ole; Verhoeven, Koen J. F.; de Jager, Victor; Megens, Hendrik-Jan; Warren, Wesley C.; Minx, Patrick; Crooijmans, Richard P. M. A.; Corcoran, Pádraic; Adriaensen, Frank; Belda, Eduardo; Bushuev, Andrey; Cichon, Mariusz; Charmantier, Anne; Dingemanse, Niels; Doligez, Blandine; Eeva, Tapio; Erikstad, Kjell Einar; Fedorov, Slava; Hau, Michaela; Hille, Sabine; Hinde, Camilla; Kempenaers, Bart; Kerimov, Anvar; Krist, Milos; Mand, Raivo; Matthysen, Erik; Nager, Reudi; Norte, Claudia; Orell, Markku; Richner, Heinz; Slagsvold, Tore; Tilgar, Vallo; Tinbergen, Joost; Torok, Janos; Tschirren, Barbara; Yuta, Tera; Sheldon, Ben C.; Slate, Jon; Zeng, Kai; van Oers, Kees; Visser, Marcel E.; Groenen, Martien A. M.

    2016-01-01

    For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species. PMID:26805030

  15. Joint phenotypes, evolutionary conflict and the fundamental theorem of natural selection

    PubMed Central

    Queller, David C.

    2014-01-01

    Multiple organisms can sometimes affect a common phenotype. For example, the portion of a leaf eaten by an insect is a joint phenotype of the plant and insect and the amount of food obtained by an offspring can be a joint trait with its mother. Here, I describe the evolution of joint phenotypes in quantitative genetic terms. A joint phenotype for multiple species evolves as the sum of additive genetic variances in each species, weighted by the selection on each species. Selective conflict between the interactants occurs when selection takes opposite signs on the joint phenotype. The mean fitness of a population changes not just through its own genetic variance but also through the genetic variance for its fitness that resides in other species, an update of Fisher's fundamental theorem of natural selection. Some similar results, using inclusive fitness, apply to within-species interactions. The models provide a framework for understanding evolutionary conflicts at all levels. PMID:24686940

  16. Optimal Wavelengths Selection Using Hierarchical Evolutionary Algorithm for Prediction of Firmness and Soluble Solids Content in Apples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hyperspectral scattering is a promising technique for rapid and noninvasive measurement of multiple quality attributes of apple fruit. A hierarchical evolutionary algorithm (HEA) approach, in combination with subspace decomposition and partial least squares (PLS) regression, was proposed to select o...

  17. Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today.

    PubMed

    Kutschera, Ulrich

    2009-11-01

    The book On the Origin of Species, published in November 1859, is an "abstract" without references, compiled by Charles Darwin from a much longer manuscript entitled "Natural Selection." Here, I summarize the five theories that can be extracted from Darwin's monograph, explain the true meaning of the phrase "struggle for life" (i.e., competition and cooperation), and outline Darwin's original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that "selection only eliminates but is not creative" is still alive today. However, I document that August Weismann (Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen (Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this "Weismann-Schmalhausen principle" with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky (Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by prokaryotic microbes. Eubacteria

  18. Structural Dynamics of GaN Microcrystals in Evolutionary Selection Selective Area Growth probed by X-ray Microdiffraction

    PubMed Central

    Kachkanov, V.; Leung, B.; Song, J.; Zhang, Y.; Tsai, M.-C.; Yuan, G.; Han, J.; O'Donnell, K. P.

    2014-01-01

    A method to grow high quality, single crystalline semiconductor material irrespective of the substrate would allow a cost-effective improvement to functionality and performance of optoelectronic devices. Recently, a novel type of substrate-insensitive growth process called Evolutionary Selection Selective Area Growth (ES-SAG) has been proposed. Here we report the use of X-ray microdiffraction to study the structural properties of GaN microcrystals grown by ES-SAG. Utilizing high resolution in both direct and reciprocal spaces, we have unraveled structural dynamics of GaN microcrystals in growth structures of different dimensions. It has been found that the geometric proportions of the growth constrictions play an important role: 2.6 μm and 4.5 μm wide growth tunnels favor the evolutionary selection mechanism, contrary to the case of 8.6 μm growth tunnels. It was also found that GaN microcrystal ensembles are dominated by slight tensile strain irrespective of growth tunnel shape. PMID:24722064

  19. Unintentional selection, unanticipated insights: introductions, stocking and the evolutionary ecology of fishes.

    PubMed

    Hutchings, J A

    2014-12-01

    Natural environmental change has produced countless opportunities for species to disperse into and persist in habitats where they previously did not exist. Introduction and stocking programmes have facilitated similar sorts of colonization opportunities across considerably greater geographical scales and often in much shorter periods of time. Even though the mechanism of colonization differs, the result can be the same: evolutionary change in the colonizing population in response to novel selection pressures. As a consequence, some human-mediated fish transfers have unintentionally yielded novel research opportunities to study how phenotypes and genes interact with their environment and affect ecological and evolutionary change. The primary purpose here is to explore how work, directly or indirectly involved with human-mediated transfers, has unintentionally yielded novel research and research opportunities in fish ecology and evolution. Insights have produced new knowledge or altered previously held perceptions on topics such as local adaptation, rate of evolutionary change, phenotypic plasticity, alternative reproductive strategies, population structure and colonization probability. Well-documented stocking programmes, especially in terms of history, numbers and original population sources, can provide highly fertile ground for generating further insights on the ecology and evolution of fishes and of the factors likely to influence the success of conservation-based, restoration programmes. PMID:25469951

  20. Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

    PubMed Central

    Offman, Marc N; Tournier, Alexander L; Bates, Paul A

    2008-01-01

    Background Automatic protein modelling pipelines are becoming ever more accurate; this has come hand in hand with an increasingly complicated interplay between all components involved. Nevertheless, there are still potential improvements to be made in template selection, refinement and protein model selection. Results In the context of an automatic modelling pipeline, we analysed each step separately, revealing several non-intuitive trends and explored a new strategy for protein conformation sampling using Genetic Algorithms (GA). We apply the concept of alternating evolutionary pressure (AEP), i.e. intermediate rounds within the GA runs where unrestrained, linear growth of the model populations is allowed. Conclusion This approach improves the overall performance of the GA by allowing models to overcome local energy barriers. AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA. PMID:18673557

  1. Differential Evolutionary Selection and Natural Evolvability Observed in ALT Proteins of Human Filarial Parasites

    PubMed Central

    Devoe, Neil C.; Corbett, Ian J.; Barker, Linsey; Chang, Robert; Gudis, Polyxeni; Mullen, Nathan; Perez, Kailey; Raposo, Hugo; Scholz, John; May, Meghan

    2016-01-01

    The abundant larval transcript (ALT-2) protein is present in all members of the Filarioidea, and has been reported as a potential candidate antigen for a subunit vaccine against lymphatic filariasis. To assess the potential for vaccine escape or heterologous protection, we examined the evolutionary selection acting on ALT-2. The ratios of nonsynonymous (K(a)) to synonymous (K(s)) mutation frequencies (ω) were calculated for the alt-2 genes of the lymphatic filariasis agents Brugia malayi and Wuchereria bancrofti and the agents of river blindness and African eyeworm disease Onchocerca volvulus and Loa loa. Two distinct Bayesian models of sequence evolution showed that ALT-2 of W. bancrofti and L. loa were under significant (P<0.05; P < 0.001) diversifying selection, while ALT-2 of B. malayi and O. volvulus were under neutral to stabilizing selection. Diversifying selection as measured by ω values was notably strongest on the region of ALT-2 encoding the signal peptide of L. loa and was elevated in the variable acidic domain of L. loa and W. bancrofti. Phylogenetic analysis indicated that the ALT-2 consensus sequences formed three clades: the first consisting of B. malayi, the second consisting of W. bancrofti, and the third containing both O. volvulus and L. loa. ALT-2 selection was therefore not predictable by phylogeny or pathology, as the two species parasitizing the eye were selected differently, as were the two species parasitizing the lymphatic system. The most immunogenic regions of L. loa and W. bancrofti ALT-2 sequence as modeled by antigenicity prediction analysis did not correspond with elevated levels of diversifying selection, and were not selected differently than predicted antigenic epitopes in B. malayi and O. volvulus. Measurements of ALT-2 evolvability made by χ2 analysis between alleles that were stable (O. volvulus and B. malayi) and those that were under diversifying selection (W. bancrofti and L. loa) indicated significant (P<0

  2. Differential Evolutionary Selection and Natural Evolvability Observed in ALT Proteins of Human Filarial Parasites.

    PubMed

    Devoe, Neil C; Corbett, Ian J; Barker, Linsey; Chang, Robert; Gudis, Polyxeni; Mullen, Nathan; Perez, Kailey; Raposo, Hugo; Scholz, John; May, Meghan

    2016-01-01

    The abundant larval transcript (ALT-2) protein is present in all members of the Filarioidea, and has been reported as a potential candidate antigen for a subunit vaccine against lymphatic filariasis. To assess the potential for vaccine escape or heterologous protection, we examined the evolutionary selection acting on ALT-2. The ratios of nonsynonymous (K(a)) to synonymous (K(s)) mutation frequencies (ω) were calculated for the alt-2 genes of the lymphatic filariasis agents Brugia malayi and Wuchereria bancrofti and the agents of river blindness and African eyeworm disease Onchocerca volvulus and Loa loa. Two distinct Bayesian models of sequence evolution showed that ALT-2 of W. bancrofti and L. loa were under significant (P<0.05; P < 0.001) diversifying selection, while ALT-2 of B. malayi and O. volvulus were under neutral to stabilizing selection. Diversifying selection as measured by ω values was notably strongest on the region of ALT-2 encoding the signal peptide of L. loa and was elevated in the variable acidic domain of L. loa and W. bancrofti. Phylogenetic analysis indicated that the ALT-2 consensus sequences formed three clades: the first consisting of B. malayi, the second consisting of W. bancrofti, and the third containing both O. volvulus and L. loa. ALT-2 selection was therefore not predictable by phylogeny or pathology, as the two species parasitizing the eye were selected differently, as were the two species parasitizing the lymphatic system. The most immunogenic regions of L. loa and W. bancrofti ALT-2 sequence as modeled by antigenicity prediction analysis did not correspond with elevated levels of diversifying selection, and were not selected differently than predicted antigenic epitopes in B. malayi and O. volvulus. Measurements of ALT-2 evolvability made by χ2 analysis between alleles that were stable (O. volvulus and B. malayi) and those that were under diversifying selection (W. bancrofti and L. loa) indicated significant (P<0

  3. If there is an evolutionary selection pressure for the high frequency of MBL2 polymorphisms, what is it?

    PubMed Central

    Eisen, D P; Osthoff, M

    2014-01-01

    Either immune selection or stochastic processes may have influenced the frequency of highly polymorphic genes such as mannose-binding lectin 2 (MBL2). This pattern recognition receptor of the innate immune system recognizes and binds to pathogenic microorganisms and apoptotic cells leading to lectin pathway complement killing or clearance. In almost all of a large number of studies in different ethnic groups worldwide there is 20–25% carriage of low MBL2 haplotypes, with 8–10% of each population having no MBL detectable in the blood. The source of this high variability of MBL2 remains cryptic. It arises from six main snps in the prompter and exon regions of the gene that assort into seven common haplotypes under linkage disequilibrium. While global studies of MBL2 show that it is not under immune selection pressure, these results are not the same when the same population genetic tools are used on large national studies. Other analyses point to the silenced MBL1 pseudogene and development of promoter polymorphisms in humans as evidence of selection pressure favouring low-producing haplotypes. While these analyses cannot be reconciled readily, there are two processes by which MBL heterozygosity could have been advantageous in an evolutionary sense; protection against adverse effects of various infectious diseases and lethal manifestations of atherosclerosis – a disease that now seems to have a more ancient history than assumed previously. Ultimately, consideration of the context for possible future therapeutic manipulation of MBL means that this can proceed independently of resolution of the evolutionary forces that have shaped MBL2 polymorphism. PMID:24255984

  4. If there is an evolutionary selection pressure for the high frequency of MBL2 polymorphisms, what is it?

    PubMed

    Eisen, D P; Osthoff, M

    2014-05-01

    Either immune selection or stochastic processes may have influenced the frequency of highly polymorphic genes such as mannose-binding lectin 2 (MBL2). This pattern recognition receptor of the innate immune system recognizes and binds to pathogenic microorganisms and apoptotic cells leading to lectin pathway complement killing or clearance. In almost all of a large number of studies in different ethnic groups worldwide there is 20-25% carriage of low MBL2 haplotypes, with 8-10% of each population having no MBL detectable in the blood. The source of this high variability of MBL2 remains cryptic. It arises from six main snps in the prompter and exon regions of the gene that assort into seven common haplotypes under linkage disequilibrium. While global studies of MBL2 show that it is not under immune selection pressure, these results are not the same when the same population genetic tools are used on large national studies. Other analyses point to the silenced MBL1 pseudogene and development of promoter polymorphisms in humans as evidence of selection pressure favouring low-producing haplotypes. While these analyses cannot be reconciled readily, there are two processes by which MBL heterozygosity could have been advantageous in an evolutionary sense; protection against adverse effects of various infectious diseases and lethal manifestations of atherosclerosis - a disease that now seems to have a more ancient history than assumed previously. Ultimately, consideration of the context for possible future therapeutic manipulation of MBL means that this can proceed independently of resolution of the evolutionary forces that have shaped MBL2 polymorphism. PMID:24255984

  5. Selection of relevant input variables in storm water quality modeling by multiobjective evolutionary polynomial regression paradigm

    NASA Astrophysics Data System (ADS)

    Creaco, E.; Berardi, L.; Sun, Siao; Giustolisi, O.; Savic, D.

    2016-04-01

    The growing availability of field data, from information and communication technologies (ICTs) in "smart" urban infrastructures, allows data modeling to understand complex phenomena and to support management decisions. Among the analyzed phenomena, those related to storm water quality modeling have recently been gaining interest in the scientific literature. Nonetheless, the large amount of available data poses the problem of selecting relevant variables to describe a phenomenon and enable robust data modeling. This paper presents a procedure for the selection of relevant input variables using the multiobjective evolutionary polynomial regression (EPR-MOGA) paradigm. The procedure is based on scrutinizing the explanatory variables that appear inside the set of EPR-MOGA symbolic model expressions of increasing complexity and goodness of fit to target output. The strategy also enables the selection to be validated by engineering judgement. In such context, the multiple case study extension of EPR-MOGA, called MCS-EPR-MOGA, is adopted. The application of the proposed procedure to modeling storm water quality parameters in two French catchments shows that it was able to significantly reduce the number of explanatory variables for successive analyses. Finally, the EPR-MOGA models obtained after the input selection are compared with those obtained by using the same technique without benefitting from input selection and with those obtained in previous works where other data-modeling techniques were used on the same data. The comparison highlights the effectiveness of both EPR-MOGA and the input selection procedure.

  6. Detection Progress of Selected Drugs in TLC

    PubMed Central

    Pyka, Alina

    2014-01-01

    This entry describes applications of known indicators and dyes as new visualizing reagents and various visualizing systems as well as photocatalytic reactions and bioautography method for the detection of bioactive compounds including drugs and compounds isolated from herbal extracts. Broadening index, detection index, characteristics of densitometric band, modified contrast index, limit of detection, densitometric visualizing index, and linearity range of detected compounds were used for the evaluation of visualizing effects of applied visualizing reagents. It was shown that visualizing effect depends on the chemical structure of the visualizing reagent, the structure of the substance detected, and the chromatographic adsorbent applied. The usefulness of densitometry to direct detection of some drugs was also shown. Quoted papers indicate the detection progress of selected drugs investigated by thin-layer chromatography (TLC). PMID:24551853

  7. Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials

    PubMed Central

    Meyer-Lucht, Yvonne; Otten, Celine; Püttker, Thomas; Sommer, Simone

    2008-01-01

    Background Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined. Results G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species. Conclusion Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism. PMID:18534008

  8. Charles Darwin's Origin of Species, directional selection, and the evolutionary sciences today

    NASA Astrophysics Data System (ADS)

    Kutschera, Ulrich

    2009-11-01

    The book On the Origin of Species, published in November 1859, is an “abstract” without references, compiled by Charles Darwin from a much longer manuscript entitled “Natural Selection.” Here, I summarize the five theories that can be extracted from Darwin’s monograph, explain the true meaning of the phrase “struggle for life” (i.e., competition and cooperation), and outline Darwin’s original concept of natural selection in populations of animals and plants. Since neither Darwin nor Alfred R. Wallace distinguished between stabilizing and directional natural selection, the popular argument that “selection only eliminates but is not creative” is still alive today. However, I document that August Weismann ( Die Bedeutung der sexuellen Fortpflanzung für die Selektions-Theorie. Gustav Fischer-Verlag, Jena, 1886) and Ivan Schmalhausen ( Factors of evolution. The theory of stabilizing selection. The Blackiston Company, Philadelphia, 1949) provided precise definitions for directional (dynamic) selection in nature and illustrate this “Weismann-Schmalhausen principle” with respect to the evolutionary development of novel phenotypes. Then, the modern (synthetic) theory of biological evolution that is based on the work of Theodosius Dobzhansky ( Genetics and the origin of species. Columbia University Press, New York, 1937) and others, and the expanded version of this system of theories, are outlined. Finally, I document that symbiogenesis (i.e., primary endosymbiosis, a process that gave rise to the first eukaryotic cells), ongoing directional natural selection, and the dynamic Earth (plate tectonics, i.e., geological events that both created and destroyed terrestrial and aquatic habitats) were the key processes responsible for the documented macroevolutionary patterns in all five kingdoms of life. Since the evolutionary development of the earliest archaic bacteria more than 3,500 mya, the biosphere of our dynamic planet has been dominated by

  9. Similarly Strong Purifying Selection Acts on Human Disease Genes of All Evolutionary Ages

    PubMed Central

    Cai, James J.; Borenstein, Elhanan; Chen, Rong

    2009-01-01

    A number of studies have showed that recently created genes differ from the genes created in deep evolutionary past in many aspects. Here, we determined the age of emergence and propensity for gene loss (PGL) of all human protein–coding genes and compared disease genes with non-disease genes in terms of their evolutionary rate, strength of purifying selection, mRNA expression, and genetic redundancy. The older and the less prone to loss, non-disease genes have been evolving 1.5- to 3-fold slower between humans and chimps than young non-disease genes, whereas Mendelian disease genes have been evolving very slowly regardless of their ages and PGL. Complex disease genes showed an intermediate pattern. Disease genes also have higher mRNA expression heterogeneity across multiple tissues than non-disease genes regardless of age and PGL. Young and middle-aged disease genes have fewer similar paralogs as non-disease genes of the same age. We reasoned that genes were more likely to be involved in human disease if they were under a strong functional constraint, expressed heterogeneously across tissues, and lacked genetic redundancy. Young human genes that have been evolving under strong constraint between humans and chimps might also be enriched for genes that encode important primate or even human-specific functions. PMID:20333184

  10. Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits.

    PubMed

    Lau, Jennifer A; Lennon, Jay T

    2011-10-01

    • Below-ground microbial communities influence plant diversity, plant productivity, and plant community composition. Given these strong ecological effects, are interactions with below-ground microbes also important for understanding natural selection on plant traits? • Here, we manipulated below-ground microbial communities and the soil moisture environment on replicated populations of Brassica rapa to examine how microbial community structure influences selection on plant traits and mediates plant responses to abiotic environmental stress. • In soils with experimentally simplified microbial communities, plants were smaller, had reduced chlorophyll content, produced fewer flowers, and were less fecund when compared with plant populations grown in association with more complex soil microbial communities. Selection on plant growth and phenological traits also was stronger when plants were grown in simplified, less diverse soil microbial communities, and these effects typically were consistent across soil moisture treatments. • Our results suggest that microbial community structure affects patterns of natural selection on plant traits. Thus, the below-ground microbial community can influence evolutionary processes, just as recent studies have demonstrated that microbial diversity can influence plant community and ecosystem processes. PMID:21658184

  11. Negative Selection Algorithm for Aircraft Fault Detection

    NASA Technical Reports Server (NTRS)

    Dasgupta, D.; KrishnaKumar, K.; Wong, D.; Berry, M.

    2004-01-01

    We investigated a real-valued Negative Selection Algorithm (NSA) for fault detection in man-in-the-loop aircraft operation. The detection algorithm uses body-axes angular rate sensory data exhibiting the normal flight behavior patterns, to generate probabilistically a set of fault detectors that can detect any abnormalities (including faults and damages) in the behavior pattern of the aircraft flight. We performed experiments with datasets (collected under normal and various simulated failure conditions) using the NASA Ames man-in-the-loop high-fidelity C-17 flight simulator. The paper provides results of experiments with different datasets representing various failure conditions.

  12. An evolutionary theory of large-scale human warfare: Group-structured cultural selection.

    PubMed

    Zefferman, Matthew R; Mathew, Sarah

    2015-01-01

    When humans wage war, it is not unusual for battlefields to be strewn with dead warriors. These warriors typically were men in their reproductive prime who, had they not died in battle, might have gone on to father more children. Typically, they are also genetically unrelated to one another. We know of no other animal species in which reproductively capable, genetically unrelated individuals risk their lives in this manner. Because the immense private costs borne by individual warriors create benefits that are shared widely by others in their group, warfare is a stark evolutionary puzzle that is difficult to explain. Although several scholars have posited models of the evolution of human warfare, these models do not adequately explain how humans solve the problem of collective action in warfare at the evolutionarily novel scale of hundreds of genetically unrelated individuals. We propose that group-structured cultural selection explains this phenomenon. PMID:25914359

  13. Hybridization of Evolutionary Mechanisms for Feature Subset Selection in Unsupervised Learning

    NASA Astrophysics Data System (ADS)

    Torres, Dolores; Ponce-de-León, Eunice; Torres, Aurora; Ochoa, Alberto; Díaz, Elva

    Feature subset selection for unsupervised learning, is a very important topic in artificial intelligence because it is the base for saving computational resources. In this implementation we use a typical testor’s methodology in order to incorporate an importance index for each variable. This paper presents the general framework and the way two hybridized meta-heuristics work in this NP-complete problem. The evolutionary mechanisms are based on the Univariate Marginal Distribution Algorithm (UMDA) and the Genetic Algorithm (GA). GA and UMDA - Estimation of Distribution Algorithm (EDA) use a very useful rapid operator implemented for finding typical testors on a very large dataset and also, both algorithms, have a local search mechanism for improving time and fitness. Experiments show that EDA is faster than GA because it has a better exploitation performance; nevertheless, GA’ solutions are more consistent.

  14. Detection and characterization of flaws in CFRP by SQUID gradiometer using evolutionary computation

    NASA Astrophysics Data System (ADS)

    Kojima, F.; Kawai, R.; Kasai, N.; Hatsukade, H.

    2002-05-01

    This paper is concerned with a quantitative nondestructive evaluation of a carbon fiberglass reinforced plastic (CFRP) using the low temperature superconductor (LTS) SQUID gradiometer. The evaluation can be implemented by applying the alternative current injection to the CFRP with a defect. A 3D finite element code is developed for analyzing the SQUID based nondestructive system. Using the evolutionary programming, an efficient inverse scheme is proposed for recovering flaws in CFRP. The proposed algorithm is tested for the detection and characterization of flaws in the CFRP samples.

  15. Orientation Selectivity Sharpens Motion Detection in Drosophila.

    PubMed

    Fisher, Yvette E; Silies, Marion; Clandinin, Thomas R

    2015-10-21

    Detecting the orientation and movement of edges in a scene is critical to visually guided behaviors of many animals. What are the circuit algorithms that allow the brain to extract such behaviorally vital visual cues? Using in vivo two-photon calcium imaging in Drosophila, we describe direction selective signals in the dendrites of T4 and T5 neurons, detectors of local motion. We demonstrate that this circuit performs selective amplification of local light inputs, an observation that constrains motion detection models and confirms a core prediction of the Hassenstein-Reichardt correlator (HRC). These neurons are also orientation selective, responding strongly to static features that are orthogonal to their preferred axis of motion, a tuning property not predicted by the HRC. This coincident extraction of orientation and direction sharpens directional tuning through surround inhibition and reveals a striking parallel between visual processing in flies and vertebrate cortex, suggesting a universal strategy for motion processing. PMID:26456048

  16. Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments.

    PubMed

    McNamara, John M; Dall, Sasha R X; Hammerstein, Peter; Leimar, Olof

    2016-10-01

    There are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist. PMID:27600658

  17. Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria

    PubMed Central

    2013-01-01

    Background Actinobacteria have adapted to contrasted ecological niches such as the soil, and among others to plants or animals as pathogens or symbionts. Mycobacterium genus contains mostly pathogens that cause a variety of mammalian diseases, among which the well-known leprosy and tuberculosis, it also has saprophytic relatives. Streptomyces genus is mostly a soil microbe known for its secondary metabolites, it contains also plant pathogens, animal pathogens and symbionts. Frankia, a nitrogen-fixing actinobacterium establishes a root symbiosis with dicotyledonous pionneer plants. Pathogens and symbionts live inside eukaryotic cells and tissues and interact with their cellular environment through secreted proteins and effectors transported through transmembrane systems; nevertheless they also need to avoid triggering host defense reactions. A comparative genome analysis of the secretomes of symbionts and pathogens allows a thorough investigation of selective pressures shaping their evolution. In the present study, the rates of silent mutations to non-silent mutations in secretory proteins were assessed in different strains of Frankia, Streptomyces and Mycobacterium, of which several genomes have recently become publicly available. Results It was found that secreted proteins as a whole have a stronger purifying evolutionary rate (non-synonymous to synonymous substitutions or Ka/Ks ratio) than the non-secretory proteins in most of the studied genomes. This difference becomes statistically significant in cases involving obligate symbionts and pathogens. Amongst the Frankia, secretomes of symbiotic strains were found to have undergone evolutionary trends different from those of the mainly saprophytic strains. Even within the secretory proteins, the signal peptide part has a higher Ka/Ks ratio than the mature part. Two contrasting trends were noticed amongst the Frankia genomes regarding the relation between selection strength (i.e. Ka/Ks ratio) and the codon adaptation

  18. PROTECTED POLYMORPHISMS AND EVOLUTIONARY STABILITY OF PATCH-SELECTION STRATEGIES IN STOCHASTIC ENVIRONMENTS

    PubMed Central

    EVANS, STEVEN N.; HENING, ALEXANDRU; SCHREIBER, SEBASTIAN J.

    2015-01-01

    We consider a population living in a patchy environment that varies stochastically in space and time. The population is composed of two morphs (that is, individuals of the same species with different genotypes). In terms of survival and reproductive success, the associated phenotypes differ only in their habitat selection strategies. We compute invasion rates corresponding to the rates at which the abundance of an initially rare morph increases in the presence of the other morph established at equilibrium. If both morphs have positive invasion rates when rare, then there is an equilibrium distribution such that the two morphs coexist; that is, there is a protected polymorphism for habitat selection. Alternatively, if one morph has a negative invasion rate when rare, then it is asymptotically displaced by the other morph under all initial conditions where both morphs are present. We refine the characterization of an evolutionary stable strategy for habitat selection from [Schreiber, 2012] in a mathematically rigorous manner. We provide a necessary and sufficient condition for the existence of an ESS that uses all patches and determine when using a single patch is an ESS. We also provide an explicit formula for the ESS when there are two habitat types. We show that adding environmental stochasticity results in an ESS that, when compared to the ESS for the corresponding model without stochasticity, spends less time in patches with larger carrying capacities and possibly makes use of sink patches, thereby practicing a spatial form of bet hedging. PMID:25151369

  19. Detecting genetic drift versus selection in human evolution

    PubMed Central

    Ackermann, Rebecca Rogers; Cheverud, James M.

    2004-01-01

    Recent paleoanthropological discoveries reveal a diverse, potentially speciose human fossil record. Such extensive morphological diversity results from the action of divergent evolutionary forces on an evolving lineage. Here, we apply quantitative evolutionary theory to test whether random evolutionary processes alone can explain the morphological diversity seen among fossil australopith and early Homo crania from the Plio–Pleistocene. We show that although selection may have played an important role in diversifying hominin facial morphology in the late Pliocene, this is not the case during the early evolution of the genus Homo, where genetic drift was probably the primary force responsible for facial diversification. PMID:15604148

  20. Evolutionary study of a potential selection target region in the pig.

    PubMed

    Ojeda, A; Ramos-Onsins, S E; Marletta, D; Huang, L S; Folch, J M; Pérez-Enciso, M

    2011-02-01

    Domestication, modern breeding and artificial selection have shaped dramatically the genomic variability of domestic animals. In livestock, the so-called FAT1 quantitative trait locus (QTL) in porcine chromosome 4 was the first QTL uncovered although, to date, its precise molecular nature has remained elusive. Here, we characterize the nucleotide variability of 13 fragments of ∼500 bp equally spaced in a 2 Mb region in the vicinity of the FAT1 region in a wide-diversity panel of 32 pigs. Asian and European animals, including local Mediterranean and international pig breeds, were sequenced. Patterns of genetic variability were very complex and varied largely across loci and populations; they did not reveal overall a clear signal of a selective sweep in any breed, although FABP4 fragment showed a significantly higher diversity. We used an approximate Bayesian computation approach to infer the evolutionary history of this SSC4 region. Notably, we found that European pig populations have a much lower effective size than their Asian counterparts: in the order of hundreds vs hundreds of thousands. We show also an important part of extant European variability is actually due to introgression of Asian germplasm into Europe. This study shows how a potential loss in diversity caused by bottlenecks and possible selective sweeps associated with domestication and artificial selection can be counterbalanced by migration, making it much more difficult the identification of selection footprints based on naive demographic assumptions. Given the small fragment analyzed here, it remains to be studied how these conclusions apply to the rest of the genome. PMID:20502482

  1. Evolutionary neural networks for anomaly detection based on the behavior of a program.

    PubMed

    Han, Sang-Jun; Cho, Sung-Bae

    2006-06-01

    The process of learning the behavior of a given program by using machine-learning techniques (based on system-call audit data) is effective to detect intrusions. Rule learning, neural networks, statistics, and hidden Markov models (HMMs) are some of the kinds of representative methods for intrusion detection. Among them, neural networks are known for good performance in learning system-call sequences. In order to apply this knowledge to real-world problems successfully, it is important to determine the structures and weights of these call sequences. However, finding the appropriate structures requires very long time periods because there are no suitable analytical solutions. In this paper, a novel intrusion-detection technique based on evolutionary neural networks (ENNs) is proposed. One advantage of using ENNs is that it takes less time to obtain superior neural networks than when using conventional approaches. This is because they discover the structures and weights of the neural networks simultaneously. Experimental results with the 1999 Defense Advanced Research Projects Agency (DARPA) Intrusion Detection Evaluation (IDEVAL) data confirm that ENNs are promising tools for intrusion detection. PMID:16761810

  2. Chaos Enhanced Differential Evolution in the Task of Evolutionary Control of Selected Set of Discrete Chaotic Systems

    PubMed Central

    Pluhacek, Michal; Davendra, Donald; Oplatková Kominkova, Zuzana

    2014-01-01

    Evolutionary technique differential evolution (DE) is used for the evolutionary tuning of controller parameters for the stabilization of set of different chaotic systems. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used also as the chaotic pseudorandom number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudorandom sequences given by chaotic map to help differential evolution algorithm search for the best controller settings for the very same chaotic system. The optimizations were performed for three different chaotic systems, two types of case studies and developed cost functions. PMID:25243230

  3. Testing for natural selection in human exonic splicing regulators associated with evolutionary rate shifts.

    PubMed

    Ramalho, Rodrigo F; Gelfman, Sahar; de Souza, Jorge E; Ast, Gil; de Souza, Sandro J; Meyer, Diogo

    2013-04-01

    Despite evidence that at the interspecific scale, exonic splicing silencers (ESSs) are under negative selection in constitutive exons, little is known about the effects of slightly deleterious polymorphisms on these splicing regulators. Through the application of a modified version of the McDonald-Kreitman test, we compared the normalized proportions of human polymorphisms and human/rhesus substitutions affecting exonic splicing regulators (ESRs) on sequences of constitutive and alternative exons. Our results show a depletion of substitutions and an enrichment of SNPs associated with ESS gain in constitutive exons. Moreover, we show that this evolutionary pattern is also present in a set of ESRs previously involved in the transition from constitutive to skipped exons in the mammalian lineage. The similarity between these two sets of ESRs suggests that the transition from constitutive to skipped exons in mammals is more frequently associated with the inhibition than with the promotion of splicing signals. This is in accordance with the hypothesis of a constitutive origin of exon skipping and corroborates previous findings about the antagonistic role of certain exonic splicing enhancers. PMID:23529588

  4. Delayed life history effects, multilevel selection, and evolutionary trade-offs in the California tiger salamander.

    PubMed

    Searcy, Christopher A; Gray, Levi N; Trenham, Peter C; Shaffer, H Bradley

    2014-01-01

    Delayed life history effects (DLHEs) occur when fitness in one life stage affects fitness in subsequent life stages. Given their biphasic life cycle, pond-breeding amphibians provide a natural system for studying DLHEs, although these effects are not restricted to species with biphasic life histories. In this study, we used multiple mark-recapture techniques enabled by a large trapping array to monitor components of fitness and resulting DLHEs in a population of the endangered California tiger salamander (Ambystoma californiense). We found that DLHEs are prominent across all life stage transitions and that there is variation in whether selection acts primarily at the individual or cohort level. We also demonstrated that there is more than an order of magnitude variation in mean cohort fitness, providing tremendous variation for DLHEs to act upon. We documented an evolutionary trade-off between mass at emergence and date of emergence, which may play a role in maintaining the variation in mass (fitness) at emergence. A literature review revealed that such high levels of intercohort variation occur in many other pond-breeding amphibians, and that appropriately documenting the magnitude of intercohort variation requires long-term studies (roughly two population turnovers). Given the profound effect that DLHEs can have on population dynamics, quantifying intercohort variation in mean fitness and the level(s) at which selection acts will be very important for developing accurate models of population dynamics. In general, when developing models of population dynamics, more attention should be paid to variation in mean fitness and not just variation in total numbers. PMID:24649647

  5. Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome

    PubMed Central

    Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

    2016-01-01

    Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts. PMID:26927064

  6. Detecting signatures of positive selection associated with musical aptitude in the human genome

    PubMed Central

    Liu, Xuanyao; Kanduri, Chakravarthi; Oikkonen, Jaana; Karma, Kai; Raijas, Pirre; Ukkola-Vuoti, Liisa; Teo, Yik-Ying; Järvelä, Irma

    2016-01-01

    Abilities related to musical aptitude appear to have a long history in human evolution. To elucidate the molecular and evolutionary background of musical aptitude, we compared genome-wide genotyping data (641 K SNPs) of 148 Finnish individuals characterized for musical aptitude. We assigned signatures of positive selection in a case-control setting using three selection methods: haploPS, XP-EHH and FST. Gene ontology classification revealed that the positive selection regions contained genes affecting inner-ear development. Additionally, literature survey has shown that several of the identified genes were known to be involved in auditory perception (e.g. GPR98, USH2A), cognition and memory (e.g. GRIN2B, IL1A, IL1B, RAPGEF5), reward mechanisms (RGS9), and song perception and production of songbirds (e.g. FOXP1, RGS9, GPR98, GRIN2B). Interestingly, genes related to inner-ear development and cognition were also detected in a previous genome-wide association study of musical aptitude. However, the candidate genes detected in this study were not reported earlier in studies of musical abilities. Identification of genes related to language development (FOXP1 and VLDLR) support the popular hypothesis that music and language share a common genetic and evolutionary background. The findings are consistent with the evolutionary conservation of genes related to auditory processes in other species and provide first empirical evidence for signatures of positive selection for abilities that contribute to musical aptitude. PMID:26879527

  7. Detecting signatures of positive selection associated with musical aptitude in the human genome.

    PubMed

    Liu, Xuanyao; Kanduri, Chakravarthi; Oikkonen, Jaana; Karma, Kai; Raijas, Pirre; Ukkola-Vuoti, Liisa; Teo, Yik-Ying; Järvelä, Irma

    2016-01-01

    Abilities related to musical aptitude appear to have a long history in human evolution. To elucidate the molecular and evolutionary background of musical aptitude, we compared genome-wide genotyping data (641 K SNPs) of 148 Finnish individuals characterized for musical aptitude. We assigned signatures of positive selection in a case-control setting using three selection methods: haploPS, XP-EHH and FST. Gene ontology classification revealed that the positive selection regions contained genes affecting inner-ear development. Additionally, literature survey has shown that several of the identified genes were known to be involved in auditory perception (e.g. GPR98, USH2A), cognition and memory (e.g. GRIN2B, IL1A, IL1B, RAPGEF5), reward mechanisms (RGS9), and song perception and production of songbirds (e.g. FOXP1, RGS9, GPR98, GRIN2B). Interestingly, genes related to inner-ear development and cognition were also detected in a previous genome-wide association study of musical aptitude. However, the candidate genes detected in this study were not reported earlier in studies of musical abilities. Identification of genes related to language development (FOXP1 and VLDLR) support the popular hypothesis that music and language share a common genetic and evolutionary background. The findings are consistent with the evolutionary conservation of genes related to auditory processes in other species and provide first empirical evidence for signatures of positive selection for abilities that contribute to musical aptitude. PMID:26879527

  8. Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes.

    PubMed

    Ganu, Radhika S; Ishida, Yasuko; Koutmos, Markos; Kolokotronis, Sergios-Orestis; Roca, Alfred L; Garrow, Timothy A; Schook, Lawrence B

    2015-01-01

    Betaine-homocysteine S-methyltransferase (BHMT) and BHMT2 convert homocysteine to methionine using betaine and S-methylmethionine, respectively, as methyl donor substrates. Increased levels of homocysteine in blood are associated with cardiovascular disease. Given their role in human health and nutrition, we identified BHMT and BHMT2 genes and proteins from 38 species of deuterostomes including human and non-human primates. We aligned the genes to look for signatures of selection, to infer evolutionary rates and events across lineages, and to identify the evolutionary timing of a gene duplication event that gave rise to two genes, BHMT and BHMT2. We found that BHMT was present in the genomes of the sea urchin, amphibians, reptiles, birds and mammals; BHMT2 was present only across mammals. BHMT and BHMT2 were present in tandem in the genomes of all monotreme, marsupial and placental species examined. Evolutionary rates were accelerated for BHMT2 relative to BHMT. Selective pressure varied across lineages, with the highest dN/dS ratios for BHMT and BHMT2 occurring immediately following the gene duplication event, as determined using GA Branch analysis. Nine codons were found to display signatures suggestive of positive selection; these contribute to the enzymatic or oligomerization domains, suggesting involvement in enzyme function. Gene duplication likely occurred after the divergence of mammals from other vertebrates but prior to the divergence of extant mammalian subclasses, followed by two deletions in BHMT2 that affect oligomerization and methyl donor specificity. The faster evolutionary rate of BHMT2 overall suggests that selective constraints were reduced relative to BHMT. The dN/dS ratios in both BHMT and BHMT2 was highest following the gene duplication, suggesting that purifying selection played a lesser role as the two paralogs diverged in function. PMID:26213999

  9. Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes

    PubMed Central

    Ganu, Radhika S.; Ishida, Yasuko; Koutmos, Markos; Kolokotronis, Sergios-Orestis; Roca, Alfred L.; Garrow, Timothy A.; Schook, Lawrence B.

    2015-01-01

    Betaine-homocysteine S-methyltransferase (BHMT) and BHMT2 convert homocysteine to methionine using betaine and S-methylmethionine, respectively, as methyl donor substrates. Increased levels of homocysteine in blood are associated with cardiovascular disease. Given their role in human health and nutrition, we identified BHMT and BHMT2 genes and proteins from 38 species of deuterostomes including human and non-human primates. We aligned the genes to look for signatures of selection, to infer evolutionary rates and events across lineages, and to identify the evolutionary timing of a gene duplication event that gave rise to two genes, BHMT and BHMT2. We found that BHMT was present in the genomes of the sea urchin, amphibians, reptiles, birds and mammals; BHMT2 was present only across mammals. BHMT and BHMT2 were present in tandem in the genomes of all monotreme, marsupial and placental species examined. Evolutionary rates were accelerated for BHMT2 relative to BHMT. Selective pressure varied across lineages, with the highest dN/dS ratios for BHMT and BHMT2 occurring immediately following the gene duplication event, as determined using GA Branch analysis. Nine codons were found to display signatures suggestive of positive selection; these contribute to the enzymatic or oligomerization domains, suggesting involvement in enzyme function. Gene duplication likely occurred after the divergence of mammals from other vertebrates but prior to the divergence of extant mammalian subclasses, followed by two deletions in BHMT2 that affect oligomerization and methyl donor specificity. The faster evolutionary rate of BHMT2 overall suggests that selective constraints were reduced relative to BHMT. The dN/dS ratios in both BHMT and BHMT2 was highest following the gene duplication, suggesting that purifying selection played a lesser role as the two paralogs diverged in function. PMID:26213999

  10. On detecting selective sweeps using single genomes.

    PubMed

    Sinha, Priyanka; Dincer, Aslihan; Virgil, Daniel; Xu, Guang; Poh, Yu-Ping; Jensen, Jeffrey D

    2011-01-01

    Identifying the genetic basis of human adaptation has remained a central focal point of modern population genetics. One major area of interest has been the use of polymorphism data to detect so-called "footprints" of selective sweeps - patterns produced as a beneficial mutation arises and rapidly fixes in the population. Based on numerous simulation studies and power analyses, the necessary sample size for achieving appreciable power has been shown to vary from a few individuals to a few dozen, depending on the test statistic. And yet, the sequencing of multiple copies of a single region, or of multiple genomes as is now often the case, incurs considerable cost. Enard et al. (2010) have recently proposed a method to identify patterns of selective sweeps using a single genome - and apply this approach to human and non-human primates (chimpanzee, orangutan, and macaque). They employ essentially a modification of the Hudson, Kreitman, and Aguade test - using heterozygous single nucleotide polymorphisms from single individuals, and divergence data from two closely related species (human-chimpanzee, human-orangutan, and human-macaque). Given the potential importance of this finding, we here investigate the properties of this statistic. We demonstrate through simulation that this approach is neither robust to demography nor background selection; nor is it robust to variable recombination rates. PMID:22303379

  11. Macroevolutionary patterns of bumblebee body size: detecting the interplay between natural and sexual selection

    PubMed Central

    del Castillo, Raúl Cueva; Fairbairn, Daphne J

    2012-01-01

    Bumblebees and other eusocial bees offer a unique opportunity to analyze the evolution of body size differences between sexes. The workers, being sterile females, are not subject to selection for reproductive function and thus provide a natural control for parsing the effects of selection on reproductive function (i.e., sexual and fecundity selection) from other natural selection. Using a phylogenetic comparative approach, we explored the allometric relationships among queens, males, and workers in 70 species of bumblebees (Bombus sp.). We found hyperallometry in thorax width for males relative to workers, indicating greater evolutionary divergence of body size in males than in sterile females. This is consistent with the hypothesis that selection for reproductive function, most probably sexual selection, has caused divergence in male size among species. The slope for males on workers was significantly steeper than that for queens on workers and the latter did not depart from isometry, providing further evidence of greater evolutionary divergence in male size than female size, and no evidence that reproductive selection has accelerated divergence of females. We did not detect significant hyperallometry when male size was regressed directly on queen size and our results thus add the genus Bombus to the increasing list of clades that have female-larger sexual size dimorphism and do not conform to Rensch's rule when analyzed according to standard methodology. Nevertheless, by using worker size as a common control, we were able to demonstrate that bumblee species do show the evolutionary pattern underlying Rensch's rule, that being correlated evolution of body size in males and females, but with greater evolutionary divergence in males. PMID:22408725

  12. Evolutionary and Experimental Assessment of Novel Markers for Detection of Xanthomonas euvesicatoria in Plant Samples

    PubMed Central

    Albuquerque, Pedro; Caridade, Cristina M. R.; Rodrigues, Arlete S.; Marcal, Andre R. S.; Cruz, Joana; Cruz, Leonor; Santos, Catarina L.; Mendes, Marta V.; Tavares, Fernando

    2012-01-01

    Background Bacterial spot-causing xanthomonads (BSX) are quarantine phytopathogenic bacteria responsible for heavy losses in tomato and pepper production. Despite the research on improved plant spraying methods and resistant cultivars, the use of healthy plant material is still considered as the most effective bacterial spot control measure. Therefore, rapid and efficient detection methods are crucial for an early detection of these phytopathogens. Methodology In this work, we selected and validated novel DNA markers for reliable detection of the BSX Xanthomonas euvesicatoria (Xeu). Xeu-specific DNA regions were selected using two online applications, CUPID and Insignia. Furthermore, to facilitate the selection of putative DNA markers, a customized C program was designed to retrieve the regions outputted by both databases. The in silico validation was further extended in order to provide an insight on the origin of these Xeu-specific regions by assessing chromosomal location, GC content, codon usage and synteny analyses. Primer-pairs were designed for amplification of those regions and the PCR validation assays showed that most primers allowed for positive amplification with different Xeu strains. The obtained amplicons were labeled and used as probes in dot blot assays, which allowed testing the probes against a collection of 12 non-BSX Xanthomonas and 23 other phytopathogenic bacteria. These assays confirmed the specificity of the selected DNA markers. Finally, we designed and tested a duplex PCR assay and an inverted dot blot platform for culture-independent detection of Xeu in infected plants. Significance This study details a selection strategy able to provide a large number of Xeu-specific DNA markers. As demonstrated, the selected markers can detect Xeu in infected plants both by PCR and by hybridization-based assays coupled with automatic data analysis. Furthermore, this work is a contribution to implement more efficient DNA-based methods of bacterial

  13. A likelihood method for the detection of selection and recombination using nucleotide sequences.

    PubMed

    Grassly, N C; Holmes, E C

    1997-03-01

    Different regions along nucleotide sequences are often subject to different evolutionary forces. Recombination will result in regions having different evolutionary histories, while selection can cause regions to evolve at different rates. This paper presents a statistical method based on likelihood for detecting such processes by identifying the regions which do not fit with a single phylogenetic topology and nucleotide substitution process along the entire sequence. Subsequent reanalysis of these anomalous regions may then be possible. The method is tested using simulations, and its application is demonstrated using the primate psi eta-globin pseudogene, the V3 region of the envelope gene of HIV-1, and argF sequences from Neisseria bacteria. Reanalysis of anomalous regions is shown to reveal possible immune selection in HIV-1 and recombination in Neisseria. A computer program which implements the method is available. PMID:9066792

  14. Evidence of Positive Selection of Aquaporins Genes from Pontoporia blainvillei during the Evolutionary Process of Cetaceans

    PubMed Central

    São Pedro, Simone Lima; Alves, João Marcelo Pereira; Barreto, André Silva; Lima, André Oliveira de Souza

    2015-01-01

    Background Marine mammals are well adapted to their hyperosmotic environment. Several morphological and physiological adaptations for water conservation and salt excretion are known to be present in cetaceans, being responsible for regulating salt balance. However, most previous studies have focused on the unique renal physiology of marine mammals, but the molecular bases of these mechanisms remain poorly explored. Many genes have been identified to be involved in osmotic regulation, including the aquaporins. Considering that aquaporin genes were potentially subject to strong selective pressure, the aim of this study was to analyze the molecular evolution of seven aquaporin genes (AQP1, AQP2, AQP3, AQP4, AQP6, AQP7, and AQP9) comparing the lineages of cetaceans and terrestrial mammals. Results Our results demonstrated strong positive selection in cetacean-specific lineages acting only in the gene for AQP2 (amino acids 23, 83, 107,179, 180, 181, 182), whereas no selection was observed in terrestrial mammalian lineages. We also analyzed the changes in the 3D structure of the aquaporin 2 protein. Signs of strong positive selection in AQP2 sites 179, 180, 181, and 182 were unexpectedly identified only in the baiji lineage, which was the only river dolphin examined in this study. Positive selection in aquaporins AQP1 (45), AQP4 (74), AQP7 (342, 343, 356) was detected in cetaceans and artiodactyls, suggesting that these events are not related to maintaining water and electrolyte homeostasis in seawater. Conclusions Our results suggest that the AQP2 gene might reflect different selective pressures in maintaining water balance in cetaceans, contributing to the passage from the terrestrial environment to the aquatic. Further studies are necessary, especially those including other freshwater dolphins, who exhibit osmoregulatory mechanisms different from those of marine cetaceans for the same essential task of maintaining serum electrolyte balance. PMID:26226365

  15. Evolutionary pattern in the OXT-OXTR system in primates: Coevolution and positive selection footprints

    PubMed Central

    Vargas-Pinilla, Pedro; Paré, Pamela; Tovo-Rodrigues, Luciana; Vieira, Carlos Meton de Alencar Gadelha; Xavier, Agatha; Comas, David; Pissinatti, Alcides; Sinigaglia, Marialva; Rigo, Maurício Menegatti; Vieira, Gustavo Fioravanti; Lucion, Aldo B.; Salzano, Francisco Mauro; Bortolini, Maria Cátira

    2015-01-01

    Oxytocin is a nonapeptide involved in a wide range of physiologic and behavioral functions. Until recently, it was believed that an unmodified oxytocin sequence was present in all placental mammals. This study analyzed oxytocin (OXT) in 29 primate species and the oxytocin receptor (OXTR) in 21 of these species. We report here three novel OXT forms in the New World monkeys, as well as a more extensive distribution of a previously described variant (Leu8Pro). In structural terms, these OXTs share the same three low-energy conformations in solution during molecular dynamic simulations, with subtle differences in their side chains. A consistent signal of positive selection was detected in the Cebidae family, and OXT position 8 showed a statistically significant (P = 0.013) correlation with litter size. Several OXTR changes were identified, some of them promoting gain or loss of putative phosphorylation sites, with possible consequences for receptor internalization and desensitization. OXTR amino acid sites are under positive selection, and intramolecular and intermolecular coevolutionary processes with OXT were also detected. We suggest that some New World monkey OXT-OXTR forms can be correlated to male parental care through the increase of cross-reactivity with its correlated vasopressin system. PMID:25535371

  16. Evolutionary pattern in the OXT-OXTR system in primates: coevolution and positive selection footprints.

    PubMed

    Vargas-Pinilla, Pedro; Paixão-Côrtes, Vanessa Rodrigues; Paré, Pamela; Tovo-Rodrigues, Luciana; Vieira, Carlos Meton de Alencar Gadelha; Xavier, Agatha; Comas, David; Pissinatti, Alcides; Sinigaglia, Marialva; Rigo, Maurício Menegatti; Vieira, Gustavo Fioravanti; Lucion, Aldo B; Salzano, Francisco Mauro; Bortolini, Maria Cátira

    2015-01-01

    Oxytocin is a nonapeptide involved in a wide range of physiologic and behavioral functions. Until recently, it was believed that an unmodified oxytocin sequence was present in all placental mammals. This study analyzed oxytocin (OXT) in 29 primate species and the oxytocin receptor (OXTR) in 21 of these species. We report here three novel OXT forms in the New World monkeys, as well as a more extensive distribution of a previously described variant (Leu8Pro). In structural terms, these OXTs share the same three low-energy conformations in solution during molecular dynamic simulations, with subtle differences in their side chains. A consistent signal of positive selection was detected in the Cebidae family, and OXT position 8 showed a statistically significant (P = 0.013) correlation with litter size. Several OXTR changes were identified, some of them promoting gain or loss of putative phosphorylation sites, with possible consequences for receptor internalization and desensitization. OXTR amino acid sites are under positive selection, and intramolecular and intermolecular coevolutionary processes with OXT were also detected. We suggest that some New World monkey OXT-OXTR forms can be correlated to male parental care through the increase of cross-reactivity with its correlated vasopressin system. PMID:25535371

  17. Capability of the Maximax&Maximin selection operator in the evolutionary algorithm for a nurse scheduling problem

    NASA Astrophysics Data System (ADS)

    Ramli, Razamin; Tein, Lim Huai

    2016-08-01

    A good work schedule can improve hospital operations by providing better coverage with appropriate staffing levels in managing nurse personnel. Hence, constructing the best nurse work schedule is the appropriate effort. In doing so, an improved selection operator in the Evolutionary Algorithm (EA) strategy for a nurse scheduling problem (NSP) is proposed. The smart and efficient scheduling procedures were considered. Computation of the performance of each potential solution or schedule was done through fitness evaluation. The best so far solution was obtained via special Maximax&Maximin (MM) parent selection operator embedded in the EA, which fulfilled all constraints considered in the NSP.

  18. Decomposition-Based Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Social Networks

    PubMed Central

    Ma, Jingjing; Liu, Jie; Ma, Wenping; Gong, Maoguo; Jiao, Licheng

    2014-01-01

    Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms. PMID:24723806

  19. Selective spectral detection of continuum terahertz radiation

    NASA Astrophysics Data System (ADS)

    Kaufmann, P.; Marcon, R.; Marun, A.; Kudaka, A. S.; Bortolucci, E.; Zakia, M. B.; Diniz, J. A.; Cassiano, M. M.; Pereyra, P.; Godoy, R.; Timofeevsky, A. V.; Nikolaev, V. A.; Pereira Alves da Silva, A. M.; Fernandes, L. O. T.

    2010-07-01

    The knowledge of THz continuum spectra is essential to investigate the emission mechanisms by high energy particle acceleration processes. Technical challenges appear for obtaining selective spectral sensing in the far infrared range to diagnose radiation produced by solar flare burst emissions measured from space as well as radiation produced by high energy electrons in laboratory accelerators. Efforts are been carried out intended for the development of solar flare high cadence radiometers at two THz frequencies to operate outside the terrestrial atmosphere (i.e. at 3 and 7 THz). One essential requirement is the efficient suppression of radiation in the visible and near infrared. Experimental setups have been assembled for testing (a) THz transmission of "low-pass" filters: rough surface mirrors; membranes Zitex G110G and TydexBlack; (b) a fabricated 2.4 THz resonant grid band-pass filter transmission response for polarization and angle of incidence; (c) radiation response from distinct detectors: adapted commercial microbolometer array using HRFZ-Si window, pyroelectric module and Golay cell; qualitative detection of solar radiation at a sub-THz frequency has been tested with a microbolometer array placed at the focus of the 1.5 m reflector for submillimeter waves (SST) at El Leoncito, Argentina Andes.

  20. The ghosts of selection past reduces the probability of plastic rescue but increases the likelihood of evolutionary rescue to novel stressors in experimental populations of wild yeast.

    PubMed

    Samani, Pedram; Bell, Graham

    2016-03-01

    Persistence by adaptation is called evolutionary rescue. Evolutionary rescue is more likely in populations that have been previously exposed to lower doses of the same stressor. Environmental fluctuations might also reduce the possibility of rescue, but little is known about the effect of evolutionary history on the likelihood of rescue. In this study, we hypothesised that the ubiquitous operation of generalised stress responses in many organisms increases the likelihood of rescue after exposure to other stressors. We tested this hypothesis with experimental populations that had been exposed to long-term starvation and were then selected on different, unrelated stressors. We found that prior adaptation to starvation imposes contrary effects on the plastic and evolutionary responses of populations to subsequent stressors. When first exposed to new stressors, such populations become extinct more often. If they survive the initial exposure to the new stressors, however, they are more likely to undergo evolutionary rescue. PMID:26777785

  1. Japanese monkeys (Macaca fuscata) quickly detect snakes but not spiders: Evolutionary origins of fear-relevant animals.

    PubMed

    Kawai, Nobuyuki; Koda, Hiroki

    2016-08-01

    Humans quickly detect the presence of evolutionary threats through visual perception. Many theorists have considered humans to be predisposed to respond to both snakes and spiders as evolutionarily fear-relevant stimuli. Evidence supports that human adults, children, and snake-naive monkeys all detect pictures of snakes among pictures of flowers more quickly than vice versa, but recent neurophysiological and behavioral studies suggest that spiders may, in fact, be processed similarly to nonthreat animals. The evidence of quick detection and rapid fear learning by primates is limited to snakes, and no such evidence exists for spiders, suggesting qualitative differences between fear of snakes and fear of spiders. Here, we show that snake-naive Japanese monkeys detect a single snake picture among 8 nonthreat animal pictures (koala) more quickly than vice versa; however, no such difference in detection was observed between spiders and pleasant animals. These robust differences between snakes and spiders are the most convincing evidence that the primate visual system is predisposed to pay attention to snakes but not spiders. These findings suggest that attentional bias toward snakes has an evolutionary basis but that bias toward spiders is more due to top-down, conceptually driven effects of emotion on attention capture. (PsycINFO Database Record PMID:27078076

  2. Evolutionary responses of tree phenology to the combined effects of assortative mating, gene flow and divergent selection

    PubMed Central

    Soularue, J-P; Kremer, A

    2014-01-01

    The timing of bud burst (TBB) in temperate trees is a key adaptive trait, the expression of which is triggered by temperature gradients across the landscape. TBB is strongly correlated with flowering time and is therefore probably mediated by assortative mating. We derived theoretical predictions and realized numerical simulations of evolutionary changes in TBB in response to divergent selection and gene flow in a metapopulation. We showed that the combination of the environmental gradient of TBB and assortative mating creates contrasting genetic clines, depending on the direction of divergent selection. If divergent selection acts in the same direction as the environmental gradient (cogradient settings), genetic clines are established and inflated by assortative mating. Conversely, under divergent selection of the same strength but acting in the opposite direction (countergradient selection), genetic clines are slightly constrained. We explored the consequences of these dynamics for population maladaptation, by monitoring pollen swamping. Depending on the direction of divergent selection with respect to the environmental gradient, pollen filtering owing to assortative mating either facilitates or impedes adaptation in peripheral populations. PMID:24924591

  3. Novel and selective detection of Tabun mimics.

    PubMed

    Jang, Yoon Jeong; Tsay, Olga G; Murale, Dhiraj P; Jeong, Jeong A; Segev, Aviv; Churchill, David G

    2014-07-18

    Detection of nerve agent-related molecules based on BODIPY-salicylaldehyde oxime conjugation was studied. Fluorescence intensity of the B-SAL-OXIME species increases in the presence of DECP, whereas it decreases in the presence of DCP and DEMP (limit of detection = 997 nM). Benzonitrile formation in the novel fluorescent B-SAL-OXIME system was elucidated using model substrates. PMID:24888625

  4. Molecular sieve sensors for selective detection at the nanogram level

    DOEpatents

    Bein, Thomas; Brown, Kelly D.; Frye, Gregory C.; Brinker, Charles J.

    1992-01-01

    The invention relates to a selective chemical sensor for selective detection of chemical entities even at the nanogram level. The invention further relates to methods of using the sensor. The sensor comprises: (a) a piezoelectric substrate capable of detecting mass changes resulting from adsorption of material thereon; and (b) a coating applied to the substrate, which selectively sorbs chemical entities of a size smaller than a preselected magnitude.

