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Sample records for means-end chain analysis

  1. A customer value analysis of Taiwan ice cream market: a means-end chain approach across consumption situations.

    PubMed

    Chen, Yan-Kwang; Tsai, Pei-Shan; Chiu, Fei-Rung

    2015-01-01

    In the highly competitive market, it is increasingly hard for ice cream stores to develop creative marketing strategies to retain existing customers and attract new ones. This study applies the means-end chain approach to identify the customer value, consequences, and attributes of ice cream and to suggest useful information for ice cream sellers to develop differential marketing strategies across various consumption situations (i.e. on a date, gathering with friends, craving for ice cream). This study conducted one-on-one in-depth interviews with participants. The interview content was subsequently analyzed and coded to produce an implication matrix and a hierarchical value map, which was further used to determine customers' value perceptions. The results indicate the terminal values of the highest strength comprised economy, pleasure, and efficiency. Pleasure was emphasized among consumers who were on a date or gathering with friends, whereas satisfaction was emphasized among consumers who craved ice cream. Based on the results, the study also provides suggestions to the industry and future researchers.

  2. A customer value analysis of Taiwan ice cream market: a means-end chain approach across consumption situations.

    PubMed

    Chen, Yan-Kwang; Tsai, Pei-Shan; Chiu, Fei-Rung

    2015-01-01

    In the highly competitive market, it is increasingly hard for ice cream stores to develop creative marketing strategies to retain existing customers and attract new ones. This study applies the means-end chain approach to identify the customer value, consequences, and attributes of ice cream and to suggest useful information for ice cream sellers to develop differential marketing strategies across various consumption situations (i.e. on a date, gathering with friends, craving for ice cream). This study conducted one-on-one in-depth interviews with participants. The interview content was subsequently analyzed and coded to produce an implication matrix and a hierarchical value map, which was further used to determine customers' value perceptions. The results indicate the terminal values of the highest strength comprised economy, pleasure, and efficiency. Pleasure was emphasized among consumers who were on a date or gathering with friends, whereas satisfaction was emphasized among consumers who craved ice cream. Based on the results, the study also provides suggestions to the industry and future researchers. PMID:26682112

  3. Measuring product meaning for prescribed medication using a means-end chain model.

    PubMed

    Doucette, W R; Wiederholt, J B

    1992-03-01

    On the basis of a means-end chain model, the product attribute and consequence levels of consumers' product meaning for prescribed medication were measured for a sample of 550 consumers. Using exploratory factor analysis on a 30-item scale, the authors identified five product attribute dimensions and three consequence dimensions. The means-end chain model can help marketers of health care learn more about how consumers categorize product meanings, which in turn can be used in the development of marketing strategies.

  4. Three Randomized Controlled Trials of Early Long-Chain Polyunsaturated Fatty Acid Supplementation on Means-End Problem Solving in Nine-Month Olds

    PubMed Central

    Drover, James R.; Hoffman, Dennis R.; Castañeda, Yolanda S.; Morale, Sarah E.; Birch, Eileen E.

    2009-01-01

    This study examines whether feeding infants formula supplemented with long-chain polyunsaturated fatty acids (LCPUFA) improves cognitive function of 9-month olds. Participants included 229 infants from 3, randomized controlled trials. Children received either formula supplemented with docosahexaenoic acid and arachidonic acid, or a control formula beginning at 1 to 5 d (12 month feeding study), or following 6 weeks (6-week weaning study) or 4 to 6 months of breastfeeding (4-to 6-month weaning study). Infants were assessed with a two-step problem solving task. In the 12-month feeding and 6-week weaning studies, supplemented children had more intentional solutions (successful task completions) and higher intention scores (goal-directed behaviors) than controls. These results suggest that LCPUFA-supplementation improves means-end problem solving. PMID:19765006

  5. Three Randomized Controlled Trials of Early Long-Chain Polyunsaturated Fatty Acid Supplementation on Means-End Problem Solving in 9-Month-Olds

    ERIC Educational Resources Information Center

    Drover, James; Hoffman, Dennis R.; Castaneda, Yolanda S.; Morale, Sarah E.; Birch, Eileen E.

    2009-01-01

    This study examines whether feeding infants formula supplemented with long-chain polyunsaturated fatty acids (LCPUFA) improves cognitive function of 9-month-olds. Participants included 229 infants from 3 randomized controlled trials. Children received either formula supplemented with docosahexaenoic acid and arachidonic acid, or a control formula…

  6. Means-End Theory: Getting the Service Customer's Attention.

    ERIC Educational Resources Information Center

    Rosen, Deborah E.; Greenlee, Timothy B.

    2001-01-01

    Examined the usefulness of Means-End Theory in developing effective college recruitment brochures. Found evidence that brochures that emphasize attributes (e.g., cost, location) over consequences (e.g., getting a job) or values (e.g., security) will generate greater interest in an educational institution. (EV)

  7. Using Means-End Theory To Understand the Outdoor Adventure Experience.

    ERIC Educational Resources Information Center

    Goldenberg, Marni; Klenosky, David; McAvoy, Leo; Holman, Tom

    Means-end analysis was used to examine the linkages between elements of an Outward Bound course and the personal benefits and outcomes obtained or reinforced by course completion. A self-administered questionnaire was completed by 216 persons, who completed a course at the North Carolina Outward Bound School. Respondents were aged 14-66 (83…

  8. Dogs are able to solve a means-end task

    PubMed Central

    Range, Friederike; Hentrup, Marleen; Viranyi, Zsofia

    2014-01-01

    Dogs, although very skilled in social communicative tasks, have shown limited abilities in the domain of physical cognition. Consequently, several researchers hypothesized that domestication enhanced dogs’ cognitive abilities in the social realm, but relaxed selection on the physical one. For instance, dogs failed to demonstrate means-end understanding, an important form of relying on physical causal connection, when tested in a string-pulling task. Here, we tested dogs in an ‘on/off’ task using a novel approach. Thirty-two dogs were confronted with four different conditions in which they could choose between two boards one with a reward ‘on’ and another one with a reward ‘off’ (reward was placed next to the board). The dogs chose the correct board when 1) both rewards were placed at the same distance from the dog, when 2) the reward placed ‘on’ the board was closer to the dog, and 3) even when the reward placed ‘off’ the board was much closer to the dog and was food. Interestingly, in the latter case dogs did not perform above chance, if instead of a direct reward, the dogs had to retrieve an object placed on the board to get a food reward. In contrast to previous string pulling studies, our results show that dogs are able to solve a means-end task even if proximity of the unsupported reward is a confounding factor. PMID:21445577

  9. Means-End Behavior in Young Infants: The Interplay of Action Perception and Action Production

    ERIC Educational Resources Information Center

    Daum, Moritz M.; Prinz, Wolfgang; Aschersleben, Gisa

    2009-01-01

    In 2 experiments, the interplay of action perception and action production was investigated in 6-month-old infants. In Experiment 1, infants received 2 versions of a means-end task in counterbalanced order. In the action perception version, a preferential looking paradigm in which infants were shown an actor performing means-end behavior with an…

  10. "Insight" in pigeons: absence of means-end processing in displacement tests.

    PubMed

    Cook, Robert G; Fowler, Catherine

    2014-03-01

    The understanding of functional relations between action and consequence is a critical component of intelligence. To examine this linkage in pigeons, we investigated their understanding of the relations of the elements tested in an extension of Köhler's box stacking task to this species. In the experiments, the pigeons had to move a spatially displaced box under an out-of-reach target. Experiment 1 successfully replicated and extended the previous finding showing that when separately trained to move a box and stand on it to peck the target, pigeons can synthesize these behaviors to solve the single-box displacement problem quickly on their first attempt. Experiment 2 tested whether pigeons, when given a simultaneous choice between two boxes with identical reinforcement histories, would selectively choose the box with the correct functional affordance (i.e., permitting standing) to solve the problem rather than a non-functional one. Their extensive, equivalent, and undirected behavior in moving both boxes during these tests suggests the pigeons did not possess a means-end understanding of the functional properties of the boxes. Instead, their results were consistent with an analysis of their earlier synthetic behavior as being due to the temporal and spatial relations of the physical elements in the task and their prior learned behaviors.

  11. Postural and Object-Oriented Experiences Advance Early Reaching, Object Exploration, and Means-End Behavior

    ERIC Educational Resources Information Center

    Lobo, Michele A.; Galloway, James C.

    2008-01-01

    The effects of 3 weeks of social (control), postural, or object-oriented experiences on 9- to 21-week-old infants' (N = 42) reaching, exploration, and means-end behaviors were assessed. Coders recorded object contacts, mouthing, fingering, attention, and affect from video. Postural and object-oriented experiences advanced reaching, haptic…

  12. Infants' Sensitivity to the Causal Features of Means-End Support Sequences in Action and Perception

    ERIC Educational Resources Information Center

    Sommerville, Jessica A.; Woodward, Amanda L.

    2005-01-01

    Current work has yielded differential findings regarding infants' ability to perceptually detect the causal structure of a means-end support sequence. Resolving this debate has important implications for perception-action dissociations in this domain of object knowledge. In Study 1, 12-month-old infants' ability to perceive the causal structure of…

  13. How Group Experience Affects Outcomes from NOLS Programs: A Means-End Investigation

    ERIC Educational Resources Information Center

    Goldenberg, Marni; Soule, Katherine

    2011-01-01

    Using means-end theory, this study evaluates how being part of a group influences outcomes of National Outdoor Leadership School (NOLS) participants. This study examines outcomes from NOLS courses during the summer of 2006 in the Wind River Mountain Range of Wyoming. Immediately following 2006 course completion, a convenience sample of 345…

  14. A Four-Year Follow-Up of Means-End Outcomes from Outdoor Adventure Programs

    ERIC Educational Resources Information Center

    Goldenberg, Marni; Soule, Katherine E.

    2015-01-01

    Means-end theory was used to analyze differences in outcomes from original interviews and follow-up interviews occurring four years after Outward Bound (OB) and National Outdoor Leadership School (NOLS) 2006 course participation. In 2006, a semi-structured, in-person interview was conducted after participants (N = 510) completed their course. In…

  15. An episodic specificity induction enhances means-end problem solving in young and older adults.

    PubMed

    Madore, Kevin P; Schacter, Daniel L

    2014-12-01

    Episodic memory plays an important role not only in remembering past experiences, but also in constructing simulations of future experiences and solving means-end social problems. We recently found that an episodic specificity induction-brief training in recollecting details of past experiences-enhances performance of young and older adults on memory and imagination tasks. Here we tested the hypothesis that this specificity induction would also positively impact a means-end problem-solving task on which age-related changes have been linked to impaired episodic memory. Young and older adults received the specificity induction or a control induction before completing a means-end problem-solving task, as well as memory and imagination tasks. Consistent with previous findings, older adults provided fewer relevant steps on problem solving than did young adults, and their responses also contained fewer internal (i.e., episodic) details across the 3 tasks. There was no difference in the number of other (e.g., irrelevant) steps on problem solving or external (i.e., semantic) details generated on the 3 tasks as a function of age. Critically, the specificity induction increased the number of relevant steps and internal details (but not other steps or external details) that both young and older adults generated in problem solving compared with the control induction, as well as the number of internal details (but not external details) generated for memory and imagination. Our findings support the idea that episodic retrieval processes are involved in means-end problem solving, extend the range of tasks on which a specificity induction targets these processes, and show that the problem-solving performance of older adults can benefit from a specificity induction as much as that of young adults.

  16. Bridging the Gap: Solving Spatial Means-Ends Relations in a Locomotor Task

    ERIC Educational Resources Information Center

    Berger, Sarah E.; Adolph, Karen E.; Kavookjian, Alisan E.

    2010-01-01

    Using a means-means-ends problem-solving task, this study examined whether 16-month-old walking infants (N = 28) took into account the width of a bridge as a means for crossing a precipice and the location of a handrail as a means for augmenting balance on a narrow bridge. Infants were encouraged to cross from one platform to another over narrow…

  17. An episodic specificity induction enhances means-end problem solving in young and older adults

    PubMed Central

    Madore, Kevin P.; Schacter, Daniel L.

    2014-01-01

    Episodic memory plays an important role not only in remembering past experiences, but also in constructing simulations of future experiences and solving means-end social problems. We recently found that an episodic specificity induction- brief training in recollecting details of past experiences- enhances performance of young and older adults on memory and imagination tasks. Here we tested the hypothesis that this specificity induction would also positively impact a means-end problem solving task on which age-related changes have been linked to impaired episodic memory. Young and older adults received the specificity induction or a control induction before completing a means-end problem solving task as well as memory and imagination tasks. Consistent with previous findings, older adults provided fewer relevant steps on problem solving than did young adults, and their responses also contained fewer internal (i.e., episodic) details across the three tasks. There was no difference in the number of other (e.g., irrelevant) steps on problem solving or external (i.e., semantic) details generated on the three tasks as a function of age. Critically, the specificity induction increased the number of relevant steps and internal details (but not other steps or external details) that both young and older adults generated in problem solving compared with the control induction, as well as the number of internal details (but not external details) generated for memory and imagination. Our findings support the idea that episodic retrieval processes are involved in means-end problem solving, extend the range of tasks on which a specificity induction targets these processes, and show that the problem solving performance of older adults can benefit from a specificity induction as much as that of young adults. PMID:25365688

  18. Domestication has not affected the understanding of means-end connections in dogs

    PubMed Central

    Range, Friederike; Möslinger, Helene; Virányi, Zs

    2015-01-01

    Recent studies have revealed that dogs often perform well in cognitive tasks in the social domain, but rather poorly in the physical domain. This dichotomy has led to the hypothesis that the domestication process might have enhanced the social cognitive skills of dogs (Hare et al. in Science 298:1634–1636, 2002; Miklósi et al. in Curr Biol 13:763–766, 2003) but at the same time had a detrimental effect on their physical cognition (Frank in Z Tierpsychol 5:389–399, 1980). Despite the recent interest in dog cognition and especially the effects of domestication, the latter hypothesis has hardly been tested and we lack detailed knowledge of the physical understanding of wolves in comparison with dogs. Here, we set out to examine whether adult wolves and dogs rely on means-end connections using the string-pulling task, to test the prediction that wolves would perform better than dogs in such a task of physical cognition. We found that at the group level, dogs were more prone to commit the proximity error, while the wolves showed a stronger side bias. Neither wolves nor dogs showed an instantaneous understanding of means-end connection, but made different mistakes. Thus, the performance of the wolves and dogs in this string-pulling task did not confirm that domestication has affected the physical cognition of dogs. PMID:22460629

  19. Biofuel supply chain, market, and policy analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Leilei

    Renewable fuel is receiving an increasing attention as a substitute for fossil based energy. The US Department of Energy (DOE) has employed increasing effort on promoting the advanced biofuel productions. Although the advanced biofuel remains at its early stage, it is expected to play an important role in climate policy in the future in the transportation sector. This dissertation studies the emerging biofuel supply chain and markets by analyzing the production cost, and the outcomes of the biofuel market, including blended fuel market price and quantity, biofuel contract price and quantity, profitability of each stakeholder (farmers, biofuel producers, biofuel blenders) in the market. I also address government policy impacts on the emerging biofuel market. The dissertation is composed with three parts, each in a paper format. The first part studies the supply chain of emerging biofuel industry. Two optimization-based models are built to determine the number of facilities to deploy, facility locations, facility capacities, and operational planning within facilities. Cost analyses have been conducted under a variety of biofuel demand scenarios. It is my intention that this model will shed light on biofuel supply chain design considering operational planning under uncertain demand situations. The second part of the dissertation work focuses on analyzing the interaction between the key stakeholders along the supply chain. A bottom-up equilibrium model is built for the emerging biofuel market to study the competition in the advanced biofuel market, explicitly formulating the interactions between farmers, biofuel producers, blenders, and consumers. The model simulates the profit maximization of multiple market entities by incorporating their competitive decisions in farmers' land allocation, biomass transportation, biofuel production, and biofuel blending. As such, the equilibrium model is capable of and appropriate for policy analysis, especially for those policies

  20. The Goal Trumps the Means: Highlighting Goals is More Beneficial than Highlighting Means in Means-End Training

    ERIC Educational Resources Information Center

    Gerson, Sarah A.; Woodward, Amanda L.

    2013-01-01

    Means-end actions are an early-emerging form of problem solving. These actions require initiating initial behaviors with a goal in mind. In this study, we explored the origins of 8-month-old infants' means-end action production using a cloth-pulling training paradigm. We examined whether highlighting the goal (toy) or the means (cloth) was more…

  1. Development of Means-End Behavior in Young Infants: Pulling a Support To Retrieve a Distant Object.

    ERIC Educational Resources Information Center

    Willatts, Peter

    1999-01-01

    Three longitudinal studies examined means-ends behavior of 6- to 8-month olds. Found that intentional means-end behavior increased between 6 and 7 months, with 7-month olds' performance influenced by the presence of a toy on the cloth. Performance was the same when cloth was attached to or separate from the toy. By 8 months, infants adjusted…

  2. Means-end comprehension in four parrot species: explained by social complexity.

    PubMed

    Krasheninnikova, Anastasia; Bräger, Stefan; Wanker, Ralf

    2013-09-01

    A comparative approach is required to investigate the evolutionary origins of cognitive abilities. In this paper, we compare the performance of four parrot species, spectacled parrotlets (Forpus conspicillatus), rainbow lorikeets (Trichoglossus haematodus), green-winged macaws (Ara chloroptera) and sulphur-crested cockatoos (Cacatua galerita triton) in standardized string-pulling and string-choice paradigms. We varied the spatial relationship between the strings, the presence of a reward and the physical contact between the string and the reward to test different cognitive skills requiring means-end comprehension. The species tested showed a high individual and inter-specific variation in their ability to solve the tasks. Spectacled parrotlets performed best among the four species and solved the most complex choice tasks, namely crossed-string task and broken-string task, spontaneously. In contrast, macaws and cockatoos failed to identify the correct string in these two tasks. The rainbow lorikeets were outperformed by the parrotlets, but outperformed in turn the macaws and the cockatoos. The findings can be best explained by the variation in social complexity among species, rather than in their ecology.

  3. Deubiquitinase–based analysis of ubiquitin chain architecture using Ubiquitin Chain Restriction (UbiCRest)

    PubMed Central

    Komander, David

    2016-01-01

    Protein ubiquitination is a versatile protein modification that regulates virtually all cellular processes. This versatility originates from polyubiquitin chains, which can be linked in eight distinct ways. The combinatorial complexity of eight linkage types in homotypic (one chain type per polymer) and heterotypic (multiple linkage types per polymer) chains poses significant problems for biochemical analysis. Here we describe UbiCRest, in which substrates (ubiquitinated proteins or polyubiquitin chains) are treated with a panel of linkage-specific deubiquitinating enzymes (DUBs) in parallel reactions, followed by gel-based analysis. UbiCRest can be used to show that a protein is ubiquitinated, to identify which linkage type(s) are present on polyubiquitinated proteins and to assess the architecture of heterotypic polyubiquitin chains. DUBs used in UbiCRest can be obtained commercially; however, we include details for generating a toolkit of purified DUBs and for profiling their linkage preferences in vitro. UbiCRest is a qualitative method that yields insights into ubiquitin chain linkage types and architecture within hours, and it can be performed on western blotting quantities of endogenously ubiquitinated proteins. PMID:25633630

  4. Markov Chain Analysis of Musical Dice Games

    NASA Astrophysics Data System (ADS)

    Volchenkov, D.; Dawin, J. R.

    2012-07-01

    A system for using dice to compose music randomly is known as the musical dice game. The discrete time MIDI models of 804 pieces of classical music written by 29 composers have been encoded into the transition matrices and studied by Markov chains. Contrary to human languages, entropy dominates over redundancy, in the musical dice games based on the compositions of classical music. The maximum complexity is achieved on the blocks consisting of just a few notes (8 notes, for the musical dice games generated over Bach's compositions). First passage times to notes can be used to resolve tonality and feature a composer.

  5. Fast analysis of radionuclide decay chain migration

    NASA Astrophysics Data System (ADS)

    Chen, J. S.; Liang, C. P.; Liu, C. W.; Li, L.

    2014-12-01

    A novel tool for rapidly predicting the long-term plume behavior of an arbitrary length radionuclide decay chain is presented in this study. This fast tool is achieved based on generalized analytical solutions in compact format derived for a set of two-dimensional advection-dispersion equations coupled with sequential first-order decay reactions in groundwater system. The performance of the developed tool is evaluated by a numerical model using a Laplace transform finite difference scheme. The results of performance evaluation indicate that the developed model is robust and accurate. The developed model is then used to fast understand the transport behavior of a four-member radionuclide decay chain. Results show that the plume extents and concentration levels of any target radionuclide are very sensitive to longitudinal, transverse dispersion, decay rate constant and retardation factor. The developed model are useful tools for rapidly assessing the ecological and environmental impact of the accidental radionuclide releases such as the Fukushima nuclear disaster where multiple radionuclides leaked through the reactor, subsequently contaminating the local groundwater and ocean seawater in the vicinity of the nuclear plant.

  6. Modeling methodology for supply chain synthesis and disruption analysis

    NASA Astrophysics Data System (ADS)

    Wu, Teresa; Blackhurst, Jennifer

    2004-11-01

    The concept of an integrated or synthesized supply chain is a strategy for managing today's globalized and customer driven supply chains in order to better meet customer demands. Synthesizing individual entities into an integrated supply chain can be a challenging task due to a variety of factors including conflicting objectives, mismatched incentives and constraints of the individual entities. Furthermore, understanding the effects of disruptions occurring at any point in the system is difficult when working toward synthesizing supply chain operations. Therefore, the goal of this research is to present a modeling methodology to manage the synthesis of a supply chain by linking hierarchical levels of the system and to model and analyze disruptions in the integrated supply chain. The contribution of this research is threefold: (1) supply chain systems can be modeled hierarchically (2) the performance of synthesized supply chain system can be evaluated quantitatively (3) reachability analysis is used to evaluate the system performance and verify whether a specific state is reachable, allowing the user to understand the extent of effects of a disruption.

  7. Analysis of a complex shape chain plate using Transmission Photoelasticity

    NASA Astrophysics Data System (ADS)

    Dasari, N.; Ramesh, K.

    2010-06-01

    fixture was used to load the model during stress freezing in the furnace. The integrated fringe pattern of the offset chain plate is shown in Figure 2. Slices are cut in the offset zone to understand the nature of the stress distribution. A Simple photoelastic analysis of this has revealed a wealth of information to take suitable decision on the design of such plates taking into account the constraints in manufacturing.

  8. Mathematics analysis of polymerase chain reaction kinetic curves.

    PubMed

    Sochivko, D G; Fedorov, A A; Varlamov, D A; Kurochkin, V E; Petrov, R V

    2016-01-01

    The paper reviews different approaches to the mathematical analysis of polymerase chain reaction (PCR) kinetic curves. The basic principles of PCR mathematical analysis are presented. Approximation of PCR kinetic curves and PCR efficiency curves by various functions is described. Several PCR models based on chemical kinetics equations are suggested. Decision criteria for an optimal function to describe PCR efficiency are proposed.

  9. [Analysis of complexity in Chinese meteria medica industrial chain].

    PubMed

    Liu, Ying; Li, Qi; Wang, Xiao-Fan

    2014-08-01

    Chinese meteria medica (CMM) chain is a long-span chain covering agriculture which mainly depends on the forces of nature as well as high-tech CMM industry, CMM expertise industry and fast developing CMM circulation industry. Imbalance among the development of these industries produces bottlenecks and hinders the operation of the entire production chain. After analyzing the structure of Chinese meteria medica industrial chain from the perspective of national economy industry, three industry classifications and differentiation of factor intensity, we conclude that the complex structure of CMM industry chain is attributable to these three aspects. And the complexity is mainly shown at complex industry, varied product types, different coordination of various industrial sections and different technical growth speed of varied industry. We propose that structural complexity is the natural property of the chain, which is the main reason of industry sector development imbalance and bottleneck. Results of this research could provide theoretical analysis for future research on the coordination of industrial chain and the efficiency of resource allocation.

  10. Food chain analysis at a mining waste-contaminated wetland

    SciTech Connect

    Pascoe, G.A.; Blanchet, R.J.; Linder, G.

    1994-12-31

    A food chain analysis was performed in support of a baseline ecological risk assessment oat the Milltown Reservoir Sediments Superfund site in Montana. The site consists of over 450 acres of primarily palustrine wetland contaminated with metals from mining-wastes transported from upstream sources. The food chain analysis focused on several species of terrestrial and aquatic animals indigenous to montane wetlands of the northern Rocky Mountains. Samples of small mammal tissues, grasses, forbs, invertebrates, soils, sediment, aquatic plants, and fish were collected and analyzed for As, Cd, Cu, Pb, and Zn. A linear multimedia food-chain model was constructed to estimate daily intakes of the metals for each receptor, with assumed values for aquatic and terrestrial food items from the site, ingestion of local surface water, incidental ingestion of soils or sediments, and estimated bioavailability of soil metals. Evaluation of health risks was performed by the quotient method, where exposures expressed as daily intakes were compared to literature toxicity values. Results from the food chain analysis suggested that the health of primary consumers and higher trophic organisms (including mice, voles, muskrats, beaver, various waterfowl species, osprey, bald eagles, and deer) is not at risk due to the presence of elevated metals in sediments or upland soils at the site.

  11. Rich Interpretation vs. Deflationary Accounts in Cognitive Development: The Case of Means-End Skills in 7-Month-Old Infants.

    ERIC Educational Resources Information Center

    Munakata, Yuko; Bauer, David; Stackhouse, Tracy; Landgraf, Laura; Huddleston, Jennifer

    2002-01-01

    Tested whether 7-month-olds' means-end behaviors were genuine or the repetition of trained behaviors under conditions of greater arousal. Found that infants' learned button-pushing to light a set of distant lights differed from button-pushing to retrieve toys. Infants demonstrated means-end skills with behaviors that they had not been trained to…

  12. Effects of enterprise technology on supply chain collaboration: analysis of China-linked supply chain

    NASA Astrophysics Data System (ADS)

    Li, Ling

    2012-02-01

    Supply chain collaboration has received increasing attention from scholars and practitioners in recent years. However, our understanding of how enterprise information technology facilitates supply chain collaboration is still very limited, especially with regard to Chinese enterprise ownerships such as state-owned firms, joint-venture firms and local village-owned firms. This paper extends the theory established in enterprise information technology (IT) and supply chain collaboration literature and relates it with coordination in China-linked supply chain. Drawing upon an empirical study from 177 Chinese companies, we provide three major findings: (i) uncovered the importance of leveraging enterprise IT through supply chain collaboration; (ii) identified the relationship between enterprise ownership and enterprise technology use and supply chain collaboration in China-linked supply chain and (iii) illustrated effects of supply chain collaborative activities on operational and market performance.

  13. Bayesian statistical analysis of protein side-chain rotamer preferences.

    PubMed Central

    Dunbrack, R. L.; Cohen, F. E.

    1997-01-01

    We present a Bayesian statistical analysis of the conformations of side chains in proteins from the Protein Data Bank. This is an extension of the backbone-dependent rotamer library, and includes rotamer populations and average chi angles for a full range of phi, psi values. The Bayesian analysis used here provides a rigorous statistical method for taking account of varying amounts of data. Bayesian statistics requires the assumption of a prior distribution for parameters over their range of possible values. This prior distribution can be derived from previous data or from pooling some of the present data. The prior distribution is combined with the data to form the posterior distribution, which is a compromise between the prior distribution and the data. For the chi 2, chi 3, and chi 4 rotamer prior distributions, we assume that the probability of each rotamer type is dependent only on the previous chi rotamer in the chain. For the backbone-dependence of the chi 1 rotamers, we derive prior distributions from the product of the phi-dependent and psi-dependent probabilities. Molecular mechanics calculations with the CHARMM22 potential show a strong similarity with the experimental distributions, indicating that proteins attain their lowest energy rotamers with respect to local backbone-side-chain interactions. The new library is suitable for use in homology modeling, protein folding simulations, and the refinement of X-ray and NMR structures. PMID:9260279

  14. Modelling and analysis of workflow for lean supply chains

    NASA Astrophysics Data System (ADS)

    Ma, Jinping; Wang, Kanliang; Xu, Lida

    2011-11-01

    Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

  15. Modeling Value Chain Analysis of Distance Education using UML

    NASA Astrophysics Data System (ADS)

    Acharya, Anal; Mukherjee, Soumen

    2010-10-01

    Distance education continues to grow as a methodology for the delivery of course content in higher education in India as well as abroad. To manage this growing demand and to provide certain flexibility, there must be certain strategic planning about the use of ICT tools. Value chain analysis is a framework for breaking down the sequence of business functions into a set of activities through which utility could be added to service. Thus it can help to determine the competitive advantage that is enjoyed by an institute. To implement these business functions certain visual representation is required. UML allows for this representation by using a set of structural and behavioral diagrams. In this paper, the first section defines a framework for value chain analysis and highlights its advantages. The second section gives a brief overview of related work in this field. The third section gives a brief discussion on distance education. The fourth section very briefly introduces UML. The fifth section models value chain of distance education using UML. Finally we discuss the limitations and the problems posed in this domain.

  16. Analysis of Chains of Metric Solar Type I Bursts

    NASA Astrophysics Data System (ADS)

    Sodré, Z. A. L.; Cunha-Silva, R. D.; Fernandes, F. C. R.

    2015-01-01

    Type I radio noise storms are believed to provide a diagnostic of electron acceleration in the corona. Most type I bursts appear in chains of five or more individual bursts. An analysis of the chain properties may indicate electron density, height of emission source, and magnetic-field intensity. We studied 255 chains of solar type I solar bursts recorded by the Compact Astronomical Low-cost Low-frequency Instrument for Spectroscopy and Transportable Observatory (CALLISTO-BLEN) spectrograph from 30 July to 9 August 2011 in the frequency range 170 - 870 MHz. Based on the morphological characteristics identified in the dynamic spectra, we determined the physical parameters for the events. The source electron density was found to be in the range 0.5 - 1.6×109 cm-3, the radial velocity of the emitting plasma varied from -1600 - 1500 km s-1, the magnetic-field strength was in the range 2.2 - 3.3 G, and the height of the source ranged from 0.95 to 1.15 solar radii. The results are consistent with previously reported values.

  17. Image Chain Analysis For Digital Image Rectification System

    NASA Astrophysics Data System (ADS)

    Arguello, Roger J.

    1981-07-01

    An image chain analysis, utilizing a comprehensive computer program, has been gen-erated for the key elements of a digital image rectification system. System block dia-grams and analyses for three system configurations employing film scanner input have been formulated with a parametric specification of pertinent element modulation transfer functions and input film scene spectra. The major elements of the system for this analy-sis include a high-resolution, high-speed charge-coupled device film scanner, three candidate digital resampling option algorithms (i.e., nearest neighbor, bilinear inter-polation and cubic convolution methods), and two candidate printer reconstructor implemen-tations (solid-state light-emitting diode printer and laser beam recorder). Suitable metrics for the digital rectification system, incorporating the effects of interpolation and resolution error, were established, and the image chain analysis program was used to perform a quantitative comparison of the three resampling options with the two candi-date printer reconstructor implementations. The nearest neighbor digital resampling function is found to be a good compromise choice when cascaded with either a light-emit-ting diode printer or laser beam recorder. The resulting composite intensity point spread functions, including resampling, and both types of reconstruction are bilinear and quadratic, respectively.

  18. Managing Distance Education Institutions through Value Chain Analysis: the Nigerian Experience.

    ERIC Educational Resources Information Center

    Aderinto, J. A.; Akintayo, M. O.

    Value chain analysis can gauge, analyze, and predict organization effects to control cost in light of achieving strategic organization objectives of distance education. Value chain analysis enables organizations to accomplish their goal or mission through cost effectiveness or differentiation. The value chain activity structure in a distance…

  19. Analysis of the gravitaxis signal transduction chain in Euglena gracilis

    NASA Astrophysics Data System (ADS)

    Nasir, Adeel

    Abstract Euglena gracilis is a photosynthetic, eukaryotic flagellate. It can adapt autotrophic and heterotrophic mode of growth and respond to different stimuli, this makes it an organism of choice for different research disciplines. It swims to reach a suitable niche by employing different stimuli such as oxygen, light, gravity and different chemicals. Among these stimuli light and gravity are the most important. Phototaxis (locomotion under light stimulus) and gravitaxis (locomotion under gravity stimulus) synergistically help cells to attain an optimal niche in the environment. However, in the complete absence of light or under scarcity of detectable light, cells can totally depend on gravity to find its swimming path. Therefore gravity has certain advantages over other stimuli.Unlike phototatic signal transduction chain of Euglena gracilis no clear primary gravity receptor has been identified in Euglena cells so far. However, there are some convincing evidence that TRP like channels act as a primary gravity receptor in Euglena gracilis.Use of different inhibitors gave rise to the involvement of protein kinase and calmodulin proteins in signal transduction chain of Euglena gracilis. Recently, specific calmodulin (Calmodulin 2) and protein kinase (PKA) have been identified as potential candidates of gravitactic signal transduction chain. Further characterization and investigation of these candidates was required. Therefore a combination of biochemical and genetic techniques was employed to localize proteins in cells and also to find interacting partners. For localization studies, specific antibodies were raised and characterized. Specificity of antibodies was validated by knockdown mutants, Invitro-translated proteins and heterologously expressed proteins. Cell fractionation studies, involving separation of the cell body and flagella for western blot analysis and confocal immunofluorescence studies were performed for subcellular localization. In order to find

  20. IT-Supported Modeling, Analysis and Design of Supply Chains

    NASA Astrophysics Data System (ADS)

    Nienhaus, Jörg; Alard, Robert; Sennheiser, Andreas

    A common language is a prerequisite for analyzing and optimizing supply chains. Based on experiences with three case studies, this paper identifies the aspects of a supply chain that have to be mapped to take informed decisions on its operations. Current, integrated modeling approaches for supply chains, like the SCOR and the GSCM model, will be analyzed and an advanced approach will be defined. The resulting approach takes advantage of IT-support.

  1. Identifying Innovative Interventions to Promote Healthy Eating Using Consumption-Oriented Food Supply Chain Analysis.

    PubMed

    Hawkes, Corinna

    2009-07-01

    The mapping and analysis of supply chains is a technique increasingly used to address problems in the food system. Yet such supply chain management has not yet been applied as a means of encouraging healthier diets. Moreover, most policies recommended to promote healthy eating focus on the consumer end of the chain. This article proposes a consumption-oriented food supply chain analysis to identify the changes needed in the food supply chain to create a healthier food environment, measured in terms of food availability, prices, and marketing. Along with established forms of supply chain analysis, the method is informed by a historical overview of how food supply chains have changed over time. The method posits that the actors and actions in the chain are affected by organizational, financial, technological, and policy incentives and disincentives, which can in turn be levered for change. It presents a preliminary example of the supply of Coca-Cola beverages into school vending machines and identifies further potential applications. These include fruit and vegetable supply chains, local food chains, supply chains for health-promoting versions of food products, and identifying financial incentives in supply chains for healthier eating. PMID:23144674

  2. Identifying Innovative Interventions to Promote Healthy Eating Using Consumption-Oriented Food Supply Chain Analysis

    PubMed Central

    Hawkes, Corinna

    2009-01-01

    The mapping and analysis of supply chains is a technique increasingly used to address problems in the food system. Yet such supply chain management has not yet been applied as a means of encouraging healthier diets. Moreover, most policies recommended to promote healthy eating focus on the consumer end of the chain. This article proposes a consumption-oriented food supply chain analysis to identify the changes needed in the food supply chain to create a healthier food environment, measured in terms of food availability, prices, and marketing. Along with established forms of supply chain analysis, the method is informed by a historical overview of how food supply chains have changed over time. The method posits that the actors and actions in the chain are affected by organizational, financial, technological, and policy incentives and disincentives, which can in turn be levered for change. It presents a preliminary example of the supply of Coca-Cola beverages into school vending machines and identifies further potential applications. These include fruit and vegetable supply chains, local food chains, supply chains for health-promoting versions of food products, and identifying financial incentives in supply chains for healthier eating. PMID:23144674

  3. Rouse mode analysis of chain relaxation in homopolymer melts

    SciTech Connect

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2014-09-15

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inversely with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.

  4. Rouse mode analysis of chain relaxation in homopolymer melts

    DOE PAGES

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2014-09-15

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inverselymore » with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.« less

  5. Rouse Mode Analysis of Chain Relaxation in Homopolymer Melts

    PubMed Central

    2015-01-01

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inversely with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. These facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion. PMID:25328247

  6. Diagnostic challenges of tuberculous lymphadenitis using polymerase chain reaction analysis: a case study.

    PubMed

    Taniguchi, Hirokazu; Nakamura, Masahiko; Shimokawa, Kazuki; Kamiseki, Fumi; Ishizawa, Shin; Abo, Hitoshi; Furuse, Hideaki; Tsuda, Takeshi; Masaki, Yasuaki; Suzuki, Kensuke

    2015-01-01

    This report presents a case of tuberculous lymphadenitis that was difficult to diagnose using polymerase chain reaction analysis. An 80-year-old Japanese female was hospitalized due to swollen cervical lymph nodes. Her lymph node tests revealed paradoxical polymerase chain reaction results. Polymerase chain reaction analysis of two biopsy tissues using the Cobas TaqMan revealed a positive result for Mycobacterium avium and a negative result for Mycobacterium tuberculosis. However, polymerase chain reaction analysis of a cultured colony of acid-fast bacteria from biopsy tissue using the Cobas TaqMan and an alternative polymerase chain reaction analysis of biopsy tissue yielded discordant results. The patient was diagnosed as having tuberculous lymphadenitis. She was treated with antitubercular drugs and subsequently had a reduction in cervical lymph node swelling. Polymerase chain reaction analysis is not 100% accurate; hence, its use as a diagnostic tool for mycobacterial infection requires increased attention.

  7. Causal chain analysis and root causes: the GIWA approach.

    PubMed

    Belausteguigoitia, Juan Carlos

    2004-02-01

    The Global International Waters Assessment (GIWA) was created to help develop a priority setting mechanism for actions in international waters. Apart from assessing the severity of environmental problems in ecosystems, the GIWA's task is to analyze potential policy actions that could solve or mitigate these problems. Given the complex nature of the problems, understanding their root causes is essential to develop effective solutions. The GIWA provides a framework to analyze these causes, which is based on identifying the factors that shape human behavior in relation to the use (direct or indirect) of aquatic resources. Two sets of factors are analyzed. The first one consists of social coordination mechanisms (institutions). Faults in these mechanisms lead to wasteful use of resources. The second consists of factors that do not cause wasteful use of resources per se (poverty, trade, demographic growth, technology), but expose and magnify the faults of the first group of factors. The picture that comes out is that diagnosing simple generic causes, e.g. poverty or trade, without analyzing the case specific ways in which the root causes act and interact to degrade the environment, will likely ignore important links that may put the effectiveness of the recommended policies at risk. A summary of the causal chain analysis for the Colorado River Delta is provided as an example. PMID:15083645

  8. Design and analysis of the Gemini chain system in dual clutch transmission of automobile

    NASA Astrophysics Data System (ADS)

    Cheng, Yabing; Guo, Haitao; Fu, Zhenming; Wan, Nen; Li, Lei; Wang, Yang

    2015-01-01

    Chain drive system is widely used in the conditions of high-speed, overload, variable speed and load. Many studies are focused on the meshing theory and wear characteristics of chain drive system, but system design, analysis, and noise characteristics of the chain drive system are weak. System design and noise characteristic are studied for a new type Gemini chain of dual-clutch automatic transmission. Based on the meshing theory of silent chain, the design parameters of the Gemini chain system are calculated and the mathematical models and dynamic analysis models of the Gemini chain system are established. Dynamic characteristics of the Gemini chain system is simulated and the contact force of plate and pin, plate and sprockets, the chain tension forces, the transmission error and the stress of plates and pins are analyzed. According to the simulation results of the Gemini chain system, the noise experiment about system is carried out. The noise values are tested at different speed and load and spectral characteristics are analyzed. The results of simulation and experimental show that the contact forces of plate and pin, plate and sprockets are smaller than the allowable stress values, the chain tension force is less than ultimate tension and transmission error is limited in 1.2%. The noise values can meet the requirements of industrial design, and it is proved that the design and analysis method of the Gemini chain system is scientific and feasible. The design and test system is built from analysis to test of Gemini chain system. This research presented will provide a corresponding theoretical guidance for the design and dynamic characteristics and noise characteristics of chain drive system.

  9. Analysis of Magnetosome Chains in Magnetotactic Bacteria by Magnetic Measurements and Automated Image Analysis of Electron Micrographs

    PubMed Central

    Katzmann, E.; Eibauer, M.; Lin, W.; Pan, Y.; Plitzko, J. M.

    2013-01-01

    Magnetotactic bacteria (MTB) align along the Earth's magnetic field by the activity of intracellular magnetosomes, which are membrane-enveloped magnetite or greigite particles that are assembled into well-ordered chains. Formation of magnetosome chains was found to be controlled by a set of specific proteins in Magnetospirillum gryphiswaldense and other MTB. However, the contribution of abiotic factors on magnetosome chain assembly has not been fully explored. Here, we first analyzed the effect of growth conditions on magnetosome chain formation in M. gryphiswaldense by electron microscopy. Whereas higher temperatures (30 to 35°C) and high oxygen concentrations caused increasingly disordered chains and smaller magnetite crystals, growth at 20°C and anoxic conditions resulted in long chains with mature cuboctahedron-shaped crystals. In order to analyze the magnetosome chain in electron microscopy data sets in a more quantitative and unbiased manner, we developed a computerized image analysis algorithm. The collected data comprised the cell dimensions and particle size and number as well as the intracellular position and extension of the magnetosome chain. The chain analysis program (CHAP) was used to evaluate the effects of the genetic and growth conditions on magnetosome chain formation. This was compared and correlated to data obtained from bulk magnetic measurements of wild-type (WT) and mutant cells displaying different chain configurations. These techniques were used to differentiate mutants due to magnetosome chain defects on a bulk scale. PMID:24096429

  10. Rouse Mode Analysis of Chain Relaxation in Polymer Nanocomposites

    PubMed Central

    Kalathi, Jagannathan T.; Rubinstein, Michael; Grest, Gary S.

    2016-01-01

    Large-scale Molecular Dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, as in the case of a polymer-solvent system. However, for NPs larger than half the entanglement mesh size, effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Thus, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect. PMID:25939276

  11. Rouse mode analysis of chain relaxation in polymer nanocomposites

    DOE PAGES

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2015-04-20

    Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, asmore » in the case of a polymer–solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Furthermore, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.« less

  12. Rouse mode analysis of chain relaxation in polymer nanocomposites

    SciTech Connect

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2015-04-20

    Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, as in the case of a polymer–solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Furthermore, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.

  13. Analysis of Escherichia coli mutants with a linear respiratory chain.

    PubMed

    Steinsiek, Sonja; Stagge, Stefan; Bettenbrock, Katja

    2014-01-01

    The respiratory chain of E. coli is branched to allow the cells' flexibility to deal with changing environmental conditions. It consists of the NADH:ubiquinone oxidoreductases NADH dehydrogenase I and II, as well as of three terminal oxidases. They differ with respect to energetic efficiency (proton translocation) and their affinity to the different quinone/quinol species and oxygen. In order to analyze the advantages of the branched electron transport chain over a linear one and to assess how usage of the different terminal oxidases determines growth behavior at varying oxygen concentrations, a set of isogenic mutant strains was created, which lack NADH dehydrogenase I as well as two of the terminal oxidases, resulting in strains with a linear respiratory chain. These strains were analyzed in glucose-limited chemostat experiments with defined oxygen supply, adjusting aerobic, anaerobic and different microaerobic conditions. In contrast to the wild-type strain MG1655, the mutant strains produced acetate even under aerobic conditions. Strain TBE032, lacking NADH dehydrogenase I and expressing cytochrome bd-II as sole terminal oxidase, showed the highest acetate formation rate under aerobic conditions. This supports the idea that cytochrome bd-II terminal oxidase is not able to catalyze the efficient oxidation of the quinol pool at higher oxygen conditions, but is functioning mainly under limiting oxygen conditions. Phosphorylation of ArcA, the regulator of the two-component system ArcBA, besides Fnr the main transcription factor for the response towards different oxygen concentrations, was studied. Its phosphorylation pattern was changed in the mutant strains. Dephosphorylation and therefore inactivation of ArcA started at lower aerobiosis levels than in the wild-type strain. Notably, not only the micro- and aerobic metabolism was affected by the mutations, but also the anaerobic metabolism, where the respiratory chain should not be important. PMID:24475268

  14. OTU Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis

    PubMed Central

    Mevissen, Tycho E.T.; Hospenthal, Manuela K.; Geurink, Paul P.; Elliott, Paul R.; Akutsu, Masato; Arnaudo, Nadia; Ekkebus, Reggy; Kulathu, Yogesh; Wauer, Tobias; El Oualid, Farid; Freund, Stefan M.V.; Ovaa, Huib; Komander, David

    2013-01-01

    Summary Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1’ and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates. PMID:23827681

  15. Mathematical supply-chain modelling: Product analysis of cost and time

    NASA Astrophysics Data System (ADS)

    Easters, D. J.

    2014-03-01

    Establishing a mathematical supply-chain model is a proposition that has received attention due to its inherent benefits of evolving global supply-chain efficiencies. This paper discusses the prevailing relationships found within apparel supply-chain environments, and contemplates the complex issues indicated for constituting a mathematical model. Principal results identified within the data suggest, that the multifarious nature of global supply-chain activities require a degree of simplification in order to fully dilate the necessary factors which affect, each sub-section of the chain. Subsequently, the research findings allowed the division of supply-chain components into sub-sections, which amassed a coherent method of product development activity. Concurrently, the supply-chain model was found to allow systematic mathematical formulae analysis, of cost and time, within the multiple contexts of each subsection encountered. The paper indicates the supply-chain model structure, the mathematics, and considers how product analysis of cost and time can improve the comprehension of product lifecycle management.

  16. Analysis of a simulated heroin distribution chain by HPLC.

    PubMed

    Zelkowicz, Avraham; Magora, Amir; Ravreby, Mark D; Levy, Rina

    2005-07-01

    A heroin distribution chain was simulated by taking three different seizures and preparing four additional samples from each seizure by adding a paracetamol-caffeine mixture in varying amounts, resulting in three different batches each composed of five samples. All of the samples from the three batches were analyzed using HPLC with a UV-PDA detector at a wavelength of 230 nm. The area ratio of various opium alkaloids, acetylation products and components were compared. From the results of the UV area ratios, the fifteen samples could readily be separated into three batches of five samples, with each batch of five samples having a common origin.

  17. Kinematic performance analysis of a parallel-chain hexapod machine

    SciTech Connect

    Jing Song; Jong-I Mou; Calvin King

    1998-05-18

    Inverse and forward kinematic models were derived to analyze the performance of a parallel-chain hexapod machine. Analytical models were constructed for both ideal and real structures. Performance assessment and enhancement algorithms were developed to determine the strut lengths for both ideal and real structures. The strut lengths determined from both cases can be used to analyze the effect of structural imperfections on machine performance. In an open-architecture control environment, strut length errors can be fed back to the controller to compensate for the displacement errors and thus improve the machine's accuracy in production.

  18. Theory analysis of mass spectra of long-chain isocyanates.

    PubMed

    Liu, Dongliang; Hao, Ce; Zhang, Hua; Qiao, Weihong; Li, Zongshi; Yu, Guanghui; Yan, Kelu; Guo, Yuliang; Cheng, Lvbo

    2008-07-01

    Electron impact mass spectra of four long-chain isocyanates, lauryl isocyanate, tetradecyl isocyanate, hexadecyl isocyanate and octadecyl isocyanate, were obtained with a GCT high-resolution time-of-flight mass spectrometer. The four isocyanates studied gave a common base peak of m/z 99, which suggested the formation of a stable six-membered ring structure to decentralize the positive charge. Quantum-mechanical energy calculation justified that the six-membered ring base peak had the lowest energy. The positive charge assigned during the fragmentation of the radical cation, and the relative intensity of the fragment ion peaks, were explained by quantum-mechanical calculations as well.

  19. A BENCHMARKING ANALYSIS FOR FIVE RADIONUCLIDE VADOSE ZONE MODELS (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, AND CHAIN 2D) IN SOIL SCREENING LEVEL CALCULATIONS

    EPA Science Inventory

    Five radionuclide vadose zone models with different degrees of complexity (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, and CHAIN 2D) were selected for use in soil screening level (SSL) calculations. A benchmarking analysis between the models was conducted for a radionuclide (99Tc) rele...

  20. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains.

    PubMed

    Lautala, Pasi T; Hilliard, Michael R; Webb, Erin; Busch, Ingrid; Richard Hess, J; Roni, Mohammad S; Hilbert, Jorge; Handler, Robert M; Bittencourt, Roger; Valente, Amir; Laitinen, Tuuli

    2015-12-01

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term 'supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmost importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. The paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Finally gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study. PMID:26122631

  1. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains

    SciTech Connect

    Lautala, Pasi T.; Hilliard, Michael R.; Webb, Erin; Busch, Ingrid; Richard Hess, J.; Roni, Mohammad S.; Hilbert, Jorge; Handler, Robert M.; Bittencourt, Roger; Valente, Amir; Laitinen, Tuuli

    2015-06-30

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term 'supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmost importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. Our paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Lastly, gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study.

  2. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains

    NASA Astrophysics Data System (ADS)

    Lautala, Pasi T.; Hilliard, Michael R.; Webb, Erin; Busch, Ingrid; Richard Hess, J.; Roni, Mohammad S.; Hilbert, Jorge; Handler, Robert M.; Bittencourt, Roger; Valente, Amir; Laitinen, Tuuli

    2015-12-01

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term `supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmost importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. The paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Finally gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study.

  3. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains.

    PubMed

    Lautala, Pasi T; Hilliard, Michael R; Webb, Erin; Busch, Ingrid; Richard Hess, J; Roni, Mohammad S; Hilbert, Jorge; Handler, Robert M; Bittencourt, Roger; Valente, Amir; Laitinen, Tuuli

    2015-12-01

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term 'supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmost importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. The paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Finally gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study.

  4. Analysis of a closed-kinematic chain robot manipulator

    NASA Technical Reports Server (NTRS)

    Nguyen, Charles C.; Pooran, Farhad J.

    1988-01-01

    Presented are the research results from the research grant entitled: Active Control of Robot Manipulators, sponsored by the Goddard Space Flight Center (NASA) under grant number NAG-780. This report considers a class of robot manipulators based on the closed-kinematic chain mechanism (CKCM). This type of robot manipulators mainly consists of two platforms, one is stationary and the other moving, and they are coupled together through a number of in-parallel actuators. Using spatial geometry and homogeneous transformation, a closed-form solution is derived for the inverse kinematic problem of the six-degree-of-freedom manipulator, built to study robotic assembly in space. Iterative Newton Raphson method is employed to solve the forward kinematic problem. Finally, the equations of motion of the above manipulators are obtained by employing the Lagrangian method. Study of the manipulator dynamics is performed using computer simulation whose results show that the robot actuating forces are strongly dependent on the mass and centroid locations of the robot links.

  5. Functional Analysis of a Mosquito Short Chain Dehydrogenase Cluster

    PubMed Central

    Mayoral, Jaime G.; Leonard, Kate T.; Defelipe, Lucas A.; Turjansksi, Adrian G.; Nouzova, Marcela; Noriegal, Fernando G.

    2013-01-01

    The short chain dehydrogenases (SDR) constitute one the oldest and largest families of enzymes with over 46,000 members in sequence databases. About 25% of all known dehydrogenases belong to the SDR family. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. This family is present in archaea, bacteria, and eukaryota, emphasizing their versatility and fundamental importance for metabolic processes. We identified a cluster of eight SDRs in the mosquito Aedes aegypti (AaSDRs). Members of the cluster differ in tissue specificity and developmental expression. Heterologous expression produced recombinant proteins that had diverse substrate specificities, but distinct from the conventional insect alcohol (ethanol) dehydrogenases. They are all NADP+-dependent and they have S-enantioselectivity and preference for secondary alcohols with 8–15 carbons. Homology modeling was used to build the structure of AaSDR1 and two additional cluster members. The computational study helped explain the selectivity towards the (10S)-isomers as well as the reduced activity of AaSDR4 and AaSDR9 for longer isoprenoid substrates. Similar clusters of SDRs are present in other species of insects, suggesting similar selection mechanisms causing duplication and diversification of this family of enzymes. PMID:23238893

  6. Analysis of human cytomegalovirus using the polymerase chain reaction.

    PubMed

    Mendelson, M

    2000-01-01

    As with numerous other branches of science, the study of human cytomegalovirus (HCMV) infection has been revolutionized by the polymerase chain reaction (PCR) method first devised by Mullis and Faloona (1). PCR allows the in vitro amplification of HCMV DNA sequences by the simultaneous primer extension of complementary DNA strands. Similarly, reverse transcription-PCR (RT-PCR) allows the study of targeted gene expression, by reverse transcription of RNA to complementary DNA (cDNA), followed by amplification of target DNA using predetermined primers. The PCR method is used in the clinical diagnosis of HCMV infection, particularly in the setting of transplantation medicine and in those patients infected with the human immunodeficiency virus (HIV). In addition, the advent of PCR and RT-PCR has transformed our understanding of the pathogenesis of HCMV infection, central to which is the definition of the sites of latency, the degree and type of gene expression within the latently infected cell, and the factors influencing both the maintenance of latency and reactivation of the virus during immunosuppression.

  7. Kinematic and dynamic modeling and approximate analysis of a roller chain drive

    NASA Astrophysics Data System (ADS)

    Fuglede, Niels; Thomsen, Jon Juel

    2016-03-01

    A simple roller chain drive consisting of two sprockets connected by tight chain spans is investigated. First, a kinematic model is presented which include both spans and sprockets. An approach for calculating the chain wrapping length is presented, which also allows for the exact calculation of sprocket center positions for a given chain length. The kinematic analysis demonstrates that the total length of the chain wrapped around the sprockets generally varies during one tooth period. Analytical predictions for the wrapping length are compared to multibody simulation results and show very good agreement. It is thereby demonstrated that chain drives with tight chain spans must include compliant components to function. Second, a dynamic model is presented which includes the two spans and the driven sprocket. Assuming the presence of a stationary operating state, the presented dynamic model allows for analytical studies of the coupled motion of the chain spans and driven sprocket. Parametric excitation of the spans come from sprocket angular displacements, and the driven sprocket acts as a boundary which can be compliant in the axial direction. External transverse excitation of the spans comes from polygonal action, and is treated through kinematic forcing at the moving string boundaries. Perturbation analysis of the model is carried out using the method of multiple scales. Results show a multitude of internal and external resonance conditions, and some examples are presented of both decoupled and coupled motion. Together, the kinematic and dynamic model are aimed toward providing a framework for conducting and understanding both numerical, and experimental investigations of roller chain drive dynamics.

  8. A Markov Chain Monte Carlo Approach to Confirmatory Item Factor Analysis

    ERIC Educational Resources Information Center

    Edwards, Michael C.

    2010-01-01

    Item factor analysis has a rich tradition in both the structural equation modeling and item response theory frameworks. The goal of this paper is to demonstrate a novel combination of various Markov chain Monte Carlo (MCMC) estimation routines to estimate parameters of a wide variety of confirmatory item factor analysis models. Further, I show…

  9. Detection and analysis of polymerase chain reaction products by mass spectrometry

    SciTech Connect

    Hurst, G.B., Doktycz, M.J., Britt, P.F., Vass, A.A., Buchanan, M.V.

    1997-02-01

    This paper describes recent and ongoing efforts to overcome some of the obstacles to more routine and robust application of MALDI-TOF to analysis of polymerase chain reaction products and other information- bearing nucleic acid molecules. Methods for purifying nucleic acid samples are described, as is the application of delayed extraction TOF mass spectrometry to analysis of short oligonucleotides.

  10. Supply chain analysis of e-tailing versus retailing operation - a case study

    NASA Astrophysics Data System (ADS)

    Kumar, Sameer; Tiffany, Maryellen; Vaidya, Salil

    2016-07-01

    The swift growth of e-commerce or e-tailing as a consumer retail channel has made it a serious competitor to traditional retail channels and is changing consumers' purchasing behaviour. The purpose of this case study, based on Target and Amazon.com, is to analyse the attributes of traditional retailing, e-tailing, and hybrid supply chain models to form conclusions about the feasibility of an idealised supply chain model for the future. An integrated and generalised modelling framework is used that incorporates Six Sigma - define, measure, analyse, improve, control methodology leveraging various tools, including process flow maps, cause and effect diagram, performance efficiency metrics, failure mode and effects analysis (FMEA), and Monte Carlo simulation. Based on this analysis and research, the conclusion is that the idealised supply chain of the future may evolve into a hybrid supply chain, which includes both e-tail and retail channels. The main recommendations from this study include assessing the risks of migrating to such a hybrid supply chain and to leverage the recommended actions provided in the hybrid FMEA. To facilitate more effective and mature processes, this study can guide researchers in exhaustive empirical evaluations of hybrid supply chains, gather experiences and lessons learned for practitioners.

  11. Analysis of the sensitivity of a model of terrestrial food chains

    SciTech Connect

    Ganushik, V.; Mitro, A.; Musatova, O.; Sabova, T.

    1985-10-01

    This paper estimates, by means of a sensitivity analysis, the importance of the individual parameters of the model for terrestrial food chains. This method creates the basis for the calculation of the numerical values of the buildup factors of radionuclides in the chain deposited from the atmosphere-the content in food products. The ORB-11 model describes the transportation of radioactive substances through food chains. Several principal food products are considered: wheat, fruits, cucumbers, cabbage, potato, milk, and meat. The coefficient of sensitivity (CS) was computed for each input parameter, radionuclide, contamination route, and given change of input parameter by formula. The data obtained can be used for a stochastic approach to the mnDeling of the transportation of radioactive substances through the food chains, and to the planning of radioecological investigations.

  12. Analysis of liver connexin expression using reverse transcription quantitative real-time polymerase chain reaction

    PubMed Central

    Maes, Michaël; Willebrords, Joost; Crespo Yanguas, Sara; Cogliati, Bruno; Vinken, Mathieu

    2016-01-01

    Summary Although connexin production is mainly regulated at the protein level, altered connexin gene expression has been identified as the underlying mechanism of several pathologies. When studying the latter, appropriate methods to quantify connexin mRNA levels are required. The present chapter describes a well-established reverse transcription quantitative real-time polymerase chain reaction procedure optimized for analysis of hepatic connexins. The method includes RNA extraction and subsequent quantification, generation of complementary DNA, quantitative real-time polymerase chain reaction and data analysis. PMID:27207283

  13. Analysis of Liver Connexin Expression Using Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction.

    PubMed

    Maes, Michaël; Willebrords, Joost; Crespo Yanguas, Sara; Cogliati, Bruno; Vinken, Mathieu

    2016-01-01

    Although connexin production is mainly regulated at the protein level, altered connexin gene expression has been identified as the underlying mechanism of several pathologies. When studying the latter, appropriate methods to quantify connexin RNA levels are required. The present chapter describes a well-established reverse transcription quantitative real-time polymerase chain reaction procedure optimized for analysis of hepatic connexins. The method includes RNA extraction and subsequent quantification, generation of complementary DNA, quantitative real-time polymerase chain reaction, and data analysis. PMID:27207283

  14. Reliability analysis and prediction of mixed mode load using Markov Chain Model

    NASA Astrophysics Data System (ADS)

    Nikabdullah, N.; Singh, S. S. K.; Alebrahim, R.; Azizi, M. A.; K, Elwaleed A.; Noorani, M. S. M.

    2014-06-01

    The aim of this paper is to present the reliability analysis and prediction of mixed mode loading by using a simple two state Markov Chain Model for an automotive crankshaft. The reliability analysis and prediction for any automotive component or structure is important for analyzing and measuring the failure to increase the design life, eliminate or reduce the likelihood of failures and safety risk. The mechanical failures of the crankshaft are due of high bending and torsion stress concentration from high cycle and low rotating bending and torsional stress. The Markov Chain was used to model the two states based on the probability of failure due to bending and torsion stress. In most investigations it revealed that bending stress is much serve than torsional stress, therefore the probability criteria for the bending state would be higher compared to the torsion state. A statistical comparison between the developed Markov Chain Model and field data was done to observe the percentage of error. The reliability analysis and prediction was derived and illustrated from the Markov Chain Model were shown in the Weibull probability and cumulative distribution function, hazard rate and reliability curve and the bathtub curve. It can be concluded that Markov Chain Model has the ability to generate near similar data with minimal percentage of error and for a practical application; the proposed model provides a good accuracy in determining the reliability for the crankshaft under mixed mode loading.

  15. Reliability analysis and prediction of mixed mode load using Markov Chain Model

    SciTech Connect

    Nikabdullah, N.; Singh, S. S. K.; Alebrahim, R.; Azizi, M. A.; K, Elwaleed A.; Noorani, M. S. M.

    2014-06-19

    The aim of this paper is to present the reliability analysis and prediction of mixed mode loading by using a simple two state Markov Chain Model for an automotive crankshaft. The reliability analysis and prediction for any automotive component or structure is important for analyzing and measuring the failure to increase the design life, eliminate or reduce the likelihood of failures and safety risk. The mechanical failures of the crankshaft are due of high bending and torsion stress concentration from high cycle and low rotating bending and torsional stress. The Markov Chain was used to model the two states based on the probability of failure due to bending and torsion stress. In most investigations it revealed that bending stress is much serve than torsional stress, therefore the probability criteria for the bending state would be higher compared to the torsion state. A statistical comparison between the developed Markov Chain Model and field data was done to observe the percentage of error. The reliability analysis and prediction was derived and illustrated from the Markov Chain Model were shown in the Weibull probability and cumulative distribution function, hazard rate and reliability curve and the bathtub curve. It can be concluded that Markov Chain Model has the ability to generate near similar data with minimal percentage of error and for a practical application; the proposed model provides a good accuracy in determining the reliability for the crankshaft under mixed mode loading.

  16. Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis.

    PubMed

    Tivendale, Nathan D; Jewett, Erin M; Hegeman, Adrian D; Cohen, Jerry D

    2016-08-15

    Dynamic metabolic flux analysis requires efficient and effective methods for extraction, purification and analysis of a plethora of naturally-occurring compounds. One area of metabolism that would be highly informative to study using metabolic flux analysis is the tricarboxylic acid (TCA) cycle, which consists of short-chain carboxylic acids. Here, we describe a newly-developed method for extraction, purification, derivatization and analysis of short-chain carboxylic acids involved in the TCA cycle. The method consists of snap-freezing the plant material, followed by maceration and a 12-15h extraction at -80 °C. The extracts are then subject to reduction (to stabilize β-keto acids), purified by strong anion exchange solid phase extraction and methylated with methanolic HCl. This method could also be readily adapted to quantify many other short-chain carboxylic acids.

  17. Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis.

    PubMed

    Tivendale, Nathan D; Jewett, Erin M; Hegeman, Adrian D; Cohen, Jerry D

    2016-08-15

    Dynamic metabolic flux analysis requires efficient and effective methods for extraction, purification and analysis of a plethora of naturally-occurring compounds. One area of metabolism that would be highly informative to study using metabolic flux analysis is the tricarboxylic acid (TCA) cycle, which consists of short-chain carboxylic acids. Here, we describe a newly-developed method for extraction, purification, derivatization and analysis of short-chain carboxylic acids involved in the TCA cycle. The method consists of snap-freezing the plant material, followed by maceration and a 12-15h extraction at -80 °C. The extracts are then subject to reduction (to stabilize β-keto acids), purified by strong anion exchange solid phase extraction and methylated with methanolic HCl. This method could also be readily adapted to quantify many other short-chain carboxylic acids. PMID:27348709

  18. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains

    DOE PAGES

    Lautala, Pasi T.; Hilliard, Michael R.; Webb, Erin; Busch, Ingrid; Richard Hess, J.; Roni, Mohammad S.; Hilbert, Jorge; Handler, Robert M.; Bittencourt, Roger; Valente, Amir; et al

    2015-06-30

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term 'supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmostmore » importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. Our paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Lastly, gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study.« less

  19. Supply Chain Sustainability Analysis of Three Biofuel Pathways

    SciTech Connect

    Jacob J. Jacobson; Erin Searcy; Kara Cafferty; Jennifer B. Dunn; Michael Johnson; Zhichao Wang; Michael Wang; Mary Biddy; Abhijit Dutta; Daniel Inman; Eric Tan; Sue Jones; Lesley Snowden-Swan

    2013-11-01

    The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) collaborates with industrial, agricultural, and non-profit partners to develop and deploy biofuels and other biologically-derived products. As part of this effort, BETO and its national laboratory teams conduct in-depth techno-economic assessments (TEA) of technologies to produce biofuels as part state of technology (SOT) analyses. An SOT assesses progress within and across relevant technology areas based on actual experimental results relative to technical targets and cost goals from design cases and includes technical, economic, and environmental criteria as available. Overall assessments of biofuel pathways begin with feedstock production and the logistics of transporting the feedstock from the farm or plantation to the conversion facility or biorefinery. The conversion process itself is modeled in detail as part of the SOT analysis. The teams then develop an estimate of the biofuel minimum selling price (MSP) and assess the cost competitiveness of the biofuel with conventional fuels such as gasoline.

  20. Chain of custody; recommendations for acceptance and analysis of evidentiary geochemical samples

    USGS Publications Warehouse

    Murphy, Christine M.; Briggs, Paul H.; Adrian, Betty M.; Wilson, Steve A.; Hageman, Phil L.; Theodorakos, Pete M.

    1997-01-01

    Personnel from the Analytical Chemistry Services Group (ACSG), Mineral Resource Survey Program, formed a team to determine the policies for acceptance and analysis of geochemical samples. This team contacted law enforcement agencies that handle litigious samples, laboratories that work with samples of special nature, and the Solicitor General, Department of the Interior. Using the knowledge from these agencies as well as the expertise of ACSG personnel, sample control routine procedures, sample control evidentiary procedures, personnel policy governing chain-of-custody samples, and the general polices governing physical security of chain-of custody samples have been enacted.

  1. Markov chain Monte Carlo segregation and linkage analysis for oligogenic models.

    PubMed Central

    Heath, S C

    1997-01-01

    A new method for segregation and linkage analysis, with pedigree data, is described. Reversible jump Markov chain Monte Carlo methods are used to implement a sampling scheme in which the Markov chain can jump between parameter subspaces corresponding to models with different numbers of quantitative-trait loci (QTL's). Joint estimation of QTL number, position, and effects is possible, avoiding the problems that can arise from misspecification of the number of QTL's in a linkage analysis. The method is illustrated by use of a data set simulated for the 9th Genetic Analysis Workshop; this data set had several oligogenic traits, generated by use of a 1,497-member pedigree. The mixing characteristics of the method appear to be good, and the method correctly recovers the simulated model from the test data set. The approach appears to have great potential both for robust linkage analysis and for the answering of more general questions regarding the genetic control of complex traits. PMID:9326339

  2. Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms.

    PubMed

    Rechner, Steffen; Berger, Annabell

    2016-01-01

    We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. PMID:26824442

  3. Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms.

    PubMed

    Rechner, Steffen; Berger, Annabell

    2016-01-01

    We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time.

  4. Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms

    PubMed Central

    Rechner, Steffen; Berger, Annabell

    2016-01-01

    We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. PMID:26824442

  5. Improving food safety within the dairy chain: an application of conjoint analysis.

    PubMed

    Valeeva, N I; Meuwissen, M P M; Lansink, A G J M Oude; Huirne, R B M

    2005-04-01

    This study determined the relative importance of attributes of food safety improvement in the production chain of fluid pasteurized milk. The chain was divided into 4 blocks: "feed" (compound feed production and its transport), "farm" (dairy farm), "dairy processing" (transport and processing of raw milk, delivery of pasteurized milk), and "consumer" (retailer/catering establishment and pasteurized milk consumption). The concept of food safety improvement focused on 2 main groups of hazards: chemical (antibiotics and dioxin) and microbiological (Salmonella, Escherichia coli, Mycobacterium paratuberculosis, and Staphylococcus aureus). Adaptive conjoint analysis was used to investigate food safety experts' perceptions of the attributes' importance. Preference data from individual experts (n = 24) on 101 attributes along the chain were collected in a computer-interactive mode. Experts perceived the attributes from the "feed" and "farm" blocks as being more vital for controlling the chemical hazards; whereas the attributes from the "farm" and "dairy processing" were considered more vital for controlling the microbiological hazards. For the chemical hazards, "identification of treated cows" and "quality assurance system of compound feed manufacturers" were considered the most important attributes. For the microbiological hazards, these were "manure supply source" and "action in salmonellosis and M. paratuberculosis cases". The rather high importance of attributes relating to quality assurance and traceability systems of the chain participants indicates that participants look for food safety assurance from the preceding participants. This information has substantial decision-making implications for private businesses along the chain and for the government regarding the food safety improvement of fluid pasteurized milk.

  6. The Creative Use of Chain Analysis Techniques in Counseling Clients Who Engage in Nonsuicidal Self-Injury

    ERIC Educational Resources Information Center

    Kinch, Stephanie; Kress, Victoria E.

    2012-01-01

    The purpose of this article is to present creative ways that chain analysis techniques, an intervention used in dialectical behavior therapy, can be used to address clients' nonsuicidal self-injurious behaviors. A description and rationale for using chain analysis techniques with clients who self-injure is provided. An illustrative case example is…

  7. Thermal analysis of brazing seal and sterilizing technique to break contamination chain for Mars sample return

    NASA Astrophysics Data System (ADS)

    Bao, Xiaoqi; Badescu, Mircea; Bar-Cohen, Yoseph

    2015-03-01

    The potential to return Martian samples to Earth for extensive analysis is in great interest of the planetary science community. It is important to make sure the mission would securely contain any microbes that may possibly exist on Mars so that they would not be able to cause any adverse effects on Earth's environment. A brazing sealing and sterilizing technique has been proposed to break the Mars-to-Earth contamination chain. Thermal analysis of the brazing process was conducted for several conceptual designs that apply the technique. Control of the increase of the temperature of the Martian samples is a challenge. The temperature profiles of the Martian samples being sealed in the container were predicted by finite element thermal models. The results show that the sealing and sterilization process can be controlled such that the samples' temperature is maintained below the potentially required level, and that the brazing technique is a feasible approach to break the contamination chain.

  8. Genetic and physiological analysis of branched-chain alcohols and isoamyl acetate production in Saccharomyces cerevisiae.

    PubMed

    Yoshimoto, H; Fukushige, T; Yonezawa, T; Sone, H

    2002-08-01

    Branched-chain alcohols, such as isoamyl alcohol and isobutanol, and isoamyl acetate are important flavor components of yeast-fermented alcoholic beverages. Analysis of a null mutant of the BAT2 gene encoding cytosolic branched-chain amino acid aminotransferase, and a transformant with multi-copy plasmids containing the BAT2 gene showed that the BAT2 gene product plays an important role in the production of branched-chain alcohols and isoamyl acetate. Fermentation tests using the bat2 null mutant transformed with multi-copy plasmids carrying the ATF1 gene, which encodes alcohol acetyltransferase, indicated that modified expression of BAT2 and ATF1 genes could significantly alter the proportion of branched-chain alcohols and isoamyl acetate synthesized. Furthermore, fermentation tests using different ratios of nitrogen source and RNA blot analyses demonstrated that transcription of L-leucine biosynthetic ( LEU) and BAT genes is co-regulated by nitrogen source, that production of isoamyl alcohol depends on this transcription, and that ATF transcription increased with increased concentrations of nitrogen source. Our data suggest that changes in isoamyl alcohol production by nitrogen source are due to transcriptional co-regulation of LEU and BAT genes, and that production of isoamyl acetate is dependent on isoamyl alcohol production and ATF transcription. PMID:12172617

  9. Food chain analysis of exposures and risks to wildlife at a metals-contaminated wetland.

    PubMed

    Pascoe, G A; Blanchet, R J; Linder, G

    1996-03-01

    A food chain analysis of risks to wetland receptors was performed in support of a baseline ecological risk assessment at the Milltown Reservoir Sediments Superfund site in Montana. The study area consisted of over 450 acres of primarily palustrine wetland contaminated with metals from mining wastes transported from upstream sources (average of 465 mg/kg for Cu in sediments, and 585 mg/kg in soils). The food chain analysis focused on several species of terrestrial and semiaquatic animals indigenous to montane wetlands of the northern Rocky Mountains. Receptors consisted of mice, voles, muskrats, beaver, various waterfowl species, osprey, bald eagles, and deer. Samples of aquatic and terrestrial invertebrates, small mammal tissues, fish tissue, aquatic and terrestrial vegetation, soils, sediment, and surface water were collected and analyzed for As, Cd, Cu, and Zn. A linear multimedia food-chain model was constructed to estimate daily intakes of the metals for each receptor, with assumed values for ingestion of aquatic and terrestrial food items, ingestion of local surface water, and incidental ingestion of soils and/or sediments. Evaluation of health risks to the receptors was performed by comparison of exposures expressed as daily intakes to a suite of toxicity values. The range of values consisted of the lower end of chronic toxicity data found in toxicology databases or the literature for the same or similar species, modified to account for extrapolation uncertainties. Daily intakes of chemicals of concern were below or within the range of toxicity values for all receptors. The weight of evidence from the food chain analysis and earlier bioassessment and ecological studies suggest that the health of the wetland receptors is at minimal risk due to the presence of elevated metals in sediments, upland soils, water, or food items at the site.

  10. Family of G protein alpha chains: amphipathic analysis and predicted structure of functional domains.

    PubMed

    Masters, S B; Stroud, R M; Bourne, H R

    1986-01-01

    The G proteins transduce hormonal and other signals into regulation of enzymes such as adenylyl cyclase and retinal cGMP phosphodiesterase. Each G protein contains an alpha subunit that binds and hydrolyzes guanine nucleotides and interacts with beta gamma subunits and specific receptor and effector proteins. Amphipathic and secondary structure analysis of the primary sequences of five different alpha chains (bovine alpha s, alpha t1 and alpha t2, mouse alpha i, and rat alpha o) predicted the secondary structure of a composite alpha chain (alpha avg). The alpha chains contain four short regions of sequence homologous to regions in the GDP binding domain of bacterial elongation factor Tu (EF-Tu). Similarities between the predicted secondary structures of these regions in alpha avg and the known secondary structure of EF-Tu allowed us to construct a three-dimensional model of the GDP binding domain of alpha avg. Identification of the GDP binding domain of alpha avg defined three additional domains in the composite polypeptide. The first includes the amino terminal 41 residues of alpha avg, with a predicted amphipathic alpha helical structure; this domain may control binding of the alpha chains to the beta gamma complex. The second domain, containing predicted beta strands and alpha helices, several of which are strongly amphipathic, probably contains sequences responsible for interaction of alpha chains with effector enzymes. The predicted structure of the third domain, containing the carboxy terminal 100 amino acids, is predominantly beta sheet with an amphipathic alpha helix at the carboxy terminus. We propose that this domain is responsible for receptor binding.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3148932

  11. Bayesian data analysis of severe fatal accident risk in the oil chain.

    PubMed

    Eckle, Petrissa; Burgherr, Peter

    2013-01-01

    We analyze the risk of severe fatal accidents causing five or more fatalities and for nine different activities covering the entire oil chain. Included are exploration and extraction, transport by different modes, refining and final end use in power plants, heating or gas stations. The risks are quantified separately for OECD and non-OECD countries and trends are calculated. Risk is analyzed by employing a Bayesian hierarchical model yielding analytical functions for both frequency (Poisson) and severity distributions (Generalized Pareto) as well as frequency trends. This approach addresses a key problem in risk estimation-namely the scarcity of data resulting in high uncertainties in particular for the risk of extreme events, where the risk is extrapolated beyond the historically most severe accidents. Bayesian data analysis allows the pooling of information from different data sets covering, for example, the different stages of the energy chains or different modes of transportation. In addition, it also inherently delivers a measure of uncertainty. This approach provides a framework, which comprehensively covers risk throughout the oil chain, allowing the allocation of risk in sustainability assessments. It also permits the progressive addition of new data to refine the risk estimates. Frequency, severity, and trends show substantial differences between the activities, emphasizing the need for detailed risk analysis. PMID:22642363

  12. Analysis of the necessity and the effectiveness of countermeasures to prevent a chain reaction of collisions

    NASA Astrophysics Data System (ADS)

    Eichler, Peter

    At present, the collision risk with space debris, which is increasingly endangering all spaceflight activities, is probably predominated by fragments from explosions of payloads and rocket upper stages in Earth orbits. In the future, interactive collisions between objects in Earth orbit could become the main source for the generation of fragments. The risk of a catastrophic collision, i.e. with the total destruction of the target object, is presently in the order of some per cent per year, and it will rise squared to the number of larger objects in Earth orbit. The larger fragments generated by such a collision could produce new catastrophic collisions and this could successively lead to the formation of an artificial debris belt in the way of a chain reaction. As a steady increase of the population will always lead to a chain reaction of collisions, the necessity of effective countermeasures is evident. Hence, in this paper the results of a new analysis of the possible evolution of the population in Earth orbit including fragment generation by collisions using an advanced version of the simulation program CHAIN will be presented. Of special interest in this concern is the analysis of the effectiveness of the different kinds of possible countermeasures.

  13. Empirical Analysis of Green Supply Chain Management Practices in Indian Automobile Industry

    NASA Astrophysics Data System (ADS)

    Luthra, S.; Garg, D.; Haleem, A.

    2014-04-01

    Environmental sustainability and green environmental issues have an increasing popularity among researchers and supply chain practitioners. An attempt has been made to identify and empirically analyze green supply chain management (GSCM) practices in Indian automobile industry. Six main GSCM practices (having 37 sub practices) and four expected performance outcomes (having 16 performances) have been identified by implementing GSCM practices from literature review. Questionnaire based survey has been made to validate these practices and performance outcomes. 123 complete questionnaires were collected from Indian automobile organizations and used for empirical analysis of GSCM practices in Indian automobile industry. Descriptive statistics have been used to know current implementation status of GSCM practices in Indian automobile industry and multiple regression analysis has been carried out to know the impact on expected organizational performance outcomes by current GSCM practices adopted by Indian automobile industry. The results of study suggested that environmental, economic, social and operational performances improve with the implementation of GSCM practices. This paper may play an important role to understand various GSCM implementation issues and help practicing managers to improve their performances in the supply chain.

  14. Bayesian data analysis of severe fatal accident risk in the oil chain.

    PubMed

    Eckle, Petrissa; Burgherr, Peter

    2013-01-01

    We analyze the risk of severe fatal accidents causing five or more fatalities and for nine different activities covering the entire oil chain. Included are exploration and extraction, transport by different modes, refining and final end use in power plants, heating or gas stations. The risks are quantified separately for OECD and non-OECD countries and trends are calculated. Risk is analyzed by employing a Bayesian hierarchical model yielding analytical functions for both frequency (Poisson) and severity distributions (Generalized Pareto) as well as frequency trends. This approach addresses a key problem in risk estimation-namely the scarcity of data resulting in high uncertainties in particular for the risk of extreme events, where the risk is extrapolated beyond the historically most severe accidents. Bayesian data analysis allows the pooling of information from different data sets covering, for example, the different stages of the energy chains or different modes of transportation. In addition, it also inherently delivers a measure of uncertainty. This approach provides a framework, which comprehensively covers risk throughout the oil chain, allowing the allocation of risk in sustainability assessments. It also permits the progressive addition of new data to refine the risk estimates. Frequency, severity, and trends show substantial differences between the activities, emphasizing the need for detailed risk analysis.