  5. Microbial Biosensors for Selective Detection of Disaccharides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seven microbial strains were screened for their ability to detect disaccharides as components of Clark-type oxygen biosensors. Sensors responded to varying degrees to maltose, cellobiose, sucrose, and melibiose, but none responded strongly to lactose. Although microbial sensors are relatively nons...

  6. Sexual selection and the evolutionary dynamics of the major histocompatibility complex

    PubMed Central

    Jan Ejsmond, Maciej; Radwan, Jacek; Wilson, Anthony B.

    2014-01-01

    The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection produce distinctive signatures of MHC allelic diversity with critical implications for understanding host–pathogen dynamics. While natural selection produces the Red Queen dynamics characteristic of host–parasite interactions, disassortative mating stabilizes allele frequencies, damping major fluctuations in dominant alleles and protecting functional variants against drift. This subtle difference generates a complex interaction between MHC allelic diversity and population size. In small populations, the stabilizing effects of sexual selection moderate the effects of drift, whereas pathogen-mediated selection accelerates the loss of functionally important genetic diversity. Natural selection enhances MHC allelic variation in larger populations, with the highest levels of diversity generated by the combined action of pathogen-mediated selection and disassortative mating. MHC-based sexual selection may help to explain how functionally important genetic variation can be maintained in populations of conservation concern. PMID:25339723

  7. The ecological–evolutionary interplay: density-dependent sexual selection in a migratory songbird

    PubMed Central

    Ryder, Thomas B; Fleischer, Robert C; Shriver, W Greg; Marra, Peter P

    2012-01-01

    Little is understood about how environmental heterogeneity influences the spatial dynamics of sexual selection. Within human-dominated systems, habitat modification creates environmental heterogeneity that could influence the adaptive value of individual phenotypes. Here, we used the gray catbird to examine if the ecological conditions experienced in the suburban matrix (SM) and embedded suburban parks (SP) influence reproductive strategies and the strength of sexual selection. Our results show that these habitats varied in a key ecological factor, breeding density. Moreover, this ecological factor was closely tied to reproductive strategies such that local breeding density predicted the probability that a nest would contain extra-pair offspring. Partitioning reproductive variance showed that while within-pair success was more important in both habitats, extra-pair success increased the opportunity for sexual selection by 39% at higher breeding densities. Body size was a strong predictor of relative reproductive success and was under directional selection in both habitats. Importantly, our results show that the strength of sexual selection did not differ among habitats at the landscape scale but rather that fine-scale variation in an ecological factor, breeding density, influenced sexual selection on male phenotypes. Here, we document density-dependent sexual selection in a migratory bird and hypothesize that coarse-scale environmental heterogeneity, in this case generated by anthropogenic habitat modification, changed the fine-scale ecological conditions that drove the spatial dynamics of sexual selection. PMID:22837842

  8. Embryonic development of goldfish (Carassius auratus): A model for the study of evolutionary change in developmental mechanisms by artificial selection

    PubMed Central

    Tsai, Hsin-Yuan; Chang, Mariann; Liu, Shih-Chieh; Abe, Gembu; Ota, Kinya G

    2013-01-01

    Background: Highly divergent morphology among the different goldfish strains (Carassius auratus) may make it a suitable model for investigating how artificial selection has altered developmental mechanisms. Here we describe the embryological development of the common goldfish (the single fin Wakin), which retains the ancestral morphology of this species. Results: We divided goldfish embryonic development into seven periods consisting of 34 stages, using previously reported developmental indices of zebrafish and goldfish. Although several differences were identified in terms of their yolk size, epiboly process, pigmentation patterns, and development rate, our results indicate that the embryonic features of these two teleost species are highly similar in their overall morphology from the zygote to hatching stage. Conclusions: These results provide an opportunity for further study of the evolutionary relationship between domestication and development, through applying well-established zebrafish molecular biological resources to goldfish embryos. Developmental Dynamics 242:1262–1283, 2013. © 2013 Wiley Periodicals, Inc. Key findings This study provides the first reliable descriptions of normal embryonic stages of wild-type goldfish. The embryonic features of goldfish and zebrafish are almost directly comparable. Goldfish embryos provide a novel model for the investigation of the evolutionary relationship between domestication and development. PMID:23913853

  9. Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets.

    PubMed Central

    Shi, Hua; Fan, Xiaochun; Ni, Zhuoyu; Lis, John T

    2002-01-01

    Iterative cycles of in vitro selection and amplification allow rare functional nucleic acid molecules, aptamers, to be isolated from large sequence pools. Here we present an analysis of the progression of a selection experiment that simultaneously yielded two families of RNA aptamers against two disparate targets: the intended target protein (B52/SRp55) and the partitioning matrix. We tracked the sequence abundance and binding activity to reveal the enrichment of the aptamers through successive generations of selected pools. The two aptamer families showed distinct trajectories of evolution, as did members within a single family. We also developed a method to control the relative abundance of an aptamer family in selected pools. This method, involving specific ribonuclease digestion, can be used to reduce the background selection for aptamers that bind the matrix. Additionally, it can be used to isolate a full spectrum of aptamers in a sequential and exhaustive manner for all the different targets in a mixture. PMID:12458799

  10. Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

    PubMed Central

    Nguyen Ba, Alex N.; Strome, Bob; Hua, Jun Jie; Desmond, Jonathan; Gagnon-Arsenault, Isabelle; Weiss, Eric L.; Landry, Christian R.; Moses, Alan M.

    2014-01-01

    Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication. PMID:25474245

  11. Dense cores in Ophiuchus and Chamaeleon molecular clouds: detection and evolutionary trends

    NASA Astrophysics Data System (ADS)

    Benedettini, Milena; Burton, Michael; Busquet, Gemma; Caselli, Paola; Pezzuto, Stefano; Viti, Serena

    2012-04-01

    We propose to map the densest regions of the Ophiucus, Chamaeleon I and Chamaeleon III molecular clouds in high density tracers in order to derive the distribution of the dense cores and their evolutionary stage with the aim to study the core mass function and its relationship to the stellar initial mass function. Spectroscopic surveys of star forming regions in chemical species copiously produced in the first stages of star formation are essential to derive the kinematics and the physical conditions of the pre- and proto-stellar cores, as well as their evolutionary stage. A previous study of the Lupus molecular cloud carried out with Mopra has shown the high potential of the multi-line spectroscopic surveys in identifying the dense condensations and their evolutionary stage. We ask to observe several key species: HCN, HNC, HC3N, N2H+ and HCO+ whose chemical abundance ratios are good chemical clocks for the first stages of the star formation process. The Mopra antenna is ideal for observations at 3mm of the close-by, high southern declination Ophiucus and Chamaeleon clouds since the beam size at 90GHz corresponds to about 0.03pc, well-matched to sampling the dense cores with typical sizes of 0.1pc.

  12. Analysis of channel confined selective area growth in evolutionary growth of GaN on SiO2

    NASA Astrophysics Data System (ADS)

    Leung, Benjamin; Tsai, Miao-Chan; Song, Jie; Zhang, Yu; Xiong, Kanglin; Yuan, Ge; Coltrin, Michael E.; Han, Jung

    2015-09-01

    Here, we analyze the chemical vapor deposition of semiconductor crystals by selective area growth in a non-planar geometry. Specifically, the growth process in laterally and vertically confined masks forming single-crystal GaN on SiO2 by metal-organic chemical vapor deposition is considered in detail. A textured AlN seed is used to initiate growth of oriented GaN selectively through the mask, allowing the reduction of degrees of freedom by the evolutionary grain selection process. As shown by measurements of growth rates within the mask, the sub micron length scale of the channel opening is comparable to the mean free path of precursors in the gas phase, resulting in transport characteristics that can be described by an intermediate flow regime between continuum and free-molecular. Mass transport is modeled through kinetic theory to explain the growth rate enhancements of more than a factor of two by changes in reactor pressure. The growth conditions that enable the modification of nucleation density within the channel are then discussed, and are measured by electron-back scatter diffraction of the nucleated grains on the AlN seed. Finally, the selectivity behavior using the low fill factor masks needed in these configurations has been optimized by control of precursor flow rates and the H2 enhanced etching of the polycrystalline GaN nuclei.

  13. Divergent natural selection promotes immigrant inviability at early and late stages of evolutionary divergence.

    PubMed

    Ingley, Spencer J; Johnson, Jerald B

    2016-03-01

    Natural selection's role in speciation has been of fundamental importance since Darwin first outlined his theory. Recently, work has focused on understanding how selection drives trait divergence, and subsequently reproductive isolation. "Immigrant inviability," a barrier that arises from selection against immigrants in their nonnative environment, appears to be of particular importance. Although immigrant inviability is likely ubiquitous, we know relatively little about how selection acts on traits to drive immigrant inviability, and how important immigrant inviability is at early-versus-late stages of divergence. We present a study evaluating the role of predation in the evolution of immigrant inviability in recently diverged population pairs and a well-established species pair of Brachyrhaphis fishes. We evaluate performance in a high-predation environment by assessing survival in the presence of a predator, and swimming endurance in a low-predation environment. We find strong signatures of local adaptation and immigrant inviability of roughly the same magnitude both early and late in divergence. We find remarkably conserved selection for burst-speed swimming (important in predator evasion), and selection for increased size in low-predation environments. Our results highlight the consistency with which selection acts during speciation, and suggest that similar factors might promote initial population differentiation and maintain differentiation at late stages of divergence. PMID:26831519

  14. Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family

    PubMed Central

    Mallika, V.; Sivakumar, K.C.; Soniya, E.V.

    2011-01-01

    Type III polyketide synthases have a substantial role in the biosynthesis of various polyketides in plants and microorganisms. Comparative proteomic analysis of type III polyketide synthases showed evolutionarily and structurally related positions in a compilation of amino acid sequences from different families. Bacterial and fungal type III polyketide synthase proteins showed <50% similarity but in higher plants, it exhibited >80% among chalcone synthases and >70% in the case of non-chalcone synthases. In a consensus phylogenetic tree based on 1000 replicates; bacterial, fungal and plant proteins were clustered in separate groups. Proteins from bryophytes and pteridophytes grouped immediately near to the fungal cluster, demonstrated how evolutionary lineage has occurred among type III polyketide synthase proteins. Upon physicochemical analysis, it was observed that the proteins localized in the cytoplasm and were hydrophobic in nature. Molecular structural analysis revealed comparatively stable structure comprising of alpha helices and random coils as major structural components. It was found that there was a decline in the structural stability with active site mutation as prophesied by the in silico mutation studies. PMID:21697991

  15. Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease.

    PubMed

    Brüniche-Olsen, Anna; Austin, Jeremy J; Jones, Menna E; Holland, Barbara R; Burridge, Christopher P

    2016-01-01

    Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer--devil facial tumor disease (DFTD)--that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series 'restriction site associated DNA' (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results. PMID:26930198

  16. Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease

    PubMed Central

    Brüniche-Olsen, Anna; Austin, Jeremy J.; Jones, Menna E.; Holland, Barbara R.; Burridge, Christopher P.

    2016-01-01

    Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer—devil facial tumor disease (DFTD)—that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series ‘restriction site associated DNA’ (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results. PMID:26930198

  17. Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates.

    PubMed

    He, Wenwu; Tang, Yanyan; Qi, Bin; Lu, Chuansen; Qin, Chao; Wei, Yunfei; Yi, Jiachao; Chen, Mingwu

    2014-02-10

    Vascular endothelial growth factor (VEGF), known to play an important role in vascular homeostasis, vascular integrity and angiogenesis, is little known about the evolutionary relationship of its five members especially the role of gene duplication and natural selection in the evolution of the VEGF family. In this study, seventy-five full-length cDNA sequences from 33 vertebrate species were extracted from the NCBI's GenBank, UniProt protein database and the Ensembl database. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the VEGFs. Five VEGF family members in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain the relationship of the site-specific evolution in the vertebrate VEGF family. Eleven positive selection sites, one transmembrane region and the active sites were detected in this process. PMID:24200960

  18. Evolutionary Game Dynamics in Finite Populations with Strong Selection and Weak Mutation

    PubMed Central

    Fudenberg, Drew; Nowak, Martin A.; Taylor, Christine

    2011-01-01

    We study stochastic game dynamics in finite populations. To this end we extend the classical Moran process to incorporate frequency-dependent selection and mutation. For 2 × 2 games, we give a complete analysis of the long-run behavior when mutation rates are small. For 3 × 3 coordination games, we provide a simple rule to determine which strategy will be selected in large populations. The expected motion in our model resembles the standard replicator dynamics when the population is large, but is qualitatively different when the population is small. Our analysis shows that even in large finite populations the behavior of a replicator-like system can be different from that of the standard replicator dynamics. As an application, we consider selective language dynamics. We determine which language will be spoken in finite large populations. The results have an intuitive interpretation but would not be expected from an analysis of the replicator dynamics. PMID:16987535

  19. Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow

    PubMed Central

    Rivas, M. J.; Domínguez-García, S.; Carvajal-Rodríguez, A.

    2015-01-01

    The study of local adaptation is a main focus of evolutionary biology since it may contribute to explain the current species diversity. The genomic scan procedures permit for the first time to study the connection between specific DNA patterns and processes as natural selection, genetic drift, recombination, mutation and gene flow. Accordingly, the information on genomes from non-model organisms increases and the interest on detecting the signal of natural selection in the DNA sequences of different populations also raises. The main goal of the present work is to explore a sequence-based method for detecting natural selection in divergent populations connected by migration. In doing so, we rely on a recently published statistic based upon th e definition of haplotype allelic classes (HAC). The original measure was modified to be more sensitive to intermediate frequencies in non-model species. A linkage-disequilibrium-based method was also assayed and individual-based simulations were performed to test the methods. The results suggest that the HAC-based methods and, specifically, the new proposed method are quite powerful for detecting the footprint of moderate divergent selection. They are also robust to reasonable model misspecification. One obvious advantage of the new algorithm is that it does not require knowledge of the allelic state. PMID:26069460

  20. Semiconducting Metal Oxide Based Sensors for Selective Gas Pollutant Detection

    PubMed Central

    Kanan, Sofian M.; El-Kadri, Oussama M.; Abu-Yousef, Imad A.; Kanan, Marsha C.

    2009-01-01

    A review of some papers published in the last fifty years that focus on the semiconducting metal oxide (SMO) based sensors for the selective and sensitive detection of various environmental pollutants is presented. PMID:22408500

  1. Multi-objective entropy evolutionary algorithm for marine oil spill detection using cosmo-skymed satellite data

    NASA Astrophysics Data System (ADS)

    Marghany, M.

    2015-06-01

    Oil spill pollution has a substantial role in damaging the marine ecosystem. Oil spill that floats on top of water, as well as decreasing the fauna populations, affects the food chain in the ecosystem. In fact, oil spill is reducing the sunlight penetrates the water, limiting the photosynthesis of marine plants and phytoplankton. Moreover, marine mammals for instance, disclosed to oil spills their insulating capacities are reduced, and so making them more vulnerable to temperature variations and much less buoyant in the seawater. This study has demonstrated a design tool for oil spill detection in SAR satellite data using optimization of Entropy based Multi-Objective Evolutionary Algorithm (E-MMGA) which based on Pareto optimal solutions. The study also shows that optimization entropy based Multi-Objective Evolutionary Algorithm provides an accurate pattern of oil slick in SAR data. This shown by 85 % for oil spill, 10 % look-alike and 5 % for sea roughness using the receiver-operational characteristics (ROC) curve. The E-MMGA also shows excellent performance in SAR data. In conclusion, E-MMGA can be used as optimization for entropy to perform an automatic detection of oil spill in SAR satellite data.

  2. A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure

    NASA Astrophysics Data System (ADS)

    Tsai, Ming-Chi; Blelloch, Guy; Ravi, R.; Schwartz, Russell

    The random accumulation of variations in the human genome over time implicitly encodes a history of how human populations have arisen, dispersed, and intermixed since we emerged as a species. Reconstructing that history is a challenging computational and statistical problem but has important applications both to basic research and to the discovery of genotype-phenotype correlations. In this study, we present a novel approach to inferring human evolutionary history from genetic variation data. Our approach uses the idea of consensus trees, a technique generally used to reconcile species trees from divergent gene trees, adapting it to the problem of finding the robust relationships within a set of intraspecies phylogenies derived from local regions of the genome. We assess the quality of the method on two large-scale genetic variation data sets: the HapMap Phase II and the Human Genome Diversity Project. Qualitative comparison to a consensus model of the evolution of modern human population groups shows that our inferences closely match our best current understanding of human evolutionary history. A further comparison with results of a leading method for the simpler problem of population substructure assignment verifies that our method provides comparable accuracy in identifying meaningful population subgroups in addition to inferring the relationships among them.

  3. Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs

    PubMed Central

    Reinharz, Vladimir

    2013-01-01

    Abstract The analysis of the sequence–structure relationship in RNA molecules is not only essential for evolutionary studies but also for concrete applications such as error-correction in next generation sequencing (NGS) technologies. The prohibitive sizes of the mutational and conformational landscapes, combined with the volume of data to process, require efficient algorithms to compute sequence–structure properties. In this article, we address the correction of NGS errors by calculating which mutations most increase the likelihood of a sequence to a given structure and RNA family. We introduce RNApyro, an efficient, linear time and space inside–outside algorithm that computes exact mutational probabilities under secondary structure and evolutionary constraints given as a multiple sequence alignment with a consensus structure. We develop a scoring scheme combining classical stacking base-pair energies to novel isostericity scores and apply our techniques to correct pointwise errors in 5s and 16s rRNA sequences. Our results suggest that RNApyro is a promising algorithm to complement existing tools in the NGS error-correction pipeline. PMID:24134390

  4. Exact solutions for the selection-mutation equilibrium in the Crow-Kimura evolutionary model.

    PubMed

    Semenov, Yuri S; Novozhilov, Artem S

    2015-08-01

    We reformulate the eigenvalue problem for the selection-mutation equilibrium distribution in the case of a haploid asexually reproduced population in the form of an equation for an unknown probability generating function of this distribution. The special form of this equation in the infinite sequence limit allows us to obtain analytically the steady state distributions for a number of particular cases of the fitness landscape. The general approach is illustrated by examples; theoretical findings are compared with numerical calculations. PMID:26005029

  5. Bands selection and classification of hyperspectral images based on hybrid kernels SVM by evolutionary algorithm

    NASA Astrophysics Data System (ADS)

    Hu, Yan-Yan; Li, Dong-Sheng

    2016-01-01

    The hyperspectral images(HSI) consist of many closely spaced bands carrying the most object information. While due to its high dimensionality and high volume nature, it is hard to get satisfactory classification performance. In order to reduce HSI data dimensionality preparation for high classification accuracy, it is proposed to combine a band selection method of artificial immune systems (AIS) with a hybrid kernels support vector machine (SVM-HK) algorithm. In fact, after comparing different kernels for hyperspectral analysis, the approach mixed radial basis function kernel (RBF-K) with sigmoid kernel (Sig-K) and applied the optimized hybrid kernels in SVM classifiers. Then the SVM-HK algorithm used to induce the bands selection of an improved version of AIS. The AIS was composed of clonal selection and elite antibody mutation, including evaluation process with optional index factor (OIF). Experimental classification performance was on a San Diego Naval Base acquired by AVIRIS, the HRS dataset shows that the method is able to efficiently achieve bands redundancy removal while outperforming the traditional SVM classifier.

  6. Ion-Selective Detection with Glass Nanopipette for Living Cells

    NASA Astrophysics Data System (ADS)

    Takami, T.; Son, J. W.; Kang, E. J.; Deng, X. L.; Kawai, T.; Lee, S.-W.; Park, B. H.

    2013-05-01

    We developed a method to probe local ion concentration with glass nanopipette in which poly(vinyl chloride) membrane containing ionophore for separate ion detection is prepared. Here we demonstrate how ion-selective detections are available for living cells such as HeLa cell, rat vascular myocyte, and neuron cell.

  7. Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.

    PubMed

    Thomas, Cristel G; Wang, Wei; Jovelin, Richard; Ghosh, Rajarshi; Lomasko, Tatiana; Trinh, Quang; Kruglyak, Leonid; Stein, Lincoln D; Cutter, Asher D

    2015-05-01

    The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the "Temperate" and "Tropical" phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes. PMID:25783854

  8. MOEPGA: A novel method to detect protein complexes in yeast protein-protein interaction networks based on MultiObjective Evolutionary Programming Genetic Algorithm.

    PubMed

    Cao, Buwen; Luo, Jiawei; Liang, Cheng; Wang, Shulin; Song, Dan

    2015-10-01

    The identification of protein complexes in protein-protein interaction (PPI) networks has greatly advanced our understanding of biological organisms. Existing computational methods to detect protein complexes are usually based on specific network topological properties of PPI networks. However, due to the inherent complexity of the network structures, the identification of protein complexes may not be fully addressed by using single network topological property. In this study, we propose a novel MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. Our approach first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally we describe our algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of our method, we compared MOEPGA with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, our approach can cover a certain number of proteins in the input PPI network in terms of the normalized clustering score. Taken together, our method can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions. PMID:26298638

  9. Combining evolutionary algorithms with oblique decision trees to detect bent-double galaxies

    NASA Astrophysics Data System (ADS)

    Cantu-Paz, Erick; Kamath, Chandrika

    2000-10-01

    Decision tress have long been popular in classification as they use simple and easy-to-understand tests at each node. Most variants of decision trees test a single attribute at a node, leading to axis- parallel trees, where the test results in a hyperplane which is parallel to one of the dimensions in the attribute space. These trees can be rather large and inaccurate in cases where the concept to be learned is best approximated by oblique hyperplanes. In such cases, it may be more appropriate to use an oblique decision tree, where the decision at each node is a linear combination of the attributes. Oblique decision trees have not gained wide popularity in part due to the complexity of constructing good oblique splits and the tendency of existing splitting algorithms to get stuck in local minima. Several alternatives have been proposed to handle these problems including randomization in conjunction wiht deterministic hill-climbing and the use of simulated annealing. In this paper, we use evolutionary algorithms (EAs) to determine the split. EAs are well suited for this problem because of their global search properties, their tolerance to noisy fitness evaluations, and their scalability to large dimensional search spaces. We demonstrate our technique on a synthetic data set, and then we apply it to a practical problem from astronomy, namely, the classification of galaxies with a bent-double morphology. In addition, we describe our experiences with several split evaluation criteria. Our results suggest that, in some cases, the evolutionary approach is faster and more accurate than existing oblique decision tree algorithms. However, for our astronomical data, the accuracy is not significantly different than the axis-parallel trees.

  10. Colour variation in cichlid fish: Developmental mechanisms, selective pressures and evolutionary consequences☆

    PubMed Central

    Maan, Martine E.; Sefc, Kristina M.

    2013-01-01

    Cichlid fishes constitute one of the most species-rich families of vertebrates. In addition to complex social behaviour and morphological versatility, they are characterised by extensive diversity in colouration, both within and between species. Here, we review the cellular and molecular mechanisms underlying colour variation in this group and the selective pressures responsible for the observed variation. We specifically address the evidence for the hypothesis that divergence in colouration is associated with the evolution of reproductive isolation between lineages. While we conclude that cichlid colours are excellent models for understanding the role of animal communication in species divergence, we also identify taxonomic and methodological biases in the current research effort. We suggest that the integration of genomic approaches with ecological and behavioural studies, across the entire cichlid family and beyond it, will contribute to the utility of the cichlid model system for understanding the evolution of biological diversity. PMID:23665150

  11. Reflections on Behavior Analysis and Evolutionary Biology: A Selective Review of Evolution Since Darwin—The First 150 Years. Edited by M. A. Bell, D. J. Futuyama, W. F. Eanes, & J. S. Levinton

    PubMed Central

    Donahoe, John W

    2012-01-01

    This review focuses on parallels between the selectionist sciences of evolutionary biology and behavior analysis. In selectionism, complex phenomena are interpreted as the cumulative products of relatively simple processes acting over time—natural selection in evolutionary biology and reinforcement in behavior analysis. Because evolutionary biology is the more mature science, an examination of the factors that led to the triumph of natural selection provides clues whereby reinforcement may achieve a similar fate in the science of behavior.

  12. ATLASGAL-selected massive clumps in the inner Galaxy. II. Characterisation of different evolutionary stages and their SiO emission

    NASA Astrophysics Data System (ADS)

    Csengeri, T.; Leurini, S.; Wyrowski, F.; Urquhart, J. S.; Menten, K. M.; Walmsley, M.; Bontemps, S.; Wienen, M.; Beuther, H.; Motte, F.; Nguyen-Luong, Q.; Schilke, P.; Schuller, F.; Zavagno, A.; Sanna, C.

    2016-02-01

    Context. The processes leading to the birth of high-mass stars are poorly understood. The key first step to reveal their formation processes is characterising the clumps and cores from which they form. Aims: We define a representative sample of massive clumps in different evolutionary stages selected from the APEX Telescope Large Area Survey of the Galaxy (ATLASGAL), from which we aim to establish a census of molecular tracers of their evolution. As a first step, we study the shock tracer, SiO, mainly associated with shocks from jets probing accretion processes. In low-mass young stellar objects (YSOs), outflow and jet activity decreases with time during the star formation processes. Recently, a similar scenario was suggested for massive clumps based on SiO observations. Here we analyse observations of the SiO (2-1) and (5-4) lines in a statistically significant sample to constrain the change of SiO abundance and the excitation conditions as a function of evolutionary stage of massive star-forming clumps. Methods: We performed an unbiased spectral line survey covering the 3-mm atmospheric window between 84-117 GHz with the IRAM 30 m telescope of a sample of 430 sources of the ATLASGAL survey, covering various evolutionary stages of massive clumps. A smaller sample of 128 clumps has been observed in the SiO (5-4) transition with the APEX telescope to complement the (2-1) line and probe the excitation conditions of the emitting gas. We derived detection rates to assess the star formation activity of the sample, and we estimated the column density and abundance using both an LTE approximation and non-LTE calculations for a smaller subsample, where both transitions have been observed. Results: We characterise the physical properties of the selected sources, which greatly supersedes the largest samples studied so far, and show that they are representative of different evolutionary stages. We report a high detection rate of >75% of the SiO (2-1) line and a >90% detection

  13. A neutrality test for detecting selection on DNA methylation using single methylation polymorphism frequency spectrum.

    PubMed

    Wang, Jun; Fan, Chuanzhu

    2015-01-01

    Inheritable epigenetic mutations (epimutations) can contribute to transmittable phenotypic variation. Thus, epimutations can be subject to natural selection and impact the fitness and evolution of organisms. Based on the framework of the modified Tajima's D test for DNA mutations, we developed a neutrality test with the statistic "D(m)" to detect selection forces on DNA methylation mutations using single methylation polymorphisms. With computer simulation and empirical data analysis, we compared the D(m) test with the original and modified Tajima's D tests and demonstrated that the D(m) test is suitable for detecting selection on epimutations and outperforms original/modified Tajima's D tests. Due to the higher resetting rate of epimutations, the interpretation of D(m) on epimutations and Tajima's D test on DNA mutations could be different in inferring natural selection. Analyses using simulated and empirical genome-wide polymorphism data suggested that genes under genetic and epigenetic selections behaved differently. We applied the D(m) test to recently originated Arabidopsis and human genes, and showed that newly evolved genes contain higher level of rare epialleles, suggesting that epimutation may play a role in origination and evolution of genes and genomes. Overall, we demonstrate the utility of the D(m) test to detect whether the loci are under selection regarding DNA methylation. Our analytical metrics and methodology could contribute to our understanding of evolutionary processes of genes and genomes in the field of epigenetics. The Perl script for the "D(m)" test is available at http://fanlab.wayne.edu/ (last accessed December 18, 2014). PMID:25539727

  14. Recursive SAM-based band selection for hyperspectral anomaly detection

    NASA Astrophysics Data System (ADS)

    He, Yuanlei; Liu, Daizhi; Yi, Shihua

    2010-10-01

    Band selection has been widely used in hyperspectral image processing for dimension reduction. In this paper, a recursive SAM-based band selection (RSAM-BBS) method is proposed. Once two initial bands are given, RSAM-BBS is performed in a sequential manner, and at each step the band that can best describe the spectral separation of two hyperspectral signatures is added to the bands already selected until the spectral angle reaches its maximum. In order to demonstrate the utility of the proposed band selection method, an anomaly detection algorithm is developed, which first extracts the anomalous target spectrum from the original image using automatic target detection and classification algorithm (ATDCA), followed by maximum spectral screening (MSS) to estimate the background average spectrum, then implements RSAM-BBS to select bands that participate in the subsequent adaptive cosine estimator (ACE) target detection. As shown in the experimental result on the AVIRIS dataset, less than five bands selected by the RSAM-BBS can achieve comparable detection performance using the full bands.

  15. Double-layer evolutionary algorithm for distributed optimization of particle detection on the Grid

    NASA Astrophysics Data System (ADS)

    Padée, Adam; Kurek, Krzysztof; Zaremba, Krzysztof

    2013-08-01

    Reconstruction of particle tracks from information collected by position-sensitive detectors is an important procedure in HEP experiments. It is usually controlled by a set of numerical parameters which have to be manually optimized. This paper proposes an automatic approach to this task by utilizing evolutionary algorithm (EA) operating on both real-valued and binary representations. Because of computational complexity of the task a special distributed architecture of the algorithm is proposed, designed to be run in grid environment. It is two-level hierarchical hybrid utilizing asynchronous master-slave EA on the level of clusters and island model EA on the level of the grid. The technical aspects of usage of production grid infrastructure are covered, including communication protocols on both levels. The paper deals also with the problem of heterogeneity of the resources, presenting efficiency tests on a benchmark function. These tests confirm that even relatively small islands (clusters) can be beneficial to the optimization process when connected to the larger ones. Finally a real-life usage example is presented, which is an optimization of track reconstruction in Large Angle Spectrometer of NA-58 COMPASS experiment held at CERN, using a sample of Monte Carlo simulated data. The overall reconstruction efficiency gain, achieved by the proposed method, is more than 4%, compared to the manually optimized parameters.

  16. Parallelized evolutionary learning for detection of biclusters in gene expression data.

    PubMed

    Huang, Qinghua; Tao, Dacheng; Li, Xuelong; Liew, Alan Wee-Chung

    2012-01-01

    The analysis of gene expression data obtained from microarray experiments is important for discovering the biological process of genes. Biclustering algorithms have been proven to be able to group the genes with similar expression patterns under a number of experimental conditions. In this paper, we propose a new biclustering algorithm based on evolutionary learning. By converting the biclustering problem into a common clustering problem, the algorithm can be applied in a search space constructed by the conditions. To further reduce the size of the search space, we randomly separate the full conditions into a number of condition subsets (subspaces), each of which has a smaller number of conditions. The algorithm is applied to each subspace and is able to discover bicluster seeds within a limited computing time. Finally, an expanding and merging procedure is employed to combine the bicluster seeds into larger biclusters according to a homogeneity criterion. We test the performance of the proposed algorithm using synthetic and real microarray data sets. Compared with several previously developed biclustering algorithms, our algorithm demonstrates a significant improvement in discovering additive biclusters. PMID:21383419

  17. Combining evolutionary algorithms with oblique decision trees to detect bent double galaxies

    SciTech Connect

    Cantu-Paz, E; Kamath, C

    2000-06-22

    Decision trees have long been popular in classification as they use simple and easy-to-understand tests at each node. Most variants of decision trees test a single attribute at a node, leading to axis-parallel trees, where the test results in a hyperplane which is parallel to one of the dimensions in the attribute space. These trees can be rather large and inaccurate in cases where the concept to be learnt is best approximated by oblique hyperplanes. In such cases, it may be more appropriate to use an oblique decision tree, where the decision at each node is a linear combination of the attributes. Oblique decision trees have not gained wide popularity in part due to the complexity of constructing good oblique splits and the tendency of existing splitting algorithms to get stuck in local minima. Several alternatives have been proposed to handle these problems including randomization in conjunction with deterministic hill climbing and the use of simulated annealing. In this paper, they use evolutionary algorithms (EAs) to determine the split. EAs are well suited for this problem because of their global search properties, their tolerance to noisy fitness evaluations, and their scalability to large dimensional search spaces. They demonstrate the technique on a practical problem from astronomy, namely, the classification of galaxies with a bent-double morphology, and describe their experiences with several split evaluation criteria.

  18. Open and closed evolutionary paths for drastic morphological changes, involving serial gene duplication, sub-functionalization, and selection

    PubMed Central

    Abe, Gembu; Lee, Shu-Hua; Li, Ing-Jia; Chang, Chun-Ju; Tamura, Koji; Ota, Kinya G.

    2016-01-01

    Twin-tail goldfish strains are examples of drastic morphological alterations that emerged through domestication. Although this mutation is known to be caused by deficiency of one of two duplicated chordin genes, it is unknown why equivalent mutations have not been observed in other domesticated fish species. Here, we compared the chordin gene morphant phenotypes of single-tail goldfish and common carp (close relatives, both of which underwent chordin gene duplication and domestication). Morpholino-induced knockdown depleted chordin gene expression in both species; however, while knockdown reproduced twin-tail morphology in single-tail goldfish, it had no effect on common carp morphology. This difference can be explained by the observation that expression patterns of the duplicated chordin genes overlap completely in common carp, but are sub-functionalized in goldfish. Our finding implies that goldfish drastic morphological changes might be enhanced by the subsequent occurrence of three different types of evolutionary event (duplication, sub-functionalization, and selection) in a certain order. PMID:27220684

  19. Open and closed evolutionary paths for drastic morphological changes, involving serial gene duplication, sub-functionalization, and selection.

    PubMed

    Abe, Gembu; Lee, Shu-Hua; Li, Ing-Jia; Chang, Chun-Ju; Tamura, Koji; Ota, Kinya G

    2016-01-01

    Twin-tail goldfish strains are examples of drastic morphological alterations that emerged through domestication. Although this mutation is known to be caused by deficiency of one of two duplicated chordin genes, it is unknown why equivalent mutations have not been observed in other domesticated fish species. Here, we compared the chordin gene morphant phenotypes of single-tail goldfish and common carp (close relatives, both of which underwent chordin gene duplication and domestication). Morpholino-induced knockdown depleted chordin gene expression in both species; however, while knockdown reproduced twin-tail morphology in single-tail goldfish, it had no effect on common carp morphology. This difference can be explained by the observation that expression patterns of the duplicated chordin genes overlap completely in common carp, but are sub-functionalized in goldfish. Our finding implies that goldfish drastic morphological changes might be enhanced by the subsequent occurrence of three different types of evolutionary event (duplication, sub-functionalization, and selection) in a certain order. PMID:27220684

  20. A model of selective masking in chromatic detection.

    PubMed

    Shepard, Timothy G; Swanson, Emily A; McCarthy, Comfrey L; Eskew, Rhea T

    2016-07-01

    Narrowly tuned, selective noise masking of chromatic detection has been taken as evidence for the existence of a large number of color mechanisms (i.e., higher order color mechanisms). Here we replicate earlier observations of selective masking of tests in the (L,M) plane of cone space when the noise is placed near the corners of the detection contour. We used unipolar Gaussian blob tests with three different noise color directions, and we show that there are substantial asymmetries in the detection contours-asymmetries that would have been missed with bipolar tests such as Gabor patches. We develop a new chromatic detection model, which is based on probability summation of linear cone combinations, and incorporates a linear contrast energy versus noise power relationship that predicts how the sensitivity of these mechanisms changes with noise contrast and chromaticity. With only six unipolar color mechanisms (the same number as the cardinal model), the new model accounts for the threshold contours across the different noise conditions, including the asymmetries and the selective effects of the noises. The key for producing selective noise masking in the (L,M) plane is having more than two mechanisms with opposed L- and M-cone inputs, in which case selective masking can be produced without large numbers of color mechanisms. PMID:27442723

  1. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    PubMed Central

    Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

    2015-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

  2. A dynamic evolutionary clustering perspective: Community detection in signed networks by reconstructing neighbor sets

    NASA Astrophysics Data System (ADS)

    Chen, Jianrui; Wang, Hua; Wang, Lina; Liu, Weiwei

    2016-04-01

    Community detection in social networks has been intensively studied in recent years. In this paper, a novel similarity measurement is defined according to social balance theory for signed networks. Inter-community positive links are found and deleted due to their low similarity. The positive neighbor sets are reconstructed by this method. Then, differential equations are proposed to imitate the constantly changing states of nodes. Each node will update its state based on the difference between its state and average state of its positive neighbors. Nodes in the same community will evolve together with time and nodes in the different communities will evolve far away. Communities are detected ultimately when states of nodes are stable. Experiments on real world and synthetic networks are implemented to verify detection performance. The thorough comparisons demonstrate the presented method is more efficient than two acknowledged better algorithms.

  3. Greenhouse Effect Detection Experiment (GEDEX). Selected data sets

    NASA Technical Reports Server (NTRS)

    Olsen, Lola M.; Warnock, Archibald, III

    1992-01-01

    This CD-ROM contains selected data sets compiled by the participants of the Greenhouse Effect Detection Experiment (GEDEX) workshop on atmospheric temperature. The data sets include surface, upper air, and/or satellite-derived measurements of temperature, solar irradiance, clouds, greenhouse gases, fluxes, albedo, aerosols, ozone, and water vapor, along with Southern Oscillation Indices and Quasi-Biennial Oscillation statistics.

  4. Detecting Bias in Selection for Higher Education: Three Different Methods

    ERIC Educational Resources Information Center

    Kennet-Cohen, Tamar; Turvall, Elliot; Oren, Carmel

    2014-01-01

    This study examined selection bias in Israeli university admissions with respect to test language and gender, using three approaches for the detection of such bias: Cleary's model of differential prediction, boundary conditions for differential prediction and difference between "d's" (the Constant Ratio Model). The university…

  5. Efficient feature selection using a hybrid algorithm for the task of epileptic seizure detection

    NASA Astrophysics Data System (ADS)

    Lai, Kee Huong; Zainuddin, Zarita; Ong, Pauline

    2014-07-01

    Feature selection is a very important aspect in the field of machine learning. It entails the search of an optimal subset from a very large data set with high dimensional feature space. Apart from eliminating redundant features and reducing computational cost, a good selection of feature also leads to higher prediction and classification accuracy. In this paper, an efficient feature selection technique is introduced in the task of epileptic seizure detection. The raw data are electroencephalography (EEG) signals. Using discrete wavelet transform, the biomedical signals were decomposed into several sets of wavelet coefficients. To reduce the dimension of these wavelet coefficients, a feature selection method that combines the strength of both filter and wrapper methods is proposed. Principal component analysis (PCA) is used as part of the filter method. As for wrapper method, the evolutionary harmony search (HS) algorithm is employed. This metaheuristic method aims at finding the best discriminating set of features from the original data. The obtained features were then used as input for an automated classifier, namely wavelet neural networks (WNNs). The WNNs model was trained to perform a binary classification task, that is, to determine whether a given EEG signal was normal or epileptic. For comparison purposes, different sets of features were also used as input. Simulation results showed that the WNNs that used the features chosen by the hybrid algorithm achieved the highest overall classification accuracy.

  6. Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering

    PubMed Central

    Srivastava, Amit Kumar; Chopra, Rupali; Ali, Shafat; Aggarwal, Shweta; Vig, Lovekesh; Koul Bamezai, Rameshwar Nath

    2014-01-01

    Inundation of evolutionary markers expedited in Human Genome Project and 1000 Genome Consortium has necessitated pruning of redundant and dependent variables. Various computational tools based on machine-learning and data-mining methods like feature selection/extraction have been proposed to escape the curse of dimensionality in large datasets. Incidentally, evolutionary studies, primarily based on sequentially evolved variations have remained un-facilitated by such advances till date. Here, we present a novel approach of recursive feature selection for hierarchical clustering of Y-chromosomal SNPs/haplogroups to select a minimal set of independent markers, sufficient to infer population structure as precisely as deduced by a larger number of evolutionary markers. To validate the applicability of our approach, we optimally designed MALDI-TOF mass spectrometry-based multiplex to accommodate independent Y-chromosomal markers in a single multiplex and genotyped two geographically distinct Indian populations. An analysis of 105 world-wide populations reflected that 15 independent variations/markers were optimal in defining population structure parameters, such as FST, molecular variance and correlation-based relationship. A subsequent addition of randomly selected markers had a negligible effect (close to zero, i.e. 1 × 10−3) on these parameters. The study proves efficient in tracing complex population structures and deriving relationships among world-wide populations in a cost-effective and expedient manner. PMID:25030906

  7. Pattern recognition for selective odor detection with gas sensor arrays.

    PubMed

    Kim, Eungyeong; Lee, Seok; Kim, Jae Hun; Kim, Chulki; Byun, Young Tae; Kim, Hyung Seok; Lee, Taikjin

    2012-01-01

    This paper presents a new pattern recognition approach for enhancing the selectivity of gas sensor arrays for clustering intelligent odor detection. The aim of this approach was to accurately classify an odor using pattern recognition in order to enhance the selectivity of gas sensor arrays. This was achieved using an odor monitoring system with a newly developed neural-genetic classification algorithm (NGCA). The system shows the enhancement in the sensitivity of the detected gas. Experiments showed that the proposed NGCA delivered better performance than the previous genetic algorithm (GA) and artificial neural networks (ANN) methods. We also used PCA for data visualization. Our proposed system can enhance the reproducibility, reliability, and selectivity of odor sensor output, so it is expected to be applicable to diverse environmental problems including air pollution, and monitor the air quality of clean-air required buildings such as a kindergartens and hospitals. PMID:23443378

  8. Pattern Recognition for Selective Odor Detection with Gas Sensor Arrays

    PubMed Central

    Kim, Eungyeong; Lee, Seok; Kim, Jae Hun; Kim, Chulki; Byun, Young Tae; Kim, Hyung Seok; Lee, Taikjin

    2012-01-01

    This paper presents a new pattern recognition approach for enhancing the selectivity of gas sensor arrays for clustering intelligent odor detection. The aim of this approach was to accurately classify an odor using pattern recognition in order to enhance the selectivity of gas sensor arrays. This was achieved using an odor monitoring system with a newly developed neural-genetic classification algorithm (NGCA). The system shows the enhancement in the sensitivity of the detected gas. Experiments showed that the proposed NGCA delivered better performance than the previous genetic algorithm (GA) and artificial neural networks (ANN) methods. We also used PCA for data visualization. Our proposed system can enhance the reproducibility, reliability, and selectivity of odor sensor output, so it is expected to be applicable to diverse environmental problems including air pollution, and monitor the air quality of clean-air required buildings such as a kindergartens and hospitals. PMID:23443378

  9. Selective detection of bacterial layers with terahertz plasmonic antennas.

    PubMed

    Berrier, Audrey; Schaafsma, Martijn C; Nonglaton, Guillaume; Bergquist, Jonas; Rivas, Jaime Gómez

    2012-11-01

    Current detection and identification of micro-organisms is based on either rather unspecific rapid microscopy or on more accurate but complex and time-consuming procedures. In a medical context, the determination of the bacteria Gram type is of significant interest. The diagnostic of microbial infection often requires the identification of the microbiological agent responsible for the infection, or at least the identification of its family (Gram type), in a matter of minutes. In this work, we propose to use terahertz frequency range antennas for the enhanced selective detection of bacteria types. Several microorganisms are investigated by terahertz time-domain spectroscopy: a fast, contactless and damage-free investigation method to gain information on the presence and the nature of the microorganisms. We demonstrate that plasmonic antennas enhance the detection sensitivity for bacterial layers and allow the selective recognition of the Gram type of the bacteria. PMID:23162730

  10. Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes

    PubMed Central

    Reineke, Anna R.; Bornberg-Bauer, Erich; Gu, Jenny

    2011-01-01

    The discovery of regulatory motifs embedded in upstream regions of plants is a particularly challenging bioinformatics task. Previous studies have shown that motifs in plants are short compared with those found in vertebrates. Furthermore, plant genomes have undergone several diversification mechanisms such as genome duplication events which impact the evolution of regulatory motifs. In this article, a systematic phylogenomic comparison of upstream regions is conducted to further identify features of the plant regulatory genomes, the component of genomes regulating gene expression, to enable future de novo discoveries. The findings highlight differences in upstream region properties between major plant groups and the effects of divergence times and duplication events. First, clear differences in upstream region evolution can be detected between monocots and dicots, thus suggesting that a separation of these groups should be made when searching for novel regulatory motifs, particularly since universal motifs such as the TATA box are rare. Second, investigating the decay rate of significantly aligned regions suggests that a divergence time of ∼100 mya sets a limit for reliable conserved non-coding sequence (CNS) detection. Insights presented here will set a framework to help identify embedded motifs of functional relevance by understanding the limits of bioinformatics detection for CNSs. PMID:21470961

  11. An Evolutionary Approach for Joint Blind Multichannel Estimation and Order Detection

    NASA Astrophysics Data System (ADS)

    Fangjiong, Chen; Kwong, Sam; Gang, Wei

    2003-12-01

    A joint blind order-detection and parameter-estimation algorithm for a single-input multiple-output (SIMO) channel is presented. Based on the subspace decomposition of the channel output, an objective function including channel order and channel parameters is proposed. The problem is resolved by using a specifically designed genetic algorithm (GA). In the proposed GA, we encode both the channel order and parameters into a single chromosome, so they can be estimated simultaneously. Novel GA operators and convergence criteria are used to guarantee correct and high convergence speed. Simulation results show that the proposed GA achieves satisfactory convergence speed and performance.

  12. Selective media for detecting and enumerating foodborne yeasts.

    PubMed

    Beuchat, L R

    1993-06-25

    No one medium is satisfactory for detecting, isolating and enumerating all yeasts in all foods. Antibiotic-supplemented media such as dichloran rose Bengal chloramphenicol agar, tryptone glucose yeast extract chloramphenicol agar, oxytetracycline glucose yeast extract agar and rose Bengal chloramphenicol agar are superior to acidified potato dextrose agar and other acidified media for enumeration of the vast majority of spoilage yeasts. Dichloran glycerol (18%) agar performs well for enumerating moderately xerotolerant yeasts. Malt extract yeast extract glucose (up to 60%) can be used for detecting and enumerating moderate and extreme xerophiles. These media also support the growth of moulds. Lysine agar, Schwarz differential agar and Lin's wild yeast differential agar are used by the brewing industry to differentiate wild yeasts from brewer's strains. Lysine agar is selective for apiculate yeasts and ethanol sulfite yeast extract agar is selective for Saccharomyces. Both have application in wineries. Modified molybdate agar can be used to selectively isolate yeasts from tropical fruits. Preservative-resistant yeasts can be detected on malt acetic agar. The recommended incubation temperature is 25 degrees C, but incubation time between plating and counting colonies ranges from 5 days for determination of general populations of yeasts to 10 days for more for xerotolerant yeasts. There is need for new and improved media for selectively isolating various groups, genera, species and strains of yeasts capable of growing only under specific environmental conditions in specific types of foods and beverages. PMID:8357752

  13. Wavelength band selection method for multispectral target detection.

    PubMed

    Karlholm, Jörgen; Renhorn, Ingmar

    2002-11-10

    A framework is proposed for the selection of wavelength bands for multispectral sensors by use of hyperspectral reference data. Using the results from the detection theory we derive a cost function that is minimized by a set of spectral bands optimal in terms of detection performance for discrimination between a class of small rare targets and clutter with known spectral distribution. The method may be used, e.g., in the design of multispectral infrared search and track and electro-optical missile warning sensors, where a low false-alarm rate and a high-detection probability for detection of small targets against a clutter background are of critical importance, but the required high frame rate prevents the use of hyperspectral sensors. PMID:12440532

  14. Considerations in detecting CDC select agents under field conditions

    NASA Astrophysics Data System (ADS)

    Spinelli, Charles; Soelberg, Scott; Swanson, Nathaneal; Furlong, Clement; Baker, Paul

    2008-04-01

    Surface Plasmon Resonance (SPR) has become a widely accepted technique for real-time detection of interactions between receptor molecules and ligands. Antibody may serve as receptor and can be attached to the gold surface of the SPR device, while candidate analyte fluids contact the detecting antibody. Minute, but detectable, changes in refractive indices (RI) indicate that analyte has bound to the antibody. A decade ago, an inexpensive, robust, miniature and fully integrated SPR chip, called SPREETA, was developed. University of Washington (UW) researchers subsequently developed a portable, temperature-regulated instrument, called SPIRIT, to simultaneously use eight of these three-channel SPREETA chips. A SPIRIT prototype instrument was tested in the field, coupled to a remote reporting system on a surrogate unmanned aerial vehicle (UAV). Two target protein analytes were released sequentially as aerosols with low analyte concentration during each of three flights and were successfully detected and verified. Laboratory experimentation with a more advanced SPIRIT instrument demonstrated detection of very low levels of several select biological agents that might be employed by bioterrorists. Agent detection under field-like conditions is more challenging, especially as analyte concentrations are reduced and complex matricies are introduced. Two different sample preconditioning protocols have been developed for select agents in complex matrices. Use of these preconditioning techniques has allowed laboratory detection in spiked heavy mud of Francisella tularensis at 10 3 CFU/ml, Bacillus anthracis spores at 10 3 CFU/ml, Staphylococcal enterotoxin B (SEB) at 1 ng/ml, and Vaccinia virus (a smallpox simulant) at 10 5 PFU/ml. Ongoing experiments are aimed at simultaneous detection of multiple agents in spiked heavy mud, using a multiplex preconditioning protocol.

  15. Comparative Genomics Uncovers Unique Gene Turnover and Evolutionary Rates in a Gene Family Involved in the Detection of Insect Cuticular Pheromones

    PubMed Central

    Torres-Oliva, Montserrat; Almeida, Francisca C.; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-01-01

    Chemoreception is an essential process for the survival and reproduction of animals. Many of the proteins responsible for recognizing and transmitting chemical stimuli in insects are encoded by genes that are members of moderately sized multigene families. The members of the CheB family are specialized in gustatory-mediated detection of long-chain hydrocarbon pheromones in Drosophila melanogaster and play a central role in triggering and modulating mating behavior in this species. Here, we present a comprehensive comparative genomic analysis of the CheB family across 12 species of the Drosophila genus. We have identified a total of 102 new CheB genes in the genomes of these species, including a functionally divergent member previously uncharacterized in D. melanogaster. We found that, despite its relatively small repertory size, the CheB family has undergone multiple gain and loss events and various episodes of diversifying selection during the divergence of the surveyed species. Present estimates of gene turnover and coding sequence substitution rates show that this family is evolving faster than any known Drosophila chemosensory family. To date, only other insect gustatory-related genes among these families had shown evolutionary dynamics close to those observed in CheBs. Our findings reveal the high adaptive potential of molecular components of the gustatory system in insects and anticipate a key role of genes involved in this sensory modality in species adaptation and diversification.

  16. Detecting and measuring selection from gene frequency data.

    PubMed

    Vitalis, Renaud; Gautier, Mathieu; Dawson, Kevin J; Beaumont, Mark A

    2014-03-01

    The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily and cost effectively, large amounts of detailed data on the genotype composition of populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best to identify these selected regions, loci, or single nucleotides remains a challenging issue. Here, we introduce a new model-based method, called SelEstim, to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former. The underlying population genetic model is a diffusion approximation for the distribution of allele frequency in a population subdivided into a number of demes that exchange migrants. We use a Markov chain Monte Carlo algorithm for sampling from the joint posterior distribution of the model parameters, in a hierarchical Bayesian framework. We present evidence from stochastic simulations, which demonstrates the good power of SelEstim to identify loci targeted by selection and to estimate the strength of selection acting on these loci, within each deme. We also reanalyze a subset of SNP data from the Stanford HGDP-CEPH Human Genome Diversity Cell Line Panel to illustrate the performance of SelEstim on real data. In agreement with previous studies, our analyses point to a very strong signal of positive selection upstream of the LCT gene, which encodes for the enzyme lactase-phlorizin hydrolase and is associated with adult-type hypolactasia. The geographical distribution of the strength of positive selection across the Old World matches the interpolated map of lactase persistence phenotype frequencies, with the strongest selection coefficients in Europe and in the Indus Valley. PMID:24361938

  17. Fast Selective Detection of Pyocyanin Using Cyclic Voltammetry

    PubMed Central

    Alatraktchi, Fatima AlZahra’a; Breum Andersen, Sandra; Krogh Johansen, Helle; Molin, Søren; Svendsen, Winnie E.

    2016-01-01

    Pyocyanin is a virulence factor uniquely produced by the pathogen Pseudomonas aeruginosa. The fast and selective detection of pyocyanin in clinical samples can reveal important information about the presence of this microorganism in patients. Electrochemical sensing of the redox-active pyocyanin is a route to directly quantify pyocyanin in real time and in situ in hospitals and clinics. The selective quantification of pyocyanin is, however, limited by other redox-active compounds existing in human fluids and by other metabolites produced by pathogenic bacteria. Here we present a direct selective method to detect pyocyanin in a complex electroactive environment using commercially available electrodes. It is shown that cyclic voltammetry measurements between −1.0 V to 1.0 V reveal a potential detection window of pyocyanin of 0.58–0.82 V that is unaffected by other redox-active interferents. The linear quantification of pyocyanin has an R2 value of 0.991 across the clinically relevant concentration range of 2–100 µM. The proposed method was tested on human saliva showing a standard deviation of 2.5% ± 1% (n = 5) from the known added pyocyanin concentration to the samples. This inexpensive procedure is suggested for clinical use in monitoring the presence and state of P. aeruginosa infection in patients. PMID:27007376

  18. Selection of advanced technologies for detection of trucks

    NASA Astrophysics Data System (ADS)

    Middleton, Dan

    1998-01-01

    The North American Free Trade Agreement is anticipated an already increasing trend in highway freight movement across the international border between Texas and Mexico. The Texas Department of Transportation is concerned about safeguarding its motoring public and protection of its highway infrastructure. By sponsoring this research, it hopes to improve traffic signal operations, especially at isolated intersections. Recent advances in sensing technologies and signalization enable safer and more efficient intersection control. This research evaluated advanced detection technologies that can be used to increase green time to trucks and reduce their stops and delays. Equipment selection criteria required devices that were reasonably accurate in classification of vehicles under all weather and lighting conditions and determination of vehicle speeds. The research team selected active IR and passive acoustic technologies. Components of the detection system include: an Industrial PC, proprietary boards inside the computer, IR and acoustic detectors, a pole for mounting the selected systems, and a classifier system using pavement sensors for verification purposes. The purpose of the node computer was to interpret signals from detectors, store data, and communicate with the controller cabinet upon detection of a truck.

  19. Binding-regulated click ligation for selective detection of proteins.

    PubMed

    Cao, Ya; Han, Peng; Wang, Zhuxin; Chen, Weiwei; Shu, Yongqian; Xiang, Yang

    2016-04-15

    Herein, a binding-regulated click ligation (BRCL) strategy for endowing selective detection of proteins is developed with the incorporation of small-molecule ligand and clickable DNA probes. The fundamental principle underlying the strategy is the regulating capability of specific protein-ligand binding against the ligation between clickable DNA probes, which could efficiently combine the detection of particular protein with enormous DNA-based sensing technologies. In this work, the feasibly of the BRCL strategy is first verified through agarose gel electrophoresis and electrochemical impedance spectroscopy measurements, and then confirmed by transferring it to a nanomaterial-assisted fluorescence assay. Significantly, the BRCL strategy-based assay is able to respond to target protein with desirable selectivity, attributing to the specific recognition between small-molecule ligand and its target. Further experiments validate the general applicability of the sensing method by tailoring the ligand toward different proteins (i.e., avidin and folate receptor), and demonstrate its usability in complex biological samples. To our knowledge, this work pioneers the practice of click chemistry in probing specific small-molecule ligand-protein binding, and therefore may pave a new way for selective detection of proteins. PMID:26599478

  20. Interest area selection for navigation based on structured edge detection

    NASA Astrophysics Data System (ADS)

    Sun, Xiao; Shang, Ke; Li, ShaoJun; Dou, Hao; Tian, JinWen; Ming, Delie

    2015-12-01

    The scene matching based navigation is an important precision navigation technology for unmanned aerial vehicles (UAV). Selection of interest area where reference image is made has an important influence on the precision of matching result besides the performance of match algorithm. In this paper, a method to select interest area based on structured edge detection is proposed. We use a data driven approach that classifies each pixel with a typical structured edge label. We propose a method that combines these labels into a feature measuring suitable to match of a region. Then a SVM classifier is trained to classify the features and get the final result of the selection of interest area. The experimental result shows that the proposed method is valid and effective.

  1. Drosophila melanogaster Selection for Survival after Infection with Bacillus cereus Spores: Evolutionary Genetic and Phenotypic Investigations of Respiration and Movement

    PubMed Central

    Ma, Junjie; Benson, Andrew K.; Kachman, Stephen D.; Jacobsen, Deidra J.; Harshman, Lawrence G.

    2013-01-01

    Laboratory populations of D. melanogaster have been subjected to selection for survival after live spores of B. cereus were introduced as a pathogenic agent. The present study was designed to investigate correlated traits: respiration as a metabolic trait and movement as a behavioral trait. An underlying hypothesis was that the evolution of increased survival after B. cereus infection exerts a metabolic cost associated with elevated immunity and this would be detected by increased respiration rates. There was support for this hypothesis in the male response to selection, but not for selected-line females. Two phenotypic effects were also observed in the study. Females especially showed a marked increase in respiration after mating compared to the other assay stages regardless of whether respiration was measured per fly or adjusted by lean mass or dry weight. Given that mating stimulates egg production, it is feasible that elevated metabolism was needed to provision oocytes with yolk. Females also moved less than males, perhaps due to behaviors related to oviposition whereas elevated male activity might be due to behaviors associated with seeking females and courtship. Relatively low movement of females indicated that their elevated respiration after mating was not due to a change in locomotion. PMID:23634317

  2. ULTRASENSITIVE HIGH-TEMPERATURE SELECTIVE GAS DETECTION USING PIEZOELECTRIC MICROCANTILEVERS

    SciTech Connect

    Wan Y. Shih; Tejas Patil; Qiang Zhao; Yi-Shi Chiu; Wei-Heng Shih

    2004-03-05

    We have obtained very promising results in the Phase I study. Specifically, for temperature effects, we have established that piezoelectric cantilever sensors could retain their resonance peak strength at high temperatures, i.e., the Q values of the resonance peaks remained above 10 even when the temperature was very close to the Curie temperature. This confirms that a piezoelectric cantilever sensor can be used as a sensor up to its Curie temperature. Furthermore, we have shown that the mass detection sensitivity remained unchanged at different temperatures. For selective gas detection, we have demonstrated selective NH{sub 3} detection using piezoelectric cantilever sensors coated with mesoporous SiO{sub 2}. For high-temperature sensor materials development, we have achieved highly oriented Sr-doped lead titanate thin films that possessed superior dielectric and ferroelectric properties. Such highly oriented films can be microfabricated into high-performance piezoelectric microcantilever sensors that can be used up to 490 C. We have accomplished the goal of Phase I study in exploring the various aspects of a high-temperature gas sensor. We propose to continue the study in Phase II to develop a sensor that is suitable for high-temperature applications using piezoelectrics with a high Curie temperature and by controlling the effects of temperature. The lead titanate based thin film developed in Phase I is good for applications up to 490 C. In phase II, we will develop lithium niobate thin film based cantilevers for applications up to 1000 C.