  15. Exploring extraction/dissolution procedures for analysis of starch chain-length distributions.

    PubMed

    Wu, Alex Chi; Li, EnPeng; Gilbert, Robert G

    2014-12-19

    The analysis of starch chain-length distributions (CLDs) is important for understanding starch biosythesis-structure-property relations. It is obtained by analyzing the number distribution of the linear glucan chains released by enzymatic debranching of starch α-(1→6) glycosidic bonds for subsequent characterization by techniques such as fluorophore-assisted carbohydrate electrophoresis (FACE) or size-exclusion chromatography (SEC). Current literature pretreatments for debranching prior to CLD determination involve varying protocols, which might yield artifactual results. This paper examines the two widely used starch dissolution treatments with dimethyl sulfoxide (DMSO) containing 0.5% (w/w) lithium bromide (DMSO-LiBr) at 80°C and with aqueous alkaline (i.e. NaOH) solvents at 100 ˚C. Analyses by FACE with a very high range of degree of polymerization, and by SEC, of the CLD of barley starches with different structures show the following. (1) The NaOH treatment, even at a dilute concentration, causes significant degradation at higher degrees of polymerization, leading to quantitatively incorrect CLD results in longer amylopectin and in amylose chains. (2) Certain features in both amylopectin and amylose fractions of the CLD reduced to bumps or are missing with NaOH treatment. (3) Overestimation of amylose chains in starch CLD due to incomplete amylopectin dissolution with dilute NaOH concentration. These results indicate starch dissolution with DMSO-LiBr is the method of choice for minimizing artifacts. An improved pretreatment protocol is presented for starch CLD analysis by FACE and SEC. PMID:25263861

  16. Genome-Wide Analysis of Branched-Chain Amino Acid Levels in Arabidopsis Seeds[W

    PubMed Central

    Angelovici, Ruthie; Lipka, Alexander E.; Deason, Nicholas; Gonzalez-Jorge, Sabrina; Lin, Haining; Cepela, Jason; Buell, Robin; Gore, Michael A.; DellaPenna, Dean

    2013-01-01

    Branched-chain amino acids (BCAAs) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in development and growth. However, seed BCAA levels in major crops are insufficient to meet dietary requirements, making genetic improvement for increased and balanced seed BCAAs an important nutritional target. Addressing this issue requires a better understanding of the genetics underlying seed BCAA content and composition. Here, a genome-wide association study and haplotype analysis for seed BCAA traits in Arabidopsis thaliana revealed a strong association with a chromosomal interval containing two BRANCHED-CHAIN AMINO ACID TRANSFERASES, BCAT1 and BCAT2. Linkage analysis, reverse genetic approaches, and molecular complementation analysis demonstrated that allelic variation at BCAT2 is responsible for the natural variation of seed BCAAs in this interval. Complementation analysis of a bcat2 null mutant with two significantly different alleles from accessions Bayreuth-0 and Shahdara is consistent with BCAT2 contributing to natural variation in BCAA levels, glutamate recycling, and free amino acid homeostasis in seeds in an allele-dependent manner. The seed-specific phenotype of bcat2 null alleles, its strong transcription induction during late seed development, and its subcellular localization to the mitochondria are consistent with a unique, catabolic role for BCAT2 in BCAA metabolism in seeds. PMID:24368787

  17. Applying different independent component analysis algorithms and support vector regression for IT chain store sales forecasting.

    PubMed

    Dai, Wensheng; Wu, Jui-Yu; Lu, Chi-Jie

    2014-01-01

    Sales forecasting is one of the most important issues in managing information technology (IT) chain store sales since an IT chain store has many branches. Integrating feature extraction method and prediction tool, such as support vector regression (SVR), is a useful method for constructing an effective sales forecasting scheme. Independent component analysis (ICA) is a novel feature extraction technique and has been widely applied to deal with various forecasting problems. But, up to now, only the basic ICA method (i.e., temporal ICA model) was applied to sale forecasting problem. In this paper, we utilize three different ICA methods including spatial ICA (sICA), temporal ICA (tICA), and spatiotemporal ICA (stICA) to extract features from the sales data and compare their performance in sales forecasting of IT chain store. Experimental results from a real sales data show that the sales forecasting scheme by integrating stICA and SVR outperforms the comparison models in terms of forecasting error. The stICA is a promising tool for extracting effective features from branch sales data and the extracted features can improve the prediction performance of SVR for sales forecasting.

  18. Applying Different Independent Component Analysis Algorithms and Support Vector Regression for IT Chain Store Sales Forecasting

    PubMed Central

    Dai, Wensheng

    2014-01-01

    Sales forecasting is one of the most important issues in managing information technology (IT) chain store sales since an IT chain store has many branches. Integrating feature extraction method and prediction tool, such as support vector regression (SVR), is a useful method for constructing an effective sales forecasting scheme. Independent component analysis (ICA) is a novel feature extraction technique and has been widely applied to deal with various forecasting problems. But, up to now, only the basic ICA method (i.e., temporal ICA model) was applied to sale forecasting problem. In this paper, we utilize three different ICA methods including spatial ICA (sICA), temporal ICA (tICA), and spatiotemporal ICA (stICA) to extract features from the sales data and compare their performance in sales forecasting of IT chain store. Experimental results from a real sales data show that the sales forecasting scheme by integrating stICA and SVR outperforms the comparison models in terms of forecasting error. The stICA is a promising tool for extracting effective features from branch sales data and the extracted features can improve the prediction performance of SVR for sales forecasting. PMID:25165740

  19. Flow cytometric analysis of expression of interleukin-2 receptor beta chain (p70-75) on various leukemic cells

    SciTech Connect

    Hoshino, S.; Oshimi, K.; Tsudo, M.; Miyasaka, M.; Teramura, M.; Masuda, M.; Motoji, T.; Mizoguchi, H. )

    1990-08-15

    We analyzed the expression of the interleukin-2 receptor (IL-2R) beta chain (p70-75) on various leukemic cells from 44 patients by flow cytometric analysis using the IL-2R beta chain-specific monoclonal antibody, designated Mik-beta 1. Flow cytometric analysis demonstrated the expression of the IL-2R beta chain on granular lymphocytes (GLs) from all eight patients with granular lymphocyte proliferative disorders (GLPDs), on adult T-cell leukemia (ATL) cells from all three patients with ATL, and on T-cell acute lymphoblastic leukemia (T-ALL) cells from one of three patients with T-ALL. Although GLs from all the GLPD patients expressed the IL-2R beta chain alone and not the IL-2R alpha chain (Tac-antigen: p55), ATL and T-ALL cells expressing the beta chain coexpressed the alpha chain. In two of seven patients with common ALL (cALL) and in both patients with B-cell chronic lymphocytic leukemia, the leukemic cells expressed the alpha chain alone. Neither the alpha chain nor the beta chain was expressed on leukemic cells from the remaining 28 patients, including all 18 patients with acute nonlymphocytic leukemia, five of seven patients with cALL, all three patients with multiple myeloma, and two of three patients with T-ALL. These results indicate that three different forms of IL-2R chain expression exist on leukemic cells: the alpha chain alone; the beta chain alone; and both the alpha and beta chains. To examine whether the results obtained by flow cytometric analysis actually reflect functional aspects of the expressed IL-2Rs, we studied the specific binding of 125I-labeled IL-2 (125I-IL-2) to leukemic cells in 18 of the 44 patients. In addition, we performed 125I-IL-2 crosslinking studies in seven patients. The results of IL-2R expression of both 125I-IL-2 binding assay and crosslinking studies were in agreement with those obtained by flow cytometric analysis.

  20. Conformation Analysis of Peptides Derived from Laminin Alpha 1-2 Chain Using Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Yamada, Hironao; Fukuda, Masaki; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako

    Laminin is one of the components of the basement membrane and has diverse biological activities. Several functional peptides (EF1-EF5) are identified from LG4 modules of laminin alpha 1-5 chains. Thus, we perform conformation analysis of EF1 and EF2 using molecular dynamics simulations. In this study, we perform structure sampling with NPT ensemble (300 K, 1 bar). Our results show that EF1 peptide has β-sheet structure in water, and EF2 peptide does not have. Likewise, the EF2 peptide has unstable structure compared with the EF1 peptide in water.

  1. Brief Communication: Earthquake sequencing: analysis of time series constructed from the Markov chain model

    NASA Astrophysics Data System (ADS)

    Cavers, M. S.; Vasudevan, K.

    2015-10-01

    Directed graph representation of a Markov chain model to study global earthquake sequencing leads to a time series of state-to-state transition probabilities that includes the spatio-temporally linked recurrent events in the record-breaking sense. A state refers to a configuration comprised of zones with either the occurrence or non-occurrence of an earthquake in each zone in a pre-determined time interval. Since the time series is derived from non-linear and non-stationary earthquake sequencing, we use known analysis methods to glean new information. We apply decomposition procedures such as ensemble empirical mode decomposition (EEMD) to study the state-to-state fluctuations in each of the intrinsic mode functions. We subject the intrinsic mode functions, derived from the time series using the EEMD, to a detailed analysis to draw information content of the time series. Also, we investigate the influence of random noise on the data-driven state-to-state transition probabilities. We consider a second aspect of earthquake sequencing that is closely tied to its time-correlative behaviour. Here, we extend the Fano factor and Allan factor analysis to the time series of state-to-state transition frequencies of a Markov chain. Our results support not only the usefulness of the intrinsic mode functions in understanding the time series but also the presence of power-law behaviour exemplified by the Fano factor and the Allan factor.

  2. U.S. Wind Energy Manufacturing and Supply Chain: A Competitiveness Analysis

    SciTech Connect

    Fullenkamp, Patrick H; Holody, Diane S

    2014-06-15

    The goal of the project was to develop a greater understanding of the key factors determining wind energy component manufacturing costs and pricing on a global basis in order to enhance the competitiveness of U.S. manufacturers, and to reduce installed systems cost. Multiple stakeholders including DOE, turbine OEMs, and large component manufactures will all benefit by better understanding the factors determining domestic competitiveness in the emerging offshore and next generation land-based wind industries. Major objectives of this project were to: 1. Carry out global cost and process comparisons for 5MW jacket foundations, blades, towers, and permanent magnet generators; 2. Assess U.S. manufacturers’ competitiveness and potential for cost reduction; 3. Facilitate informed decision-making on investments in U.S. manufacturing; 4. Develop an industry scorecard representing the readiness of the U.S. manufacturers’ to produce components for the next generations of wind turbines, nominally 3MW land-based and 5MW offshore; 5. Disseminate results through the GLWN Wind Supply Chain GIS Map, a free website that is the most comprehensive public database of U.S. wind energy suppliers; 6. Identify areas and develop recommendations to DOE on potential R&D areas to target for increasing domestic manufacturing competitiveness, per DOE’s Clean Energy Manufacturing Initiative (CEMI). Lists of Deliverables 1. Cost Breakdown Competitive Analyses of four product categories: tower, jacket foundation, blade, and permanent magnet (PM) generator. The cost breakdown for each component includes a complete Bill of Materials with net weights; general process steps for labor; and burden adjusted by each manufacturer for their process categories of SGA (sales general and administrative), engineering, logistics cost to a common U.S. port, and profit. 2. Value Stream Map Competitiveness Analysis: A tool that illustrates both information and material flow from the point of getting a

  3. An example of neutronic penalizations in reactivity transient analysis using 3D coupled chain HEMERA

    SciTech Connect

    Dubois, F.; Normand, B.; Sargeni, A.

    2012-07-01

    HEMERA (Highly Evolutionary Methods for Extensive Reactor Analyses), is a fully coupled 3D computational chain developed jointly by IRSN and CEA. It is composed of CRONOS2 (core neutronics, cross sections library from APOLLO2), FLICA4 (core thermal-hydraulics) and the system code CATHARE. Multi-level and multi-dimensional models are developed to account for neutronics, core thermal-hydraulics, fuel thermal analysis and system thermal-hydraulics, dedicated to best-estimate, conservative simulations and sensitivity analysis. In IRSN, the HEMERA chain is widely used to study several types of reactivity accidents and for sensitivity studies. Just as an example of the HEMERA possibilities, we present here two types of neutronic penalizations and their impact on a power transient due to a REA (Rod Ejection Accident): in the first one, we studied a bum-up distribution modification and in the second one, a delayed-neutron fraction modification. Both modifications are applied to the whole core or localized in a few assemblies. Results show that it is possible to use global or local changes but 1) in case of bum-up modification, the total core power can increase when assembly peak power decrease so, care has to be taken if the goal is to maximize a local power peak and 2) for delayed-neutron fraction, a local modification can have the same effect as the one on the whole core, provided that it is large enough. (authors)

  4. A Markov Chain Analysis of Fish Movements to Determine Entrainment Zones

    SciTech Connect

    Johnson, Gary E.; Hedgepeth, J; Skalski, John R.; Giorgi, Albert E.

    2004-10-01

    Fish can become entrained at water withdrawal locations such as fish bypasses or cooling water intakes. Accordingly, the size of a fish entrainment zone (FEZ) is often of interest to fisheries managers and facility operators. This study developed a new technique to map the FEZ, defined here as the region immediately upstream of a portal where the probability of fish movement toward the portal is greater than 90%. To map the FEZ, we applied a Markov chain analysis to fish movement data collected with an active tracking sonar. This device locks onto and follows a target, recording positions through a set of volumetric cells comprising the sampled volume. The probability of a fish moving from one cell to another was calculated from fish position data, which was used to populate a Markov transition matrix. We developed and applied the technique using data on salmon smolts migrating near the ice/trash sluiceway at The Dalles Dam on the Columbia River. The FEZ of the sluiceway entrance in 2000 as determined with this procedure was approximately 5 m across and extended 6-8 m out from the face of the dam in the surface layer 2-3 m deep. In conclusion, using a Markov chain analysis of fish track data we were able to describe and quantify the FEZ of the sluiceway at The Dalles Dam. This technique for FEZ mapping is applicable to other bioengineering efforts aimed at protecting fish populations affected by water withdrawals.

  5. Comparative Analysis of Immune Repertoires between Bactrian Camel's Conventional and Heavy-Chain Antibodies

    PubMed Central

    Yang, Kai; Zhang, Wei; Zhang, Changjiang; Fu, Longfei; Ren, Zhe; Wang, Changxi; Wu, Jinghua; Lu, Ruxue; Ye, Yanrui; He, Mengying; Nie, Chao; Yang, Naibo; Wang, Jian; Yang, Huanming; Liu, Xiao

    2016-01-01

    Compared to classical antibodies, camel heavy chain antibodies (HCAbs) are smaller in size due to lack of the light chain and the first constant domain of the heavy chain (CH1 region). The variable regions of HCAbs (VHHs) are more soluble and stable than that of conventional antibodies (VHs). Even with such simple structure, they are still functional in antigen binding. Although HCAbs have been extensively investigated over the past two decades, most efforts have been based upon low throughput sequence analysis, and there are only limited reports trying to analyze and describe the complete immune repertoire (IR) of camel HCAbs. Here we leveraged the high-throughput data generated by Next Generation Sequencing (NGS) of the variable domains of the antibody heavy chains from three Bactrian camels to conduct in-depth comparative analyses of the immunoglobulin repertoire. These include analyses of the complementary determining region 3 (CDR3) length and distribution, mutation rate, antibody characteristic amino acids, the distribution of the cysteine (Cys) codons, and the non-classical VHHs. We found that there is higher diversity in the CDR2 than in the other sub-regions, and there is a higher mutation rate in the VHHs than in the VHs (P < 0.05). In addition to substitutions at amino acid (AA) residue positions NO.49/50/52 between VH and VHH clones, we also observed other substitutions at the positions NO.40/54/57/96/101 that could lead to additional structural alterations. We also found that VH-derived VHH clones, referred to as non-classical VHH clones in this study, accounted for about 8% of all clones. Further, only 5%-10% clones had the Trp > Arg AA substitution at the first position of framework 4 for all types of clones. We present, for the first time, a relatively complete picture of the Bactrian camel antibody immune repertoire, including conventional antibody (Ab) and HCAbs, using PCR and in silico analysis based on high-throughput NGS data. PMID:27588755

  6. Comparative Analysis of Immune Repertoires between Bactrian Camel's Conventional and Heavy-Chain Antibodies.

    PubMed

    Li, Xinyang; Duan, Xiaobo; Yang, Kai; Zhang, Wei; Zhang, Changjiang; Fu, Longfei; Ren, Zhe; Wang, Changxi; Wu, Jinghua; Lu, Ruxue; Ye, Yanrui; He, Mengying; Nie, Chao; Yang, Naibo; Wang, Jian; Yang, Huanming; Liu, Xiao; Tan, Wen

    2016-01-01

    Compared to classical antibodies, camel heavy chain antibodies (HCAbs) are smaller in size due to lack of the light chain and the first constant domain of the heavy chain (CH1 region). The variable regions of HCAbs (VHHs) are more soluble and stable than that of conventional antibodies (VHs). Even with such simple structure, they are still functional in antigen binding. Although HCAbs have been extensively investigated over the past two decades, most efforts have been based upon low throughput sequence analysis, and there are only limited reports trying to analyze and describe the complete immune repertoire (IR) of camel HCAbs. Here we leveraged the high-throughput data generated by Next Generation Sequencing (NGS) of the variable domains of the antibody heavy chains from three Bactrian camels to conduct in-depth comparative analyses of the immunoglobulin repertoire. These include analyses of the complementary determining region 3 (CDR3) length and distribution, mutation rate, antibody characteristic amino acids, the distribution of the cysteine (Cys) codons, and the non-classical VHHs. We found that there is higher diversity in the CDR2 than in the other sub-regions, and there is a higher mutation rate in the VHHs than in the VHs (P < 0.05). In addition to substitutions at amino acid (AA) residue positions NO.49/50/52 between VH and VHH clones, we also observed other substitutions at the positions NO.40/54/57/96/101 that could lead to additional structural alterations. We also found that VH-derived VHH clones, referred to as non-classical VHH clones in this study, accounted for about 8% of all clones. Further, only 5%-10% clones had the Trp > Arg AA substitution at the first position of framework 4 for all types of clones. We present, for the first time, a relatively complete picture of the Bactrian camel antibody immune repertoire, including conventional antibody (Ab) and HCAbs, using PCR and in silico analysis based on high-throughput NGS data. PMID:27588755

  7. Comparative Analysis of Immune Repertoires between Bactrian Camel's Conventional and Heavy-Chain Antibodies.

    PubMed

    Li, Xinyang; Duan, Xiaobo; Yang, Kai; Zhang, Wei; Zhang, Changjiang; Fu, Longfei; Ren, Zhe; Wang, Changxi; Wu, Jinghua; Lu, Ruxue; Ye, Yanrui; He, Mengying; Nie, Chao; Yang, Naibo; Wang, Jian; Yang, Huanming; Liu, Xiao; Tan, Wen

    2016-01-01

    Compared to classical antibodies, camel heavy chain antibodies (HCAbs) are smaller in size due to lack of the light chain and the first constant domain of the heavy chain (CH1 region). The variable regions of HCAbs (VHHs) are more soluble and stable than that of conventional antibodies (VHs). Even with such simple structure, they are still functional in antigen binding. Although HCAbs have been extensively investigated over the past two decades, most efforts have been based upon low throughput sequence analysis, and there are only limited reports trying to analyze and describe the complete immune repertoire (IR) of camel HCAbs. Here we leveraged the high-throughput data generated by Next Generation Sequencing (NGS) of the variable domains of the antibody heavy chains from three Bactrian camels to conduct in-depth comparative analyses of the immunoglobulin repertoire. These include analyses of the complementary determining region 3 (CDR3) length and distribution, mutation rate, antibody characteristic amino acids, the distribution of the cysteine (Cys) codons, and the non-classical VHHs. We found that there is higher diversity in the CDR2 than in the other sub-regions, and there is a higher mutation rate in the VHHs than in the VHs (P < 0.05). In addition to substitutions at amino acid (AA) residue positions NO.49/50/52 between VH and VHH clones, we also observed other substitutions at the positions NO.40/54/57/96/101 that could lead to additional structural alterations. We also found that VH-derived VHH clones, referred to as non-classical VHH clones in this study, accounted for about 8% of all clones. Further, only 5%-10% clones had the Trp > Arg AA substitution at the first position of framework 4 for all types of clones. We present, for the first time, a relatively complete picture of the Bactrian camel antibody immune repertoire, including conventional antibody (Ab) and HCAbs, using PCR and in silico analysis based on high-throughput NGS data.

  8. Prenatal diagnosis of alpha-thalassemia by polymerase chain reaction and dual restriction enzyme analysis.

    PubMed

    Lebo, R V; Saiki, R K; Swanson, K; Montano, M A; Erlich, H A; Golbus, M S

    1990-08-01

    Asian couples at risk for a fetus with homozygous alpha-thalassemia (hydrops fetalis) are often identified by their low erythrocyte mean corpuscular volume (MCV) and normal hemoglobin electrophoresis when little time remains to test their genotypes by restriction enzyme analysis. DNA analysis is performed directly on chorionic villi or amniocytes remaining after an aliquot is used to establish a backup cell culture. The polymerase chain reaction (PCR) protocol quickly determines whether the fetus has hydrops fetalis without waiting for cultured cells to grow. Previously, growing cultured fetal cells to obtain more fetal material to establish unambiguously the fetal genotype with two independent restriction enzyme digests absorbed a significant portion of the time remaining to complete prenatal diagnosis. A dual restriction enzyme digestion protocol was development using a 3' zeta-globin probe to clearly distinguish the most common alpha-thalassemia deletions that represent nearly all the alpha-thalassemia haplotypes in Southeast Asia.

  9. Real-time reverse-transcription polymerase chain reaction: technical considerations for gene expression analysis.

    PubMed

    Doak, Shareen H; Zaïr, Zoulikha M

    2012-01-01

    The reverse transcription - polymerase chain reaction (RT-PCR) is a sensitive technique for the quantification of steady-state mRNA levels, particularly in samples with limited quantities of extracted RNA, or for analysis of low level transcripts. The procedure amplifies defined mRNA transcripts by taking advantage of retroviral enzymes with reverse transcriptase (RT) activity, coupled to PCR. The resultant PCR product concentration is directly proportional to the initial starting quantity of mRNA, therefore allowing quantification of gene expression by incorporation of a fluorescence detector for the appropriate amplicons. In this chapter, we describe a number of the most popular techniques for performing RT-PCR and detail the subsequent analysis methodologies required to interpret the resultant data in either a relative manner or through absolute quantification of gene expression levels.

  10. Analysis of myosin heavy chain mRNA expression by RT-PCR

    NASA Technical Reports Server (NTRS)

    Wright, C.; Haddad, F.; Qin, A. X.; Baldwin, K. M.

    1997-01-01

    An assay was developed for rapid and sensitive analysis of myosin heavy chain (MHC) mRNA expression in rodent skeletal muscle. Only 2 microg of total RNA were necessary for the simultaneous analysis of relative mRNA expression of six different MHC genes. We designed synthetic DNA fragments as internal standards, which contained the relevant primer sequences for the adult MHC mRNAs type I, IIa, IIx, IIb as well as the embryonic and neonatal MHC mRNAs. A known amount of the synthetic fragment was added to each polymerase chain reaction (PCR) and yielded a product of different size than the amplified MHC mRNA fragment. The ratio of amplified MHC fragment to synthetic fragment allowed us to calculate percentages of the gene expression of the different MHC genes in a given muscle sample. Comparison with the traditional Northern blot analysis demonstrated that our reverse transcriptase-PCR-based assay was reliable, fast, and quantitative over a wide range of relative MHC mRNA expression in a spectrum of adult and neonatal rat skeletal muscles. Furthermore, the high sensitivity of the assay made it very useful when only small quantities of tissue were available. Statistical analysis of the signals for each MHC isoform across the analyzed samples showed a highly significant correlation between the PCR and the Northern signals as Pearson correlation coefficients ranged between 0.77 and 0.96 (P < 0.005). This assay has potential use in analyzing small muscle samples such as biopsies and samples from pre- and/or neonatal stages of development.

  11. Empirical Study on Relationship Capital in Supply Chain-Based on Analysis of Enterprises in Hunan Province

    NASA Astrophysics Data System (ADS)

    Shan, Lu; Qiang-Bin, Ou-Yang

    Based on the existing theories and studies, this thesis aims to propose a theoretical model for describing the relationship between the relationship capital in the supply chain and its influencing factors, and meanwhile, the EFA (exploratory factor analysis) and CFA (confirmatory factor analysis) are carried out on 188 sample data. Through the evaluation of goodness of fit on the structure model as well as assumption testing, it turns out that there are four influencing factors for the relationship capital in the supply chain, namely, capability and reputation of the cooperation companies in the supply chain, input in specific assets and transfer cost, which are in a positive correlation with relationship capital separately. Then a decision-making basis is provided for the practice of relationship capital in the supply chain.

  12. Perchlorate in the United States. Analysis of relative source contributions to the food chain.

    PubMed

    Dasgupta, Purnendu K; Dyke, Jason V; Kirk, Andrea B; Jackson, W Andrew

    2006-11-01

    Perchlorate has been considered by some a potential threat to human health, especially to developing infants and children because it may inhibit iodide uptake by the sodium iodide symporter (NIS) of the thyroid. In the United States, during the last several decades, environmental perchlorate has had three recognized sources stemming from (a) its use as an oxidizer (including in rocket propellants), (b) its presence in Chilean nitrate fertilizer (CNF), and (c) natural production. An analysis of the relative source strengths and how they may influence entry into the food chain has not been conducted. Averaged over the last --60 years, we estimate that the source strengths have been (a) 10.6, (b) 0.75, and (c) 0.13-0.64 Gg/y for the United States as a whole. Of this, while (b) and (c) represent actual dispersed amounts, the figure in (a) is the amount of perchlorate produced and only a fraction (f) of it has been dispersed and often in a more localized fashion. In addition, dispersal of (b) has taken place only over agricultural land. Considering that the total land area in the United States is 5.5 x the arable land area, in terms of incorporation into the food chain,the figure cited in (b) has a proportionately greater impact. Most estimates of fwill thus suggest that over the considered period, the contribution of CNF to incorporation of perchlorate in the food chain has likely been comparable to oxidizer perchlorate, with natural production being a lesser source. Fireworks presently constitute a potentially important source of increasing importance but a quantitative impact cannotyet be assessed.

  13. Markov chain modelling of reliability analysis and prediction under mixed mode loading

    NASA Astrophysics Data System (ADS)

    Singh, Salvinder; Abdullah, Shahrum; Nik Mohamed, Nik Abdullah; Mohd Noorani, Mohd Salmi

    2015-03-01

    The reliability assessment for an automobile crankshaft provides an important understanding in dealing with the design life of the component in order to eliminate or reduce the likelihood of failure and safety risks. The failures of the crankshafts are considered as a catastrophic failure that leads towards a severe failure of the engine block and its other connecting subcomponents. The reliability of an automotive crankshaft under mixed mode loading using the Markov Chain Model is studied. The Markov Chain is modelled by using a two-state condition to represent the bending and torsion loads that would occur on the crankshaft. The automotive crankshaft represents a good case study of a component under mixed mode loading due to the rotating bending and torsion stresses. An estimation of the Weibull shape parameter is used to obtain the probability density function, cumulative distribution function, hazard and reliability rate functions, the bathtub curve and the mean time to failure. The various properties of the shape parameter is used to model the failure characteristic through the bathtub curve is shown. Likewise, an understanding of the patterns posed by the hazard rate onto the component can be used to improve the design and increase the life cycle based on the reliability and dependability of the component. The proposed reliability assessment provides an accurate, efficient, fast and cost effective reliability analysis in contrast to costly and lengthy experimental techniques.

  14. Evaluation of Supply Chain Efficiency Based on a Novel Network of Data Envelopment Analysis Model

    NASA Astrophysics Data System (ADS)

    Fu, Li Fang; Meng, Jun; Liu, Ying

    2015-12-01

    Performance evaluation of supply chain (SC) is a vital topic in SC management and inherently complex problems with multilayered internal linkages and activities of multiple entities. Recently, various Network Data Envelopment Analysis (NDEA) models, which opened the “black box” of conventional DEA, were developed and applied to evaluate the complex SC with a multilayer network structure. However, most of them are input or output oriented models which cannot take into consideration the nonproportional changes of inputs and outputs simultaneously. This paper extends the Slack-based measure (SBM) model to a nonradial, nonoriented network model named as U-NSBM with the presence of undesirable outputs in the SC. A numerical example is presented to demonstrate the applicability of the model in quantifying the efficiency and ranking the supply chain performance. By comparing with the CCR and U-SBM models, it is shown that the proposed model has higher distinguishing ability and gives feasible solution in the presence of undesirable outputs. Meanwhile, it provides more insights for decision makers about the source of inefficiency as well as the guidance to improve the SC performance.

  15. Locations of Racism in Education: A Speech Act Analysis of a Policy Chain

    ERIC Educational Resources Information Center

    Arneback, Emma; Quennerstedt, Ann

    2016-01-01

    This article explores how racism is located in an educational policy chain and identifies how its interpretation changes throughout the chain. A basic assumption is that the policy formation process can be seen as a chain in which international, national and local policies are "links"--separate entities yet joined. With Sweden as the…

  16. Improving Markov Chain Monte Carlo algorithms in LISA Pathfinder Data Analysis

    NASA Astrophysics Data System (ADS)

    Karnesis, N.; Nofrarias, M.; Sopuerta, C. F.; Lobo, A.

    2012-06-01

    The LISA Pathfinder mission (LPF) aims to test key technologies for the future LISA mission. The LISA Technology Package (LTP) on-board LPF will consist of an exhaustive suite of experiments and its outcome will be crucial for the future detection of gravitational waves. In order to achieve maximum sensitivity, we need to have an understanding of every instrument on-board and parametrize the properties of the underlying noise models. The Data Analysis team has developed algorithms for parameter estimation of the system. A very promising one implemented for LISA Pathfinder data analysis is the Markov Chain Monte Carlo. A series of experiments are going to take place during flight operations and each experiment is going to provide us with essential information for the next in the sequence. Therefore, it is a priority to optimize and improve our tools available for data analysis during the mission. Using a Bayesian framework analysis allows us to apply prior knowledge for each experiment, which means that we can efficiently use our prior estimates for the parameters, making the method more accurate and significantly faster. This, together with other algorithm improvements, will lead us to our main goal, which is no other than creating a robust and reliable tool for parameter estimation during the LPF mission.

  17. Purification, Characterization, and Analysis of the Allergenic Properties of Myosin Light Chain in Procambarus clarkii.

    PubMed

    Zhang, Yong-Xia; Chen, Heng-Li; Maleki, Soheila J; Cao, Min-Jie; Zhang, Ling-Jing; Su, Wen-Jin; Liu, Guang-Ming

    2015-07-15

    Myosin light chain (MLC) plays a vital role in cell and muscle functions and has been identified as an allergen in shrimp. In this study, MLC with a molecular mass of 18 kDa was purified from crayfish (Procambarus clarkii) muscle. Its physicochemical characterization showed that the purified MLC is a glycoprotein with 4.3% carbohydrate, highly stable to heat, acid-alkali, and digestion, and weakly retains IgE-binding activity when its secondary structure was altered. Serological assays suggested that conformational epitopes predominate over linear epitopes in the purified MLC. Two isoforms of the MLC gene (MLC1 and MLC2) were cloned, and the purified MLC was identified as MLC1. Analysis of the secondary and tertiary structures of the MLCs indicated that MLC1 has four conformational epitopes and three linear epitopes, whereas MLC2 had a major conformational epitope and three linear epitopes. These results are significant for understanding hypersensitization of humans to crayfish.

  18. IDENTIFICATION OF MOSQUITO AVIAN-DERIVED BLOOD MEALS BY POLYMERASE CHAIN REACTION-HETERODUPLEX ANALYSIS

    PubMed Central

    LEE, JOON HAK; HASSAN, HASSAN; HILL, GEOFF; CUPP, EDDIE W.; HIGAZI, TARIG B.; MITCHELL, CARL J.; GODSEY, MARVIN S.; UNNASCH, THOMAS R.

    2008-01-01

    A polymerase chain reaction (PCR) heteroduplex assay (HDA) was developed to identify avian derived mosquito blood meals to the species level. The assay used primers amplifying a fragment of the cytochrome B gene from vertebrate but not invertebrate species. In Culex tarsalis fed on quail, PCR products derived from the quail cytochrome B gene were detected seven days post-engorgement. In an analysis of wild-caught mosquitoes, 85% of blood-fed mosquitoes produced detectable PCR products. Heteroduplex patterns obtained from bird-derived PCR products were found to permit the unambiguous identification of all species examined. No intraspecific variation in HDA patterns was found. The PCR-HDA was used to characterize blood meals in wild caught Cx. tarsalis. Of the 67 blood meals analyzed, 60% were derived from avian sources. Of the avian blood meals, 65% were derived from a single host, the common grackle. PMID:12201598

  19. Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction.

    PubMed

    Jackson, D P; Lewis, F A; Taylor, G R; Boylston, A W; Quirke, P

    1990-06-01

    Several DNA extraction techniques were quantitatively and qualitatively compared using both fresh and paraffin wax embedded tissue and their suitability investigated for providing DNA and RNA for the polymerase chain reaction (PCR). A one hour incubation with proteinase K was the most efficient DNA extraction procedure for fresh tissue. For paraffin wax embedded tissue a five day incubation with proteinase K was required to produce good yields of DNA. Incubation with sodium dodecyl sulphate produced very poor yields, while boiling produced 20% as much DNA as long enzyme digestion. DNA extracted by these methods was suitable for the PCR amplification of a single copy gene. Proteinase K digestion also produced considerable amounts of RNA which has previously been shown to be suitable for PCR analysis. A delay before fixation had no effect on the amount of DNA obtained while fixation in Carnoy's reagent results in a much better preservation of DNA than formalin fixation, allowing greater yields to be extracted.

  20. Single Quantum Dot Analysis Enables Multiplexed Point Mutation Detection by Gap Ligase Chain Reaction

    PubMed Central

    Song, Yunke; Zhang, Yi; Wang, Tza-Huei

    2014-01-01

    Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and tedious assay processes. In this report, we propose an assay technology which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single molecule coincidence detection and superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification. PMID:23239594

  1. Gene analysis of multiple oral bacteria by the polymerase chain reaction coupled with capillary polymer electrophoresis.

    PubMed

    Liu, Chenchen; Yamaguchi, Yoshinori; Sekine, Shinichi; Ni, Yi; Li, Zhenqing; Zhu, Xifang; Dou, Xiaoming

    2016-03-01

    Capillary polymer electrophoresis is identified as a promising technology for the analysis of DNA from bacteria, virus and cell samples. In this paper, we propose an innovative capillary polymer electrophoresis protocol for the quantification of polymerase chain reaction products. The internal standard method was modified and applied to capillary polymer electrophoresis. The precision of our modified internal standard protocol was evaluated by measuring the relative standard deviation of intermediate capillary polymer electrophoresis experiments. Results showed that the relative standard deviation was reduced from 12.4-15.1 to 0.6-2.3%. Linear regression tests were also implemented to validate our protocol. The modified internal standard method showed good linearity and robust properties. Finally, the ease of our method was illustrated by analyzing a real clinical oral sample using a one-run capillary polymer electrophoresis experiment. PMID:26648455

  2. In vitro reconstitution and analysis of the chain initiating enzymes of the R1128 polyketide synthase.

    PubMed

    Meadows, E S; Khosla, C

    2001-12-11

    Biosynthesis of the carbon chain backbone of the R1128 substances is believed to involve the activity of a ketosynthase/chain length factor (ZhuB/ZhuA), an additional ketosynthase (ZhuH), an acyl transferase (ZhuC), and two acyl carrier proteins (ACPs; ZhuG and ZhuN). A subset of these proteins initiate chain synthesis via decarboxylative condensation between an acetyl-, propionyl-, isobutyryl-, or butyryl-CoA derived primer unit and a malonyl-CoA derived extender unit to yield an acetoacetyl-, beta-ketopentanoyl-, 3-oxo-4-methylpentanoyl-, or beta-ketohexanoyl-ACP product, respectively. To investigate the precise roles of ZhuH, ZhuC, ZhuG, and ZhuN, each protein was expressed in Escherichia coli and purified to homogeneity. Although earlier reports had proposed that ZhuC and its homologues played a role in primer unit selection, direct in vitro analysis of ZhuC showed that it was in fact a malonyl-CoA:ACP malonyltransferase (MAT). The enzyme could catalyze malonyl transfer but not acetyl- or propionyl-transfer onto R1128 ACPs or onto ACPs from other biosynthetic pathways, suggesting that ZhuC has broad substrate specificity with respect to the holo-ACP substrate but is specific for malonyl-CoA. Thus, ZhuC supplies extender units to both the initiating and elongating ketosynthases from this pathway. To interrogate the primer unit specificity of ZhuH, the kinetics of beta-ketoacyl-ACP formation in the presence of various acyl-CoAs and malonyl-ZhuG were measured. Propionyl-CoA and isobutyryl-CoA were the two most preferred substrates of ZhuH, although acetyl-CoA and butyryl-CoA could also be accepted and elongated. This specificity is not only consistent with earlier reports demonstrating that R1128B and R1128C are the major products of the R1128 pathway in vivo, but is also in good agreement with the properties of the ZhuH substrate binding pocket, as deduced from a recently solved crystal structure of the enzyme. Finally, to investigate the molecular logic for the

  3. A simple RNA probe system for analysis of Listeria monocytogenes polymerase chain reaction products.

    PubMed Central

    Blais, B W; Phillippe, L M

    1993-01-01

    The synthesis of an RNA probe specific for the hlyA gene of Listeria monocytogenes by in vitro transcription from a polymerase chain reaction (PCR)-generated template incorporating bacteriophage T7 promoter sequences is described. This simple method produced a high yield of RNA which hybridized specifically with hlyA PCR products on a membrane, resulting in RNA-DNA hybrids which were detected by an immunoenzymatic assay with an anti-RNA-DNA hybrid antibody. The RNA probe hybridization system was more sensitive in the analysis of the PCR products than was the conventional agarose gel electrophoresis method. When applied to the analysis of PCR samples from cultures of various Listeria and non-Listeria organisms, the RNA probe was reactive in the assay of 62 different L. monocytogenes isolates but not other Listeria species. Among the non-Listeria organisms tested, only Enterococcus faecalis gave a weak positive reaction with more than 10(9) cells per ml. This reactivity disappeared at lower cell densities. This strategy for the synthesis and application of RNA probes should facilitate the analysis of PCR products in the detection of L. monocytogenes and possibly other food pathogens. Images PMID:8215354

  4. Preliminary identification of hemoglobin q-iran in an Iranian family from central province of Iran by globin chain analysis on HPLC.

    PubMed

    Khatami, Shohreh; Najmabadi, Hossein; Rouhi, Soghra; Mirzazadeh, Roghieh; Bayat, Parastoo; Sadeghi, Sedigheh

    2013-12-01

    Many abnormal α-chain hemoglobins (Hbs) are caused by single nucleotide mutations in α1- or α2-goblin genes. One of these Hbs is Hb Q-Iran which is resulted from a point mutation at codon 75 of the α1-globin gene (Asp→His). The identification of Hb Q-Iran was observed in two members of a family from the Central Province of Iran. In this study, Globin chain analysis on high performance liquid chromatography (HPLC) and DNA sequencing were applied. An unusual Hb variant, like HbS on alkaline pH electrophoresis was identified from samples of a father and his son from Arak city in the Central Province of Iran. The variant was further characterized by globin chain analysis and DNA sequencing methods. Globin chain analysis revealed an unknown globin chain peak after α-globin chain peak with a different retention time from βs-globin chain, as the control in both samples. Genetic analysis led to the identification of an unknown Hb variant, Hb Q-Iran. Globin chain analysis showed the presence of an unknown globin chain, and likewise DNA sequencing revealed HbQ-Iran. In other words, Globin chain analysis procedure could preliminarily detect an unknown globin chain.