  3. Frequency selective detection of nuclear quadrupole resonance (NQR) spin echoes

    NASA Astrophysics Data System (ADS)

    Somasundaram, Samuel D.; Jakobsson, Andreas; Smith, John A. S.; Althoefer, Kaspar A.

    2006-05-01

    Nuclear Quadrupole Resonance (NQR) is a radio frequency (RF) technique that can be used to detect the presence of quadrupolar nuclei, such as the 14N nucleus prevalent in many explosives and narcotics. The technique has been hampered by low signal-to-noise ratios and is further aggravated by the presence of RF interference (RFI). To ensure accurate detection, proposed detectors should exploit the rich form of the NQR signal. Furthermore, the detectors should also be robust to any remaining residual interference, left after suitable RFI mitigation has been employed. In this paper, we propose a new NQR data model, particularly for the realistic case where multiple pulse sequences are used to generate trains of spin echoes. Furthermore, we refine two recently proposed approximative maximum likelihood (AML) detectors, enabling the algorithm to optimally exploit the data model of the entire echo train and also incorporate knowledge of the temperature dependent spin-echo decay time. The AML-based detectors ensure accurate detection and robustness against residual RFI, even when the temperature of the sample is not precisely known, by exploiting the dependencies of the NQR resonant lines on temperature. Further robustness against residual interference is gained as the proposed detector is frequency selective; exploiting only those regions of the spectrum where the NQR signal is expected. Extensive numerical evaluations based on both simulated and measured NQR data indicate that the proposed Frequency selective Echo Train AML (FETAML) detector offers a significant improvement as compared to other existing detectors.

  4. Multitemporal spectroscopy for crop stress detection using band selection methods

    NASA Astrophysics Data System (ADS)

    Mewes, Thorsten; Franke, Jonas; Menz, Gunter

    2008-08-01

    A fast and precise sensor-based identification of pathogen infestations in wheat stands is essential for the implementation of site-specific fungicide applications. Several works have shown possibilities and limitations for the detection of plant stress using spectral sensor data. Hyperspectral data provide the opportunity to collect spectral reflectance in contiguous bands over a broad range of the electromagnetic spectrum. Individual phenomena like the light absorption of leaf pigments can be examined in detail. The precise knowledge of stress-dependent shifting in certain spectral wavelengths provides great advantages in detecting fungal infections. This study focuses on band selection techniques for hyperspectral data to identify relevant and redundant information in spectra regarding a detection of plant stress caused by pathogens. In a laboratory experiment, five 1 sqm boxes with wheat were multitemporarily measured by a ASD Fieldspec® 3 FR spectroradiometer. Two stands were inoculated with Blumeria graminis - the pathogen causing powdery mildew - and one stand was used to simulate the effect of water deficiency. Two stands were kept healthy as control stands. Daily measurements of the spectral reflectance were taken over a 14-day period. Three ASD Pro Lamps were used to illuminate the plots with constant light. By applying band selection techniques, the three types of different wheat vitality could be accurately differentiated at certain stages. Hyperspectral data can provide precise information about pathogen infestations. The reduction of the spectral dimension of sensor data by means of band selection procedures is an appropriate method to speed up the data supply for precision agriculture.

  5. Evaluation of Selected Features for CAR Detection in Aerial Images

    NASA Astrophysics Data System (ADS)

    Tuermer, S.; Leitloff, J.; Reinartz, P.; Stilla, U.

    2011-09-01

    The extraction of vehicles from aerial images provides a wide area traffic situation within a short time. Applications for the gathered data are various and reach from smart routing in the case of congestions to usability validation of roads in the case of disasters. The challenge of the vehicle detection task is finding adequate features which are capable to separate cars from other objects; especially those that look similar. We present an experiment where selected features show their ability of car detection. Precisely, Haar-like and HoG features are utilized and passed to the AdaBoost algorithm for calculating the final detector. Afterwards the classifying power of the features is accurately analyzed and evaluated. The tests a carried out on aerial data from the inner city of Munich, Germany and include small inner city roads with rooftops close by which raise the complexity factor.

  6. Method for detection of selected chemicals in an open environment

    NASA Technical Reports Server (NTRS)

    Duong, Tuan (Inventor); Ryan, Margaret (Inventor)

    2009-01-01

    The present invention relates to a space-invariant independent component analysis and electronic nose for detection of selective chemicals in an unknown environment, and more specifically, an approach to analysis of sensor responses to mixtures of unknown chemicals by an electronic nose in an open and changing environment. It is intended to fill the gap between an alarm, which has little or no ability to distinguish among chemical compounds causing a response, and an analytical instrument, which can distinguish all compounds present but with no real-time or continuous event monitoring ability.

  7. Element Selective X-ray Detected Magnetic Resonance

    SciTech Connect

    Goulon, J.; Rogalev, A.; Wilhelm, F.; Jaouen, N.; Goulon-Ginet, C.; Goujon, G.; Youssef, J. Ben; Indenbom, M. V.

    2007-01-19

    Element selective X-ray Detected Magnetic Resonance (XDMR) was measured on exciting the Fe K-edge in a high quality YIG thin film. Resonant pumping at high microwave power was achieved in the nonlinear foldover regime and X-ray Magnetic Circular Dichroism (XMCD) was used to probe the time-invariant change of the magnetization {delta}Mz due to the precession of orbital magnetization densities of states (DOS) at the Fe sites. This challenging experiment required us to design a specific instrumentation which is briefly described.

  8. Evolutionary process of Bos taurus cattle in favourable versus unfavourable environments and its implications for genetic selection

    PubMed Central

    O'Neill, Christopher J; Swain, David L; Kadarmideen, Haja N

    2010-01-01

    The evolutionary processes that have enabled Bos taurus cattle to establish around the globe are at the core to the future success of livestock production. Our study focuses on the history of cattle domestication including the last 60 years of B. taurus breeding programmes in both favourable and unfavourable environments and its consequences on evolution and fitness of cattle. We discuss the emergence of ‘production diseases’ in temperate production systems and consider the evolutionary genetics of tropical adaptation in cattle and conclude that the Senepol, N'Dama, Adaptaur and Criollo breeds, among others with similar evolutionary trajectories, would possess genes capable of improving the productivity of cattle in challenging environments. Using our own experimental evidence from northern Australia, we review the evolution of the Adaptaur cattle breed which has become resistant to cattle tick. We emphasize that the knowledge of interactions between genotype, environment and management in the livestock systems will be required to generate genotypes for efficient livestock production that are both economically and environmentally sustainable. Livestock producers in the 21st century will have less reliance on infrastructure and veterinary products to alleviate environmental stress and more on the animal's ability to achieve fitness in a given production environment. PMID:25567936

  9. Possible evolutionary relationships between streptomycin and bluensomycin biosynthetic pathways: detection of novel inositol kinase and O-carbamoyltransferase activities.

    PubMed Central

    Walker, J B

    1990-01-01

    Bluensomycin (glebomycin) is an aminocyclitol antibiotic that differs structurally from dihydrostreptomycin in having bluensidine (1D-1-O-carbamoyl-3-guanidinodeoxy-scyllo-inositol) rather than streptidine (1,3-diguanidino-1,3-dideoxy-scyllo-inositol) as its aminocyclitol moiety. Extracts of the bluensomycin producer Streptomyces hygroscopicus form glebosus ATCC 14607 (S. glebosus) were found to have aminodeoxy-scyllo-inositol kinase activity but to lack 1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol kinase activity, showing for the first time that these two reactions in streptomycin producers must be catalyzed by different enzymes. S. glebosus extracts therefore possess the same five enzymes required for synthesis of guanidinodeoxy-scyllo-inositol from myo-inositol that are found in streptomycin producers but lack the next three of the four enzymes found in streptomycin producers that are required to synthesize the second guanidino group of streptidine-P. In place of a second guanidino group, S. glebosus extracts were found to catalyze a Mg2(+)-dependent carbamoylation of guanidinodeoxy-scyllo-inositol to form bluensidine, followed by a phosphorylation to form bluensidine-P. The novel carbamoyl-P:guanidinodeoxy-scyllo-inositol O-carbamoyltransferase and ATP:bluensidine phosphotransferase activities were not detected in streptomycin producers or in S. glebosus during its early rapid growth phase. Free bluensidine appears to be a normal intermediate in bluensomycin biosynthesis, in contrast to the case of streptomycin biosynthesis; in the latter, although exogenous streptidine can enter the pathway via streptidine-P, free streptidine is not an intermediate in the endogenous biosynthetic pathway. Comparison of the streptomycin and bluensomycin biosynthetic pathways provides a unique opportunity to evaluate those proposed mechanisms for the evolutionary acquisition of new biosynthetic capabilities that involve gene duplication and subsequent mutational changes in

  10. Evolutionary biology of language.

    PubMed Central

    Nowak, M A

    2000-01-01

    Language is the most important evolutionary invention of the last few million years. It was an adaptation that helped our species to exchange information, make plans, express new ideas and totally change the appearance of the planet. How human language evolved from animal communication is one of the most challenging questions for evolutionary biology The aim of this paper is to outline the major principles that guided language evolution in terms of mathematical models of evolutionary dynamics and game theory. I will discuss how natural selection can lead to the emergence of arbitrary signs, the formation of words and syntactic communication. PMID:11127907

  11. Bayesian Variable Selection for Detecting Adaptive Genomic Differences Among Populations

    PubMed Central

    Riebler, Andrea; Held, Leonhard; Stephan, Wolfgang

    2008-01-01

    We extend an Fst-based Bayesian hierarchical model, implemented via Markov chain Monte Carlo, for the detection of loci that might be subject to positive selection. This model divides the Fst-influencing factors into locus-specific effects, population-specific effects, and effects that are specific for the locus in combination with the population. We introduce a Bayesian auxiliary variable for each locus effect to automatically select nonneutral locus effects. As a by-product, the efficiency of the original approach is improved by using a reparameterization of the model. The statistical power of the extended algorithm is assessed with simulated data sets from a Wright–Fisher model with migration. We find that the inclusion of model selection suggests a clear improvement in discrimination as measured by the area under the receiver operating characteristic (ROC) curve. Additionally, we illustrate and discuss the quality of the newly developed method on the basis of an allozyme data set of the fruit fly Drosophila melanogaster and a sequence data set of the wild tomato Solanum chilense. For data sets with small sample sizes, high mutation rates, and/or long sequences, however, methods based on nucleotide statistics should be preferred. PMID:18245358

  12. Bayesian variable selection for detecting adaptive genomic differences among populations.

    PubMed

    Riebler, Andrea; Held, Leonhard; Stephan, Wolfgang

    2008-03-01

    We extend an F(st)-based Bayesian hierarchical model, implemented via Markov chain Monte Carlo, for the detection of loci that might be subject to positive selection. This model divides the F(st)-influencing factors into locus-specific effects, population-specific effects, and effects that are specific for the locus in combination with the population. We introduce a Bayesian auxiliary variable for each locus effect to automatically select nonneutral locus effects. As a by-product, the efficiency of the original approach is improved by using a reparameterization of the model. The statistical power of the extended algorithm is assessed with simulated data sets from a Wright-Fisher model with migration. We find that the inclusion of model selection suggests a clear improvement in discrimination as measured by the area under the receiver operating characteristic (ROC) curve. Additionally, we illustrate and discuss the quality of the newly developed method on the basis of an allozyme data set of the fruit fly Drosophila melanogaster and a sequence data set of the wild tomato Solanum chilense. For data sets with small sample sizes, high mutation rates, and/or long sequences, however, methods based on nucleotide statistics should be preferred. PMID:18245358

  13. Selective TERS Detection and Imaging through Controlled Plasmonics

    PubMed Central

    Wang, Hao; Carrier, Stacey L.; Park, Sheldon; Schultz, Zachary D.

    2014-01-01

    Enhanced Raman spectroscopy offers capabilities to detect molecules in the complex molecular environments and image chemical heterogeneity in a wide range of samples. It has been shown that plasmonic interactions between a TERS tip and a metal surface produce significant enhancements. In this report we show how SERS spectra from purified molecules can be used to selectively image proteins on surfaces and in cell membranes. The SERS response from the purified protein can be used to create a multivariate regression model that can be applied to nanoparticles that bind to protein receptors. Filtering the observed TERS spectra with the regression model can then selectively image the protein receptor. Experiments with mutant proteins suggest that key amino acids provide significant contributions to the observed TERS signal, which enables differentiating protein receptors. These results demonstrate the selectivity that can be obtained in TERS images through a controlled plasmonic interaction. This approach has further implications for identifying membrane receptors that bind specific molecules relevant to drug targeting and chemical signaling. PMID:25759958

  14. Selective Detection of Neurotransmitters by Fluorescence and Chemiluminescence Imaging

    SciTech Connect

    Ziqiang Wang; Edward S. Yeung

    2001-08-06

    In recent years, luminescence imaging has been widely employed in neurochemical analysis. It has a number of advantages for the study of neuronal and other biological cells: (1) a particular molecular species or cellular constituent can be selectively visualized in the presence of a large excess of other species in a heterogeneous environment; (2) low concentration detection limits can be achieved because of the inherent sensitivity associated with fluorescence and chemiluminescence; (3) low excitation intensities can be used so that long-term observation can be realized while the viability of the specimen is preserved; and (4) excellent spatial resolution can be obtained with the light microscope so subcellular compartments can be identified. With good sensitivity, temporal and spatial resolution, the flux of ions and molecules and the distribution and dynamics of intracellular species can be measured in real time with specific luminescence probes, substrates, or with native fluorescence. A noninvasive detection scheme based on glutamate dehydrogenase (GDH) enzymatic assay combined with microscopy was developed to measure the glutamate release in cultured cells from the central nervous system (CNS). The enzyme reaction is very specific and sensitive. The detection limit with CCD imaging is down to {micro}M levels of glutamate with reasonable response time. They also found that chemiluminescence associated with the ATP-dependent reaction between luciferase and luciferin can be used to image ATP at levels down to 10 nM in the millisecond time scale. Similar imaging experiments should be feasible in a broad spectrum of biological systems.

  15. Ratiometric fluorescent nanosensors for selective detecting cysteine with upconversion luminescence.

    PubMed

    Guan, Yunlong; Qu, Songnan; Li, Bin; Zhang, Liming; Ma, Heping; Zhang, Ligong

    2016-03-15

    Fluorescent sensors based on upconversion (UC) luminescence have been considered as a promising strategy to detect bio-analyte due to their advantages in deep penetration, minimum autofluorescence, and ratiometric fluorescent output. A prototype of nanosensors combined with mesoporous silica coated upconversion nanoparticles (UCNPs) and a fluorescein-based fluorescent probe loaded in pores was therefore designed to detect cysteine (Cys). The silica shell provided loading space for the probe and enabled the nanosensors to disperse in water. In the presence of Cys, the fluorescent probe was transformed into 5(6)-carboxyfluorescein with an emission band centering at 518 nm which was secondarily excited by the light at around 475 nm from NaYF4:Yb(3+), Tm(3+) UCNPs driven by 980 nm near-infrared (NIR) laser. The intensity ratio between green and blue luminescence (I518/I475) grew exponentially with increasing concentrations of Cys over a range of 20-200 μmolL(-1). The response of the nanosensors towards Cys was recognizable with naked eyes by luminescence color change. Evidences suggest that these nanosensors are capable of sensing Cys in aqueous solution and distinguishing Cys from homocysteine (Hcy) with kinetically-controlled selectivity. The system was further employed to detect Cys in human serum and the result was in agreement with it tested by high performance liquid chromatography with acceptable recovery. PMID:26402589

  16. Statistical feature selection for enhanced detection of brain tumor

    NASA Astrophysics Data System (ADS)

    Chaddad, Ahmad; Colen, Rivka R.

    2014-09-01

    Feature-based methods are widely used in the brain tumor recognition system. Robust of early cancer detection is one of the most powerful image processing tools. Specifically, statistical features, such as geometric mean, harmonic mean, mean excluding outliers, median, percentiles, skewness and kurtosis, have been extracted from brain tumor glioma to aid in discriminating two levels namely, Level I and Level II using fluid attenuated inversion recovery (FLAIR) sequence in the diagnosis of brain tumor. Statistical feature describes the major characteristics of each level from glioma which is an important step to evaluate heterogeneity of cancer area pixels. In this paper, we address the task of feature selection to identify the relevant subset of features in the statistical domain, while discarding those that are either redundant or confusing, thereby improving the performance of feature-based scheme to distinguish between Level I and Level II. We apply a Decision Structure algorithm to find the optimal combination of nonhomogeneity based statistical features for the problem at hand. We employ a Naïve Bayes classifier to evaluate the performance of the optimal statistical feature based scheme in terms of its glioma Level I and Level II discrimination capability and use real-data collected from 17 patients have a glioblastoma multiforme (GBM). Dataset provided from 3 Tesla MR imaging system by MD Anderson Cancer Center. For the specific data analyzed, it is shown that the identified dominant features yield higher classification accuracy, with lower number of false alarms and missed detections, compared to the full statistical based feature set. This work has been proposed and analyzed specific GBM types which Level I and Level II and the dominant features were considered as feature aid to prognostic indicators. These features were selected automatically to be better able to determine prognosis from classical imaging studies.

  17. Selective detection of Escherichia coli DNA using fluorescent carbon spindles.

    PubMed

    Roy, Anurag; Chatterjee, Sabyasachi; Pramanik, Srikrishna; Devi, Parukuttyamma Sujatha; Suresh Kumar, Gopinatha

    2016-04-28

    We investigate the interaction of hydrophilic blue emitting carbon spindles with various deoxyribonucleic acids (DNA) having different base pair compositions, such as Herring testes (HT), calf thymus (CT), Escherichia coli (EC) and Micrococcus lysodeikticus (ML) DNA, to understand the mode of interaction. Interestingly, the fluorescent carbon spindles selectively interacted with E. coli DNA resulting in enhanced fluorescence of the former. Interaction of the same carbon with other DNAs exhibited insignificant changes in fluorescence. In addition, in the presence of EC DNA, the D band in the Raman spectrum attributed to the defect state completely disappeared, resulting in enhanced crystallinity. Microscopy images confirmed the wrapping of DNA on the carbon spindles leading to the assembly of spindles in the form of flowers. Dissociation of double-stranded DNA occurred upon interaction with carbon spindles, resulting in selective E. coli DNA interaction. The carbon spindles also exhibited a similar fluorescence enhancement upon treating with E. coli bacteria. These results confirm the possibility of E. coli detection in water and other liquid foods using such fluorescent carbon. PMID:27081680

  18. Active link selection for efficient semi-supervised community detection

    PubMed Central

    Yang, Liang; Jin, Di; Wang, Xiao; Cao, Xiaochun

    2015-01-01

    Several semi-supervised community detection algorithms have been proposed recently to improve the performance of traditional topology-based methods. However, most of them focus on how to integrate supervised information with topology information; few of them pay attention to which information is critical for performance improvement. This leads to large amounts of demand for supervised information, which is expensive or difficult to obtain in most fields. For this problem we propose an active link selection framework, that is we actively select the most uncertain and informative links for human labeling for the efficient utilization of the supervised information. We also disconnect the most likely inter-community edges to further improve the efficiency. Our main idea is that, by connecting uncertain nodes to their community hubs and disconnecting the inter-community edges, one can sharpen the block structure of adjacency matrix more efficiently than randomly labeling links as the existing methods did. Experiments on both synthetic and real networks demonstrate that our new approach significantly outperforms the existing methods in terms of the efficiency of using supervised information. It needs ~13% of the supervised information to achieve a performance similar to that of the original semi-supervised approaches. PMID:25761385

  19. Visual target detection paradigm for the study of selective attention.

    PubMed

    Tabert, M H; Chokron, S; Tang, C Y; Wei, T; Brickman, A M; Buchsbaum, M S

    2000-11-01

    The current protocol can be used to examine selective attention. It has been used to acquire behavioral performance data in neurologically healthy normal control subjects and schizophrenic patients. A modified version, also described here, has been used to acquire functional neuroimaging data in normal subjects using positron emission tomography. Subject response accuracy and reaction times are recorded while subjects detect visual stimuli in either hemifield (left vs. right of a fixation point) or along the vertical meridian (above or below fixation). The lateralized presentation of stimuli permits the study of hemispheric specialization for selective attentional processes. Attentional load is manipulated by presenting larger-sized target stimuli alone (i.e., the letter 'O') or smaller-sized target stimuli surrounded by flanking letters. This protocol report includes a description of subject exclusion criteria, procedural details, relevant experimental conditions and variables, suggestions for data analysis, expected results, and a discussion of the protocol's significance for attentional research along with suggestions for future research. PMID:11086266

  20. Active link selection for efficient semi-supervised community detection.

    PubMed

    Yang, Liang; Jin, Di; Wang, Xiao; Cao, Xiaochun

    2015-01-01

    Several semi-supervised community detection algorithms have been proposed recently to improve the performance of traditional topology-based methods. However, most of them focus on how to integrate supervised information with topology information; few of them pay attention to which information is critical for performance improvement. This leads to large amounts of demand for supervised information, which is expensive or difficult to obtain in most fields. For this problem we propose an active link selection framework, that is we actively select the most uncertain and informative links for human labeling for the efficient utilization of the supervised information. We also disconnect the most likely inter-community edges to further improve the efficiency. Our main idea is that, by connecting uncertain nodes to their community hubs and disconnecting the inter-community edges, one can sharpen the block structure of adjacency matrix more efficiently than randomly labeling links as the existing methods did. Experiments on both synthetic and real networks demonstrate that our new approach significantly outperforms the existing methods in terms of the efficiency of using supervised information. It needs ~13% of the supervised information to achieve a performance similar to that of the original semi-supervised approaches. PMID:25761385

  1. Genomic resources and their influence on the detection of the signal of positive selection in genome scans.

    PubMed

    Manel, S; Perrier, C; Pratlong, M; Abi-Rached, L; Paganini, J; Pontarotti, P; Aurelle, D

    2016-01-01

    Genome scans represent powerful approaches to investigate the action of natural selection on the genetic variation of natural populations and to better understand local adaptation. This is very useful, for example, in the field of conservation biology and evolutionary biology. Thanks to Next Generation Sequencing, genomic resources are growing exponentially, improving genome scan analyses in non-model species. Thousands of SNPs called using Reduced Representation Sequencing are increasingly used in genome scans. Besides, genome sequences are also becoming increasingly available, allowing better processing of short-read data, offering physical localization of variants, and improving haplotype reconstruction and data imputation. Ultimately, genome sequences are also becoming the raw material for selection inferences. Here, we discuss how the increasing availability of such genomic resources, notably genome sequences, influences the detection of signals of selection. Mainly, increasing data density and having the information of physical linkage data expand genome scans by (i) improving the overall quality of the data, (ii) helping the reconstruction of demographic history for the population studied to decrease false-positive rates and (iii) improving the statistical power of methods to detect the signal of selection. Of particular importance, the availability of a high-quality reference genome can improve the detection of the signal of selection by (i) allowing matching the potential candidate loci to linked coding regions under selection, (ii) rapidly moving the investigation to the gene and function and (iii) ensuring that the highly variable regions of the genomes that include functional genes are also investigated. For all those reasons, using reference genomes in genome scan analyses is highly recommended. PMID:26562485

  2. Photo-SRM: laser-induced dissociation improves detection selectivity of Selected Reaction Monitoring mode.

    PubMed

    Enjalbert, Quentin; Simon, Romain; Salvador, Arnaud; Antoine, Rodolphe; Redon, Sébastien; Ayhan, Mehmet Menaf; Darbour, Florence; Chambert, Stéphane; Bretonnière, Yann; Dugourd, Philippe; Lemoine, Jérôme

    2011-11-30

    Selected Reaction Monitoring (SRM) carried out on triple-quadrupole mass spectrometers coupled to liquid chromatography has been a reference method to develop quantitative analysis of small molecules in biological or environmental matrices for years and is currently emerging as a promising tool in clinical proteomic. However, sensitive assays in complex matrices are often hampered by the presence of co-eluted compounds that share redundant transitions with the target species. On-the-fly better selection of the precursor ion by high-field asymmetric waveform ion mobility spectrometry (FAIMS) or increased quadrupole resolution is one way to escape from interferences. In the present work we document the potential interest of substituting classical gas-collision activation mode by laser-induced dissociation in the visible wavelength range to improve the specificity of the fragmentation step. Optimization of the laser beam pathway across the different quadrupoles to ensure high photo-dissociation yield in Q2 without detectable fragmentation in Q1 was assessed with sucrose tagged with a push-pull chromophore. Next, the proof of concept that photo-SRM ensures more specific detection than does conventional collision-induced dissociation (CID)-based SRM was carried out with oxytocin peptide. Oxytocin was derivatized by the thiol-reactive QSY® 7 C(5)-maleimide quencher on cysteine residues to shift its absorption property into the visible range. Photo-SRM chromatograms of tagged oxytocin spiked in whole human plasma digest showed better detection specificity and sensitivity than CID, that resulted in extended calibration curve linearity. We anticipate that photo-SRM might significantly improve the limit of quantification of classical SRM-based assays targeting cysteine-containing peptides. PMID:22002689

  3. Evolutionary Theory of Mate Selection and Partners of Trans People: A Qualitative Study Using Interpretative Phenomenological Analysis

    ERIC Educational Resources Information Center

    Forde, Amanda

    2011-01-01

    Despite much research into mate selection, non-heterosexual populations are often only included for comparison purposes, while trans people and their partners are overlooked. This study attempts to address this using qualitative methodology to explore the mate selection of the partners of trans people. Six participants were recruited from online…

  4. Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs)

    PubMed Central

    2015-01-01

    Background Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outcome. Because evolutionary processes tend to act on gene regulation, we test whether regulatory variants are under positive selection. We introduce a new approach to enhance detection of genetic markers undergoing positive selection, using conditional entropy to capture recent local selection signals. Results We use conditional logistic regression to compare our Adjusted Haplotype Conditional Entropy (H|H) measure of positive selection to existing positive selection measures. H|H and existing measures were applied to published regulatory variants acting in cis (cis-eQTLs), with conditional logistic regression testing whether regulatory variants undergo stronger positive selection than the surrounding gene. These cis-eQTLs were drawn from six independent studies of genotype and RNA expression. The conditional logistic regression shows that, overall, H|H is substantially more powerful than existing positive-selection methods in identifying cis-eQTLs against other Single Nucleotide Polymorphisms (SNPs) in the same genes. When broken down by Gene Ontology, H|H predictions are particularly strong in some biological process categories, where regulatory variants are under strong positive selection compared to the bulk of the gene, distinct from those GO categories under overall positive selection. . However, cis-eQTLs in a second group of genes lack positive selection signatures detectable by H|H, consistent with ancient short haplotypes compared to the surrounding gene (for example, in innate immunity GO:0042742); under such other modes of selection, H|H would not be expected to be a strong predictor.. These conditional logistic regression models are

  5. Evolutionary thinking

    PubMed Central

    Hunt, Tam

    2014-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

  6. Evolutionary Consequences of Male Driven Sexual Selection and Sex-Biased Fitness Modifications in Drosophila melanogaster and Members of the simulans Clade

    PubMed Central

    Jagadeeshan, Santosh; Haerty, Wilfried; Moglinicka, Monika; Ahuja, Abha; De Vito, Scot; Singh, Rama S.

    2015-01-01

    Males have evolved a variety of behavioral, morphological, and physiological traits to manipulate their mates in order to maximize their chances of success. These traits are bound to influence how females respond to male behaviors and influence the nature of sexual selection/conflict. A common consequence of aggressive male mating strategies in Drosophila melanogaster is the reduction of female lifespan. Our study shows that this is common across members of the simulans clade. Reduced life expectancy of females implies that female contribution to a population is less than that of males per generation. Fitness differences between the sexes in every generation will invariably affect overall population fitness. How natural selection responds to the female deaths and thereby the unequal fitness of the sexes has rarely been addressed. We shed light on this issue and provide evidence, which suggests that additional gains of fitness by males due to their longevity and continued mating may provide one explanation as to why the loss of female fitness may be “invisible” (effectively neutral) to natural selection. Male driven sexual selection and additional, transgenerational gains of male fitness can be an important force of evolutionary change and need to be tested with other organisms. PMID:26421208

  7. Selective ciprofloxacin antibiotic detection by fluorescent siderophore pyoverdin.

    PubMed

    Pawar, Madhuri K; Tayade, Kundan C; Sahoo, Suban K; Mahulikar, Pramod P; Kuwar, Anil S; Chaudhari, Bhushan L

    2016-07-15

    Fluorescent siderophore pyoverdin (PVD) was produced from a soil isolate Pseudomonas monteilii strain MKP 213. The PVD was purified near to homogeneity and applied for the fluorescent chemosensing of various antibiotics in aqueous solution (pH=7.0). Upon addition of ciprofloxacin, PVD showed new UV-vis absorption bands at 252 and 321nm due to an internal charge transfer mechanism. Also, the addition of ciprofloxacin induced a highly selective fluorescence enhancement of PVD with a 13nm blue shift from 458 to 445nm. The combination of a long peptide chain along with the chromophore unit of PVD generates a converging cleft for ciprofloxacin recognition with LOD and LOQ of 7.13μM and 21.6μM, respectively without interference from other studied antibiotics. The association constant (Ka) of PVD with ciprofloxacin was calculated to be as low as 1.40×10(5)M(-1) using Benesi-Hildebrand plot depicting its significance in detection. The pharmaceutical tablet analysis measures the sensing with negligible matrix effect and quantitative recovery. PMID:26971273

  8. Fluorescent Peptide Beacons for the Selective Ratiometric Detection of Heparin.

    PubMed

    Maity, Debabrata; Schmuck, Carsten

    2016-09-01

    Heparin is extensively used as an anticoagulant drug during surgery. Two fluorophore-functionalized cationic oligopeptides HS 1 and HS 2 were developed to monitor heparin ratiometrically in aqueous media. Upon binding to heparin, HS 1 and HS 2 undergo a conformational change from an open form to a folded form, which leads to a distinct change in the fluorescence properties. HS 1 switches from pyrene monomer emission to an excimer emission. For HS 2, a fluorescence resonance energy transfer (FRET) process is enabled between a naphthalene donor and a dansyl acceptor. This method is highly selective for heparin relative to other similar biological analytes such as hyaluronic acid or chondroitin sulfate. HS 1 and HS 2 could also detect heparin ratiometrically in diluted bovine serum. The strong ratiometric emission color change can also be observed by the naked eye. Addition of the polycationic protein protamine releases both HS 1 and HS 2 from their heparin complex, which simultaneously restores pyrene monomer emission for the first case and decreases the FRET process for the latter case, respectively. Dynamic light scattering (DLS) and AFM studies confirm aggregate formation of heparin with HS 1 and HS 2. PMID:27534383

  9. SNP Detection from De Novo Transcriptome Sequencing in the Bivalve Macoma balthica: Marker Development for Evolutionary Studies

    PubMed Central

    Becquet, Vanessa; Belkhir, Khalid; Bierne, Nicolas; Garcia, Pascale

    2012-01-01

    Hybrid zones are noteworthy systems for the study of environmental adaptation to fast-changing environments, as they constitute reservoirs of polymorphism and are key to the maintenance of biodiversity. They can move in relation to climate fluctuations, as temperature can affect both selection and migration, or remain trapped by environmental and physical barriers. There is therefore a very strong incentive to study the dynamics of hybrid zones subjected to climate variations. The infaunal bivalve Macoma balthica emerges as a noteworthy model species, as divergent lineages hybridize, and its native NE Atlantic range is currently contracting to the North. To investigate the dynamics and functioning of hybrid zones in M. balthica, we developed new molecular markers by sequencing the collective transcriptome of 30 individuals. Ten individuals were pooled for each of the three populations sampled at the margins of two hybrid zones. A single 454 run generated 277 Mb from which 17K SNPs were detected. SNP density averaged 1 polymorphic site every 14 to 19 bases, for mitochondrial and nuclear loci, respectively. An scan detected high genetic divergence among several hundred SNPs, some of them involved in energetic metabolism, cellular respiration and physiological stress. The high population differentiation, recorded for nuclear-encoded ATP synthase and NADH dehydrogenase as well as most mitochondrial loci, suggests cytonuclear genetic incompatibilities. Results from this study will help pave the way to a high-resolution study of hybrid zone dynamics in M. balthica, and the relative importance of endogenous and exogenous barriers to gene flow in this system. PMID:23300636

  10. Contrasting evolutionary histories of MHC class I and class II loci in grouse-effects of selection and gene conversion.

    PubMed

    Minias, P; Bateson, Z W; Whittingham, L A; Johnson, J A; Oyler-McCance, S; Dunn, P O

    2016-05-01

    Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens. PMID:26860199

  11. Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion

    USGS Publications Warehouse

    Minias, Piotr; Bateson, Zachary W; Whittingham, Linda A; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O

    2016-01-01

    Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

  12. Child Development and Evolutionary Psychology.

    ERIC Educational Resources Information Center

    Bjorklund, David F.; Pellegrini, Anthony D.

    2000-01-01

    Argues that an evolutionary account provides insight into developmental function and individual differences. Outlines some assumptions of evolutionary psychology related to development. Introduces the developmental systems approach, differential influence of natural selection at different points in ontogeny, and development of evolved…

  13. SELECTED METHODS FOR DETECTING AND TRACING HAZARDOUS MATERIALS SPILLS

    EPA Science Inventory

    Detection of hazardous chemicals by a wide range of phenomena including electrical conductivity, catalytic combustion, and colorimetry was investigated. This study showed that simple, fieldable instruments are available or can readily be made available for detecting spills of mos...

  14. Feature Extraction and Selection From the Perspective of Explosive Detection

    SciTech Connect

    Sengupta, S K

    2009-09-01

    -dimensional attenuation images with a voxel resolution of the order of one quarter of a milimeter. In the task of feature extraction and subsequent selection of an appropriate subset thereof, several important factors need to be considered. Foremost among them are: (1) Definition of the sampling unit from which the features will be extracted for the purpose of detection/ identification of the explosives. (2) The choice of features ( given the sampling unit) to be extracted that can be used to signal the existence / identity of the explosive. (3) Robustness of the computed features under different inspection conditions. To attain robustness, invariance under the transformations of translation, scaling, rotation and change of orientation is highly desirable. (4) The computational costs in the process of feature extraction, selection and their use in explosive detection/ identification In the search for extractable features, we have done a thorough literature survey with the above factors in mind and come out with a list of features that could possibly help us in meeting our objective. We are assuming that features will be based on sampling units that are single CT slices of the target. This may however change when appropriate modifications should be made to the feature extraction process. We indicate below some of the major types of features in 2- or 3-dimensional images that have been used in the literature on application of pattern recognition (PR) techniques in image understanding and are possibly pertinent to our study. In the following paragraph, we briefly indicate the motivation that guided us in the choice of these features, and identify the nature of the constraints. The principal feature types derivable from an image will be discussed in section 2. Once the features are extracted, one must select a subset of this feature set that will retain the most useful information and remove any redundant and irrelevant information that may have a detrimental effect on the

  15. Evolutionary awareness.

    PubMed

    Gorelik, Gregory; Shackelford, Todd K

    2014-01-01

    In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment. PMID:25300054

  16. How competition affects evolutionary rescue

    PubMed Central

    Osmond, Matthew Miles; de Mazancourt, Claire

    2013-01-01

    Populations facing novel environments can persist by adapting. In nature, the ability to adapt and persist will depend on interactions between coexisting individuals. Here we use an adaptive dynamic model to assess how the potential for evolutionary rescue is affected by intra- and interspecific competition. Intraspecific competition (negative density-dependence) lowers abundance, which decreases the supply rate of beneficial mutations, hindering evolutionary rescue. On the other hand, interspecific competition can aid evolutionary rescue when it speeds adaptation by increasing the strength of selection. Our results clarify this point and give an additional requirement: competition must increase selection pressure enough to overcome the negative effect of reduced abundance. We therefore expect evolutionary rescue to be most likely in communities which facilitate rapid niche displacement. Our model, which aligns to previous quantitative and population genetic models in the absence of competition, provides a first analysis of when competitors should help or hinder evolutionary rescue. PMID:23209167

  17. The chemically homogeneous evolutionary channel for binary black hole mergers: rates and properties of gravitational-wave events detectable by advanced LIGO

    NASA Astrophysics Data System (ADS)

    de Mink, S. E.; Mandel, I.

    2016-08-01

    We explore the predictions for detectable gravitational-wave signals from merging binary black holes formed through chemically homogeneous evolution in massive short-period stellar binaries. We find that ˜500 events per year could be detected with advanced ground-based detectors operating at full sensitivity. We analyse the distribution of detectable events, and conclude that there is a very strong preference for detecting events with nearly equal components (mass ratio >0.66 at 90 per cent confidence in our default model) and high masses (total source-frame mass between 57 and 103 M⊙ at 90 per cent confidence). We consider multiple alternative variations to analyse the sensitivity to uncertainties in the evolutionary physics and cosmological parameters, and conclude that while the rates are sensitive to assumed variations, the mass distributions are robust predictions. Finally, we consider the recently reported results of the analysis of the first 16 double-coincident days of the O1 LIGO (Laser Interferometer Gravitational-wave Observatory) observing run, and find that this formation channel is fully consistent with the inferred parameters of the GW150914 binary black hole detection and the inferred merger rate.

  18. The chemically homogeneous evolutionary channel for binary black hole mergers: rates and properties of gravitational-wave events detectable by advanced LIGO

    NASA Astrophysics Data System (ADS)

    de Mink, S. E.; Mandel, I.

    2016-08-01

    We explore the predictions for detectable gravitational-wave signals from merging binary black holes formed through chemically homogeneous evolution in massive short-period stellar binaries. We find that $\\sim 500$ events per year could be detected with advanced ground-based detectors operating at full sensitivity. We analyze the distribution of detectable events, and conclude that there is a very strong preference for detecting events with nearly equal components (mass ratio $>0.66$ at 90\\% confidence in our default model) and high masses (total source-frame mass between $57$ and $103\\, M_\\odot$ at 90\\% confidence). We consider multiple alternative variations to analyze the sensitivity to uncertainties in the evolutionary physics and cosmological parameters, and conclude that while the rates are sensitive to assumed variations, the mass distributions are robust predictions. Finally, we consider the recently reported results of the analysis of the first 16 double-coincident days of the O1 LIGO (Laser Interferometer Gravitational-wave Observatory) observing run, and find that this formation channel is fully consistent with the inferred parameters of the GW150914 binary black hole detection and the inferred merger rate.

  19. The chemically homogeneous evolutionary channel for binary black hole mergers: Rates and Properties of gravitational-wave events detectable by advanced LIGO

    NASA Astrophysics Data System (ADS)

    de Mink, S. E.; Mandel, I.

    2016-05-01

    We explore the predictions for detectable gravitational-wave signals from merging binary black holes formed through chemically homogeneous evolution in massive short-period stellar binaries. We find that ˜500 events per year could be detected with advanced ground-based detectors operating at full sensitivity. We analyze the distribution of detectable events, and conclude that there is a very strong preference for detecting events with nearly equal components (mass ratio >0.66 at 90% confidence in our default model) and high masses (total source-frame mass between 57 and 103 M⊙ at 90% confidence). We consider multiple alternative variations to analyze the sensitivity to uncertainties in the evolutionary physics and cosmological parameters, and conclude that while the rates are sensitive to assumed variations, the mass distributions are robust predictions. Finally, we consider the recently reported results of the analysis of the first 16 double-coincident days of the O1 LIGO observing run, and find that this formation channel is fully consistent with the inferred parameters of the GW150914 binary black hole detection and the inferred merger rate.

  20. Paleoanthropology and evolutionary theory.

    PubMed

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted. PMID:23272602

  1. Applying Evolutionary Anthropology

    PubMed Central

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

  2. Critical Reflections on Evolutionary Psychology and Sexual Selection Theory as Explanatory Account of Emergence of Sex Differences in Psychopathology: Comment on Martel (2013)

    PubMed Central

    Hankin, Benjamin L.

    2014-01-01

    Martel (2013) proposed a meta-theory, based on sexual selection theory and broad evolutionary psychological (EP) principles, to account for well-known sex differences in the emergence of common behavioral and certain internalizing disorders across childhood and adolescence, respectively. This Comment first enumerates several strengths and then offers two primary critiques about Martel’s proposal. Martel provides an exceptional, integrative review that organizes several disparate literatures that hold promise to enhance understanding of such sex differences. At the same time, I raise critical questions regarding EP generally, and sexual selection theory specifically, as the meta-theoretical framework chosen to bind together these different influences and mechanisms as drivers of the sex difference in different psychopathologies. Indeed, it is not clear that EP is necessary—nor does it provide unique explanatory power—to explicate the emergence of sex differences in internalizing and externalizing disorders among youth. Moreover, Martel’s EP-based proposal pertains to adolescent-onset depression and social phobia but does not provide an explanation for known sex differences in other common childhood-onset and early adult-onset anxiety disorders. PMID:24188421

  3. BMD Loci Contribute to Ethnic and Developmental Differences in Skeletal Fragility across Populations: Assessment of Evolutionary Selection Pressures

    PubMed Central

    Medina-Gómez, Carolina; Chesi, Alessandra; Heppe, Denise H.M.; Zemel, Babette S.; Yin, Jia-Lian; Kalkwarf, Heidi J.; Hofman, Albert; Lappe, Joan M.; Kelly, Andrea; Kayser, Manfred; Oberfield, Sharon E.; Gilsanz, Vicente; Uitterlinden, André G.; Shepherd, John A.; Jaddoe, Vincent W.V.; Grant, Struan F.A.; Lao, Oscar; Rivadeneira, Fernando

    2015-01-01

    Bone mineral density (BMD) is a highly heritable trait used both for the diagnosis of osteoporosis in adults and to assess bone health in children. Ethnic differences in BMD have been documented, with markedly higher levels in individuals of African descent, which partially explain disparity in osteoporosis risk across populations. To date, 63 independent genetic variants have been associated with BMD in adults of Northern-European ancestry. Here, we demonstrate that at least 61 of these variants are predictive of BMD early in life by studying their compound effect within two multiethnic pediatric cohorts. Furthermore, we show that within these cohorts and across populations worldwide the frequency of those alleles associated with increased BMD is systematically elevated in individuals of Sub-Saharan African ancestry. The amount of differentiation in the BMD genetic scores among Sub-Saharan and non-Sub-Saharan populations together with neutrality tests, suggest that these allelic differences are compatible with the hypothesis of selective pressures acting on the genetic determinants of BMD. These findings constitute an explorative contribution to the role of selection on ethnic BMD differences and likely a new example of polygenic adaptation acting on a human trait. PMID:26226985

  4. A common evolutionary origin for the ON- and OFF-edge motion detection pathways of the Drosophila visual system

    PubMed Central

    Shinomiya, Kazunori; Takemura, Shin-ya; Rivlin, Patricia K.; Plaza, Stephen M.; Scheffer, Louis K.; Meinertzhagen, Ian A.

    2015-01-01

    Synaptic circuits for identified behaviors in the Drosophila brain have typically been considered from either a developmental or functional perspective without reference to how the circuits might have been inherited from ancestral forms. For example, two candidate pathways for ON- and OFF-edge motion detection in the visual system act via circuits that use respectively either T4 or T5, two cell types of the fourth neuropil, or lobula plate (LOP), that exhibit narrow-field direction-selective responses and provide input to wide-field tangential neurons. T4 or T5 both have four subtypes that terminate one each in the four strata of the LOP. Representatives are reported in a wide range of Diptera, and both cell types exhibit various similarities in: (1) the morphology of their dendritic arbors; (2) their four morphological and functional subtypes; (3) their cholinergic profile in Drosophila; (4) their input from the pathways of L3 cells in the first neuropil, or lamina (LA), and by one of a pair of LA cells, L1 (to the T4 pathway) and L2 (to the T5 pathway); and (5) their innervation by a single, wide-field contralateral tangential neuron from the central brain. Progenitors of both also express the gene atonal early in their proliferation from the inner anlage of the developing optic lobe, being alone among many other cell type progeny to do so. Yet T4 receives input in the second neuropil, or medulla (ME), and T5 in the third neuropil or lobula (LO). Here we suggest that these two cell types were originally one, that their ancestral cell population duplicated and split to innervate separate ME and LO neuropils, and that a fiber crossing—the internal chiasma—arose between the two neuropils. The split most plausibly occurred, we suggest, with the formation of the LO as a new neuropil that formed when it separated from its ancestral neuropil to leave the ME, suggesting additionally that ME input neurons to T4 and T5 may also have had a common origin. PMID:26217193

  5. Practical Approaches for Detecting Selection in Microbial Genomes

    PubMed Central

    Hedge, Jessica; Wilson, Daniel J.

    2016-01-01

    Microbial genome evolution is shaped by a variety of selective pressures. Understanding how these processes occur can help to address important problems in microbiology by explaining observed differences in phenotypes, including virulence and resistance to antibiotics. Greater access to whole-genome sequencing provides microbiologists with the opportunity to perform large-scale analyses of selection in novel settings, such as within individual hosts. This tutorial aims to guide researchers through the fundamentals underpinning popular methods for measuring selection in pathogens. These methods are transferable to a wide variety of organisms, and the exercises provided are designed for researchers with any level of programming experience. PMID:26867134

  6. First detections of FS Canis Majoris stars in clusters. Evolutionary state as constrained by coeval massive stars

    NASA Astrophysics Data System (ADS)

    de la Fuente, D.; Najarro, F.; Trombley, C.; Davies, B.; Figer, D. F.

    2015-03-01

    Context. FS CMa stars are low-luminosity objects showing the B[e] phenomenon whose evolutionary state remains a puzzle. These stars are surrounded by compact disks of warm dust of unknown origin. Hitherto, membership of FS CMa stars to coeval populations has never been confirmed. Aims: The discovery of low-luminosity line emitters in the young massive clusters Mercer 20 and Mercer 70 prompts us to investigate the nature of such objects. We intend to confirm membership to coeval populations in order to characterize these emission-line stars through the cluster properties. Methods: Based on ISAAC/VLT medium-resolution spectroscopy and NICMOS/HST photometry of massive cluster members, new characterizations of Mercer 20 and Mercer 70 are performed. Coevality of each cluster and membership of the newly-discovered B[e] objects are investigated using our observations as well as literature data of the surroundings. Infrared excess and narrow-band photometric properties of the B[e] stars are also studied. Results: We confirm and classify 22 new cluster members, including Wolf-Rayet stars and blue hypergiants. Spectral types (O9-B1.5 V) and radial velocities of B[e] objects are compatible with the remaining cluster members, while emission features of Mg ii, Fe ii], and [Fe ii] are identified in their spectra. The ages of these stars are 4.5 and 6 Myr, and they show mild infrared excesses. Conclusions: We confirm the presence of FS CMa stars in the coeval populations of Mercer 20 and Mercer 70. We discuss the nature and evolutionary state of FS CMa stars, discarding a post-AGB nature and introducing a new hypothesis about mergers. A new search method for FS CMa candidates in young massive clusters based on narrow-band Paschen-α photometry is proposed and tested in photometric data of other clusters, yielding three new candidates. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile, under program IDs 083.D

  7. Proteomics in evolutionary ecology.

    PubMed

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  8. Evolutionary Computing

    SciTech Connect

    Patton, Robert M; Cui, Xiaohui; Jiao, Yu; Potok, Thomas E

    2008-01-01

    The rate at which information overwhelms humans is significantly more than the rate at which humans have learned to process, analyze, and leverage this information. To overcome this challenge, new methods of computing must be formulated, and scientist and engineers have looked to nature for inspiration in developing these new methods. Consequently, evolutionary computing has emerged as new paradigm for computing, and has rapidly demonstrated its ability to solve real-world problems where traditional techniques have failed. This field of work has now become quite broad and encompasses areas ranging from artificial life to neural networks. This chapter focuses specifically on two sub-areas of nature-inspired computing: Evolutionary Algorithms and Swarm Intelligence.

  9. Evolutionary Adaptations to Dietary Changes

    PubMed Central

    Luca, F.; Perry, G.H.; Di Rienzo, A.

    2014-01-01

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  10. Evolutionary adaptations to dietary changes.

    PubMed

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  11. Stereochemical and Regiochemical Trends in the Selective Detection of Saccharides

    PubMed Central

    Jiang, Shan; Escobedo, Jorge O.; Kim, Kyu Kwang; Alptürk, Onur; Samoei, George K.; Fakayode, Sayo O.; Warner, Isiah M.; Rusin, Oleksandr; Strongin, Robert M.

    2009-01-01

    Several discreet sugar–boronate complexes exist in solution. This is due to the complex equilibria between isomeric species of even the simplest monosaccharides. In the current investigation, we determine the regio- and stereochemical features of the various equilibrating sugar isomers that induce signal transduction in boronic acid chemosensors such as 1 as well as 2 and 3. We present a unique example of a chemosensor (1) that is selective for ribose, adenosine, nucleotides, nucleosides, and congeners. As a result of this study, we are able to predict and achieve selective fluorescence and colorimetric responses to specific disaccharides as a consequence of their terminal sugar residue linkage patterns and configurations. We also find that the combined use of chemosensors exhibiting complementary reactivities may be used cooperatively to obtain enhanced selectivity for ribose and rare saccharides. PMID:16967973

  12. Detecting kin selection at work using inclusive fitness.

    PubMed

    Grafen, Alan

    2007-03-01

    A recent model shows that altruism can evolve with limited migration and variable group sizes, and the authors claim that kin selection cannot provide a sufficient explanation of their results. It is demonstrated, using a recent reformulation of Hamilton's original arguments, that the model falls squarely within the scope of inclusive fitness theory, which furthermore shows how to calculate inclusive fitness and the relevant relatedness. A distinction is drawn between inclusive fitness, which is a method of analysing social behaviour; and kin selection, a process that operates through genetic similarity brought about by common ancestry, but not by assortation by genotype or by direct assessment of genetic similarity. The recent model is analysed, and it turns out that kin selection provides a sufficient explanation to considerable quantitative accuracy, contrary to the authors' claims. A parallel analysis is possible and would be illuminating for all models of social behaviour in which individuals' effects on each other's offspring numbers combine additively. PMID:17254996

  13. Role of selective sorption in chemiresistor sensors for organophosphorus detection

    SciTech Connect

    Grate, J.W.; Klusty, M.; Barger, W.R.; Snow, A.W. )

    1990-09-15

    Nickel, palladium, platinum, and copper tetrakis(cumylphenoxy)phthalocyanines were combined with an elastomeric, oligomeric fluoropolyol material in mixed Langmuir-Blodgett films on chemiresistor sensors for organophosphorus vapors. The phthalocyanine carried the electronic current, while the fluoropolyol improved the sorption characteristics of the film. This strategy produced sensors with improved response and recovery times and high sensitivity. Factors influencing the selectivity of the sensor responses were analyzed in terms of two steps: sorption and transduction. Sorption was shown to be the primary determinant of selectivity among the organic vapors tested.

  14. Geographic Variation in the Acoustic Traits of Greater Horseshoe Bats: Testing the Importance of Drift and Ecological Selection in Evolutionary Processes

    PubMed Central

    Sun, Keping; Luo, Li; Kimball, Rebecca T.; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Li, Guohong; Feng, Jiang

    2013-01-01

    Patterns of intraspecific geographic variation of signaling systems provide insight into the microevolutionary processes driving phenotypic divergence. The acoustic calls of bats are sensitive to diverse evolutionary forces, but processes that shape call variation are largely unexplored. In China, Rhinolophus ferrumequinum displays a diverse call frequency and inhabits a heterogeneous landscape, presenting an excellent opportunity for this kind of research. We quantified geographic variation in resting frequency (RF) of echolocation calls, estimated genetic structure and phylogeny of R. ferrumequinum populations, and combined this with climatic factors to test three hypotheses to explain acoustic variation: genetic drift, cultural drift, and local adaptation. Our results demonstrated significant regional divergence in frequency and phylogeny among the bat populations in China's northeast (NE), central-east (CE) and southwest (SW) regions. The CE region had higher frequencies than the NE and SW regions. Drivers of RF divergence were estimated in the entire range and just the CE/NE region (since these two regions form a clade). In both cases, RF divergence was not correlated with mtDNA or nDNA genetic distance, but was significantly correlated with geographic distance and mean annual temperature, indicating cultural drift and ecological selection pressures are likely important in shaping RF divergence among different regions in China. PMID:23950926

  15. Selected References on Asbestos: Its Nature, Hazards, Detection, and Control.

    ERIC Educational Resources Information Center

    National Education Association, Washington, DC.

    This document provides teachers with sources of information about the nature, hazards, detection, and control of asbestos. Because many school buildings include asbestos-containing materials, teachers and other school personnel must be aware of the potential dangers to students and to themselves and take steps to have asbestos hazards contained or…

  16. Radiography by selective detection of scatter field velocity components

    NASA Technical Reports Server (NTRS)

    Jacobs, Alan M. (Inventor); Dugan, Edward T. (Inventor); Shedlock, Daniel (Inventor)

    2007-01-01

    A reconfigurable collimated radiation detector, system and related method includes at least one collimated radiation detector. The detector has an adjustable collimator assembly including at least one feature, such as a fin, optically coupled thereto. Adjustments to the adjustable collimator selects particular directions of travel of scattered radiation emitted from an irradiated object which reach the detector. The collimated detector is preferably a collimated detector array, where the collimators are independently adjustable. The independent motion capability provides the capability to focus the image by selection of the desired scatter field components. When an array of reconfigurable collimated detectors is provided, separate image data can be obtained from each of the detectors and the respective images cross-correlated and combined to form an enhanced image.

  17. Orientation-selective building detection in aerial images

    NASA Astrophysics Data System (ADS)

    Manno-Kovacs, Andrea; Sziranyi, Tamas

    2015-10-01

    This paper introduces a novel aerial building detection method based on region orientation as a new feature, which is used in various steps throughout the presented framework. As building objects are expected to be connected with each other on a regional level, exploiting the main orientation obtained from the local gradient analysis provides further information for detection purposes. The orientation information is applied for an improved edge map design, which is integrated with classical features like shadow and color. Moreover, an orthogonality check is introduced for finding building candidates, and their final shapes defined by the Chan-Vese active contour algorithm are refined based on the orientation information, resulting in smooth and accurate building outlines. The proposed framework is evaluated on multiple data sets, including aerial and high resolution optical satellite images, and compared to six state-of-the-art methods in both object and pixel level evaluation, proving the algorithm's efficiency.

  18. Evolutionary dynamics in structured populations

    PubMed Central

    Nowak, Martin A.; Tarnita, Corina E.; Antal, Tibor

    2010-01-01

    Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces. PMID:20008382

  19. Reagent Selection Methodology for a Novel Explosives Detection Platform

    ScienceCinema

    None

    2012-12-31

    This video describes research being conducted by Dr. Marvin Warner, a research scientist at Pacific Northwest National Laboratory, in the individual pieces of antibodies used to set up a chemical reaction that will give off light just by mixing reagents together with a sample that contains an explosive molecule. This technology would help detect if explosives are present with just the use of a handheld system or container.

  20. Reagent Selection Methodology for a Novel Explosives Detection Platform

    SciTech Connect

    2010-06-01

    This video describes research being conducted by Dr. Marvin Warner, a research scientist at Pacific Northwest National Laboratory, in the individual pieces of antibodies used to set up a chemical reaction that will give off light just by mixing reagents together with a sample that contains an explosive molecule. This technology would help detect if explosives are present with just the use of a handheld system or container.

  1. Feature Selection and Pedestrian Detection Based on Sparse Representation.

    PubMed

    Yao, Shihong; Wang, Tao; Shen, Weiming; Pan, Shaoming; Chong, Yanwen; Ding, Fei

    2015-01-01

    Pedestrian detection have been currently devoted to the extraction of effective pedestrian features, which has become one of the obstacles in pedestrian detection application according to the variety of pedestrian features and their large dimension. Based on the theoretical analysis of six frequently-used features, SIFT, SURF, Haar, HOG, LBP and LSS, and their comparison with experimental results, this paper screens out the sparse feature subsets via sparse representation to investigate whether the sparse subsets have the same description abilities and the most stable features. When any two of the six features are fused, the fusion feature is sparsely represented to obtain its important components. Sparse subsets of the fusion features can be rapidly generated by avoiding calculation of the corresponding index of dimension numbers of these feature descriptors; thus, the calculation speed of the feature dimension reduction is improved and the pedestrian detection time is reduced. Experimental results show that sparse feature subsets are capable of keeping the important components of these six feature descriptors. The sparse features of HOG and LSS possess the same description ability and consume less time compared with their full features. The ratios of the sparse feature subsets of HOG and LSS to their full sets are the highest among the six, and thus these two features can be used to best describe the characteristics of the pedestrian and the sparse feature subsets of the combination of HOG-LSS show better distinguishing ability and parsimony. PMID:26295480

  2. Feature Selection and Pedestrian Detection Based on Sparse Representation

    PubMed Central

    Yao, Shihong; Wang, Tao; Shen, Weiming; Pan, Shaoming; Chong, Yanwen; Ding, Fei

    2015-01-01

    Pedestrian detection have been currently devoted to the extraction of effective pedestrian features, which has become one of the obstacles in pedestrian detection application according to the variety of pedestrian features and their large dimension. Based on the theoretical analysis of six frequently-used features, SIFT, SURF, Haar, HOG, LBP and LSS, and their comparison with experimental results, this paper screens out the sparse feature subsets via sparse representation to investigate whether the sparse subsets have the same description abilities and the most stable features. When any two of the six features are fused, the fusion feature is sparsely represented to obtain its important components. Sparse subsets of the fusion features can be rapidly generated by avoiding calculation of the corresponding index of dimension numbers of these feature descriptors; thus, the calculation speed of the feature dimension reduction is improved and the pedestrian detection time is reduced. Experimental results show that sparse feature subsets are capable of keeping the important components of these six feature descriptors. The sparse features of HOG and LSS possess the same description ability and consume less time compared with their full features. The ratios of the sparse feature subsets of HOG and LSS to their full sets are the highest among the six, and thus these two features can be used to best describe the characteristics of the pedestrian and the sparse feature subsets of the combination of HOG-LSS show better distinguishing ability and parsimony. PMID:26295480

  3. Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly.

    PubMed

    Wragg, David; Marti-Marimon, Maria; Basso, Benjamin; Bidanel, Jean-Pierre; Labarthe, Emmanuelle; Bouchez, Olivier; Le Conte, Yves; Vignal, Alain

    2016-01-01

    Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail. PMID:27255426

  4. Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly

    PubMed Central

    Wragg, David; Marti-Marimon, Maria; Basso, Benjamin; Bidanel, Jean-Pierre; Labarthe, Emmanuelle; Bouchez, Olivier; Le Conte, Yves; Vignal, Alain

    2016-01-01

    Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail. PMID:27255426

  5. Fluorescent Cancer-Selective Alkylphosphocholine Analogs For Intraoperative Glioma Detection

    PubMed Central

    Swanson, Kyle I.; Clark, Paul A.; Zhang, Ray R.; Kandela, Irawati K.; Farhoud, Mohammed; Weichert, Jamey P.; Kuo, John S.

    2015-01-01

    Background 5-ALA induced tumor fluorescence aids brain tumor resections but is not approved for routine use in the United States. We developed and describe testing of two novel fluorescent, cancer-selective alkylphosphocholine analogs, CLR1501 (green) and CLR1502 (near-infrared), in a proof-of-principle study for fluorescence-guided glioma surgery. Objective To demonstrate CLR1501 and CLR1502 are cancer cell-selective fluorescence agents in glioblastoma models and compare tumor (T) to normal brain (N) fluorescence ratios with 5-ALA. Methods CLR1501, CLR1502, 5-ALA were administered to mice with MRI-verified orthotopic U251 GBM and GSC-derived xenografts. Harvested brains were imaged using confocal microscopy (CLR1501), IVIS Spectrum imaging system (CLR1501, CLR1502, and 5-ALA), or Fluobeam near-infrared fluorescence imaging system (CLR1502). Imaging and quantitative analysis of T:N fluorescence ratios were performed. Results Excitation/emission peaks are 500/517nm for CLR1501, and 760/778nm for CLR1502. The observed T:N ratio of CLR1502 (9.28±1.08) was significantly higher (p<0.01) than CLR1501 (3.51±0.44 on confocal imaging; 7.23±1.63 on IVIS imaging) and 5-ALA (4.81±0.92). Near-infrared Fluobeam CLR1502 imaging in a mouse xenograft model demonstrated high contrast tumor visualization compatible with surgical applications. Conclusion CLR1501 (green) and CLR1502 (near infrared) are novel tumor-selective fluorescent agents for discriminating tumor from normal brain. CLR1501 exhibits a tumor to brain fluorescence ratio similar to 5-ALA, whereas CLR1502 has a superior tumor to brain fluorescence ratio. This study demonstrates the potential use of CLR1501 and CLR1502 in fluorescence-guided tumor surgery. PMID:25549194

  6. Quality-of-service sensitivity to bio-inspired/evolutionary computational methods for intrusion detection in wireless ad hoc multimedia sensor networks

    NASA Astrophysics Data System (ADS)

    Hortos, William S.

    2012-06-01

    In the author's previous work, a cross-layer protocol approach to wireless sensor network (WSN) intrusion detection an identification is created with multiple bio-inspired/evolutionary computational methods applied to the functions of the protocol layers, a single method to each layer, to improve the intrusion-detection performance of the protocol over that of one method applied to only a single layer's functions. The WSN cross-layer protocol design embeds GAs, anti-phase synchronization, ACO, and a trust model based on quantized data reputation at the physical, MAC, network, and application layer, respectively. The construct neglects to assess the net effect of the combined bioinspired methods on the quality-of-service (QoS) performance for "normal" data streams, that is, streams without intrusions. Analytic expressions of throughput, delay, and jitter, coupled with simulation results for WSNs free of intrusion attacks, are the basis for sensitivity analyses of QoS metrics for normal traffic to the bio-inspired methods.

  7. Selection of peptides for serological detection of equine infectious anemia.

    PubMed

    Santos, E M; Cardoso, R; Souza, G R L; Goulart, L R; Heinemann, M B; Leite, R C; Reis, J K P

    2012-01-01

    Equine infectious anemia caused by equine infectious anemia virus is an important disease due to its high severity and incidence in animals. We used a phage display library to isolate peptides that can be considered potential markers for equine infectious anemia diagnosis. We selected peptides using IgG purified from a pool comprised of 20 sera from animals naturally infected with equine infectious anemia virus. The diagnostic potential of these peptides was investigated by ELISA, Western blot and dot blot with purified IgG and serum samples. Based on the results, we chose a peptide mimetic for glycoprotein gp45 epitopes of equine infectious anemia virus, with potential for use as an antigen in indirect diagnostic assays. Synthesis of this peptide has possible applications for the development of new diagnostic tools for this disease. PMID:22653674

  8. Selective chemical detection by energy modulation of sensors

    DOEpatents

    Stetter, J.R.; Otagawa, T.

    1985-05-20

    A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulating means for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor means compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. 4 figs.

  9. Urban Detection, Delimitation and Morphology: Comparative Analysis of Selective "MEGACITIES"

    NASA Astrophysics Data System (ADS)

    Alhaddad, B.; Arellano, B. E.; Roca, J.

    2012-08-01

    Over the last 50 years, the world has faced an impressive growth of urban population. The walled city, close to the outside, an "island"for economic activities and population density within the rural land, has led to the spread of urban life and urban networks in almost all the territory. There was, as said Margalef (1999), "a topological inversion of the landscape". The "urban" has gone from being an island in the ocean of rural land vastness, to represent the totally of the space in which are inserted natural and rural "systems". New phenomena such as the fall of the fordist model of production, the spread of urbanization known as urban sprawl, and the change of scale of the metropolis, covering increasingly large regions, called "megalopolis" (Gottmann, 1961), have characterized the century. However there are no rigorous databases capable of measuring and evaluating the phenomenon of megacities and in general the process of urbanization in the contemporary world. The aim of this paper is to detect, identify and analyze the morphology of the megacities through remote sensing instruments as well as various indicators of landscape. To understand the structure of these heterogeneous landscapes called megacities, land consumption and spatial complexity needs to be quantified accurately. Remote sensing might be helpful in evaluating how the different land covers shape urban megaregions. The morphological landscape analysis allows establishing the analogies and the differences between patterns of cities and studying the symmetry, growth direction, linearity, complexity and compactness of the urban form. The main objective of this paper is to develop a new methodology to detect urbanized land of some megacities around the world (Tokyo, Mexico, Chicago, New York, London, Moscow, Sao Paulo and Shanghai) using Landsat 7 images.

  10. A New Multiplex-PCR for Urinary Tract Pathogen Detection Using Primer Design Based on an Evolutionary Computation Method.

    PubMed

    García, Liliana Torcoroma; Cristancho, Laura Maritza; Vera, Erika Patricia; Begambre, Oscar

    2015-10-28

    This work describes a new strategy for optimal design of Multiplex-PCR primer sequences. The process is based on the Particle Swarm Optimization-Simplex algorithm (Mult-PSOS). Diverging from previous solutions centered on heuristic tools, the Mult-PSOS is selfconfigured because it does not require the definition of the algorithm's initial search parameters. The successful performance of this method was validated in vitro using Multiplex- PCR assays. For this validation, seven gene sequences of the most prevalent bacteria implicated in urinary tract infections were taken as DNA targets. The in vitro tests confirmed the good performance of the Mult-PSOS, with respect to infectious disease diagnosis, in the rapid and efficient selection of the optimal oligonucleotide sequences for Multiplex-PCRs. The predicted sequences allowed the adequate amplification of all amplicons in a single step (with the correct amount of DNA template and primers), reducing significantly the need for trial and error experiments. In addition, owing to its independence from the initial selection of the heuristic constants, the Mult-PSOS can be employed by non-expert users in computational techniques or in primer design problems. PMID:26059514

  11. Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs

    PubMed Central

    Zhao, Pengju; Li, Junhui; Kang, Huimin; Wang, Haifei; Fan, Ziyao; Yin, Zongjun; Wang, Jiafu; Zhang, Qin; Wang, Zhiquan; Liu, Jian-Feng

    2016-01-01

    In this study, we performed a genome-wide SV detection among the genomes of thirteen pigs from diverse Chinese and European originated breeds by next genetation sequencing, and constrcuted a single-nucleotide resolution map involving 56,930 putative SVs. We firstly identified a SV hotspot spanning 35 Mb region on the X chromosome specifically in the genomes of Chinese originated individuals. Further scrutinizing this region by large-scale sequencing data of extra 111 individuals, we obtained the confirmatory evidence on our initial finding. Moreover, thirty five SV-related genes within the hotspot region, being of importance for reproduction ability, rendered significant different evolution rates between Chinese and European originated breeds. The SV hotspot identified herein offers a novel evidence for assessing phylogenetic relationships, as well as likely explains the genetic difference of corresponding phenotypes and features, among Chinese and European pig breeds. Furthermore, we employed various SVs to infer genetic structure of individuls surveyed. We found SVs can clearly detect the difference of genetic background among individuals. This clues us that genome-wide SVs can capture majority of geneic variation and be applied into cladistic analyses. Characterizing whole genome SVs demonstrated that SVs are significantly enriched/depleted with various genomic features. PMID:26729041

  12. Surface plasmon resonance enhanced upconversion luminescence in aqueous media for TNT selective detection.

    PubMed

    Tu, Nina; Wang, Leyu

    2013-07-18

    We present a novel report on a surface plasmon resonance enhanced upconversion luminescence strategy in aqueous media for highly sensitive and selective detection of 2,4,6-trinitrotoluene (TNT). PMID:23739225

  13. Robust Ground Target Detection by SAR and IR Sensor Fusion Using Adaboost-Based Feature Selection.

    PubMed

    Kim, Sungho; Song, Woo-Jin; Kim, So-Hyun

    2016-01-01

    Long-range ground targets are difficult to detect in a noisy cluttered environment using either synthetic aperture radar (SAR) images or infrared (IR) images. SAR-based detectors can provide a high detection rate with a high false alarm rate to background scatter noise. IR-based approaches can detect hot targets but are affected strongly by the weather conditions. This paper proposes a novel target detection method by decision-level SAR and IR fusion using an Adaboost-based machine learning scheme to achieve a high detection rate and low false alarm rate. The proposed method consists of individual detection, registration, and fusion architecture. This paper presents a single framework of a SAR and IR target detection method using modified Boolean map visual theory (modBMVT) and feature-selection based fusion. Previous methods applied different algorithms to detect SAR and IR targets because of the different physical image characteristics. One method that is optimized for IR target detection produces unsuccessful results in SAR target detection. This study examined the image characteristics and proposed a unified SAR and IR target detection method by inserting a median local average filter (MLAF, pre-filter) and an asymmetric morphological closing filter (AMCF, post-filter) into the BMVT. The original BMVT was optimized to detect small infrared targets. The proposed modBMVT can remove the thermal and scatter noise by the MLAF and detect extended targets by attaching the AMCF after the BMVT. Heterogeneous SAR and IR images were registered automatically using the proposed RANdom SAmple Region Consensus (RANSARC)-based homography optimization after a brute-force correspondence search using the detected target centers and regions. The final targets were detected by feature-selection based sensor fusion using Adaboost. The proposed method showed good SAR and IR target detection performance through feature selection-based decision fusion on a synthetic database generated

  14. Robust Ground Target Detection by SAR and IR Sensor Fusion Using Adaboost-Based Feature Selection

    PubMed Central

    Kim, Sungho; Song, Woo-Jin; Kim, So-Hyun

    2016-01-01

    Long-range ground targets are difficult to detect in a noisy cluttered environment using either synthetic aperture radar (SAR) images or infrared (IR) images. SAR-based detectors can provide a high detection rate with a high false alarm rate to background scatter noise. IR-based approaches can detect hot targets but are affected strongly by the weather conditions. This paper proposes a novel target detection method by decision-level SAR and IR fusion using an Adaboost-based machine learning scheme to achieve a high detection rate and low false alarm rate. The proposed method consists of individual detection, registration, and fusion architecture. This paper presents a single framework of a SAR and IR target detection method using modified Boolean map visual theory (modBMVT) and feature-selection based fusion. Previous methods applied different algorithms to detect SAR and IR targets because of the different physical image characteristics. One method that is optimized for IR target detection produces unsuccessful results in SAR target detection. This study examined the image characteristics and proposed a unified SAR and IR target detection method by inserting a median local average filter (MLAF, pre-filter) and an asymmetric morphological closing filter (AMCF, post-filter) into the BMVT. The original BMVT was optimized to detect small infrared targets. The proposed modBMVT can remove the thermal and scatter noise by the MLAF and detect extended targets by attaching the AMCF after the BMVT. Heterogeneous SAR and IR images were registered automatically using the proposed RANdom SAmple Region Consensus (RANSARC)-based homography optimization after a brute-force correspondence search using the detected target centers and regions. The final targets were detected by feature-selection based sensor fusion using Adaboost. The proposed method showed good SAR and IR target detection performance through feature selection-based decision fusion on a synthetic database generated

  15. Selective chemical detection by energy modulation of sensors

    DOEpatents

    Stetter, Joseph R.; Otagawa, Takaaki

    1991-01-01

    A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulator for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor which compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. In particular, the concentration of the component of interest is proportional to the amplitude of the modulated output signal, while the identifying activation output energy of the chemical interaction indicative of that component is proportional to a normalized parameter equal to the peak-to-peak amplitude divided by the height of the upper peaks above a base line signal level.

  16. Selective chemical detection by energy modulation of sensors

    DOEpatents

    Stetter, J.R.; Otagawa, T.

    1991-09-10

    A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulator for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor which compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. In particular, the concentration of the component of interest is proportional to the amplitude of the modulated output signal, while the identifying activation output energy of the chemical interaction indicative of that component is proportional to a normalized parameter equal to the peak-to-peak amplitude divided by the height of the upper peaks above a base line signal level. 5 figures.

  17. Gas chromatographic identification of Clostridium difficile and detection of cytotoxin from a modified selective medium.

    PubMed Central

    Levett, P N; Phillips, K D

    1985-01-01

    A modification of an existing selective medium for Clostridium difficile is described. Inclusion in the medium of DL nor-leucine and p-hydroxyphenylacetic acid enables identification of C difficile to be made directly from primary isolation plates by gas chromatographic detection of caproic acid and p-cresol. Plugs of agar withdrawn from the selective medium also allow the detection of cytotoxin production in vitro. PMID:3968212

  18. Modeling Network Intrusion Detection System Using Feature Selection and Parameters Optimization

    NASA Astrophysics Data System (ADS)

    Kim, Dong Seong; Park, Jong Sou

    Previous approaches for modeling Intrusion Detection System (IDS) have been on twofold: improving detection model(s) in terms of (i) feature selection of audit data through wrapper and filter methods and (ii) parameters optimization of detection model design, based on classification, clustering algorithms, etc. In this paper, we present three approaches to model IDS in the context of feature selection and parameters optimization: First, we present Fusion of Genetic Algorithm (GA) and Support Vector Machines (SVM) (FuGAS), which employs combinations of GA and SVM through genetic operation and it is capable of building an optimal detection model with only selected important features and optimal parameters value. Second, we present Correlation-based Hybrid Feature Selection (CoHyFS), which utilizes a filter method in conjunction of GA for feature selection in order to reduce long training time. Third, we present Simultaneous Intrinsic Model Identification (SIMI), which adopts Random Forest (RF) and shows better intrusion detection rates and feature selection results, along with no additional computational overheads. We show the experimental results and analysis of three approaches on KDD 1999 intrusion detection datasets.

  19. Gene discovery, evolutionary affinity and molecular detection of Oxyspirura petrowi, an eye worm parasite of game birds

    PubMed Central

    2013-01-01

    Background Oxyspirura petrowi appears to be emerging as a nematode parasite that could negatively impact Northern Bobwhite quail individuals and populations within Texas and other regions of the United States. Despite this eye worm's potential importance in the conservation of wild quail, little is known about the general biology and genome composition of O. petrowi. To fill the knowledge gap, we performed a small scale random genome sequence survey, sequenced its 18S rRNA and the intergenic region between the 18S and 28S rRNA genes, studied its phylogenetic affinity, and developed a PCR protocol for the detection of this eye worm. Results We have generated ~240 kb of genome sequence data derived from 348 clones by a random genome survey of an O. petrowi genomic library. The eye worm genome is AT-rich (i.e., 62.2% AT-content), and contains a high number of microsatellite sequences. The discovered genes encode a wide-range of proteins including hypothetical proteins, enzymes, nematode-specific proteins. Phylogenetic analysis based on 18S rRNA sequences indicate that the Spiruroidea is paraphyletic, in which Oxyspirura and its closely related species are sisters to the filarial nematodes. We have also developed a PCR protocol based on the ITS2 sequence that allows sensitive and specific detection of eye worm DNA in feces. Using this newly developed protocol, we have determined that ~28% to 33% of the fecal samples collected from Northern Bobwhites and Scaled Quail in Texas in the spring of 2013 are O. petrowi positive. Conclusions The O. petrowi genome is rich in microsatellite sequences that may be used in future genotyping and molecular fingerprinting analysis. This eye worm is evolutionarily close to the filarial nematodes, implying that therapeutic strategies for filariasis such as Loa loa would be referential in developing treatments for the Thelazoidea parasites. Our qPCR-based survey has confirmed that O. petrowi infection is of potential concern to quail

  20. Mitochondrial DNA Detects a Complex Evolutionary History with Pleistocene Epoch Divergence for the Neotropical Malaria Vector Anopheles nuneztovari Sensu Lato

    PubMed Central

    Scarpassa, Vera Margarete; Conn, Jan E.

    2011-01-01

    Cryptic species and lineages characterize Anopheles nuneztovari s.l. Gabaldón, an important malaria vector in South America. We investigated the phylogeographic structure across the range of this species with cytochrome oxidase subunit I (COI) mitochondrial DNA sequences to estimate the number of clades and levels of divergence. Bayesian and maximum-likelihood phylogenetic analyses detected four groups distributed in two major monophyletic clades (I and II). Samples from the Amazon Basin were clustered in clade I, as were subclades II-A and II-B, whereas those from Bolivia/Colombia/Venezuela were restricted to one basal subclade (II-C). These data, together with a statistical parsimony network, confirm results of previous studies that An. nuneztovari is a species complex consisting of at least two cryptic taxa, one occurring in Colombia and Venezuela and the another occurring in the Amazon Basin. These data also suggest that additional incipient species may exist in the Amazon Basin. Divergence time and expansion tests suggested that these groups separated and expanded in the Pleistocene Epoch. In addition, the COI sequences clearly separated An. nuneztovari s.l. from the closely related species An. dunhami Causey, and three new records are reported for An. dunhami in Amazonian Brazil. These findings are relevant for vector control programs in areas where both species occur. Our analyses support dynamic geologic and landscape changes in northern South America, and infer particularly active divergence during the Pleistocene Epoch for New World anophelines. PMID:22049039

  1. Detection of Bacillus cereus on selected retail chicken products.

    PubMed

    Smith, D P; Berrang, M E; Feldner, P W; Phillips, R W; Meinersmann, R J

    2004-08-01

    Samples from five chicken meat products, obtained at retail stores, were evaluated for the presence of Bacillus cereus. The products tested were as follows: breaded, fully cooked, frozen nuggets (NUGGETS); breaded, fully cooked, frozen tenders (TENDERS); fully cooked, frozen, white-meat fajita-style strips (STRIPS); raw, refrigerated, boneless, skinless, marinated breast fillets (FILLETS); and raw, refrigerated, cut-up, tray-pack bone-in parts (PARTS), either split breasts or thighs. Four packages of each item were obtained on three different days (n = 60). Frozen and refrigerated products were held overnight in their respective environments as appropriate; then packages were opened aseptically, and a total of 25 g of tissue was excised from multiple pieces within a package. The 25-g samples were enriched in 225 ml of Trypticase soy-polymixin broth for 18 to 24 h at 30 degrees C and then plated on mannitol-egg yolk-polymixin agar and incubated for 18 to 24 h at 30 degrees C. Colonies characteristic of B. cereus were chosen and replated for isolation on mannitol-egg yolk-polymixin agar. Suspect colonies were confirmed as Bacillus spp. by Gram stain, hemolysis on blood agar, and a biochemical test strip. Isolates were further confirmed as B. cereus using Bacteriological Analytical Manual procedures, including tests for motility, rhizoid growth, hemolysis, and protein toxin crystal production. B. cereus was detected in 27 of 60 total samples. By product, the prevalence levels were as follows: NUGGETS, 11 of 12 positive; TENDERS, 8 of 12 positive; STRIPS, 6 of 12 positive; FILLETS, 0 of 12 positive; and PARTS, 2 of 12 positive. Isolates were tested by PCR for presence of the toxin-encoding genes bceT, nheABC, hblACD, and cytK. Results indicate that B. cereus organisms were present on four of the five retail poultry products tested in this study, with the highest rates reported for the three fully cooked items, especially the two breaded products. All strains isolated

  2. Evolutionary foundations for cancer biology

    PubMed Central

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles—cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations—provide a foundation for understanding, preventing, and treating cancer. PMID:23396885

  3. Selective detection and characterization of nanoparticles from motor vehicles.

    PubMed

    Johnston, Murray V; Klems, Joseph P; Zordan, Christopher A; Pennington, M Ross; Smith, James N

    2013-02-01

    distance or transit time from emission to sampling increased, the size distribution shifted to a larger particle size, which confirmed the source assignments. To determine the distribution of emissions from individual vehicles, we correlated camera images with the spike contribution to particle number concentration at each time point. A small percentage of motor vehicles were found to emit a disproportionally large concentration of nanoparticles, and these high emitters included both spark-ignition (SI) and heavy-duty diesel (HDD) vehicles. In addition to characterizing the contribution of the spikes (local sources) to the ambient number concentration, we developed a method to determine the net contribution of motor vehicles (all sources) to the total mass concentration of ambient nanoparticles. To do this, we correlated the concentration of spikes with measurements of fast changes in the chemical composition of nanoparticles measured with the nano aerosol mass spectrometer (NAMS; built by the Johnston group). The NAMS irradiates individual, size-selected nanoparticles with a high-energy laser pulse to generate a mass spectrum consisting of multiply charged atomic ions. The elemental composition of each particle was determined from the ion signal intensities of each element. However, overlapping mass-to-charge ratios (m/z) at 4 m/z (O(+4) and C(+3)) and at 8 m/z (O(+2) and S(+4)) needed to be separated into their component ions to obtain a representative composition. To do this, we developed a method to deconvolute these ion signals using sucrose and ammonium sulfate [(NH4)2SO4] as calibration standards. With this approach, the differences between the expected and measured elemental mole fractions of carbon (C), oxygen (O), nitrogen (N), and sulfur (S) for a variety of test particles were generally much less than 10%. Ambient nanoparticles were found to consist mostly of C, O, N, and S. Many particles also contained silicon (Si). The elemental compositions were apportioned

  4. A naphthalimide based PET probe with Fe3+ selective detection ability: theoretical and experimental study.

    PubMed

    Chereddy, Narendra Reddy; Niladri Raju, M V; Nagaraju, Peethani; Krishnaswamy, Venkat Raghavan; Korrapati, Purna Sai; Bangal, Prakriti Ranjan; Rao, Vaidya Jayathirtha

    2014-12-21

    A naphthalimide based fluorescent probe '1' that operates based on photoinduced electron transfer phenomenon is synthesized and its chemosensory application is explored. Among various metal ions, 1 selectively detects Fe(3+) with a detection limit of 3.0 × 10(-8) M. 1 is stable at physiological pH, nontoxic under experimental conditions and suitable for the detection of Fe(3+) ions present in aqueous samples and live cells. PMID:25340936

  5. Sequential Model Selection based Segmentation to Detect DNA Copy Number Variation

    PubMed Central

    Hu, Jianhua; Zhang, Liwen; Wang, Huixia Judy

    2016-01-01

    Summary Array-based CGH experiments are designed to detect genomic aberrations or regions of DNA copy-number variation that are associated with an outcome, typically a state of disease. Most of the existing statistical methods target on detecting DNA copy number variations in a single sample or array. We focus on the detection of group effect variation, through simultaneous study of multiple samples from multiple groups. Rather than using direct segmentation or smoothing techniques, as commonly seen in existing detection methods, we develop a sequential model selection procedure that is guided by a modified Bayesian information criterion. This approach improves detection accuracy by accumulatively utilizing information across contiguous clones, and has computational advantage over the existing popular detection methods. Our empirical investigation suggests that the performance of the proposed method is superior to that of the existing detection methods, in particular, in detecting small segments or separating neighboring segments with differential degrees of copy-number variation. PMID:26954760

  6. Evolutionary optimum for male sexual traits characterized using the multivariate Robertson–Price Identity

    PubMed Central

    Delcourt, Matthieu; Blows, Mark W.; Aguirre, J. David; Rundle, Howard D.

    2012-01-01

    Phenotypes tend to remain relatively constant in natural populations, suggesting a limit to trait evolution. Although stationary phenotypes suggest stabilizing selection, directional selection is more commonly reported. However, selection on phenotypes will have no evolutionary consequence if the traits do not genetically covary with fitness, a covariance known as the Robertson–Price Identity. The nature of this genetic covariance determines if phenotypes will evolve directionally or whether they reside at an evolutionary optimum. Here, we show how a set of traits can be shown to be under net stabilizing selection through an application of the multivariate Robertson–Price Identity. We characterize how a suite of male sexual displays genetically covaries with fitness in a population of Drosophila serrata. Despite strong directional sexual selection on these phenotypes directly and significant genetic variance in them, little genetic covariance was detected with overall fitness. Instead, genetic analysis of trait deviations showed substantial stabilizing selection on the genetic variance of these traits with respect to overall fitness, indicating that they reside at an evolutionary optimum. In the presence of widespread pleiotropy, stabilizing selection on focal traits will arise through the net effects of selection on other, often unmeasured, traits and will tend to be stronger on trait combinations than single traits. Such selection may be difficult to detect in phenotypic analyses if the environmental covariance between the traits and fitness obscures the underlying genetic associations. The genetic analysis of trait deviations provides a way of detecting the missing stabilizing selection inferred by recent metaanalyses. PMID:22615415

  7. Evolutionary dynamics in set structured populations

    PubMed Central

    Tarnita, Corina E.; Antal, Tibor; Ohtsuki, Hisashi; Nowak, Martin A.

    2009-01-01

    Evolutionary dynamics are strongly affected by population structure. The outcome of an evolutionary process in a well-mixed population can be very different from that in a structured population. We introduce a powerful method to study dynamical population structure: evolutionary set theory. The individuals of a population are distributed over sets. Individuals interact with others who are in the same set. Any 2 individuals can have several sets in common. Some sets can be empty, whereas others have many members. Interactions occur in terms of an evolutionary game. The payoff of the game is interpreted as fitness. Both the strategy and the set memberships change under evolutionary updating. Therefore, the population structure itself is a consequence of evolutionary dynamics. We construct a general mathematical approach for studying any evolutionary game in set structured populations. As a particular example, we study the evolution of cooperation and derive precise conditions for cooperators to be selected over defectors. PMID:19433793

  8. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

    PubMed Central

    Zaitlen, Noah A.; Ye, Chun Jimmie; Witte, John S.

    2016-01-01

    The role of rare alleles in complex phenotypes has been hotly debated, but most rare variant association tests (RVATs) do not account for the evolutionary forces that affect genetic architecture. Here, we use simulation and numerical algorithms to show that explosive population growth, as experienced by human populations, can dramatically increase the impact of very rare alleles on trait variance. We then assess the ability of RVATs to detect causal loci using simulations and human RNA-seq data. Surprisingly, we find that statistical performance is worst for phenotypes in which genetic variance is due mainly to rare alleles, and explosive population growth decreases power. Although many studies have attempted to identify causal rare variants, few have reported novel associations. This has sometimes been interpreted to mean that rare variants make negligible contributions to complex trait heritability. Our work shows that RVATs are not robust to realistic human evolutionary forces, so general conclusions about the impact of rare variants on complex traits may be premature. PMID:27197206

  9. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.

    PubMed

    Uricchio, Lawrence H; Zaitlen, Noah A; Ye, Chun Jimmie; Witte, John S; Hernandez, Ryan D

    2016-07-01

    The role of rare alleles in complex phenotypes has been hotly debated, but most rare variant association tests (RVATs) do not account for the evolutionary forces that affect genetic architecture. Here, we use simulation and numerical algorithms to show that explosive population growth, as experienced by human populations, can dramatically increase the impact of very rare alleles on trait variance. We then assess the ability of RVATs to detect causal loci using simulations and human RNA-seq data. Surprisingly, we find that statistical performance is worst for phenotypes in which genetic variance is due mainly to rare alleles, and explosive population growth decreases power. Although many studies have attempted to identify causal rare variants, few have reported novel associations. This has sometimes been interpreted to mean that rare variants make negligible contributions to complex trait heritability. Our work shows that RVATs are not robust to realistic human evolutionary forces, so general conclusions about the impact of rare variants on complex traits may be premature. PMID:27197206

  10. Culturomics as a data playground for tests of selection: Mathematical approaches to detecting selection in word use.

    PubMed

    Sindi, Suzanne S; Dale, Rick

    2016-09-21

    In biological evolution traits may rise and fall in frequency due to genetic drift, where variant frequencies change by chance, or by selection where advantageous variants will rise in frequency. The neutral model of evolution, first developed by Kimura in the 1960s, has become the standard against which selection is detected. While the balance between these two important forces - drift and selection - has been well established in biology there are other domains where the contribution of these processes is still coming together. Although the idea of natural selection has been applied to the cultural domain since the time of Darwin, it has proven more challenging to positively identify cultural traits under selection both because of a lack of established tests for selection and a lack of large cultural data sets. However, in recent years with the accumulation of large cultural data sets many cultural features from pre-history pottery to modern baby names have been shown to evolve according to the neutral theory. But there is accumulating empirical evidence from cultural processes suggesting that the neutral theory alone cannot account for all features of the data. As such, there has been a renewed interest in determining whether there is selection amidst drift. Here we analyze a subset English word frequencies, and determine whether frequency change reveals processes of selection. Inspired by the Moran and Wright-Fisher models in population genetics, we developed a neutral model of word frequency variation to assess when linguistic data appears to depart from neutral evolution. As such, our model represents a possible "test for selection" in the linguistic domain. We explore how the distribution of word use has changed for sets of words in English for more than 100 years (1901-2008) as expressed in vocabulary usage in published books, made available by Google Ngram. When comparing empirical word frequency changes to our neutral model we find pervasive and systematic

  11. Joint Skewness and Its Application in Unsupervised Band Selection for Small Target Detection

    NASA Astrophysics Data System (ADS)

    Geng, Xiurui; Sun, Kang; Ji, Luyan; Tang, Hairong; Zhao, Yongchao

    2015-04-01

    Few band selection methods are specially designed for small target detection. It is well known that the information of small targets is most likely contained in non-Gaussian bands, where small targets are more easily separated from the background. On the other hand, correlation of band set also plays an important role in the small target detection. When the selected bands are highly correlated, it will be unbeneficial for the subsequent detection. However, the existing non-Gaussianity-based band selection methods have not taken the correlation of bands into account, which generally result in high correlation of obtained bands. In this paper, combining the third-order (third-order tensor) and second-order (correlation) statistics of bands, we define a new concept, named joint skewness, for multivariate data. Moreover, we also propose an easy-to-implement approach to estimate this index based on high-order singular value decomposition (HOSVD). Based on the definition of joint skewness, we present an unsupervised band selection for small target detection for hyperspectral data, named joint skewness band selection (JSBS). The evaluation results demonstrate that the bands selected by JSBS are very effective in terms of small target detection.

  12. Joint Skewness and Its Application in Unsupervised Band Selection for Small Target Detection

    PubMed Central

    Geng, Xiurui; Sun, Kang; Ji, Luyan; Tang, Hairong; Zhao, Yongchao

    2015-01-01

    Few band selection methods are specially designed for small target detection. It is well known that the information of small targets is most likely contained in non-Gaussian bands, where small targets are more easily separated from the background. On the other hand, correlation of band set also plays an important role in the small target detection. When the selected bands are highly correlated, it will be unbeneficial for the subsequent detection. However, the existing non-Gaussianity-based band selection methods have not taken the correlation of bands into account, which generally result in high correlation of obtained bands. In this paper, combining the third-order (third-order tensor) and second-order (correlation) statistics of bands, we define a new concept, named joint skewness, for multivariate data. Moreover, we also propose an easy-to-implement approach to estimate this index based on high-order singular value decomposition (HOSVD). Based on the definition of joint skewness, we present an unsupervised band selection for small target detection for hyperspectral data, named joint skewness band selection (JSBS). The evaluation results demonstrate that the bands selected by JSBS are very effective in terms of small target detection. PMID:25873018

  13. Detecting and characterizing genomic signatures of positive selection in global populations.

    PubMed

    Liu, Xuanyao; Ong, Rick Twee-Hee; Pillai, Esakimuthu Nisha; Elzein, Abier M; Small, Kerrin S; Clark, Taane G; Kwiatkowski, Dominic P; Teo, Yik-Ying

    2013-06-01

    Natural selection is a significant force that shapes the architecture of the human genome and introduces diversity across global populations. The question of whether advantageous mutations have arisen in the human genome as a result of single or multiple mutation events remains unanswered except for the fact that there exist a handful of genes such as those that confer lactase persistence, affect skin pigmentation, or cause sickle cell anemia. We have developed a long-range-haplotype method for identifying genomic signatures of positive selection to complement existing methods, such as the integrated haplotype score (iHS) or cross-population extended haplotype homozygosity (XP-EHH), for locating signals across the entire allele frequency spectrum. Our method also locates the founder haplotypes that carry the advantageous variants and infers their corresponding population frequencies. This presents an opportunity to systematically interrogate the whole human genome whether a selection signal shared across different populations is the consequence of a single mutation process followed subsequently by gene flow between populations or of convergent evolution due to the occurrence of multiple independent mutation events either at the same variant or within the same gene. The application of our method to data from 14 populations across the world revealed that positive-selection events tend to cluster in populations of the same ancestry. Comparing the founder haplotypes for events that are present across different populations revealed that convergent evolution is a rare occurrence and that the majority of shared signals stem from the same evolutionary event. PMID:23731540

  14. Detecting and Characterizing Genomic Signatures of Positive Selection in Global Populations

    PubMed Central

    Liu, Xuanyao; Ong, Rick Twee-Hee; Pillai, Esakimuthu Nisha; Elzein, Abier M.; Small, Kerrin S.; Clark, Taane G.; Kwiatkowski, Dominic P.; Teo, Yik-Ying

    2013-01-01

    Natural selection is a significant force that shapes the architecture of the human genome and introduces diversity across global populations. The question of whether advantageous mutations have arisen in the human genome as a result of single or multiple mutation events remains unanswered except for the fact that there exist a handful of genes such as those that confer lactase persistence, affect skin pigmentation, or cause sickle cell anemia. We have developed a long-range-haplotype method for identifying genomic signatures of positive selection to complement existing methods, such as the integrated haplotype score (iHS) or cross-population extended haplotype homozygosity (XP-EHH), for locating signals across the entire allele frequency spectrum. Our method also locates the founder haplotypes that carry the advantageous variants and infers their corresponding population frequencies. This presents an opportunity to systematically interrogate the whole human genome whether a selection signal shared across different populations is the consequence of a single mutation process followed subsequently by gene flow between populations or of convergent evolution due to the occurrence of multiple independent mutation events either at the same variant or within the same gene. The application of our method to data from 14 populations across the world revealed that positive-selection events tend to cluster in populations of the same ancestry. Comparing the founder haplotypes for events that are present across different populations revealed that convergent evolution is a rare occurrence and that the majority of shared signals stem from the same evolutionary event. PMID:23731540

  15. Inference of Evolutionary Forces Acting on Human Biological Pathways

    PubMed Central

    Daub, Josephine T.; Dupanloup, Isabelle; Robinson-Rechavi, Marc; Excoffier, Laurent

    2015-01-01

    Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald–Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects and evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their two-dimensional null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of nonsynonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures. PMID:25971280

  16. Evolutionary Dynamics of Biological Games

    NASA Astrophysics Data System (ADS)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  17. Evolutionary mysteries in meiosis.

    PubMed

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

    2016-10-19

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. PMID:27619705

  18. Guidelines for Improving the Lower Detection Limit of Ion-Selective Electrodes: A Systematic Approach

    SciTech Connect

    Radu, Aleksandar; Peper, Shane M.; Bakker, Eric; Diamond, Dermot

    2007-01-01

    Zero-current membrane fluxes are the principal source of bias that has prohibited researchers from obtaining true, thermodynamic selectivity coefficients for membrane-based ion selective electrodes (ISEs). They are also responsible for the mediocre detection limits historically seen with these types of potentiometric sensors. By choosing an experimental protocol that suppresses these fluxes, it becomes possible to obtain unbiased thermodynamic selectivity coefficients that are needed to produce ISEs with greatly improved detection limits. In this work, a Cs+-selective electrode based on calix[6]arene-hexaacetic acid hexaethyl ester (Cs I) is used to systematically demonstrate how unbiased selectivity coefficients can be obtained, and how they can be used to optimize inner filling solutions for low detection limit measurements. A comparison of biased selectivity methods (e.g., classical separate solution method (SSM), fixed interference method (FIM), matched potential method (MPM)) with the unbiased modified separate solution method (MSSM) found that selectivity coefficients were underestimated in several cases by more than 4 orders of magnitude. The importance of key experimental parameters, including diffusion coefficients and diffusion layer thicknesses in the aqueous and organic phases, on the minimization of ion fluxes and the improvement of lower detection limits is also described. A dramatic reduction of membrane fluxes by the covalent attachment of a Ca2+-selective ionophore to a methyl methacrylate-decyl methacrylate copolymer matrix is also demonstrated. The ionophore-immobilized ISE exhibited no super-Nernstian response and yielded a detection limit of 40 ppt with an inner filling solution of 1 x 10-3 M KCl. Finally, a set of guidelines for experimental protocols leading to obtaining unbiased selectivity coefficients and producing ISEs for trace level analyses is given.

  19. Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data.

    PubMed

    Kadota, Koji; Konishi, Tomokazu; Shimizu, Kentaro

    2007-01-01

    Large-scale expression profiling using DNA microarrays enables identification of tissue-selective genes for which expression is considerably higher and/or lower in some tissues than in others. Among numerous possible methods, only two outlier-detection-based methods (an AIC-based method and Sprent's non-parametric method) can treat equally various types of selective patterns, but they produce substantially different results. We investigated the performance of these two methods for different parameter settings and for a reduced number of samples. We focused on their ability to detect selective expression patterns robustly. We applied them to public microarray data collected from 36 normal human tissue samples and analyzed the effects of both changing the parameter settings and reducing the number of samples. The AIC-based method was more robust in both cases. The findings confirm that the use of the AIC-based method in the recently proposed ROKU method for detecting tissue-selective expression patterns is correct and that Sprent's method is not suitable for ROKU. PMID:19936074

  20. Environmental changes bridge evolutionary valleys

    PubMed Central

    Steinberg, Barrett; Ostermeier, Marc

    2016-01-01

    In the basic fitness landscape metaphor for molecular evolution, evolutionary pathways are presumed to follow uphill steps of increasing fitness. How evolution can cross fitness valleys is an open question. One possibility is that environmental changes alter the fitness landscape such that low-fitness sequences reside on a hill in alternate environments. We experimentally test this hypothesis on the antibiotic resistance gene TEM-15 β-lactamase by comparing four evolutionary strategies shaped by environmental changes. The strategy that included initial steps of selecting for low antibiotic resistance (negative selection) produced superior alleles compared with the other three strategies. We comprehensively examined possible evolutionary pathways leading to one such high-fitness allele and found that an initially deleterious mutation is key to the allele’s evolutionary history. This mutation is an initial gateway to an otherwise relatively inaccessible area of sequence space and participates in higher-order, positive epistasis with a number of neutral to slightly beneficial mutations. The ability of negative selection and environmental changes to provide access to novel fitness peaks has important implications for natural evolutionary mechanisms and applied directed evolution. PMID:26844293

  1. Environmental changes bridge evolutionary valleys.

    PubMed

    Steinberg, Barrett; Ostermeier, Marc

    2016-01-01

    In the basic fitness landscape metaphor for molecular evolution, evolutionary pathways are presumed to follow uphill steps of increasing fitness. How evolution can cross fitness valleys is an open question. One possibility is that environmental changes alter the fitness landscape such that low-fitness sequences reside on a hill in alternate environments. We experimentally test this hypothesis on the antibiotic resistance gene TEM-15 β-lactamase by comparing four evolutionary strategies shaped by environmental changes. The strategy that included initial steps of selecting for low antibiotic resistance (negative selection) produced superior alleles compared with the other three strategies. We comprehensively examined possible evolutionary pathways leading to one such high-fitness allele and found that an initially deleterious mutation is key to the allele's evolutionary history. This mutation is an initial gateway to an otherwise relatively inaccessible area of sequence space and participates in higher-order, positive epistasis with a number of neutral to slightly beneficial mutations. The ability of negative selection and environmental changes to provide access to novel fitness peaks has important implications for natural evolutionary mechanisms and applied directed evolution. PMID:26844293

  2. Predicting outbreak detection in public health surveillance: quantitative analysis to enable evidence-based method selection.

    PubMed

    Buckeridge, David L; Okhmatovskaia, Anna; Tu, Samson; O'Connor, Martin; Nyulas, Csongor; Musen, Mark A

    2008-01-01

    Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however, remains limited and mainly qualitative. Using simulated outbreak data, we developed and validated quantitative models for predicting the ability of commonly used surveillance algorithms to detect different types of outbreaks. The developed models accurately predict the ability of different algorithms to detect different types of outbreaks. These models enable evidence-based algorithm selection and can guide research into algorithm development. PMID:18999264

  3. Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection

    PubMed Central

    Buckeridge, David L.; Okhmatovskaia, Anna; Tu, Samson; O’Connor, Martin; Nyulas, Csongor; Musen, Mark A.

    2008-01-01

    Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however, remains limited and mainly qualitative. Using simulated outbreak data, we developed and validated quantitative models for predicting the ability of commonly used surveillance algorithms to detect different types of outbreaks. The developed models accurately predict the ability of different algorithms to detect different types of outbreaks. These models enable evidence-based algorithm selection and can guide research into algorithm development. PMID:18999264

  4. [Evolutionary medicine: the future looking at the past].

    PubMed

    Carvalho, Serafim; Rosado, Margarida

    2008-01-01

    Evolutionary medicine is an emergent basic science that offers new and varied perspectives to the comprehension of the human health and disease, considering them as a result of a gap between our modern lives and the environment where human beings evolve. This work's goals are to understand the importance of the evolutionary theories on concepts of health and disease, providing a new insight on medicine investigation. This bibliography review is based on Medline and PsycINFO articles research between 1996 and 2007 about review and experimental studies published in English, using the key words evolutionary and medicine, psychiatry, psychology, behaviour, health, disease, gene. There were selected forty-five articles based on and with special interest on the authors' practice. There were also consulted some allusive books. The present human genome and phenotypes are essentially Palaeolithic ones: they are not adapted to the modern life style, thus favouring the so called diseases of civilization. Fitting evolutionary strategies, apparently protective ones, when excessive, are the core syndromes of many emotional disruptive behaviours and diseases. Having the stone age's genes, we are obliged to live in the space age. With the evolutionary approach, postmodern medicine is detecting better the vulnerabilities, restrictions, biases, adaptations and maladaptations of human body, its actual diseases and its preventions and treatment. PMID:19331793

  5. Selective immobilization and detection of DNA on biopolymer supports for the design of microarrays.

    PubMed

    Kargl, R; Vorraber, V; Ribitsch, V; Köstler, S; Stana-Kleinschek, K; Mohan, T

    2015-06-15

    DNA immobilization for the manufacturing of microarrays requires sufficient probe density, low unspecific binding and high interaction efficiency with complementary strands that are detected from solutions. Many of these important parameters are affected by the surface chemistry and the blocking steps conducted during DNA spotting and hybridization. This work describes an alternative method to selectively immobilize probes and to detect DNA on biocompatible, hydrophilic cellulose coated supports with low unspecific binding, high selectivity and appropriate sensitivity. It takes advantage of a relatively selective adsorption of water soluble polysaccharides on a solid cellulose matrix. Single strands of DNA were conjugated to this soluble polysaccharide and subsequently micro-spotted on solid cellulose thin films that were coated on glass and polymer slides. This resulted in adsorptively bound DNA-probes that were used to detect complementary, labelled DNA strands with different lengths and sequences by hybridization. The interaction of the DNA-conjugates with cellulose surfaces and the selectivity of hybridization were investigated by a quartz crystal microbalance with dissipation monitoring (QCM-D) and fluorescence scanning. The method of non-covalent immobilization of DNA probes on an uncharged, non-reactive, hydrophilic support lowers the unspecific binding and the number of handling steps required to conduct the experiments for the detection of DNA on microarrays. Simultaneously selectivity, hybridization efficiency and detection limits are maintained. PMID:25618375

  6. Neuronal boost to evolutionary dynamics.

    PubMed

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

  7. Neuronal boost to evolutionary dynamics

    PubMed Central

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

  8. Sensitive and selective detection of thrombin by using a cyclic peptide as affinity ligand.

    PubMed

    Zhao, Qiang; Gao, Jie

    2015-01-15

    Here we describe a sensitive assay for thrombin by using a high binding-affinity cyclic peptide against thrombin as affinity ligand. The cyclic peptide is immobilized on the magnetic beads or microplates to selectively capture thrombin. The enriched thrombin then catalyzes the cleavage of a substrate of thrombin to a detectable product. The detection of thrombin is finally achieved by measuring the generated product. This assay enables the detection of thrombin at tens fM in 100 µL of sample solution when fluorogenic substrate was applied, while detection limits reached pM level when chromogenic substrate was used. Thrombin in plasma sample can be detected with this assay. This cyclic peptide affinity ligand shows potentials for thrombin analysis in other detection formats. PMID:25048449

  9. A Genomics Approach to the Detection of Positive Selection in Cattle:

    PubMed Central

    Lynn, David J.; Freeman, Abigail R.; Murray, Caitriona; Bradley, Daniel G.

    2005-01-01

    The detection of adaptive evolution at the molecular level is of interest not only as an insight into the process of evolution but also because of its functional implications for genes of interest. Here, we present the first genomics approach to detecting positive selection operating on the Bos taurus lineage, an important domestic species. This analysis led to the identification of the T-cell and natural killer (NK) cell receptor cluster of differentiation 2 (CD2) as having a strong signal of selection. Further detailed investigation of CD2 revealed that this gene was subject to positive selection during the evolution of a number of mammalian lineages. Moreover, we show that selection has operated primarily on the extracellular domain of CD2 and discuss the implications of this for an important regulator of the adaptive immune response.

  10. Selective fluorescence and fluorescence-free detection of single biomolecules on nanobiochips.

    PubMed

    Lee, Seungah; Kang, Seong Ho

    2014-10-01

    This topical review provides an overview of selective fluorescence and fluorescence-free detection on nanobiochips fabricated by nanopatterning techniques such as nanolithography and the use of artificial nanostructures (arrays of pillars, holes, and wires). The unique properties of nanostructured surfaces have led to applications in biomedical nanoarrays used for either diagnostic or functional assays on chips. Some targets can be optically detected using not only colorimetry, chemiluminescence or the most developed fluorescence mode, but also more recent non-conventional optical methods. Two main approaches have been used: fluorescence (e.g., epifluorescence and total internal reflection) and fluorescence-free (e.g., surface plasmon resonance, optical resonance, dark-field scattering, atom force microscopy, electrochemical method, etc.) detection. The aim of the present paper is to review the most recent progress in nanobiochips in the development of new selective fluorescence and fluorescence-free detection at the single-molecule level. PMID:25992412

  11. Effective Sensor Selection and Data Anomaly Detection for Condition Monitoring of Aircraft Engines.

    PubMed

    Liu, Liansheng; Liu, Datong; Zhang, Yujie; Peng, Yu

    2016-01-01

    In a complex system, condition monitoring (CM) can collect the system working status. The condition is mainly sensed by the pre-deployed sensors in/on the system. Most existing works study how to utilize the condition information to predict the upcoming anomalies, faults, or failures. There is also some research which focuses on the faults or anomalies of the sensing element (i.e., sensor) to enhance the system reliability. However, existing approaches ignore the correlation between sensor selecting strategy and data anomaly detection, which can also improve the system reliability. To address this issue, we study a new scheme which includes sensor selection strategy and data anomaly detection by utilizing information theory and Gaussian Process Regression (GPR). The sensors that are more appropriate for the system CM are first selected. Then, mutual information is utilized to weight the correlation among different sensors. The anomaly detection is carried out by using the correlation of sensor data. The sensor data sets that are utilized to carry out the evaluation are provided by National Aeronautics and Space Administration (NASA) Ames Research Center and have been used as Prognostics and Health Management (PHM) challenge data in 2008. By comparing the two different sensor selection strategies, the effectiveness of selection method on data anomaly detection is proved. PMID:27136561

  12. Effective Sensor Selection and Data Anomaly Detection for Condition Monitoring of Aircraft Engines

    PubMed Central

    Liu, Liansheng; Liu, Datong; Zhang, Yujie; Peng, Yu

    2016-01-01

    In a complex system, condition monitoring (CM) can collect the system working status. The condition is mainly sensed by the pre-deployed sensors in/on the system. Most existing works study how to utilize the condition information to predict the upcoming anomalies, faults, or failures. There is also some research which focuses on the faults or anomalies of the sensing element (i.e., sensor) to enhance the system reliability. However, existing approaches ignore the correlation between sensor selecting strategy and data anomaly detection, which can also improve the system reliability. To address this issue, we study a new scheme which includes sensor selection strategy and data anomaly detection by utilizing information theory and Gaussian Process Regression (GPR). The sensors that are more appropriate for the system CM are first selected. Then, mutual information is utilized to weight the correlation among different sensors. The anomaly detection is carried out by using the correlation of sensor data. The sensor data sets that are utilized to carry out the evaluation are provided by National Aeronautics and Space Administration (NASA) Ames Research Center and have been used as Prognostics and Health Management (PHM) challenge data in 2008. By comparing the two different sensor selection strategies, the effectiveness of selection method on data anomaly detection is proved. PMID:27136561

  13. Active surfaces engineered by immobilizing protein-polymer nanoreactors for selectively detecting sugar alcohols.

    PubMed

    Zhang, Xiaoyan; Lomora, Mihai; Einfalt, Tomaz; Meier, Wolfgang; Klein, Noreen; Schneider, Dirk; Palivan, Cornelia G

    2016-05-01

    We introduce active surfaces generated by immobilizing protein-polymer nanoreactors on a solid support for sensitive sugar alcohols detection. First, such selective nanoreactors were engineered in solution by simultaneous encapsulation of specific enzymes in copolymer polymersomes, and insertion of membrane proteins for selective conduct of sugar alcohols. Despite the artificial surroundings, and the thickness of the copolymer membrane, functionality of reconstituted Escherichia coli glycerol facilitator (GlpF) was preserved, and allowed selective diffusion of sugar alcohols to the inner cavity of the polymersome, where encapsulated ribitol dehydrogenase (RDH) enzymes served as biosensing entities. Ribitol, selected as a model sugar alcohol, was detected quantitatively by the RDH-nanoreactors with GlpF-mediated permeability in a concentration range of 1.5-9 mM. To obtain "active surfaces" for detecting sugar alcohols, the nanoreactors optimized in solution were then immobilized on a solid support: aldehyde groups exposed at the compartment external surface reacted via an aldehyde-amino reaction with glass surfaces chemically modified with amino groups. The nanoreactors preserved their architecture and activity after immobilization on the glass surface, and represent active biosensing surfaces for selective detection of sugar alcohols, with high sensitivity. PMID:26950167

  14. Recursive spectral similarity measure-based band selection for anomaly detection in hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    He, Yuanlei; Liu, Daizhi; Yi, Shihua

    2011-01-01

    Band selection has been widely used in hyperspectral image processing for dimension reduction. In this paper, a recursive spectral similarity measure-based band selection (RSSM-BBS) method is presented. Unlike most of the existing image-based band selection techniques, it is for two hyperspectral signatures with its main focus on their spectral separability. Furthermore, it is unsupervised and based on the recursive calculation of the spectral similarity measure with an additional band. In order to demonstrate the utility of the proposed method, an anomaly detection algorithm is developed, which first extracts the anomalous target spectrum from the image using the automatic target detection and classification algorithm (ATDCA), followed by the maximum spectral screening (MSS) to obtain a good estimate of the background, and then implements RSSM-BBS to select bands that participate in the subsequent adaptive cosine/coherence estimator (ACE) target detection. As shown in the experimental result on the AVIRIS dataset, the detection performance of the ACE has been improved greatly with the bands selected by RSSM-BBS over that using full bands.

  15. Improved ion-selective detection method using nanopipette with poly(vinyl chloride)-based membrane.

    PubMed

    Kang, Eun Ji; Takami, Tomohide; Deng, Xiao Long; Son, Jong Wan; Kawai, Tomoji; Park, Bae Ho

    2014-05-15

    Ion-selective electrodes (ISEs) are widely used to detect targeted ions in solution selectively. Application of an ISE to a small area detection system with a nanopipette requires a special measurement method in order to avoid the enhanced background signal problem caused by a cation-rich layer near the charged inner surface of the nanopipette and the selectivity change problem due to relatively fast saturation of the ISE inside the nanopipette. We developed a novel ion-selective detection system using a nanopipette that measures an alternating current (AC) signal mediated by saturated ionophores in a poly(vinyl chloride) (PVC) membrane located at the conical shank of the nanopipette to solve the above problems. Small but reliable K(+) and Na(+) ionic current passing through a PVC membrane containing saturated bis(benzo-15-crown-5) and bis(12-crown-4) ionophore, respectively, could be selectively detected using the AC signal measurement system equipped with a lock-in amplifier. PMID:24766420

  16. BODIPY based colorimetric fluorescent probe for selective thiophenol detection: theoretical and experimental studies.

    PubMed

    Kand, Dnyaneshwar; Mishra, Pratyush Kumar; Saha, Tanmoy; Lahiri, Mayurika; Talukdar, Pinaki

    2012-09-01

    A BODIPY-based selective thiophenol probe capable of discriminating aliphatic thiols is reported. The fluorescence off-on effect upon reaction with thiol is elucidated with theoretical calculations. The sensing of thiophenol is associated with a color change from red to yellow and 63-fold enhancement in green fluorescence. Application of the probe for selective thiophenol detection is demonstrated by live cell imaging. PMID:22751002

  17. Multi-Layer Approach for the Detection of Selective Forwarding Attacks

    PubMed Central

    Alajmi, Naser; Elleithy, Khaled

    2015-01-01

    Security breaches are a major threat in wireless sensor networks (WSNs). WSNs are increasingly used due to their broad range of important applications in both military and civilian domains. WSNs are prone to several types of security attacks. Sensor nodes have limited capacities and are often deployed in dangerous locations; therefore, they are vulnerable to different types of attacks, including wormhole, sinkhole, and selective forwarding attacks. Security attacks are classified as data traffic and routing attacks. These security attacks could affect the most significant applications of WSNs, namely, military surveillance, traffic monitoring, and healthcare. Therefore, there are different approaches to detecting security attacks on the network layer in WSNs. Reliability, energy efficiency, and scalability are strong constraints on sensor nodes that affect the security of WSNs. Because sensor nodes have limited capabilities in most of these areas, selective forwarding attacks cannot be easily detected in networks. In this paper, we propose an approach to selective forwarding detection (SFD). The approach has three layers: MAC pool IDs, rule-based processing, and anomaly detection. It maintains the safety of data transmission between a source node and base station while detecting selective forwarding attacks. Furthermore, the approach is reliable, energy efficient, and scalable. PMID:26610499

  18. Multi-Layer Approach for the Detection of Selective Forwarding Attacks.

    PubMed

    Alajmi, Naser; Elleithy, Khaled

    2015-01-01

    Security breaches are a major threat in wireless sensor networks (WSNs). WSNs are increasingly used due to their broad range of important applications in both military and civilian domains. WSNs are prone to several types of security attacks. Sensor nodes have limited capacities and are often deployed in dangerous locations; therefore, they are vulnerable to different types of attacks, including wormhole, sinkhole, and selective forwarding attacks. Security attacks are classified as data traffic and routing attacks. These security attacks could affect the most significant applications of WSNs, namely, military surveillance, traffic monitoring, and healthcare. Therefore, there are different approaches to detecting security attacks on the network layer in WSNs. Reliability, energy efficiency, and scalability are strong constraints on sensor nodes that affect the security of WSNs. Because sensor nodes have limited capabilities in most of these areas, selective forwarding attacks cannot be easily detected in networks. In this paper, we propose an approach to selective forwarding detection (SFD). The approach has three layers: MAC pool IDs, rule-based processing, and anomaly detection. It maintains the safety of data transmission between a source node and base station while detecting selective forwarding attacks. Furthermore, the approach is reliable, energy efficient, and scalable. PMID:26610499

  19. Optimal neural network architecture selection: effects on computer-aided detection of mammographic microcalcifications

    NASA Astrophysics Data System (ADS)

    Gurcan, Metin N.; Chan, Heang-Ping; Sahiner, Berkman; Hadjiiski, Lubomir M.; Petrick, Nicholas; Helvie, Mark A.

    2002-05-01

    We evaluated the effectiveness of an optimal convolution neural network (CNN) architecture selected by simulated annealing for improving the performance of a computer-aided diagnosis (CAD) system designed for the detection of microcalcification clusters on digitized mammograms. The performances of the CAD programs with manually and optimally selected CNNs were compared using an independent test set. This set included 472 mammograms and contained 253 biopsy-proven malignant clusters. Free-response receiver operating characteristic (FROC) analysis was used for evaluation of the detection accuracy. At a false positive (FP) rate of 0.7 per image, the film-based sensitivity was 84.6% with the optimized CNN, in comparison with 77.2% with the manually selected CNN. If clusters having images in both craniocaudal and mediolateral oblique views were analyzed together and a cluster was considered to be detected when it was detected in one or both views, at 0.7 FPs/image, the sensitivity was 93.3% with the optimized CNN and 87.0% with the manually selected CNN. This study indicates that classification of true positive and FP signals is an important step of the CAD program and that the detection accuracy of the program can be considerably improved by optimizing this step with an automated optimization algorithm.