  5. Diagnostic value of immunoglobulin κ light chain gene rearrangement analysis in B-cell lymphomas

    PubMed Central

    KOKOVIC, IRA; NOVAKOVIC, BARBARA JEZERSEK; NOVAKOVIC, SRDJAN

    2015-01-01

    Analysis of the immunoglobulin κ light chain (IGK) gene is an alternative method for B-cell clonality assessment in the diagnosis of mature B-cell proliferations in which the detection of clonal immunoglobulin heavy chain (IGH) gene rearrangements fails. The aim of the present study was to evaluate the added value of standardized BIOMED-2 assay for the detection of clonal IGK gene rearrangements in the diagnostic setting of suspected B-cell lymphomas. With this purpose, 92 specimens from 80 patients with the final diagnosis of mature B-cell lymphoma (37 specimens), mature T-cell lymphoma (26 specimens) and reactive lymphoid proliferation (29 specimens) were analyzed for B-cell clonality. B-cell clonality analysis was performed using the BIOMED-2 IGH and IGK gene clonality assays. The determined sensitivity of the IGK assay was 67.6%, while the determined sensitivity of the IGH assay was 75.7%. The sensitivity of combined IGH+IGK assay was 81.1%. The determined specificity of the IGK assay was 96.2% in the group of T-cell lymphomas and 96.6% in the group of reactive lesions. The determined specificity of the IGH assay was 84.6% in the group of lymphomas and 86.2% in the group of reactive lesions. The comparison of GeneScan (GS) and heteroduplex pretreatment-polyacrylamide gel electrophoresis (HD-PAGE) methods for the analysis of IGK gene rearrangements showed a higher efficacy of GS analysis in a series of 27 B-cell lymphomas analyzed by both methods. In the present study, we demonstrated that by applying the combined IGH+IGK clonality assay the overall detection rate of B-cell clonality was increased by 5.4%. Thus, we confirmed the added value of the standardized BIOMED-2 IGK assay for assessment of B-cell clonality in suspected B-cell lymphomas with inconclusive clinical and cyto/histological diagnosis. PMID:25501347

  6. BMI Affects the Relationship between Long Chain N-3 Polyunsaturated Fatty Acid Intake and Stroke Risk: a Meta-Analysis.

    PubMed

    Cheng, Pengfei; Huang, Wen; Bai, Shunjie; Wu, Yu; Yu, Jia; Zhu, Xiaofeng; Qi, Zhiguo; Shao, Weihua; Xie, Peng

    2015-01-01

    We performed a meta-analysis to clarify the relationship between long chain n-3 polyunsaturated fatty acid (PUFA) intake and stroke risk. Relevant studies were identified by searching online databases through May 2015. Log relative risks (RRs) of the highest versus the lowest for cohort studies were weighed by the inverse variance method to obtain pooled RRs. Fourteen prospective cohort studies including 514,483 individuals and 9,065 strokes were included. The pooled RR of overall stroke risk for long chain n-3 PUFA intake was 0.87 [95% confidence interval (CI), 0.79-0.95]. Stratification analysis showed that higher long chain n-3 PUFAs intake was associated with reduced fatal stroke risk (RR = 0.84; 95% CI, 0.73-0.97), reduced stroke risk for BMI < 24 (RR = 0.86; 95% CI, 0.75-0.98) and reduced stroke risk for females (RR = 0.81; 95% CI, 0.71-0.92), but was not associated with stroke risk for either BMI ≥ 24 or men. This meta-analysis reveals that higher long chain n-3 PUFA intake is inversely associated with risk of stroke morbidity and mortality with BMI and sex as key factors influencing this risk. Individuals should be encouraged to manage their body weight while increasing their intake of long chain n-3 PUFAs. PMID:26369699

  7. Effects of tour boats on dolphin activity examined with sensitivity analysis of Markov chains.

    PubMed

    Dans, Silvana Laura; Degrati, Mariana; Pedraza, Susana Noemí; Crespo, Enrique Alberto

    2012-08-01

    In Patagonia, Argentina, watching dolphins, especially dusky dolphins (Lagenorhynchus obscurus), is a new tourist activity. Feeding time decreases and time to return to feeding after feeding is abandoned and time it takes a group of dolphins to feed increase in the presence of boats. Such effects on feeding behavior may exert energetic costs on dolphins and thus reduce an individual's survival and reproductive capacity or maybe associated with shifts in distribution. We sought to predict which behavioral changes modify the activity pattern of dolphins the most. We modeled behavioral sequences of dusky dolphins with Markov chains. We calculated transition probabilities from one activity to another and arranged them in a stochastic matrix model. The proportion of time dolphins dedicated to a given activity (activity budget) and the time it took a dolphin to resume that activity after it had been abandoned (recurrence time) were calculated. We used a sensitivity analysis of Markov chains to calculate the sensitivity of the time budget and the activity-resumption time to changes in behavioral transition probabilities. Feeding-time budget was most sensitive to changes in the probability of dolphins switching from traveling to feeding behavior and of maintaining feeding behavior. Thus, an increase in these probabilities would be associated with the largest reduction in the time dedicated to feeding. A reduction in the probability of changing from traveling to feeding would also be associated with the largest increases in the time it takes dolphins to resume feeding. To approach dolphins when they are traveling would not affect behavior less because presence of the boat may keep dolphins from returning to feeding. Our results may help operators of dolphin-watching vessels minimize negative effects on dolphins. PMID:22624561

  8. Effect of specimen type on free immunoglobulin light chains analysis on the Roche Diagnostics cobas 8000 analyzer.

    PubMed

    Nelson, Louis S; Steussy, Bryan; Morris, Cory S; Krasowski, Matthew D

    2015-01-01

    The measurement of free immunoglobulin light chains is typically performed on serum; however, the use of alternative specimen types has potential benefits. Using the Freelite™ kappa and lambda free light chains assay on a Roche Diagnostics cobas 8000 c502 analyzer, we compared three specimen types (serum, EDTA-plasma and lithium heparin plasma separator gel-plasma) on 100 patients. Using Deming regression and eliminating outliers (limiting data to light chain concentrations below 400 mg/L), the three specimen types showed comparable results for kappa light chain concentration, lambda light chain concentration, and kappa/lambda ratio with slopes close to 1.0 and y-intercepts close to zero. EDTA-plasma showed slightly more positive bias relative to serum than lithium heparin. Analysis using EDTA-plasma and lithium heparin plasma showed comparable linearity, precision, and temperature stability. A single sample showing hook effect (not in the comparison set) gave comparable results using either plasma specimen type. For the Freelite™ kappa and lambda free light chains assay, both EDTA-plasma or lithium heparin-plasma can serve as acceptable substitutes for serum, at least for the Roche cobas 8000 analyzer. PMID:26682113

  9. Accuracy of mucocutaneous leishmaniasis diagnosis using polymerase chain reaction: systematic literature review and meta-analysis

    PubMed Central

    Gomes, Ciro Martins; Mazin, Suleimy Cristina; dos Santos, Elisa Raphael; Cesetti, Mariana Vicente; Bächtold, Guilherme Albergaria Brízida; Cordeiro, João Henrique de Freitas; Theodoro, Fabrício Claudino Estrela Terra; Damasco, Fabiana dos Santos; Carranza, Sebastián Andrés Vernal; Santos, Adriana de Oliveira; Roselino, Ana Maria; Sampaio, Raimunda Nonata Ribeiro

    2015-01-01

    The diagnosis of mucocutaneous leishmaniasis (MCL) is hampered by the absence of a gold standard. An accurate diagnosis is essential because of the high toxicity of the medications for the disease. This study aimed to assess the ability of polymerase chain reaction (PCR) to identify MCL and to compare these results with clinical research recently published by the authors. A systematic literature review based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses: the PRISMA Statement was performed using comprehensive search criteria and communication with the authors. A meta-analysis considering the estimates of the univariate and bivariate models was performed. Specificity near 100% was common among the papers. The primary reason for accuracy differences was sensitivity. The meta-analysis, which was only possible for PCR samples of lesion fragments, revealed a sensitivity of 71% [95% confidence interval (CI) = 0.59; 0.81] and a specificity of 93% (95% CI = 0.83; 0.98) in the bivariate model. The search for measures that could increase the sensitivity of PCR should be encouraged. The quality of the collected material and the optimisation of the amplification of genetic material should be prioritised. PMID:25946238

  10. Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis

    PubMed Central

    Selivanov, Vitaly A.; Cascante, Marta; Friedman, Mark; Schumaker, Mark F.; Trucco, Massimo; Votyakova, Tatyana V.

    2012-01-01

    The mitochondrial electron transport chain transforms energy satisfying cellular demand and generates reactive oxygen species (ROS) that act as metabolic signals or destructive factors. Therefore, knowledge of the possible modes and bifurcations of electron transport that affect ROS signaling provides insight into the interrelationship of mitochondrial respiration with cellular metabolism. Here, a bifurcation analysis of a sequence of the electron transport chain models of increasing complexity was used to analyze the contribution of individual components to the modes of respiratory chain behavior. Our algorithm constructed models as large systems of ordinary differential equations describing the time evolution of the distribution of redox states of the respiratory complexes. The most complete model of the respiratory chain and linked metabolic reactions predicted that condensed mitochondria produce more ROS at low succinate concentration and less ROS at high succinate levels than swelled mitochondria. This prediction was validated by measuring ROS production under various swelling conditions. A numerical bifurcation analysis revealed qualitatively different types of multistationary behavior and sustained oscillations in the parameter space near a region that was previously found to describe the behavior of isolated mitochondria. The oscillations in transmembrane potential and ROS generation, observed in living cells were reproduced in the model that includes interaction of respiratory complexes with the reactions of TCA cycle. Whereas multistationarity is an internal characteristic of the respiratory chain, the functional link of respiration with central metabolism creates oscillations, which can be understood as a means of auto-regulation of cell metabolism. PMID:23028295

  11. Histochemical Analysis of Laminin α Chains in Diethylstilbestrol-Induced Prolactinoma in Rats.

    PubMed

    Ramadhani, Dini; Tofrizal, Alimuddin; Tsukada, Takehiro; Yashiro, Takashi

    2015-04-28

    Laminin, a major basement membrane component, is important in structural support and cell proliferation and differentiation. Its 19 isoforms are assemblies of α, β, and γ chains, and the α chains (α1-5) determine the isoform characteristics. Although our previous studies showed alterations in α chain expressions during anterior pituitary development, their expressions in pituitary tumors yet to be determined. The present study used a rat model of diethylstilbestrol (DES)-induced prolactinoma to examine α chain expressions during prolactinoma tumorigenesis (0-12 weeks of DES treatment) by in situ hybridization and immunohistochemistry. mRNA of α1, α3, and α4 chains was detected in control and after 4 weeks of DES treatment. These expressions were undetectable after 8 weeks of DES treatment and in prolactinoma (12 weeks of DES treatment). Immunohistochemistry showed that the α1 chain was localized in some anterior pituitary cells in control and after 4 weeks of treatment and in endothelial cells after 8 weeks of treatment. The α3 and α4 chains were expressed in endothelial cells, and immunoreactivity and the number of immunopositive cells decreased during DES treatment. These findings suggest that alteration of laminin α chains is related to abnormal cell proliferation and neovascularization during development of DES-induced prolactinoma.

  12. Cloning and functional analysis of novel short-chain cis-prenyltransferases.

    PubMed

    Ambo, Takanori; Noike, Motoyoshi; Kurokawa, Hirofumi; Koyama, Tanetoshi

    2008-10-31

    cis-Prenyltransferase catalyzes the synthesis of Z,E-mixed prenyl diphosphates by sequential condensation of isopentenyl diphosphate with allylic diphosphate. cis-Prenyltransferases can be classified into three subgroups: short-, medium-, and long-chain cis-prenyltransferase, according to their product chain lengths. cis-Farnesyl diphosphate synthase from Mycobacterium tuberculosis has been the only example as short-chain cis-prenyltransferase so far characterized. In this study, we cloned the novel short-chain cis-prenyltransferases from three different bacteria, and characterized their enzymatic activities to compare and elucidate a common feature of the short-chain cis-prenyltransferases. Furthermore, we identified a specific isoleucine that is conserved in short-chain cis-prenyltransferases and located in close proximity of the omega-end of the geranyl diphosphate. Several site-directed mutants with respect to the isoleucine residue synthesized longer prenyl chain products and showed broader allylic substrate specificity. These results suggested that the isoleucine plays an important role in the substrate specificity and chain length determination mechanism of cis-prenyltransferase.

  13. [Analysis of the vegetable productive chain in Ribeirão Preto, SP].

    PubMed

    Takayanagui, Osvaldo M; Capuano, Divani M; Oliveira, Carlos A D; Bergamini, Alzira M M; Okino, Madalena H T; Castro e Silva, Ana A M C; Oliveira, Maria A; Ribeiro, Eliana G A; Takayanagui, Angela M M

    2006-01-01

    With the aim of assessing the cumulative risk of lettuce contamination, 45 production chains were investigated. The presence of thermotolerant coliforms, Salmonella and/or parasites was detected in 69% of these, in all steps of the production chain. Quality control in all steps of the lettuce production process should be intensified. PMID:16699655

  14. Falling Chains as Variable-Mass Systems: Theoretical Model and Experimental Analysis

    ERIC Educational Resources Information Center

    de Sousa, Celia A.; Gordo, Paulo M.; Costa, Pedro

    2012-01-01

    In this paper, we revisit, theoretically and experimentally, the fall of a folded U-chain and of a pile-chain. The model calculation implies the division of the whole system into two subsystems of variable mass, allowing us to explore the role of tensional contact forces at the boundary of the subsystems. This justifies, for instance, that the…

  15. Analysis of gene amplification in archival tissue by differential polymerase chain reaction.

    PubMed

    Neubauer, A; Neubauer, B; He, M; Effert, P; Iglehart, D; Frye, R A; Liu, E

    1992-05-01

    Oncogene amplification is found in many human tumors, and its detection may have important prognostic value. However, analysis of gene amplification may be hampered by inadequate tissue or poor DNA quality. We have previously described a polymerase chain reaction (PCR)-based procedure called differential PCR that can detect variations in gene dosage using miniscule amounts of tumor DNA [Frye, R.A., Benz, C.C. & Liu, E. (1989). Oncogene, 4, 1153-1157]. We now report the optimization of this technique for the analysis of oncogene amplification in paraffin-embedded archival tissues. We find that differential PCR is able to detect amplification of the HER2 (c-erbB-2) and the epidermal growth factor receptor (EGFR) genes and can be used to arrive at a semiquantitative estimate of gene dosage. Furthermore, our approach can determine gene amplification in samples in which the DNA is significantly degraded. Using differential PCR on paraffin-embedded tissues from cases previously investigated by standard DNA extraction and dot-blot procedures, good correlation between the two methods was found. Approaches are described to overcome technical problems posed by factors that affect the differential PCR, including the method of DNA extraction and extreme fragmentation of the DNA (less than 200 base pairs). Furthermore, the resulting analytical algorithm reported herein has proved effective in detecting oncogene amplification in archival breast cancer specimens from standard pathology laboratories. Thus, differential PCR will be particularly helpful in the analysis of tumor specimens that are archived, small in size or rare in occurrence.

  16. Kinetic analysis of mechanochemical chain scission of linear poly(phthalaldehyde).

    PubMed

    Peterson, Gregory I; Boydston, Andrew J

    2014-09-01

    The kinetics of mechanochemical chain scission of poly(phthalaldehyde) (PPA) are investigated. Ultrasound-induced cavitation is capable of causing chain scission in the PPA backbone that ultimately leads to rapid depolymerization of each resulting polymer fragment when above the polymer's ceiling temperature (Tc ). An interesting feature of the mechanochemical breakdown of PPA is that "half-chain" daughter fragments are not observed, since the depolymerization is rapid following chain scission. These features facilitate the determination of rate constants of activation for multiple molecular weights from a single sonication experiment. Additionally, the degradation kinetics are modified with chain-end trapping agents through variation of the nature and amount of small molecule nucleophile or electrophile.

  17. Time-based analysis of the apheresis platelet supply chain in England.

    PubMed

    Wilding, R; Cotton, S; Dobbin, J; Chapman, J; Yates, N

    2011-10-01

    During 2009/2010 loss of platelets within NHS Blood and Transplant (NHSBT) due to time expiry was 9.3%. Hospitals remain reluctant to hold stocks of platelets due to the poor shelf life at issue. The purpose of this study was to identify areas for time compression in the apheresis platelet supply chain to extend the shelf life available for hospitals and reduce wastage in NHSBT. This was done within the context of NHSBT reconfiguring their supply chain and moving towards a consolidated and centralised approach. Time based process mapping was applied to identify value and non-value adding time in two manufacturing models. A large amount of the non-value adding time in the apheresis platelet supply chain is due to transportation and waiting for the next process in the manufacturing process to take place. Time based process mapping provides an effective 'lens' for supply chain professionals to identify opportunities for improvement in the platelet supply chain.

  18. Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

    PubMed

    Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

    2016-06-01

    We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. PMID:25827436

  19. Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

    PubMed

    Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

    2016-06-01

    We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing.

  20. Analysis of polymorphism in the bovine casein genes by use of the polymerase chain reaction.

    PubMed

    Pinder, S J; Perry, B N; Skidmore, C J; Savva, D

    1991-01-01

    Methods have been devised for detecting polymorphisms in the bovine beta- and kappa-casein genes using the polymerase chain reaction (PCR) followed either by restriction enzyme digestion (to reveal a restriction fragment length polymorphism (RFLP] or by hybridization of an allele-specific oligonucleotide. These methods, as well as being faster and more sensitive than traditional RFLP methods, are of more general applicability since they can detect any change in DNA sequence. They require only a small sample of blood or semen and are applicable to animals of any age or sex. These methods make possible large-scale screening and thus selection for alleles at these loci. Typing of blood DNA can give erroneous results when the animal concerned is a twin; however, this can be overcome by retesting using milk or semen. Analysis of the kappa-casein genotype of Holstein-Friesian bulls gives frequencies for the A and B alleles of 0.80 and 0.20 respectively. Selection in favour of the B allele, which is superior for cheese production, could thus have a large effect. The A3 and B alleles at the beta-casein locus have been shown to be rare in the Holstein-Friesian population. Linkage disequilibrium exists between beta-casein B and kappa-casein B.

  1. Polymerase chain reaction analysis of aqueous humour samples in necrotising retinitis

    PubMed Central

    Tran, T H C; Rozenberg, F; Cassoux, N; Rao, N A; LeHoang, P; Bodaghi, B

    2003-01-01

    Aim: To evaluate the diagnostic value of polymerase chain reaction (PCR) performed on aqueous humour for the detection of viral DNA in patients with necrotising herpetic retinitis. Methods: The clinical features and laboratory results of 22 patients (29 eyes) presenting with necrotising herpetic retinitis between March 1999 and June 2001 were reviewed retrospectively. Aqueous humour was obtained after anterior chamber paracentesis and PCR was performed in all cases. Results: Viral DNA was detected in the aqueous humour of 19 patients (86.4%). Epstein-Barr virus (EBV) seroconversion was evidenced in one additional patient. In the acute retinal necrosis (ARN) group (n = 19), varicella zoster virus (VZV) DNA was identified in six patients, herpes simplex virus 1 (HSV-1) DNA in two patients, herpes simplex virus 2 (HSV-2) DNA in four patients, and cytomegalovirus (CMV) genome in four patients. In the progressive outer retinal necrosis (PORN) group (n = 3), VZV DNA was detected in all patients. No sample was positive for more than one virus. Conclusions: PCR analysis of aqueous humour in patients with clinical features of necrotising viral retinitis can provide specific aetiological orientation and the method appears to be safe and highly sensitive. PMID:12488268

  2. Conformational analysis of the oligosaccharides related to side chains of holothurian fucosylated chondroitin sulfates.

    PubMed

    Gerbst, Alexey G; Dmitrenok, Andrey S; Ustyuzhanina, Nadezhda E; Nifantiev, Nikolay E

    2015-02-01

    Anionic polysaccharides fucosylated chondroitin sulfates (FCS) from holothurian species were shown to affect various biological processes, such as metastasis, angiogenesis, clot formation, thrombosis, inflammation, and some others. To understand the mechanism of FCSs action, knowledge about their spatial arrangement is required. We have started the systematic synthesis, conformational analysis, and study of biological activity of the oligosaccharides related to various fragments of these types of natural polysaccharides. In this communication, five molecules representing distinct structural fragments of chondroitin sulfate have been studied by means of molecular modeling and NMR. These are three disaccharides and two trisaccharides containing fucose and glucuronic acid residues with one sulfate group per each fucose residue or without it. Long-range C-H coupling constants were used for the verification of the theoretical models. The presence of two conformers for both linkage types was revealed. For the Fuc-GlA linkage, the dominant conformer was the same as described previously in a literature as the molecular dynamics (MD) average in a dodechasaccharide FCS fragment representing the backbone chain of the polysaccharide including GalNAc residues. This shows that the studied oligosaccharides, in addition to larger ones, may be considered as reliable models for Quantitative Structure-Activity Relationship (QSAR) studies to reveal pharmacophore fragments of FCS.

  3. Gene-expression analysis of single cells-nested polymerase chain reaction after laser microdissection

    PubMed Central

    Shi, Xin; Kleeff, JÖrg; Zhu, Zhao-Wen; Schmied, Bruno; Tang, Wen-Hao; Zimmermann, Arthur; BÜchler, Markus W.; Friess, Helmut

    2003-01-01

    AIM: The structural and functional characteristics of cells are dependent on the specific gene expression profile. The ability to study and compare gene expression at the cellular level will therefore provide valuable insights into cell physiology and pathophysiology. METHODS: Individual cells were isolated from frozen colon tissue sections using laser microdissection. DNA as well as RNA were extracted, and total RNA was reversely transcribed to complementary DNA (cDNA). Both DNA and cDNA were analyzed by nested polymerase chain reaction (PCR). The quality of isolated DNA and RNA was satisfactory. RESULTS: Single cells were successfully microdissected using an ultraviolet laser micromanipulator. Nested PCR amplification products of DNA and cDNA of single cells could clearly be visualized by agarose gel electrophoresis. CONCLUSION: The combined use of laser microdissection and nested-PCR provides an opportunity to analyze gene expression in single cells. This method allows the analysis and identification of specific genes which are involved in physiological and pathophysiological processes in a complex of variable cell phenotypes. PMID:12800252

  4. Conformational Analysis of the Oligosaccharides Related to Side Chains of Holothurian Fucosylated Chondroitin Sulfates

    PubMed Central

    Gerbst, Alexey G.; Dmitrenok, Andrey S.; Ustyuzhanina, Nadezhda E.; Nifantiev, Nikolay E.

    2015-01-01

    Anionic polysaccharides fucosylated chondroitin sulfates (FCS) from holothurian species were shown to affect various biological processes, such as metastasis, angiogenesis, clot formation, thrombosis, inflammation, and some others. To understand the mechanism of FCSs action, knowledge about their spatial arrangement is required. We have started the systematic synthesis, conformational analysis, and study of biological activity of the oligosaccharides related to various fragments of these types of natural polysaccharides. In this communication, five molecules representing distinct structural fragments of chondroitin sulfate have been studied by means of molecular modeling and NMR. These are three disaccharides and two trisaccharides containing fucose and glucuronic acid residues with one sulfate group per each fucose residue or without it. Long-range C–H coupling constants were used for the verification of the theoretical models. The presence of two conformers for both linkage types was revealed. For the Fuc–GlA linkage, the dominant conformer was the same as described previously in a literature as the molecular dynamics (MD) average in a dodechasaccharide FCS fragment representing the backbone chain of the polysaccharide including GalNAc residues. This shows that the studied oligosaccharides, in addition to larger ones, may be considered as reliable models for Quantitative Structure-Activity Relationship (QSAR) studies to reveal pharmacophore fragments of FCS. PMID:25686272

  5. Markov chain Monte Carlo analysis to constrain dark matter properties with directional detection

    SciTech Connect

    Billard, J.; Mayet, F.; Santos, D.

    2011-04-01

    Directional detection is a promising dark matter search strategy. Indeed, weakly interacting massive particle (WIMP)-induced recoils would present a direction dependence toward the Cygnus constellation, while background-induced recoils exhibit an isotropic distribution in the Galactic rest frame. Taking advantage of these characteristic features, and even in the presence of a sizeable background, it has recently been shown that data from forthcoming directional detectors could lead either to a competitive exclusion or to a conclusive discovery, depending on the value of the WIMP-nucleon cross section. However, it is possible to further exploit these upcoming data by using the strong dependence of the WIMP signal with: the WIMP mass and the local WIMP velocity distribution. Using a Markov chain Monte Carlo analysis of recoil events, we show for the first time the possibility to constrain the unknown WIMP parameters, both from particle physics (mass and cross section) and Galactic halo (velocity dispersion along the three axis), leading to an identification of non-baryonic dark matter.

  6. Combined survival analysis of cardiac patients by a Cox PH model and a Markov chain.

    PubMed

    Shauly, Michal; Rabinowitz, Gad; Gilutz, Harel; Parmet, Yisrael

    2011-10-01

    The control and treatment of dyslipidemia is a major public health challenge, particularly for patients with coronary heart diseases. In this paper we propose a framework for survival analysis of patients who had a major cardiac event, focusing on assessment of the effect of changing LDL-cholesterol level and statins consumption on survival. This framework includes a Cox PH model and a Markov chain, and combines their results into reinforced conclusions regarding the factors that affect survival time. We prospectively studied 2,277 cardiac patients, and the results show high congruence between the Markov model and the PH model; both evidence that diabetes, history of stroke, peripheral vascular disease and smoking significantly increase hazard rate and reduce survival time. On the other hand, statin consumption is correlated with a lower hazard rate and longer survival time in both models. The role of such a framework in understanding the therapeutic behavior of patients and implementing effective secondary and primary prevention of heart diseases is discussed here. PMID:21735134

  7. A Markov chain analysis of fish movements to determine entrainment zones

    SciTech Connect

    Johnson, Gary E.; Hedgepeth, J.; Skalski, John R.; Giorgi, Albert E.

    2004-06-01

    The extent of the biological zone of influence (BZI) of a water withdrawal port, such as a cooling water intake or a smolt bypass, directly reflects its local effect on fish. This study produced a new technique to determine the BZI, defined as the region immediately upstream of a portal where the probability of fish movement toward the portal is greater than 90%. We developed and applied the technique at The Dalles Dam on the Columbia River, where the ice/trash sluiceway functions as a surface flow smolt bypass. To map the BZI, we applied a Markov-Chain analysis to smolt movement data collected with an active fish tracking sonar system. Probabilities of fish movement from cell to cell in the sample volume, calculated from tracked fish data, formed a Markov transition matrix. Multiplying this matrix by itself many times with absorption at the boundaries produced estimates of probability of passage out each side of the sample volume from the cells within. The BZI of a sluiceway entrance at The Dalles Dam was approximately 5 m across and extended 6-8 m out from the face of the dam in the surface layer 2-3 m deep. BZI mapping is applicable to many bioengineering efforts to protect fish populations.

  8. Assessment of the Cotton Industry Using the Global Commodity Chain Analysis Approach in Katsina State, Nigeria

    NASA Astrophysics Data System (ADS)

    Kudi, T. M.; Akpoko, J. G.; Abdulsalam, Z.

    The study examines the cotton commodity chain and assessed the share of each actor in the cotton industry and identified the constraints encountered in cotton production, marketing and processing. A sample of thirty cotton producers, 50 traders, 500 agents and 3 ginneries were selected from Funtua Local Government Area of Katsina State using both random and purposive sampling techniques. Both qualitative and quantitative data were collected from the participants using focus group discussion and structured questionnaire during the 2004/2005 cropping season. Analysis of the data was done using descriptive statistics and budgeting technique. The farmersN budget analysis indicated that from an investment cost of N 33,146.00 ha-1, farmers obtained a revenue of N 44,544-00 ha-1, thus making a net income of N 11,398 ha-1, while the agent analysis shows that an agent is paid a commission of N 500.00 ton-1 of seed cotton purchase on behalf of the merchant. The analysis of the tradersN budget revealed that from an investment cost of N 36,746.00 ton-1 of seed cotton purchased, traders` N 41,700.00 (lint + seed) and a net profit of N 4,954.00 ton h-1 of seed cotton. The analysis of the ginnery budget revealed that from one ton of seed cotton processed, a ginnery is making a net profit of N 2,178.00. These analyses indicated that cotton production, marketing and processing under the current price and cost setting is profitable. In spite of the profitability in cotton business, the following problems were identified: adulteration of seed cotton with foreign materials, heterogeneous seeds resale in the market, inappropriate packaging systems, no good prices for improving the quality and no mechanism for ensuring transparency in the quality (trust between actors). There is the need for intensification and expansion of the cotton sector in terms of provision of high quality inputs, clean seed cotton, introduction of jute bags for packaging, introduction of quality control

  9. Dynamic Models and Coordination Analysis of Reverse Supply Chain with Remanufacturing

    NASA Astrophysics Data System (ADS)

    Yan, Nina

    In this paper, we establish a reverse chain system with one manufacturer and one retailer under demand uncertainties. Distinguishing between the recycling process of the retailer and the remanufacturing process of the manufacturer, we formulate a two-stage dynamic model for reverse supply chain based on remanufacturing. Using buyback contract as coordination mechanism and applying dynamic programming the optimal decision problems for each stage are analyzed. It concluded that the reverse supply chain system could be coordinated under the given condition. Finally, we carry out numerical calculations to analyze the expected profits for the manufacturer and the retailer under different recovery rates and recovery prices and the outcomes validate the theoretical analyses.

  10. The Analysis of Rush Orders Risk in Supply Chain: A Simulation Approach

    NASA Technical Reports Server (NTRS)

    Mahfouz, Amr; Arisha, Amr

    2011-01-01

    Satisfying customers by delivering demands at agreed time, with competitive prices, and in satisfactory quality level are crucial requirements for supply chain survival. Incidence of risks in supply chain often causes sudden disruptions in the processes and consequently leads to customers losing their trust in a company's competence. Rush orders are considered to be one of the main types of supply chain risks due to their negative impact on the overall performance, Using integrated definition modeling approaches (i.e. IDEF0 & IDEF3) and simulation modeling technique, a comprehensive integrated model has been developed to assess rush order risks and examine two risk mitigation strategies. Detailed functions sequence and objects flow were conceptually modeled to reflect on macro and micro levels of the studied supply chain. Discrete event simulation models were then developed to assess and investigate the mitigation strategies of rush order risks, the objective of this is to minimize order cycle time and cost.

  11. RFID Application Strategy in Agri-Food Supply Chain Based on Safety and Benefit Analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Li, Peichong

    Agri-food supply chain management (SCM), a management method to optimize internal costs and productivities, has evolved as an application of e-business technologies. These days, RFID has been widely used in many fields. In this paper, we analyze the characteristics of agri-food supply chain. Then the disadvantages of RFID are discussed. After that, we study the application strategies of RFID based on benefit and safety degree.

  12. Early detection of Brucella canis via quantitative polymerase chain reaction analysis.

    PubMed

    Kauffman, L K; Bjork, J K; Gallup, J M; Boggiatto, P M; Bellaire, B H; Petersen, C A

    2014-02-01

    Canine brucellosis is a reportable zoonotic disease that can lead to canine reproductive losses and human infection through contact with infected urine or other genitourinary secretions. Although many locations require testing and euthanasia of positive dogs, current diagnosis is limited by the time required for seroconversion, for example, presence of B. canis-specific antibodies. The goal of this study was to determine the diagnostic ability of Brucella canis-specific quantitative polymerase chain reaction (qPCR) assay to detect B. canis in field samples prior to serological positivity for faster diagnosis and prevention of transmission within kennels or in households. Two kennels, one of which was located in the owner's home, were sampled following observation of suggestive clinical signs and positive serology of at least one dog. Specimens obtained were comparatively analysed via serology and qPCR analysis. 107 dogs were analysed for B. canis infection via qPCR: 105 via whole-blood samples, 65 via vaginal swab, six via urine and seven via genitourinary tract tissue taken at necropsy. Forty-five dogs were found to be infected with canine brucellosis via qPCR, of which 22 (48.89%) were seropositive. A statistically significant number (P = 0.0228) of qPCR-positive dogs, 5/25 (20.00%), seroconverted within a 30-day interval after initial serologic testing. As compared to serology, qPCR analysis of DNA from vaginal swabs had a sensitivity of 92.31% and specificity of 51.92%, and qPCR analysis of DNA from whole-blood samples had a sensitivity of 16.67% and specificity of 100%. B. canis outer membrane protein 25 DNA qPCR from non-invasive vaginal swab and urine samples provided early detection of B. canis infection in dogs prior to detection of antibodies. This assay provides a critical tool to decrease zoonotic spread of canine brucellosis, its associated clinical presentation(s), and emotional and economic repercussions.

  13. Supply Chain Sustainability Analysis of Indirect Liquefaction of Blended Biomass to Produce High Octane Gasoline

    SciTech Connect

    Cai, Hao; Canter, Christina E.; Dunn, Jennifer B.; Tan, Eric; Biddy, Mary; Talmadge, Michael; Hartley, Damon S.; Snowden-Swan, Lesley

    2015-09-01

    The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) aims at developing and deploying technologies to transform renewable biomass resources into commercially viable, high-performance biofuels, bioproducts and biopower through public and private partnerships (DOE, 2015). BETO also performs a supply chain sustainability analysis (SCSA). This report describes the SCSA of the production of renewable high octane gasoline (HOG) via indirect liquefaction (IDL) of lignocellulosic biomass. This SCSA was developed for the 2017 design case for feedstock logistics (INL, 2014) and for the 2022 target case for HOG production via IDL (Tan et al., 2015). The design includes advancements that are likely and targeted to be achieved by 2017 for the feedstock logistics and 2022 for the IDL conversion process. The 2017 design case for feedstock logistics demonstrated a delivered feedstock cost of $80 per dry U.S. short ton by the year 2017 (INL, 2014). The 2022 design case for the conversion process, as modeled in Tan et al. (2015), uses the feedstock 2017 design case blend of biomass feedstocks consisting of pulpwood, wood residue, switchgrass, and construction and demolition waste (C&D) with performance properties consistent with a sole woody feedstock type (e.g., pine or poplar). The HOG SCSA case considers the 2017 feedstock design case (the blend) as well as individual feedstock cases separately as alternative scenarios when the feedstock blend ratio varies as a result of a change in feedstock availability. These scenarios could be viewed as bounding SCSA results because of distinctive requirements for energy and chemical inputs for the production and logistics of different components of the blend feedstocks.

  14. Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Santos, M S; Souza, E S; S Junior, R M; Talhari, S; Souza, J V B

    2010-08-01

    Prompt and specific identification of fungemia agents is important in order to define clinical treatment. However, in most cases conventional culture identification can be considered to be time-consuming and not without errors. The aim of the present study was to identify the following fungemia agents: Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Cryptococcus gattii, and Histoplasma capsulatum using the polymerase chain reaction and restriction fragment length polymorphism analysis (PCR/RFLP). More specifically: a) to evaluate 3 different amplification regions, b) to investigate 3 different restriction enzymes, and c) to use the best PCR/RFLP procedure to indentify 60 fungemia agents from a culture collection. All 3 pairs of primers (ITS1/ITS4, NL4/ITS5 and Primer1/Primer2) were able to amplify DNA from the reference strains. However, the size of these PCR products did not permit the identification of all the species studied. Three restriction enzymes were used to digest the PCR products: HaeIII, Ddel and Bfal. Among the combinations of pairs of primers and restriction enzymes, only one (primer pair NL4/ITS5 and restriction enzyme Ddel) produced a specific RFLP pattern for each microorganism studied. Sixty cultures of fungemia agents (selected from the culture collection of Fundação de Medicina Tropical do Amazonas--FMTAM) were correctly identified by PCR/RFLP using the prime pair NL4/ITS5 and Ddel. We conclude that the method proved to be both simple and reproducible, and may offer potential advantages over phenotyping methods.

  15. Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Santos, M S; Souza, E S; S Junior, R M; Talhari, S; Souza, J V B

    2010-08-01

    Prompt and specific identification of fungemia agents is important in order to define clinical treatment. However, in most cases conventional culture identification can be considered to be time-consuming and not without errors. The aim of the present study was to identify the following fungemia agents: Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Cryptococcus gattii, and Histoplasma capsulatum using the polymerase chain reaction and restriction fragment length polymorphism analysis (PCR/RFLP). More specifically: a) to evaluate 3 different amplification regions, b) to investigate 3 different restriction enzymes, and c) to use the best PCR/RFLP procedure to indentify 60 fungemia agents from a culture collection. All 3 pairs of primers (ITS1/ITS4, NL4/ITS5 and Primer1/Primer2) were able to amplify DNA from the reference strains. However, the size of these PCR products did not permit the identification of all the species studied. Three restriction enzymes were used to digest the PCR products: HaeIII, Ddel and Bfal. Among the combinations of pairs of primers and restriction enzymes, only one (primer pair NL4/ITS5 and restriction enzyme Ddel) produced a specific RFLP pattern for each microorganism studied. Sixty cultures of fungemia agents (selected from the culture collection of Fundação de Medicina Tropical do Amazonas--FMTAM) were correctly identified by PCR/RFLP using the prime pair NL4/ITS5 and Ddel. We conclude that the method proved to be both simple and reproducible, and may offer potential advantages over phenotyping methods. PMID:20640387

  16. Plasma lipidomics analysis finds long chain cholesteryl esters to be associated with Alzheimer's disease.

    PubMed

    Proitsi, P; Kim, M; Whiley, L; Pritchard, M; Leung, R; Soininen, H; Kloszewska, I; Mecocci, P; Tsolaki, M; Vellas, B; Sham, P; Lovestone, S; Powell, J F; Dobson, R J B; Legido-Quigley, C

    2015-01-13

    There is an urgent need for the identification of Alzheimer's disease (AD) biomarkers. Studies have now suggested the promising use of associations with blood metabolites as functional intermediate phenotypes in biomedical and pharmaceutical research. The aim of this study was to use lipidomics to identify a battery of plasma metabolite molecules that could predict AD patients from controls. We performed a comprehensive untargeted lipidomic analysis, using ultra-performance liquid chromatography/mass spectrometry on plasma samples from 35 AD patients, 40 elderly controls and 48 individuals with mild cognitive impairment (MCI) and used multivariate analysis methods to identify metabolites associated with AD status. A combination of 10 metabolites could discriminate AD patients from controls with 79.2% accuracy (81.8% sensitivity, 76.9% specificity and an area under curve of 0.792) in a novel test set. Six of the metabolites were identified as long chain cholesteryl esters (ChEs) and were reduced in AD (ChE 32:0, odds ratio (OR)=0.237, 95% confidence interval (CI)=0.10-0.48, P=4.19E-04; ChE 34:0, OR=0.152, 95% CI=0.05-0.37, P=2.90E-04; ChE 34:6, OR=0.126, 95% CI=0.03-0.35, P=5.40E-04; ChE 32:4, OR=0.056, 95% CI=0.01-0.24, P=6.56E-04 and ChE 33:6, OR=0.205, 95% CI=0.06-0.50, P=2.21E-03, per (log2) metabolite unit). The levels of these metabolites followed the trend control>MCI>AD. We, additionally, found no association between cholesterol, the precursor of ChE and AD. This study identified new ChE molecules, involved in cholesterol metabolism, implicated in AD, which may help identify new therapeutic targets; although, these findings need to be replicated in larger well-phenotyped cohorts.