  20. A fluorescence-based microbial sensor for the selective detection of gold.

    PubMed

    Tseng, Hsueh-Wei; Tsai, Yi-Jung; Yen, Jia-Ho; Chen, Pei-Hsuan; Yeh, Yi-Chun

    2014-02-18

    This study presents a fluorescence-based microbial sensor for the detection of metal ions as a novel analytical tool for environmental applications. Our results demonstrate the effectiveness of whole-cell sensors in the selective detection of gold ions. Two heavy-metal-tolerant proteobacteria, Cupriavidus metallidurans and Ralstonia eutropha, were examined and showed great specificity. This work highlights the potential of employing engineered microbial strains as robust analytical tools. PMID:24394407

  1. An aqueous fluorescent probe for Hg(2+) detection with high selectivity and sensitivity.

    PubMed

    Fang, Qian; Liu, Qian; Song, Xiangzhi; Kang, Jian

    2015-12-01

    An aqueous fluorescent probe, 1, was developed for the rapid detection of Hg(2+) with high sensitivity and excellent selectivity. Upon the addition of Hg(2+) in pure aqueous media, the Hg(2+)-mediated hydrolysis of vinyl ether and subsequent cyclization reactions converted probe 1 into the corresponding iminocoumarin dye, which is strongly fluorescent when excited. The application of this probe for the detection of intracellular Hg(2+) was successfully demonstrated in living cells. PMID:25761896

  2. Selective Detection of Sulfur Derivatives Using Microfabricated Tuning Fork-Based Sensors

    PubMed Central

    Rai, Anant; Tsow, Francis; Nassirpour, Sanam; Bankers, Jeffrey; Spinatsch, Martina; He, M. Pete; Forzani, Erica; Tao, N. J.

    2009-01-01

    The paper describes an integtrated sensor system that can selectively and reversibly detect sulfur derivatives in the presence of interferent molecules. This is accomplished by integrating analyte-specific sensing materials with optimized filter materials. Microfabricated quartz tuning fork arrays are used to provide fast, accurate and low-cost transduction of the analyte binding events into electronic signals. The concept is demonstrated for detection of three sulfur derivatives – dimethyl disulfide, ethanethiol and methylsulfide. PMID:20160943

  3. Evolutionary genetics of maternal effects

    PubMed Central

    Wolf, Jason B.; Wade, Michael J.

    2016-01-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

  4. Evolutionary genetics of maternal effects.

    PubMed

    Wolf, Jason B; Wade, Michael J

    2016-04-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single-locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype-phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype-phenotype relationship frequency dependent, resulting in the appearance of negative frequency-dependent selection, while additive MGEs contribute a component of parent-of-origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be "available" to the evolving population. PMID:26969266

  5. A bioinformatics workflow for detecting signatures of selection in genomic data.

    PubMed

    Cadzow, Murray; Boocock, James; Nguyen, Hoang T; Wilcox, Phillip; Merriman, Tony R; Black, Michael A

    2014-01-01

    The detection of "signatures of selection" is now possible on a genome-wide scale in many plant and animal species, and can be performed in a population-specific manner due to the wealth of per-population genome-wide genotype data that is available. With genomic regions that exhibit evidence of having been under selection shown to also be enriched for genes associated with biologically important traits, detection of evidence of selective pressure is emerging as an additional approach for identifying novel gene-trait associations. While high-density genotype data is now relatively easy to obtain, for many researchers it is not immediately obvious how to go about identifying signatures of selection in these data sets. Here we describe a basic workflow, constructed from open source tools, for detecting and examining evidence of selection in genomic data. Code to install and implement the pipeline components, and instructions to run a basic analysis using the workflow described here, can be downloaded from our public GitHub repository: http://www.github.com/smilefreak/selectionTools/ PMID:25206364

  6. Scedo-Select III: a new semi-selective culture medium for detection of the Scedosporium apiospermum species complex.

    PubMed

    Pham, Trâm; Giraud, Sandrine; Schuliar, Gaëlle; Rougeron, Amandine; Bouchara, Jean-Philippe

    2015-06-01

    The Scedosporium apiospermum complex is responsible for a large variety of infections in human. Members of this complex have become emerging fungal pathogens with an increasing occurrence in patients with underlying conditions such as immunosuppression or cystic fibrosis. A better knowledge of these fungi and of the sources of contamination of the patients is required and more accurate detection methods from the environment are needed. In this context, a highly selective culture medium was developed in the present study. Thus, various aliphatic, cyclic, or aromatic compounds were tested as the sole carbon source, in combination with some inorganic nitrogen sources and fungicides. The best results were obtained with 4-hydroxy-benzoate combined with ammonium sulfate and the fungicides dichloran and benomyl. This new culture medium called Scedo-Select III was shown to support growth of all species of the S. apiospermum complex. Subsequently, this new culture medium was evaluated successfully on water and soil samples, exhibiting higher sensitivity and selectivity than the previously described SceSel+ culture medium. Therefore, this easy-to-prepare and synthetic semi-selective culture medium may be useful to clarify the ecology of these fungi and to identify their reservoirs in patients' environment. PMID:25841055

  7. Eigenvalue-weighting and feature selection for computer-aided polyp detection in CT colonography

    NASA Astrophysics Data System (ADS)

    Zhu, Hongbin; Wang, Su; Fan, Yi; Lu, Hongbing; Liang, Zhengrong

    2010-03-01

    With the development of computer-aided polyp detection towards virtual colonoscopy screening, the trade-off between detection sensitivity and specificity has gained increasing attention. An optimum detection, with least number of false positives and highest true positive rate, is desirable and involves interdisciplinary knowledge, such as feature extraction, feature selection as well as machine learning. Toward that goal, various geometrical and textural features, associated with each suspicious polyp candidate, have been individually extracted and stacked together as a feature vector. However, directly inputting these high-dimensional feature vectors into a learning machine, e.g., neural network, for polyp detection may introduce redundant information due to feature correlation and induce the curse of dimensionality. In this paper, we explored an indispensable building block of computer-aided polyp detection, i.e., principal component analysis (PCA)-weighted feature selection for neural network classifier of true and false positives. The major concepts proposed in this paper include (1) the use of PCA to reduce the feature correlation, (2) the scheme of adaptively weighting each principal component (PC) by the associated eigenvalue, and (3) the selection of feature combinations via the genetic algorithm. As such, the eigenvalue is also taken as part of the characterizing feature, and the necessary number of features can be exposed to mitigate the curse of dimensionality. Learned and tested by radial basis neural network, the proposed computer-aided polyp detection has achieved 95% sensitivity at a cost of average 2.99 false positives per polyp.

  8. SweeD: likelihood-based detection of selective sweeps in thousands of genomes.

    PubMed

    Pavlidis, Pavlos; Živkovic, Daniel; Stamatakis, Alexandros; Alachiotis, Nikolaos

    2013-09-01

    The advent of modern DNA sequencing technology is the driving force in obtaining complete intra-specific genomes that can be used to detect loci that have been subject to positive selection in the recent past. Based on selective sweep theory, beneficial loci can be detected by examining the single nucleotide polymorphism patterns in intraspecific genome alignments. In the last decade, a plethora of algorithms for identifying selective sweeps have been developed. However, the majority of these algorithms have not been designed for analyzing whole-genome data. We present SweeD (Sweep Detector), an open-source tool for the rapid detection of selective sweeps in whole genomes. It analyzes site frequency spectra and represents a substantial extension of the widely used SweepFinder program. The sequential version of SweeD is up to 22 times faster than SweepFinder and, more importantly, is able to analyze thousands of sequences. We also provide a parallel implementation of SweeD for multi-core processors. Furthermore, we implemented a checkpointing mechanism that allows to deploy SweeD on cluster systems with queue execution time restrictions, as well as to resume long-running analyses after processor failures. In addition, the user can specify various demographic models via the command-line to calculate their theoretically expected site frequency spectra. Therefore, (in contrast to SweepFinder) the neutral site frequencies can optionally be directly calculated from a given demographic model. We show that an increase of sample size results in more precise detection of positive selection. Thus, the ability to analyze substantially larger sample sizes by using SweeD leads to more accurate sweep detection. We validate SweeD via simulations and by scanning the first chromosome from the 1000 human Genomes project for selective sweeps. We compare SweeD results with results from a linkage-disequilibrium-based approach and identify common outliers. PMID:23777627

  9. The Evolving Theory of Evolutionary Radiations.

    PubMed

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology. PMID:26632984

  10. Unsupervised Spectral-Spatial Feature Selection-Based Camouflaged Object Detection Using VNIR Hyperspectral Camera

    PubMed Central

    2015-01-01

    The detection of camouflaged objects is important for industrial inspection, medical diagnoses, and military applications. Conventional supervised learning methods for hyperspectral images can be a feasible solution. Such approaches, however, require a priori information of a camouflaged object and background. This letter proposes a fully autonomous feature selection and camouflaged object detection method based on the online analysis of spectral and spatial features. The statistical distance metric can generate candidate feature bands and further analysis of the entropy-based spatial grouping property can trim the useless feature bands. Camouflaged objects can be detected better with less computational complexity by optical spectral-spatial feature analysis. PMID:25879073

  11. Standoff explosives trace detection and imaging by selective stimulated Raman scattering

    NASA Astrophysics Data System (ADS)

    Bremer, Marshall T.; Dantus, Marcos

    2013-08-01

    We introduce a sensitive method for laser based standoff detection of chemicals based on stimulated Raman scattering. Selective excitation of a particular Raman transition is detected by measuring the diffusely reflected laser light from a distant surface. The method simultaneously measures stimulated Raman loss and gain within a single laser shot and is insensitive to the optical properties (reflectivity/absorptivity) of the substrate. We demonstrate the specificity and sensitivity by detecting and imaging nanogram analyte micro-crystals on paper, fabric, and plastic substrates at 1 to 10 m standoff distance using only 10 mW of laser power from a single femtosecond laser.

  12. Highly Efficient State-Selective Submicrosecond Photoionization Detection of Single Atoms

    SciTech Connect

    Henkel, F.; Krug, M.; Hofmann, J.; Rosenfeld, W.; Weber, M.; Weinfurter, H.

    2010-12-17

    We experimentally demonstrate a detection scheme suitable for state analysis of single optically trapped atoms in less than 1 {mu}s with an overall detection efficiency {eta} exceeding 98%. The method is based on hyperfine-state-selective photoionization and subsequent registration of the correlated photoion-electron pairs by coincidence counting via two opposing channel electron multipliers. The scheme enables the calibration of absolute detection efficiencies and might be a key ingredient for future quantum information applications or precision spectroscopy of ultracold atoms.

  13. Performance of SaSelect, a Chromogenic Medium for Detection of Staphylococci in Clinical Specimens

    PubMed Central

    Kerttula, Anne-Marie; Kaukoranta, Suvi-Sirkku

    2014-01-01

    In a preliminary study, known staphylococcus (n = 86) and other microbial (n = 12) isolates were plated on three chromogenic media, SaSelect (Bio-Rad, Hercules, CA, USA), CHROMagar Staph. aureus (CHROMagar Microbiology, Paris, France), and S. aureus ID (bioMérieux, Marcy l'Etoile, France). The sensitivities of all the media to detect Staphylococcus aureus after 24 h of incubation were high (100.0%). However, their specificities varied at 93.3% (95% confidence interval [CI], 86.0% to 100.0%) (CHROMagar Staph. aureus), 97.8% (95% CI, 93.5% to 100.0%) (S. aureus ID), and 100.0% (SaSelect). SaSelect also showed the highest sensitivity for recovery and differentiation of other staphylococci. As the best performing chromogenic medium, SaSelect was then prospectively compared to conventional culture and identification tests for the detection of staphylococci from 2,780 clinical specimens. A total of 1,589 staphylococcal isolates were recovered. Of these, 912 were S. aureus and 677 were other staphylococci. The sensitivity and specificity of SaSelect to detect S. aureus in clinical specimens after 24 h of incubation were 99.6% and 99.9% (95% CI, 99.2% to 100.0% and 99.8% to 100.0%), respectively, whereas the sensitivity and specificity using conventional plates combined with laboratory identification methods were 96.8% and 99.5% (95% CI, 95.7 to 97.9% and 99.2% to 99.8%). For the recovery and preliminary identification of other staphylococci, the sensitivity and specificity of SaSelect were 94.4% and 99.9%. SaSelect is a well-performing chromogenic medium that significantly improved the detection of staphylococci, especially S. aureus, compared to conventional culture (P < 0.0001). PMID:24430448

  14. Highly Sensitive and Selective Detection of Nanomolar Ferric Ions Using Dopamine Functionalized Graphene Quantum Dots.

    PubMed

    Dutta Chowdhury, Ankan; Doong, Ruey-An

    2016-08-17

    The good stability, low cytotoxicity, and excellent photoluminescence property of graphene quantum dots (GQDs) make them an emerging class of promising materials in various application fields ranging from sensor to drug delivery. In the present work, the dopamine-functionalized GQDs (DA-GQDs) with stably bright blue fluorescence were successfully synthesized for low level Fe(3+) ions detection. The as-synthesized GQDs are uniform in size with narrow-distributed particle size of 4.5 ± 0.6 nm and high quantum yield of 10.2%. The amide linkage of GQDs with dopamine, confirmed by using XPS and FTIR spectra, results in the specific interaction between Fe(3+) and catechol moiety of dopamine at the interfaces for highly sensitive and selective detection of Fe(3+). A linear range of 20 nM to 2 μM with a detection limit of 7.6 nM is obtained for Fe(3+) detection by DA-GQDs. The selectivity of DA-GQDs sensing probe is significantly excellent in the presence of other interfering metal ions. In addition, the reaction mechanism for Fe(3+) detection based on the complexation and oxidation of dopamine has been proposed and validated. Results obtained in this study clearly demonstrate the superiority of surface functionalized GQDs to Fe(3+) detection, which can pave an avenue for the development of high performance and robust sensing probes for detection of metal ions and other organic metabolites in environmental and biomedical applications. PMID:27472083

  15. A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

    PubMed Central

    Zhang, Jing; Wu, Huizhe; Chen, Qiuchen; Zhao, Pengfei; Zhao, Haishan; Yao, Weifan; Wei, Minjie

    2015-01-01

    Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1 C3435T/A) from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature. PMID:26347880

  16. A highly sensitive and selective immunoassay for the detection of tetrabromobisphenol A in soil and sediment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. A sensitive and selective enzyme-linked immunosorbent assay (ELISA) for the detection of TBBPA was developed. Six haptens (T1-T6) mimicking different structural elements of TBBPA were synthesized and coupled to keyhole...

  17. Hyperspectral imaging-based classification and wavebands selection for internal defect detection of pickling cucumbers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hyperspectral imaging is useful for detecting internal defect of pickling cucumbers. The technique, however, is not yet suitable for high-speed online implementation due to the challenges for analyzing large-scale hyperspectral images. This research was aimed to select the optimal wavebands from the...

  18. Hyperspectral Waveband Selection for Internal Defect Detection of Pickling Cucumbers and Whole Pickles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hyperspectral imaging under transmittance mode has shown potential for detecting internal defect, however, the technique still cannot meet the on-line speed requirement because it needs to acquire and analyze a large amount of image data. This study was carried out to select important wavebands that...

  19. A bioinformatics workflow for detecting signatures of selection in genomic data

    PubMed Central

    Cadzow, Murray; Boocock, James; Nguyen, Hoang T.; Wilcox, Phillip; Merriman, Tony R.; Black, Michael A.

    2014-01-01

    The detection of “signatures of selection” is now possible on a genome-wide scale in many plant and animal species, and can be performed in a population-specific manner due to the wealth of per-population genome-wide genotype data that is available. With genomic regions that exhibit evidence of having been under selection shown to also be enriched for genes associated with biologically important traits, detection of evidence of selective pressure is emerging as an additional approach for identifying novel gene-trait associations. While high-density genotype data is now relatively easy to obtain, for many researchers it is not immediately obvious how to go about identifying signatures of selection in these data sets. Here we describe a basic workflow, constructed from open source tools, for detecting and examining evidence of selection in genomic data. Code to install and implement the pipeline components, and instructions to run a basic analysis using the workflow described here, can be downloaded from our public GitHub repository: http://www.github.com/smilefreak/selectionTools/ PMID:25206364

  20. Electrochemical plasmonic sensing system for highly selective multiplexed detection of biomolecules based on redox nanoswitches.

    PubMed

    Dallaire, Anne-Marie; Patskovsky, Sergiy; Vallée-Bélisle, Alexis; Meunier, Michel

    2015-09-15

    In this paper, we present the development of a nanoswitch-based electrochemical surface plasmon resonance (eSPR) transducer for the multiplexed and selective detection of DNA and other biomolecules directly in complex media. To do so, we designed an experimental set-up for the synchronized measurements of electrochemical and electro-plasmonic responses to the activation of multiple electrochemically labeled structure-switching biosensors. As a proof of principle, we adapted this strategy for the detection of DNA sequences that are diagnostic of two pathogens (drug-resistant tuberculosis and Escherichia coli) by using methylene blue-labeled structure-switching DNA stem-loop. The experimental sensitivity of the switch-based eSPR sensor is estimated at 5 nM and target detection is achieved within minutes. Each sensor is reusable several times with a simple 8M urea washing procedure. We then demonstrated the selectivity and multiplexed ability of these switch-based eSPR by simultaneously detecting two different DNA sequences. We discuss the advantages of the proposed eSPR approach for the development of highly selective sensor devices for the rapid and reliable detection of multiple molecular markers in complex samples. PMID:25889347

  1. Nanomolar colorimetric quantitative detection of Fe3 + and PPi with high selectivity

    NASA Astrophysics Data System (ADS)

    Li, Zhanxian; Li, Haixia; Shi, Caixia; Yu, Mingming; Wei, Liuhe; Ni, Zhonghai

    2016-04-01

    A novel rhodamine and 8-hydroxyquinoline-based derivative was synthesized, which is shown to act as a colorimetric chemosensor for Fe3 + in aqueous solution with high selectivity over various environmentally and biologically relevant metal ions and anions with a distinct color change from colorless to pink in very fast response time (< 1 min). Fe3 + can be detected quantitatively in the concentration range from 6.7 to 16 μM and the detection limit (LOD) on UV-vis response of the sensor can be as low as 15 nM. The 'in situ' prepared Fe3 + complex (1 ṡ Fe) showed high selectivity toward PPi against many common anions, and sensitivity (the LOD can be as low as 71 nM). In addition, both the chemosensor and the 'in situ' prepared Fe3 + complex are reusable for the detection of Fe3 + and PPi respectively.

  2. Nanomolar colorimetric quantitative detection of Fe(3+) and PPi with high selectivity.

    PubMed

    Li, Zhanxian; Li, Haixia; Shi, Caixia; Yu, Mingming; Wei, Liuhe; Ni, Zhonghai

    2016-04-15

    A novel rhodamine and 8-hydroxyquinoline-based derivative was synthesized, which is shown to act as a colorimetric chemosensor for Fe(3+) in aqueous solution with high selectivity over various environmentally and biologically relevant metal ions and anions with a distinct color change from colorless to pink in very fast response time (<1min). Fe(3+) can be detected quantitatively in the concentration range from 6.7 to 16μM and the detection limit (LOD) on UV-vis response of the sensor can be as low as 15nM. The 'in situ' prepared Fe(3+) complex (1⋅Fe) showed high selectivity toward PPi against many common anions, and sensitivity (the LOD can be as low as 71nM). In addition, both the chemosensor and the 'in situ' prepared Fe(3+) complex are reusable for the detection of Fe(3+) and PPi respectively. PMID:26878355

  3. Highly selective and sensitive fluorescent paper sensor for nitroaromatic explosive detection.

    PubMed

    Ma, Yingxin; Li, Hao; Peng, Shan; Wang, Leyu

    2012-10-01

    Rapid, sensitive, and selective detection of explosives such as 2,4,6-trinitrotoluene (TNT) and 2,4,6-trinitrophenol (TNP), especially using a facile paper sensor, is in high demand for homeland security and public safety. Although many strategies have been successfully developed for the detection of TNT, it is not easy to differentiate the influence from TNP. Also, few methods were demonstrated for the selective detection of TNP. In this work, via a facile and versatile method, 8-hydroxyquinoline aluminum (Alq(3))-based bluish green fluorescent composite nanospheres were successfully synthesized through self-assembly under vigorous stirring and ultrasonic treatment. These polymer-coated nanocomposites are not only water-stable but also highly luminescent. Based on the dramatic and selective fluorescence quenching of the nanocomposites via adding TNP into the aqueous solution, a sensitive and robust platform was developed for visual detection of TNP in the mixture of nitroaromatics including TNT, 2,4-dinitrotoluene (DNT), and nitrobenzene (NB). Meanwhile, the fluorescence intensity is proportional to the concentration of TNP in the range of 0.05-7.0 μg/mL with the 3σ limit of detection of 32.3 ng/mL. By handwriting or finger printing with TNP solution as ink on the filter paper soaked with the fluorescent nanocomposites, the bluish green fluorescence was instantly and dramatically quenched and the dark patterns were left on the paper. Therefore, a convenient and rapid paper sensor for TNP-selective detection was fabricated. PMID:22946839

  4. Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds

    PubMed Central

    Zhu, Caiye; Fan, Hongying; Yuan, Zehu; Hu, Shijin; Zhang, Li; Wei, Caihong; Zhang, Qin; Zhao, Fuping; Du, Lixin

    2015-01-01

    Artificial selection has played a critical role in animal breeding. Detection of artificial selection footprints in genomic regions can provide insights for understanding the function of specific phenotypic traits and better guide animal breeding. To more fully understand the relationship between genomic composition and phenotypic diversity arising from breed development, a genome-wide scan was conducted using an OvineSNP50 BeadChip and integrated haplotype score and fixation index analyses to detect selection signatures on the X chromosome in three sheep breeds. We identified 49, 34, and 55 candidate selection regions with lengths of 27.49, 16.47, and 25.42 Mb in German Mutton, Dorper, and Sunit sheep, respectively. Bioinformatics analysis showed that some of the genes in these regions with selection signatures, such as BMP15, were relevant to reproduction. We also identified some selection regions harboring genes that had human orthologs, including BKT, CENPI, GUCY2F, MSN, PCDH11X, PLP1, VSIG4, PAK3, WAS, PCDH19, PDHA1, and SRPX2. The VSIG4 and PCDH11X genes are associated with the immune system and disease, PDHA1 is associated with biosynthetic related pathways, and PCDH19 is expressed in the nervous system and skin. These genes may be useful as candidate genes for molecular breeding. PMID:26343642

  5. Evolutionary direction of processed pseudogenes.

    PubMed

    Liu, Guoqing; Cui, Xiangjun; Li, Hong; Cai, Lu

    2016-08-01

    While some pseudogenes have been reported to play important roles in gene regulation, little is known about the possible relationship between pseudogene functions and evolutionary process of pseudogenes, or about the forces responsible for the pseudogene evolution. In this study, we characterized human processed pseudogenes in terms of evolutionary dynamics. Our results show that pseudogenes tend to evolve toward: lower GC content, strong dinucleotide bias, reduced abundance of transcription factor binding motifs and short palindromes, and decreased ability to form nucleosomes. We explored possible evolutionary forces that shaped the evolution pattern of pseudogenes, and concluded that mutations in pseudogenes are likely determined, at least partially, by neighbor-dependent mutational bias and recombination-associated selection. PMID:27333782

  6. Enhanced Photoelectrochemical Proximity Assay for Highly Selective Protein Detection in Biological Matrixes.

    PubMed

    Wen, Guangming; Ju, Huangxian

    2016-08-16

    This work proposes the first photoelectrochemical proximity assay (PECPA) method via the sensitization of CdTe quantum dots (QDs) on photoelectrochemical response of ITO/TiO2/CdS electrode for highly selective and sensitive detection of proteins. This detection was performed on a sensing interface formed via the hybridization of capture DNA immobilized on ITO/TiO2/CdS electrode with labeled antibody-DNA (DNA-Ab1). Upon the recognition of Ab1 to target protein, the immunocomplex of DNA-Ab1, target, and the detection antibody-DNA (DNA-Ab2) was formed, which led to the proximity hybridization of the DNA in DNA-Ab2, capture DNA, and signal DNA-CdTe QDs, and brought CdTe QDs to the ITO/TiO2/CdS electrode to produce a sensitized photocurrent. The photocurrent intensity increased with the increasing concentration of the specific target protein. Using insulin as a target, this sensitized method showed a detectable range of 10 fM to 10 nM and a detection limit of 3.0 fM without the need of a washing step. It possessed high selectivity and good accuracy for detection of proteins in biological matrixes. This method is extremely flexible and can be extended to varieties of protein targets. PMID:27464227

  7. Feature Transformation Detection Method with Best Spectral Band Selection Process for Hyper-spectral Imaging

    NASA Astrophysics Data System (ADS)

    Chen, Hai-Wen; McGurr, Mike; Brickhouse, Mark

    2015-11-01

    We present a newly developed feature transformation (FT) detection method for hyper-spectral imagery (HSI) sensors. In essence, the FT method, by transforming the original features (spectral bands) to a different feature domain, may considerably increase the statistical separation between the target and background probability density functions, and thus may significantly improve the target detection and identification performance, as evidenced by the test results in this paper. We show that by differentiating the original spectral, one can completely separate targets from the background using a single spectral band, leading to perfect detection results. In addition, we have proposed an automated best spectral band selection process with a double-threshold scheme that can rank the available spectral bands from the best to the worst for target detection. Finally, we have also proposed an automated cross-spectrum fusion process to further improve the detection performance in lower spectral range (<1000 nm) by selecting the best spectral band pair with multivariate analysis. Promising detection performance has been achieved using a small background material signature library for concept-proving, and has then been further evaluated and verified using a real background HSI scene collected by a HYDICE sensor.

  8. Selective Detection of Peptide-Oligonucleotide Heteroconjugates Utilizing Capillary HPLC-ICPMS

    NASA Astrophysics Data System (ADS)

    Catron, Brittany; Caruso, Joseph A.; Limbach, Patrick A.

    2012-06-01

    A method for the selective detection and quantification of peptide:oligonucleotide heteroconjugates, such as those generated by protein:nucleic acid cross-links, using capillary reversed-phase high performance liquid chromatography (cap-RPHPLC) coupled with inductively coupled plasma mass spectrometry detection (ICPMS) is described. The selective detection of phosphorus as 31P+, the only natural isotope, in peptide-oligonucleotide heteroconjugates is enabled by the elemental detection capabilities of the ICPMS. Mobile phase conditions that allow separation of heteroconjugates while maintaining ICPMS compatibility were investigated. We found that trifluoroacetic acid (TFA) mobile phases, used in conventional peptide separations, and hexafluoroisopropanol/triethylamine (HFIP/TEA) mobile phases, used in conventional oligonucleotide separations, both are compatible with ICPMS and enable heteroconjugate separation. The TFA-based separations yielded limits of detection (LOD) of ~40 ppb phosphorus, which is nearly seven times lower than the LOD for HFIP/TEA-based separations. Using the TFA mobile phase, 1-2 pmol of a model heteroconjugate were routinely separated and detected by this optimized capLC-ICPMS method.

  9. Development of a selective agar plate for the detection of Campylobacter spp. in fresh produce.

    PubMed

    Yoo, Jin-Hee; Choi, Na-Young; Bae, Young-Min; Lee, Jung-Su; Lee, Sun-Young

    2014-10-17

    This study was conducted to develop a selective medium for the detection of Campylobacter spp. in fresh produce. Campylobacter spp. (n=4), non-Campylobacter (showing positive results on Campylobacter selective agar) strains (n=49) isolated from fresh produce, indicator bacteria (n=13), and spoilage bacteria isolated from fresh produce (n=15) were plated on four Campylobacter selective media. Bolton agar and modified charcoal cefoperazone deoxycholate agar (mCCDA) exhibited higher sensitivity for Campylobacter spp. than did Preston agar and Hunt agar, although certain non-Campylobacter strains isolated from fresh produce by using a selective agar isolation method, were still able to grow on Bolton agar and mCCDA. To inhibit the growth of non-Campylobacter strains, Bolton agar and mCCDA were supplemented with 5 antibiotics (rifampicin, polymyxin B, sodium metabisulfite, sodium pyruvate, ferrous sulfate) and the growth of Campylobacter spp. (n=7) and non-Campylobacter strains (n=44) was evaluated. Although Bolton agar supplemented with rifampicin (BR agar) exhibited a higher selectivity for Campylobacter spp. than did mCCDA supplemented with antibiotics, certain non-Campylobacter strains were still able to grow on BR agar (18.8%). When BR agar with various concentrations of sulfamethoxazole-trimethoprim were tested with Campylobacter spp. (n=8) and non-Campylobacter (n=7), sulfamethoxazole-trimethoprim was inhibitory against 3 of 7 non-Campylobacter strains. Finally, we validated the use of BR agar containing 50mg/L sulfamethoxazole (BRS agar) or 0.5mg/L ciprofloxacin (BRCS agar) and other selective agars for the detection of Campylobacter spp. in chicken and fresh produce. All chicken samples were positive for Campylobacter spp. when tested on mCCDA, BR agar, and BRS agar. In fresh produce samples, BRS agar exhibited the highest selectivity for Campylobacter spp., demonstrating its suitability for the detection of Campylobacter spp. in fresh produce. PMID:25126968

  10. Reactive chromophores for sensitive and selective detection of chemical warfare agents and toxic industrial chemicals

    NASA Astrophysics Data System (ADS)

    Frye-Mason, Greg; Leuschen, Martin; Wald, Lara; Paul, Kateri; Hancock, Lawrence F.

    2005-05-01

    A reactive chromophore developed at MIT exhibits sensitive and selective detection of surrogates for G-class nerve agents. This reporter acts by reacting with the agent to form an intermediate that goes through an internal cyclization reaction. The reaction locks the molecule into a form that provides a strong fluorescent signal. Using a fluorescent sensor platform, Nomadics has demonstrated rapid and sensitive detection of reactive simulants such as diethyl chloro-phosphate (simulant for sarin, soman, and related agents) and diethyl cyanophosphate (simulant for tabun). Since the unreacted chromophore does not fluoresce at the excitation wavelength used for the cyclized reporter, the onset of fluo-rescence can be easily detected. This fluorescence-based detection method provides very high sensitivity and could enable rapid detection at permissible exposure levels. Tests with potential interferents show that the reporter is very selective, with responses from only a few highly toxic, electrophilic chemicals such as phosgene, thionyl chloride, and strong acids such as HF, HCl, and nitric acid. Dimethyl methyl phosphonate (DMMP), a common and inactive simu-lant for other CW detectors, is not reactive enough to generate a signal. The unique selectivity to chemical reactivity means that a highly toxic and hazardous chemical is present when the reporter responds and illustrates that this sensor can provide very low false alarm rates. Current efforts focus on demonstrating the sensitivity and range of agents and toxic industrial chemicals detected with this reporter as well as developing additional fluorescent reporters for a range of chemical reactivity classes. The goal is to produce a hand-held sensor that can sensitively detect a broad range of chemical warfare agent and toxic industrial chemical threats.

  11. Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected “sword” out of a caudal fin

    PubMed Central

    Kang, Ji Hyoun; Manousaki, Tereza; Franchini, Paolo; Kneitz, Susanne; Schartl, Manfred; Meyer, Axel

    2015-01-01

    Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the “sword genes” those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the “older” gonopodium than in the “younger,” and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails. PMID:25750712

  12. Selection of Ceratitis capitata (Diptera: Tephritidae) Specific Recombinant Monoclonal Phage Display Antibodies for Prey Detection Analysis

    PubMed Central

    Monzó, César; Urbaneja, Alberto; Ximénez-Embún, Miguel; García-Fernández, Julia; García, José Luis; Castañera, Pedro

    2012-01-01

    Several recombinant antibodies against the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), one of the most important pests in agriculture worldwide, were selected for the first time from a commercial phage display library of human scFv antibodies. The specificity and sensitivity of the selected recombinant antibodies were compared with that of a rabbit polyclonal serum raised in parallel using a wide range of arthropod species as controls. The selected recombinant monoclonal antibodies had a similar or greater specificity when compared with classical monoclonal antibodies. The selected recombinant antibodies were successfully used to detect the target antigen in the gut of predators and the scFv antibodies were sequenced and compared. These results demonstrate the potential for recombinant scFv antibodies to be used as an alternative to the classical monoclonal antibodies or even molecular probes in the post-mortem analysis studies of generalist predators. PMID:23272105

  13. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.

    PubMed

    Pérez-Losada, Marcos; Arenas, Miguel; Galán, Juan Carlos; Palero, Ferran; González-Candelas, Fernando

    2015-03-01

    Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure. PMID:25541518

  14. Leveraging zinc interstitials and oxygen vacancies for sensitive biomolecule detection through selective surface functionalization

    NASA Astrophysics Data System (ADS)

    Radha Shanmugam, Nandhinee; Muthukumar, Sriram; Chaudhry, Shajee; Prasad, Shalini

    2015-03-01

    In this study, functionally engineered EIS technique was implemented to investigate the influence of surface functionalization on sensitivity of biomolecule detection using nanostructured ZnO platform. Organic molecules with thiol and carboxylic functional groups were chosen to control biomolecule immobilization on zinc and oxygen-terminated 2D planar and 1D nanostructured ZnO surfaces. The amount of functionalization and its influence on charge perturbations at the ZnO-electrolyte interface were studied using fluorescence and EIS measurements. We observed the dependence of charge transfer on both the polarity of platform and concentration of cross-linker molecules. Such selectively modified surfaces were used for detection of cortisol, a major stress indicator. Results demonstrated preferential binding of thiol groups to Zn terminations and thus leveraging ZnO interstitials increases the sensitivity of detection over larger dynamic range with detection limit at 10fg/mL.

  15. Selective detection of homocysteine by laser desorption/ionization mass spectrometry.

    PubMed

    Su, Chih-Lin; Tseng, Wei-Lung

    2006-01-01

    This article describes the use of 2,3-naphthalenedicarboxaldehyde (NDA) as a selective probe for the determination of homocysteine (HCys) via fluorescence measurement and laser desorption/ionization mass spectrometry (LDI-MS). The derivatives of three aminothiols-HCys, glutathione (GSH), and gamma-glutamylcysteine (gamma-Glu-Cys)-with NDA under alkaline conditions possess different fluorescence emission characteristics, which allow us to identify them from amines, amino acids, and thiols. By selecting appropriate pH and excitation wavelengths, the limits of detection (LODs) at a signal-to-noise ratio of 3 were 5.2, 1.4 and 16 nM for HCys, GSH and gamma-Glu-Cys, respectively. Additionally, strong UV absorption of the NDA-HCys derivative was further observed at 331 nm; it could be directly detected by LDI-MS with a 337-nm nitrogen laser. Selective detection of HCys has been achieved by conducting the LDI-MS of the NDA-HCys derivative, which was found at m/z 406.9. The lowest detectable concentration of the NDA-HCys derivative in this approach was 500 nM. Quantitative determination of HCys in urine samples was accomplished by LDI-MS. Also, a calibration curve was created from plasma samples spiked with standard HCys (20-100 microM). The experimental results suggest that our proposed methods have great potential in clinical diagnosis and metabolomics application. PMID:17044125

  16. A ROC-based feature selection method for computer-aided detection and diagnosis

    NASA Astrophysics Data System (ADS)

    Wang, Songyuan; Zhang, Guopeng; Liao, Qimei; Zhang, Junying; Jiao, Chun; Lu, Hongbing

    2014-03-01

    Image-based computer-aided detection and diagnosis (CAD) has been a very active research topic aiming to assist physicians to detect lesions and distinguish them from benign to malignant. However, the datasets fed into a classifier usually suffer from small number of samples, as well as significantly less samples available in one class (have a disease) than the other, resulting in the classifier's suboptimal performance. How to identifying the most characterizing features of the observed data for lesion detection is critical to improve the sensitivity and minimize false positives of a CAD system. In this study, we propose a novel feature selection method mR-FAST that combines the minimal-redundancymaximal relevance (mRMR) framework with a selection metric FAST (feature assessment by sliding thresholds) based on the area under a ROC curve (AUC) generated on optimal simple linear discriminants. With three feature datasets extracted from CAD systems for colon polyps and bladder cancer, we show that the space of candidate features selected by mR-FAST is more characterizing for lesion detection with higher AUC, enabling to find a compact subset of superior features at low cost.

  17. New adaptive branch and bound algorithm for hyperspectral waveband selection for chicken skin tumor detection

    NASA Astrophysics Data System (ADS)

    Nakariyakul, Songyot; Casasent, David

    2006-10-01

    Detection of skin tumors on chicken carcasses is considered. A chicken skin tumor consists of an ulcerous lesion region surrounded by a region of thickened-skin. We use a new adaptive branch-and-bound (ABB) feature selection algorithm to choose only a few useful wavebands from hyperspectral data for use in a real-time multispectral camera. The ABB algorithm selects an optimal feature subset and is shown to be much faster than any other versions of the branch and bound algorithm. We found that the spectral responses of the lesion and the thickened-skin regions of tumors are considerably different; thus we train our feature selection algorithm to separately detect the lesion regions and thickened-skin regions of tumors. We then fuse the two HS detection results of lesion and thickened-skin regions to reduce false alarms. Initial results on six hyperspectral cubes show that our method gives an excellent tumor detection rate and a low false alarm rate.

  18. Polymer-oligopeptide composite coating for selective detection of explosives in water.

    PubMed

    Cerruti, Marta; Jaworski, Justyn; Raorane, Digvijay; Zueger, Chris; Varadarajan, John; Carraro, Carlo; Lee, Seung-Wuk; Maboudian, Roya; Majumdar, Arun

    2009-06-01

    The selective detection of a specific target molecule in a complex environment containing potential contaminants presents a significant challenge in chemical sensor development. Utilizing phage display techniques against trinitrotoluene (TNT) and dinitrotoluene (DNT) targets, peptide receptors have previously been identified with selective binding capabilities for these molecules. For practical applications, these receptors must be immobilized onto the surface of sensor platforms at high density while maintaining their ability to bind target molecules. In this paper, a polymeric matrix composed of poly(ethylene-co-glycidyl methacrylate) (PEGM) has been prepared. A high density of receptors was covalently linked through reaction of amino groups present in the receptor with epoxy groups present in the co-polymer. Using X-ray photoelectron spectroscopy (XPS) and gas-chromatography/mass spectroscopy (GC/MS), this attachment strategy is demonstrated to lead to stably bound receptors, which maintain their selective binding ability for TNT. The TNT receptor/PEGM conjugates retained 10-fold higher TNT binding ability in liquid compared to the lone PEGM surface and 3-fold higher TNT binding compared to non-specific receptor conjugates. In contrast, non-target DNT exposure yielded undetectable levels of binding. These results indicate that this polymeric construct is an effective means of facilitating selective target interaction both in an aqueous environment. Finally, real-time detection experiments were performed using a quartz crystal microbalance (QCM) as the sensing platform. Selective detection of TNT vs DNT was demonstrated using QCM crystals coated with PEGM/TNT receptor, highlighting that this receptor coating can be incorporated as a sensing element in a standard detection device for practical applications. PMID:19476386

  19. Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps.

    PubMed

    Garud, Nandita R; Rosenberg, Noah A

    2015-06-01

    Soft selective sweeps represent an important form of adaptation in which multiple haplotypes bearing adaptive alleles rise to high frequency. Most statistical methods for detecting selective sweeps from genetic polymorphism data, however, have focused on identifying hard selective sweeps in which a favored allele appears on a single haplotypic background; these methods might be underpowered to detect soft sweeps. Among exceptions is the set of haplotype homozygosity statistics introduced for the detection of soft sweeps by Garud et al. (2015). These statistics, examining frequencies of multiple haplotypes in relation to each other, include H12, a statistic designed to identify both hard and soft selective sweeps, and H2/H1, a statistic that conditional on high H12 values seeks to distinguish between hard and soft sweeps. A challenge in the use of H2/H1 is that its range depends on the associated value of H12, so that equal H2/H1 values might provide different levels of support for a soft sweep model at different values of H12. Here, we enhance the H12 and H2/H1 haplotype homozygosity statistics for selective sweep detection by deriving the upper bound on H2/H1 as a function of H12, thereby generating a statistic that normalizes H2/H1 to lie between 0 and 1. Through a reanalysis of resequencing data from inbred lines of Drosophila, we show that the enhanced statistic both strengthens interpretations obtained with the unnormalized statistic and leads to empirical insights that are less readily apparent without the normalization. PMID:25891325

  20. Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection.

    PubMed

    Lucotte, Elise A; Laurent, Romain; Heyer, Evelyne; Ségurel, Laure; Toupance, Bruno

    2016-01-01

    Sexually antagonistic (SA) selection, a form of selection that can occur when both sexes have different fitness optima for a trait, is a major force shaping the evolution of organisms. A seminal model developed by Rice (Rice WR. 1984. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38:735-742.) predicts that the X chromosome should be a hotspot for the accumulation of loci under SA selection as compared with the autosomes. Here, we propose a methodological framework designed to detect a specific signature of SA selection on viability, differences in allelic frequencies between the sexes. Applying this method on genome-wide single nucleotide polymorphism (SNP) data in human populations where no sex-specific population stratification could be detected, we show that there are overall significantly more SNPs exhibiting differences in allelic frequencies between the sexes on the X chromosome as compared with autosomes, supporting the predictions of Rice's model. This pattern is consistent across populations and is robust to correction for potential biases such as differences in linkage disequilibrium, sample size, and genotyping errors between chromosomes. Although SA selection is not the only factor resulting in allelic frequency differences between the sexes, we further show that at least part of the identified X-linked loci is caused by such a sex-specific processes. PMID:27189992

  1. Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection

    PubMed Central

    Lucotte, Elise A.; Laurent, Romain; Heyer, Evelyne; Ségurel, Laure; Toupance, Bruno

    2016-01-01

    Sexually antagonistic (SA) selection, a form of selection that can occur when both sexes have different fitness optima for a trait, is a major force shaping the evolution of organisms. A seminal model developed by Rice (Rice WR. 1984. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38:735–742.) predicts that the X chromosome should be a hotspot for the accumulation of loci under SA selection as compared with the autosomes. Here, we propose a methodological framework designed to detect a specific signature of SA selection on viability, differences in allelic frequencies between the sexes. Applying this method on genome-wide single nucleotide polymorphism (SNP) data in human populations where no sex-specific population stratification could be detected, we show that there are overall significantly more SNPs exhibiting differences in allelic frequencies between the sexes on the X chromosome as compared with autosomes, supporting the predictions of Rice’s model. This pattern is consistent across populations and is robust to correction for potential biases such as differences in linkage disequilibrium, sample size, and genotyping errors between chromosomes. Although SA selection is not the only factor resulting in allelic frequency differences between the sexes, we further show that at least part of the identified X-linked loci is caused by such a sex-specific processes. PMID:27189992

  2. Highly selective detection of oil spill polycyclic aromatic hydrocarbons using molecularly imprinted polymers for marine ecosystems.

    PubMed

    Krupadam, Reddithota J; Nesterov, Evgueni E; Spivak, David A

    2014-06-15

    Im*plications due to oil spills on marine ecosystems have created a great interest toward developing more efficient and selective materials for oil spill toxins detection and remediation. This research paper highlights the application of highly efficient molecularly imprinted polymer (MIP) adsorbents based on a newly developed functional crosslinker (N,O-bismethacryloyl ethanolamine, NOBE) for detection of highly toxic polycyclic aromatic hydrocarbons (PAHs) in seawater. The binding capacity of MIP for oil spill toxin pyrene is 35 mg/g as compared to the value of 3.65 mg/g obtained using a non-imprinted polymer (NIP). The selectivity of all three high molecular weight PAHs (pyrene, chrysene and benzo[a]pyrene) on the NOBE-MIP shows an excellent selective binding with only 5.5% and 7% cross-reactivity for chrysene and benzo[a]pyrene, respectively. Not only is this particularly significant because the rebinding solvent is water, which is known to promote non-selective hydrophobic interactions; the binding remains comparable under salt-water conditions. These selective and high capacity adsorbents will find wide application in industrial and marine water monitoring/remediation. PMID:24759433

  3. Contrast based band selection for optimized weathered oil detection in hyperspectral images

    NASA Astrophysics Data System (ADS)

    Levaux, Florian; Bostater, Charles R., Jr.; Neyt, Xavier

    2012-09-01

    Hyperspectral imagery offers unique benefits for detection of land and water features due to the information contained in reflectance signatures such as the bi-directional reflectance distribution function or BRDF. The reflectance signature directly shows the relative absorption and backscattering features of targets. These features can be very useful in shoreline monitoring or surveillance applications, for example to detect weathered oil. In real-time detection applications, processing of hyperspectral data can be an important tool and Optimal band selection is thus important in real time applications in order to select the essential bands using the absorption and backscatter information. In the present paper, band selection is based upon the optimization of target detection using contrast algorithms. The common definition of the contrast (using only one band out of all possible combinations available within a hyperspectral image) is generalized in order to consider all the possible combinations of wavelength dependent contrasts using hyperspectral images. The inflection (defined here as an approximation of the second derivative) is also used in order to enhance the variations in the reflectance spectra as well as in the contrast spectrua in order to assist in optimal band selection. The results of the selection in term of target detection (false alarms and missed detection) are also compared with a previous method to perform feature detection, namely the matched filter. In this paper, imagery is acquired using a pushbroom hyperspectral sensor mounted at the bow of a small vessel. The sensor is mechanically rotated using an optical rotation stage. This opto-mechanical scanning system produces hyperspectral images with pixel sizes on the order of mm to cm scales, depending upon the distance between the sensor and the shoreline being monitored. The motion of the platform during the acquisition induces distortions in the collected HSI imagery. It is therefore

  4. Validation of the ANSR® Listeria Method for Detection of Listeria spp. in Selected Foods.

    PubMed

    Caballero, Oscar; Alles, Susan; Wendorf, Michael; Gray, R Lucas; Walton, Kayla; Pinkava, Lisa; Mozola, Mark; Rice, Jennifer

    2015-01-01

    ANSR® Listeria was previously certified as Performance Tested Method(SM) 101202 for detection of Listeria spp. on selected environmental surfaces. This study proposes a matrix extension to the method for detection of Listeria spp. in selected food matrixes. The method is an isothermal nucleic acid amplification assay based on the nicking enzyme amplification reaction technology. Following single-step sample enrichment for 16-24 h, the assay is completed in less than 50 min, requiring only simple instrumentation. Inclusivity testing was performed using a panel of 51 strains of Listeria spp., representing the species L. grayi, L. innocua, L. ivanovii, L. monocytogenes, L. seeligeri, and L. welshimeri. All strains tested were detected by the ANSR assay. Exclusivity testing of 30 strains representing non-Listeria Gram-positive bacteria yielded no evidence of cross-reactivity. Performance of the ANSR method for detection of Listeria spp. was compared to that of reference culture procedures for pasteurized liquid egg, pasteurized 2% milk, Mexican-style cheese, ice cream, smoked salmon, lettuce, cantaloupe, and guacamole. Data obtained in these unpaired studies and analyzed using a probability of detection model demonstrated that there were no statistically significant differences in results between the ANSR and reference culture methods, except for milk at 16 h and cantaloupe. In milk and smoked salmon, ANSR sensitivity was low at 16 h and therefore the recommended incubation time is 24 h. In cantaloupe, ANSR was found to be more sensitive than the reference culture method at both 16 and 24 h in independent laboratory testing. The ANSR Listeria method can be used as an accurate, rapid, and simple alternative to standard culture methods for detection of Listeria spp. in selected food types. PMID:26525248

  5. Algorithmic Mechanism Design of Evolutionary Computation

    PubMed Central

    Pei, Yan

    2015-01-01

    We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

  6. Algorithmic Mechanism Design of Evolutionary Computation.

    PubMed

    Pei, Yan

    2015-01-01

    We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

  7. A ratiometric fluorescence nanosensor for highly selective and sensitive detection of selenite.

    PubMed

    Chen, Linfeng; Tian, Xike; Zhao, Yuan; Li, Yong; Yang, Chao; Zhou, Zhaoxin; Liu, Xiangwen

    2016-08-01

    The instant and on-site detection of selenium still remains a challenge for environmental monitoring and medical prevention. We herein developed a ratiometric fluorescent nanosensor for accurate and on-site sensing of SeO3(2-) by linking the recognition molecule 3,3'-diaminobenzidine (DAB) onto the surface of carboxyl group modified CdTe@SiO2. The fluorescence of DAB on the surface of silica nanospheres could be selectively and efficiently enhanced by SeO3(2-) through a surface chelating reaction between DAB and SeO3(2-). Thus, in the presence of SeO3(2-), the nanosensor would show two characteristic fluorescence emissions of Se-DAB and CdTe QDs under a single excitation wavelength. The selectivity and the optimal conditions for the detection of SeO3(2-) were carefully investigated. The ratio of F530/F635 linearly increased with increasing SeO3(2-) concentration in the range of 0 to 2.5 μM and the detection limit reaches as low as 6.68 nM (0.53 ppb). This developed nanosensor has the capability of on-site detection in an aqueous system without any separation step. The Se concentrations in selenium-rich food were detected and the results were consistent with the values determined by ICP-AES. PMID:27241591

  8. Label-free and selective photoelectrochemical detection of chemical DNA methylation damage using DNA repair enzymes.

    PubMed

    Wu, Yiping; Zhang, Bintian; Guo, Liang-Hong

    2013-07-16

    Exogenous chemicals may produce DNA methylation that is potentially toxic to living systems. Methylated DNA bases are difficult to detect with biosensors because the methyl group is small and chemically inert. In this report, a label-free photoelectrochemical sensor was developed for the selective detection of chemically methylated bases in DNA films. The sensor employed two DNA repair enzymes, human alkyladenine DNA glycosylase and human apurinic/apyrimidinic endonuclease, to convert DNA methylation sites in DNA films on indium tin oxide electrodes into strand breaks. A DNA intercalator, Ru(bpy)2(dppz)(2+) (bpy=2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine) was then used as the photoelectrochemical signal indicator to detect the DNA strand breaks. Its photocurrent signal was found to correlate inversely with the amount of 3-methyladenines (metAde) produced with a methylating agent, methylmethane sulfonate (MMS). The sensor detected the methylated bases produced with as low as 1 mM MMS, at which concentration the amount of metAde on the sensor surface was estimated to be 0.5 pg, or 1 metAde in 1.6 × 10(5) normal bases. Other DNA base modification products, such as 5-methylcytosine and DNA adducts with ethyl and styrene groups did not attenuate the photocurrent, demonstrating good selectivity of the sensor. This strategy can be utilized to develop sensors for the detection of other modified DNA bases with specific DNA repair enzymes. PMID:23777269

  9. Feature selection and classifier parameters estimation for EEG signals peak detection using particle swarm optimization.

    PubMed

    Adam, Asrul; Shapiai, Mohd Ibrahim; Tumari, Mohd Zaidi Mohd; Mohamad, Mohd Saberi; Mubin, Marizan

    2014-01-01

    Electroencephalogram (EEG) signal peak detection is widely used in clinical applications. The peak point can be detected using several approaches, including time, frequency, time-frequency, and nonlinear domains depending on various peak features from several models. However, there is no study that provides the importance of every peak feature in contributing to a good and generalized model. In this study, feature selection and classifier parameters estimation based on particle swarm optimization (PSO) are proposed as a framework for peak detection on EEG signals in time domain analysis. Two versions of PSO are used in the study: (1) standard PSO and (2) random asynchronous particle swarm optimization (RA-PSO). The proposed framework tries to find the best combination of all the available features that offers good peak detection and a high classification rate from the results in the conducted experiments. The evaluation results indicate that the accuracy of the peak detection can be improved up to 99.90% and 98.59% for training and testing, respectively, as compared to the framework without feature selection adaptation. Additionally, the proposed framework based on RA-PSO offers a better and reliable classification rate as compared to standard PSO as it produces low variance model. PMID:25243236

  10. Feature Selection and Classifier Parameters Estimation for EEG Signals Peak Detection Using Particle Swarm Optimization

    PubMed Central

    Adam, Asrul; Mohd Tumari, Mohd Zaidi; Mohamad, Mohd Saberi

    2014-01-01

    Electroencephalogram (EEG) signal peak detection is widely used in clinical applications. The peak point can be detected using several approaches, including time, frequency, time-frequency, and nonlinear domains depending on various peak features from several models. However, there is no study that provides the importance of every peak feature in contributing to a good and generalized model. In this study, feature selection and classifier parameters estimation based on particle swarm optimization (PSO) are proposed as a framework for peak detection on EEG signals in time domain analysis. Two versions of PSO are used in the study: (1) standard PSO and (2) random asynchronous particle swarm optimization (RA-PSO). The proposed framework tries to find the best combination of all the available features that offers good peak detection and a high classification rate from the results in the conducted experiments. The evaluation results indicate that the accuracy of the peak detection can be improved up to 99.90% and 98.59% for training and testing, respectively, as compared to the framework without feature selection adaptation. Additionally, the proposed framework based on RA-PSO offers a better and reliable classification rate as compared to standard PSO as it produces low variance model. PMID:25243236

  11. Ultra-sensitive and selective Hg{sup 2+} detection based on fluorescent carbon dots

    SciTech Connect

    Liu, Ruihua; Li, Haitao; Kong, Weiqian; Liu, Juan; Liu, Yang; Tong, Cuiyan; Zhang, Xing; Kang, Zhenhui

    2013-07-15

    Graphical abstract: Fluorescent carbon dots were efficiently synthesized by one-step sodium hydroxide-assisted reflux method from PEG and demonstrated to show high selectivity toward Hg2+ ions detection. - Highlights: • FCDs were synthesized by one-step sodium hydroxide-assisted reflux method from PEG. • The FCDs emit blue photoluminescence and have upconversion fluorescent property. • The FCDs show ultra-sensitive detective ability for Hg{sup 2+} ions. - Abstract: Fluorescent carbon dots (FCDs) were efficiently synthesized by one-step sodium hydroxide-assisted reflux method from poly(ethylene glycol) (PEG). The obtained FCDs exhibit excellent water-solubility and high stability. Under the UV irradiation, the FCDs could emit bright blue photoluminescence, and also they were found to show excellent up-conversion fluorescence. It was further demonstrated that such FCDs can serve as effective fluorescent sensing platform for Hg{sup 2+} ions detection with ultra-sensitivity and selectivity. The sensing system achieved a limit of detection as low as 1 fM, which is much lower than all the previous reported sensing systems for Hg{sup 2+} ions detection. This FCDs sensing system has been successfully applied for the analysis of Hg{sup 2+} ions in water samples from river, lake, and tap water, showing good practical feasibility.

  12. FTIR gas analysis with improved sensitivity and selectivity for CWA and TIC detection

    NASA Astrophysics Data System (ADS)

    Phillips, Charles M.; Tan, Huwei

    2010-04-01

    This presentation describes the use of an FTIR (Fourier Transform Infrared)-based spectrometer designed to continuously monitor ambient air for the presence of chemical warfare agents (CWAs) and toxic industrial chemicals (TICs). The necessity of a reliable system capable of quickly and accurately detecting very low levels of CWAs and TICs while simultaneously retaining a negligible false alarm rate will be explored. Technological advancements in FTIR sensing have reduced noise while increasing selectivity and speed of detection. These novel analyzer design characteristics are discussed in detail and descriptions are provided which show how optical throughput, gas cell form factor, and detector response are optimized. The hardware and algorithms described here will explain why this FTIR system is very effective for the simultaneous detection and speciation of a wide variety of toxic compounds at ppb concentrations. Analytical test data will be reviewed demonstrating the system's sensitivity to and selectivity for specific CWAs and TICs; this will include recent data acquired as part of the DHS ARFCAM (Autonomous Rapid Facility Chemical Agent Monitor) project. These results include analyses of the data from live agent testing for the determination of CWA detection limits, immunity to interferences, detection times, residual noise analysis and false alarm rates. Sensing systems such as this are critical for effective chemical hazard identification which is directly relevant to the CBRNE community.

  13. Ecological aspects of the evolutionary processes.

    PubMed

    Bock, Walter J

    2003-03-01

    Darwin in his On the Origin of species made it clear that evolutionary change depends on the combined action of two different causes, the first being the origin of genetically based phenotypic variation in the individual organisms comprising the population and the second being the action of selective agents of the external environment placing demands on the individual organisms. For over a century following Darwin, most evolutionists focused on the origin of inherited variation and its transmission; many workers continue to regard genetics to be the core of evolutionary theory. Far less attention has been given to the exact nature of the selective agents with most evolutionists still treating this cause imprecisely to the detriment of our understanding of both nomological and historical evolutionary theory. Darwin was vague in the meaning of his new concept of "Natural Selection," using it interchangeably as one of the causes for evolutionary change and as the final outcome (= evolutionary change). In 1930, natural selection was defined clearly as "non-random, differential reproduction of genes" by R. Fisher and J.B.S. Haldane which is a statement of the outcome of evolutionary process and which omits mention of the causes bringing about this change. Evolutionists quickly accepted this outcome definition of natural selection, and have used interchangeably selection both as a cause and as the result of evolutionary change, causing great confusion. Herein, the details will be discussed of how the external environment (i.e., the environment-phenotype interaction) serves as selective agents and exerts demands on the phenotypic organisms. Included are the concepts of fitness and of the components of fitness (= adaptations) which are respectively (a) survival, (b) direct reproductive and (c) indirect reproductive features. Finally, it will be argued that historical-narrative analyses of organisms, including classification and phylogenetic history, are possible only with

  14. Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides.

    PubMed

    Verga, Daniela; Welter, Moritz; Marx, Andreas

    2016-02-01

    DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye. PMID:26774580

  15. Selective fluorogenic and chromogenic probe for detection of silver ions and silver nanoparticles in aqueous media.

    PubMed

    Chatterjee, Amrita; Santra, Mithun; Won, Nayoun; Kim, Sungjee; Kim, Jae Kyung; Kim, Seung Bin; Ahn, Kyo Han

    2009-02-18

    A novel rhodamine-based fluorogenic and chromogenic probe for Ag(+) ions in aqueous media is developed, which can be also used for the detection of AgNPs. The sensing mechanism is based on irreversible tandem ring-opening and -forming processes promoted by Ag(+)-coordination to the iodide of the probe, which is accompanied by both color and turn-on type fluorescence changes. The probe shows remarkably high selectivity over other metal ions and detects silver ions up to 14 ppb. PMID:19159289

  16. Chloride accelerated Fenton chemistry for the ultrasensitive and selective colorimetric detection of copper.

    PubMed

    Shan, Zhi; Lu, Mingsheng; Wang, Li; MacDonald, Bruce; MacInnis, Judy; Mkandawire, Martin; Zhang, Xu; Oakes, Ken D

    2016-02-01

    A highly selective, ultrasensitive (visual and instrumental detection limits of 40 nM and 0.1 nM, respectively), environmentally-friendly, simple and rapid colorimetric sensor was developed for the detection of copper(II) in water. This sensor is based on a novel signal-amplification mechanism involving reactive halide species (RHSs) including chlorides or bromides, which accelerate copper Fenton reactions oxidizing the chromogenic substrate to develop colour. The results of this study expand our understanding of copper-based Fenton chemistry. PMID:26685747

  17. Selective detection of bacteria in urine with a long-range surface plasmon waveguide biosensor

    PubMed Central

    Béland, Paul; Krupin, Oleksiy; Berini, Pierre

    2015-01-01

    Experimentation demonstrates long-range surface plasmon polariton waveguides as a useful biosensor to selectively detect gram negative or gram positive bacteria in human urine having a low concentration of constituents. The biosensor can detect bacteria at concentrations of 105 CFU/ml, the internationally recommended threshold for diagnostic of urinary tract infection. Using a negative control urine solution of bacterial concentration 1000☓ higher than the targeted bacteria, we obtain a ratio of 5.4 for the positive to negative signals. PMID:26309755

  18. Fluorescent probes for the selective detection of chemical species inside mitochondria.

    PubMed

    Xu, Zheng; Xu, Lin

    2016-01-21

    During the last few years, the preparation of novel fluorescent probes for the selective detection of chemical species inside mitochondria has attracted considerable attention because of their wide applications in chemistry, biology, and medical science. This feature article focuses on the recent advances in the design principles and recognition mechanisms of these kinds of fluorescent probes. In addition, their applications for the detection of reactive oxygen species (ROS), nitric oxide, reactive sulfur species (RSS), thioredoxin (Trx), metal ions, anions, etc. in the mitochondrion is discussed as well. PMID:26621071

  19. Screening and selection of synthetic peptides for a novel and optimized endotoxin detection method.

    PubMed

    Mujika, M; Zuzuarregui, A; Sánchez-Gómez, S; Martínez de Tejada, G; Arana, S; Pérez-Lorenzo, E

    2014-09-30

    The current validated endotoxin detection methods, in spite of being highly sensitive, present several drawbacks in terms of reproducibility, handling and cost. Therefore novel approaches are being carried out in the scientific community to overcome these difficulties. Remarkable efforts are focused on the development of endotoxin-specific biosensors. The key feature of these solutions relies on the proper definition of the capture protocol, especially of the bio-receptor or ligand. The aim of the presented work is the screening and selection of a synthetic peptide specifically designed for LPS detection, as well as the optimization of a procedure for its immobilization onto gold substrates for further application to biosensors. PMID:25034430

  20. Liquid crystal-based sensors for selective and quantitative detection of nitrogen dioxide.

    PubMed

    Sen, Avijit; Kupcho, Kurt A; Grinwald, Bart A; Vantreeck, Heidi J; Acharya, Bharat R

    2013-03-01

    A highly sensitive nitrogen dioxide (NO2) sensor based on orientational transition of a thin film of liquid crystal (LC) supported on a gold surface is reported. Transport of NO2 molecules through the LC film to the LC-gold interface induces an orientation transition in the LC film. The dynamic behavior of the sensor response exhibits a concentration-dependent response rate that is employed to generate an algorithm for quantitative determination of unknown concentrations. Sensitive, selective and reversible detection with minimal effects of environmental fluctuations suggest that these sensors can be used for quantitative NO2 detection for a number of applications. PMID:23526230

  1. A highly selective fluorescent probe for direct detection and isolation of mouse embryonic stem cells.

    PubMed

    Chandran, Yogeswari; Kang, Nam-Young; Park, Sung-Jin; Alamudi, Samira Husen; Kim, Jun-Young; Sahu, Srikanta; Su, Dongdong; Lee, Jungyeol; Vendrell, Marc; Chang, Young-Tae

    2015-11-01

    Stem cell research has gathered immense attention in the past decade due to the remarkable ability of stem cells for self-renewal and tissue-specific differentiation. Despite having numerous advancements in stem cell isolation and manipulation techniques, there is a need for highly reliable probes for the specific detection of live stem cells. Herein we developed a new fluorescence probe (CDy9) with high selectivity for mouse embryonic stem cells. CDy9 allows the detection and isolation of intact stem cells with marginal impact on their function and capabilities. PMID:26115574

  2. The evolutionary genetics of canalization.

    PubMed

    Flatt, Thomas

    2005-09-01

    Evolutionary genetics has recently made enormous progress in understanding how genetic variation maps into phenotypic variation. However why some traits are phenotypically invariant despite apparent genetic and environmental changes has remained a major puzzle. In the 1940s, Conrad Hal Waddington coined the concept and term "canalization" to describe the robustness of phenotypes to perturbation; a similar concept was proposed by Waddington's contemporary Ivan Ivanovich Schmalhausen. This paper reviews what has been learned about canalization since Waddington. Canalization implies that a genotype's phenotype remains relatively invariant when individuals of a particular genotype are exposed to different environments (environmental canalization) or when individuals of the same single- or multilocus genotype differ in their genetic background (genetic canalization). Consequently, genetic canalization can be viewed as a particular kind of epistasis, and environmental canalization and phenotypic plasticity are two aspects of the same phenomenon. Canalization results in the accumulation of phenotypically cryptic genetic variation, which can be released after a "decanalizing" event. Thus, canalized genotypes maintain a cryptic potential for expressing particular phenotypes, which are only uncovered under particular decanalizing environmental or genetic conditions. Selection may then act on this newly released genetic variation. The accumulation of cryptic genetic variation by canalization may therefore increase evolvability at the population level by leading to phenotypic diversification under decanalizing conditions. On the other hand, under canalizing conditions, a major part of the segregating genetic variation may remain phenotypically cryptic; canalization may therefore, at least temporarily, constrain phenotypic evolution. Mechanistically, canalization can be understood in terms of transmission patterns, such as epistasis, pleiotropy, and genotype by environment

  3. Quantitative evolutionary design

    PubMed Central

    Diamond, Jared

    2002-01-01

    The field of quantitative evolutionary design uses evolutionary reasoning (in terms of natural selection and ultimate causation) to understand the magnitudes of biological reserve capacities, i.e. excesses of capacities over natural loads. Ratios of capacities to loads, defined as safety factors, fall in the range 1.2-10 for most engineered and biological components, even though engineered safety factors are specified intentionally by humans while biological safety factors arise through natural selection. Familiar examples of engineered safety factors include those of buildings, bridges and elevators (lifts), while biological examples include factors of bones and other structural elements, of enzymes and transporters, and of organ metabolic performances. Safety factors serve to minimize the overlap zone (resulting in performance failure) between the low tail of capacity distributions and the high tail of load distributions. Safety factors increase with coefficients of variation of load and capacity, with capacity deterioration with time, and with cost of failure, and decrease with costs of initial construction, maintenance, operation, and opportunity. Adaptive regulation of many biological systems involves capacity increases with increasing load; several quantitative examples suggest sublinear increases, such that safety factors decrease towards 1.0. Unsolved questions include safety factors of series systems, parallel or branched pathways, elements with multiple functions, enzyme reaction chains, and equilibrium enzymes. The modest sizes of safety factors imply the existence of costs that penalize excess capacities. Those costs are likely to involve wasted energy or space for large or expensive components, but opportunity costs of wasted space at the molecular level for minor components. PMID:12122135

  4. Selectable Ultrasensitive Detection of Hg2+ with Rhodamine 6G-Modified Nanoporous Gold Optical Sensor

    NASA Astrophysics Data System (ADS)

    Wang, Zheng; Yang, Min; Chen, Chao; Zhang, Ling; Zeng, Heping

    2016-07-01

    An extremely sensitive fluorescence sensor has been developed for selectively detection of mercury ions based on metallophilic Hg2+-Au+ interactions, which results in an effective release of pre-adsorbed rhodamine 6G (R6G) molecules from the nanoporous gold substrate, associated with a significant decrease of fluorescence intensity. The optical sensor has a detection sensitivity down to 0.6 pM for Hg2+ and CH3Hg+ ions, in particular a superior selectivity in a complex aqueous system containing 13 different types of metal ions, meanwhile maintaining a long-term stability after 10 cycles. Such a fluorescence sensor combining multiple advantages therefore present promising potentials in various applications.

  5. Rhodium Nanoparticle-mesoporous Silicon Nanowire Nanohybrids for Hydrogen Peroxide Detection with High Selectivity

    NASA Astrophysics Data System (ADS)

    Song, Zhiqian; Chang, Hucheng; Zhu, Weiqin; Xu, Chenlong; Feng, Xinjian

    2015-01-01

    Developing nanostructured electrocatalysts, with low overpotential, high selectivity and activity has fundamental and technical importance in many fields. We report here rhodium nanoparticle and mesoporous silicon nanowire (RhNP@mSiNW) hybrids for hydrogen peroxide (H2O2) detection with high electrocatalytic activity and selectivity. By employing electrodes that loaded with RhNP@mSiNW nanohybrids, interference caused from both many electroactive substances and dissolved oxygen were eliminated by electrochemical assaying at an optimal potential of +75 mV. Furthermore, the electrodes exhibited a high detection sensitivity of 0.53 μA/mM and fast response (< 5 s). This high-performance nanohybrid electrocatalyst has great potential for future practical application in various oxidase-base biosensors.

  6. Selectable Ultrasensitive Detection of Hg(2+) with Rhodamine 6G-Modified Nanoporous Gold Optical Sensor.

    PubMed

    Wang, Zheng; Yang, Min; Chen, Chao; Zhang, Ling; Zeng, Heping

    2016-01-01

    An extremely sensitive fluorescence sensor has been developed for selectively detection of mercury ions based on metallophilic Hg(2+)-Au(+) interactions, which results in an effective release of pre-adsorbed rhodamine 6G (R6G) molecules from the nanoporous gold substrate, associated with a significant decrease of fluorescence intensity. The optical sensor has a detection sensitivity down to 0.6 pM for Hg(2+) and CH3Hg(+) ions, in particular a superior selectivity in a complex aqueous system containing 13 different types of metal ions, meanwhile maintaining a long-term stability after 10 cycles. Such a fluorescence sensor combining multiple advantages therefore present promising potentials in various applications. PMID:27403721

  7. Oligomer-coated carbon nanotube chemiresistive sensors for selective detection of nitroaromatic explosives.

    PubMed

    Zhang, Yaqiong; Xu, Miao; Bunes, Benjamin R; Wu, Na; Gross, Dustin E; Moore, Jeffrey S; Zang, Ling

    2015-04-15

    High-performance chemiresistive sensors were made using a porous thin film of single-walled carbon nanotubes (CNTs) coated with a carbazolylethynylene (Tg-Car) oligomer for trace vapor detection of nitroaromatic explosives. The sensors detect low concentrations of 4-nitrotoluene (NT), 2,4,6-trinitrotoluene (TNT), and 2,4-dinitrotoluene (DNT) vapors at ppb to ppt levels. The sensors also show high selectivity to NT from other common organic reagents at significantly higher vapor concentrations. Furthermore, by using Tg-Car/CNT sensors and uncoated CNT sensors in parallel, differential sensing of NT, TNT, and DNT vapors was achieved. This work provides a methodology to create selective CNT-based sensors and sensor arrays. PMID:25823968

  8. Magnetically recoverable fluorescence chemosensor for the adsorption and selective detection of Hg2+ in water.

    PubMed

    Lv, Qiang; Li, Gang; Cheng, Zhuhong; Lu, Hong; Gao, Xiaoxia

    2014-01-01

    In order to conveniently and effectively detect the heavy metal ion Hg(2+) existing in water, a magnetic fluorescence chemosensor has been strategically prepared by immobilizing a Rhodamine B derivative RhB-tris(2-aminoethyl)amine on Fe3O4@SiO2-Au@PSiO2 composites via gold particles. The adsorption and detection for Hg(2+) ions were investigated with fluorophotometry. This chemosensor shows high sensitivity and high selectivity for Hg(2+) over other metal cations owing to the ring opening of the rhodamine fluorophore selectively induced by Hg(2+). In addition, the presence of Fe3O4 in the sensor also facilitates the magnetic separation of the Fe3O4@SiO2-Au-Hg(2+)@PSiO2 from the solution. PMID:24270323

  9. Selectable Ultrasensitive Detection of Hg2+ with Rhodamine 6G-Modified Nanoporous Gold Optical Sensor

    PubMed Central

    Wang, Zheng; Yang, Min; Chen, Chao; Zhang, Ling; Zeng, Heping

    2016-01-01

    An extremely sensitive fluorescence sensor has been developed for selectively detection of mercury ions based on metallophilic Hg2+-Au+ interactions, which results in an effective release of pre-adsorbed rhodamine 6G (R6G) molecules from the nanoporous gold substrate, associated with a significant decrease of fluorescence intensity. The optical sensor has a detection sensitivity down to 0.6 pM for Hg2+ and CH3Hg+ ions, in particular a superior selectivity in a complex aqueous system containing 13 different types of metal ions, meanwhile maintaining a long-term stability after 10 cycles. Such a fluorescence sensor combining multiple advantages therefore present promising potentials in various applications. PMID:27403721

  10. Rhodium Nanoparticle-mesoporous Silicon Nanowire Nanohybrids for Hydrogen Peroxide Detection with High Selectivity

    PubMed Central

    Song, Zhiqian; Chang, Hucheng; Zhu, Weiqin; Xu, Chenlong; Feng, Xinjian

    2015-01-01

    Developing nanostructured electrocatalysts, with low overpotential, high selectivity and activity has fundamental and technical importance in many fields. We report here rhodium nanoparticle and mesoporous silicon nanowire (RhNP@mSiNW) hybrids for hydrogen peroxide (H2O2) detection with high electrocatalytic activity and selectivity. By employing electrodes that loaded with RhNP@mSiNW nanohybrids, interference caused from both many electroactive substances and dissolved oxygen were eliminated by electrochemical assaying at an optimal potential of +75 mV. Furthermore, the electrodes exhibited a high detection sensitivity of 0.53 μA/mM and fast response (< 5 s). This high-performance nanohybrid electrocatalyst has great potential for future practical application in various oxidase-base biosensors. PMID:25588953

  11. A simple ratiometric and colorimetric chemosensor for the selective detection of fluoride in DMSO buffered solution

    NASA Astrophysics Data System (ADS)

    Niu, Hu; Shu, Qinghai; Jin, Shaohua; Li, Bingjun; Zhu, Jiaping; Li, Lijie; Chen, Shusen

    2016-01-01

    A derivative of squaramide (cyclobuta[b]quinoxaline-1, 2(3H, 8H)-dione) has been synthesized for the ratiometric and colorimetric sensing of F- in aqueous solution in competitive fashion. With F-, probe 1 showed a highly selective naked-eye detectable color change along with a characteristic UV-Vis absorbance over other tested ions, which probably originates from the deprotonation occurred between 1 and F-, as proved by the 1H NMR titration experiments and DFT calculations.

  12. A novel donor-acceptor receptor for selective detection of Pb2+ and Fe3+ ions.

    PubMed

    Nandre, Kamlakar P; Puyad, Avinash L; Bhosale, Sheshanath V; Bhosale, Sidhanath V

    2014-12-01

    An efficient and highly selective colorimetric and fluorescent receptor DTPDA has been synthesized for sensitive detection of Pb(2+) and Fe(3+) cations. The sensor DTPDA produces a facile, cost-effective and naked eye sensing platform to determine trace amounts of Pb(2+) and Fe(3+) metal ions by complexation with pendent S-termini of thiophenes, which commonly coordinates to central N-termini of pyridine. PMID:25159385

  13. Analyte-directed formation of emissive excimers for the selective detection of polyamines.

    PubMed

    Kim, Tae-Il; Kim, Youngmi

    2016-08-23

    A convenient and selective method for the sensing of polyamines, which are important biomarkers for cancers, has been developed. The fluorescence light-up mechanism utilizes the analyte-induced formation of emissive excimers of a sulfonated probe. Detection is achieved in aqueous media and artificial urine samples, as indicated by an excellent fluorescence turn-on signal with a large spectral shift. PMID:27501825

  14. An adapted modulation transfer function for x-ray backscatter radiography by selective detection

    NASA Astrophysics Data System (ADS)

    Sabri, Nissia; Dugan, Edward T.; Jacobs, Alan M.; Shedlock, Daniel

    2007-09-01

    The Modulation Transfer Function (MTF) is a quantitative function based on frequency resolution that characterizes imaging system performance. In this study, a new MTF methodology is investigated for application to Radiography by Selective Detection (RSD), an enhanced single-side x-ray Compton backscatter imaging (CBI) technique which detects selected scatter components. The RSD imaging modality is a unique type of real-time radiography that uses a set of fin and sleeve collimators to preferentially select different components of the x-ray backscattered field. Radiography by selective detection has performed successfully in different non-destructive evaluation (NDE) applications. A customized RSD imaging system was built at the University of Florida for inspection of the space shuttle external tank spray-on foam insulation (SOFI). The x-ray backscatter RSD imaging system has been successfully used for crack and corrosion detection in a variety of materials. The conventional transmission x-ray image quality characterization tools do not apply for RSD because of the different physical process involved. Thus, the main objective of this project is to provide an adapted tool for dynamic evaluation of RSD system image quality. For this purpose, an analytical model of the RSD imaging system response is developed and supported. Two approaches are taken for the MTF calculations: one using the Fourier Transform of a line spread function and the other one using a sine function pattern. Calibration and test targets are then designed according to this proposed model. A customized Matlab code using image contrast and digital curve recognition is developed to support the experimental data and provide the Modulation Transfer Functions for RSD.

  15. Interdigitated gate electrode field effect transistor for the selective detection of nitrogen dioxide and diisopropyl methylphosphonate

    SciTech Connect

    Kolesar, E.S. Jr.; Wiseman, J.M. )

    1989-11-01

    An interdigitated gate electrode field effect transistor (IGE-FET) coupled to an electron beam evaporated copper phthalocyanine thin film was used to selectively detect part-per-billion concentration levels of nitrogen dioxide (NO{sub 2}) and diisopropyl methylphosphonate (DIMP). The sensor is excited with a voltage pulse, and the time- and frequency-domain responses are measured. The envelopes of the magnitude of the normalized difference frequency spectrums reveal features that unambiguously distinguish NO{sub 2} and DIMP exposures.

  16. Rapid and highly selective chromogenic detection of nerve agents with a cleft-shaped host.

    PubMed

    Kumar, Vinod; Kaushik, Mahabir Parshad

    2011-12-21

    A new chromogenic protocol has been developed for rapid and selective detection of nerve agents like tabun. The chemsensor displayed a drastic color change from its colorless solution to yellow instantaneously with an 89 nm bathochromic shift. No inference of other chemical warfare agents and its mimics was observed either with the naked-eye or by UV-Vis spectroscopy. The development of a portable chemosensor kit for tabun demonstrates its practical application in real-time monitoring. PMID:22013586

  17. Selective Detection of Live Pathogens via Surface-Confined Electric Field Perturbation on Interdigitated Silicon Transducers

    PubMed Central

    de la Rica, Roberto; Baldi, Antonio; Fernández-Sánchez, César; Matsui, Hiroshi

    2010-01-01

    Detection of physical changes of cells is emerging as a new diagnostic approach to determine their phenotypical features. One of such changes is related to their viability; live (viable) cells are more voluminous than the dead ones, and monitoring this parameter in tissue cells becomes essential in fields such as drug discovery and hazard evaluation. In the area of pathogen detection, an analytical system capable of specifically detecting viable cells with the simple sample preparation and detection process would be highly desirable since live microorganisms can rapidly increase their numbers even at extremely low concentration and become a severe health risk. However, current sensing strategies cannot clearly determine the viability of cells, and hence they are susceptible to false-positive signals from harmless dead pathogens. Here we developed a robust electronic immunoassay that uses a pair of polycrystalline silicon interdigitated electrodes for the rapid detection of pathogens with high specificity for live cells. After bacterial cells were specifically anchored to the surface of the antibody-modified electrode, the characteristic geometry of the transducer enables the selective detection of viable cells with a limit of detection of 3 × 102 cfu/mL and an incubation time of only 1 h. The CMOS compatible fabrication process of the chip along with the label-free, reagentless electronic detection and the easy electrode regeneration to recycle for another impedance measurement make this approach an excellent candidate for oncoming economical in-field viable-cell detection systems, fully integrable with sophisticated signal processing circuits. PMID:19334738

  18. Detection limits of thin layer coulometry with ionophore based ion-selective membranes.

    PubMed

    Shvarev, Alexey; Neel, Bastien; Bakker, Eric

    2012-09-18

    We report here on a significant improvement in lowering the low detection limit of thin layer coulometric sensors based on liquid ion-selective membranes, using a potassium-selective system as a model example. Various possible processes that may result in an elevated residual current reading after electrolysis were eliminated. Self-dissolution of AgCl on the Ag/AgCl inner element may result in a residual ion flux that could adversely affect the lower detection limit. It was here replaced with an Ag/AgI inner pseudoreference electrode where the self-dissolution equilibrium is largely suppressed. Possible residual currents originating from a direct contact between inner element and ion-selective membranes were eliminated by introducing an inert PVDF separator of 50 μm diameter that was coiled around the inner element by a custom-made instrument. Finally, the influence of electrolyte fluxes from the outer solution across the membrane into the sample was evaluated by altering its lipophilic nature and reducing its concentration. It was found that this last effect is most likely responsible for the observed residual current for the potassium-selective membranes studied here. For the optimized conditions, the calibration curves demonstrated a near zero intercept, thereby paving the way to the coulometric calibration-free sensing of ionic species. A linear calibration curve for the coulometric cell with valinomycin potassium-selective membrane was obtained in the range of 100 nM to 10 μM potassium in the presence of a 10 μM sodium background. In the presence of a higher (100 μM) concentration of sodium, a reliable detection of 1-100 μM of potassium was achieved. PMID:22917023

  19. Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

    PubMed Central

    Shim, Hyunjin; Laurent, Stefan; Matuszewski, Sebastian; Foll, Matthieu; Jensen, Jeffrey D.

    2016-01-01

    During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of analyses, with the focus of discussion centering mainly on random or oscillatory fluctuations of selection intensities. Here, we present a novel method to consider nonrandom changes in selection intensities using Wright-Fisher approximate Bayesian (ABC)-based approaches, in order to detect and evaluate a change in selection strength from time-sampled data. This novel method jointly estimates the position of a change point as well as the strength of both corresponding selection coefficients (and dominance for diploid cases) from the allele trajectory. The simulation studies of this method reveal the combinations of parameter ranges and input values that optimize performance, thus indicating optimal experimental design strategies. We apply this approach to both the historical dataset of P. dominula in order to shed light on this historical debate, as well as to whole-genome time-serial data from influenza virus in order to identify sites with changing selection intensities in response to drug treatment. PMID:26869618

  20. Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data.

    PubMed

    Shim, Hyunjin; Laurent, Stefan; Matuszewski, Sebastian; Foll, Matthieu; Jensen, Jeffrey D

    2016-01-01

    During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of analyses, with the focus of discussion centering mainly on random or oscillatory fluctuations of selection intensities. Here, we present a novel method to consider nonrandom changes in selection intensities using Wright-Fisher approximate Bayesian (ABC)-based approaches, in order to detect and evaluate a change in selection strength from time-sampled data. This novel method jointly estimates the position of a change point as well as the strength of both corresponding selection coefficients (and dominance for diploid cases) from the allele trajectory. The simulation studies of this method reveal the combinations of parameter ranges and input values that optimize performance, thus indicating optimal experimental design strategies. We apply this approach to both the historical dataset of P. dominula in order to shed light on this historical debate, as well as to whole-genome time-serial data from influenza virus in order to identify sites with changing selection intensities in response to drug treatment. PMID:26869618

  1. Selective and sensitive detection of chromium(VI) in waters using electrospray ionization mass spectrometry.

    PubMed

    Weldy, Effie; Wolff, Chloe; Miao, Zhixin; Chen, Hao

    2013-09-01

    From 2000 through 2011, there were 14 criminal cases of violations of the Clean Water Act involving the discharge of chromium, a toxic heavy metal, into drinking and surface water sources. As chromium(VI), a potential carcinogen present in the environment, represents a significant safety concern, it is currently the subject of an EPA health risk assessment. Therefore, sensitive and selective detection of this species is highly desired. This study reports the analysis of chromium(VI) in water samples by electrospray ionization mass spectrometry (ESI-MS) following its reduction and complexation with ammonium pyrrolidinedithiocarbamate (APDC). The reduction and subsequent complexation produce a characteristic [Cr(III)O]-PDC complex which can be detected as a protonated ion of m/z 507 in the positive ion mode. The detection is selective to chromium(VI) under acidic pH, even in the presence of chromium(III) and other metal ions, providing high specificity. Different water samples were examined, including deionized, tap, and river waters, and sensitive detection was achieved. In the case of deionized water, quantification over the concentration range of 3.7 to 148ppb gave an excellent correlation coefficient of 0.9904 using the enhanced MS mode scan. Using the single-reaction monitoring (SRM) mode (monitoring the characteristic fragmentation of m/z 507 to m/z 360), the limit of detection (LOD) was found to be 0.25ppb. The LOD of chromium(VI) for both tap and river water samples was determined to be 2.0ppb. A preconcentration strategy using simple vacuum evaporation of the aqueous sample was shown to further improve the ESI signal by 15 fold. This method, with high sensitivity and selectivity, should provide a timely solution for the real-world analysis of toxic chromium(VI). PMID:23937937

  2. A nonionic surfactant-decorated liquid crystal sensor for sensitive and selective detection of proteins.

    PubMed

    Wang, Yi; Hu, Qiongzheng; Tian, Tongtong; Gao, Yan'an; Yu, Li

    2016-09-21

    Proteins are responsible for most biochemical events in human body. It is essential to develop sensitive and selective methods for the detection of proteins. In this study, liquid crystal (LC)-based sensor for highly selective and sensitive detection of lysozyme, concanavalin A (Con A), and bovine serum albumin (BSA) was constructed by utilizing the LC interface decorated with a nonionic surfactant, dodecyl β-d-glucopyranoside. A change of the LC optical images from bright to dark appearance was observed after transferring dodecyl β-d-glucopyranoside onto the aqueous/LC interface due to the formation of stable self-assembled surfactant monolayer, regardless of pH and ion concentrations studied in a wide range. The optical images turned back from dark to bright appearance after addition of lysozyme, Con A and BSA, respectively. Noteworthy is that these proteins can be further distinguished by adding enzyme inhibitors and controlling incubation temperature of the protein solutions based on three different interaction mechanisms between proteins and dodecyl β-d-glucopyranoside, viz. enzymatic hydrolysis, specific saccharide binding, and physical absorption. The LC-based sensor decorated with dodecyl β-d-glucopyranoside shows high sensitivity for protein detection. The limit of detection (LOD) for lysozyme, Con A and BSA reaches around 0.1 μg/mL, 0.01 μg/mL and 0.001 μg/mL, respectively. These results might provide new insights into increasing selectivity and sensitivity of LC-based sensors for the detection of proteins. PMID:27590553

  3. Supersensitive and selective detection of picric acid explosive by fluorescent Ag nanoclusters.

    PubMed

    Zhang, Jian Rong; Yue, Yuan Yuan; Luo, Hong Qun; Li, Nian Bing

    2016-02-01

    Picric acid (PA) explosive is a hazard to public safety and health, so the sensitive and selective detection of PA is very important. In the present work, polyethyleneimine stabilized Ag nanoclusters were successfully used for the sensitive and selective quantification of PA on the basis of fluorescence quenching. The quenching efficiency of Ag nanoclusters is proportional to the concentration of PA and the logarithm of PA concentration over two different concentration ranges (1.0 nM-1 μM for the former and 0.25-20 μM for the latter), thus the proposed quantitative strategy for PA provides a wide linear range of 1.0 nM-20 μM. The detection limit based on 3σ/K is 0.1 nM. The quenching mechanism of Ag nanoclusters by PA is discussed in detail. The results indicate that the selective detection of PA over other nitroaromatics including 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), p-nitrotoluene (p-NT), m-dinitrobenzene (m-DNB), and nitrobenzene (NB), is due to the electron transfer and energy transfer between PA and polyethyleneimine-capped Ag nanoclusters. In addition, the experimental data obtained for the analysis of artificial samples show that the proposed PA sensor is potentially applicable in the determination of trace PA explosive in real samples. PMID:26661456

  4. Highly sensitive and selective sugar detection by terahertz nano-antennas

    NASA Astrophysics Data System (ADS)

    Lee, Dong-Kyu; Kang, Ji-Hun; Lee, Jun-Seok; Kim, Hyo-Seok; Kim, Chulki; Hun Kim, Jae; Lee, Taikjin; Son, Joo-Hiuk; Park, Q.-Han; Seo, Minah

    2015-10-01

    Molecular recognition and discrimination of carbohydrates are important because carbohydrates perform essential roles in most living organisms for energy metabolism and cell-to-cell communication. Nevertheless, it is difficult to identify or distinguish various carbohydrate molecules owing to the lack of a significant distinction in the physical or chemical characteristics. Although there has been considerable effort to develop a sensing platform for individual carbohydrates selectively using chemical receptors or an ensemble array, their detection and discrimination limits have been as high in the millimolar concentration range. Here we show a highly sensitive and selective detection method for the discrimination of carbohydrate molecules using nano-slot-antenna array-based sensing chips which operate in the terahertz (THz) frequency range (0.5-2.5 THz). This THz metamaterial sensing tool recognizes various types of carbohydrate molecules over a wide range of molecular concentrations. Strongly localized and enhanced terahertz transmission by nano-antennas can effectively increase the molecular absorption cross sections, thereby enabling the detection of these molecules even at low concentrations. We verified the performance of nano-antenna sensing chip by both THz spectra and images of transmittance. Screening and identification of various carbohydrates can be applied to test even real market beverages with a high sensitivity and selectivity.

  5. Highly sensitive and selective sugar detection by terahertz nano-antennas.

    PubMed

    Lee, Dong-Kyu; Kang, Ji-Hun; Lee, Jun-Seok; Kim, Hyo-Seok; Kim, Chulki; Kim, Jae Hun; Lee, Taikjin; Son, Joo-Hiuk; Park, Q-Han; Seo, Minah

    2015-01-01

    Molecular recognition and discrimination of carbohydrates are important because carbohydrates perform essential roles in most living organisms for energy metabolism and cell-to-cell communication. Nevertheless, it is difficult to identify or distinguish various carbohydrate molecules owing to the lack of a significant distinction in the physical or chemical characteristics. Although there has been considerable effort to develop a sensing platform for individual carbohydrates selectively using chemical receptors or an ensemble array, their detection and discrimination limits have been as high in the millimolar concentration range. Here we show a highly sensitive and selective detection method for the discrimination of carbohydrate molecules using nano-slot-antenna array-based sensing chips which operate in the terahertz (THz) frequency range (0.5-2.5 THz). This THz metamaterial sensing tool recognizes various types of carbohydrate molecules over a wide range of molecular concentrations. Strongly localized and enhanced terahertz transmission by nano-antennas can effectively increase the molecular absorption cross sections, thereby enabling the detection of these molecules even at low concentrations. We verified the performance of nano-antenna sensing chip by both THz spectra and images of transmittance. Screening and identification of various carbohydrates can be applied to test even real market beverages with a high sensitivity and selectivity. PMID:26494203

  6. Highly sensitive and selective sugar detection by terahertz nano-antennas

    PubMed Central

    Lee, Dong-Kyu; Kang, Ji-Hun; Lee, Jun-Seok; Kim, Hyo-Seok; Kim, Chulki; Hun Kim, Jae; Lee, Taikjin; Son, Joo-Hiuk; Park, Q-Han; Seo, Minah

    2015-01-01

    Molecular recognition and discrimination of carbohydrates are important because carbohydrates perform essential roles in most living organisms for energy metabolism and cell-to-cell communication. Nevertheless, it is difficult to identify or distinguish various carbohydrate molecules owing to the lack of a significant distinction in the physical or chemical characteristics. Although there has been considerable effort to develop a sensing platform for individual carbohydrates selectively using chemical receptors or an ensemble array, their detection and discrimination limits have been as high in the millimolar concentration range. Here we show a highly sensitive and selective detection method for the discrimination of carbohydrate molecules using nano-slot-antenna array-based sensing chips which operate in the terahertz (THz) frequency range (0.5–2.5 THz). This THz metamaterial sensing tool recognizes various types of carbohydrate molecules over a wide range of molecular concentrations. Strongly localized and enhanced terahertz transmission by nano-antennas can effectively increase the molecular absorption cross sections, thereby enabling the detection of these molecules even at low concentrations. We verified the performance of nano-antenna sensing chip by both THz spectra and images of transmittance. Screening and identification of various carbohydrates can be applied to test even real market beverages with a high sensitivity and selectivity. PMID:26494203

  7. Using identity by descent estimation with dense genotype data to detect positive selection.

    PubMed

    Han, Lide; Abney, Mark

    2013-02-01

    Identification of genomic loci and segments that are identical by descent (IBD) allows inference on problems such as relatedness detection, IBD disease mapping, heritability estimation and detection of recent or ongoing positive selection. Here, employing a novel statistical method, we use IBD to find signals of selection in the Maasai from Kinyawa, Kenya (MKK). In doing so, we demonstrate the advantage of statistical tools that can probabilistically estimate IBD sharing without having to thin genotype data because of linkage disequilibrium (LD), and that allow for both inbreeding and more than one allele to be shared IBD. We use our novel method, GIBDLD, to estimate IBD sharing between all pairs of individuals at all genotyped SNPs in the MKK, and, by looking for genomic regions showing excess IBD sharing in unrelated pairs, find loci that are known to have undergone recent selection (eg, the LCT gene and the HLA region) as well as many novel loci. Intriguingly, those loci that show the highest amount of excess IBD, with the exception of HLA, also show a substantial number of unrelated pairs sharing all four of their alleles IBD. In contrast to other IBD detection methods, GIBDLD provides accurate probabilistic estimates at each locus for all nine possible IBD sharing states between a pair of individuals, thus allowing for consanguinity, while also modeling LD, thus removing the need to thin SNPs. These characteristics will prove valuable for those doing genetic studies, and estimating IBD, in the wide variety of human populations. PMID:22781100

  8. Organic transistors with ordered nanoparticle arrays as a tailorable platform for selective, in situ detection.

    PubMed

    Hammock, Mallory L; Sokolov, Anatoliy N; Stoltenberg, Randall M; Naab, Benjamin D; Bao, Zhenan

    2012-04-24

    The use of organic transistors as sensing platforms provides a number of distinct advantages over conventional detection technologies, including their tunability, portability, and ability to directly transduce binding events without tedious and expensive labeling procedures. However, detection efforts using organic transistors lack a general method to uniquely specify and detect a target of interest. While highly sensitive liquid- and vapor-phase sensors have been previously reported, detection has been restricted either to the serendipitous interaction of the analyte molecules with the organic semiconductor or to the covalent functionalization of the semiconductor with receptor groups to enhance specificity. However, the former technique cannot be regularly relied upon for tailorable sensing while the latter may result in unpredictable decreases in electronic performance. Thus, a method to provide modular receptor sites on the surface of an organic transistor without damaging the device will significantly advance the field, especially regarding biological species detection. In this work, we utilized a block copolymer to template ordered, large-area arrays of gold nanoparticles, with sub-100 nm center-to-center spacing onto the surface of an organic transistor. This highly modular platform is designed for orthogonal modification with a number of available chemical and biological functional groups by taking advantage of the well-studied gold-thiol linkage. Herein, we demonstrate the functionalization of gold nanoparticles with a mercury-binding oligonucleotide sequence. Finally, we demonstrate the highly selective and robust detection of mercury(II) using this platform in an underwater environment. PMID:22397363

  9. Sensitive and selective electrochemical detection of artemisinin based on its reaction with p-aminophenylboronic acid.

    PubMed

    Wang, Chao; Zholudov, Yuriy T; Nsabimana, Anaclet; Xu, Guobao; Li, Jianping

    2016-09-21

    The electrochemical detection of artemisinin generally requires high oxidation potential or the use of complex electrode modification. We find that artemisinin can react with p-aminophenylboronic acid to produce easily electrochemically detectable aminophenol for the first time. By making use of the new reaction, we report an alternative method to detect artemisinin through the determination of p-aminophenol. The calibration curve for the determination of artemisinin is linear in the range of 2 μmol L(-1) to 200 μmol L(-1) with the detection limit of 0.8 μmol L(-1), which is more sensitive than other reported electrochemical methods. The relative standard deviation is 4.83% for the determination of 10 μM artemisinin. Because the oxidation potential of p-aminophenol is around 0 V, the present method is high selective. When 40 μM, 90 μM and 140 μM of artemisinin were spiked to compound naphthoquine phosphate tablet samples, the recoveries are 107.6%, 105.4% and 101.7%, respectively. This detection strategy is attractive for the detection of artemisinin and its derivatives. The finding that artemisinin can react with aromatic boronic acid has the potential to be exploited for the development of other sensors, such as fluorescence artemisinin sensors. PMID:27590543

  10. Renovating the chromoionophores and detection modes in carrier-based ion-selective optical sensors.

    PubMed

    Xie, Xiaojiang

    2016-04-01

    Ion-selective optical sensing is an important branch of analytical and bioanalytical chemistry. Conventional ion-selective optodes are based on H(+) chromoionophores. These sensors are known to be pH dependent and usually operated in a passive mode. In view of the applications in complex real samples, the sensors must exhibit not only excellent chemical selectivity but also the ability to eliminate the optical background interference such as autofluorescence and light scattering. In this article, recent advances to renovate the chromoionophores and detection modes to overcome the pH cross-response and to eliminate the background optical interference are summarized. Topics include sensors based on solvatochromic dyes, alternative chromoionophores, photoswitchable sensors, upconverting nanoparticles, luminescence decay time, and others. PMID:26922342

  11. Selective detection of heavy metal ions by self assembled chemical field effect transistors

    NASA Astrophysics Data System (ADS)

    Ruan, Hang; Kang, Yuhong; Gladwin, Elizabeth; Claus, Richard O.

    2015-04-01

    Multiple layer-by-layer sensor material modifications were designed and implemented to achieve selectivity of semiconductor based chemical field effect transistors (ChemFETs) to particular heavy metal ions. The ChemFET sensors were fabricated and modified in three ways, with the intent to initially target first mercury and lead ions and then chromium ions, respectively. Sensor characterization was performed with the gate regions of the sensor elements exposed to different concentrations of target heavy metal ion solutions. A minimum detection level in the range of 0.1 ppm and a 10%-90% response time of less than 10 s were demonstrated. By combining layer-by-layer gold nanoparticles and lead ionophores, a sensor is produced that is sensitive and selective not only to chromium but also to Cr3+ and Cr6+. This result supports the claim that high selectivity can be achieved by designing self-assembled bonding for lead, arsenic, chromium, cesium, mercury, and cadmium.

  12. Small sample training and test selection method for optimized anomaly detection algorithms in hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Mindrup, Frank M.; Friend, Mark A.; Bauer, Kenneth W.

    2012-01-01

    There are numerous anomaly detection algorithms proposed for hyperspectral imagery. Robust parameter design (RPD) techniques provide an avenue to select robust settings capable of operating consistently across a large variety of image scenes. Many researchers in this area are faced with a paucity of data. Unfortunately, there are no data splitting methods for model validation of datasets with small sample sizes. Typically, training and test sets of hyperspectral images are chosen randomly. Previous research has developed a framework for optimizing anomaly detection in HSI by considering specific image characteristics as noise variables within the context of RPD; these characteristics include the Fisher's score, ratio of target pixels and number of clusters. We have developed method for selecting hyperspectral image training and test subsets that yields consistent RPD results based on these noise features. These subsets are not necessarily orthogonal, but still provide improvements over random training and test subset assignments by maximizing the volume and average distance between image noise characteristics. The small sample training and test selection method is contrasted with randomly selected training sets as well as training sets chosen from the CADEX and DUPLEX algorithms for the well known Reed-Xiaoli anomaly detector.

  13. A highly selective and picomolar level photoelectrochemical sensor for PCB 101 detection in environmental water samples.

    PubMed

    Shi, Huijie; Zhao, Jinzhi; Wang, Yingling; Zhao, Guohua

    2016-07-15

    A highly selective and sensitive photoelectrochemical (PEC) sensor was fabricated for fast and convenient detection of PCB 101 in environmental water samples with a low detection limit of 1.0×10(-14)molL(-1) based on single crystalline TiO2 nanorods (NRs). By integration with molecular imprinting (MI) technique, the PEC sensor's selectivity towards PCB 101 was significantly improved, so that the interference caused by 100-fold excess of PCB 126 and PCB 77 which had similar structure with PCB 101 was below 37%, not to mention other coexisted pollutants. This high selectivity could be attributed to the high-quality expression of the molecular imprinting sites on the rigid and smooth surface of single crystalline TiO2 NRs on which PCB 101 could be selectively and preferentially adsorbed. The oriented and multiple halogen bonds formed between PCB 101 and the molecular imprinting sites played a critical role in improving the recognition ability of the PEC sensor. Meanwhile, the one dimensional nanorods structure of TiO2 was beneficial for the efficient separation of photogenerated electrons and holes, leading to enhanced photocurrent response and further improving the sensitivity of the PEC sensor. PMID:27016911

  14. A surface acoustic wave sensor functionalized with a polypyrrole molecularly imprinted polymer for selective dopamine detection.

    PubMed

    Maouche, Naima; Ktari, Nadia; Bakas, Idriss; Fourati, Najla; Zerrouki, Chouki; Seydou, Mahamadou; Maurel, François; Chehimi, Mohammed Mehdi

    2015-11-01

    A surface acoustic wave sensor operating at 104 MHz and functionalized with a polypyrrole molecularly imprinted polymer has been designed for selective detection of dopamine (DA). Optimization of pyrrole/DA ratio, polymerization and immersion times permitted to obtain a highly selective sensor, which has a sensitivity of 0.55°/mM (≈ 550 Hz/mM) and a detection limit of ≈ 10 nM. Morphology and related roughness parameters of molecularly imprinted polymer surfaces, before and after extraction of DA, as well as that of the non imprinted polymer were characterized by atomic force microscopy. The developed chemosensor selectively recognized dopamine over the structurally similar compound 4-hydroxyphenethylamine (referred as tyramine), or ascorbic acid,which co-exists with DA in body fluids at a much higher concentration. Selectivity tests were also carried out with dihydroxybenzene, for which an unexpected phase variation of order of 75% of the DA one was observed. Quantum chemical calculations, based on the density functional theory, were carried out to determine the nature of interactions between each analyte and the PPy matrix and the DA imprinted PPy polypyrrole sensing layer in order to account for the important phase variation observed during dihydroxybenzene injection. PMID:26095144

  15. Amplified electrochemical detection of nucleic acid hybridization via selective preconcentration of unmodified gold nanoparticles.

    PubMed

    Li, Yuan; Tian, Rui; Zheng, Xingwang; Huang, Rongfu

    2016-08-31

    The common drawback of optical methods for rapid detection of nucleic acid by exploiting the differential affinity of single-/double-stranded nucleic acids for unmodified gold nanoparticles (AuNPs) is its relatively low sensitivity. In this article, on the basis of selective preconcentration of AuNPs unprotected by single-stranded DNA (ssDNA) binding, a novel electrochemical strategy for nucleic acid sequence identification assay has been developed. Through detecting the redox signal mediated by AuNPs on 1, 6-hexanedithiol blocked gold electrode, the proposed method is able to ensure substantial signal amplification and a low background current. This strategy is demonstrated for quantitative analysis of the target microRNA (let-7a) in human breast adenocarcinoma cells, and a detection limit of 16 fM is readily achieved with desirable specificity and sensitivity. These results indicate that the selective preconcentration of AuNPs for electrochemical signal readout can offer a promising platform for the detection of specific nucleic acid sequence. PMID:27506344

  16. Novel selective dyeing method for chrysotile asbestos detection in concrete materials.

    PubMed

    Oke, Yoshihiko; Yamasaki, Nakamichi; Amamoto, Go Y; Sasaki, Kazuhiro; Maeta, Naomi; Fujimaki, Hirokazu; Hashida, Toshiyuki

    2008-03-01

    There are a tremendous number of asbestos-containing buildings without any surveys on the presence of asbestos because of the difficulty to detect asbestos in building materials simply and quickly, although a great deal of worldwide effort was put into removing asbestos of which inhalation causes serious diseases. In this study, we newly developed a simple dyeing method to detect chrysotile asbestos, the most commonly used type of asbestos, in asbestos-cement composite materials using magnesium-chelating organic dyes. As an essential process for selective dyeing of chrysotile asbestos, special pretreatment with a calcium-chelating agent was developed to prevent the dyes from reacting with calcium, which is the major component of concrete materials. Our developed selective dyeing method was shown to possess sufficient sensitivity for detecting chrysotile asbestos in an amount greater than 0.1 mass% in concrete specimens, and there was an approximately linear relationship between the area fraction of dyed spots and the mass fraction of chrysotile asbestos. Our results may provide a basis for further development of a simple on-site detection method for chrysotile asbestos in building materials and may facilitate the progress of control and removal of asbestos in the environment. PMID:18441814

  17. A highly facile and selective Chemo-Paper-Sensor (CPS) for detection of strontium.

    PubMed

    Kang, Sung-Min; Jang, Sung-Chan; Huh, Yun Suk; Lee, Chang-Soo; Roh, Changhyun

    2016-06-01

    Chemosensors have attracted increasing attention for their usefulness on-site detection and monitoring. In this study, we elucidated a novel, facile, and highly selective Chemo-Paper-Sensor (CPS) for detection and monitoring of strontium (Sr(2+)) ions, which means a potent colorimetric sensor based on a Chrysoidine G (CG)-coated paper strip. The CPS for highly selective colorimetric detection of strontium ion was handily analyzed to determine the red-green-blue (RGB) value using portable devices such as desktop digital scanner and mobile phone camera, quantitatively. Interestingly, an orange to dark orange color transition was observed when the aqueous and solid paper colorimetric sensor was introduced to Sr(2+) ion, respectively. It was demonstrated that the value of the signal has a linear relationship with concentrations of the strontium in the 500 ppm to 100 ppb range with a detection limit of 200 ppb. We believe that a newly developed Chemo-Paper-Sensor will be useful in a wide range of sensing applications. PMID:26953730

  18. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles.

    PubMed

    Elghanian, R; Storhoff, J J; Mucic, R C; Letsinger, R L; Mirkin, C A

    1997-08-22

    A highly selective, colorimetric polynucleotide detection method based on mercaptoalkyloligonucleotide-modified gold nanoparticle probes is reported. Introduction of a single-stranded target oligonucleotide (30 bases) into a solution containing the appropriate probes resulted in the formation of a polymeric network of nanoparticles with a concomitant red-to-pinkish/purple color change. Hybridization was facilitated by freezing and thawing of the solutions, and the denaturation of these hybrid materials showed transition temperatures over a narrow range that allowed differentiation of a variety of imperfect targets. Transfer of the hybridization mixture to a reverse-phase silica plate resulted in a blue color upon drying that could be detected visually. The unoptimized system can detect about 10 femtomoles of an oligonucleotide. PMID:9262471

  19. Sensitive and Selective Detection of HIV-1 RRE RNA Using Vertical Silicon Nanowire Electrode Array.

    PubMed

    Lee, Jaehyung; Hong, Min-Ho; Han, Sanghun; Na, Jukwan; Kim, Ilsoo; Kwon, Yong-Joon; Lim, Yong-Beom; Choi, Heon-Jin

    2016-12-01

    In this study, HIV-1 Rev response element (RRE) RNA was detected via an Au-coated vertical silicon nanowire electrode array (VSNEA). The VSNEA was fabricated by combining bottom-up and top-down approaches and then immobilized by artificial peptides for the recognition of HIV-1 RRE. Differential pulse voltammetry (DPV) analysis was used to measure the electrochemical response of the peptide-immobilized VSNEA to the concentration and types of HIV-1 RRE RNA. DPV peaks showed linearity to the concentration of RNA with a detection limit down to 1.513 fM. It also showed the clear different peaks to the mutated HIV-1 RRE RNA. The high sensitivity and selectivity of VSNEA for the detection of HIV-1 RRE RNA may be attributed to the high surface-to-volume ratio and total overlap diffusion mode of ions of the one-dimensional nanowire electrodes. PMID:27448026

  20. Novel pyridyl based azo-derivative for the selective and colorimetric detection of nickel(II)

    NASA Astrophysics Data System (ADS)

    Biswas, Sujan; Acharyya, Samik; Sarkar, Deblina; Gharami, Saswati; Mondal, Tapan Kumar

    2016-04-01

    A highly sensitive and selective pyridyl based colorimetric chemosensor (H2L) for the efficient detection of Ni2 + has been reported. The synthesized chemosensor H2L is highly efficient in detecting Ni2 + even in the presence of other metal ions that commonly co-exist with Ni2 +. H2L also shows distinct color change from green to deep red visible under naked eye due to specific binding with Ni2 +. This color change is due to formation of a new band at 510 nm upon gradual addition of Ni2 +. The association constant has been found to be 1.27 × 105 M- 1 with limit of detection (LOD) of 8.3 × 10- 7 M. Electronic structure of the H2L-Ni2 + complex and sensing mechanism have been interpreted theoretically by DFT and TDDFT calculations.

  1. Advanced selective non-invasive ketone body detection sensors based on new ionophores

    NASA Astrophysics Data System (ADS)

    Sathyapalan, A.; Sarswat, P. K.; Zhu, Y.; Free, M. L.

    2014-12-01

    New molecules and methods were examined that can be used to detect trace level ketone bodies. Diseases such as type 1 diabetes, childhood hypo-glycaemia-growth hormone deficiency, toxic inhalation, and body metabolism changes are linked with ketone bodies concentration. Here we introduce, selective ketone body detection sensors based on small, environmentally friendly organic molecules with Lewis acid additives. Density functional theory (DFT) simulation of the sensor molecules (Bromo-acetonaphthone tungstate (BANT) and acetonaphthophenyl ether propiono hydroxyl tungstate (APPHT)), indicated a fully relaxed geometry without symmetry attributes and specific coordination which enhances ketone bodies sensitivity. A portable sensing unit was made in which detection media containing ketone bodies at low concentration and new molecules show color change in visible light as well as unique irradiance during UV illumination. RGB analysis, electrochemical tests, SEM characterization, FTIR, absorbance and emission spectroscopy were also performed in order to validate the ketone sensitivity of these new molecules.

  2. Selectivity and sensitivity of some thin-layer chromatographic detection systems.

    PubMed

    Fodor-Csorba, K; Dutka, F

    1986-09-19

    The selectivity and sensitivity of some thin-layer chromatographic detection systems widely used internationally and developed in our laboratory were studied. Halogenated organophosphorus pesticides were found to interfere with the detection of organochlorine pesticides when using silver nitrate-2-phenoxyethanol. The stability of colours formed by the 4-(4'-nitrobenzyl)pyridine-tetraethylenepentamine system was enhanced by spraying with acetic acid and allowed densitometric evaluation. The most sensitive detection method for thiocarbamates is the reaction with 2,6-dichlorobenzoquinone-N-chloroimine or its dibromo analogue (50 ng). Application of this method for sulphur-containing organophosphorus insecticides results in the same or better sensitivity. Quantitation of these compounds was carried out by densitometry. PMID:3771705

  3. Sensitive and Selective Detection of HIV-1 RRE RNA Using Vertical Silicon Nanowire Electrode Array

    NASA Astrophysics Data System (ADS)

    Lee, Jaehyung; Hong, Min-Ho; Han, Sanghun; Na, Jukwan; Kim, Ilsoo; Kwon, Yong-Joon; Lim, Yong-beom; Choi, Heon-Jin

    2016-07-01

    In this study, HIV-1 Rev response element (RRE) RNA was detected via an Au-coated vertical silicon nanowire electrode array (VSNEA). The VSNEA was fabricated by combining bottom-up and top-down approaches and then immobilized by artificial peptides for the recognition of HIV-1 RRE. Differential pulse voltammetry (DPV) analysis was used to measure the electrochemical response of the peptide-immobilized VSNEA to the concentration and types of HIV-1 RRE RNA. DPV peaks showed linearity to the concentration of RNA with a detection limit down to 1.513 fM. It also showed the clear different peaks to the mutated HIV-1 RRE RNA. The high sensitivity and selectivity of VSNEA for the detection of HIV-1 RRE RNA may be attributed to the high surface-to-volume ratio and total overlap diffusion mode of ions of the one-dimensional nanowire electrodes.

  4. Ag@poly(m-phenylenediamine) core-shell nanoparticles for highly selective, multiplex nucleic acid detection.

    PubMed

    Zhang, Yingwei; Wang, Lei; Tian, Jingqi; Li, Hailong; Luo, Yonglan; Sun, Xuping

    2011-03-15

    In this letter, we report on the one-step synthesis of Ag@poly(m-phenylenediamine) core-shell nanoparticles (APCSNPs), carried out by direct mixing of aqueous silver nitrate and m-phenylenediamine solutions at room temperature. We further demonstrate the use of APCSNP as a novel fluorescent sensing platform for nucleic acid detection. In this regard, the detection of DNA is accomplished in two steps. First, APCSNP absorbs and quenches the fluorescence of dye-labeled single-stranded DNA (ssDNA) as a probe. Second, hybridizing of the probe with its target produces a double-stranded DNA (dsDNA) that detaches from APCSNP, resulting in the recovery of dye fluorescence. It suggests that this sensing system has a high selectivity down to single-base mismatch, and the results exhibit good reproducibility. Furthermore, we also demonstrate its application for the multiplex detection of nucleic acid sequences. PMID:21302954

  5. Novel pyridyl based azo-derivative for the selective and colorimetric detection of nickel(II).

    PubMed

    Biswas, Sujan; Acharyya, Samik; Sarkar, Deblina; Gharami, Saswati; Mondal, Tapan Kumar

    2016-04-15

    A highly sensitive and selective pyridyl based colorimetric chemosensor (H2L) for the efficient detection of Ni(2+) has been reported. The synthesized chemosensor H2L is highly efficient in detecting Ni(2+) even in the presence of other metal ions that commonly co-exist with Ni(2+). H2L also shows distinct color change from green to deep red visible under naked eye due to specific binding with Ni(2+). This color change is due to formation of a new band at 510nm upon gradual addition of Ni(2+). The association constant has been found to be 1.27×10(5)M(-1) with limit of detection (LOD) of 8.3×10(-7)M. Electronic structure of the H2L-Ni(2+) complex and sensing mechanism have been interpreted theoretically by DFT and TDDFT calculations. PMID:26845582

  6. Sensitive and selective detection of copper ions with highly stable polyethyleneimine-protected silver nanoclusters.

    PubMed

    Yuan, Zhiqin; Cai, Na; Du, Yi; He, Yan; Yeung, Edward S

    2014-01-01

    Copper is a highly toxic environmental pollutant with bioaccumulative properties. Therefore, sensitive Cu(2+) detection is very important to prevent over-ingestion, and visual detection using unaugmented vision is preferred for practical applications. In this study, hyperbranched polyethyleneimine-protected silver nanoclusters (hPEI-AgNCs) were successfully synthesized using a facile, one-pot reaction under mild conditions. The hPEI-AgNCs were very stable against extreme pH, ionic strength, temperature, and photoillumination and could act as sensitive and selective Cu(2+) sensing nanoprobes in aqueous solutions with a 10 nM limit of detection. In addition, hPEI-AgNCs-doped agarose hydrogels were developed as an instrument-free and regenerable platform for visual Cu(2+) and water quality monitoring. PMID:24274096

  7. Molecularly imprinted plasmonic nanosensor for selective SERS detection of protein biomarkers.

    PubMed

    Lv, Yongqin; Qin, Yating; Svec, Frantisek; Tan, Tianwei

    2016-06-15

    Molecularly imprinted plasmonic nanosensor has been prepared via the rational design of an ultrathin polymer layer on the surface of gold nanorods imprinted with the target protein. This nanosensor enabled selective fishing-out of the target protein biomarker even from a complex real sample such as human serum. Sensitive SERS detection of the protein biomarkers with a strong Raman enhancement was achieved by formation of protein imprinted gold nanorods aggregates, stacking of protein imprinted gold nanorods onto a glass plate, or self-assembly of protein imprinted gold nanorods into close-packed array. High specificity and sensitivity of this method were demonstrated with a detection limit of at least 10(-8)mol/L for the target protein. This could provide a promising alternative for the currently used immunoassays and fluorescence detection, and offer an ultrasensitive, non-destructive, and label-free technique for clinical diagnosis applications. PMID:26874111

  8. Change-Point Detection of Natural Frequency Using Dynamic Model Selection and Clustering

    NASA Astrophysics Data System (ADS)

    Matsuoka, Kodai; Kaito, Kiyoyuki; Sogabe, Masamichi

    In order to apply structural monitoring into practice, it is indispensable to develop a method for change-point detection of bridge vibrational properties. In this study, the authors have developed a methodology using sequential prediction, dynamic model selection, and clustering, with the purpose of evaluating vibrational properties and its change timings. In order to examine the validity, the time series that had the change in frequency was calculated, and proposal method was applied. As a results, it was found that the natural frequency is detected. As for change timings, these were evaluated as change intervals. On the other hand, when the proposed method was applied to the acceleration response of a bridge when a train passes, it was found that bridge frequency can be extracted stably, and it is difficult to detect change timings when the change is small. Based on these results, factors were studied, and some solutions to the problems were proposed.

  9. Detecting recent positive selection with high accuracy and reliability by conditional coalescent tree.

    PubMed

    Wang, Minxian; Huang, Xin; Li, Ran; Xu, Hongyang; Jin, Li; He, Yungang

    2014-11-01

    Studies of natural selection, followed by functional validation, are shedding light on understanding of genetic mechanisms underlying human evolution and adaptation. Classic methods for detecting selection, such as the integrated haplotype score (iHS) and Fay and Wu's H statistic, are useful for candidate gene searching underlying positive selection. These methods, however, have limited capability to localize causal variants in selection target regions. In this study, we developed a novel method based on conditional coalescent tree to detect recent positive selection by counting unbalanced mutations on coalescent gene genealogies. Extensive simulation studies revealed that our method is more robust than many other approaches against biases due to various demographic effects, including population bottleneck, expansion, or stratification, while not sacrificing its power. Furthermore, our method demonstrated its superiority in localizing causal variants from massive linked genetic variants. The rate of successful localization was about 20-40% higher than that of other state-of-the-art methods on simulated data sets. On empirical data, validated functional causal variants of four well-known positive selected genes were all successfully localized by our method, such as ADH1B, MCM6, APOL1, and HBB. Finally, the computational efficiency of this new method was much higher than that of iHS implementations, that is, 24-66 times faster than the REHH package, and more than 10,000 times faster than the original iHS implementation. These magnitudes make our method suitable for applying on large sequencing data sets. Software can be downloaded from https://github.com/wavefancy/scct. PMID:25135945

  10. Investigation of microcantilever array with ordered nanoporous coatings for selective chemical detection

    NASA Astrophysics Data System (ADS)

    Lee, J.-H.; Houk, R. T. J.; Robinson, A.; Greathouse, J. A.; Thornberg, S. M.; Allendorf, M. D.; Hesketh, P. J.