  17. Plasma lipidomics analysis finds long chain cholesteryl esters to be associated with Alzheimer's disease.

    PubMed

    Proitsi, P; Kim, M; Whiley, L; Pritchard, M; Leung, R; Soininen, H; Kloszewska, I; Mecocci, P; Tsolaki, M; Vellas, B; Sham, P; Lovestone, S; Powell, J F; Dobson, R J B; Legido-Quigley, C

    2015-01-01

    There is an urgent need for the identification of Alzheimer's disease (AD) biomarkers. Studies have now suggested the promising use of associations with blood metabolites as functional intermediate phenotypes in biomedical and pharmaceutical research. The aim of this study was to use lipidomics to identify a battery of plasma metabolite molecules that could predict AD patients from controls. We performed a comprehensive untargeted lipidomic analysis, using ultra-performance liquid chromatography/mass spectrometry on plasma samples from 35 AD patients, 40 elderly controls and 48 individuals with mild cognitive impairment (MCI) and used multivariate analysis methods to identify metabolites associated with AD status. A combination of 10 metabolites could discriminate AD patients from controls with 79.2% accuracy (81.8% sensitivity, 76.9% specificity and an area under curve of 0.792) in a novel test set. Six of the metabolites were identified as long chain cholesteryl esters (ChEs) and were reduced in AD (ChE 32:0, odds ratio (OR)=0.237, 95% confidence interval (CI)=0.10-0.48, P=4.19E-04; ChE 34:0, OR=0.152, 95% CI=0.05-0.37, P=2.90E-04; ChE 34:6, OR=0.126, 95% CI=0.03-0.35, P=5.40E-04; ChE 32:4, OR=0.056, 95% CI=0.01-0.24, P=6.56E-04 and ChE 33:6, OR=0.205, 95% CI=0.06-0.50, P=2.21E-03, per (log2) metabolite unit). The levels of these metabolites followed the trend control>MCI>AD. We, additionally, found no association between cholesterol, the precursor of ChE and AD. This study identified new ChE molecules, involved in cholesterol metabolism, implicated in AD, which may help identify new therapeutic targets; although, these findings need to be replicated in larger well-phenotyped cohorts. PMID:25585166

  18. Quantitative Polymerase Chain Reaction Analysis of the Mouse Cyp2j Subfamily: Tissue Distribution and Regulation.

    PubMed

    Graves, Joan P; Gruzdev, Artiom; Bradbury, J Alyce; DeGraff, Laura M; Li, Huiling; House, John S; Hoopes, Samantha L; Edin, Matthew L; Zeldin, Darryl C

    2015-08-01

    Members of the cytochrome P450 CYP2J subfamily are expressed in multiple tissues in mice and humans. These enzymes are active in the metabolism of fatty acids to generate bioactive compounds. Herein we report new methods and results for quantitative polymerase chain reaction (qPCR) analysis for the seven genes (Cyp2j5, Cyp2j6, Cyp2j8, Cyp2j9, Cyp2j11, Cyp2j12, and Cyp2j13) of the mouse Cyp2j subfamily. SYBR Green primer sets were developed and compared with commercially available TaqMan primer/probe assays for specificity toward mouse Cyp2j cDNA, and analysis of tissue distribution and regulation of Cyp2j genes. Each TaqMan primer/probe set and SYBR Green primer set were shown to be specific for their intended mouse Cyp2j cDNA. Tissue distribution of the mouse Cyp2j isoforms confirmed similar patterns of expression between the two qPCR methods. Cyp2j5 and Cyp2j13 were highly expressed in male kidneys, and Cyp2j11 was highly expressed in both male and female kidneys. Cyp2j6 was expressed in multiple tissues, with the highest expression in the small intestine and duodenum. Cyp2j8 was detected in various tissues, with highest expression found in the skin. Cyp2j9 was highly expressed in the brain, liver, and lung. Cyp2j12 was predominately expressed in the brain. We also determined the Cyp2j isoform expression in Cyp2j5 knockout mice to determine whether there was compensatory regulation of other Cyp2j isoforms, and we assessed Cyp2j isoform regulation during various inflammatory models, including influenza A, bacterial lipopolysaccharide, house dust mite allergen, and corn pollen. Both qPCR methods detected similar suppression of Cyp2j6 and Cyp2j9 during inflammation in the lung.

  19. Time-based analysis of the apheresis platelet supply chain in England.

    PubMed

    Wilding, R; Cotton, S; Dobbin, J; Chapman, J; Yates, N

    2011-10-01

    During 2009/2010 loss of platelets within NHS Blood and Transplant (NHSBT) due to time expiry was 9.3%. Hospitals remain reluctant to hold stocks of platelets due to the poor shelf life at issue. The purpose of this study was to identify areas for time compression in the apheresis platelet supply chain to extend the shelf life available for hospitals and reduce wastage in NHSBT. This was done within the context of NHSBT reconfiguring their supply chain and moving towards a consolidated and centralised approach. Time based process mapping was applied to identify value and non-value adding time in two manufacturing models. A large amount of the non-value adding time in the apheresis platelet supply chain is due to transportation and waiting for the next process in the manufacturing process to take place. Time based process mapping provides an effective 'lens' for supply chain professionals to identify opportunities for improvement in the platelet supply chain. PMID:21521234

  20. Scalability analysis of the synchronizability for ring or chain networks with dense clusters

    NASA Astrophysics Data System (ADS)

    Lu, Jun-An; Zhang, Yong; Chen, Juan; Lü, Jinhu

    2014-03-01

    It is well known that most real-world complex networks, such as the Internet and the World Wide Web, are evolving networks. An interesting fundamental question is: how do some important functions or dynamical behaviors of complex networks evolve with increasing network scale? This paper aims at investigating the scalability of the synchronizability for ring or chain networks with dense clusters as the network size increases. We discover some interesting phenomena as follows: (i) the synchronizability of ring or chain networks with clusters decreases with increasing network scale regardless of the inner structures of all communities; (ii) for the same network scale, the network synchronizability decreases more quickly with increasing number of cluster blocks than with increasing number of nodes within the cluster block; (iii) the number of rings or chains has a much more significant influence on the network synchronizability than the size of the rings or chains. Our results indicate that network synchronizability can be maintained with increasing network scale by avoiding ring and chain structures.

  1. A comparative analysis of accident risks in fossil, hydro, and nuclear energy chains

    SciTech Connect

    Burgherr, P.; Hirschberg, S.

    2008-07-01

    This study presents a comparative assessment of severe accident risks in the energy sector, based on the historical experience of fossil (coal, oil, natural gas, and LPG (Liquefied Petroleum Gas)) and hydro chains contained in the comprehensive Energy-related Severe Accident Database (ENSAD), as well as Probabilistic Safety Assessment (PSA) for the nuclear chain. Full energy chains were considered because accidents can take place at every stage of the chain. Comparative analyses for the years 1969-2000 included a total of 1870 severe ({>=} 5 fatalities) accidents, amounting to 81,258 fatalities. Although 79.1% of all accidents and 88.9% of associated fatalities occurred in less developed, non-OECD countries, industrialized OECD countries dominated insured losses (78.0%), reflecting their substantially higher insurance density and stricter safety regulations. Aggregated indicators and frequency-consequence (F-N) curves showed that energy-related accident risks in non-OECD countries are distinctly higher than in OECD countries. Hydropower in non-OECD countries and upstream stages within fossil energy chains are most accident-prone. Expected fatality rates are lowest for Western hydropower and nuclear power plants; however, the maximum credible consequences can be very large. Total economic damages due to severe accidents are substantial, but small when compared with natural disasters. Similarly, external costs associated with severe accidents are generally much smaller than monetized damages caused by air pollution.

  2. Analysis of solitary wave impulses in granular chains using ultrasonic excitation

    NASA Astrophysics Data System (ADS)

    Yang, J.; Hutchins, D. A.; Akanji, O.; Thomas, P. J.; Davis, L. A. J.; Harput, S.; Gelat, P.; Freear, S.; Saffari, N.

    2016-06-01

    The propagation of broad bandwidth solitary wave impulses, generated within granular chains by narrow bandwidth ultrasonic excitation, is studied in detail. Theoretical predictions are compared to experimental results. It is demonstrated that the observed effects result from a sum of a solitary wave traveling out from the source with a wave that reflects from the far end of the chain. It is shown that this combination, when used with an excitation in the form of a long-duration tone burst, encourages the generation of multiple impulses with a characteristic periodicity. This study shows that the properties of the chain structure and the excitation can be adjusted so as to generate ultrasonic solitary wave impulses with a high amplitude and known frequency content, which are of interest in applications such as biomedical ultrasound.

  3. Electromyographic and Force Plate Analysis of the Deadlift Performed With and Without Chains.

    PubMed

    Nijem, Ramsey M; Coburn, Jared W; Brown, Lee E; Lynn, Scott K; Ciccone, Anthony B

    2016-05-01

    The purpose of this study was to determine the effects of deadlift chain variable resistance on surface electromyography (EMG) of the gluteus maximus, erector spinae, and vastus lateralis muscles, ground reaction forces (GRFs), and rate of force development (RFD). Thirteen resistance-trained men (24.0 ± 2.1 years, 179.3 ± 4.8 cm, 87.0 ± 10.6 kg) volunteered for the study. On day 1, subjects performed 1 repetition maximum (1RM) testing of the deadlift exercise. On day 2, subjects performed one set of 3 repetitions with a load of 85% 1RM with chains (CH) and without chains (NC). The order of the CH and NC conditions was randomly determined for each subject. For the CH condition, the chains accounted for approximately 20% (19.9 ± 0.6%) of the 85% 1RM load, matched at the top of the lift. Surface EMG was recorded to differentiate muscle activity between conditions (CH, NC), range of motion (ROM; bottom, top), and phase (concentric, eccentric). Peak GRFs and RFD were measured using a force plate. Electromyography results revealed that for the gluteus maximus there was significantly greater EMG activity during the NC condition vs. the CH condition. For the erector spinae, EMG activity was greater at the bottom than the top ROM (p ≤ 0.05). Force plate results revealed that deadlifting at 85% 1RM with an accommodating chain resistance of approximately 20% results in a reduction in GRFs (p ≤ 0.05) and no change in RFD (p > 0.05). Collectively, these results suggest that the use of chain resistance during deadlifting can alter muscle activation and force characteristics of the lift. PMID:26840441

  4. Serum-free light-chain analysis in diagnosis and management of multiple myeloma and related conditions.

    PubMed

    Milani, Paolo; Palladini, Giovanni; Merlini, Giampaolo

    2016-01-01

    The introduction of the serum-free light-chain (S-FLC) assay has been a breakthrough in the diagnosis and management of plasma cell dyscrasias, particularly monoclonal light-chain diseases. The first method, proposed in 2001, quantifies serum-free light-chains using polyclonal antibodies. More recently, assays based on monoclonal antibodies have entered into clinical practice. S-FLC measurement plays a central role in the screening for multiple myeloma and related conditions, in association with electrophoretic techniques. Analysis of S-FLC is essential in assessing the risk of progression of precursor diseases to overt plasma cell dyscrasias. It is also useful for risk stratification in solitary plasmacytoma and AL amyloidosis. The S-FLC measurement is part of the new diagnostic criteria for multiple myeloma, and provides a marker to follow changes in clonal substructure over time. Finally, the evaluation of S-FLC is fundamental for assessing the response to treatment in monoclonal light chain diseases. PMID:27467897

  5. An Analysis on Distribution of Cooperative Profit in Supply Chain Based on Multi-Agent

    NASA Astrophysics Data System (ADS)

    Zhang, Yaofeng; Geng, Hilin

    The problem about the distribution of profit in supply chain cooperation has been widespreadly concerned in recent years. This paper formulates an evolutionary game model of the profit distribution in supply chain. Using the Multi-Agent Simulation technology, we analyze the influences of the profit distribution to the level of cooperation and average individual income. The results show that it's only the profit disribution coefficient in the vicinity of 0.5, the ratio of cooperation can keep relatively high level, and the changes of average individual income caused by cost-benefit ratio are smaller than by knowledge spillover revenue.

  6. Comparison of Bootstrapping and Markov Chain Monte Carlo for Copula Analysis of Hydrological Droughts

    NASA Astrophysics Data System (ADS)

    Yang, P.; Ng, T. L.; Yang, W.

    2015-12-01

    Effective water resources management depends on the reliable estimation of the uncertainty of drought events. Confidence intervals (CIs) are commonly applied to quantify this uncertainty. A CI seeks to be at the minimal length necessary to cover the true value of the estimated variable with the desired probability. In drought analysis where two or more variables (e.g., duration and severity) are often used to describe a drought, copulas have been found suitable for representing the joint probability behavior of these variables. However, the comprehensive assessment of the parameter uncertainties of copulas of droughts has been largely ignored, and the few studies that have recognized this issue have not explicitly compared the various methods to produce the best CIs. Thus, the objective of this study to compare the CIs generated using two widely applied uncertainty estimation methods, bootstrapping and Markov Chain Monte Carlo (MCMC). To achieve this objective, (1) the marginal distributions lognormal, Gamma, and Generalized Extreme Value, and the copula functions Clayton, Frank, and Plackett are selected to construct joint probability functions of two drought related variables. (2) The resulting joint functions are then fitted to 200 sets of simulated realizations of drought events with known distribution and extreme parameters and (3) from there, using bootstrapping and MCMC, CIs of the parameters are generated and compared. The effect of an informative prior on the CIs generated by MCMC is also evaluated. CIs are produced for different sample sizes (50, 100, and 200) of the simulated drought events for fitting the joint probability functions. Preliminary results assuming lognormal marginal distributions and the Clayton copula function suggest that for cases with small or medium sample sizes (~50-100), MCMC to be superior method if an informative prior exists. Where an informative prior is unavailable, for small sample sizes (~50), both bootstrapping and MCMC

  7. Purification, Characterization and Analysis of the Allergenic Properties of Myosin Light Chain in Procambarus clarkia.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Myosin light chain (MLC) plays a vital role in cell and muscle functions and has been identified as an allergen in close species. In this study, MLC with the molecular mass of 18kDa was purified from crayfish (Procambarus clarkii) muscle fibrils. Its physicochemical characterization showed that the...

  8. Understanding Latina and Latino College Choice: A Social Capital and Chain Migration Analysis

    ERIC Educational Resources Information Center

    Perez, Patricia A.; McDonough, Patricia M.

    2008-01-01

    Through interviews and focus groups with 106 high school juniors and seniors, this research examined the college choice process for Latina and Latino students in the greater Los Angeles basin. Using chain migration theory within a social capital framework, the results indicated that as primarily first-generation college students, the students in…

  9. Analysis of the Ketosynthase-Chain Length Factor Heterodimer from the Fredericamycin Polyketide Synthase

    PubMed Central

    Szu, Ping-Hui; Govindarajan, Sridhar; Meehan, Michael J.; Das, Abhirup; Nguyen, Don D.; Dorrestein, Pieter C.; Minshull, Jeremy; Khosla, Chaitan

    2011-01-01

    SUMMARY The pentadecaketide fredericamycin has the longest carbon chain backbone among polycyclic aromatic polyketide antibiotics whose biosynthetic genes have been sequenced. This backbone is synthesized by the bimodular fdm polyketide synthase (PKS). The initiation module is thought to synthesize a C6 intermediate that is then transferred onto the elongation PKS module, which extends it into a C30 poly-β-ketoacyl product. Here we demonstrate that the bimodular fdm PKS as well as its elongation module alone synthesize undecaketides and dodecaketides. Thus, unlike other homologues, the fdm ketosynthase – chain length factor (KS-CLF) heterodimer does not exclusively control the backbone length of its natural product. Using sequence- and structure-based approaches, 48 multiple mutants of the CLF were engineered and analyzed. Unexpectedly, the I134F mutant was unable to turn over, but could initiate and at least partially elongate the polyketide chain. This unprecedented mutant suggests that the KS-CLF heterodimer harbors an as yet uncharacterized chain termination mechanism. Together, our findings reveal fundamental mechanistic differences between the fdm PKS and its well-studied homologues. PMID:21867917

  10. Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire.

    PubMed

    de Wildt, R M; Hoet, R M; van Venrooij, W J; Tomlinson, I M; Winter, G

    1999-01-22

    In the bone marrow, diversity in the primary antibody repertoire is created by the combinatorial rearrangement of different gene segments and by the association of different heavy and light chains. During the secondary response in the germinal centres, antibodies are diversified by somatic mutation and possibly by further rearrangements, or "receptor editing". Here, we have analysed the pairings of heavy and light chain variable domains (VH and VL) in 365 human IgG+ B cells from peripheral blood, and established that these pairings are largely random. The repertoire is dominated by a limited number of pairings of segments and folds. Among these pairings we identified two identical mutated heavy chains in combination with two different mutated light chains (one kappa and one lambda). This shows that receptor editing occurs in the human periphery and that the same antibody lineage can be subjected to both receptor editing and somatic hypermutation. This suggests that receptor editing may be used together with somatic mutation for the affinity maturation of antibodies. We also propose that receptor editing has shaped variable gene segment use and the evolution of V gene families.

  11. Functional analysis and molecular docking identify two active short-chain prenyltransferases in the green peach aphid, Myzus persicae.

    PubMed

    Zhang, Yong-Lei; Li, Zheng-Xi

    2012-10-01

    Short-chain prenyltransferases are responsible for biosynthesis of the C(10)-C(20) precursors of a variety of isoprenoids. We previously isolated two different short-chain prenyltransferases from the green peach aphid, Myzus persicae (MpIPPS1 and MpIPPS2). In this study, the activity of the two aphid prenyltransferases was analyzed in vitro. Kinetic analysis using recombinant enzymes showed that both prenyltransferases could efficiently catalyze the formation of C(10) geranyl diphosphate (GPP) and C(15) farnesyl diphosphate (FPP) from the C(5) substrates isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), and MpIPPS2 had higher catalytic activity than MpIPPS1. Product analysis by gas chromatography-mass spectrometry demonstrated that FPP was generated as the major product, but GPP could be detected at low enzyme concentrations. Molecular docking revealed that MpIPPS2 had higher binding affinity with the substrates DMAPP, IPP, and GPP than MpIPPS1, which supported the experimentally determined kinetic parameters. Molecular docking also identified an amino acid residue (K266) critical to the catalytic activity of both MpIPPS1 and MpIPPS2. This prediction was subsequently confirmed by site-directed mutagenesis, in which a point mutation (K266I) abolished the activity of both MpIPPS1 and MpIPPS2. Our data illustrate that both aphid short-chain prenyltransferases are active forms, which is in contrast to the previously reported results.

  12. An integrated one-chip-sensor system for microRNA quantitative analysis based on digital droplet polymerase chain reaction

    NASA Astrophysics Data System (ADS)

    Tsukuda, Masahiko; Wiederkehr, Rodrigo Sergio; Cai, Qing; Majeed, Bivragh; Fiorini, Paolo; Stakenborg, Tim; Matsuno, Toshinobu

    2016-04-01

    A silicon microfluidic chip was developed for microRNA (miRNA) quantitative analysis. It performs sequentially reverse transcription and polymerase chain reaction in a digital droplet format. Individual processes take place on different cavities, and reagent and sample mixing is carried out on a chip, prior to entering each compartment. The droplets are generated on a T-junction channel before the polymerase chain reaction step. Also, a miniaturized fluorescence detector was developed, based on an optical pick-up head of digital versatile disc (DVD) and a micro-photomultiplier tube. The chip integrated in the detection system was tested using synthetic miRNA with known concentrations, ranging from 300 to 3,000 templates/µL. Results proved the functionality of the system.

  13. Purification, crystallization and preliminary X-ray crystallographic analysis of branched-chain aminotransferase from Deinococcus radiodurans

    SciTech Connect

    Chen, Chung-Der; Huang, Tien-Feng; Lin, Chih-Hao; Guan, Hong-Hsiang; Hsieh, Yin-Cheng; Lin, Yi-Hung; Huang, Yen-Chieh; Liu, Ming-Yih; Chang, Wen-Chang; Chen, Chun-Jung

    2007-06-01

    The crystallization of branched-chain aminotransferase from D. radiodurans is described. The branched-chain amino-acid aminotransferase (BCAT), which requires pyridoxal 5′-phosphate (PLP) as a cofactor, is a key enzyme in the biosynthetic pathway of the hydrophobic amino acids leucine, isoleucine and valine. DrBCAT from Deinococcus radiodurans, which has a molecular weight of 40.9 kDa, was crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction data to 2.50 Å resolution from a DrBCAT crystal, the crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 56.37, b = 90.70, c = 155.47 Å. Preliminary analysis indicates the presence of two DrBCAT molecules in the asymmetric unit, with a solvent content of 47.52%.

  14. From puffins to plankton: a DNA-based analysis of a seabird food chain in the northern Gulf of Maine.

    PubMed

    Bowser, A Kirsten; Diamond, Antony W; Addison, Jason A

    2013-01-01

    The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis. PMID:24358258

  15. From Puffins to Plankton: A DNA-Based Analysis of a Seabird Food Chain in the Northern Gulf of Maine

    PubMed Central

    Bowser, A. Kirsten; Diamond, Antony W.; Addison, Jason A.

    2013-01-01

    The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis. PMID:24358258

  16. From puffins to plankton: a DNA-based analysis of a seabird food chain in the northern Gulf of Maine.

    PubMed

    Bowser, A Kirsten; Diamond, Antony W; Addison, Jason A

    2013-01-01

    The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis.

  17. Probabilistic accident consequence uncertainty analysis: Food chain uncertainty assessment. Volume 2: Appendices

    SciTech Connect

    Brown, J.; Goossens, L.H.J.; Kraan, B.C.P.

    1997-06-01

    This volume is the second of a two-volume document that summarizes a joint project by the US Nuclear Regulatory and the Commission of European Communities to assess uncertainties in the MACCS and COSYMA probabilistic accident consequence codes. These codes were developed primarily for estimating the risks presented by nuclear reactors based on postulated frequencies and magnitudes of potential accidents. This two-volume report, which examines mechanisms and uncertainties of transfer through the food chain, is the first in a series of five such reports. A panel of sixteen experts was formed to compile credible and traceable uncertainty distributions for food chain transfer that affect calculations of offsite radiological consequences. Seven of the experts reported on transfer into the food chain through soil and plants, nine reported on transfer via food products from animals, and two reported on both. The expert judgment elicitation procedure and its outcomes are described in these volumes. This volume contains seven appendices. Appendix A presents a brief discussion of the MAACS and COSYMA model codes. Appendix B is the structure document and elicitation questionnaire for the expert panel on soils and plants. Appendix C presents the rationales and responses of each of the members of the soils and plants expert panel. Appendix D is the structure document and elicitation questionnaire for the expert panel on animal transfer. The rationales and responses of each of the experts on animal transfer are given in Appendix E. Brief biographies of the food chain expert panel members are provided in Appendix F. Aggregated results of expert responses are presented in graph format in Appendix G.

  18. Adaptive Markov chain Monte Carlo forward projection for statistical analysis in epidemic modelling of human papillomavirus.

    PubMed

    Korostil, Igor A; Peters, Gareth W; Cornebise, Julien; Regan, David G

    2013-05-20

    A Bayesian statistical model and estimation methodology based on forward projection adaptive Markov chain Monte Carlo is developed in order to perform the calibration of a high-dimensional nonlinear system of ordinary differential equations representing an epidemic model for human papillomavirus types 6 and 11 (HPV-6, HPV-11). The model is compartmental and involves stratification by age, gender and sexual-activity group. Developing this model and a means to calibrate it efficiently is relevant because HPV is a very multi-typed and common sexually transmitted infection with more than 100 types currently known. The two types studied in this paper, types 6 and 11, are causing about 90% of anogenital warts. We extend the development of a sexual mixing matrix on the basis of a formulation first suggested by Garnett and Anderson, frequently used to model sexually transmitted infections. In particular, we consider a stochastic mixing matrix framework that allows us to jointly estimate unknown attributes and parameters of the mixing matrix along with the parameters involved in the calibration of the HPV epidemic model. This matrix describes the sexual interactions between members of the population under study and relies on several quantities that are a priori unknown. The Bayesian model developed allows one to estimate jointly the HPV-6 and HPV-11 epidemic model parameters as well as unknown sexual mixing matrix parameters related to assortativity. Finally, we explore the ability of an extension to the class of adaptive Markov chain Monte Carlo algorithms to incorporate a forward projection strategy for the ordinary differential equation state trajectories. Efficient exploration of the Bayesian posterior distribution developed for the ordinary differential equation parameters provides a challenge for any Markov chain sampling methodology, hence the interest in adaptive Markov chain methods. We conclude with simulation studies on synthetic and recent actual data. PMID

  19. Applying commodity chain analysis to changing modes of alcohol supply in a developing country.

    PubMed

    Jernigan, D H

    2000-12-01

    Development sociology has used global commodity chains as one way of analyzing the dynamics of power and profit-taking in globalized production networks made up of multiple firms and occurring in multiple national settings. A substantial portion of the alcohol supply in developing countries is now produced through such production networks. Particularly in the beer and spirits trade, a small number of transnational firms control networks of local producers, importers, advertisers and distributors. These networks serve to embed transnational or transnationally backed brands in the local culture, using the tools of market research, product design and marketing to influence local drinking practices. Case materials from Malaysia's beer industry help to illustrate how the transnational firms dominate in those links of the commodity chain in which monopoly or oligopoly control is most likely to be found: the design/recipe and marketing/advertising nodes. Their control of the commodity chains and extraction of monopoly or oligopoly profits from them places substantial resources and influence over drinking settings and practices in foreign hands. The impact of this influence on state efficacy and autonomy in setting alcohol policy is an important subject for future research on the creation and implementation of effective alcohol policies in developing societies.

  20. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

    PubMed

    Kohda, Masakazu; Tokuzawa, Yoshimi; Kishita, Yoshihito; Nyuzuki, Hiromi; Moriyama, Yohsuke; Mizuno, Yosuke; Hirata, Tomoko; Yatsuka, Yukiko; Yamashita-Sugahara, Yzumi; Nakachi, Yutaka; Kato, Hidemasa; Okuda, Akihiko; Tamaru, Shunsuke; Borna, Nurun Nahar; Banshoya, Kengo; Aigaki, Toshiro; Sato-Miyata, Yukiko; Ohnuma, Kohei; Suzuki, Tsutomu; Nagao, Asuteka; Maehata, Hazuki; Matsuda, Fumihiko; Higasa, Koichiro; Nagasaki, Masao; Yasuda, Jun; Yamamoto, Masayuki; Fushimi, Takuya; Shimura, Masaru; Kaiho-Ichimoto, Keiko; Harashima, Hiroko; Yamazaki, Taro; Mori, Masato; Murayama, Kei; Ohtake, Akira; Okazaki, Yasushi

    2016-01-01

    Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder.

  1. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

    PubMed

    Kohda, Masakazu; Tokuzawa, Yoshimi; Kishita, Yoshihito; Nyuzuki, Hiromi; Moriyama, Yohsuke; Mizuno, Yosuke; Hirata, Tomoko; Yatsuka, Yukiko; Yamashita-Sugahara, Yzumi; Nakachi, Yutaka; Kato, Hidemasa; Okuda, Akihiko; Tamaru, Shunsuke; Borna, Nurun Nahar; Banshoya, Kengo; Aigaki, Toshiro; Sato-Miyata, Yukiko; Ohnuma, Kohei; Suzuki, Tsutomu; Nagao, Asuteka; Maehata, Hazuki; Matsuda, Fumihiko; Higasa, Koichiro; Nagasaki, Masao; Yasuda, Jun; Yamamoto, Masayuki; Fushimi, Takuya; Shimura, Masaru; Kaiho-Ichimoto, Keiko; Harashima, Hiroko; Yamazaki, Taro; Mori, Masato; Murayama, Kei; Ohtake, Akira; Okazaki, Yasushi

    2016-01-01

    Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder. PMID:26741492

  2. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies

    PubMed Central

    Nyuzuki, Hiromi; Moriyama, Yohsuke; Mizuno, Yosuke; Hirata, Tomoko; Yatsuka, Yukiko; Yamashita-Sugahara, Yzumi; Nakachi, Yutaka; Kato, Hidemasa; Okuda, Akihiko; Tamaru, Shunsuke; Borna, Nurun Nahar; Banshoya, Kengo; Aigaki, Toshiro; Sato-Miyata, Yukiko; Ohnuma, Kohei; Suzuki, Tsutomu; Nagao, Asuteka; Maehata, Hazuki; Matsuda, Fumihiko; Higasa, Koichiro; Nagasaki, Masao; Yasuda, Jun; Yamamoto, Masayuki; Fushimi, Takuya; Shimura, Masaru; Kaiho-Ichimoto, Keiko; Harashima, Hiroko; Yamazaki, Taro; Mori, Masato; Murayama, Kei; Ohtake, Akira; Okazaki, Yasushi

    2016-01-01

    Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder. PMID:26741492

  3. Real-time polymerase chain reaction for diagnosing infectious mononucleosis in pediatric patients: A systematic review and meta-analysis.

    PubMed

    Jiang, Sha-Yi; Yang, Jing-Wei; Shao, Jing-Bo; Liao, Xue-Lian; Lu, Zheng-Hua; Jiang, Hui

    2016-05-01

    In this meta-analysis, we evaluated the diagnostic role of Epstein-Barr virus deoxyribonucleic acid detection and quantitation in the serum of pediatric and young adult patients with infectious mononucleosis. The primary outcome of this meta-analysis was the sensitivity and specificity of Epstein-Barr virus (EBV) deoxyribonucleic acid (DNA) detection and quantitation using polymerase chain reaction (PCR). A systematic review and meta-analysis was performed by searching for articles that were published through September 24, 2014 in the following databases: Medline, Cochrane, EMBASE, and Google Scholar. The following keywords were used for the search: "Epstein-Barr virus," "infectious mononucleosis," "children/young adults/infant/pediatric," and "polymerase chain reaction or PCR." Three were included in this analysis. We found that for detection by PCR, the pooled sensitivity for detecting EBV DNA was 77% (95%CI, 66-86%) and the pooled specificity for was 98% (95%CI, 93-100%). Our findings indicate that this PCR-based assay has high specificity and good sensitivity for detecting of EBV DNA, indicating it may useful for identifying patients with infectious mononucleosis. This assay may also be helpful to identify young athletic patients or highly physically active pediatric patients who are at risk for a splenic rupture due to acute infectious mononucleosis.

  4. Designing Performance Measurement For Supply Chain's Actors And Regulator Using Scale Balanced Scorecard And Data Envelopment Analysis

    NASA Astrophysics Data System (ADS)

    Kusrini, Elisa; Subagyo; Aini Masruroh, Nur

    2016-01-01

    This research is a sequel of the author's earlier conducted researches in the fields of designing of integrated performance measurement between supply chain's actors and regulator. In the previous paper, the design of performance measurement is done by combining Balanced Scorecard - Supply Chain Operation Reference - Regulator Contribution model and Data Envelopment Analysis. This model referred as B-S-Rc-DEA model. The combination has the disadvantage that all the performance variables have the same weight. This paper investigates whether by giving weight to performance variables will produce more sensitive performance measurement in detecting performance improvement. Therefore, this paper discusses the development of the model B-S-Rc-DEA by giving weight to its performance'variables. This model referred as Scale B-S-Rc-DEA model. To illustrate the model of development, some samples from small medium enterprises of leather craft industry supply chain in province of Yogyakarta, Indonesia are used in this research. It is found that Scale B-S-Rc-DEA model is more sensitive to detecting performance improvement than B-S- Rc-DEA model.

  5. Mitigation of ammonia, nitrous oxide and methane emissions from manure management chains: a meta-analysis and integrated assessment.

    PubMed

    Hou, Yong; Velthof, Gerard L; Oenema, Oene

    2015-03-01

    Livestock manure contributes considerably to global emissions of ammonia (NH3 ) and greenhouse gases (GHG), especially methane (CH4 ) and nitrous oxide (N2 O). Various measures have been developed to mitigate these emissions, but most of these focus on one specific gas and/or emission source. Here, we present a meta-analysis and integrated assessment of the effects of mitigation measures on NH3 , CH4 and (direct and indirect) N2 O emissions from the whole manure management chain. We analysed the effects of mitigation technologies on NH3 , CH4 and N2 O emissions from individual sources statistically using results of 126 published studies. Whole-chain effects on NH3 and GHG emissions were assessed through scenario analysis. Significant NH3 reduction efficiencies were observed for (i) housing via lowering the dietary crude protein (CP) content (24-65%, compared to the reference situation), for (ii) external slurry storages via acidification (83%) and covers of straw (78%) or artificial films (98%), for (iii) solid manure storages via compaction and covering (61%, compared to composting), and for (iv) manure application through band spreading (55%, compared to surface application), incorporation (70%) and injection (80%). Acidification decreased CH4 emissions from stored slurry by 87%. Significant increases in N2 O emissions were found for straw-covered slurry storages (by two orders of magnitude) and manure injection (by 26-199%). These side-effects of straw covers and slurry injection on N2 O emission were relatively small when considering the total GHG emissions from the manure chain. Lowering the CP content of feed and acidifying slurry are strategies that consistently reduce NH3 and GHG emissions in the whole chain. Other strategies may reduce emissions of a specific gas or emissions source, by which there is a risk of unwanted trade-offs in the manure management chain. Proper farm-scale combinations of mitigation measures are important to minimize impacts of

  6. Mitigation of ammonia, nitrous oxide and methane emissions from manure management chains: a meta-analysis and integrated assessment.

    PubMed

    Hou, Yong; Velthof, Gerard L; Oenema, Oene

    2015-03-01

    Livestock manure contributes considerably to global emissions of ammonia (NH3 ) and greenhouse gases (GHG), especially methane (CH4 ) and nitrous oxide (N2 O). Various measures have been developed to mitigate these emissions, but most of these focus on one specific gas and/or emission source. Here, we present a meta-analysis and integrated assessment of the effects of mitigation measures on NH3 , CH4 and (direct and indirect) N2 O emissions from the whole manure management chain. We analysed the effects of mitigation technologies on NH3 , CH4 and N2 O emissions from individual sources statistically using results of 126 published studies. Whole-chain effects on NH3 and GHG emissions were assessed through scenario analysis. Significant NH3 reduction efficiencies were observed for (i) housing via lowering the dietary crude protein (CP) content (24-65%, compared to the reference situation), for (ii) external slurry storages via acidification (83%) and covers of straw (78%) or artificial films (98%), for (iii) solid manure storages via compaction and covering (61%, compared to composting), and for (iv) manure application through band spreading (55%, compared to surface application), incorporation (70%) and injection (80%). Acidification decreased CH4 emissions from stored slurry by 87%. Significant increases in N2 O emissions were found for straw-covered slurry storages (by two orders of magnitude) and manure injection (by 26-199%). These side-effects of straw covers and slurry injection on N2 O emission were relatively small when considering the total GHG emissions from the manure chain. Lowering the CP content of feed and acidifying slurry are strategies that consistently reduce NH3 and GHG emissions in the whole chain. Other strategies may reduce emissions of a specific gas or emissions source, by which there is a risk of unwanted trade-offs in the manure management chain. Proper farm-scale combinations of mitigation measures are important to minimize impacts of

  7. Anaerobic Fe(III) reduction by Shewanella putrefaciens: Analysis of the electron transport chain

    SciTech Connect

    Daad Saffarini

    2004-01-20

    The goals of the project were to isolate mutants that are deficient in metal reduction, identify components of the electron transport chain that are involved in this process, and purify some of these proteins for biochemical analyses. In the 3-year period since the start of the project, we have accomplished many of these goals. We have isolated several new S. oneidensis mutants that are deficient in metal reduction, and have initiated the development of vectors for the overexpression of cytochromes and other proteins in S. oneidensis. We have also overexpressed CymA, one of the c cytochromes that are involved in metal reduction.

  8. Markov chain Monte Carlo methods for statistical analysis of RF photonic devices.

    PubMed

    Piels, Molly; Zibar, Darko

    2016-02-01

    The microwave reflection coefficient is commonly used to characterize the impedance of high-speed optoelectronic devices. Error and uncertainty in equivalent circuit parameters measured using this data are systematically evaluated. The commonly used nonlinear least-squares method for estimating uncertainty is shown to give unsatisfactory and incorrect results due to the nonlinear relationship between the circuit parameters and the measured data. Markov chain Monte Carlo methods are shown to provide superior results, both for individual devices and for assessing within-die variation. PMID:26906783

  9. Stability and bifurcation analysis on a three-species food chain system with two delays

    NASA Astrophysics Data System (ADS)

    Cui, Guo-Hu; Yan, Xiang-Ping

    2011-09-01

    The present paper deals with a three-species Lotka-Volterra food chain system with two discrete delays. By linearizing the system at the positive equilibrium and analyzing the associated characteristic equation, the asymptotic stability of the positive equilibrium and existence of local Hopf bifurcations are investigated. Furthermore, by using the normal form theory and the center manifold reduction, explicit formulae are derived to determine the direction of bifurcations and the stability of bifurcating periodic solutions. Finally, to verify our theoretical predictions, some numerical simulations are also included at the end of this paper.

  10. Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data

    PubMed Central

    Sieh, Weiva; Basu, Saonli; Fu, Audrey Q; Rothstein, Joseph H; Scheet, Paul A; Stewart, William CL; Sung, Yun J; Thompson, Elizabeth A; Wijsman, Ellen M

    2005-01-01

    We performed multipoint linkage analysis of the electrophysiological trait ECB21 on chromosome 4 in the full pedigrees provided by the Collaborative Study on the Genetics of Alcoholism (COGA). Three Markov chain Monte Carlo (MCMC)-based approaches were applied to the provided and re-estimated genetic maps and to five different marker panels consisting of microsatellite (STRP) and/or SNP markers at various densities. We found evidence of linkage near the GABRB1 STRP using all methods, maps, and marker panels. Difficulties encountered with SNP panels included convergence problems and demanding computations. PMID:16451566

  11. Ionic polymer cluster energetics: Computational analysis of pendant chain stiffness and charge imbalance

    NASA Astrophysics Data System (ADS)

    Weiland, Lisa Mauck; Leo, Donald J.

    2005-06-01

    In recent years there has been considerable study of the potential mechanisms underlying the electromechanical response of ionic-polymer-metal composites. The most recent models have been based on the response of the ion-containing clusters that are formed when the material is synthesized. Most of these efforts have employed assumptions of uniform ion distribution within spherical cluster shapes. This work investigates the impact of dispensing with these assumptions in order to better understand the parameters that impact cluster shape, size, and ion transport potential. A computational micromechanics model applying Monte Carlo methodology is employed to predict the equilibrium state of a single cluster of a solvated ionomeric polymer. For a constant solvated state, the model tracks the position of individual ions within a given cluster in response to ion-ion interaction, mechanical stiffness of the pendant chain, cluster surface energy, and external electric-field loading. Results suggest that cluster surface effects play a significant role in the equilibrium cluster state, including ion distribution; pendant chain stiffness also plays a role in ion distribution but to a lesser extent. Moreover, ion pairing is rarely complete even in cation-rich clusters; this in turn supports the supposition of the formation of anode and cathode boundary layers.

  12. Vaccine instability in the cold chain: mechanisms, analysis and formulation strategies.

    PubMed

    Kumru, Ozan S; Joshi, Sangeeta B; Smith, Dawn E; Middaugh, C Russell; Prusik, Ted; Volkin, David B

    2014-09-01

    Instability of vaccines often emerges as a key challenge during clinical development (lab to clinic) as well as commercial distribution (factory to patient). To yield stable, efficacious vaccine dosage forms for human use, successful formulation strategies must address a combination of interrelated topics including stabilization of antigens, selection of appropriate adjuvants, and development of stability-indicating analytical methods. This review covers key concepts in understanding the causes and mechanisms of vaccine instability including (1) the complex and delicate nature of antigen structures (e.g., viruses, proteins, carbohydrates, protein-carbohydrate conjugates, etc.), (2) use of adjuvants to further enhance immune responses, (3) development of physicochemical and biological assays to assess vaccine integrity and potency, and (4) stabilization strategies to protect vaccine antigens and adjuvants (and their interactions) during storage. Despite these challenges, vaccines can usually be sufficiently stabilized for use as medicines through a combination of formulation approaches combined with maintenance of an efficient cold chain (manufacturing, distribution, storage and administration). Several illustrative case studies are described regarding mechanisms of vaccine instability along with formulation approaches for stabilization within the vaccine cold chain. These include live, attenuated (measles, polio) and inactivated (influenza, polio) viral vaccines as well as recombinant protein (hepatitis B) vaccines.