    2010-04-01

    In this paper we demonstrate the potential for novel nanoporous framework materials (NFM) such as metal-organic frameworks (MOFs) to provide selectivity and sensitivity to a broad range of analytes including explosives, nerve agents, and volatile organic compounds (VOCs). NFM are highly ordered, crystalline materials with considerable synthetic flexibility resulting from the presence of both organic and inorganic components within their structure. Detection of chemical weapons of mass destruction (CWMD), explosives, toxic industrial chemicals (TICs), and volatile organic compounds (VOCs) using micro-electro-mechanical-systems (MEMS) devices, such as microcantilevers and surface acoustic wave sensors, requires the use of recognition layers to impart selectivity. Traditional organic polymers are dense, impeding analyte uptake and slowing sensor response. The nanoporosity and ultrahigh surface areas of NFM enhance transport into and out of the NFM layer, improving response times, and their ordered structure enables structural tuning to impart selectivity. Here we describe experiments and modeling aimed at creating NFM layers tailored to the detection of water vapor, explosives, CWMD, and VOCs, and their integration with the surfaces of MEMS devices. Force field models show that a high degree of chemical selectivity is feasible. For example, using a suite of MOFs it should be possible to select for explosives vs. CWMD, VM vs. GA (nerve agents), and anthracene vs. naphthalene (VOCs). We will also demonstrate the integration of various NFM with the surfaces of MEMS devices and describe new synthetic methods developed to improve the quality of VFM coatings. Finally, MOF-coated MEMS devices show how temperature changes can be tuned to improve response times, selectivity, and sensitivity.

  11. Investigation of microcantilever array with ordered nanoporous coatings for selective chemical detection.

    SciTech Connect

    Allendorf, Mark D.; Thornberg, Steven Michael; Lee, J. -H.; Robinson, Alex Lockwood; Hesketh, Peter J.; Greathouse, Jeffery A.; Houk, Ronald J. T.

    2010-03-01

    In this paper we demonstrate the potential for novel nanoporous framework materials (NFM) such as metal-organic frameworks (MOFs) to provide selectivity and sensitivity to a broad range of analytes including explosives, nerve agents, and volatile organic compounds (VOCs). NFM are highly ordered, crystalline materials with considerable synthetic flexibility resulting from the presence of both organic and inorganic components within their structure. Detection of chemical weapons of mass destruction (CWMD), explosives, toxic industrial chemicals (TICs), and volatile organic compounds (VOCs) using micro-electro-mechanical-systems (MEMS) devices, such as microcantilevers and surface acoustic wave sensors, requires the use of recognition layers to impart selectivity. Traditional organic polymers are dense, impeding analyte uptake and slowing sensor response. The nanoporosity and ultrahigh surface areas of NFM enhance transport into and out of the NFM layer, improving response times, and their ordered structure enables structural tuning to impart selectivity. Here we describe experiments and modeling aimed at creating NFM layers tailored to the detection of water vapor, explosives, CWMD, and VOCs, and their integration with the surfaces of MEMS devices. Force field models show that a high degree of chemical selectivity is feasible. For example, using a suite of MOFs it should be possible to select for explosives vs. CWMD, VM vs. GA (nerve agents), and anthracene vs. naphthalene (VOCs). We will also demonstrate the integration of various NFM with the surfaces of MEMS devices and describe new synthetic methods developed to improve the quality of VFM coatings. Finally, MOF-coated MEMS devices show how temperature changes can be tuned to improve response times, selectivity, and sensitivity.

  12. The Predictive Power of Evolutionary Biology and the Discovery of Eusociality in the Naked Mole-Rat.

    ERIC Educational Resources Information Center

    Braude, Stanton

    1997-01-01

    Discusses how biologists use evolutionary theory and provides examples of how evolutionary biologists test hypotheses on specific modes of selection and evolution. Presents an example of the successful predictive power of one evolutionary hypothesis. Contains 38 references. (DDR)

  13. [Research on fast detecting tomato seedlings nitrogen content based on NIR characteristic spectrum selection].

    PubMed

    Wu, Jing-zhu; Wang, Feng-zhu; Wang, Li-li; Zhang, Xiao-chao; Mao, Wen-hua

    2015-01-01

    In order to improve the accuracy and robustness of detecting tomato seedlings nitrogen content based on near-infrared spectroscopy (NIR), 4 kinds of characteristic spectrum selecting methods were studied in the present paper, i. e. competitive adaptive reweighted sampling (CARS), Monte Carlo uninformative variables elimination (MCUVE), backward interval partial least squares (BiPLS) and synergy interval partial least squares (SiPLS). There were totally 60 tomato seedlings cultivated at 10 different nitrogen-treatment levels (urea concentration from 0 to 120 mg . L-1), with 6 samples at each nitrogen-treatment level. They are in different degrees of over nitrogen, moderate nitrogen, lack of nitrogen and no nitrogen status. Each sample leaves were collected to scan near-infrared spectroscopy from 12 500 to 3 600 cm-1. The quantitative models based on the above 4 methods were established. According to the experimental result, the calibration model based on CARS and MCUVE selecting methods show better performance than those based on BiPLS and SiPLS selecting methods, but their prediction ability is much lower than that of the latter. Among them, the model built by BiPLS has the best prediction performance. The correlation coefficient (r), root mean square error of prediction (RMSEP) and ratio of performance to standard derivate (RPD) is 0. 952 7, 0. 118 3 and 3. 291, respectively. Therefore, NIR technology combined with characteristic spectrum selecting methods can improve the model performance. But the characteristic spectrum selecting methods are not universal. For the built model based or single wavelength variables selection is more sensitive, it is more suitable for the uniform object. While the anti-interference ability of the model built based on wavelength interval selection is much stronger, it is more suitable for the uneven and poor reproducibility object. Therefore, the characteristic spectrum selection will only play a better role in building model

  14. New Detection Systems of Bacteria Using Highly Selective Media Designed by SMART: Selective Medium-Design Algorithm Restricted by Two Constraints

    PubMed Central

    Kawanishi, Takeshi; Shiraishi, Takuya; Okano, Yukari; Sugawara, Kyoko; Hashimoto, Masayoshi; Maejima, Kensaku; Komatsu, Ken; Kakizawa, Shigeyuki; Yamaji, Yasuyuki; Hamamoto, Hiroshi; Oshima, Kenro; Namba, Shigetou

    2011-01-01

    Culturing is an indispensable technique in microbiological research, and culturing with selective media has played a crucial role in the detection of pathogenic microorganisms and the isolation of commercially useful microorganisms from environmental samples. Although numerous selective media have been developed in empirical studies, unintended microorganisms often grow on such media probably due to the enormous numbers of microorganisms in the environment. Here, we present a novel strategy for designing highly selective media based on two selective agents, a carbon source and antimicrobials. We named our strategy SMART for highly Selective Medium-design Algorithm Restricted by Two constraints. To test whether the SMART method is applicable to a wide range of microorganisms, we developed selective media for Burkholderia glumae, Acidovorax avenae, Pectobacterium carotovorum, Ralstonia solanacearum, and Xanthomonas campestris. The series of media developed by SMART specifically allowed growth of the targeted bacteria. Because these selective media exhibited high specificity for growth of the target bacteria compared to established selective media, we applied three notable detection technologies: paper-based, flow cytometry-based, and color change-based detection systems for target bacteria species. SMART facilitates not only the development of novel techniques for detecting specific bacteria, but also our understanding of the ecology and epidemiology of the targeted bacteria. PMID:21304596

  15. Monochromatic wavelength dispersive x-ray fluorescence providing sensitive and selective detection of uranium

    SciTech Connect

    Havrilla, George J; Collins, Michael L; Montoya, Velma M; Chen, Zewu; Wei, Fuzhong

    2010-01-01

    Monochromatic wavelength dispersive X-ray fluorescence (MWDXRF) is a sensitive and selective method for elemental compositional analyses. The basis for this instrumental advance is the doubly curved crystal (DCC) optic. Previous work has demonstrated the feasibility of sensitive trace element detection for yttrium as a surrogate for curium in aqueous solutions. Additional measurements have demonstrated similar sensitivity in several different matrix environments which attests to the selectivity of the DCC optic as well as the capabilities of the MWDXRF concept. The objective of this effort is to develop an improved Pu characterization method for nuclear fuel reprocessing plants. The MWDXRF prototype instrument is the second step in a multi-year effort to achieve an improved Pu assay. This work will describe a prototype MWDXRF instrument designed for uranium detection and characterization. The prototype consists of an X-ray tube with a rhodium anode and a DCC excitation optic incorporated into the source. The DCC optic passes the RhK{alpha} line at 20.214 keV for monochromatic excitation of the sample. The source is capable of 50 W power at 50 kV and 1.0 mA operation. The x-ray emission from the sample is collected by a DCC optic set at the UL{alpha} line of 13.613 keV. The collection optic transmits the UL{alpha} x-rays to the silicon drift detector. The x-ray source, sample, collection optic and detector are all mounted on motion controlled stages for the critical alignment of these components. The sensitivity and selectivity of the instrument is obtained through the monochromatic excitation and the monochromatic detection. The prototype instrument performance has a demonstrated for sensitivity for uranium detection of around 2 ppm at the current state of development. Further improvement in sensitivity is expected with more detailed alignment.

  16. Evolutionary principles and their practical application

    PubMed Central

    Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

    2011-01-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

  17. Identifying signatures of sexual selection using genomewide selection components analysis

    PubMed Central

    Flanagan, Sarah P; Jones, Adam G

    2015-01-01

    Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual-based model to investigate the utility of genome-wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a quantitative trait to simulate sexual selection. Genome-wide allele frequencies in adults and offspring were compared using weighted FST values. The average number of outlier peaks (i.e., those with significantly large FST values) with a quantitative trait locus in close proximity (“real” peaks) represented correct diagnoses of loci under selection, whereas peaks above the FST significance threshold without a quantitative trait locus reflected spurious peaks. We found that, even with moderate sample sizes, signatures of strong sexual selection were detectable, but larger sample sizes improved detection rates. The model was better able to detect selection with more neutral markers, and when quantitative trait loci and neutral markers were distributed across multiple chromosomes. Although environmental variation decreased detection rates, the identification of real peaks nevertheless remained feasible. We also found that detection rates can be improved by sampling multiple populations experiencing similar selection regimes. In short, genome-wide selection components analysis is a challenging but feasible approach for the identification of regions of the genome under selection. PMID:26257884

  18. Reactive chromophores for sensitive and selective detection of chemical warfare agents

    NASA Astrophysics Data System (ADS)

    Frye-Mason, Greg; Leuschen, Martin; la Grone, Marcus; Wald, Lara; Aker, Craig; Dock, Matt; Hancock, Lawrence F.; Fagan, Steve; Paul, Kateri

    2004-08-01

    A new sensor for highly toxic species including chemical warfare (CW) agents has been developed. This sensor is based on a unique CW indicating chromophore (CWIC) developed by Professor Tim Swager at MIT. The CWIC was designed to be sensitive to the reactivity that makes these chemicals so toxic. Since it requires the reactivity of the agent to be detected, the CWIC technology has shown remarkable selectivity for nerve agent surrogates and some other highly toxic species, thereby demonstrating the potential to provide low false alarm rate detection. Since the chromophore has mini-mal fluorescence prior to reaction with an electrophilic and toxic chemical, the sensor acts in a dark field fluorescence mode. This provides the sensor with exceptional sensitivity and a potential to detect priority analytes well below levels detected by current hand held sensors. Finally, it is based on a simple optical detection scheme that enables small and rugged sensors to be developed and produced at a low enough cost so they can be widely utilized.

  19. Evolutionary origins of invasive populations

    PubMed Central

    Lee, Carol Eunmi; Gelembiuk, Gregory William

    2008-01-01

    What factors shape the evolution of invasive populations? Recent theoretical and empirical studies suggest that an evolutionary history of disturbance might be an important factor. This perspective presents hypotheses regarding the impact of disturbance on the evolution of invasive populations, based on a synthesis of the existing literature. Disturbance might select for life-history traits that are favorable for colonizing novel habitats, such as rapid population growth and persistence. Theoretical results suggest that disturbance in the form of fluctuating environments might select for organismal flexibility, or alternatively, the evolution of evolvability. Rapidly fluctuating environments might favor organismal flexibility, such as broad tolerance or plasticity. Alternatively, longer fluctuations or environmental stress might lead to the evolution of evolvability by acting on features of the mutation matrix. Once genetic variance is generated via mutations, temporally fluctuating selection across generations might promote the accumulation and maintenance of genetic variation. Deeper insights into how disturbance in native habitats affects evolutionary and physiological responses of populations would give us greater capacity to predict the populations that are most likely to tolerate or adapt to novel environments during habitat invasions. Moreover, we would gain fundamental insights into the evolutionary origins of invasive populations. PMID:25567726

  20. DETECTING SELECTION IN NATURAL POPULATIONS: MAKING SENSE OF GENOME SCANS AND TOWARDS ALTERNATIVE SOLUTIONS

    PubMed Central

    Haasl, Ryan J.; Payseur, Bret A.

    2016-01-01

    Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example FST, cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach. PMID:26224644

  1. Selective Electrochemical Detection of Ciprofloxacin with a Porous Nafion/Multiwalled Carbon Nanotube Composite Film Electrode.

    PubMed

    Gayen, Pralay; Chaplin, Brian P

    2016-01-27

    This study focuses on the development of electrochemical sensors for the detection of Ciprofloxacin (CFX) in natural waters and wastewater effluents. The sensors are prepared by depositing a layer of multiwalled carbon nanotubes (MWCNTs) dispersed in a porous Nafion film on to a boron-doped diamond (BDD) electrode substrate. The porous-Nafion-MWCNT/BDD electrode enhanced detection of CFX due to selective adsorption, which was accomplished by a combination of electrostatic attraction at -SO3(-) sites in the porous Nafion film and the formation of charge assisted hydrogen bonding between CFX and -COOH MWCNT surface functional groups. By contrast, the bare BDD electrode did not show any activity for CFX oxidation. The sensors were selective for CFX detection in the presence of other antibiotics (i.e., amoxicillin) and other nontarget water constituents (i.e., Cl(-), Ca(2+), humic acid, sodium dodecylbenzenesulfonate, salicylic acid, 4-aminobenzoic acid, and 4-hydroxybenzoic acid). A limit of detection of 5 nM (S/N = 5.04 ± 0.26) in a 0.1 M KH2PO4 supporting electrolyte (pH = 4.5) was obtained using differential pulse voltammetry. The linear dynamic ranges with respect to CFX concentration were 0.005-0.05 μM and 0.05-10 μM, and the sensitivities were 41 ± 5.2 μA μM(-1) and 2.1 ± 0.22 μA μM(-1), respectively. Sensor fouling was observed at high concentrations of some organic compounds such as 1 mM 4-aminobenzoic acid and 4-hydroxybenzoic acid. However, a short cathodic treatment fully restores sensor response. The results indicate that these sensors have application in detecting CFX in natural waters and wastewater effluents. PMID:26711553

  2. Feature selection of seismic waveforms for long period event detection at Cotopaxi Volcano

    NASA Astrophysics Data System (ADS)

    Lara-Cueva, R. A.; Benítez, D. S.; Carrera, E. V.; Ruiz, M.; Rojo-Álvarez, J. L.

    2016-04-01

    Volcano Early Warning Systems (VEWS) have become a research topic in order to preserve human lives and material losses. In this setting, event detection criteria based on classification using machine learning techniques have proven useful, and a number of systems have been proposed in the literature. However, to the best of our knowledge, no comprehensive and principled study has been conducted to compare the influence of the many different sets of possible features that have been used as input spaces in previous works. We present an automatic recognition system of volcano seismicity, by considering feature extraction, event classification, and subsequent event detection, in order to reduce the processing time as a first step towards a high reliability automatic detection system in real-time. We compiled and extracted a comprehensive set of temporal, moving average, spectral, and scale-domain features, for separating long period seismic events from background noise. We benchmarked two usual kinds of feature selection techniques, namely, filter (mutual information and statistical dependence) and embedded (cross-validation and pruning), each of them by using suitable and appropriate classification algorithms such as k Nearest Neighbors (k-NN) and Decision Trees (DT). We applied this approach to the seismicity presented at Cotopaxi Volcano in Ecuador during 2009 and 2010. The best results were obtained by using a 15 s segmentation window, feature matrix in the frequency domain, and DT classifier, yielding 99% of detection accuracy and sensitivity. Selected features and their interpretation were consistent among different input spaces, in simple terms of amplitude and spectral content. Our study provides the framework for an event detection system with high accuracy and reduced computational requirements.

  3. Erotomanic stalking in evolutionary perspective.

    PubMed

    Brüne, Martin

    2003-01-01

    Erotomania, the delusion of being loved by another person, comprises marked sex differences concerning prevalence rates and behavior. Whereas traditional psychiatry has considered erotomania to be almost entirely restricted to women, recent studies have revealed that criminal offenses associated with the condition occur much more frequently in men. The main hypothesis of this article is that these findings may be explained in terms of evolutionary theory. Erotomania, accordingly, may be viewed as a pathological variant of a specific sexual strategy that evolved under selection pressures of the human environment of evolutionary adaptedness. The overt behavior is related to the pursuit of long-term mating, its potentially beneficial effect on inclusive fitness of the individual, and disparate strategies of the sexes to ensure sexual fidelity of the potential partner. Therefore, the evolutionary approach provides a plausible explanation as to why forensically relevant erotomania prevails in men. The pathological process of delusional misinterpretation of perceived signals from the social environment itself may result from poor reality testing due to a failure of social meta-cognition. The evolutionary perspective may provide additional insights into the nature of sex-specific behaviors and may improve our understanding of forensically relevant behaviors. PMID:12579619

  4. Cyclometallated ruthenium complex-modified upconversion nanophosphors for selective detection of Hg2+ ions in water

    NASA Astrophysics Data System (ADS)

    Li, Xianghong; Wu, Yongquan; Liu, Yi; Zou, Xianmei; Yao, Liming; Li, Fuyou; Feng, Wei

    2013-12-01

    Upconversion detection nanocomposites were assembled for the selective luminescent detection of mercury ions in water. A hydrophobic cyclometallated ruthenium complex [RuII(bpy)2(thpy)]PF6 (abbreviated as Ru1; bpy = 2,2'-bipyridine and thpy = 2-(2-thienyl)pyridine) is employed as a chemodosimeter to assemble on amphiphilic polymer-coating upconversion nanophosphors (UCNPs) based on the hydrophobic-hydrophobic interaction. Upon addition of Hg2+, the nanocomposite not only exhibits a remarkable color change from deep-red to yellow, but also an enhanced upconversion luminescence (UCL) emission by hindering the luminescent resonance energy transfer (LRET) process from the upconversion emission of UCNPs to Ru1. Using the ratiometric UCL emission as a detection signal, the detection limit of Hg2+ for this nanoprobe in aqueous solution is 8.2 ppb, which is much lower than that (329 ppb) determined by UV/Vis technology. Such an Hg2+-tunable LRET process provides a general strategy for fabricating a water-soluble upconversion-based nanoprobe for some special analyte.Upconversion detection nanocomposites were assembled for the selective luminescent detection of mercury ions in water. A hydrophobic cyclometallated ruthenium complex [RuII(bpy)2(thpy)]PF6 (abbreviated as Ru1; bpy = 2,2'-bipyridine and thpy = 2-(2-thienyl)pyridine) is employed as a chemodosimeter to assemble on amphiphilic polymer-coating upconversion nanophosphors (UCNPs) based on the hydrophobic-hydrophobic interaction. Upon addition of Hg2+, the nanocomposite not only exhibits a remarkable color change from deep-red to yellow, but also an enhanced upconversion luminescence (UCL) emission by hindering the luminescent resonance energy transfer (LRET) process from the upconversion emission of UCNPs to Ru1. Using the ratiometric UCL emission as a detection signal, the detection limit of Hg2+ for this nanoprobe in aqueous solution is 8.2 ppb, which is much lower than that (329 ppb) determined by UV/Vis technology

  5. A multiobjective evolutionary algorithm to find community structures based on affinity propagation

    NASA Astrophysics Data System (ADS)

    Shang, Ronghua; Luo, Shuang; Zhang, Weitong; Stolkin, Rustam; Jiao, Licheng

    2016-07-01

    Community detection plays an important role in reflecting and understanding the topological structure of complex networks, and can be used to help mine the potential information in networks. This paper presents a Multiobjective Evolutionary Algorithm based on Affinity Propagation (APMOEA) which improves the accuracy of community detection. Firstly, APMOEA takes the method of affinity propagation (AP) to initially divide the network. To accelerate its convergence, the multiobjective evolutionary algorithm selects nondominated solutions from the preliminary partitioning results as its initial population. Secondly, the multiobjective evolutionary algorithm finds solutions approximating the true Pareto optimal front through constantly selecting nondominated solutions from the population after crossover and mutation in iterations, which overcomes the tendency of data clustering methods to fall into local optima. Finally, APMOEA uses an elitist strategy, called "external archive", to prevent degeneration during the process of searching using the multiobjective evolutionary algorithm. According to this strategy, the preliminary partitioning results obtained by AP will be archived and participate in the final selection of Pareto-optimal solutions. Experiments on benchmark test data, including both computer-generated networks and eight real-world networks, show that the proposed algorithm achieves more accurate results and has faster convergence speed compared with seven other state-of-art algorithms.

  6. 3,5-Dinitrobenzoic acid-capped upconverting nanocrystals for the selective detection of melamine.

    PubMed

    Hazra, Chanchal; Adusumalli, Venkata N K B; Mahalingam, Venkataramanan

    2014-05-28

    In this Research Article, we report for the first time the use of upconverting nanoparticles to detect melamine up to nanomolar concentration. Detection of melamine is important as it is one of the adulterant in protein rich food products due to its high nitrogen content. In this work, we have shown how the electron deficient 3,5-dinitrobenzoic acid (DNB)-coated Er/Yb-NaYF4 nanocrystals can specifically bind to electron rich melamine and alter the upconverting property of the nanocrystals. This selective binding led to the quenching of the upconversion emission from the nanocrystals. The high selectivity is verified by the addition of various analytes similar in structure with that of melamine. In addition, the selective quenching of the upconversion emission is reversible with the addition of dilute acid. This process has been repeated for more than five cycles with only a slight decrease in the sensing ability. The study was also extended to real milk samples, where the milk adulterated with melamine quenches the emission intensity of the DNB coated NaYF4:Er/Yb nanocrystals, whereas hardly any change is noted for the unadulterated milk sample. The high robustness and the sharp emission peaks make Er(3+)/Yb(3+)-doped NaYF4 nanocrystals a potential melamine sensing material over other organic fluorophores and nanocrystals possessing broad emissions. PMID:24742261

  7. Hydrazide d-luciferin for in vitro selective detection and intratumoral imaging of Cu(2.).

    PubMed

    Zheng, Zhen; Wang, Lin; Tang, Wei; Chen, Peiyao; Zhu, Hui; Yuan, Yue; Li, Gongyu; Zhang, Huafeng; Liang, Gaolin

    2016-09-15

    Copper is an essential micronutrient involved in fundamental life processes but using a bioluminescence (BL) probe to selectively sense Cu(2+)in vitro or image Cu(2+)in vivo is still unavailable. Herein, a latent BL probe hydrazide d-luciferin (1) was rationally designed and successfully applied it for selective detection of Cu(2+)in vitro and imaging Cu(2+) in living cells and in tumors. Upon the catalysis of Cu(2+), 1 was converted to d-luciferin and turned on the BL in the presence of firefly luciferase (fLuc). In vitro tests indicated that 1 could be applied for highly selective sensing Cu(2+) within the range of 0-80μM with a limit of detection (LOD) of 39.0nM. Cell and animal experiments indicated that 1 could be applied for specific BL imaging of Cu(2+) in living cells and tumors and the BL signal of 1 was more stable and longer than that of d-luciferin. We envision that this unique probe 1 might serve as an elucidative tool for further exploration of the biological roles of Cu(2+) in physiological and pathological processes in the near future. PMID:27131992

  8. Triazole-based highly selective supramolecular sensor for the detection of diclofenac in real samples.

    PubMed

    Ahmed, Farid; Shah, Kiramat; Awan, Iqra Zubair; Shah, Muhammad Raza

    2016-07-01

    A triazole-based supramolecular chemosensor 6 for the selective spectrophotometric detection of diclofenac in human plasma and tap water was developed. The 6 was synthesized through click approach and characterized via UV-vis spectroscopy, FT-IR, Mass and NMR spectroscopy. The supramolecular interaction of compound 6 with commonly used drugs has been investigated with the help of UV-vis spectral titrations, FT-IR and (1)H, (13)C NMR spectroscopy. The UV-visible spectral changes upon addition of various commonly used drugs showed that compound 6 is highly selective for diclofenac over other drugs. The supramolecule 6 exhibited a selective enhancement in the absorbance intensity after mixing with diclofenac in human plasma and water samples in the presence of other drugs at pH 6-7, with a linear range of 0.938 (R(2)=0.938) and a limit of detection 10µM. The relative standard deviation (RSD) for 100µM diclofenac was found to be 0.462. The Job's plot analysis revealed that diclofenac bind to compound 6 in 1:1 stoichiometry. PMID:27003618

  9. A highly selective electrochemical impedance spectroscopy-based aptasensor for sensitive detection of acetamiprid.

    PubMed

    Fan, Lifang; Zhao, Guohua; Shi, Huijie; Liu, Meichuan; Li, Zhengxin

    2013-05-15

    A simple aptasensor for sensitive and selective detection of acetamiprid has been developed based on electrochemical impedance spectroscopy (EIS). To improve sensitivity of the aptasensor, gold nanoparticles (AuNPs) were electrodeposited on the bare gold electrode surface by cycle voltammetry (CV), which was employed as a platform for aptamer immobilization. With the addition of acetamiprid, the formation of acetamiprid-aptamer complex on the AuNPs-deposited electrode surface resulted in an increase of electron transfer resistance (Ret). The change of Ret strongly depends on acetamiprid concentration, which is applied for acetamiprid quantification. A wide linear range was obtained from 5 to 600nM with a low detection limit of 1nM. The control experiments performed by employing the pesticides that may coexist or have similar structure with acetamiprid demonstrate that the aptasensor has only specific recognition to acetamiprid, resulting in high selectivity of the aptasensor. The dissociation constant, Kd of 23.41nM for acetamiprid-aptamer complex has been determined from the differential capacitance (Cd) by assuming a Langmuir isotherm, which indicates strong interaction between acetamiprid and aptamer, further proving high selectivity of the aptasensor. Besides, the applicability of the developed aptasensor has been successfully evaluated by determining acetamiprid in the real samples, wastewater and tomatoes. PMID:23274191

  10. Fluorescent sensors for selective detection of thiols: expanding the intramolecular displacement based mechanism to new chromophores.

    PubMed

    Niu, Li-Ya; Zheng, Hai-Rong; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

    2014-03-21

    Biological thiols, including cysteine (Cys), homocystein (Hcy) and glutathione (GSH), play crucial roles in maintaining the appropriate redox status of biological systems. An abnormal level of biothiols is associated with different diseases, therefore, the discrimination between them is of great importance. Herein, we present two fluorescent sensors for selective detection of biothiols based on our recently reported intramolecular displacement mechanism. We expanded this mechanism to commercially available chromophores, 4-chloro-7-nitro-2,1,3-benzoxadiazole (NBD-Cl) and heptamethine cyanine dye IR-780. The sensors operate by undergoing displacement of chloride by thiolate. The amino groups of Cys/Hcy further replace the thiolate to form amino-substituted products, which exhibit dramatically different photophysical properties compared to sulfur-substituted products from the reaction with GSH. NBD-Cl is highly selective towards Cys/Hcy and exhibits significant fluorescence enhancement. IR-780 showed a variation in its fluorescence ratio towards Cys over other thiols. Both of the sensors can be used for live-cell imaging of Cys. The wide applicability of the mechanism may provide a powerful tool for developing novel fluorescent sensors for selective detection of biothiols. PMID:24466567

  11. A research of selected textural features for detection of asbestos-cement roofing sheets using orthoimages

    NASA Astrophysics Data System (ADS)

    Książek, Judyta

    2015-10-01

    At present, there has been a great interest in the development of texture based image classification methods in many different areas. This study presents the results of research carried out to assess the usefulness of selected textural features for detection of asbestos-cement roofs in orthophotomap classification. Two different orthophotomaps of southern Poland (with ground resolution: 5 cm and 25 cm) were used. On both orthoimages representative samples for two classes: asbestos-cement roofing sheets and other roofing materials were selected. Estimation of texture analysis usefulness was conducted using machine learning methods based on decision trees (C5.0 algorithm). For this purpose, various sets of texture parameters were calculated in MaZda software. During the calculation of decision trees different numbers of texture parameters groups were considered. In order to obtain the best settings for decision trees models cross-validation was performed. Decision trees models with the lowest mean classification error were selected. The accuracy of the classification was held based on validation data sets, which were not used for the classification learning. For 5 cm ground resolution samples, the lowest mean classification error was 15.6%. The lowest mean classification error in the case of 25 cm ground resolution was 20.0%. The obtained results confirm potential usefulness of the texture parameter image processing for detection of asbestos-cement roofing sheets. In order to improve the accuracy another extended study should be considered in which additional textural features as well as spectral characteristics should be analyzed.

  12. Enhancing the Detection Limit of Nanoscale Biosensors via Topographically Selective Functionalization

    PubMed Central

    Lifson, Mark A.; Roy, Dhrubajyoti Basu; Miller, Benjamin L.

    2014-01-01

    Nanoscale biosensors have remarkable theoretical sensitivities, but often suffer from sub-optimal limits of detection in practice. This is in part because the sensing area of nanoscale sensors is orders of magnitude smaller than the total device substrate. Current strategies to immobilize probes (capture molecules) functionalize both sensing and non-sensing regions, leading to target depletion and diminished limits of detection. The difference in topography between these regions on nanoscale biosensors offers a way to selectively address only the sensing area. We developed a bottom-up, topographically selective approach employing self-assembled poly(N-isopropylacrylamide) (PNIPAM) hydrogel nanoparticles as a mask to preferentially bind target to only the active sensing region of a photonic crystal (PhC) biosensor. This led to over one order of magnitude improvement in the limit of detection for the device, in agreement with finite element simulations. Since the sensing elements in many nanoscale sensors are topographically distinct, this approach should be widely applicable. PMID:24372197

  13. Rapidly responsive and highly selective fluorescent probe for sulfite detection in real samples and living cells.

    PubMed

    Li, Hongda

    2015-10-15

    Sulfites (HSO3(-) or SO3(-)) have very significant toxicity in the environment and in the system. However, developing specific identification of sulfite probes is still very important. In this paper, a highly selective colorimetric and fluorescent probe (HHC) was synthesized to detect HSO3(-) in real samples and living cells. Sensing performance and preponderance are listed as follows. First, probe HHC showed remarkable selectivity for HSO3(-) over varieties of other species, including cysteine, glutathione, S(2-), CN(-), and reactive oxygen species, mainly because of the introduction of the electron-poor C=C double bond for HSO3(-). Second, probe HHC has great molar absorptivity, allowing it to act as a visual detection of probe for HSO3(-). Third, the fluorescence intensities of HHC linearly correlate with the concentration of HSO3(-), with a detection limit of 6.8 nm. Finally, our proposed probe can be applied to the visually determination of trace HSO3(-) in real samples and living HeLa cells with high precision. We hope that our proposed probe will greatly benefit biological sciences when biological researchers survey the role of HSO3(-) in biological systems. PMID:26515011

  14. Ultrasensitive and selective non-enzymatic glucose detection using copper nanowires.

    PubMed

    Zhang, Yuchan; Su, Liang; Manuzzi, Dan; de los Monteros, Honorio Valdés Espinosa; Jia, Wenzhao; Huo, Danqun; Hou, Changjun; Lei, Yu

    2012-01-15

    In the pursuit of more economical electrocatalysts for non-enzymatic glucose sensors, one-dimensional Cu nanowires (Cu NWs) with uniform size distribution and a large aspect ratio (>200) were synthesized by a facile, scalable, wet-chemistry approach. The morphology, crystallinity, and surface property of the as-prepared Cu NWs were examined by SEM, XRD, and XPS, respectively. The electrochemical property of Cu NWs for glucose electrooxidation was thoroughly investigated by cyclic voltammetry. In the amperometric detection of glucose, the Cu NWs modified glassy carbon electrode exhibited an extraordinary limit of detection as low as 35 nM and a wide dynamic range with excellent sensitivity of 420.3 μA cm(-2) mM(-1), which was more than 10,000 times higher than that of the control electrode without Cu NWs. The performance of the developed glucose sensor was also independent to oxygen concentration and free from chloride poisoning. Furthermore, the interference from uric acid, ascorbic acid, acetaminophen, fructose, and sucrose at the level of their physiological concentration were insignificant, indicating excellent selectivity. Finally, good accuracy and high precision for the quantification of glucose concentration in human serum samples implicate the applicability of Cu NWs in sensitive and selective non-enzymatic glucose detection. PMID:22154404

  15. Synthesis of Au/Graphene Oxide Composites for Selective and Sensitive Electrochemical Detection of Ascorbic Acid

    NASA Astrophysics Data System (ADS)

    Song, Jian; Xu, Lin; Xing, Ruiqing; Li, Qingling; Zhou, Chunyang; Liu, Dali; Song, Hongwei

    2014-12-01

    In this work, we present a novel ascorbic acid (AA) sensor applied to the detection of AA in human sera and pharmaceuticals. A series of Au nanoparticles (NPs) and graphene oxide sheets (Au NP/GO) composites were successfully synthesized by reduction of gold (III) using sodium citrate. Then the Au NP/GO composites were used to construct nonenzymatic electrodes in practical AA measurement. The electrode that has the best performance presents attractive analytical features, such as a low working potential of +0.15 V, a high sensitivity of 101.86 μA mM-1 cm-2 to AA, a low detection limit of 100 nM, good reproducibility and excellent selectivity. And more,it was also employed to accurately and practically detect AA in human serum and clinical vitamin C tablet with the existence of some food additive. The enhanced AA electrochemical properties of the Au NP/GO modified electrode in our work can be attributed to the improvement of electroactive surface area of Au NPs and the synergistic effect from the combination of Au NPs and GO sheets. This work shows that the Au NP/GO/GCEs hold the prospect for sensitive and selective determination of AA in practical clinical application.

  16. Ultrasensitive quantum dot fluorescence quenching assay for selective detection of mercury ions in drinking water.

    PubMed

    Ke, Jun; Li, Xinyong; Zhao, Qidong; Hou, Yang; Chen, Junhong

    2014-01-01

    Mercury is one of the most acutely toxic substances at trace level to human health and living thing. Developing a rapid, cheap and water soluble metal sensor for detecting mercury ions at ppb level remains a challenge. Herein, a metal sensor consisting of MPA coated Mn doped ZnSe/ZnS colloidal nanoparticles was utilized to ultrasensitively and selectively detect Hg(2+) ions with a low detection limit (0.1 nM) over a dynamic range from 0 to 20 nM. According to strong interaction between thiol(s) and mercury ions, mercaptopropionic acid (MPA) was used as a highly unique acceptor for mercury ions in the as-obtained ultrasensitive sensor. In the presence of mercury ions, colloidal nanoparticles rapidly agglomerated due to changes of surface chemical properties, which results in severe quenching of fluorescent intensity. Meanwhile, we find that the original ligands are separated from the surface of colloidal nanoparticles involving strongly chelation between mercury ion and thiol(s) proved by controlled IR analysis. The result shows that the QD-based metal ions sensor possesses satisfactory precision, high sensitivity and selectivity, and could be applied for the quantification analysis of real samples. PMID:25005836

  17. Label free selective detection of estriol using graphene oxide-based fluorescence sensor

    NASA Astrophysics Data System (ADS)

    Kushwaha, H. S.; Sao, Reshma; Vaish, Rahul

    2014-07-01

    Water-soluble and fluorescent Graphene oxide (GO) is biocompatible, easy, and economical to synthesize. Interestingly, GO is also capable of quenching fluorescence. On the basis of its fluorescence and quenching abilities, GO has been reported to serve as an energy acceptor in a fluorescence resonance energy transfer (FRET) sensor. GO-based FRET biosensors have been widely reported for sensing of proteins, nucleic acid, ATP (Adenosine triphosphate), etc. GO complexes with fluorescent dyes and enzymes have been used to sense metal ions. Graphene derivatives have been used for sensing endocrine-disrupting chemicals like bisphenols and chlorophenols with high sensitivity and good reproducibility. On this basis, a novel GO based fluorescent sensor has been successfully designed to detect estriol with remarkable selectivity and sensitivity. Estriol is one of the three estrogens in women and is considered to be medically important. Estriol content of maternal urine or plasma acts as an important screening marker for estimating foetal growth and development. In addition, estriol is also used as diagnostic marker for diseases like breast cancer, osteoporosis, neurodegenerative and cardiovascular diseases, insulin resistance, lupus erythematosus, endometriosis, etc. In this present study, we report for the first time a rapid, sensitive with detection limit of 1.3 nM, selective and highly biocompatible method for label free detection of estriol under physiological conditions using fluorescence assay.

  18. Ultrasensitive Quantum Dot Fluorescence quenching Assay for Selective Detection of Mercury Ions in Drinking Water

    PubMed Central

    Ke, Jun; Li, Xinyong; Zhao, Qidong; Hou, Yang; Chen, Junhong

    2014-01-01

    Mercury is one of the most acutely toxic substances at trace level to human health and living thing. Developing a rapid, cheap and water soluble metal sensor for detecting mercury ions at ppb level remains a challenge. Herein, a metal sensor consisting of MPA coated Mn doped ZnSe/ZnS colloidal nanoparticles was utilized to ultrasensitively and selectively detect Hg2+ ions with a low detection limit (0.1 nM) over a dynamic range from 0 to 20 nM. According to strong interaction between thiol(s) and mercury ions, mercaptopropionic acid (MPA) was used as a highly unique acceptor for mercury ions in the as-obtained ultrasensitive sensor. In the presence of mercury ions, colloidal nanoparticles rapidly agglomerated due to changes of surface chemical properties, which results in severe quenching of fluorescent intensity. Meanwhile, we find that the original ligands are separated from the surface of colloidal nanoparticles involving strongly chelation between mercury ion and thiol(s) proved by controlled IR analysis. The result shows that the QD-based metal ions sensor possesses satisfactory precision, high sensitivity and selectivity, and could be applied for the quantification analysis of real samples. PMID:25005836

  19. Synthesis of Au/Graphene Oxide Composites for Selective and Sensitive Electrochemical Detection of Ascorbic Acid

    PubMed Central

    Song, Jian; Xu, Lin; Xing, Ruiqing; Li, Qingling; Zhou, Chunyang; Liu, Dali; Song, Hongwei

    2014-01-01

    In this work, we present a novel ascorbic acid (AA) sensor applied to the detection of AA in human sera and pharmaceuticals. A series of Au nanoparticles (NPs) and graphene oxide sheets (Au NP/GO) composites were successfully synthesized by reduction of gold (III) using sodium citrate. Then the Au NP/GO composites were used to construct nonenzymatic electrodes in practical AA measurement. The electrode that has the best performance presents attractive analytical features, such as a low working potential of +0.15 V, a high sensitivity of 101.86 μA mM−1 cm−2 to AA, a low detection limit of 100 nM, good reproducibility and excellent selectivity. And more,it was also employed to accurately and practically detect AA in human serum and clinical vitamin C tablet with the existence of some food additive. The enhanced AA electrochemical properties of the Au NP/GO modified electrode in our work can be attributed to the improvement of electroactive surface area of Au NPs and the synergistic effect from the combination of Au NPs and GO sheets. This work shows that the Au NP/GO/GCEs hold the prospect for sensitive and selective determination of AA in practical clinical application. PMID:25515430

  20. Ultrasensitive Quantum Dot Fluorescence quenching Assay for Selective Detection of Mercury Ions in Drinking Water

    NASA Astrophysics Data System (ADS)

    Ke, Jun; Li, Xinyong; Zhao, Qidong; Hou, Yang; Chen, Junhong

    2014-07-01

    Mercury is one of the most acutely toxic substances at trace level to human health and living thing. Developing a rapid, cheap and water soluble metal sensor for detecting mercury ions at ppb level remains a challenge. Herein, a metal sensor consisting of MPA coated Mn doped ZnSe/ZnS colloidal nanoparticles was utilized to ultrasensitively and selectively detect Hg2+ ions with a low detection limit (0.1 nM) over a dynamic range from 0 to 20 nM. According to strong interaction between thiol(s) and mercury ions, mercaptopropionic acid (MPA) was used as a highly unique acceptor for mercury ions in the as-obtained ultrasensitive sensor. In the presence of mercury ions, colloidal nanoparticles rapidly agglomerated due to changes of surface chemical properties, which results in severe quenching of fluorescent intensity. Meanwhile, we find that the original ligands are separated from the surface of colloidal nanoparticles involving strongly chelation between mercury ion and thiol(s) proved by controlled IR analysis. The result shows that the QD-based metal ions sensor possesses satisfactory precision, high sensitivity and selectivity, and could be applied for the quantification analysis of real samples.

  1. Selecting a sensitive battery of bioassays to detect toxic effects of metals in effluents.

    PubMed

    de Paiva Magalhães, Danielly; da Costa Marques, Mônica Regina; Fernandes Baptista, Darcilio; Forsin Buss, Daniel

    2014-09-01

    The use of bioassay batteries is necessary to evaluate toxic effects at various biological levels. The selection of bioassays without prior testing and determination of the most sensitive/suitable groups for each impact may allow the discharge of effluents that pose a threat to the environment. The present study tested and selected a battery of sensitive ecotoxicological bioassays for detecting toxic effects of metals. The sensitivities of six organisms were evaluated (algae Pseudokirchneriella subcapitata and Chlorella vulgaris, Cladocera Daphnia similis and Ceriodaphnia dubia, and fish Poecilia reticulata and Danio rerio) after exposure to 10 individual metal species deemed toxic to the aquatic environment (Ag(+), Cd(2+), Cu(+), Cu(2+), Cr(3+), Cr(6+), Pb(2+), Ni(2+), Zn(2+), and Hg(2+)) and to real (steel-mill) and laboratory simulated effluents. In the bioassays, fish were the least sensitive; D. rerio showed no sensitivity to any of the effluents tested. P. subcapitata was a good bioindicator of Cr(3+) toxicity, and D. similis was the most sensitive organism to Hg(2+); but the toxic effect of effluents with higher levels of Hg(2+) was better detected by C. dubia. The most sensitive battery of bioassays to detect low concentrations of dissolved metals in effluents was the 72-h chronic test with C. vulgaris and the 48-h acute test with C. dubia. PMID:25199585

  2. Selective calcium ion detection with functionalized ZnO nanorods-extended gate MOSFET.

    PubMed

    Asif, M H; Nur, O; Willander, M; Danielsson, B

    2009-07-15

    Zinc oxide nanorod-extended gate field effect transistor (MOSFET) is demonstrated for the detection of calcium (Ca(2+)) ions. ZnO nanorods were grown on the surface of a silver wire to produce an electrochemical nanosensor for selectively detecting Ca(2+). The electrochemical response from the interaction between the ZnO nanorods and Ca(2+) in an aqueous solution is coupled directly to the gate of a field effect transistor (MOSFET). The induced voltage change on the gate results in a measureable current response. In order to adapt the sensors for Ca(2+) ions measurements in biological fluids with sufficient selectivity and stability, a plastic membrane coating containing ionophores was applied on the nanorods. The sensor exhibited a linear response within the range of interest from 1 microM to 1 mM. This work demonstrates a simple technique for sensitive detection of Ca(2+) ions by efficient transfer of the chemical response directly to a standard electronic component producing a low impedance signal. PMID:19442511

  3. Quantifying evolutionary dynamics from variant-frequency time series.

    PubMed

    Khatri, Bhavin S

    2016-01-01

    From Kimura's neutral theory of protein evolution to Hubbell's neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher's angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series. PMID:27616332

  4. Evolutionary stability on graphs

    PubMed Central

    Ohtsuki, Hisashi; Nowak, Martin A.

    2008-01-01

    Evolutionary stability is a fundamental concept in evolutionary game theory. A strategy is called an evolutionarily stable strategy (ESS), if its monomorphic population rejects the invasion of any other mutant strategy. Recent studies have revealed that population structure can considerably affect evolutionary dynamics. Here we derive the conditions of evolutionary stability for games on graphs. We obtain analytical conditions for regular graphs of degree k > 2. Those theoretical predictions are compared with computer simulations for random regular graphs and for lattices. We study three different update rules: birth-death (BD), death-birth (DB), and imitation (IM) updating. Evolutionary stability on sparse graphs does not imply evolutionary stability in a well-mixed population, nor vice versa. We provide a geometrical interpretation of the ESS condition on graphs. PMID:18295801

  5. Simultaneous detection of ascorbate and uric acid using a selectively catalytic surface.

    PubMed

    Nassef, Hossam M; Radi, Abd-Elgawad; O'Sullivan, Ciara

    2007-01-30

    The direct and selective detection of ascorbate at conventional carbon or metal electrodes is difficult due to its large overpotential and fouling by oxidation products. Electrode modification by electrochemical reduction of diazonium salts of different aryl derivatives is useful for catalytic, analytical and biotechnological applications. A monolayer of o-aminophenol (o-AP) was grafted on a glassy carbon electrode (GCE) via the electrochemical reduction of its in situ prepared diazonium salts in aqueous solution. The o-aminophenol confined surface was characterized by cyclic voltammetry. The grafted film demonstrated an excellent electrocatalytic activity towards the oxidation of ascorbate in phosphate buffer of pH 7.0 shifting the overpotential from +462 to +263 mV versus Ag/AgCl. Cyclic voltammetry and d.c. amperometric measurements were carried out for the quantitative determination of ascorbate and uric acid. The catalytic oxidation peak current was linearly dependent on the ascorbate concentration and a linear calibration curve was obtained using d.c. amperometry in the range of 2-20 microM of ascorbate with a correlation coefficient 0.9998, and limit of detection 0.3 microM. The effect of H2O2 on the electrocatalytic oxidation of ascorbate at o-aminophenol modified GC electrode has been studied, the half-life time and rate constant was estimated as 270 s, and 2.57x10(-3) s(-1), respectively. The catalytically selective electrode was applied to the simultaneous detection of ascorbate and uric acid, and used for their determination in real urine samples. This o-AP/GCE showed high stability with time, and was used as a simple and precise amperometric sensor for the selective determination of ascorbate. PMID:17386544

  6. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    SciTech Connect

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonance can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.

  7. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    DOE PAGESBeta

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonancemore » can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.« less

  8. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    PubMed Central

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-01-01

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonance can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. The method can be applied to a wide range of solid-state systems. PMID:26497777

  9. A new and fast image feature selection method for developing an optimal mammographic mass detection scheme

    PubMed Central

    Tan, Maxine; Pu, Jiantao; Zheng, Bin

    2014-01-01

    Purpose: Selecting optimal features from a large image feature pool remains a major challenge in developing computer-aided detection (CAD) schemes of medical images. The objective of this study is to investigate a new approach to significantly improve efficacy of image feature selection and classifier optimization in developing a CAD scheme of mammographic masses. Methods: An image dataset including 1600 regions of interest (ROIs) in which 800 are positive (depicting malignant masses) and 800 are negative (depicting CAD-generated false positive regions) was used in this study. After segmentation of each suspicious lesion by a multilayer topographic region growth algorithm, 271 features were computed in different feature categories including shape, texture, contrast, isodensity, spiculation, local topological features, as well as the features related to the presence and location of fat and calcifications. Besides computing features from the original images, the authors also computed new texture features from the dilated lesion segments. In order to select optimal features from this initial feature pool and build a highly performing classifier, the authors examined and compared four feature selection methods to optimize an artificial neural network (ANN) based classifier, namely: (1) Phased Searching with NEAT in a Time-Scaled Framework, (2) A sequential floating forward selection (SFFS) method, (3) A genetic algorithm (GA), and (4) A sequential forward selection (SFS) method. Performances of the four approaches were assessed using a tenfold cross validation method. Results: Among these four methods, SFFS has highest efficacy, which takes 3%–5% of computational time as compared to GA approach, and yields the highest performance level with the area under a receiver operating characteristic curve (AUC) = 0.864 ± 0.034. The results also demonstrated that except using GA, including the new texture features computed from the dilated mass segments improved the AUC

  10. A Wearable Channel Selection-Based Brain-Computer Interface for Motor Imagery Detection

    PubMed Central

    Lo, Chi-Chun; Chien, Tsung-Yi; Chen, Yu-Chun; Tsai, Shang-Ho; Fang, Wai-Chi; Lin, Bor-Shyh

    2016-01-01

    Motor imagery-based brain-computer interface (BCI) is a communication interface between an external machine and the brain. Many kinds of spatial filters are used in BCIs to enhance the electroencephalography (EEG) features related to motor imagery. The approach of channel selection, developed to reserve meaningful EEG channels, is also an important technique for the development of BCIs. However, current BCI systems require a conventional EEG machine and EEG electrodes with conductive gel to acquire multi-channel EEG signals and then transmit these EEG signals to the back-end computer to perform the approach of channel selection. This reduces the convenience of use in daily life and increases the limitations of BCI applications. In order to improve the above issues, a novel wearable channel selection-based brain-computer interface is proposed. Here, retractable comb-shaped active dry electrodes are designed to measure the EEG signals on a hairy site, without conductive gel. By the design of analog CAR spatial filters and the firmware of EEG acquisition module, the function of spatial filters could be performed without any calculation, and channel selection could be performed in the front-end device to improve the practicability of detecting motor imagery in the wearable EEG device directly or in commercial mobile phones or tablets, which may have relatively low system specifications. Finally, the performance of the proposed BCI is investigated, and the experimental results show that the proposed system is a good wearable BCI system prototype. PMID:26861347

  11. Cyclic Peptide-Decorated Self-Assembled Nanohybrids for Selective Recognition and Detection of Multivalent RNAs.

    PubMed

    Choi, Jun Shik; Han, So-hee; Kim, Hyoseok; Lim, Yong-Beom

    2016-03-16

    Although there has been substantial advancement in the development of nanostructures, the development of self-assembled nanostructures that can selectively recognize multivalent targets has been very difficult. Here we show the proof of concept that topology-controlled peptide nanoassemblies can selectively recognize and detect a multivalent RNA target. We compared the differential behaviors of peptides in a linear or cyclic topology in terms of peptide-gold nanoparticle hybrid nanostructure formation, conformational stabilization, monovalent and multivalent RNA binding in vitro, and multivalent RNA recognition in live cells. When the topology-dependent selectivity amplification of the cyclic peptide hybrids is combined with the noninvasive nature of dark-field microscopy, the cellular localization of the viral Rev response element (RRE) RNA can be monitored in situ. Because intracellular interactions are often mediated by overlapping binding partners with weak affinity, the topology-controlled peptide assemblies can provide a versatile means to convert weak ligands into multivalent ligands with high affinity and selectivity. PMID:26886413

  12. A Wearable Channel Selection-Based Brain-Computer Interface for Motor Imagery Detection.

    PubMed

    Lo, Chi-Chun; Chien, Tsung-Yi; Chen, Yu-Chun; Tsai, Shang-Ho; Fang, Wai-Chi; Lin, Bor-Shyh

    2016-01-01

    Motor imagery-based brain-computer interface (BCI) is a communication interface between an external machine and the brain. Many kinds of spatial filters are used in BCIs to enhance the electroencephalography (EEG) features related to motor imagery. The approach of channel selection, developed to reserve meaningful EEG channels, is also an important technique for the development of BCIs. However, current BCI systems require a conventional EEG machine and EEG electrodes with conductive gel to acquire multi-channel EEG signals and then transmit these EEG signals to the back-end computer to perform the approach of channel selection. This reduces the convenience of use in daily life and increases the limitations of BCI applications. In order to improve the above issues, a novel wearable channel selection-based brain-computer interface is proposed. Here, retractable comb-shaped active dry electrodes are designed to measure the EEG signals on a hairy site, without conductive gel. By the design of analog CAR spatial filters and the firmware of EEG acquisition module, the function of spatial filters could be performed without any calculation, and channel selection could be performed in the front-end device to improve the practicability of detecting motor imagery in the wearable EEG device directly or in commercial mobile phones or tablets, which may have relatively low system specifications. Finally, the performance of the proposed BCI is investigated, and the experimental results show that the proposed system is a good wearable BCI system prototype. PMID:26861347

  13. Novel Piezoelectric Fiber Transducers for Mode Selective Excitation and Detection of Lamb Waves

    NASA Astrophysics Data System (ADS)

    Koehler, B.; Frankenstein, B.; Schubert, F.; Barth, M.

    2009-03-01

    One of the most widely applied methods for Structural Health Monitoring of plate like structures, shells and tubes is based on the transmission and reception of guided elastic waves. But, dispersion of various wave modes leads to complex signals which are difficult to interpret. Piezoelectric fiber patches (PFP) have been developed which can be used to excite and detect Lamb waves. These are of low thickness having the potential to be integrated into structures. This paper deals with a novel method to excite PFP. By this method a Lamb modes can be both excited and detected selectively. In addition, also directivity can be realized. These sensors can be used to simplify the interpretation of the acoustic signals considerably.

  14. A highly selective fluorescent probe for in vitro and in vivo detection of Hg(2+) .

    PubMed

    Zhou, Quan; Wu, Zeming; Huang, Xiaohua; Zhong, Fenfen; Cai, Qingyun

    2015-10-01

    In this paper, a simple fluorescent probe, rhodamine B derivatives (RS), was designed and prepared for sensitive detection of Hg(2+) in CH3CN/H2O (5/5, v/v). RS exhibits high selectivity and sensitivity toward Hg(2+) over other common metal ions, displaying a significant color change from colorless to pink in the presence of Hg(2+). The fluorescence responses remain stable over a broad pH range (5.0 to 9.0) and are suitable for detection under physiological conditions. Experimental results of HeLa cells and zebrafish show that RS is cell and organism permeable. We also demonstrate the acquisition of images of Hg(2+) in HeLa cells and zebrafish by using a simple fluorescence confocal imaging technique. PMID:26301269

  15. Brief Report: Negative Controls to Detect Selection Bias and Measurement Bias in Epidemiologic Studies

    PubMed Central

    Ercumen, Ayse; Benjamin-Chung, Jade; Colford, John M.

    2016-01-01

    Biomedical laboratory experiments routinely use negative controls to identify possible sources of bias, but epidemiologic studies have infrequently used this type of control in their design or measurement approach. Recently, epidemiologists proposed the routine use of negative controls in observational studies and defined the structure of negative controls to detect bias due to unmeasured confounding. We extend this previous study and define the structure of negative controls to detect selection bias and measurement bias in both observational studies and randomized trials. We illustrate the strengths and limitations of negative controls in this context using examples from the epidemiologic literature. Given their demonstrated utility and broad generalizability, the routine use of prespecified negative controls will strengthen the evidence from epidemiologic studies. PMID:27182642

  16. Selective identification and quantification of saccharin by liquid chromatography and fluorescence detection.

    PubMed

    Bruno, Sergio N F; Cardoso, Carlos R; Maciel, Márcia Mosca A; Vokac, Lidmila; da Silva Junior, Ademário I

    2014-09-15

    High-pressure liquid chromatography with ultra-violet detection (HPLC-UV) is one of the most commonly used methods to identify and quantify saccharin in non-alcoholic beverages. However, due to the wide variety of interfering UV spectra in saccharin-containing beverage matrices, the same method cannot be used to measure this analyte accurately. We have developed a new, highly effective method to identify and quantify saccharin using HPLC with fluorescence detection (HPLC-FLD). The excitation wavelength (250 nm) and emission wavelength (440 nm) chosen increased selectivity for all matrices and ensured few changes were required in the mobile phase or other parameters. The presence of saccharin in non-diet beverages - a fraud commonly used to replace more expensive sucrose - was confirmed by comparing coincident peaks as well as the emission spectra of standards and samples. PMID:24767060

  17. Brief Report: Negative Controls to Detect Selection Bias and Measurement Bias in Epidemiologic Studies.

    PubMed

    Arnold, Benjamin F; Ercumen, Ayse; Benjamin-Chung, Jade; Colford, John M

    2016-09-01

    Biomedical laboratory experiments routinely use negative controls to identify possible sources of bias, but epidemiologic studies have infrequently used this type of control in their design or measurement approach. Recently, epidemiologists proposed the routine use of negative controls in observational studies and defined the structure of negative controls to detect bias due to unmeasured confounding. We extend this previous study and define the structure of negative controls to detect selection bias and measurement bias in both observational studies and randomized trials. We illustrate the strengths and limitations of negative controls in this context using examples from the epidemiologic literature. Given their demonstrated utility and broad generalizability, the routine use of prespecified negative controls will strengthen the evidence from epidemiologic studies. PMID:27182642

  18. EXONEST: Bayesian model selection applied to the detection and characterization of exoplanets via photometric variations

    SciTech Connect

    Placek, Ben; Knuth, Kevin H.; Angerhausen, Daniel E-mail: kknuth@albany.edu

    2014-11-10

    EXONEST is an algorithm dedicated to detecting and characterizing the photometric signatures of exoplanets, which include reflection and thermal emission, Doppler boosting, and ellipsoidal variations. Using Bayesian inference, we can test between competing models that describe the data as well as estimate model parameters. We demonstrate this approach by testing circular versus eccentric planetary orbital models, as well as testing for the presence or absence of four photometric effects. In addition to using Bayesian model selection, a unique aspect of EXONEST is the potential capability to distinguish between reflective and thermal contributions to the light curve. A case study is presented using Kepler data recorded from the transiting planet KOI-13b. By considering only the nontransiting portions of the light curve, we demonstrate that it is possible to estimate the photometrically relevant model parameters of KOI-13b. Furthermore, Bayesian model testing confirms that the orbit of KOI-13b has a detectable eccentricity.