  13. Cockroach fauna in the Ogasawara Chain Islands of Japan and analysis of their habitats.

    PubMed

    Komatsu, Noriyuki; Kishimoto, Toshio; Uchida, Akihiko; Ooi, Hong-Kean

    2013-03-01

    A survey of cockroach fauna was carried out on the 3 inhabited islands of the Ogasawara chain island of Japan, namely, Chichijima island, Hahajima island and Iwo island. Seven species, namely, Periplaneta americana (Linnaeus, 1758), Periplaneta australasiae (Fabricius, 1775), Blattella lituricollis (Walker, 1868), Onychostylus vilis (Brunner von Wattenwyl, 1865), Supella longipalpa (Fabricius, 1798), Pycnoscelus surinamensis (Linnaeus, 1758) and Opisthoplatia orientalis (Burmeister, 1838), were collected on Chichijima island. Four species, namely, P. americana, P. australasiae, O. vilis and P. surinamensis were collected on Hahajima island and 6 species, namely, P. americana, P. australasiae, B. lituricollis, O. vilis, P. surinamensis and Neostylopyga rhombifolia were collected on Iwo island. This is the first record of N. rhombifolia and Onychostylus orientalis on the Ogasawara chain islands. Our study increases the recorded taxon of cockroaches on the Ogasawara from 3 families, 5 genera 10 species to 4 families, 7 genera, 12 species. A list of the cockroach species on Ogasawara islands reported to date as well as a key for their identification is also presented. Periplaneta americana and P. australasiae, being the dominant species, together with S. longipalpa, were collected mostly in the indoor environment, indicating their preference for this habitat. Pycnoscelus surinamensis, which is considered as an outdoor insect has been found in semi-household environments such as greenhouse and shed, indicating their new adaptation to the changing environment.

  14. Analysis of Information on Food Chain in Europe and Piedmont Region, Italy

    PubMed Central

    Pattono, Daniele; Bertolina, Barbara; Chiesa, Francesco; Civera, Tiziana

    2014-01-01

    Food chain information (FCI) is an innovation of the new European regulation. Its purpose is to enhance the concept of food security. FCI includes specifications such as: health status, information on treatments and diseases, analytical reports on control plans, zoonoses or environmental contaminants, production performance, etc. The aim of this article is to compare the different European guidelines and analyse the situation in Piedmont in order to assess potential problems and propose solutions. European guidelines are similar one another, but they have been tailored to the epidemiological situations of each state. Except for Spain and Germany, FCI models are different for each species and the poultry sector is the most detailed. Unfortunately, Italy has not provided guidelines yet, and this has generated considerable differences. Overall, the number of FCI models with incomplete information is the largest group compared to the models not completed for each entry. The main deficiencies are related to pharmacological treatments. The health status of the farm is listed consistently regarding the compulsory eradication plans, but other national voluntary or accreditation plans are rarely mentioned. The situation is similar in other European countries. In conclusion, FCI is an effective tool if applied with consistency and reason. Only in this way the collection of data will be effective and representative of the food chain. PMID:27800357

  15. Falling chains

    NASA Astrophysics Data System (ADS)

    Wong, Chun Wa; Yasui, Kosuke

    2006-06-01

    The one-dimensional fall of a folded chain with one end suspended from a rigid support and a chain falling from a resting heap on a table is studied. Because their Lagrangians contain no explicit time dependence, the falling chains are conservative systems. Their equations of motion are shown to contain a term that enforces energy conservation when masses are transferred between subchains. We show that Cayley's 1857 energy nonconserving solution for a chain falling from a resting heap is incorrect because it neglects the energy gained when a link leaves a subchain. The maximum chain tension measured by Calkin and March for the falling folded chain is given a simple if rough interpretation. Other aspects of the falling folded chain are briefly discussed.

  16. Quantitative analysis of the free energy coupling in the system calmodulin, calcium, smooth muscle myosin light chain kinase.

    PubMed

    Mamar-Bachi, A; Cox, J A

    1987-12-01

    Interactions between Ca2+, calmodulin and turkey gizzard myosin light chain kinase have been studied by equilibrium gel filtration and analyzed in terms of the theory of free energy coupling as formulated by Huang and King for calmodulin-regulated systems (Current Topics in Cellular Regulation 27, 1966-1971, 1985). Direct binding studies revealed that upon interaction with the enzyme, calmodulin acquires strong positive cooperativity in Ca2+-binding. The determination of the Ca2+-binding constants is inherently approximative due to the apparent homotropic cooperativity; therefore a statistical chi 2 analysis was carried out to delimit the formation-, and subsequently the stoichiometric Ca2+-binding constants. Whereas the first two stoichiometric Ca2+-binding constants of enzyme-bound CaM do not differ or are at the upmost 10-fold higher than those in free calmodulin, the third Ca2+ ion binds with an at least 70-fold and more likely 3000-fold higher affinity constant. The binding constant for the fourth Ca2+ is only 5-fold higher than the corresponding one in free calmodulin, thus creating a plateau at 3 bound Ca2+ in the isotherm. Direct binding of Ca2+-free calmodulin to myosin light chain kinase at 10(-7) M free Ca2+ yielded a l/l stoichiometry and an affinity constant of 2.2 x 10(5) M-1. It is thus anticipated that in resting smooth muscle ([Ca2+] less than or equal to 10(-7) M) more than half of the enzyme is bound to metal-free calmodulin. Analysis of the enzymatic activation of myosin light chain kinase at different concentrations of calmodulin and Ca2+ revealed that this Ca2+-free complex is inactive and that activation is concomitant with the formation of the enzyme.calmodulin.Ca3 complex.

  17. Genomic Analysis of Genes Involved in the Biosynthesis of Very Long Chain Polyunsaturated Fatty Acids in Thraustochytrium sp. 26185.

    PubMed

    Zhao, Xianming; Dauenpen, Meesapyodsuk; Qu, Cunmin; Qiu, Xiao

    2016-09-01

    Thraustochytrium sp. 26185 is a marine protist that can produce a large amount of docosahexaenoic acid (DHA, 22:6n-3), an ω3 very long chain polyunsaturated fatty acid (VLCPUFA) of nutritional importance. However, the mechanism of how this fatty acid is synthesized and assembled into the storage lipid triacylglycerol is unclear. Here we report sequencing of the whole genome and genomic analysis of genes involved in the biosynthesis and assembly of the fatty acids in this species. Genome sequencing produced a total of 2,418,734,139 bp clean sequences with about 62 fold genome coverage. Annotation of the genome sequences revealed 10,797 coding genes. Among them, 10,216 genes could be assigned into 25 KOG classes where 451 genes were specifically assigned to the group of lipid transport and metabolism. Detailed analysis of these genes revealed co-existence of both aerobic pathway and anaerobic pathways for the biosynthesis of DHA in this species. However, in the aerobic pathway, a key gene encoding stearate Δ9 desaturase introducing the first double bond to long chain saturated fatty acid 18:0 was missing from the genome. Genomic survey of genes involved in the acyl trafficking among glycerolipids showed that, unlike plants, this protist did not possess phosphatidylcholine:diacylglycerol cholinephosphotransferase, an important enzyme in bridging two types of glycerolipids, diacylglycerols (DAG) and phosphatidylcholines (PtdCho). These results shed new insight on the biosynthesis and assembly of VLCPUFA in the Thraustochytrium. PMID:27514858

  18. Supply Chain Vulnerability Analysis Using Scenario-Based Input-Output Modeling: Application to Port Operations.

    PubMed

    Thekdi, Shital A; Santos, Joost R

    2016-05-01

    Disruptive events such as natural disasters, loss or reduction of resources, work stoppages, and emergent conditions have potential to propagate economic losses across trade networks. In particular, disruptions to the operation of container port activity can be detrimental for international trade and commerce. Risk assessment should anticipate the impact of port operation disruptions with consideration of how priorities change due to uncertain scenarios and guide investments that are effective and feasible for implementation. Priorities for protective measures and continuity of operations planning must consider the economic impact of such disruptions across a variety of scenarios. This article introduces new performance metrics to characterize resiliency in interdependency modeling and also integrates scenario-based methods to measure economic sensitivity to sudden-onset disruptions. The methods will be demonstrated on a U.S. port responsible for handling $36.1 billion of cargo annually. The methods will be useful to port management, private industry supply chain planning, and transportation infrastructure management. PMID:26271771

  19. Simulation analysis of formycin 5'-monophosphate analog substrates in the ricin A-chain active site.

    PubMed

    Olson, M A; Scovill, J P; Hack, D C

    1995-06-01

    Ricin is an RNA N-glycosidase that hydrolyzes a single adenine base from a conserved loop of 28S ribosomal RNA, thus inactivating protein synthesis. Molecular-dynamics simulation methods are used to analyze the structural interactions and thermodynamics that govern the binding of formycin 5'-monophosphate (FMP) and several of its analogs to the active site of ricin A-chain. Simulations are carried out initiated from the X-ray crystal structure of the ricin-FMP complex with the ligand modeled as a dianion, monoanion and zwitterion. Relative changes in binding free energies are estimated for FMP analogs constructed from amino substitutions at the 2- and 2'-positions, and from hydroxyl substitution at the 2'-position.

  20. DNA fragment length polymorphism analysis of Mycobacterium tuberculosis isolates by arbitrarily primed polymerase chain reaction.

    PubMed

    Palittapongarnpim, P; Chomyc, S; Fanning, A; Kunimoto, D

    1993-04-01

    Strain identification of Mycobacterium tuberculosis would prove whether transmission had occurred between individuals. A method to characterize strains of M. tuberculosis has been developed utilizing polymerase chain reaction (PCR). Purified chromosomal DNA of cultured clinical samples of M. tuberculosis were subjected to PCR using short (10-12 nucleotide) oligonucleotide primers. PCR products visualized after agarose gel electrophoresis and ethidium bromide staining demonstrated that different strains of M. tuberculosis give different banding patterns. This technique was used to confirm the relationship between cases of tuberculosis in several clusters, prove the lack of relationship between 2 isolates with the same antibiotic-resistance pattern, confirm a suspected mislabeling event, and suggest the source of infection in a case of tuberculous meningitis. This method is rapid and simple and does not require radioactive probes.

  1. A methodology for stochastic analysis of share prices as Markov chains with finite states.

    PubMed

    Mettle, Felix Okoe; Quaye, Enoch Nii Boi; Laryea, Ravenhill Adjetey

    2014-01-01

    Price volatilities make stock investments risky, leaving investors in critical position when uncertain decision is made. To improve investor evaluation confidence on exchange markets, while not using time series methodology, we specify equity price change as a stochastic process assumed to possess Markov dependency with respective state transition probabilities matrices following the identified state pace (i.e. decrease, stable or increase). We established that identified states communicate, and that the chains are aperiodic and ergodic thus possessing limiting distributions. We developed a methodology for determining expected mean return time for stock price increases and also establish criteria for improving investment decision based on highest transition probabilities, lowest mean return time and highest limiting distributions. We further developed an R algorithm for running the methodology introduced. The established methodology is applied to selected equities from Ghana Stock Exchange weekly trading data. PMID:25520904

  2. Analysis of a stochastic tri-trophic food-chain model with harvesting.

    PubMed

    Liu, Meng; Bai, Chuanzhi

    2016-09-01

    We consider a tri-trophic stochastic food-chain model with harvesting. We first establish critical values between persistence in mean and extinction for each species. The results show that persistence and extinction of a species only depends on the demographic impacts of environmental stochasticity on the species and species at lower tropic levels; however, the mean abundance of a species depends on the impacts of environmental stochasticity at all trophic levels. Then we consider stability in distribution of the model. Finally, we provide a necessary and sufficient condition for existence of optimal harvesting strategy and give the optimal harvesting effort and maximum of sustainable yield. The results show that the optimal harvesting strategy is closely related to the stochastic noises in the model.

  3. Supply Chain Vulnerability Analysis Using Scenario-Based Input-Output Modeling: Application to Port Operations.

    PubMed

    Thekdi, Shital A; Santos, Joost R

    2016-05-01

    Disruptive events such as natural disasters, loss or reduction of resources, work stoppages, and emergent conditions have potential to propagate economic losses across trade networks. In particular, disruptions to the operation of container port activity can be detrimental for international trade and commerce. Risk assessment should anticipate the impact of port operation disruptions with consideration of how priorities change due to uncertain scenarios and guide investments that are effective and feasible for implementation. Priorities for protective measures and continuity of operations planning must consider the economic impact of such disruptions across a variety of scenarios. This article introduces new performance metrics to characterize resiliency in interdependency modeling and also integrates scenario-based methods to measure economic sensitivity to sudden-onset disruptions. The methods will be demonstrated on a U.S. port responsible for handling $36.1 billion of cargo annually. The methods will be useful to port management, private industry supply chain planning, and transportation infrastructure management.

  4. Electro-optical and pyroelectrical thermal analysis of novel nonlinear optical side-chain polymers with high thermal stability

    NASA Astrophysics Data System (ADS)

    Gerhard-Multhaupt, Reimund; Bauer, Stefan; Molzow, Wolf-Dietrich; Ren, W.; Wirges, Werner; Yilmaz, S.; Oertel, U.; Haenel, B.; Haeussler, L.; Komber, H.; Lunkwitz, K.

    1994-01-01

    Polymers containing nonlinear optical moieties were prepared on the basis of maleic anhydride copolymers. Azo dyes such as Disperse Red 1 (DR 1) were attached to the polymer backbones via esterification, amidization, or imidization. Optimal poling conditions for the side-chain polymers were determined by means of thermal analysis. After electrode poling with a bias voltage of 200 V at a temperature of 185 degree(s)C, the spin-coated samples were slowly cooled down to room temperature with the poling field still applied. The thermal stabilities of the poled polymer films were measured by means of electro-optical (EOTA) and pyro- electrical (PTA) thermal analysis and compared to the respective responses of DR 1/polymethylmethacrylate (PMMA) guest/host polymer samples. Both experimental techniques (EOTA and PTA) are discussed in some detail together with the experimental results.

  5. Extraction of DNA from exfoliative cytology specimens and its suitability for analysis by the polymerase chain reaction.

    PubMed

    Jackson, D P; Payne, J; Bell, S; Lewis, F A; Taylor, G R; Peel, K R; Sutton, J; Quirke, P

    1990-01-01

    The extraction of DNA from archival exfoliative cytology samples would allow the molecular biological analysis of this readily available material using the polymerase chain reaction (PCR). We have quantitatively and qualitatively studied the extraction of DNA from a variety of cytological preparations. For both fresh and archival cervical smears, overnight incubation with proteinase K produces high yields of high molecular weight DNA, but simply boiling the samples produces DNA suitable for PCR amplification of a single copy gene. Increasing the proteinase K incubation to several days allows the extraction of DNA from fixed and stained archival cytology slides from a variety of sites. The extracted DNA was again suitable for PCR analysis. Fresh and archival cytological material can be utilized for molecular biological study of disease processes using PCR. Archival cytological material is probably the best source of DNA and RNA after stored frozen tissue.

  6. New insights into the properties and interactions of carbon chains as revealed by HRTEM and DFT analysis

    PubMed Central

    Casillas, Gilberto; Mayoral, Alvaro; Liu, Mingjie; Ponce, Arturo; Artyukhov, Vasilii I.; Yakobson, Boris I.; Jose-Yacaman, Miguel

    2013-01-01

    Atomic carbon chains have raised interest for their possible applications as graphene interconnectors as the thinnest nanowires; however, they are hard to synthesize and subsequently to study. We present here a reproducible method to synthesize carbon chains in situ TEM. Moreover, we present a direct observation of the bond length alternation in a pure carbon chain by aberration corrected TEM. Also, cross bonding between two carbon chains, 5 nm long, is observed experimentally and confirmed by DFT calculations. Finally, while free standing carbon chains were observed to be straight due to tensile loading, a carbon chain inside the walls of a carbon nanotube showed high flexibility. PMID:24363453

  7. Ethanol distribution, dispensing, and use: analysis of a portion of the biomass-to-biofuels supply chain using system dynamics.

    PubMed

    Vimmerstedt, Laura J; Bush, Brian; Peterson, Steve

    2012-01-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain-represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner's decision whether to offer ethanol fuel and a consumer's choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  8. Ethanol distribution, dispensing, and use: analysis of a portion of the biomass-to-biofuels supply chain using system dynamics.

    PubMed

    Vimmerstedt, Laura J; Bush, Brian; Peterson, Steve

    2012-01-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain-represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner's decision whether to offer ethanol fuel and a consumer's choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  9. Markov chains and entropy tests in genetic-based lithofacies analysis of deep-water clastic depositional systems

    NASA Astrophysics Data System (ADS)

    Borka, Szabolcs

    2016-01-01

    The aim of this study was to examine the relationship between structural elements and the so-called genetic lithofacies in a clastic deep-water depositional system. Process-sedimentology has recently been gaining importance in the characterization of these systems. This way the recognized facies attributes can be associated with the depositional processes establishing the genetic lithofacies. In this paper this approach was presented through a case study of a Tertiary deep-water sequence of the Pannonian-basin. Of course it was necessary to interpret the stratigraphy of the sequences in terms of "general" sedimentology, focusing on the structural elements. For this purpose, well-logs and standard deep-water models were applied. The cyclicity of sedimentary sequences can be easily revealed by using Markov chains. Though Markov chain analysis has broad application in mainly fluvial depositional environments, its utilization is uncommon in deep-water systems. In this context genetic lithofacies was determined and analysed by embedded Markov chains. The randomness in the presence of a lithofacies within a cycle was estimated by entropy tests (entropy after depositional, before depositional, for the whole system). Subsequently the relationships between lithofacies were revealed and a depositional model (i.e. modal cycle) was produced with 90% confidence level of stationarity. The non-randomness of the latter was tested by chi-square test. The consequences coming from the comparison of "general" sequences (composed of architectural elements), the genetic-based sequences (showing the distributions of the genetic lithofacies) and the lithofacies relationships were discussed in details. This way main depositional channel has the best, channelized lobes have good potential hydrocarbon reservoir attributes, with symmetric alternation of persistent fine-grained sandstone (Facies D) and muddy fine-grained sandstone with traction structures (Facies F)

  10. Ethanol Distribution, Dispensing, and Use: Analysis of a Portion of the Biomass-to-Biofuels Supply Chain Using System Dynamics

    SciTech Connect

    Vimmerstedt, L. J.; Bush, B.; Peterson, S.

    2012-05-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain-represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner's decision whether to offer ethanol fuel and a consumer's choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  11. Molecular characterization and expression analysis of four isotypes of immunoglobulin light chain genes in orange-spotted grouper, Epinephelus coioides.

    PubMed

    Wu, Ming-Shan; Cheng, Chao-An; Lin, Chih-Hung; Lee, Chiou-Yueh; Tseng, Shih-Jou; Tzeng, Chyng-Shyan; Chang, Chi-Yao

    2013-03-01

    To date, many immunoglobulin (Ig) genes have been identified in diverse teleost species, but the contributions of different types of light chain (IgL) to the immune response remain unclear. Screening of a stimulated kidney cDNA library from orange-spotted grouper (Osg, Epinephelus coioides) resulted in the identification of 26 full Ig light chain (OsgIgL) coding sequences. These 26 OsgIgLs encoded peptides from 235 to 248 amino acid residues and could be grouped into five variable (V(L)) and four constant (C(L)) isotypes. The C(L) regions contained three conserved cysteine residues that may participate in intra- or inter-chain disulfide bond formation. The four C(L) isotypes could be sub-grouped into two serological types: κ (C(L)-I, C(L)-II and C(L)-III) and σ (C(L)-IV), by phylogenetic analysis. The OsgIgL genes were found to be expressed in various tissues, with greatest levels of expression observed in the head-kidney and spleen. The major expression type was C(L)-I, which comprised 92% and 91% of total OsgIgL gene expression in the head-kidney and spleen, respectively. Transcription of all four C(L) isotypes was differentially affected in response to various immunostimulators, including lipopolysaccharide (LPS), poly I:C and grouper iridovirus (GIV). Induction of OsgIgL genes in response to immunostimulators was particularly dramatic in the spleen, suggesting this organ holds particular importance for the regulation of OsgIgL expression. Furthermore, vaccination of grouper with formalin-inactivated GIV also induced differential patterns of expression in all four OsgIgL isotypes. In summary, the significant and diverse patterns of transcriptional induction observed for OsgIgL isotypes in the spleen and head-kidney imply that each isotype may have unique roles in the immune response.

  12. Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics

    PubMed Central

    Tewari, Shivendra G.; Zhou, Yifan; Otto, Bradley J.; Dash, Ranjan K.; Kwok, Wai-Meng; Beard, Daniel A.

    2015-01-01

    The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance. PMID:25628567

  13. Sequence analysis of the myosin regulatory light chain gene of the vestimentiferan Riftia pachyptila.

    PubMed

    Ravaux, J; Hassanin, A; Deutsch, J; Gaill, F; Markmann-Mulisch, U

    2001-01-24

    We have isolated and characterized a cDNA (DNA complementary to RNA) clone (Rf69) from the vestimentiferan Riftia pachyptila. The cDNA insert consists of 1169 base pairs. The aminoacid sequence deduced from the longest reading frame is 193 residues in length, and clearly characterized it as a myosin regulatory light chain (RLC). The RLC primary structure is described in relation to its function in muscle contraction. The comparison with other RLCs suggested that Riftia myosin is probably regulated through its RLC either by phosphorylation like the vertebrate smooth muscle myosins, and/or by Ca2+-binding like the mollusk myosins. Riftia RLC possesses a N-terminal extension lacking in all other species besides the earthworm Lumbricus terrestris. Aminoacid sequence comparisons with a number of RLCs from vertebrates and invertebrates revealed a relatively high identity score (64%) between Riftia RLC and the homologous gene from Lumbricus. The relationships between the members of the myosin RLCs were examined by two phylogenetic methods, i.e. distance matrix and maximum parsimony. The resulting trees depict the grouping of the RLCs according to their role in myosin activity regulation. In all trees, Riftia RLC groups with RLCs that depend on Ca2+-binding for myosin activity regulation. PMID:11223252

  14. Medium chain triglycerides for treatment of spontaneous, neonatal chylothorax. Lipid analysis of the chyle.

    PubMed

    Peitersen, B; Jacobsen, B

    1977-01-01

    Volume and contents of lipid and protein in the pleural fluid from a three weeks old girl with spontaneous chylothorax were studied (a) during parenteral, nonfatty nutrition and later (b) during administration of a formula (Biosorbin) containing medium chain triglycerides (MCT). The pleural fluid production could not be correlated to the treatment employed but suddenly ceased after 20 days management. Triglyceride and total esterified fatty acid concentrations in pleural fluid were high on admission when feeded with human milk, and chylomicrons and other lipoproteins were present in the chyle. During parenteral treatment a pronounced decrease in pleural fluid concentrations of triglyceride and total fatty acids occurred concomitant with a disappearance of the chylomicrons. During the following MCT diet a pronounced increase in triglyceride and total fatty acids concentrations appeared and the chylomicrons reappeared in the chyle. The cholesterol and phospholipid concentrations in the pleural fluid showed only small changes during the different treatments. No significant changes in protein and albumin concentrations of chyle were observed. It is concluded, that administration of the Biosorbin MCT formula, containing 871/2% of the fat as MCT, seems without value ih the treatment of spontaneous, neonatal chylothorax.

  15. Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics.

    PubMed

    Tewari, Shivendra G; Zhou, Yifan; Otto, Bradley J; Dash, Ranjan K; Kwok, Wai-Meng; Beard, Daniel A

    2014-01-01

    The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance. PMID:25628567

  16. Polymerase chain reaction-based analysis to detect terrestrial animal protein in fish meal.

    PubMed

    Bellagamba, Federica; Valfrè, Franco; Panseri, Sara; Moretti, Vittorio M

    2003-04-01

    The recent European bovine spongiform encephalopathy crisis has focused attention on the importance of adopting stringent control measures to avoid the risk of the diffusion of mad cow disease through meat meal-based animal feedstuffs. Potential adulteration of such feedstuffs with bone particles from terrestrial animals is determined by microscopic examination by law before the release of these feedstuffs for free circulation in the European Community. This study describes a DNA monitoring method to examine fish meal for contamination with mammalian and poultry products. A polymerase chain reaction (PCR) method based on the nucleotide sequence variation in the 12S ribosomal RNA gene of mitochondrial DNA was developed and evaluated. Three species-specific primer pairs were designed for the identification of ruminant, pig, and poultry DNA. The specificity of the primers used in the PCR was tested by comparison with DNA samples for several vertebrate species and confirmed. The PCR specifically detected mammalian and poultry adulteration in fish meals containing 0.125% beef, 0.125% sheep, 0.125% pig, 0.125% chicken, and 0.5% goat. A multiplex PCR assay for ruminant and pig adulteration was optimized and had a detection limit of 0.25%. PMID:12696697

  17. Quantitative analysis of periodontal pathogens by ELISA and real-time polymerase chain reaction.

    PubMed

    Hamlet, Stephen M

    2010-01-01

    The development of analytical methods enabling the accurate identification and enumeration of bacterial species colonizing the oral cavity has led to the identification of a small number of bacterial pathogens that are major factors in the etiology of periodontal disease. Further, these methods also underpin more recent epidemiological analyses of the impact of periodontal disease on general health. Given the complex milieu of over 700 species of microorganisms known to exist within the complex biofilms found in the oral cavity, the identification and enumeration of oral periodontopathogens has not been an easy task. In recent years however, some of the intrinsic limitations of the more traditional microbiological analyses previously used have been overcome with the advent of immunological and molecular analytical methods. Of the plethora of methodologies reported in the literature, the enzyme-linked immunosorbent assay (ELISA), which combines the specificity of antibody with the sensitivity of simple enzyme assays and the polymerase chain reaction (PCR), has been widely utilized in both laboratory and clinical applications. Although conventional PCR does not allow quantitation of the target organism, real-time PCR (rtPCR) has the ability to detect amplicons as they accumulate in "real time" allowing subsequent quantitation. These methods enable the accurate quantitation of as few as 10(2) (using rtPCR) to 10(4) (using ELISA) periodontopathogens in dental plaque samples.

  18. From cysteine to longer chain thiols: thermodynamic analysis of cadmium binding by phytochelatins and their fragments.

    PubMed

    Chekmeneva, Elena; Gusmão, Rui; Díaz-Cruz, José Manuel; Ariño, Cristina; Esteban, Miquel

    2011-08-01

    Isothermal Titration Calorimetry (ITC) was used to study the binding of Cd(2+) by phytochelatins ((γGlu-Cys)(n)-Gly, PC(n); n = 1-5) and their selected fragments (Cys, Cys-Gly and γGlu-Cys) in order to understand the influence of the chain length on the complex stabilities and the origin of the enhanced affinities in Tris buffer at pH 7.5 and 8.5 and at 25 °C. Different complexes are formed with glutathione (GSH) and its fragments, Cys, Cys-Gly and γGlu-Cys, and their stabilities depend on the corresponding pK(a) value of the thiol group in the ligands. The stability of Cd-PC(n) complexes increases moving towards higher PC(2-5), as well as the complexing capacity expressed as the number of metal ions that can be bound by one ligand molecule. The affinity of Cd(2+) for the PC(n) can be described by the following GSH < PC(2) < PC(3)≤ PC(4)≤ PC(5) sequence. On the basis of these thermodynamic data it is possible to explain the abundance of certain Cd-PC(n) complexes found in nature. The comprehension of the thermodynamic rules that govern the interactions of Cd(2+) with PC(n) and their constituents is of great service in the research with real plant samples subjected to metal stress and in the development of new strategies of bio/phytoremediation.

  19. Analysis of adult otitis media: polymerase chain reaction versus culture for bacteria and viruses.

    PubMed

    Liederman, E M; Post, J C; Aul, J J; Sirko, D A; White, G J; Buchman, C A; Ehrlich, G D

    1998-01-01

    Recent studies using the polymerase chain reaction (PCR) have identified bacterial and viral genomic sequences in culture-negative pediatric middle ear effusions. To evaluate this technique in adults, 19 effusions were analyzed to compare bacterial and viral culture and PCR detection of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and adenovirus. Effusions from 4 subjects positive for human immunodeficiency virus (HIV) were analyzed by PCR for HIV virus. Three of 19 effusions were culture-positive for bacteria, and 0 of 19 for viruses. Fifteen of 19 effusions were PCR-positive for bacterial genomic sequences, and 0 of 19 for adenovirus. Thirteen of 15 PCR-positive specimens demonstrated S pneumoniae, 5 of 15 H influenzae, and 0 of 13 M catarrhalis. All 4 effusions from HIV-positive subjects were PCR-positive for HIV. No effusion was culture-positive and PCR-negative. These results confirm that culture-negative middle ear effusions contain genomic sequences from bacterial pathogens. Finding of HIV RNA and DNA in effusion from HIV-positives suggests replicating virus in this fluid.

  20. Probabilistic accident consequence uncertainty analysis: Food chain uncertainty assessment. Volume 1: Main report

    SciTech Connect

    Brown, J.; Goossens, L.H.J.; Kraan, B.C.P.

    1997-06-01

    This volume is the first of a two-volume document that summarizes a joint project conducted by the US Nuclear Regulatory Commission and the European Commission to assess uncertainties in the MACCS and COSYMA probabilistic accident consequence codes. These codes were developed primarily for estimating the risks presented by nuclear reactors based on postulated frequencies and magnitudes of potential accidents. This document reports on an ongoing project to assess uncertainty in the MACCS and COSYMA calculations for the offsite consequences of radionuclide releases by hypothetical nuclear power plant accidents. A panel of sixteen experts was formed to compile credible and traceable uncertainty distributions for food chain variables that affect calculations of offsite consequences. The expert judgment elicitation procedure and its outcomes are described in these volumes. Other panels were formed to consider uncertainty in other aspects of the codes. Their results are described in companion reports. Volume 1 contains background information and a complete description of the joint consequence uncertainty study. Volume 2 contains appendices that include (1) a summary of the MACCS and COSYMA consequence codes, (2) the elicitation questionnaires and case structures for both panels, (3) the rationales and results for the panels on soil and plant transfer and animal transfer, (4) short biographies of the experts, and (5) the aggregated results of their responses.

  1. Trends and advances in food analysis by real-time polymerase chain reaction.

    PubMed

    Salihah, Nur Thaqifah; Hossain, Mohammad Mosharraf; Lubis, Hamadah; Ahmed, Minhaz Uddin

    2016-05-01

    Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling.

  2. Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences.

    PubMed

    Schbath, S; Prum, B; de Turckheim, E

    1995-01-01

    Identifying exceptional motifs is often used for extracting information from long DNA sequences. The two difficulties of the method are the choice of the model that defines the expected frequencies of words and the approximation of the variance of the difference T(W) between the number of occurrences of a word W and its estimation. We consider here different Markov chain models, either with stationary or periodic transition probabilities. We estimate the variance of the difference T(W) by the conditional variance of the number of occurrences of W given the oligonucleotides counts that define the model. Two applications show how to use asymptotically standard normal statistics associated with the counts to describe a given sequence in terms of its outlying words. Sequences of Escherichia coli and of Bacillus subtilis are compared with respect to their exceptional tri- and tetranucleotides. For both bacteria, exceptional 3-words are mainly found in the coding frame. E. coli palindrome counts are analyzed in different models, showing that many overabundant words are one-letter mutations of avoided palindromes. PMID:8521272

  3. Trends and advances in food analysis by real-time polymerase chain reaction.

    PubMed

    Salihah, Nur Thaqifah; Hossain, Mohammad Mosharraf; Lubis, Hamadah; Ahmed, Minhaz Uddin

    2016-05-01

    Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling. PMID:27407185

  4. Event-specific qualitative and quantitative polymerase chain reaction analysis for genetically modified canola T45.

    PubMed

    Yang, Litao; Pan, Aihu; Zhang, Haibo; Guo, Jinchao; Yin, Changsong; Zhang, Dabing

    2006-12-27

    Polymerase chain reaction (PCR) methods have been the main technical support for the detection of genetically modified organisms (GMOs). To date, GMO-specific PCR detection strategies have been developed basically at four different levels, such as screening-, gene-, construct-, and event-specific detection methods. Event-specific PCR detection method is the primary trend in GMO detection because of its high specificity based on the flanking sequence of exogenous integrant. GM canola, event T45, with tolerance to glufosinate ammonium is one of the commercial genetically modified (GM) canola events approved in China. In this study, the 5'-integration junction sequence between host plant DNA and the integrated gene construct of T45 canola was cloned and revealed by means of TAIL-PCR. Specific PCR primers and TaqMan probes were designed based upon the revealed sequence, and qualitative and quantitative TaqMan real-time PCR detection assays employing these primers and probe were developed. In qualitative PCR, the limit of detection (LOD) was 0.1% for T45 canola in 100 ng of genomic DNA. The quantitative PCR assay showed limits of detection and quantification (LOD and LOQ) of 5 and 50 haploid genome copies, respectively. In addition, three mixed canola samples with known GM contents were detected employing the developed real-time PCR assay, and expected results were obtained. These results indicated that the developed event-specific PCR methods can be used for identification and quantification of T45 canola and its derivates.

  5. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis

    PubMed Central

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela

    2015-01-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. PMID:26590278

  6. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    PubMed

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2015-11-20

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments.

  7. Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinonnii E5202H

    PubMed Central

    Shaw, Jeffery J; Spakowicz, Daniel J; Dalal, Rahul S; Davis, Jared H; Lehr, Nina A; Dunican, Brian F; Orellana, Esteban A; Narváez-Trujillo, Alexandra; Strobel, Scott A

    2015-01-01

    An endophytic fungus was isolated that produces a series of volatile natural products, including terpenes and odd chain polyenes. Phylogenetic analysis of the isolate using five loci suggests that it is closely related to Nigrograna mackinnonii CBS 674.75. The main component of the polyene series was purified and identified as (3E,5E,7E)-nona-1,3,5,7-tetraene (NTE), a novel natural product. Non-oxygenated hydrocarbons of this chain length are uncommon and desirable as gasoline-surrogate biofuels. The biosynthetic pathway for NTE production was explored using metabolic labeling and GCMS. Two-carbon incorporation 13C acetate suggests that it is derived from a polyketide synthase (PKS) followed by decarboxylation. There are several known mechanisms for such decarboxylation, though none have been discovered in fungi. Towards identifying the PKS responsible for the production of NTE, the genome of N. mackinnonii E5202H (ATCC SD-6839) was sequenced and assembled. Of the 32 PKSs present in the genome, 17 are predicted to contain sufficient domains for the production of NTE. These results exemplify the capacity of endophytic fungi to produce novel natural products that may have many uses, such as biologically derived fuels and commodity chemicals. PMID:25672844

  8. Analysis of Factors that Affect Responding in a Two-Response Chain in Children with Developmental Disabilities

    ERIC Educational Resources Information Center

    Contrucci Kuhn, Stephanie A.; Lerman, Dorothea C.; Vorndran, Christina M.; Addison, Laura

    2006-01-01

    A sequence of behaviors consisting of appropriate responses, inappropriate responses, or a combination of both can be linked together in a behavior chain. Several operant processes may disrupt behavior chains. For example, one or more members of the behavior chain may be affected when reinforcement is withheld for the last response in the chain…

  9. The Belgian PCB/dioxin incident: analysis of the food chain contamination and health risk evaluation.

    PubMed

    Bernard, Alfred; Broeckaert, Fabrice; De Poorter, Geert; De Cock, Ann; Hermans, Cédric; Saegerman, Claude; Houins, Gilbert

    2002-01-01

    The Belgian PCB incident occurred at the end of January 1999 when a mixture of polychlorinated biphenyls (PCBs) contaminated with dioxins was accidentally added to a stock of recycled fat used in the production of animal feeds. Although signs of poultry poisoning were noticed by February, 1999, the source and the extent of the contamination were discovered only in May 1999, when it appeared that more than 2500 farms could have been supplied with contaminated feeds. This resulted in a major food crisis, which rapidly extended to the whole country and could be resolved only by the implementation of a large PCB/dioxin food monitoring program. Screening for PCB contamination was based on the determination of the seven PCB markers. When PCB concentrations exceeded the tolerance levels of 0.1 (milk), 0.2 (poultry, bovine, and pig meat), or 1 (animal feed) microg/g fat, dioxins (17 PCDD/Fs congeners) were also determined. At the end of December 1999, the database contained the results of more than 55,000 PCB and 500 dioxin analyses. The study of PCB levels and profiles in contaminated feeds delivered to poultry or pig farms confirmed that the Belgian PCB incident was due to a single source of PCB oil introduced into the food chain at the end of January 1999. This PCB oil had a congeners pattern closely matched to a mixture of Aroclor 1260/1254 in the proportion 75/25. The total amount of PCBs added to recycled fats was estimated at 50 kg (sum of the seven markers) or approximately 150 kg total PCBs, which corresponds to about 100 liters of PCB oil. This PCB mixture contained about 1g TEQ dioxins (more than 90- contributed by PCDFs) and about 2g TEQ dioxin-like PCBs. The proportions of PCB 52 and 101 congeners were fairly constant in animal feeds, excluding the possibility of secondary contamination due to fat recycling from contaminated animals. The highest concentrations of PCBs and dioxins were found in poultry and especially in the reproduction animals (hens and chicks

  10. Epistasis Test in Meta-Analysis: A Multi-Parameter Markov Chain Monte Carlo Model for Consistency of Evidence.

    PubMed

    Lin, Chin; Chu, Chi-Ming; Su, Sui-Lung

    2016-01-01

    Conventional genome-wide association studies (GWAS) have been proven to be a successful strategy for identifying genetic variants associated with complex human traits. However, there is still a large heritability gap between GWAS and transitional family studies. The "missing heritability" has been suggested to be due to lack of studies focused on epistasis, also called gene-gene interactions, because individual trials have often had insufficient sample size. Meta-analysis is a common method for increasing statistical power. However, sufficient detailed information is difficult to obtain. A previous study employed a meta-regression-based method to detect epistasis, but it faced the challenge of inconsistent estimates. Here, we describe a Markov chain Monte Carlo-based method, called "Epistasis Test in Meta-Analysis" (ETMA), which uses genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data and tested the power and type I error rates in ETMA, individual data analysis and conventional meta-regression-based method. ETMA not only successfully facilitated consistency of evidence but also yielded acceptable type I error and higher power than conventional meta-regression. We applied ETMA to three real meta-analysis data sets. We found significant gene-gene interactions in the renin-angiotensin system and the polycyclic aromatic hydrocarbon metabolism pathway, with strong supporting evidence. In addition, glutathione S-transferase (GST) mu 1 and theta 1 were confirmed to exert independent effects on cancer. We concluded that the application of ETMA to real meta-analysis data was successful. Finally, we developed an R package, etma, for the detection of epistasis in meta-analysis [etma is available via the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/etma/index.html]. PMID:27045371

  11. Epistasis Test in Meta-Analysis: A Multi-Parameter Markov Chain Monte Carlo Model for Consistency of Evidence.

    PubMed

    Lin, Chin; Chu, Chi-Ming; Su, Sui-Lung

    2016-01-01

    Conventional genome-wide association studies (GWAS) have been proven to be a successful strategy for identifying genetic variants associated with complex human traits. However, there is still a large heritability gap between GWAS and transitional family studies. The "missing heritability" has been suggested to be due to lack of studies focused on epistasis, also called gene-gene interactions, because individual trials have often had insufficient sample size. Meta-analysis is a common method for increasing statistical power. However, sufficient detailed information is difficult to obtain. A previous study employed a meta-regression-based method to detect epistasis, but it faced the challenge of inconsistent estimates. Here, we describe a Markov chain Monte Carlo-based method, called "Epistasis Test in Meta-Analysis" (ETMA), which uses genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data and tested the power and type I error rates in ETMA, individual data analysis and conventional meta-regression-based method. ETMA not only successfully facilitated consistency of evidence but also yielded acceptable type I error and higher power than conventional meta-regression. We applied ETMA to three real meta-analysis data sets. We found significant gene-gene interactions in the renin-angiotensin system and the polycyclic aromatic hydrocarbon metabolism pathway, with strong supporting evidence. In addition, glutathione S-transferase (GST) mu 1 and theta 1 were confirmed to exert independent effects on cancer. We concluded that the application of ETMA to real meta-analysis data was successful. Finally, we developed an R package, etma, for the detection of epistasis in meta-analysis [etma is available via the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/etma/index.html].

  12. Robustness and sensitivity analysis of a virtual process chain using the S-rail specimen applying random fields

    NASA Astrophysics Data System (ADS)

    Konrad, T.; Wolff, S.; Wiegand, K.; Merklein, M.

    2016-08-01

    An important part in robustness evaluation of production processes is the identification of shape deviations. A systematic approach is typically based on the numerical evaluation of a DoE and the application of metamodels. They provide knowledge on solver noise and sensitivities of individual model parameters. This article presents the sensitivity analysis workflow of a linked deep drawing and joining process chain. LS-DYNA®, optiSLang and SoS is used. The challenge is to separate simulative from process and material parameters of AA 6014. Spatial quantities like variations in geometry, thinning and strain have to be considered in the next process steps. At the same time the number of required virtual CAE model evaluations must be limited. The solution is based on nonlinear metamodels and random fields.

  13. Detection of Mycobacterium tuberculosis with nested polymerase chain reaction analysis in enucleated eye ball in Eales' disease.

    PubMed

    Verma, Aditya; Biswas, Jyotirmay; Dhanurekha, L; Gayathri, R; Lily Therese, K

    2016-06-01

    Nested polymerase chain reaction (nPCR) was performed on enucleated eyeball for detection of Mycobacterium tuberculosis (M. tb) genome in a patient with Eales' disease. PCR analysis in all previous studies has been done mainly using aqueous, vitreous and epiretinal membranes from these patients. Paraffin wax embedded tissue section of the enucleated eyeball was analyzed by histopathology and nPCR targeting MPB64 gene and IS6110 region of M. tb genome. Lymphocytic infiltration was seen in the vitreous, iris and the retinal tissue. Ziehl Neelsen stain was negative for acid fast bacilli. Caseation necrosis was not seen in any section. Agarose gel electrophoretogram showed positive results with 200 bp specific amplified product targeting MPB64 gene, whereas nPCR targeting IS6110 region was negative. Since biopsy proven M. tb is extremely difficult in ocular tissues due to extensive necrosis, the nPCR technique aided in the diagnosis.

  14. Detection of Mycobacterium tuberculosis with nested polymerase chain reaction analysis in enucleated eye ball in Eales' disease.

    PubMed

    Verma, Aditya; Biswas, Jyotirmay; Dhanurekha, L; Gayathri, R; Lily Therese, K

    2016-06-01

    Nested polymerase chain reaction (nPCR) was performed on enucleated eyeball for detection of Mycobacterium tuberculosis (M. tb) genome in a patient with Eales' disease. PCR analysis in all previous studies has been done mainly using aqueous, vitreous and epiretinal membranes from these patients. Paraffin wax embedded tissue section of the enucleated eyeball was analyzed by histopathology and nPCR targeting MPB64 gene and IS6110 region of M. tb genome. Lymphocytic infiltration was seen in the vitreous, iris and the retinal tissue. Ziehl Neelsen stain was negative for acid fast bacilli. Caseation necrosis was not seen in any section. Agarose gel electrophoretogram showed positive results with 200 bp specific amplified product targeting MPB64 gene, whereas nPCR targeting IS6110 region was negative. Since biopsy proven M. tb is extremely difficult in ocular tissues due to extensive necrosis, the nPCR technique aided in the diagnosis. PMID:26499903

  15. A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses.

    PubMed

    Wilkinson, M; Thorley, J L; Upchurch, P

    2000-12-01

    In decay analyses the support for a particular split in most-parsimonious trees is its decay index, that is, the extra steps required of the shortest trees that do not include the split. By focusing solely on the support for splits, traditional decay analysis may provide an incomplete and potentially misleading summary of the support for phylogenetic relationships common to the most-parsimonious tree or trees. Here, we introduce double decay analysis, a new approach to assessing support for phylogenetic relationships. Double decay analysis is the determination of the decay indices of all n-taxon statements/partitions common to the most-parsimonious tree. The results of double decay analyses are presented in a partition table, but various approaches to graphical representation of the results, including the use of reduced consensus support trees, are also discussed. Double decay analysis provides a more comprehensive summary and facilitates a better understanding of the strengths and weaknesses of complex phylogenetic hypotheses than does traditional decay analysis. The limitations of traditional decay analyses and the utility of double decay analyses are illustrated with both contrived data and real data for sauropod dinosaurs.

  16. Assessment of parameter uncertainty in hydrological model using a Markov-Chain-Monte-Carlo-based multilevel-factorial-analysis method

    NASA Astrophysics Data System (ADS)

    Zhang, Junlong; Li, Yongping; Huang, Guohe; Chen, Xi; Bao, Anming

    2016-07-01

    Without a realistic assessment of parameter uncertainty, decision makers may encounter difficulties in accurately describing hydrologic processes and assessing relationships between model parameters and watershed characteristics. In this study, a Markov-Chain-Monte-Carlo-based multilevel-factorial-analysis (MCMC-MFA) method is developed, which can not only generate samples of parameters from a well constructed Markov chain and assess parameter uncertainties with straightforward Bayesian inference, but also investigate the individual and interactive effects of multiple parameters on model output through measuring the specific variations of hydrological responses. A case study is conducted for addressing parameter uncertainties in the Kaidu watershed of northwest China. Effects of multiple parameters and their interactions are quantitatively investigated using the MCMC-MFA with a three-level factorial experiment (totally 81 runs). A variance-based sensitivity analysis method is used to validate the results of parameters' effects. Results disclose that (i) soil conservation service runoff curve number for moisture condition II (CN2) and fraction of snow volume corresponding to 50% snow cover (SNO50COV) are the most significant factors to hydrological responses, implying that infiltration-excess overland flow and snow water equivalent represent important water input to the hydrological system of the Kaidu watershed; (ii) saturate hydraulic conductivity (SOL_K) and soil evaporation compensation factor (ESCO) have obvious effects on hydrological responses; this implies that the processes of percolation and evaporation would impact hydrological process in this watershed; (iii) the interactions of ESCO and SNO50COV as well as CN2 and SNO50COV have an obvious effect, implying that snow cover can impact the generation of runoff on land surface and the extraction of soil evaporative demand in lower soil layers. These findings can help enhance the hydrological model

  17. Comparative functional analysis of human medium-chain dehydrogenases, short-chain dehydrogenases/reductases and aldo-keto reductases with retinoids

    PubMed Central

    Gallego, Oriol; Belyaeva, Olga V.; Porté, Sergio; Ruiz, F. Xavier; Stetsenko, Anton V.; Shabrova, Elena V.; Kostereva, Natalia V.; Farrés, Jaume; Parés, Xavier; Kedishvili, Natalia Y.

    2006-01-01

    Retinoic acid biosynthesis in vertebrates occurs in two consecutive steps: the oxidation of retinol to retinaldehyde followed by the oxidation of retinaldehyde to retinoic acid. Enzymes of the MDR (medium-chain dehydrogenase/reductase), SDR (short-chain dehydrogenase/reductase) and AKR (aldo-keto reductase) superfamilies have been reported to catalyse the conversion between retinol and retinaldehyde. Estimation of the relative contribution of enzymes of each type was difficult since kinetics were performed with different methodologies, but SDRs would supposedly play a major role because of their low Km values, and because they were found to be active with retinol bound to CRBPI (cellular retinol binding protein type I). In the present study we employed detergent-free assays and HPLC-based methodology to characterize side-by-side the retinoid-converting activities of human MDR [ADH (alcohol dehydrogenase) 1B2 and ADH4), SDR (RoDH (retinol dehydrogenase)-4 and RDH11] and AKR (AKR1B1 and AKR1B10) enzymes. Our results demonstrate that none of the enzymes, including the SDR members, are active with CRBPI-bound retinoids, which questions the previously suggested role of CRBPI as a retinol supplier in the retinoic acid synthesis pathway. The members of all three superfamilies exhibit similar and low Km values for retinoids (0.12–1.1 μM), whilst they strongly differ in their kcat values, which range from 0.35 min−1 for AKR1B1 to 302 min−1 for ADH4. ADHs appear to be more effective retinol dehydrogenases than SDRs because of their higher kcat values, whereas RDH11 and AKR1B10 are efficient retinaldehyde reductases. Cell culture studies support a role for RoDH-4 as a retinol dehydrogenase and for AKR1B1 as a retinaldehyde reductase in vivo. PMID:16787387

  18. Common Threads in Behavior Checklists, Task Analysis, Prompting, Operations Training, and Chaining Research.

    ERIC Educational Resources Information Center

    Walls, Richard T.

    The paper reviews studies on performance objectives, task analysis, and prompting and instruction sequences as they relate to the education of handicapped students. The initial section, on performance objectives, reviews the development of the Vocational Behavior Checklist and the Subsequent Independent Living Behavior Checklist. The next step in…

  19. Epistasis Test in Meta-Analysis: A Multi-Parameter Markov Chain Monte Carlo Model for Consistency of Evidence

    PubMed Central

    Lin, Chin; Chu, Chi-Ming; Su, Sui-Lung

    2016-01-01

    Conventional genome-wide association studies (GWAS) have been proven to be a successful strategy for identifying genetic variants associated with complex human traits. However, there is still a large heritability gap between GWAS and transitional family studies. The “missing heritability” has been suggested to be due to lack of studies focused on epistasis, also called gene–gene interactions, because individual trials have often had insufficient sample size. Meta-analysis is a common method for increasing statistical power. However, sufficient detailed information is difficult to obtain. A previous study employed a meta-regression-based method to detect epistasis, but it faced the challenge of inconsistent estimates. Here, we describe a Markov chain Monte Carlo-based method, called “Epistasis Test in Meta-Analysis” (ETMA), which uses genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data and tested the power and type I error rates in ETMA, individual data analysis and conventional meta-regression-based method. ETMA not only successfully facilitated consistency of evidence but also yielded acceptable type I error and higher power than conventional meta-regression. We applied ETMA to three real meta-analysis data sets. We found significant gene–gene interactions in the renin–angiotensin system and the polycyclic aromatic hydrocarbon metabolism pathway, with strong supporting evidence. In addition, glutathione S-transferase (GST) mu 1 and theta 1 were confirmed to exert independent effects on cancer. We concluded that the application of ETMA to real meta-analysis data was successful. Finally, we developed an R package, etma, for the detection of epistasis in meta-analysis [etma is available via the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/etma/index.html]. PMID:27045371

  20. Meta-Analysis of Long-Chain Omega-3 Polyunsaturated Fatty Acids (LCω-3PUFA) and Prostate Cancer

    PubMed Central

    Alexander, Dominik D.; Bassett, Julie K.; Weed, Douglas L.; Barrett, Erin Cernkovich; Watson, Heather; Harris, William

    2015-01-01

    We conducted a systematic review and meta-analysis to estimate the potential association between LCω-3PUFAs and prostate cancer (PC). A comprehensive literature search was performed through 2013 to identify prospective studies that examined dietary intakes of long-chain omega-3 polyunsaturated fatty acids (LCω-3PUFA) or blood biomarkers of LCω-3PUFA status and risk of PC. Random-effects meta-analyses were conducted to generate summary relative risk estimates (SRREs) for LCω-3PUFAs and total PC, and by stage and grade. Subgroup analyses were also conducted for specific fatty acids and other study characteristics. Twelve self-reported dietary intake and 9 biomarker studies from independent study populations were included in the analysis, with 446,243 and 14,897 total participants, respectively. No association between LCω-3PUFAs and total PC was observed (SRRE = 1.00, 95% CI: 0.93–1.09) for the dietary intake studies (high vs. low LCω-3PUFAs category comparison) or for the biomarker studies (SRRE of 1.07, 95% CI: 0.94–1.20). In general, most summary associations for the dietary intake studies were in the inverse direction, whereas the majority of summary associations for the biomarker studies were in the positive direction, but all were weak in magnitude. The results from this meta-analysis do not support an association between LCω-3PUFAs and PC. PMID:25826711

  1. Semi-quantitative digital analysis of polymerase chain reaction-electrophoresis gel: Potential applications in low-income veterinary laboratories

    PubMed Central

    Antiabong, John F.; Ngoepe, Mafora G.; Abechi, Adakole S.

    2016-01-01

    Aim: The interpretation of conventional polymerase chain reaction (PCR) assay results is often limited to either positive or negative (non-detectable). The more robust quantitative PCR (qPCR) method is mostly reserved for quantitation studies and not a readily accessible technology in laboratories across developing nations. The aim of this study was to evaluate a semi-quantitative method for conventional PCR amplicons using digital image analysis of electrophoretic gel. The potential applications are also discussed. Materials and Methods: This study describes standard conditions for the digital image analysis of PCR amplicons using the freely available ImageJ software and confirmed using the qPCR assay. Results and Conclusion: Comparison of ImageJ analysis of PCR-electrophoresis gel and qPCR methods showed similar trends in the Fusobacterium necrophorum DNA concentration associated with healthy and periodontal disease infected wallabies (p≤0.03). Based on these empirical data, this study adds descriptive attributes (“more” or “less”) to the interpretation of conventional PCR results. The potential applications in low-income veterinary laboratories are suggested, and guidelines for the adoption of the method are also highlighted. PMID:27733792

  2. Statistical models for the analysis and design of digital polymerase chain (dPCR) experiments

    USGS Publications Warehouse

    Dorazio, Robert; Hunter, Margaret

    2015-01-01

    Statistical methods for the analysis and design of experiments using digital PCR (dPCR) have received only limited attention and have been misused in many instances. To address this issue and to provide a more general approach to the analysis of dPCR data, we describe a class of statistical models for the analysis and design of experiments that require quantification of nucleic acids. These models are mathematically equivalent to generalized linear models of binomial responses that include a complementary, log–log link function and an offset that is dependent on the dPCR partition volume. These models are both versatile and easy to fit using conventional statistical software. Covariates can be used to specify different sources of variation in nucleic acid concentration, and a model’s parameters can be used to quantify the effects of these covariates. For purposes of illustration, we analyzed dPCR data from different types of experiments, including serial dilution, evaluation of copy number variation, and quantification of gene expression. We also showed how these models can be used to help design dPCR experiments, as in selection of sample sizes needed to achieve desired levels of precision in estimates of nucleic acid concentration or to detect differences in concentration among treatments with prescribed levels of statistical power.

  3. Molecular cloning and expression analysis of immunoglobulin M heavy chain gene of blunt snout bream (Megalobrama amblycephala).

    PubMed

    Xia, Hu; Wu, Kang; Liu, Wanjing; Gul, Yasmeen; Wang, Weimin; Zhang, Xuezhen

    2014-09-01

    Immunoglobulins (Igs), which bind antigens with high specificity, are essential molecules in adaptive immune system of jawed vertebrates. In this study, cDNA encoding the secreted form of the immunoglobulin heavy chain of IgM (sIgM) was cloned from the mesonephros of blunt snout bream (Megalabrama amblycephala) using RT-PCR and rapid amplification of cDNA ends (RACE). The full-length cDNA of sIgM heavy chain gene has 1961 nucleotides encoding a putative protein of 569 amino acids, constant region shares high amino acid identity with that of Ctenopharyngodon idella (80%), Carassius auratus langsdorfii (65%) and Danio rerio (59%). Multiple protein sequence alignment revealed that blunt snout bream sIgM was clustered with the homologues of cyprinid fish and constructed one clade. Using quantitative real-time PCR (qRT-PCR) analysis, the level of sIgM mRNA was determined, with a V-shape change pattern: decreased initially from unfertilized egg stage to 4 cells stage and increased from 16 cells stage to prelarva. This sharp drop indicates that sIgM mRNA is maternally transferred, and was continuously degraded until 16 cells stage. The drastic rising in sIgM level from blastula stage to prelarva might be attributed to embryonic stem cell differentiation procedure. Compared with juvenile fish, the expression of sIgM was significantly higher in pronephros, liver, spleen, gill and muscle of adult fish. After the injection of Aeromonas hydrophila, the expression pattern of sIgM was found first down-regulated at 4 h, then up-regulated and reached the peak at 7 d and 21 d in mesonephros, spleen, liver and gill, respectively. PMID:24979225

  4. Ethanol Distribution, Dispensing, and Use: Analysis of a Portion of the Biomass-to-Biofuels Supply Chain Using System Dynamics

    PubMed Central

    Vimmerstedt, Laura J.; Bush, Brian; Peterson, Steve

    2012-01-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain–represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner’s decision whether to offer ethanol fuel and a consumer’s choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  5. Immunoglobulin heavy/light chain analysis enhances the detection of residual disease and monitoring of multiple myeloma patients

    PubMed Central

    Batinić, Josip; Perić, Zinaida; Šegulja, Dragana; Last, James; Prijić, Sanja; Dubravčić, Klara; Volarić, Lidija; Sertić, Dubravka; Radman, Ivo; Bašić-Kinda, Sandra; Matišić, Danica; Batinić, Drago; Labar, Boris; Nemet, Damir

    2015-01-01

    Aim To evaluate the clinical utility of incorporating a novel heavy/light chain immunoassay (HLC) into the existing methods for the assessment of multiple myeloma (MM) patients. Methods Convenience sera samples from 90 previously treated IgG and IgA MM patients in different disease stages were analyzed. The study was conducted in Clinical Hospital Center Zagreb between 2011 and 2013. The collected sera were analyzed by standard laboratory techniques (serum protein electrophoresis, quantification of total immunoglobulins, serum immunofixation, serum free light chain [FLC] assay) and HLC assay. Results HLC ratios outside the normal range were found in 58 of 90 patients, including 28 out of 61 patients with total immunoglobulin measurements within the normal range and 5 out of 23 patients in complete response. Both elevated HLC isotype level and abnormal HLC ratio correlated with the parameters of tumor burden, including percentage of plasma cells in the bone marrow (P < 0.001 and P = 0.002, respectively) and an abnormal serum FLC ratio (for both P < 0.001). In addition, abnormal HLC isotype level correlated with serum beta-2-microglobulin level (P = 0.038). In terms of prognosis, abnormal HLC isotype level and abnormal HLC ratio were significantly associated with shorter overall survival (P < 0.001 and P = 0.002, respectively). Interestingly, suppression of the uninvolved (polyclonal) isotype pair, but not other non-myeloma immunoglobulin isotypes, was also associated with a shorter overall survival (P = 0.021). In a multivariate analysis, an abnormal HLC ratio and β2-microglobulin level >3.5mg/L were independent risk factors for survival. Conclusion The new HLC assay has greater sensitivity in detecting monoclonal protein, correlates with tumor burden markers, and affects patients' outcome. PMID:26088851

  6. Structural analysis of effector functions related motifs, complement activation and hemagglutinating activities in Lama glama heavy chain antibodies.

    PubMed

    Saccodossi, Natalia; De Simone, Emilio A; Leoni, Juliana

    2012-01-15

    Heavy chain antibodies (HCAbs), devoid of the light chains and the CH(1) domain, are present in the serum of camelids. IgG(2) and IgG(3) are HCAbs; whereas IgG(1) has the conventional structure. In order to study the immunological properties of llama HCAbs, from which to date little is known, llamas (Lama glama) HCAbs cDNA were cloned, sequenced and compared with other mammalian Igs. The sequence analysis showed that llama HCAbs cDNA organization is similar to other mammalian Igs and the presence of conserved binding motifs to Protein A, Protein G, FcγRI, FcγRIII and C1q in HCAbs were observed. In a previous work, different IgG isotypes purified by Protein A and Protein G chromatography, were assayed for their ability to fix complement. Both IgG(1) and the total serum were able to fix complement, whereas IgG(2) and IgG(3) fixed complement even in the absence of antigen (anti-complementary activity). Therefore, in this work we performed the complement activating activity of the different IgG isotypes purified under physiological conditions using Sephadex G-150 and their ability to induce hemagglutination. Llamas were immunized with sheep red blood cells (RBC) stroma and the different isotypes were purified from sera. Whole serum and IgG(1) could activate complement; however, HCAbs (IgG(2)+IgG(3)) could not, despite the presence of the C1q binding motif in their primary sequence. Unlike IgG(1), the fraction corresponding to IgG(2)+IgG(3) did not display hemagglutinating activity. Our findings suggest that HCAbs cannot crosslink efficiently with different antigens and that the C1q binding site might be hindered by the proximity of the variable domains. PMID:22197565

  7. Radionuclide migration through fractured rock for arbitrary-length decay chain: Analytical solution and global sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Shahkarami, Pirouz; Liu, Longcheng; Moreno, Luis; Neretnieks, Ivars

    2015-01-01

    This study presents an analytical approach to simulate nuclide migration through a channel in a fracture accounting for an arbitrary-length decay chain. The nuclides are retarded as they diffuse in the porous rock matrix and stagnant zones in the fracture. The Laplace transform and similarity transform techniques are applied to solve the model. The analytical solution to the nuclide concentrations at the fracture outlet is governed by nine parameters representing different mechanisms acting on nuclide transport through a fracture, including diffusion into the rock matrices, diffusion into the stagnant water zone, chain decay and hydrodynamic dispersion. Furthermore, to assess how sensitive the results are to parameter uncertainties, the Sobol method is applied in variance-based global sensitivity analyses of the model output. The Sobol indices show how uncertainty in the model output is apportioned to the uncertainty in the model input. This method takes into account both direct effects and interaction effects between input parameters. The simulation results suggest that in the case of pulse injections, ignoring the effect of a stagnant water zone can lead to significant errors in the time of first arrival and the peak value of the nuclides. Likewise, neglecting the parent and modeling its daughter as a single stable species can result in a significant overestimation of the peak value of the daughter nuclide. It is also found that as the dispersion increases, the early arrival time and the peak time of the daughter decrease while the peak value increases. More importantly, the global sensitivity analysis reveals that for time periods greater than a few thousand years, the uncertainty of the model output is more sensitive to the values of the individual parameters than to the interaction between them. Moreover, if one tries to evaluate the true values of the input parameters at the same cost and effort, the determination of priorities should follow a certain

  8. Chain Confinement in Electrospun Nanocomposites: using Thermal Analysis to Investigate Polymer-Filler Interactions

    SciTech Connect

    Q Ma; B Mao; P Cebe

    2011-12-31

    We investigate the interaction of the polymer matrix and filler in electrospun nanofibers using advanced thermal analysis methods. In particular, we study the ability of silicon dioxide nanoparticles to affect the phase structure of poly(ethylene terephthalate), PET. SiO{sub 2} nanoparticles (either unmodified or modified with silane) ranging from 0 to 2.0 wt% in PET were electrospun from hexafluoro-2-propanol solutions. The morphologies of both the electrospun (ES) nanofibers and the SiO{sub 2} powders were observed by scanning and transmission electron microscopy, while the amorphous or crystalline nature of the fibers was determined by real-time wide-angle X-ray scattering. The fractions of the crystal, mobile amorphous, and rigid amorphous phases of the non-woven, nanofibrous composite mats were quantified by using heat capacity measurements. The amount of the immobilized polymer layer, the rigid amorphous fraction, was obtained from the specific reversing heat capacity for both as-spun amorphous fibers and isothermally crystallized fibers. Existence of the rigid amorphous phase in the absence of crystallinity was verified in nanocomposite fibers, and two origins for confinement of the rigid amorphous fraction are proposed. Thermal analysis of electrospun fibers, including quasi-isothermal methods, provides new insights to quantitatively characterize the polymer matrix phase structure and thermal transitions, such as devitrification of the rigid amorphous fraction.

  9. Primer-introduced restriction analysis polymerase chain reaction method for non-invasive prenatal testing of β-thalassemia.

    PubMed

    Liu, Saijun; Chen, Liyuan; Zhang, Xiandong; Li, Jian; Lin, Haiying; Liu, Louhui; Xie, Jiansheng; Ge, Huijuan; Ye, Minglan; Chen, Caifen; Ji, Xingwen; Zhang, Caifen; Xu, Fengping; Jiang, Hui; Zhen, Hefu; Chen, Shiping; Wang, Wei

    2015-01-01

    We have developed a new method for non-invasive prenatal testing (NIPT) of paternally inherited fetal mutants for β-thalassemia (β-thal). Specially designed primer-introduced restriction analysis-polymerase chain reaction (PIRA-PCR) were used to detect four major mutations [IVS-II-654, HBB: c.316-197C > T; codon 17 (A > T), HBB: c.52A > T; -28 (A > G), HBB: c.-78A > G and codons 41/42 (-TTCT), HBB: c.126_129delCTTT] causing β-thal in China. The PIRA-PCR assay was first tested in a series of mixed DNA with different concentrations and mixed proportions. Subsequently, this assay was further tested in 10 plasma DNA samples collected from pregnant women. In the DNA mixture simulation test, the PIRA-PCR assay was able to detect 3.0% target genomic DNA (gDNA) mixed in 97.0% wild-type gDNA isolated from whole blood. For plasma DNA testing, the results detected by PIRA-PCR assay achieved 100.0% consistency with those obtained from the amniocentesis analysis. This new method could potentially be used for NIPT of paternally inherited fetal mutants for β-thal.

  10. Polymorphism analysis of Chinese Theileria sergenti using allele-specific polymerase chain reaction of the major piroplasm surface protein gene.

    PubMed

    Liu, Ai Hong; Guan, Gui Quan; Liu, Jun Long; Liu, Zhi Jie; Leblanc, Neil; Li, You Quan; Gao, Jin Liang; Ma, Mi Ling; Niu, Qing Li; Ren, Qiao Yun; Bai, Qi; Yin, Hong; Luo, Jian Xun

    2011-02-01

    Theileria sergenti is a tick-borne parasite found in many parts of the world. The major piroplasm surface protein (MPSP), a conserved protein in all Theileria species, has been used as a marker for epidemiological and phylogenetic studies of benign Theileria species. In this study, Chinese species of T. sergenti were characterized by allele-specific polymerase chain reaction (PCR) and DNA sequence analysis of the MPSP gene. Using universal or allele-specific primer sets for PCR amplification of the MPSP gene, 98 of 288 cattle blood samples, collected from 6 provinces in China, were found to be positive. Among the positive samples, only 3 allelic MPSP gene types (Chitose [C]-, Ikeda [I]-, and buffeli [B]-type) were successfully amplified. Moreover, the results revealed that the majority of the parasites sampled in this study were C- and I-type (prevalence of 84 and 69%, respectively), whereas the B-type was less common (prevalence of 36%). Co-infections with C-, I-, and B-type T. sergenti also were found. An additional known allele, Thai-type, was not detected. Phylogenetic analysis based on the MPSP gene sequences, including 3 standard stocks generated in the laboratory ( T. sergenti Wenchuan, T. sergenti Ningxian, and T. sergenti Liaoyang), revealed that the isolates of Chinese sergenti were comprised of at least 4 allelic MPSP gene types, i.e., C-, I-, B1-, and B2-type, and these parasites with 6 MPSP types 1-5 and 7 were present in China.

  11. Value Chains of Public and Private Health-care Services in a Small EU Island State: A SWOT Analysis.

    PubMed

    Buttigieg, Sandra C; Schuetz, Marcus; Bezzina, Frank

    2016-01-01

    The global financial and macroeconomic crisis of 2008/2009 and the ensuing recessions obliged policy makers to maximize use of resources and cut down on waste. Specifically, in health care, governments started to explore ways of establishing collaborations between the public and private health-care sectors. This is essential so as to ensure the best use of available resources, while securing quality of delivery of care as well as health systems sustainability and resilience. This qualitative study explores complementary and mutual attributes in the value creation process to patients by the public and private health-care systems in Malta, a small European Union island state. A workshop was conducted with 28 professionals from both sectors to generate two separate value chains, and this was followed by an analysis of strengths, weaknesses, opportunities, and threats (SWOT). The latter revealed several strengths and opportunities, which can better equip health-policy makers in the quest to maximize provision of health-care services. Moreover, the analysis also highlighted areas of weaknesses in both sectors as well as current threats of the external environment that, unless addressed, may threaten the state's health-care system sustainability and resilience to macroeconomic shocks. The study goes on to provide feasible recommendations aimed at maximizing provision of health-care services in Malta. PMID:27683658

  12. Value Chains of Public and Private Health-care Services in a Small EU Island State: A SWOT Analysis.

    PubMed

    Buttigieg, Sandra C; Schuetz, Marcus; Bezzina, Frank

    2016-01-01

    The global financial and macroeconomic crisis of 2008/2009 and the ensuing recessions obliged policy makers to maximize use of resources and cut down on waste. Specifically, in health care, governments started to explore ways of establishing collaborations between the public and private health-care sectors. This is essential so as to ensure the best use of available resources, while securing quality of delivery of care as well as health systems sustainability and resilience. This qualitative study explores complementary and mutual attributes in the value creation process to patients by the public and private health-care systems in Malta, a small European Union island state. A workshop was conducted with 28 professionals from both sectors to generate two separate value chains, and this was followed by an analysis of strengths, weaknesses, opportunities, and threats (SWOT). The latter revealed several strengths and opportunities, which can better equip health-policy makers in the quest to maximize provision of health-care services. Moreover, the analysis also highlighted areas of weaknesses in both sectors as well as current threats of the external environment that, unless addressed, may threaten the state's health-care system sustainability and resilience to macroeconomic shocks. The study goes on to provide feasible recommendations aimed at maximizing provision of health-care services in Malta.

  13. Value Chains of Public and Private Health-care Services in a Small EU Island State: A SWOT Analysis

    PubMed Central

    Buttigieg, Sandra C.; Schuetz, Marcus; Bezzina, Frank

    2016-01-01

    The global financial and macroeconomic crisis of 2008/2009 and the ensuing recessions obliged policy makers to maximize use of resources and cut down on waste. Specifically, in health care, governments started to explore ways of establishing collaborations between the public and private health-care sectors. This is essential so as to ensure the best use of available resources, while securing quality of delivery of care as well as health systems sustainability and resilience. This qualitative study explores complementary and mutual attributes in the value creation process to patients by the public and private health-care systems in Malta, a small European Union island state. A workshop was conducted with 28 professionals from both sectors to generate two separate value chains, and this was followed by an analysis of strengths, weaknesses, opportunities, and threats (SWOT). The latter revealed several strengths and opportunities, which can better equip health-policy makers in the quest to maximize provision of health-care services. Moreover, the analysis also highlighted areas of weaknesses in both sectors as well as current threats of the external environment that, unless addressed, may threaten the state’s health-care system sustainability and resilience to macroeconomic shocks. The study goes on to provide feasible recommendations aimed at maximizing provision of health-care services in Malta.

  14. Value Chains of Public and Private Health-care Services in a Small EU Island State: A SWOT Analysis

    PubMed Central

    Buttigieg, Sandra C.; Schuetz, Marcus; Bezzina, Frank

    2016-01-01

    The global financial and macroeconomic crisis of 2008/2009 and the ensuing recessions obliged policy makers to maximize use of resources and cut down on waste. Specifically, in health care, governments started to explore ways of establishing collaborations between the public and private health-care sectors. This is essential so as to ensure the best use of available resources, while securing quality of delivery of care as well as health systems sustainability and resilience. This qualitative study explores complementary and mutual attributes in the value creation process to patients by the public and private health-care systems in Malta, a small European Union island state. A workshop was conducted with 28 professionals from both sectors to generate two separate value chains, and this was followed by an analysis of strengths, weaknesses, opportunities, and threats (SWOT). The latter revealed several strengths and opportunities, which can better equip health-policy makers in the quest to maximize provision of health-care services. Moreover, the analysis also highlighted areas of weaknesses in both sectors as well as current threats of the external environment that, unless addressed, may threaten the state’s health-care system sustainability and resilience to macroeconomic shocks. The study goes on to provide feasible recommendations aimed at maximizing provision of health-care services in Malta. PMID:27683658

  15. A three-dimensional, six-segment chain analysis of forceful overarm throwing.

    PubMed

    Hong, D A; Cheung, T K; Roberts, E M

    2001-04-01

    A three-dimensional, six-segment model was applied to the pitching motion of three professional pitchers to analyze the kinematics and kinetics of the hips, upper trunk, humerus and forearm plus hand of both the upper limbs. Subjects were filmed at 250 frames per second. An inverse dynamics approach and angular momentum principle with respect to the proximal endpoint of a rigid segment were employed in the analysis. Results showed considerable similarities between subjects in the kinetic control of trunk rotation about the spine's longitudinal axis, but variability in the control of trunk lean both to the side and forward. The kinetics of the throwing shoulder and elbow joint were comparable between subjects, but the contribution of the non-throwing upper limb was minimal and variable. The upper trunk rotators played a key role in accelerating the ball to an early, low velocity near stride foot contact. After a brief pause they resumed acting strongly in a positive direction, though not enough to prevent trunk angular velocity slowing, as the musculature of the arm applied a load at the throwing shoulder. The interaction moment from the proximal segments assisted the forearm extensor in slowing flexion and producing rapid elbow extension near ball release. The temporal onset of muscular torques was not in a strictly successive proximal-to-distal sequence.

  16. Kinetic chain of overarm throwing in terms of joint rotations revealed by induced acceleration analysis.

    PubMed

    Hirashima, Masaya; Yamane, Katsu; Nakamura, Yoshihiko; Ohtsuki, Tatsuyuki

    2008-09-18

    This study investigated how baseball players generate large angular velocity at each joint by coordinating the joint torque and velocity-dependent torque during overarm throwing. Using a four-segment model (i.e., trunk, upper arm, forearm, and hand) that has 13 degrees of freedom, we conducted the induced acceleration analysis to determine the accelerations induced by these torques by multiplying the inverse of the system inertia matrix to the torque vectors. We found that the proximal joint motions (i.e., trunk forward motion, trunk leftward rotation, and shoulder internal rotation) were mainly accelerated by the joint torques at their own joints, whereas the distal joint motions (i.e., elbow extension and wrist flexion) were mainly accelerated by the velocity-dependent torques. We further examined which segment motion is the source of the velocity-dependent torque acting on the elbow and wrist accelerations. The results showed that the angular velocities of the trunk and upper arm produced the velocity-dependent torque for initial elbow extension acceleration. As a result, the elbow joint angular velocity increased, and concurrently, the forearm angular velocity relative to the ground also increased. The forearm angular velocity subsequently accelerated the elbow extension and wrist flexion. It also accelerated the shoulder internal rotation during the short period around the ball-release time. These results indicate that baseball players accelerate the distal elbow and wrist joint rotations by utilizing the velocity-dependent torque that is originally produced by the proximal trunk and shoulder joint torques in the early phase.

  17. Value-Chain Dynamics of the West Point Foundry, 1817-1911: A Historical Case Analysis in Marketing

    ERIC Educational Resources Information Center

    Petkus, Ed, Jr.

    2013-01-01

    This case provides the opportunity for students to explore marketing and value/supply-chain dynamics in a unique historical context. The West Point Foundry (WPF), located in Cold Spring, New York, was one of the most important manufacturing ventures in the United States from 1817 to 1911. The case outlines the supply-chain details of the WPF as…

  18. Unsupervised DInSAR processing chain for multi-scale displacement analysis

    NASA Astrophysics Data System (ADS)

    Casu, Francesco; Manunta, Michele

    2016-04-01

    , thus leading to the generation of Interferometric products for both global and local scale displacement analysis. Among several examples, we will show a wide displacement SBAS processing, carried out over the southern California, during which the whole ascending ENVISAT data set of more than 740 images has been fully processed on a Cloud Computing environment in less than 9 hours, leading to the generation of a displacement map of about 150,000 square kilometres. The P-SBAS characteristics allowed also us to integrate the algorithm within the ESA Geohazard Exploitation Platform (GEP), which is based on the use of GRID and Cloud Computing facilities, thus making freely available to the EO community a web tool for massive and systematic interferometric displacement time series generation. This work has been partially supported by: the Italian MIUR under the RITMARE project; the CNR-DPC agreement and the ESA GEP project.

  19. Rapid detection of HLA-B*51 by real-time polymerase chain reaction and high-resolution melting analysis.

    PubMed

    Imperiali, C; Alía-Ramos, P; Padró-Miquel, A

    2015-08-01

    HLA-B*51, a class I human leukocyte antigen (HLA) molecule, is the strongest known genetic risk factor for Behçet disease. However, there are only few articles reporting methods to determine the presence or absence of HLA-B51. For this reason, we designed and developed an easy, fast, and inexpensive real-time high-resolution melting (HRM) assay to detect HLA-B*51. We genotyped 61 samples by our HRM assay and by conventional polymerase chain reaction, and no discrepancies were found between results. Besides, a subgroup of 25 samples was also genotyped in a different laboratory, and another subgroup of 16 samples was obtained from the International Histocompatibility Working Group DNA Bank, and a full concordance of results was observed with those obtained by HRM. Regarding the identifying system evaluated, we obtained 100% of specificity, sensibility, and repeatability, and 0% of false positive and false negative rates. Therefore, this HRM analysis is easily applicable to the rapid detection of HLA-B*51, exhibits a high speed, and requires a very low budget. PMID:26176813

  20. A MARKOV CHAIN MONTE CARLO ALGORITHM FOR ANALYSIS OF LOW SIGNAL-TO-NOISE COSMIC MICROWAVE BACKGROUND DATA

    SciTech Connect

    Jewell, J. B.; O'Dwyer, I. J.; Huey, Greg; Gorski, K. M.; Eriksen, H. K.; Wandelt, B. D. E-mail: h.k.k.eriksen@astro.uio.no

    2009-05-20

    We present a new Markov Chain Monte Carlo (MCMC) algorithm for cosmic microwave background (CMB) analysis in the low signal-to-noise regime. This method builds on and complements the previously described CMB Gibbs sampler, and effectively solves the low signal-to-noise inefficiency problem of the direct Gibbs sampler. The new algorithm is a simple Metropolis-Hastings sampler with a general proposal rule for the power spectrum, C {sub l}, followed by a particular deterministic rescaling operation of the sky signal, s. The acceptance probability for this joint move depends on the sky map only through the difference of {chi}{sup 2} between the original and proposed sky sample, which is close to unity in the low signal-to-noise regime. The algorithm is completed by alternating this move with a standard Gibbs move. Together, these two proposals constitute a computationally efficient algorithm for mapping out the full joint CMB posterior, both in the high and low signal-to-noise regimes.

  1. Analysis of T cell receptor beta chain CDR3 size using RNA extracted from formalin fixed paraffin wax embedded tissue.

    PubMed Central

    O'Shea, U; Wyatt, J I; Howdle, P D

    1997-01-01

    AIMS: To isolate RNA and DNA simultaneously from formalin fixed paraffin wax embedded tissue to assess the clonality of enteropathy associated T cell lymphomas and to analyse it in detail by a non-radioactive method of T cell receptor complementarity determining region 3 (CDR3) spectratyping. METHODS: DNA and RNA were isolated simultaneously from formalin fixed paraffin wax embedded tissue blocks and subjected to the polymerase chain reaction (PCR) and semi-nested reverse transcription PCR (RT-PCR), respectively. The RT-PCR T cell receptor V beta products were analysed by CDR3 spectratyping using a denaturing polyacrylamide gel and silver staining. RESULTS: Usable DNA and RNA were isolated simultaneously from formalin fixed paraffin wax embedded tissue. The specific clonality of the tissue was successfully analysed by a non-radioactive method of T cell receptor CDR3 spectratyping of the RT-PCR products. CDR3 spectratying of the RT-PCR products demonstrated the precise clonal nature of the tumour and non-tumour tissue showing that the non-tumour tissue comprised an oligoclonal population of a number of different T cell receptor V beta families. The tumour tissue comprised two T cell subtypes of the one family, T cell receptor V beta 9. CONCLUSIONS: RNA and DNA were isolated from formalin fixed paraffin wax embedded enteropathy associated T cell lymphoma tissue. Detailed analysis of clonality can be carried out by a non-radioactive method of CDR3 spectratyping. Images PMID:9462260

  2. Rapid detection of HLA-B*51 by real-time polymerase chain reaction and high-resolution melting analysis.

    PubMed

    Imperiali, C; Alía-Ramos, P; Padró-Miquel, A

    2015-08-01

    HLA-B*51, a class I human leukocyte antigen (HLA) molecule, is the strongest known genetic risk factor for Behçet disease. However, there are only few articles reporting methods to determine the presence or absence of HLA-B51. For this reason, we designed and developed an easy, fast, and inexpensive real-time high-resolution melting (HRM) assay to detect HLA-B*51. We genotyped 61 samples by our HRM assay and by conventional polymerase chain reaction, and no discrepancies were found between results. Besides, a subgroup of 25 samples was also genotyped in a different laboratory, and another subgroup of 16 samples was obtained from the International Histocompatibility Working Group DNA Bank, and a full concordance of results was observed with those obtained by HRM. Regarding the identifying system evaluated, we obtained 100% of specificity, sensibility, and repeatability, and 0% of false positive and false negative rates. Therefore, this HRM analysis is easily applicable to the rapid detection of HLA-B*51, exhibits a high speed, and requires a very low budget.