  19. Selective Detection of 8-Oxo-2'-deoxyguanosine in Single-Stranded DNA via Nanopore Sensing Approach.

    PubMed

    Liu, Lei; Li, Yuru; Li, Ting; Xie, Jiani; Chen, Chaofei; Liu, Quansheng; Zhang, Shouwen; Wu, Hai-Chen

    2016-01-19

    We have developed a nanopore sensing approach for the selective detection of 8-oxo-2'-deoxyguanosine (8-oxoG) in single-stranded DNA. First, 1,12-dodecanediamine is coupled with 8-oxoG-containing DNA molecules in high yield which leaves a free amine group for subsequent attaching of an adamantane moiety. After incubation with cucurbit[7]uril, the host-guest complex-modified DNA hybrid is translocated through an α-hemolysin nanopore. Highly characteristic events can be recorded and used to quantify the 8-oxoG-DNA content in a DNA mixture. Compared with the existing methods, this study provides a reliable, quick, and low-cost approach for the detection of 8-oxoG site in single-stranded DNA at the single-molecule level, particularly suitable for high-throughput screening of a massive number of samples. PMID:26699617

  20. Voltammetric detection of sequence-selective DNA hybridization related to Toxoplasma gondii in PCR amplicons.

    PubMed

    Gokce, Gultekin; Erdem, Arzum; Ceylan, Cagdas; Akgöz, Muslum

    2016-03-01

    This work describes the single-use electrochemical DNA biosensor technology developed for voltammetric detection of sequence selective DNA hybridization related to important human and veterinary pathogen; Toxoplasma gondii. In the principle of electrochemical label-free detection assay, the duplex of DNA hybrid formation was detected by measuring guanine oxidation signal occured in the presence of DNA hybridization. The biosensor design consisted of the immobilization of an inosine-modified (guanine-free) probe onto the surface of pencil graphite electrode (PGE), and the detection of the duplex formation in connection with the differential pulse voltammetry(DPV) by measuring the guanine signal. Toxoplasma gondii capture probe was firstly immobilized onto the surface of the activated PGE by wet adsorption. The extent of hybridization at PGE surface between the probe and the target was then determined by measuring the guanine signal observed at +1.0V. The electrochemical monitoring of optimum DNA hybridization has been performed in the target concentration of 40µg/mL in 50min of hybridization time. The specificity of the electrochemical biosensor was then tested using non-complementary, or mismatch short DNA sequences. Under the optimum conditions, the guanine oxidation signal indicating full hybridization was measured in various target concentration from 0.5 to 25µg/mL and a detection limit was found to be 1.78µg/mL. This single-use biosensor platform was successfully applied for the voltammetric detection of DNA hybridization related to Toxoplasma gondii in PCR amplicons. PMID:26717837

  1. Validation of nested PCR and a selective biochemical method as alternatives for mycoplasma detection.

    PubMed

    Cheong, Kyung Ah; Agrawal, Santosh Rani; Lee, Ai-Young

    2011-04-01

    Direct culture is the most common way to reliably detect mycoplasma, but it is not practical for the qualitative control of cell therapeutics because of the elaborate culture medium, the prolonged incubation time, and the large sample volumes. Here, we chose two alternative methods using commercial detection kits, the PCR mycoplasma detection kit with nested PCR and the selective biochemical method, MycoAlert(®), and validated them with the direct culture method as a reference. We tested eight mycoplasma species and five validation parameters: specificity, detection limit, robustness, repeatability, and ruggedness, based on the regulatory guidelines in the US Pharmacopoeia. All experiments were performed using fibroblasts spiked with mycoplasma. Specificity tests for both methods included all mycoplasma species, except Mycoplasma pneumonia and M. genitalium for the nested PCR and Ureaplasma urealyticum for the MycoAlert(®) assay. Regarding the detection limit, the nested PCR proved to be as sensitive as the direct culture method and more sensitive than the MycoAlert(®) assay. The predicted median for probit = 0.9 was 54 (44-76) CFU/ml for M. hyorhinis and 16 (13-23) CFU/ml for M. hominis by the nested PCR, but 431 (346-593) CFU/ml and 105 (87-142) CFU/ml, respectively, with MycoAlert(®). Changes in the concentration of reagents, reagent lot, or individual analysts did not influence the results of the examined methods. The results of this study support nested PCR as a valuable alternative for mycoplasma detection. PMID:20806253

  2. Isomer-Selective Detection of Aromatic Molecules in Temperature-Programmed Desorption for Model Catalysis.

    PubMed

    Winbauer, Andreas; Kollmannsberger, Sebastian L; Walenta, Constantin A; Schreiber, Patrick; Kiermaier, Josef; Tschurl, Martin; Heiz, Ueli

    2016-05-17

    Based on three different molecules dosed on a Pt(111) single crystal the selectivity and sensitivity of REMPI-TPD in UHV is investigated for a potential application in heterogeneous catalysis. It is shown that the two structural isomers ethylbenzene and p-xylene can be discriminated by REMPI in a standard TPD experiment. The latter is not possible for the ionization with electrons in a Q-MS. It is further demonstrated by benzene TPD studies that the sensitivity of the REMPI-TOF-MS is comparable to commercial EI-Q-MS solutions and enables the detection of less than 0.6% molecules of a monolayer. PMID:27078611

  3. Model-based fault detection and identification with online aerodynamic model structure selection

    NASA Astrophysics Data System (ADS)

    Lombaerts, T.

    2013-12-01

    This publication describes a recursive algorithm for the approximation of time-varying nonlinear aerodynamic models by means of a joint adaptive selection of the model structure and parameter estimation. This procedure is called adaptive recursive orthogonal least squares (AROLS) and is an extension and modification of the previously developed ROLS procedure. This algorithm is particularly useful for model-based fault detection and identification (FDI) of aerospace systems. After the failure, a completely new aerodynamic model can be elaborated recursively with respect to structure as well as parameter values. The performance of the identification algorithm is demonstrated on a simulation data set.

  4. Non-gated laser-induced breakdown spectroscopy in bulk water by position-selective detection

    SciTech Connect

    Tian, Ye; Xue, Boyang; Song, Jiaojian; Lu, Yuan; Zheng, Ronger

    2015-09-14

    Temporal and spatial evolutions of the laser-induced plasma in bulk water are investigated using fast imaging and emission spectroscopic techniques. By tightly focusing a single-pulse nanosecond Nd: YAG laser beam into the bulk water, we generate a strongly expanded plasma with high reproducibility. Such a strong expanding plasma enables us to obtain well-resolved spectral lines by means of position-selective detection; hence, the time-gated detector becomes abdicable. The present results suggest not only a possible non-gated approach for underwater laser-induced breakdown spectroscopy but also give an insight into the plasma generation and expansion in bulk water.

  5. Fast, sensitive point of care electrochemical molecular system for point mutation and select agent detection.

    PubMed

    MacLeod, J A; Nemeth, A C; Dicke, W C; Wang, D; Manalili Wheeler, S; Hannis, J C; Collier, G B; Drader, J J

    2016-07-01

    Point of care molecular diagnostics benefits from a portable battery-operated device capable of performing a fast turnaround using reliable inexpensive cartridges. We describe a prototype device for performing a molecular diagnostics test for clinical and biodefense samples in 16 minutes using a prototype capable of an 8 minute PCR reaction, followed by hybridization and detection on an electrochemical microarray based on the i-STAT® system. We used human buccal swabs for hemochromatosis testing including in-device DNA extraction. Additional clinical and biodefense samples included influenza A and bacterial select agents Bacillus anthracis, Yersinia pestis and Francisella tularensis. PMID:27280174

  6. Simple and sensitive colorimetric sensors for the selective detection of Cu2+ in aqueous buffer.

    PubMed

    Huo, Jianzhong; Liu, Kai; Zhao, Xiaojun; Zhang, Xingxing; Wang, Ying

    2014-01-01

    Simple chromogenic sensor for the selective detection of Cu(2+) was described. With the addition of Cu(2+), a bathochromic shift about 82 nm was observed in the UV-VIS spectra, with the color change from colorless to bright yellow. This suggested that the coordination between receptor and Cu(2+) was formed, and the strong push-pull system occurred. The followed IR spectra indicated that Cu(2+) coordinated to the two phenolic oxygen atoms and one of two azomethines in the receptor. PMID:24161519

  7. A novel OFET-based biosensor for the selective and sensitive detection of lactate levels.

    PubMed

    Minami, Tsuyoshi; Sato, Tsubasa; Minamiki, Tsukuru; Fukuda, Kenjiro; Kumaki, Daisuke; Tokito, Shizuo

    2015-12-15

    Biosensors based on organic field effect transistors (OFETs) are one of the more promising device applications in organic electronics. However, OFET-based biosensors are still in their early stages of development compared to other electrochemical biosensors. This study is the first to report on an extended-gate type organic field effect transistor (OFET) for lactate detection in aqueous media. Here, the extended-gate electrode of the OFET was modified with layers of a lactate oxidase and a horseradish peroxidase osmium-redox polymer on a flexible plastic film substrate for an enzymatic redox reaction of lactate. The device exhibited both high selectivity and sensitivity. The limit of detection (LOD) and the limit of quantification (LOQ) were estimated to be 66 nM and 220 nM, respectively, which are the sufficient detection limit for practical sensor applications. The obtained results confirm that extended-gate type OFET devices are applicable to enzyme-based biosensors for detecting lactate levels. PMID:26101795

  8. Assembly of polythiophenes on responsive polymer microgels for the highly selective detection of ammonia gas

    DOE PAGESBeta

    Chang, Aiping; Peng, Yahui; Li, Zezhou; Yu, Xiang; Hong, Kunlun; Zhou, Shuiqin; Wu, Weitai

    2016-04-05

    For this study, a class of smart composite materials based on the assembly of conjugated polymers on responsive polymer microgels has been prepared. We have chosen poly(3-((2-(2-methoxyethoxy)ethoxy)methyl)-thiophene) as the model conjugated polymer and an ammonia-responsive microgel of phenoxazinium-functionalized poly(N-isopropylacrylamide-co-propargyl acrylate) as the model template. Under this design, the composite materials can combine the electrical conductivity of the conjugated polymers and the ammonia recognisability of the ammonia-responsive polymer microgels; the cooperation of these properties allows the reversible control of electrical conductivity by ammonia gas. Those composite materials can not only adapt to ammonia gas, but also convert changes in the concentrationmore » of ammonia into conductance, allowing the electrical detection of ammonia gas with high selectivity. This makes the composite materials different from the conductive polymer platforms reported previously, which may also respond to non-ammonia gases and the response induced by non-ammonia gases is close to that induced by ammonia gas. Using these composite materials as sensing materials for the electrical detection of ammonia gas, the detection limit can reach as low as 1.1 ppb. Finally, these features enable their use for the electrical detection of ammonia in breath.« less

  9. Label-Free SERS Selective Detection of Dopamine and Serotonin Using Graphene-Au Nanopyramid Heterostructure.

    PubMed

    Wang, Pu; Xia, Ming; Liang, Owen; Sun, Ke; Cipriano, Aaron F; Schroeder, Thomas; Liu, Huinan; Xie, Ya-Hong

    2015-10-20

    Ultrasensitive detection and spatially resolved mapping of neurotransmitters, dopamine and serotonin, are critical to facilitate understanding brain functions and investigate the information processing in neural networks. In this work, we demonstrated single molecule detection of dopamine and serotonin using a graphene-Au nanopyramid heterostructure platform. The quasi-periodic Au structure boosts high-density and high-homogeneity hotspots resulting in ultrahigh sensitivity with a surface enhanced Raman spectroscopic (SERS) enhancement factor ∼10(10). A single layer graphene superimposed on a Au structure not only can locate SERS hot spots but also modify the surface chemistry to realize selective enhancement Raman yield. Dopamine and serotonin could be detected and distinguished from each other at 10(-10) M level in 1 s data acquisition time without any pretreatment and labeling process. Moreover, the heterostructure realized nanomolar detection of neurotransmitters in the presence of simulated body fluids. These findings represent a step forward in enabling in-depth studies of neurological processes including those closely related to brain activity mapping (BAM). PMID:26382549

  10. Shift endpoint trace selection algorithm and wavelet analysis to detect the endpoint using optical emission spectroscopy

    NASA Astrophysics Data System (ADS)

    Ben Zakour, Sihem; Taleb, Hassen

    2016-06-01

    Endpoint detection (EPD) is very important undertaking on the side of getting a good understanding and figuring out if a plasma etching process is done on the right way. It is truly a crucial part of supplying repeatable effects in every single wafer. When the film to be etched has been completely erased, the endpoint is reached. In order to ensure the desired device performance on the produced integrated circuit, many sensors are used to detect the endpoint, such as the optical, electrical, acoustical/vibrational, thermal, and frictional. But, except the optical sensor, the other ones show their weaknesses due to the environmental conditions which affect the exactness of reaching endpoint. Unfortunately, some exposed area to the film to be etched is very low (<0.5%), reflecting low signal and showing the incapacity of the traditional endpoint detection method to determine the wind-up of the etch process. This work has provided a means to improve the endpoint detection sensitivity by collecting a huge numbers of full spectral data containing 1201 spectra for each run, then a new unsophisticated algorithm is proposed to select the important endpoint traces named shift endpoint trace selection (SETS). Then, a sensitivity analysis of linear methods named principal component analysis (PCA) and factor analysis (FA), and the nonlinear method called wavelet analysis (WA) for both approximation and details will be studied to compare performances of the methods mentioned above. The signal to noise ratio (SNR) is not only computed based on the main etch (ME) period but also the over etch (OE) period. Moreover, a new unused statistic for EPD, coefficient of variation (CV), is proposed to reach the endpoint in plasma etches process.

  11. Increasing the selectivity and sensitivity of gas sensors for the detection of explosives

    NASA Astrophysics Data System (ADS)

    Mallin, Daniel

    Over the past decade, the use of improvised explosive devices (IEDs) has increased, domestically and internationally, highlighting a growing need for a method to quickly and reliably detect explosive devices in both military and civilian environments before the explosive can cause damage. Conventional techniques have been successful in explosive detection, however they typically suffer from enormous costs in capital equipment and maintenance, costs in energy consumption, sampling, operational related expenses, and lack of continuous and real-time monitoring. The goal was thus to produce an inexpensive, portable sensor that continuously monitors the environment, quickly detects the presence of explosive compounds and alerts the user. In 2012, here at URI, a sensor design was proposed for the detection of triacetone triperoxide (TATP). The design entailed a thermodynamic gas sensor that measures the heat of decomposition between trace TATP vapor and a metal oxide catalyst film. The sensor was able to detect TATP vapor at the part per million level (ppm) and showed great promise for eventual commercial use, however, the sensor lacked selectivity. Thus, the specific objective of this work was to take the original sensor design proposed in 2012 and to make several key improvements to advance the sensor towards commercialization. It was demonstrated that a sensor can be engineered to detect TATP and ignore the effects of interferent H2O2 molecules by doping SnO2 films with varying amounts of Pd. Compared with a pure SnO2 catalyst, a SnO2, film doped with 8 wt. % Pd had the highest selectivity between TATP and H2O2. Also, at 12 wt. % Pd, the response to TATP and H2O2 was enhanced, indicating that sensitivity, not only selectivity, can be increased by modifying the composition of the catalyst. An orthogonal detection system was demonstrated. The platform consists of two independent sensing mechanisms, one thermodynamic and one conductometric, which take measurements from

  12. Evolutionary History of Cathepsin L (L-like) Family Genes in Vertebrates

    PubMed Central

    Zhou, Jin; Zhang, Yao-Yang; Li, Qing-Yun; Cai, Zhong-Hua

    2015-01-01

    Cathepsin L family, an important cysteine protease found in lysosomes, is categorized into cathepsins B, F, H, K, L, S, and W in vertebrates. This categorization is based on their sequence alignment and traditional functional classification, but the evolutionary relationship of family members is unclear. This study determined the evolutionary relationship of cathepsin L family genes in vertebrates through phylogenetic construction. Results showed that cathepsins F, H, S and K, and L and V were chronologically diverged. Tandem-repeat duplication was found to occur in the evolutionary history of cathepsin L family. Cathepsin L in zebrafish, cathepsins S and K in xenopus, and cathepsin L in mice and rats underwent evident tandem-repeat events. Positive selection was detected in cathepsin L-like members in mice and rats, and amino acid sites under positive selection pressure were calculated. Most of these sites appeared at the connection of secondary structures, suggesting that the sites may slightly change spatial structure. Severe positive selection was also observed in cathepsin V (L2) of primates, indicating that this enzyme had some special functions. Our work provided a brief evolutionary history of cathepsin L family and differentiated cathepsins S and K from cathepsin L based on vertebrate appearance. Positive selection was the specific cause of differentiation of cathepsin L family genes, confirming that gene function variation after expansion events was related to interactions with the environment and adaptability. PMID:26221069

  13. Computational Physics and Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Fontana, Walter

    2000-03-01

    One aspect of computational physics deals with the characterization of statistical regularities in materials. Computational physics meets biology when these materials can evolve. RNA molecules are a case in point. The folding of RNA sequences into secondary structures (shapes) inspires a simple biophysically grounded genotype-phenotype map that can be explored computationally and in the laboratory. We have identified some statistical regularities of this map and begin to understand their evolutionary consequences. (1) ``typical shapes'': Only a small subset of shapes realized by the RNA folding map is typical, in the sense of containing shapes that are realized significantly more often than others. Consequence: evolutionary histories mostly involve typical shapes, and thus exhibit generic properties. (2) ``neutral networks'': Sequences folding into the same shape are mutationally connected into a network that reaches across sequence space. Consequence: Evolutionary transitions between shapes reflect the fraction of boundary shared by the corresponding neutral networks in sequence space. The notion of a (dis)continuous transition can be made rigorous. (3) ``shape space covering'': Given a random sequence, a modest number of mutations suffices to reach a sequence realizing any typical shape. Consequence: The effective search space for evolutionary optimization is greatly reduced, and adaptive success is less dependent on initial conditions. (4) ``plasticity mirrors variability'': The repertoire of low energy shapes of a sequence is an indicator of how much and in which ways its energetically optimal shape can be altered by a single point mutation. Consequence: (i) Thermodynamic shape stability and mutational robustness are intimately linked. (ii) When natural selection favors the increase of stability, extreme mutational robustness -- to the point of an evolutionary dead-end -- is produced as a side effect. (iii) The hallmark of robust shapes is modularity.

  14. Telling Tales at Work: An Evolutionary Explanation

    ERIC Educational Resources Information Center

    Yang, Chulguen

    2013-01-01

    This article explores the adaptive functions of storytelling in the workplace from an evolutionary perspective. Based on the analysis of ethnographic studies on hunter-gatherer and modern work organizations, this article claims that storytelling, as an adapted cognitive device, was selectively retained by natural and sexual selection, because of…

  15. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

    PubMed Central

    2011-01-01

    Background 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle. Results We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme FST values were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant FST values were found in regions of some relevant genes such as SMCP and FGF1. Conclusions Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FST suggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported

  16. On evolutionary spatial heterogeneous games

    NASA Astrophysics Data System (ADS)

    Fort, H.

    2008-03-01

    How cooperation between self-interested individuals evolve is a crucial problem, both in biology and in social sciences, that is far from being well understood. Evolutionary game theory is a useful approach to this issue. The simplest model to take into account the spatial dimension in evolutionary games is in terms of cellular automata with just a one-parameter payoff matrix. Here, the effects of spatial heterogeneities of the environment and/or asymmetries in the interactions among the individuals are analysed through different extensions of this model. Instead of using the same universal payoff matrix, bimatrix games in which each cell at site ( i, j) has its own different ‘temptation to defect’ parameter T(i,j) are considered. First, the case in which these individual payoffs are constant in time is studied. Second, an evolving evolutionary spatial game such that T=T(i,j;t), i.e. besides depending on the position evolves (by natural selection), is used to explore the combination of spatial heterogeneity and natural selection of payoff matrices.

  17. Feature Selection for Evolutionary Commercial-off-the-Shelf Software: Studies Focusing on Time-to-Market, Innovation and Hedonic-Utilitarian Trade-Offs

    ERIC Educational Resources Information Center

    Kakar, Adarsh Kumar

    2013-01-01

    Feature selection is one of the most important decisions made by product managers. This three article study investigates the concepts, tools and techniques for making trade-off decisions of introducing new features in evolving Commercial-Off-The-Shelf (COTS) software products. The first article investigates the efficacy of various feature…

  18. Evolutionary constraints or opportunities?

    PubMed Central

    Sharov, Alexei A.

    2014-01-01

    Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term “constraint” has negative connotations, I use the term “regulated variation” to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch “on” or “off” preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). PMID:24769155

  19. GlutenTox® Pro Test for the Detection of Gluten in Select Foods and Surfaces.

    PubMed

    Síglez, Miguel A; Nocea, Bárbara; del Mar Pérez, María; Ma García, Eva; León, Laura; Galera, Carlos

    2015-01-01

    The GlutenTox® Pro Test is an immunochromatographic test for the detection of gluten in foods and on surfaces with varying compositions and levels of processing, from raw foods/ingredients to final product testing. The Method Developer evaluation for the validation of the GlutenTox Pro Test Kit (Biomedal Diagnostics, Sevilla, Spain) for the detection of gluten in foods and on surfaces was conducted at Biomedal, S. L., Camas, Sevilla, Spain. The GlutenTox Pro test method was evaluated by testing the following: cross-reactivity, interference, specificity and sensitivity, robustness, stability, lot-to-lot variation, food matrix, and environmental surface. To evaluate the performance of the GlutenToxPro test for the detection of gluten, 10 matrixes were selected: rice flour, bread/biscuit, rolled oat, pâté, and yogurt (and a second bread matrix for incurred sampled testing) for the food matrix study and food-grade painted wood, plastic, rubber, sealed ceramic, and stainless steel for the environmental surface matrix study. For the food matrix study, 30 replicates were evaluated at six spiked levels of gluten (0, 3, 8, 15, 25, and 45 ppm) against four detection thresholds (5, 10, 20, and 40 ppm) for each food matrix. Additionally, 10 replicates were evaluated at a concentration of 10,000 ppm using all four detection thresholds only for rice flour matrix. Three replicates of each concentration level of gluten were analyzed using paired samples by the AOAC OMA 2012.01 reference method for each food matrix. For the environmental surface study, 30 replicates were evaluated at a low spike level of gluten (16 ng/16 cm2), five replicates at a high spike level of gluten (400 ng/16 cm2), and five replicates at an unspiked control level (0 ng/16 cm2) for each surface matrix. Upon completion of testing, the probability of detection values and confidence intervals were calculated and plotted versus the concentration level as determined by the reference method when applicable. An

  20. Cellulose-lanthanum hydroxide nanocomposite as a selective marker for detection of toxic copper

    NASA Astrophysics Data System (ADS)

    Marwani, Hadi M.; Lodhi, Mazhar Ullah; Khan, Sher Bahadar; Asiri, Abdullah M.

    2014-09-01

    In this current report, a simple, reliable, and rapid method based on modifying the cellulose surface by doping it with different percentages of lanthanum hydroxide (i.e., 1% La(OH)3-cellulose (LC), 5% La(OH)3-cellulose (LC2), and 10% La(OH)3-cellulose (LC3)) was proposed as a selective marker for detection of copper (Cu(II)) in aqueous medium. Surface properties of the newly modified cellulose phases were confirmed by Fourier transform infrared spectroscopy, field emission scanning electron microscope, energy dispersive X-ray spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopic analysis. The effect of pH on the adsorption of modified cellulose phases for Cu(II) was evaluated, and LC3 was found to be the most selective for Cu(II) at pH 6.0. Other parameters, influencing the maximum uptake of Cu(II) on LC3, were also investigated for a deeper mechanistic understanding of the adsorption phenomena. Results showed that the adsorption capacity for Cu(II) was improved by 211% on the LC3 phase as compared to diethylaminoethyl cellulose phase after only 2 h contact time. Adsorption isotherm data established that the adsorption process nature was monolayer with a homogeneous adsorbent surface. Results displayed that the adsorption of Cu(II) onto the LC3 phase obeyed a pseudo-second-order kinetic model. Selectivity studies toward eight metal ions, i.e., Cd(II), Co(II), Cr(III), Cr(VI), Cu(II), Fe(III), Ni(II), and Zn(II), were further performed at the optimized pH value. Based on the selectivity study, it was found that Cu(II) is highly selective toward the LC3 phase. Moreover, the efficiency of the proposed method was supported by implementing it to real environmental water samples with adequate results.

  1. Cellulose-lanthanum hydroxide nanocomposite as a selective marker for detection of toxic copper.

    PubMed

    Marwani, Hadi M; Lodhi, Mazhar Ullah; Khan, Sher Bahadar; Asiri, Abdullah M

    2014-01-01

    In this current report, a simple, reliable, and rapid method based on modifying the cellulose surface by doping it with different percentages of lanthanum hydroxide (i.e., 1% La(OH)3-cellulose (LC), 5% La(OH)3-cellulose (LC2), and 10% La(OH)3-cellulose (LC3)) was proposed as a selective marker for detection of copper (Cu(II)) in aqueous medium. Surface properties of the newly modified cellulose phases were confirmed by Fourier transform infrared spectroscopy, field emission scanning electron microscope, energy dispersive X-ray spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopic analysis. The effect of pH on the adsorption of modified cellulose phases for Cu(II) was evaluated, and LC3 was found to be the most selective for Cu(II) at pH 6.0. Other parameters, influencing the maximum uptake of Cu(II) on LC3, were also investigated for a deeper mechanistic understanding of the adsorption phenomena. Results showed that the adsorption capacity for Cu(II) was improved by 211% on the LC3 phase as compared to diethylaminoethyl cellulose phase after only 2 h contact time. Adsorption isotherm data established that the adsorption process nature was monolayer with a homogeneous adsorbent surface. Results displayed that the adsorption of Cu(II) onto the LC3 phase obeyed a pseudo-second-order kinetic model. Selectivity studies toward eight metal ions, i.e., Cd(II), Co(II), Cr(III), Cr(VI), Cu(II), Fe(III), Ni(II), and Zn(II), were further performed at the optimized pH value. Based on the selectivity study, it was found that Cu(II) is highly selective toward the LC3 phase. Moreover, the efficiency of the proposed method was supported by implementing it to real environmental water samples with adequate results. PMID:25258599

  2. Cellulose-lanthanum hydroxide nanocomposite as a selective marker for detection of toxic copper

    PubMed Central

    2014-01-01

    In this current report, a simple, reliable, and rapid method based on modifying the cellulose surface by doping it with different percentages of lanthanum hydroxide (i.e., 1% La(OH)3-cellulose (LC), 5% La(OH)3-cellulose (LC2), and 10% La(OH)3-cellulose (LC3)) was proposed as a selective marker for detection of copper (Cu(II)) in aqueous medium. Surface properties of the newly modified cellulose phases were confirmed by Fourier transform infrared spectroscopy, field emission scanning electron microscope, energy dispersive X-ray spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopic analysis. The effect of pH on the adsorption of modified cellulose phases for Cu(II) was evaluated, and LC3 was found to be the most selective for Cu(II) at pH 6.0. Other parameters, influencing the maximum uptake of Cu(II) on LC3, were also investigated for a deeper mechanistic understanding of the adsorption phenomena. Results showed that the adsorption capacity for Cu(II) was improved by 211% on the LC3 phase as compared to diethylaminoethyl cellulose phase after only 2 h contact time. Adsorption isotherm data established that the adsorption process nature was monolayer with a homogeneous adsorbent surface. Results displayed that the adsorption of Cu(II) onto the LC3 phase obeyed a pseudo-second-order kinetic model. Selectivity studies toward eight metal ions, i.e., Cd(II), Co(II), Cr(III), Cr(VI), Cu(II), Fe(III), Ni(II), and Zn(II), were further performed at the optimized pH value. Based on the selectivity study, it was found that Cu(II) is highly selective toward the LC3 phase. Moreover, the efficiency of the proposed method was supported by implementing it to real environmental water samples with adequate results. PMID:25258599

  3. Highly sensitive and selective electrochemical detection of Hg(2+) through surface-initiated enzymatic polymerization.

    PubMed

    Mei, Chenyang; Lin, Dajie; Fan, Chengchao; Liu, Aili; Wang, Shun; Wang, Jichang

    2016-06-15

    A Hg(2+) electrochemical biosensor is developed by integrating thymine-Hg(2+)-thymine (T-Hg(2+)-T) base pairs for the high selectivity with surface-initiated enzymatic polymerization (SIEP) for signal amplification. The fabrication begins with the covalent conjugation of capture DNA probe labeled with thiol at its 3'terminal onto the gold electrode. The presence of Hg(2+) leads to DNA hybridization, in which complementary DNA was captured onto the biosensor surface, which subsequently catalyzed the addition of deoxynucleotides (dNTP) containing biotinlated 2'-deoxyadenosine 5'-triphosphate (biotin-dATP) by terminal deoxynucleotidyl transferase (TdT). The binding between biotin and strepavidin leads to the attachment of a large number of strepavidin functionalized silver nanoparticles (strepavidin-AgNPs), which could generate electrochemical stripping signal of silver to monitor the concentration of Hg(2+) in KCl solution. Through utilizing the T-Hg(2+)-T selectivity and SIEP amplification, this assay method can detect aqueous Hg(2+) with a wide linear range from 0.05nM to 100nM and a detection limit of 0.024nM. The application of this sensor in the analysis of drinking water demonstrates that the proposed method works well for real samples. PMID:26807524

  4. Tension promoted circular probe for highly selective microRNA detection and imaging.

    PubMed

    Tang, Yaqin; Wang, Tingting; Chen, Ming; He, Xiao; Qu, Xiaohuan; Feng, Xuli

    2016-11-15

    The crucial role of miRNA in cell regulation and its connection with diverse human cancers as a tumor suppressor or an oncogenic fragment poses great demand for an accurate and rapid approach for highly efficient miRNA detection and imaging in live cells. However, the ability to selectively detect and image miRNA remains a significant challenge in biomedical fields. Herein, a sealed circular probe (CP) has been prepared with copper free click ligation. The big tension force of the ring structure greatly increases the sequence recognition specificity. Toehold initiated strand displacement of CP further amplify the selectivity for miRNA determination. Impressively, the different site of single base mismatch could even be discriminated. More importantly, CP was successfully applied for imaging endogenous miRNA expression in live cells. We believe that this new probe would find wide application in profiling of endogenous miRNA and be potential candidate method for helping us diagnosing miRNA related diseases. PMID:27162146

  5. Molecularly Imprinted Composite Membranes for Selective Detection of 2-Deoxyadenosine in Urine Samples

    PubMed Central

    Scorrano, Sonia; Mergola, Lucia; Di Bello, Maria Pia; Lazzoi, Maria Rosaria; Vasapollo, Giuseppe; Del Sole, Roberta

    2015-01-01

    An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. In this work, a novel molecularly imprinted polymer composite membrane (MIM) was synthesized and employed for the selective detection in urine samples of 2-deoxyadenosine (2-dA), an important tumoral marker. By thermal polymerization, the 2-dA-MIM was cross-linked on the surface of a polyvinylidene-difluoride (PVDF) membrane. By characterization techniques, the linking of the imprinted polymer on the surface of the membrane was found. Batch-wise guest binding experiments confirmed the absorption capacity of the synthesized membrane towards the template molecule. Subsequently, a time-course of 2-dA retention on membrane was performed and the best minimum time (30 min) to bind the molecule was established. HPLC analysis was also performed to carry out a rapid detection of target molecule in urine sample with a recovery capacity of 85%. The experiments indicated that the MIM was highly selective and can be used for revealing the presence of 2-dA in urine samples. PMID:26086824

  6. Flow Chronopotentiometry with Ion-Selective Membranes for Cation, Anion, and Polyion Detection.

    PubMed

    Ghahraman Afshar, Majid; Crespo, Gastón A; Bakker, Eric

    2016-04-01

    We report here on the development of a chronopotentiometric readout for ion-selective electrodes that allows one to record transition times in continuous flow conditions without the necessity to stop the flow. A sample plug of 150 μL is injected into the carrier solution (0.5 mM NaCl) and subsequently transported to the detection cell (∼20 μL) at moderate flow rates (∼0.5 mL min(-1)), where a short current pulse (5s) is applied between the ionophore-based working electrode and a biocompatible and nonpolarizable Donnan exclusion anion-exchanger membrane reference/counter electrode. Flow conditions bear an influence on the thickness of the aqueous diffusion layer and result in a shift of the chronopotentiometric transition time with respect to stopped flow. Two models based on rotating disk electrodes and flow chronopotentiometry at metal-based electrodes were used to corroborate the data. The method was successfully applied to the determination of calcium, chloride, alkalinity, acidity, and protamine with a range of ion-selective membranes. Because of the limiting exposure time of ca. 20 s of the membranes with the sample, this approach is demonstrated to be useful for the detection of protamine in the therapeutic range of undiluted human blood. PMID:26932542

  7. Molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin.

    PubMed

    Wang, Xiaoyan; Yu, Jialuo; Kang, Qi; Shen, Dazhong; Li, Jinhua; Chen, Lingxin

    2016-03-15

    A facile strategy was developed to prepare molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin (PC) based on fluorescence resonance energy transfer (FRET), via a sol-gel polymerization process using nitrobenzoxadiazole (NBD) as fluorescent signal source. The ratio of two fluorescence peak emission intensities of NBD and PC was utilized to determine the concentration of PC, which could effectively reduce the background interference and fluctuation of diverse conditions. As a result, this sensor obtained high sensitivity with a low detection limit of 0.14 nM within 6 min, and excellent recognition specificity for PC over its analogues with a high imprinting factor of 9.1. Furthermore, the sensor attained high recoveries in the range of 93.8-110.2% at three spiking levels of PC, with precisions below 4.7% in seawater and lake water samples. The developed sensor strategy demonstrated simplicity, reliability, rapidity, high selectivity and high sensitivity, proving to be a feasible way to develop high efficient fluorescence sensors and thus potentially applicable for ultratrace analysis of complicated matrices. PMID:26485176

  8. A highly selective molecularly imprinted electrochemiluminescence sensor for ultra-trace beryllium detection.

    PubMed

    Li, Jianping; Ma, Fei; Wei, Xiaoping; Fu, Cong; Pan, Hongcheng

    2015-04-29

    A new molecularly imprinted electrochemiluminescence (ECL) sensor was proposed for highly sensitive and selective determination of ultratrace Be(2+) determination. The complex of Be(2+) with 4-(2-pyridylazo)-resorcinol (PAR) was chosen as the template molecule for the molecularly imprinted polymer (MIP). In this assay, the complex molecule could be eluted from the MIP, and the cavities formed could then selectively recognize the complex molecules. The cavities formed could also work as the tunnel for the transfer of probe molecules to produce sound responsive signal. The determination was based on the intensity of the signal, which was proportional to the concentrations of the complex molecule in the sample solution, and the Be(2+) concentration could then be determined indirectly. The results showed that in the range of 7×10(-11 )mol L(-1) to 8.0×10(-9) mol L(-1), the ECL intensity had a linear relationship with the Be(2+) concentrations, with the limit of detection of 2.35×10(-11) mol L(-1). This method was successfully used to detect Be(2+) in real water samples. PMID:25847161

  9. Construction and selection of lifting-based multiwavelets for mechanical fault detection

    NASA Astrophysics Data System (ADS)

    Yuan, Jing; He, Zhengjia; Zi, Yanyang; Wei, Ying

    2013-11-01

    The essence of wavelet transforms is a similar measurement between the signal and the wavelet basis functions. Thus, the construction and selection of the proper wavelet basis functions similar to the fault feature and possessing good properties such as vanishing moments have vital importance to the effective fault diagnosis. In this paper, the construction of lifting-based adaptive multiwavelets with various vanishing moments and the selection rules for different mechanical fault detection are proposed. On the basis of the fixed cubic Hermite multiwavelets, lifting schemes are adopted to construct new changeable multiwavelets with diverse vanishing moments. Then, the defined local spectral entropy minimization rules are proposed to determine the optimum multiwavelets providing the proper vanishing moments, classified into the typical shaft faults, gear faults and rolling bearing faults. The proposed method is applied to incipient fault diagnosis of rolling bearing and gearbox fault diagnosis of rolling mill to verify its effectiveness and feasibility in comparison with different wavelet transforms and spectral kurtosis. The results show that the proposed method can act as a promising tool for mechanical fault detection.

  10. Selective fluorescent Hg(II) detection in aqueous solutions with a dye intermediate

    NASA Astrophysics Data System (ADS)

    Young, Song

    2007-11-01

    A dye intermediate, 1-amino-8-naphthol-3,6-disulfonic acid sodium (ANDS) was first used to selectively recognize Hg(II) in aqueous solutions with its fluorescence being strong quenched. The fluorescence quenching of ANDS was attributed to the formation of an inclusion complex between Hg(II) and ANDS by 2:1 complex ratio ( K = 6.2 × 10 9), which has been utilized as the basis of the fabrication of the Hg(II)-sensitive fluorescent chemosensor. The analytical performance characteristics of the proposed chemosensor were investigated. The sensor shows a linear response toward Hg(II) in the concentration range 2.9 × 10 -6 to 5.5 × 10 -5 M with a limit of detection of 5.3 × 10 -7 M, and a working pH range from 5.0 to 9.0. It shows excellent selectivity for Hg(II) over a large number of cations such as alkali, alkaline earth and transitional metal ions. The proposed method was utilized successfully for the detection of Hg 2+ in water samples.

  11. DNA aptamer-based fiber optic biosensor for selective and label-free detection of dopamine

    NASA Astrophysics Data System (ADS)

    Zibaii, M. I.; Latifi, H.; Asadollahi, A.; Bayat, A. H.; Haghparast, A.

    2015-09-01

    Dopamine (DA) analysis is complicated by the interference from other electrochemically active endogenous compounds present in the brain, including DA precursors and metabolites and other neurotransmitters (NT). Here we report a simple, sensitive and selective optical fiber biosensor for the detection of DA in the presence of other NT. It is composed of a 57-mer dopamine-binding aptamer (DBA) as recognition element and nonadiabatic tapered optical fiber (NATOF) as probe. Upon the addition of DA, the conformation of DBA would change from a random coil structure to a rigid tertiary structure like a pocket. The conformational change of DBA lead to the refractive index (RI) change around the tapered fiber surface. Specific recognition of DA by the aptamer allowed a selective optical detection of DA within the physiologically relevant 500 nM to 10 μM range. Some common interferents such as epinephrine (EP) and ascorbic acid (AA) showed no or just a little interference in the determination of DA.

  12. Aptamers Selected to Postoperative Lung Adenocarcinoma Detect Circulating Tumor Cells in Human Blood

    PubMed Central

    Zamay, Galina S; Kolovskaya, Olga S; Zamay, Tatiana N; Glazyrin, Yury E; Krat, Alexey V; Zubkova, Olga; Spivak, Ekaterina; Wehbe, Mohammed; Gargaun, Ana; Muharemagic, Darija; Komarova, Mariia; Grigorieva, Valentina; Savchenko, Andrey; Modestov, Andrey A; Berezovski, Maxim V; Zamay, Anna S

    2015-01-01

    Circulating tumor cells (CTCs) are rare cells and valuable clinical markers of prognosis of metastasis formation and prediction of patient survival. Most CTC analyses are based on the antibody-based detection of a few epithelial markers; therefore miss an important portion of mesenchymal cancer cells circulating in blood. In this work, we selected and identified DNA aptamers as specific affinity probes that bind to lung adenocarcinoma cells derived from postoperative tissues. The unique feature of our selection strategy is that aptamers are produced for lung cancer cell biomarkers in their native state and conformation without previous knowledge of the biomarkers. The aptamers did not bind to normal lung cells and lymphocytes, and had very low affinity to A549 lung adenocarcinoma culture. We applied these aptamers to detect CTCs, apoptotic bodies, and microemboli in clinical samples of peripheral blood of lung cancer and metastatic lung cancer patients. We identified aptamer-associated protein biomarkers for lung cancer such as vimentin, annexin A2, annexin A5, histone 2B, neutrophil defensin, and clusterin. Tumor-specific aptamers can be produced for individual patients and synthesized many times during anticancer therapy, thereby opening up the possibility of personalized diagnostics. PMID:26061649

  13. Aptamers Selected to Postoperative Lung Adenocarcinoma Detect Circulating Tumor Cells in Human Blood.

    PubMed

    Zamay, Galina S; Kolovskaya, Olga S; Zamay, Tatiana N; Glazyrin, Yury E; Krat, Alexey V; Zubkova, Olga; Spivak, Ekaterina; Wehbe, Mohammed; Gargaun, Ana; Muharemagic, Darija; Komarova, Mariia; Grigorieva, Valentina; Savchenko, Andrey; Modestov, Andrey A; Berezovski, Maxim V; Zamay, Anna S

    2015-09-01

    Circulating tumor cells (CTCs) are rare cells and valuable clinical markers of prognosis of metastasis formation and prediction of patient survival. Most CTC analyses are based on the antibody-based detection of a few epithelial markers; therefore miss an important portion of mesenchymal cancer cells circulating in blood. In this work, we selected and identified DNA aptamers as specific affinity probes that bind to lung adenocarcinoma cells derived from postoperative tissues. The unique feature of our selection strategy is that aptamers are produced for lung cancer cell biomarkers in their native state and conformation without previous knowledge of the biomarkers. The aptamers did not bind to normal lung cells and lymphocytes, and had very low affinity to A549 lung adenocarcinoma culture. We applied these aptamers to detect CTCs, apoptotic bodies, and microemboli in clinical samples of peripheral blood of lung cancer and metastatic lung cancer patients. We identified aptamer-associated protein biomarkers for lung cancer such as vimentin, annexin A2, annexin A5, histone 2B, neutrophil defensin, and clusterin. Tumor-specific aptamers can be produced for individual patients and synthesized many times during anticancer therapy, thereby opening up the possibility of personalized diagnostics. PMID:26061649

  14. Highly sensitive and selective nonenzymatic detection of glucose using three-dimensional porous nickel nanostructures.

    PubMed

    Niu, Xiangheng; Lan, Minbo; Zhao, Hongli; Chen, Chen

    2013-04-01

    Highly sensitive and selective nonenzymatic detection of glucose has been achieved using a novel disposable electrochemical sensor based on three-dimensional (3D) porous nickel nanostructures. The enzyme-free sensor was fabricated through in situ growing porous nickel networks on a homemade screen-printed carbon electrode substrate via electrochemically reducing the Ni(2+) precursor, along with continuously liberating hydrogen bubbles. The resulting nickel-modified electrode was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectrometry (EDX), powder X-ray diffractometry (XRD), and electrochemical techniques. Cyclic voltammetric, alternating-current impedance, and amperometric methods were used to investigate the catalytic properties of the assembled sensor for glucose electro-oxidation in alkaline media. Under optimized conditions, the enzymeless sensor exhibited excellent performance for glucose analysis selectively, offering a much wider linear range (from 0.5 μM to 4 mM), an extremely low detection limit (0.07 μM, signal-to-noise ratio (S/N) of 3), and an ultrahigh sensitivity of 2.9 mA/(cm(2) mM). Importantly, favorable reproducibility and long-term performance stability were obtained thanks to the robust frameworks. Application of the proposed sensor in monitoring blood glucose was also demonstrated. PMID:23458297

  15. [THE APPLICATION OF SELECTIVE CHROMOGENIC AGAR FOR DETECTING ENTEROBACTERIA WITH PRODUCTION OF BETA-LACTAMASES].

    PubMed

    Korobova, A G; Frolova, L N; Kliasova, G A

    2015-11-01

    The detection of enterobacteria with production of beta-lactamases of extended spectrum in selective chromogenic agar was analyzed The results ofdetection of beta-lactamases of extended spectrum was compared with "double disc" technique. The smears from mucous membrane of guttur and rectum from patients were analyzed in parallel on solid growth agar (Endo or Mac Conkey) and on selective agar CHROMagartm ESBL (CHROMagar France). The production of beta-lactamases of extended spectrum was confirmed using "double discs" technique. To exclude hyper-production of ampC beta-lactamases E-test was applied containing cefotetan and cefotetan with cloxacillin. The sampling consisted of 1552 samples from patients. The study permitted to isolate 1243 strains of enterobacteria on agar Endo or Mac Conkey and 409 strains of enterobacteria on selective agar CHROMagartm ESBL (Escherichia coli n = 226, Klebsiella pneumoniae n = 105, enterobacter spp. n = 35, Citrobacter spp. n = 21, others n = 22). The application of "double discs" technique confirmed production of beta-lactamases of extended spectrum in 386 (94%) out of 409 strains isolated on agar CHROMagartm ESBL. In 23 (6%) of strains no confirmation was established and hyper-production of ampC of beta-lactamases was established 15 out of total. Additionally, 8 were sensitive to cephalosporin of third generation. All enterobacteria isolated on agar Endo or Mac Conkey also were tested by "double discs" technique. Overall, 394 strains of enterobacteria with production of beta-lactamases of extended spectrum were obtained. On all agars (agar Endo or Mac Conkey and CHROMagartm ESBL)--263 (67%) strains; only on CHROMagartm ESBL--123 (31%) and only on agar Endo or Mac Conkey--8 (2%) (p < 0.0001). The sensitivity of selective agar CHROMagartm ESBL made up to 98% and specificity--97%. The resolution about detection of enterobacteria producing beta-lactamases of extended spectrum were submitted to clinic in 18-24 hours after arrival

  16. A calixarene-based ion-selective electrode for thallium(I) detection.

    PubMed

    Chester, Ryan; Sohail, Manzar; Ogden, Mark I; Mocerino, Mauro; Pretsch, Ernö; De Marco, Roland

    2014-12-01

    Three new calixarene Tl(+) ionophores have been utilized in Tl(+) ion-selective electrodes (ISEs) yielding Nernstian response in the concentration range of 10(-2)-10(-6)M TlNO3 with a non-optimized filling solution in a conventional liquid contact ISE configuration. The complex formation constants (logβIL) for two of the calixarene derivatives with thallium(I) (i.e. 6.44 and 5.85) were measured using the sandwich membrane technique, with the other ionophore immeasurable due to eventual precipitation of the ionophore during these long-term experiments. Furthermore, the unbiased selectivity coefficients for these ionophores displayed excellent selectivity against Zn(2+), Ca(2+), Ba(2+), Cu(2+), Cd(2+) and Al(3+) with moderate selectivity against Pb(2+), Li(+), Na(+), H(+), K(+), NH4(+) and Cs(+), noting that silver was the only significant interferent with these calixarene-based ionophores. When optimizing the filling solution in a liquid contact ISE, it was possible to achieve a lower limit of detection of approximately 8nM according to the IUPAC definition. Last, the new ionophores were also evaluated in four solid-contact (SC) designs leading to Nernstian response, with the best response noted with a SC electrode utilizing a gold substrate, a poly(3-octylthiophene) (POT) ion-to-electron transducer and a poly(methyl methacrylate)-poly(decyl methacrylate) (PMMA-PDMA) co-polymer membrane. This electrode exhibited a slope of 58.4mVdecade(-1) and a lower detection limit of 30.2nM. Due to the presence of an undesirable water layer and/or leaching of redox mediator from the graphite redox buffered SC, a coated wire electrode on gold and graphite redox buffered SC yielded grossly inferior detection limits against the polypyrrole/PVC SC and POT/PMMA-PDMA SC ISEs that did not display signs of a water layer or leaching of SC ingredients into the membrane. PMID:25440668

  17. X-ray backscatter imaging for radiography by selective detection and snapshot: Evolution, development, and optimization

    NASA Astrophysics Data System (ADS)

    Shedlock, Daniel

    Compton backscatter imaging (CBI) is a single-sided imaging technique that uses the penetrating power of radiation and unique interaction properties of radiation with matter to image subsurface features. CBI has a variety of applications that include non-destructive interrogation, medical imaging, security and military applications. Radiography by selective detection (RSD), lateral migration radiography (LMR) and shadow aperture backscatter radiography (SABR) are different CBI techniques that are being optimized and developed. Radiography by selective detection (RSD) is a pencil beam Compton backscatter imaging technique that falls between highly collimated and uncollimated techniques. Radiography by selective detection uses a combination of single- and multiple-scatter photons from a projected area below a collimation plane to generate an image. As a result, the image has a combination of first- and multiple-scatter components. RSD techniques offer greater subsurface resolution than uncollimated techniques, at speeds at least an order of magnitude faster than highly collimated techniques. RSD scanning systems have evolved from a prototype into near market-ready scanning devices for use in a variety of single-sided imaging applications. The design has changed to incorporate state-of-the-art detectors and electronics optimized for backscatter imaging with an emphasis on versatility, efficiency and speed. The RSD system has become more stable, about 4 times faster, and 60% lighter while maintaining or improving image quality and contrast over the past 3 years. A new snapshot backscatter radiography (SBR) CBI technique, shadow aperture backscatter radiography (SABR), has been developed from concept and proof-of-principle to a functional laboratory prototype. SABR radiography uses digital detection media and shaded aperture configurations to generate near-surface Compton backscatter images without scanning, similar to how transmission radiographs are taken. Finally, a

  18. Chemically-modulated photoluminescence of graphene oxide for selective detection of neurotransmitter by "turn-on" response.

    PubMed

    Jeon, Su-Ji; Kwak, Seon-Yeong; Yim, DaBin; Ju, Jong-Min; Kim, Jong-Ho

    2014-08-01

    Designing artificial nanomaterials capable of selectively detecting targets without the use of expensive and fragile antibodies is of great interest in the applications of nanomedicine. Here, we show that the photoluminescence (PL) of graphene oxide (GO) was chemically modulated for the selective detection of a neurotransmitter without the use of antibodies. GO was functionalized with nitrotriacetic acid (NTA) on which four different metal ions were chelated (M-NTA-GO), which led to its different PL responses to neurotransmitters. In particular, the Cu-NTA-GO hybrid was able to selectively detect norepinephrine at nanomolar concentrations in a simple manner via its "turn-on" PL. Moreover, it was successfully applied to the selective detection of norepinephrine secreted from living PC-12 cells. PMID:25036980

  19. Selective fluorescence sensors for detection of nitroaniline and metal Ions based on ligand-based luminescent metal-organic frameworks

    NASA Astrophysics Data System (ADS)

    Yu, Zongchao; Wang, Fengqin; Lin, Xiangyi; Wang, Chengmiao; Fu, Yiyuan; Wang, Xiaojun; Zhao, Yongnan; Li, Guodong

    2015-12-01

    Metal-organic frameworks (MOFs) are porous crystalline materials with high potential for applications in fluorescence sensors. In this work, two solvent-induced Zn(II)-based metal-organic frameworks, Zn3L3(DMF)2 (1) and Zn3L3(DMA)2(H2O)3 (2) (L=4,4‧-stilbenedicarboxylic acid), were investigated as selective sensing materials for detection of nitroaromatic compounds and metal ions. The sensing experiments show that 1 and 2 both exhibit selective fluorescence quenching toward nitroaniline with a low detection limit. In addition, 1 exhibits high selectivity for detection of Fe3+ and Al3+ by significant fluorescence quenching or enhancement effect. While for 2, it only exhibits significant fluorescence quenching effect for Fe3+. The results indicate that 1 and 2 are both promising fluorescence sensors for detecting and recognizing nitroaniline and metal ions with high sensitivity and selectivity.

  20. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data

    PubMed Central

    Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; Bazin, Eric; Blum, Michael G.B.

    2016-01-01

    To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult. PMID:26715629

  1. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data.

    PubMed

    Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; Bazin, Eric; Blum, Michael G B

    2016-04-01

    To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult. PMID:26715629

  2. Functionalized polymeric magnetic nanoconstructs for selective capturing and sensitive detection of Salmonella typhimurium.

    PubMed

    Chattopadhyay, Sruti; Kaur, Avneet; Jain, Swati; Sabharwal, Prabhjot K; Singh, Harpal

    2016-09-21

    Rapid detection and enumeration of pathogens is essential for monitoring contamination and spoilage of food products to ensure improved quality control management. Functionalized polymeric magnetic nanoconstructs (FPMNCs) were developed as an effective immunomagnetic separator and sensing platform for the selective capturing of Salmonella typhimurium. Novel FPMNCs were prepared in three stages involving synthesis of iron oxide (IO) dispersion, capping with sodium oleate and encapsulation of preformed IO nanoparticles by in-situ free radical emulsion polymerization of styrene (St), methyl methacrylate (MMA) and acetoacetoxy ethylmethacrylate (AAEM). PMMA improves the stability of FPMNCs by bridging extremely hydrophobic PS and hydrophilic PAAEM. Core-shell morphology of hydrophobic core of IO, PS & PMMA and hydrophilic shell of PAAEM was demonstrated by SEM, TEM and FTIR studies. FPMNCs with surface functionalized acetoacetoxy groups were covalently attached with polyclonal antibodies against Salmonella common structural antigen (CSA-1-Ab) without using any linker and catalyst. Colorimetric readout signal was acquired using CSA-1-Ab-HRP as secondary antibody after formation of sandwich immunocomplex with bacteria where the optical density of the samples were recorded using ELISA plate reader at 450 nm. The developed immunoassay was specific and selective which captures only targeted S. typhimurium with a detection limit of 10 cells/mL lower than infectious dose of salmonellosis infection. Minimal interference of food matrix with high signal to noise ratio was shown by various food samples. In addition, the performance of developed FPMNC based immunoassay was superior to commercially available immunomagnetic microbeads demonstrating undisputed advantage for capturing and detecting specific bacteria without any pre-enrichment of sample. PMID:27590554

  3. Synthesis of Water-Dispersible Molecularly Imprinted Electroactive Nanoparticles for the Sensitive and Selective Paracetamol Detection.

    PubMed

    Luo, Jing; Ma, Qiang; Wei, Wei; Zhu, Ye; Liu, Ren; Liu, Xiaoya

    2016-08-17

    A novel kind of water-dispersible molecularly imprinted electroactive nanoparticles was prepared combining macromolecular self-assembly with molecularly imprinting technique employing paracetamol (PCM) as template molecule. An amphiphilic electroactive copolymer (P(NVC-EHA-AA), PNEA) containing carbazole group was first synthesized through a one-pot free radical copolymerization. The coassembly of the electroactive copolymers with the template molecules (PCM) in aqueous solution generated nanoparticles embedded with PCM, leading to the formation of molecularly imprinted electroactive nanoparticles (MIENPs). A robust MIP film was formed on the surface of electrode by electrodeposition of MIENPs and subsequent electropolymerization of the carbazole units in MIENPs. After the extraction of PCM molecules, a MIP sensor was successfully constructed. It should be noted that electropolymerization of the electroactive units in MIENPs creates cross-conjugated polymer network, which not only locks the recognition sites but also significantly accelerates the electron transfer and thus enhances the response signal of the MIP sensor. These advantages endowed the MIP sensor with good selectivity and high sensitivity for PCM detection. The MIP sensor could recognize PCM from its possible interfering substances with good selectivity. Under the optimal conditions, two linear ranges from 1 μM to 0.1 mM and 0.1 to 10 mM with a detection limit of 0.3 μM were obtained for PCM detection. The MIP sensor also showed good stability and repeatability, which has been successfully used to analyze PCM in tablets and human urine samples with satisfactory results. PMID:27463123

  4. Selection of informative frequency band in local damage detection in rotating machinery

    NASA Astrophysics Data System (ADS)

    Obuchowski, Jakub; Wyłomańska, Agnieszka; Zimroz, Radosław

    2014-10-01

    Problem of informative frequency band (IFB) selection in vibration signal processing for local damage detection is discussed. It is proposed to extend the concept of automatic and objective IFB selection proposed by several authors. Till now, kurtosis was preferred as criterion for IFB search. Thus, it is offered to study set of statistics, namely Jarque-Bera, Kolmogorov-Smirnov, Cramer-von Mises, Anderson-Darling, quantile-quantile plot and a method based on the local maxima approach in order to verify their abilities of IFB selection. Also similarities between them are described. It has been proved by simulation and real data analysis that proposed selectors (because they allow us to “select” frequency band) might be equivalent to the spectral kurtosis (SK) in ordinary cases. Moreover, some of the novel selectors are better, because they are less sensitive to incidental spikes that might occur during the signal acquisition process. Proposed selectors might be (as SK) the basis for filter design for informative signal extraction.

  5. Selective detection of heavy metal ions by self assembled chemical field effect transistors

    SciTech Connect

    Ruan, Hang Kang, Yuhong; Gladwin, Elizabeth; Claus, Richard O.

    2015-04-20

    Multiple layer-by-layer sensor material modifications were designed and implemented to achieve selectivity of semiconductor based chemical field effect transistors (ChemFETs) to particular heavy metal ions. The ChemFET sensors were fabricated and modified in three ways, with the intent to initially target first mercury and lead ions and then chromium ions, respectively. Sensor characterization was performed with the gate regions of the sensor elements exposed to different concentrations of target heavy metal ion solutions. A minimum detection level in the range of 0.1 ppm and a 10%–90% response time of less than 10 s were demonstrated. By combining layer-by-layer gold nanoparticles and lead ionophores, a sensor is produced that is sensitive and selective not only to chromium but also to Cr{sup 3+} and Cr{sup 6+}. This result supports the claim that high selectivity can be achieved by designing self-assembled bonding for lead, arsenic, chromium, cesium, mercury, and cadmium.

  6. Sensitive and selective system of benzene detection based on a cataluminescence sensor.

    PubMed

    Li, Bo; Zhang, Yuejin; Liu, Juefu; Xie, Xin; Zou, Dan; Li, Minqiang; Liu, Jinhuai

    2014-06-01

    Au/La2 O3 nanomaterials were prepared through calcining Au-modified La(OH)3 precursors. Scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray diffractometry (XRD) were employed to characterize the as-prepared samples. Benzene, a common volatile organic compound, was selected as a model to investigate the cataluminescence (CTL)-sensing properties of the Au/La2 O3 nanomaterials. Results indicated that the as-prepared Au/La2 O3 exhibited outstanding CTL properties such as stable intensity, high signal-to-noise values, and short response and recovery times. Under optimized conditions, the benzene assay exhibited a broad linear range of 1-4000 ppm, with a limit of detection of 0.7 ppm, which was below the standard permitted concentrations. Furthermore, the gas sensor system showed outstanding selectivity for benzene compared with seven other types of common volatile organic compounds (VOCs). The proposed gas sensor showed good characteristics with high selectivity, fast response time and long lifetime, which suggested the promising application of the Au/La2 O3 nanomaterials as a novel highly efficient CTL-sensing material. PMID:23832690

  7. Different Levels of DNA Methylation Detected in Human Sperms after Morphological Selection Using High Magnification Microscopy

    PubMed Central

    Cassuto, Nino Guy; Montjean, Debbie; Siffroi, Jean-Pierre; Bouret, Dominique; Marzouk, Flora; Copin, Henri; Benkhalifa, Moncef

    2016-01-01

    Objective. To analyze DNA methylation levels between two groups of spermatozoa taken from the same sample, following morphological selection by high magnification (HM) at 6100x microscopy. A prospective study was conducted and studied 876 spermatozoa from 10 randomly selected men. Sperm morphology was characterized at HM according to criteria previously established. High-scoring Score 6 and low-scoring Score 0 sperm were selected. Sperm DNA methylation level was assessed using an immunoassay method targeting 5-methylcytosine residues by fluorescence microscopy with imaging analysis system to detect DNA methylation in single spermatozoon. Results. In total, 448 S6 spermatozoa and 428 S0 spermatozoa were analyzed. A strong relationship was found between sperm DNA methylation levels and sperm morphology observed at HM. Sperm DNA methylation level in the S6 group was significantly lower compared with that in the S0 group (p < 10−6), OR = 2.4; and p < 0.001, as determined using the Wilcoxon test. Conclusion. Differences in DNA methylation levels are associated with sperm morphology variations as observed at HM, which allows spermatozoa with abnormal levels to be discarded and ultimately decrease birth defects, malformations, and epigenetic diseases that may be transmitted from sperm to offspring in ICSI. PMID:27148551

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