  3. Collaborative ring trial of the papaya endogenous reference gene and its polymerase chain reaction assays for genetically modified organism analysis.

    PubMed

    Wei, Jiaojun; Li, Feiwu; Guo, Jinchao; Li, Xiang; Xu, Junfeng; Wu, Gang; Zhang, Dabing; Yang, Litao

    2013-11-27

    The papaya (Carica papaya L.) Chymopapain (CHY) gene has been reported as a suitable endogenous reference gene for genetically modified (GM) papaya detection in previous studies. Herein, we further validated the use of the CHY gene and its qualitative and quantitative polymerase chain reaction (PCR) assays through an interlaboratory collaborative ring trial. A total of 12 laboratories working on detection of genetically modified organisms participated in the ring trial and returned test results. Statistical analysis of the returned results confirmed the species specificity, low heterogeneity, and single-copy number of the CHY gene among different papaya varieties. The limit of detection of the CHY qualitative PCR assay was 0.1%, while the limit of quantification of the quantitative PCR assay was ∼25 copies of haploid papaya genome with acceptable PCR efficiency and linearity. The differences between the tested and true values of papaya content in 10 blind samples ranged from 0.84 to 6.58%. These results indicated that the CHY gene was suitable as an endogenous reference gene for the identification and quantification of GM papaya.

  4. Molecular characterization and mutational analysis of the human B17 subunit of the mitochondrial respiratory chain complex I.

    PubMed

    Smeitink, J; Loeffen, J; Smeets, R; Triepels, R; Ruitenbeek, W; Trijbels, F; van den Heuvel, L

    1998-08-01

    Bovine NADH:ubiquinone oxidoreductase (complex 1) of the mitochondrial respiratory chain consists of about 36 nuclear-encoded subunits. We review the current knowledge of the 15 human complex I subunits cloned so far, and report the 598-bp cDNA sequence, the chromosomal localization and the tissue expression of an additional subunit, the B17 subunit. The cDNA open reading frame of B17 comprises 387 bp and encodes a protein of 128 amino acids (calculated Mr 15.5 kDa). There is 82.7% and 78.1% homology, respectively, at the cDNA and amino acid level with the bovine counterpart. The gene of the B17 subunit has been mapped to chromosome 2. Multiple-tissue dot-blots showed ubiquitous expression of the mRNA with relatively higher expression in tissues known for their high energy demand. Of these, kidney showed the highest expression. Mutational analysis of the subunit revealed no mutations or polymorphisms in 20 patients with isolated enzymatic complex I deficiency in cultured skin fibroblasts. PMID:9760212

  5. Detection of congenital cytomegalovirus infection by real-time polymerase chain reaction analysis of saliva or urine specimens.

    PubMed

    Ross, Shannon A; Ahmed, Amina; Palmer, April L; Michaels, Marian G; Sánchez, Pablo J; Bernstein, David I; Tolan, Robert W; Novak, Zdenek; Chowdhury, Nazma; Fowler, Karen B; Boppana, Suresh B

    2014-11-01

    Viral culture of urine or saliva has been the gold standard technique for the diagnosis of congenital cytomegalovirus (CMV) infection. Results of rapid culture and polymerase chain reaction (PCR) analysis of urine and saliva specimens from 80 children were compared to determine the clinical utility of a real-time PCR assay for diagnosis of congenital CMV infection. Results of urine PCR were positive in 98.8% of specimens. Three PCR-positive urine samples were culture negative. Results of saliva PCR and culture were concordant in 78 specimens (97.5%). Two PCR-positive saliva samples were culture negative. These findings demonstrate that PCR performs as well as rapid culture of urine or saliva specimens for diagnosing congenital CMV infection and saliva specimens are easier to collect. Because PCR also offers more rapid turnaround, is unlikely to be affected by storage and transport conditions, has lower cost, and may be adapted to high-throughput situations, it is well suited for targeted testing and large-scale screening for CMV.

  6. Application of Markov chain Monte Carlo analysis to biomathematical modeling of respirable dust in US and UK coal miners

    PubMed Central

    Sweeney, Lisa M.; Parker, Ann; Haber, Lynne T.; Tran, C. Lang; Kuempel, Eileen D.

    2015-01-01

    A biomathematical model was previously developed to describe the long-term clearance and retention of particles in the lungs of coal miners. The model structure was evaluated and parameters were estimated in two data sets, one from the United States and one from the United Kingdom. The three-compartment model structure consists of deposition of inhaled particles in the alveolar region, competing processes of either clearance from the alveolar region or translocation to the lung interstitial region, and very slow, irreversible sequestration of interstitialized material in the lung-associated lymph nodes. Point estimates of model parameter values were estimated separately for the two data sets. In the current effort, Bayesian population analysis using Markov chain Monte Carlo simulation was used to recalibrate the model while improving assessments of parameter variability and uncertainty. When model parameters were calibrated simultaneously to the two data sets, agreement between the derived parameters for the two groups was very good, and the central tendency values were similar to those derived from the deterministic approach. These findings are relevant to the proposed update of the ICRP human respiratory tract model with revisions to the alveolar-interstitial region based on this long-term particle clearance and retention model. PMID:23454101

  7. Redesigning of anti-c-Met single chain Fv antibody for the cytoplasmic folding and its structural analysis.

    PubMed

    Edwardraja, Selvakumar; Neelamegam, Rameshkumar; Ramadoss, Vijayaraj; Venkatesan, Subramanian; Lee, Sun-Gu

    2010-06-15

    Typically, single chain Fv antibodies are unable to fold properly under a reducing cytoplasm because of the reduction of disulfide bonds. The inability to fold limits both the production of the functional scFvs and their targeting against antigens, which are generally executed in a reducing cytoplasm. In this study, the target scFv CDR was grafted with stable human consensus framework sequences, which enabled the generation of a foldable scFv in a reducing cytoplasm of Escherichia coli. Additionally, the structural features affecting the folding efficiency of the engineered scFv were identified by analyzing the predicted structure. An anti-c-Met scFv, which was a cytoplasmic non-foldable protein, was redesigned as the model system. This study confirmed that the engineered anti-c-Met scFv was folded into its native form in the cytoplasm of E. coli BL21(DE3) without a significant loss in the specific binding activity against c-Met antigen. The structures of the wild-type anti-c-Met scFv and the engineered scFv were predicted using homology modeling. A comparative analysis based on the sequence and structure showed that the hydrophobicity of 12 solvent exposed residues decreased, and two newly formed salt bridges might have improved the folding efficiency of the engineered scFv under the reducing condition.

  8. Markov Chain Monte Carlo Joint Analysis of Chandra X-Ray Imaging Spectroscopy and Sunyaev-Zel'dovich Effect Data

    NASA Technical Reports Server (NTRS)

    Bonamente, Massimillano; Joy, Marshall K.; Carlstrom, John E.; Reese, Erik D.; LaRoque, Samuel J.

    2004-01-01

    X-ray and Sunyaev-Zel'dovich effect data can be combined to determine the distance to galaxy clusters. High-resolution X-ray data are now available from Chandra, which provides both spatial and spectral information, and Sunyaev-Zel'dovich effect data were obtained from the BIMA and Owens Valley Radio Observatory (OVRO) arrays. We introduce a Markov Chain Monte Carlo procedure for the joint analysis of X-ray and Sunyaev- Zel'dovich effect data. The advantages of this method are the high computational efficiency and the ability to measure simultaneously the probability distribution of all parameters of interest, such as the spatial and spectral properties of the cluster gas and also for derivative quantities such as the distance to the cluster. We demonstrate this technique by applying it to the Chandra X-ray data and the OVRO radio data for the galaxy cluster A611. Comparisons with traditional likelihood ratio methods reveal the robustness of the method. This method will be used in follow-up paper to determine the distances to a large sample of galaxy cluster.

  9. Molecular cloning and comparative analysis of immunoglobulin heavy chain genes from Phasianus colchicus, Meleagris gallopavo, and Coturnix japonica.

    PubMed

    Choi, Jin Won; Kim, Jin-Kyoo; Seo, Hee Won; Cho, Byung Wook; Song, Gwonhwa; Han, Jae Yong

    2010-08-15

    To date, immunoglobulin (Ig) genes have only been fully characterized in a small number of aves, which pose a major obstacle to understanding Ig evolution. Thus, we cloned the cDNAs of three immunoglobulin classes, IgA, IgM, and IgY, from Phasianus colchicus, Coturnix japonica, and Meleagris gallopavo. Multiple sequence alignments revealed that the highest degree of sequence homology in all Ig classes was observed between pheasant and turkey whereas the degree of homology between the galliforms and non-galliforms was relatively low compared to that among the galliforms. When the constant region domains of the four human Ig classes were compared with the corresponding regions in aves, the average percent homology between human CH2 and avian CH3, and between human CH3 and avian CH4, was greater than between identical domains in IgA and IgY, which are in partial agreement with the hypothesis that the avian CH2 domain evolved to form the mammalian hinge via domain condensation. Phylogenetic analysis showed that the galliform Ig heavy chain constant regions were divided into quail and the common ancestor of chicken, turkey, and pheasant, and that chicken was separated from turkey and pheasant, which were grouped together. These results add to our knowledge of galliform Igs and the diversification of these genes.

  10. Fish Consumption, Long-Chain Omega-3 Polyunsaturated Fatty Acid Intake and Risk of Metabolic Syndrome: A Meta-Analysis

    PubMed Central

    Kim, Yong-Seok; Xun, Pengcheng; He, Ka

    2015-01-01

    Fish and long-chain ω-3 polyunsaturated fatty acid (LCω3PUFA) intake in relation to the risk of cardiovascular diseases have been well studied. However, studies that directly link fish consumption or LCω3PUFA intake to the risk of metabolic syndrome (MetS) are sparse and the results are inconsistent. We reviewed literature through December 2014 and used random-effects or fixed-effects models, as appropriate, to pool the associations of fish or LCω3PUFA intake with the risk of MetS. Nine independent cross-sectional samples (seven cross-sectional studies) and three independent prospective cohorts (two prospective cohort studies) were identified as eligible for this meta-analysis. By pooling data from the prospective cohorts (7860 participants and 1671 incident cases), a significant inverse association between fish consumption and incidence of MetS was found. The pooled RR (95% CI) was 0.71 (0.58, 0.87), comparing the highest to the lowest category of fish consumption, and 0.94 (0.90, 0.98) for one serving/week increment. Consistent results were found for LCω3PUFA intake. Non-significant inverse association of fish or LCω3PUFA intake with risk of MetS was found when pooling the cross-sectional studies. By quantitatively summarizing the literature, a modest inverse association between fish or LCω3PUFA intake and risk of MetS cannot be excluded. PMID:25811108

  11. Identification of roots of woody species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis

    PubMed

    Bobowski; Hole; Wolf; Bryant

    1999-03-01

    Within the last two decades, substantial progress has been made in understanding seed-bank dynamics and the contribution of the soil seed bank to a postdisturbance plant community. There has been relatively little progress, however, in understanding perennial bud-bank dynamics and the contribution of the soil bud bank to secondary succession. This lack of information is due primarily to the inability to reliably identify roots, rhizomes and lignotubers that lie dormant beneath the soil surface. This investigation addressed the issue of identification of below-ground woody structures. The first objective was to develop a method that used molecular tools to identify woody plant species from subsoil tissue samples. The second objective was to develop a key in which molecular markers served as criteria for the identification and differentiation of selected tree and shrub species common to the mountains of northeast Oregon and southeast Washington. Application of restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified rbcL appears to be a reliable method to identify and differentiate 15 plants to the genus level. Two restriction enzymes, DpnII and HhaI, provided restriction site polymorphisms in the PCR product. The fragment number and length were used to develop an identification key. However, plants not analysed in this 'exploratory key' might share the same banding patterns, resulting in a false identification of unknowns. PMID:10199009

  12. Molecular characterization and mutational analysis of the human B17 subunit of the mitochondrial respiratory chain complex I.

    PubMed

    Smeitink, J; Loeffen, J; Smeets, R; Triepels, R; Ruitenbeek, W; Trijbels, F; van den Heuvel, L

    1998-08-01

    Bovine NADH:ubiquinone oxidoreductase (complex 1) of the mitochondrial respiratory chain consists of about 36 nuclear-encoded subunits. We review the current knowledge of the 15 human complex I subunits cloned so far, and report the 598-bp cDNA sequence, the chromosomal localization and the tissue expression of an additional subunit, the B17 subunit. The cDNA open reading frame of B17 comprises 387 bp and encodes a protein of 128 amino acids (calculated Mr 15.5 kDa). There is 82.7% and 78.1% homology, respectively, at the cDNA and amino acid level with the bovine counterpart. The gene of the B17 subunit has been mapped to chromosome 2. Multiple-tissue dot-blots showed ubiquitous expression of the mRNA with relatively higher expression in tissues known for their high energy demand. Of these, kidney showed the highest expression. Mutational analysis of the subunit revealed no mutations or polymorphisms in 20 patients with isolated enzymatic complex I deficiency in cultured skin fibroblasts.

  13. Determination of locust bean gum and guar gum by polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Meyer, K; Rosa, C; Hischenhuber, C; Meyer, R

    2001-01-01

    A polymerase chain reaction (PCR) was developed to differentiate the thickening agents locust bean gum (LBG) and the cheaper guar gum in finished food products. Universal primers for amplification of the intergenic spacer region between trnL 3' (UAA) exon and trnF (GAA) gene in the chloroplast (cp) genome and subsequent restriction analysis were applied to differentiate guar gum and LBG. The presence of <5% (w/w) guar gum powder added to LBG powder was detectable. Based on data obtained from sequencing this intergenic spacer region, a second PCR method for the specific detection of guar gum DNA was also developed. This assay detected guar gum powder in LBG in amounts as low as 1% (w/w). Both methods successfully detected guar gum and/or LBG in ice cream stabilizers and in foodstuffs, such as dairy products, ice cream, dry seasoning mixes, a finished roasting sauce, and a fruit jelly product, but not in products with highly degraded DNA, such as tomato ketchup and sterilized chocolate cream. Both methods detected guar gum and LBG in ice cream and fresh cheese at levels <0.1%. PMID:11234856

  14. Evaluating environmental impacts of alternative construction waste management approaches using supply-chain-linked life-cycle analysis.

    PubMed

    Kucukvar, Murat; Egilmez, Gokhan; Tatari, Omer

    2014-06-01

    Waste management in construction is critical for the sustainable treatment of building-related construction and demolition (C&D) waste materials, and recycling of these wastes has been considered as one of the best strategies in minimization of C&D debris. However, recycling of C&D materials may not always be a feasible strategy for every waste type and therefore recycling and other waste treatment strategies should be supported by robust decision-making models. With the aim of assessing the net carbon, energy, and water footprints of C&D recycling and other waste management alternatives, a comprehensive economic input-output-based hybrid life-cycle assessment model is developed by tracing all of the economy-wide supply-chain impacts of three waste management strategies: recycling, landfilling, and incineration. Analysis results showed that only the recycling of construction materials provided positive environmental footprint savings in terms of carbon, energy, and water footprints. Incineration is a better option as a secondary strategy after recycling for water and energy footprint categories, whereas landfilling is found to be as slightly better strategy when carbon footprint is considered as the main focus of comparison. In terms of construction materials' environmental footprint, nonferrous metals are found to have a significant environmental footprint reduction potential if recycled.

  15. Evaluating environmental impacts of alternative construction waste management approaches using supply-chain-linked life-cycle analysis.

    PubMed

    Kucukvar, Murat; Egilmez, Gokhan; Tatari, Omer

    2014-06-01

    Waste management in construction is critical for the sustainable treatment of building-related construction and demolition (C&D) waste materials, and recycling of these wastes has been considered as one of the best strategies in minimization of C&D debris. However, recycling of C&D materials may not always be a feasible strategy for every waste type and therefore recycling and other waste treatment strategies should be supported by robust decision-making models. With the aim of assessing the net carbon, energy, and water footprints of C&D recycling and other waste management alternatives, a comprehensive economic input-output-based hybrid life-cycle assessment model is developed by tracing all of the economy-wide supply-chain impacts of three waste management strategies: recycling, landfilling, and incineration. Analysis results showed that only the recycling of construction materials provided positive environmental footprint savings in terms of carbon, energy, and water footprints. Incineration is a better option as a secondary strategy after recycling for water and energy footprint categories, whereas landfilling is found to be as slightly better strategy when carbon footprint is considered as the main focus of comparison. In terms of construction materials' environmental footprint, nonferrous metals are found to have a significant environmental footprint reduction potential if recycled. PMID:24855225

  16. Distribution and primary source analysis of per- and poly-fluoroalkyl substances with different chain lengths in surface and groundwater in two cities, North China.

    PubMed

    Yao, Yiming; Zhu, Hongkai; Li, Bing; Hu, Hongwei; Zhang, Tao; Yamazaki, Eriko; Taniyasu, Sachi; Yamashita, Nobuyoshi; Sun, Hongwen

    2014-10-01

    Per- and poly-fluoroalkyl substances (PFASs) have been widely detected in the hydrosphere. The knowledge on the distribution and composition patterns of PFAS analogues with different chain length significantly contribute to their source analysis. In the present study, a regional scale investigation of PFASs in surface river waters and adjacent ground waters was carried out in two cities of China with potential contamination, Tianjin and Weifang. A total of 31 water samples were collected, and 20 PFASs therein were measured by a high-performance liquid chromatograph-tandem mass spectrometer (HPLC-MS/MS). The possible sources of PFASs in the aquatic environment were assessed primarily by concentration patterns as well as hierarchical cluster analysis. In all 4 rivers investigated in the two cities, perfluoroalkyl carboxylic acids (PFCAs) were the dominant compounds contributing over 70% of the PFASs detected. Perfluorooctanoic acid (PFOA) was the dominant PFCA with a concentration range of 8.58-20.3ng/L in Tianjin and 6.37-25.9ng/L in Weifang, respectively. On the average, the highest concentration was observed in samples from Dagu Drainage Canal (Dagu) in Tianjin and those short-chain PFASs (C4-C6) was detected with a comparable level of the longer-chain PFASs (>C6). Specifically, perfluorobutanoic acid (PFBA) was dominant in the short-chain analogues. This indicates that a remarkably increasing input of short-chain PFASs might be related to wastewater treatment plant effluent or industrial discharges, which could be possibly due to the switch of manufacturing to short-chain products. In Weifang, precipitation and subsequent surface runoff as non-point sources could be significant inputs of PFASs into surface water while groundwater was possibly subjected to severe point sources with ∑PFASs concentration up to ~100ng/L. The inconsistent distribution patterns in groundwater suggest complicated pathways of contamination.

  17. Facile analysis of contents and compositions of the chondroitin sulfate/dermatan sulfate hybrid chain in shark and ray tissues.

    PubMed

    Takeda, Naoko; Horai, Sawako; Tamura, Jun-ichi

    2016-04-01

    The chondroitin sulfate (CS)/dermatan sulfate (DS) hybrid chain was extracted from specific tissues of several kinds of sharks and rays. The contents and sulfation patterns of the CS/DS hybrid chain were precisely analyzed by digestion with chondroitinases ABC and AC. All samples predominantly contained the A- and C-units. Furthermore, all samples characteristically contained the D-unit. Species-specific differences were observed in the contents of the CS/DS hybrid chain, which were the highest in Mako and Blue sharks and Sharpspine skates, but were lower in Hammerhead sharks. Marked differences were observed in the ratio of the C-unit/A-unit between sharks and rays. The contents of the CS/DS hybrid chain and the ratio of the C-unit/A-unit may be related to an oxidative stress-decreasing ability. PMID:26986023

  18. When Phase Contrast Fails: ChainTracer and NucTracer, Two ImageJ Methods for Semi-Automated Single Cell Analysis Using Membrane or DNA Staining.

    PubMed

    Syvertsson, Simon; Vischer, Norbert O E; Gao, Yongqiang; Hamoen, Leendert W

    2016-01-01

    Within bacterial populations, genetically identical cells often behave differently. Single-cell measurement methods are required to observe this heterogeneity. Flow cytometry and fluorescence light microscopy are the primary methods to do this. However, flow cytometry requires reasonably strong fluorescence signals and is impractical when bacteria grow in cell chains. Therefore fluorescence light microscopy is often used to measure population heterogeneity in bacteria. Automatic microscopy image analysis programs typically use phase contrast images to identify cells. However, many bacteria divide by forming a cross-wall that is not detectable by phase contrast. We have developed 'ChainTracer', a method based on the ImageJ plugin ObjectJ. It can automatically identify individual cells stained by fluorescent membrane dyes, and measure fluorescence intensity, chain length, cell length, and cell diameter. As a complementary analysis method we developed 'NucTracer', which uses DAPI stained nucleoids as a proxy for single cells. The latter method is especially useful when dealing with crowded images. The methods were tested with Bacillus subtilis and Lactococcus lactis cells expressing a GFP-reporter. In conclusion, ChainTracer and NucTracer are useful single cell measurement methods when bacterial cells are difficult to distinguish with phase contrast.

  19. When Phase Contrast Fails: ChainTracer and NucTracer, Two ImageJ Methods for Semi-Automated Single Cell Analysis Using Membrane or DNA Staining

    PubMed Central

    Syvertsson, Simon; Vischer, Norbert O. E.; Gao, Yongqiang; Hamoen, Leendert W.

    2016-01-01

    Within bacterial populations, genetically identical cells often behave differently. Single-cell measurement methods are required to observe this heterogeneity. Flow cytometry and fluorescence light microscopy are the primary methods to do this. However, flow cytometry requires reasonably strong fluorescence signals and is impractical when bacteria grow in cell chains. Therefore fluorescence light microscopy is often used to measure population heterogeneity in bacteria. Automatic microscopy image analysis programs typically use phase contrast images to identify cells. However, many bacteria divide by forming a cross-wall that is not detectable by phase contrast. We have developed ‘ChainTracer’, a method based on the ImageJ plugin ObjectJ. It can automatically identify individual cells stained by fluorescent membrane dyes, and measure fluorescence intensity, chain length, cell length, and cell diameter. As a complementary analysis method we developed 'NucTracer', which uses DAPI stained nucleoids as a proxy for single cells. The latter method is especially useful when dealing with crowded images. The methods were tested with Bacillus subtilis and Lactococcus lactis cells expressing a GFP-reporter. In conclusion, ChainTracer and NucTracer are useful single cell measurement methods when bacterial cells are difficult to distinguish with phase contrast. PMID:27008090

  20. Chain Gang

    NASA Technical Reports Server (NTRS)

    2006-01-01

    6 August 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a chain of clustered and battered craters. These were formed by secondary impact. That is, somewhere to the south (beyond the bottom of this image), a large impact crater formed. When this occurred, material ejected from the crater was thrown tens to hundreds of kilometers away. This material then impacted the martian surface, forming clusters and chains of smaller craters.

    Location near: 15.8oN, 35.6oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Northern Spring

  1. Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis.

    PubMed

    Samah, S; Valadez-Moctezuma, E; Peláez-Luna, K S; Morales-Manzano, S; Meza-Carrera, P; Cid-Contreras, R C

    2016-01-01

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico. PMID:27323120

  2. Markov Chain Modelling Analysis of HIV/AIDS Progression: A Race-based Forecast in the United States.

    PubMed

    Lee, S; Ko, J; Tan, Xi; Patel, Isha; Balkrishnan, R; Chang, J

    2014-03-01

    HIV/AIDS has reached a pandemic level across the world with more than 33 million people who are living with HIV. In the United States, more than half a million people have been victims of AIDS. This study investigates the most vulnerable racial minority population (the African Americans) in the United States and the second least affected (the Caucasians) in order to predict the trends of the epidemic. A Markov chain analysis was used to model the progression of the disease among vulnerable people, infective people and AIDS cases for the two races separately, based on the 2009 Centers of Disease Control and Prevention HIV/AIDS Surveillance Report. Based on the Markov model, our study predicts that the number of African American people living with AIDS diagnosis and HIV infection and dead due to HIV/AIDS will be 662.2, 1225.3 and 62.9 in 2015 and 794.9, 1566.5 and 79.2 in 2030, respectively. The number of Caucasian people living with AIDS diagnosis and HIV infection and dead due to HIV/AIDS will be 96.4, 160 and 6.5 in 2015 and 118.6, 206.9 and 8.3 in 2030, respectively. The numbers of deaths due to HIV/AIDS are quite stable over the years in both the races. There is an increasing trend in the number of people living with HIV infection and AIDS diagnosis in Caucasians compared with African Americans. The absolute number of Caucasians living with AIDS diagnosis and HIV infection is quite smaller compared with African Americans. The results reveal discrepancy in HIV infection, AIDS diagnosis and deaths due to HIV/AIDS among the African Americans and the Caucasians races. There is a need for interventions focusing on HIV/AIDS prevention and management, optimum resource allocation and development of antiAIDS campaigns to reduce the infection rate. PMID:24843183

  3. Inter-helical interactions in membrane proteins: analysis based on the local backbone geometry and the side chain interactions.

    PubMed

    Jha, Anupam Nath; Vishveshwara, Saraswathi

    2009-06-01

    The availability of a significant number of the structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the mutual orientation of local axes, is able to accurately capture the details of helix-helix interaction. The analysis has been carried out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction of surface helices with the end of the trans-membrane helices. The study supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

  4. Evaluation of post-polymerase chain reaction melting temperature analysis for meat species identification in mixed DNA samples.

    PubMed

    López-Andreo, María; Garrido-Pertierra, Amando; Puyet, Antonio

    2006-10-18

    Real-time uniplex and duplex polymerase chain reaction (PCR) assays with a SYBR Green I post-PCR melting curve analysis were evaluated for the identification and quantification of bovine, porcine, horse, and wallaroo DNA in food products. Quantitative values were derived from threshold-cycle (C(t)) data obtained from serial dilutions of purified DNA. The limits of detection in uniplex reactions were 0.04 pg for porcine and wallaroo DNA and 0.4 pg for cattle and horse DNA. Species specificity of the PCR products was tested by the identification of peaks in DNA melting curves, measured as the decrease of SYBR Green I fluorescence at the dissociation temperature. The peaks could be distinguished above the background even at the lowest amount of template DNA detected by the C(t) method. The system was also tested in duplex reactions, by use of either single-species DNA or DNA admixtures containing different shares of two species. The minimum proportions of each DNA species allowing the resolution of T(m) peaks in the duplex reactions were 5% (cattle or wallaroo) in cattle/wallaroo mixtures, 5% porcine and 1% horse in porcine/horse mixtures, 60% porcine and 1% wallaroo in porcine/wallaroo mixtures, and 1% cattle and 5% horse in cattle/horse mixtures. A loss in the sensitivity of the method was observed for some DNA combinations in the duplex assay. In contrast, the results obtained from SYBR Green I uniplex and duplex reactions with single-species DNA were largely comparable to those obtained previously with species-specific TaqMan probes, showing the suitability of that simpler experimental approach for large-scale analytical applications.

  5. Detection of HLA-DRB1 microchimerism using nested polymerase chain reaction and single-strand conformation polymorphism analysis.

    PubMed

    Song, Eun Young; Chung, Hye Yoon; Joo, Shin Young; Roh, Eun Youn; Seong, Moon-Woo; Shin, Yunsu; Park, Myoung Hee

    2012-03-01

    For the detection of microchimerism, molecular methods detecting donor-specific HLA-DRB1 alleles in the recipient are most commonly used. Nested polymerase chain reaction sequence specific primer (nested PCR-SSP) methods widely used to increase the sensitivity of detection have been reported to give frequent false-positive reactions. We have developed a new method combining nested PCR with single-strand conformation polymorphism analysis (nested PCR-SSCP) and tested the 1 to 0.00001% level of microchimerism for 27 different HLA-DRB1 alleles. For most (26/27) of the HLA-DRB1 alleles tested, this method could detect 0.01 to 0.001% of microchimerism and its sensitivity was equal to or better than that of nested PCR-SSP tested in parallel. Its specificity was verified by visualizing particular DRB1-specific SSCP bands under test. Nested PCR-SSP indicated frequent false-positive reactions, mainly caused by nonspecific amplification of DRB3/B4/B5 alleles present in the major (recipient) DNAs. We have compared a real-time quantitative PCR for non-human leukocyte antigen (HLA) target (insertion/deletion marker) using a commercial kit (AlleleSEQR Chimerism assay), and its microchimerism detection sensitivity (around 0.1%) was 1 step (10 times) lower than that of nested PCR-SSP or -SSCP methods for HLA-DRB1 alleles. We validated that the newly designed nested PCR-SSCP affords good sensitivity and specificity and may be useful for studying microchimerism in clinical settings.

  6. Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis.

    PubMed

    Samah, S; Valadez-Moctezuma, E; Peláez-Luna, K S; Morales-Manzano, S; Meza-Carrera, P; Cid-Contreras, R C

    2016-06-03

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico.

  7. [Ligase chain reaction (LCR)].

    PubMed

    Yamanishi, K; Yasuno, H

    1993-06-01

    Ligase chain reaction (LCR) is a ligation-mediated amplification technique of a target DNA sequence using oligonucleotides and thermostable ligase. LCR is useful for the detection of known DNA sequences and point mutations in a limited amount of DNA. We introduce the principle, development, and protocol of this simple and convenient technique for DNA analysis.

  8. Kinematic and kinetic analysis of maximal velocity deadlifts performed with and without the inclusion of chain resistance.

    PubMed

    Swinton, Paul A; Stewart, Arthur D; Keogh, Justin W L; Agouris, Ioannis; Lloyd, Ray

    2011-11-01

    The purpose of this study was to investigate whether the deadlift could be effectively incorporated with explosive resistance training (ERT) and to investigate whether the inclusion of chains enhanced the suitability of the deadlift for ERT. Twenty-three resistance trained athletes performed the deadlift with 30, 50, and 70% 1-repetition maximum (1RM) loads at submaximal velocity, maximal velocity (MAX), and MAX with the inclusion of 2 chain loads equal to 20 or 40% of the subjects' 1RM. All trials were performed on force platforms with markers attached to the barbell to calculate velocity and acceleration using a motion capture system. Significant increases in force, velocity, power, rate of force development, and length of the acceleration phase (p < 0.05) were obtained when repetition velocity increased from submaximal to maximal. During MAX repetitions with a constant resistance, the mean length of the acceleration phase ranged from 73.2 (±7.2%) to 84.9 (±12.2%) of the overall movement. Compared to using a constant resistance, the inclusion of chains enabled greater force to be maintained to the end of the concentric action and significantly increased peak force and impulse (p < 0.05), while concurrently decreasing velocity, power, and rate of force development (p < 0.05). The effects of chains were influenced by the magnitude of the chain and barbell resistance, with greater increases and decreases in mechanical variables obtained when heavier chain and barbell loads were used. The results of the investigation suggest that the deadlift can be incorporated effectively in ERT programs. Coaches and athletes should be aware that the inclusion of heavy chains may have both positive and negative effects on kinematics and kinetics of an exercise. PMID:21993040

  9. Behavioral Analysis of Visitors to a Medical Institution’s Website Using Markov Chain Monte Carlo Methods

    PubMed Central

    Tani, Yuji

    2016-01-01

    Background Consistent with the “attention, interest, desire, memory, action” (AIDMA) model of consumer behavior, patients collect information about available medical institutions using the Internet to select information for their particular needs. Studies of consumer behavior may be found in areas other than medical institution websites. Such research uses Web access logs for visitor search behavior. At this time, research applying the patient searching behavior model to medical institution website visitors is lacking. Objective We have developed a hospital website search behavior model using a Bayesian approach to clarify the behavior of medical institution website visitors and determine the probability of their visits, classified by search keyword. Methods We used the website data access log of a clinic of internal medicine and gastroenterology in the Sapporo suburbs, collecting data from January 1 through June 31, 2011. The contents of the 6 website pages included the following: home, news, content introduction for medical examinations, mammography screening, holiday person-on-duty information, and other. The search keywords we identified as best expressing website visitor needs were listed as the top 4 headings from the access log: clinic name, clinic name + regional name, clinic name + medical examination, and mammography screening. Using the search keywords as the explaining variable, we built a binomial probit model that allows inspection of the contents of each purpose variable. Using this model, we determined a beta value and generated a posterior distribution. We performed the simulation using Markov Chain Monte Carlo methods with a noninformation prior distribution for this model and determined the visit probability classified by keyword for each category. Results In the case of the keyword “clinic name,” the visit probability to the website, repeated visit to the website, and contents page for medical examination was positive. In the case of the

  10. CMB quadrupole depression produced by early fast-roll inflation: Monte Carlo Markov chains analysis of WMAP and SDSS data

    SciTech Connect

    Destri, C.; Vega, H. J. de; Sanchez, N. G.

    2008-07-15

    Generically, the classical evolution of the inflaton has a brief fast-roll stage that precedes the slow-roll regime. The fast-roll stage leads to a purely attractive potential in the wave equations of curvature and tensor perturbations (while the potential is purely repulsive in the slow-roll stage). This attractive potential leads to a depression of the CMB quadrupole moment for the curvature and B-mode angular power spectra. A single new parameter emerges in this way in the early universe model: the comoving wave number k{sub 1} characteristic scale of this attractive potential. This mode k{sub 1} happens to exit the horizon precisely at the transition from the fast-roll to the slow-roll stage. The fast-roll stage dynamically modifies the initial power spectrum by a transfer function D(k). We compute D(k) by solving the inflaton evolution equations. D(k) effectively suppresses the primordial power for kchain analysis of the WMAP and SDSS data including the fast-roll stage and find the value k{sub 1}=0.266 Gpc{sup -1}. The quadrupole mode k{sub Q}=0.242 Gpc{sup -1} exits the horizon earlier than k{sub 1}, about one-tenth of an e-fold before the end of fast roll. We compare the fast-roll fit with a fit without fast roll but including a sharp lower cutoff on the primordial power. Fast roll provides a slightly better fit than a sharp cutoff for the temperature-temperature, temperature-E modes, and E modes-E modes. Moreover, our fits provide nonzero lower bounds for r, while the values of the other cosmological parameters are essentially those of the pure {lambda}CDM model. We display the real space two point C{sup TT}({theta}) correlator. The fact that k{sub Q} exits the horizon before the slow-roll stage implies an upper bound in the total number of e-folds N{sub tot} during inflation. Combining this with estimates during the

  11. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

    PubMed

    Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

    2015-03-01

    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.

  12. The use of heteroduplex analysis of polymerase chain reaction products to support the possible transmission of Legionella pneumophila from a malfunctioning automobile air conditioner.

    PubMed

    Pinar, Ahmet; Ramirez, Julio A; Schindler, Laura L; Miller, Richard D; Summersgill, James T

    2002-03-01

    Air conditioner condensates have not been previously associated with cases of Legionnaires' disease. We report the possible transmission of Legionella pneumophila serogroup 1 from a malfunctioning automobile air conditioning system's leaking water onto the floorboard of a car driven for a long distance by the patient. Heteroduplex analysis of polymerase chain reaction products was used to help establish an epidemiologic link between the water specimen and the patient. PMID:11918120

  13. Is food allergen analysis flawed? Health and supply chain risks and a proposed framework to address urgent analytical needs.

    PubMed

    Walker, M J; Burns, D T; Elliott, C T; Gowland, M H; Mills, E N Clare

    2016-01-01

    Food allergy is an increasing problem for those affected, their families or carers, the food industry and for regulators. The food supply chain is highly vulnerable to fraud involving food allergens, risking fatalities and severe reputational damage to the food industry. Many facets are being pursued to ameliorate the difficulties including better food labelling and the concept of thresholds of elicitation of allergy symptoms as risk management tools. These efforts depend to a high degree on the ability reliably to detect and quantify food allergens; yet all current analytical approaches exhibit severe deficiencies that jeopardise accurate results being produced particularly in terms of the risks of false positive and false negative reporting. If we fail to realise the promise of current risk assessment and risk management of food allergens through lack of the ability to measure food allergens reproducibly and with traceability to an international unit of measurement, the analytical community will have failed a significant societal challenge. Three distinct but interrelated areas of analytical work are urgently needed to address the substantial gaps identified: (a) a coordinated international programme for the production of properly characterised clinically relevant reference materials and calibrants for food allergen analysis; (b) an international programme to widen the scope of proteomics and genomics bioinformatics for the genera containing the major allergens to address problems in ELISA, MS and DNA methods; (c) the initiation of a coordinated international programme leading to reference methods for allergen proteins that provide results traceable to the SI. This article describes in more detail food allergy, the risks of inapplicable or flawed allergen analyses with examples and a proposed framework, including clinically relevant incurred allergen concentrations, to address the currently unmet and urgently required analytical requirements. Support for the

  14. Is food allergen analysis flawed? Health and supply chain risks and a proposed framework to address urgent analytical needs.

    PubMed

    Walker, M J; Burns, D T; Elliott, C T; Gowland, M H; Mills, E N Clare

    2016-01-01

    Food allergy is an increasing problem for those affected, their families or carers, the food industry and for regulators. The food supply chain is highly vulnerable to fraud involving food allergens, risking fatalities and severe reputational damage to the food industry. Many facets are being pursued to ameliorate the difficulties including better food labelling and the concept of thresholds of elicitation of allergy symptoms as risk management tools. These efforts depend to a high degree on the ability reliably to detect and quantify food allergens; yet all current analytical approaches exhibit severe deficiencies that jeopardise accurate results being produced particularly in terms of the risks of false positive and false negative reporting. If we fail to realise the promise of current risk assessment and risk management of food allergens through lack of the ability to measure food allergens reproducibly and with traceability to an international unit of measurement, the analytical community will have failed a significant societal challenge. Three distinct but interrelated areas of analytical work are urgently needed to address the substantial gaps identified: (a) a coordinated international programme for the production of properly characterised clinically relevant reference materials and calibrants for food allergen analysis; (b) an international programme to widen the scope of proteomics and genomics bioinformatics for the genera containing the major allergens to address problems in ELISA, MS and DNA methods; (c) the initiation of a coordinated international programme leading to reference methods for allergen proteins that provide results traceable to the SI. This article describes in more detail food allergy, the risks of inapplicable or flawed allergen analyses with examples and a proposed framework, including clinically relevant incurred allergen concentrations, to address the currently unmet and urgently required analytical requirements. Support for the

  15. deducing the sequence of deformations during chain building from the analysis of minor structures: the case of the Sicily Belt (Central Mediterranean)

    NASA Astrophysics Data System (ADS)

    Nigro, Fabrizio; Renda, Pietro; Favara, Rocco

    2010-05-01

    the structural evolution of the Sicily chain using overprinting mesoscopic fabrics and their relationships to larger structures. The geometric differences existing between some types of structures within the belt and their overprinting relationships allow delineating the timing of deformations during chain building and post-collision tectonic history. The overall structural setting of the mountain chain reflects therefore the deformation and the progressive thrusting migration forelandwards, with extensional faulting overprinting and inverting formed thrusts. Most of the data available for this work come from detailed analysis in a few key areas, ranging along the Northern Sicily, where minor structures are overprinted to form a single sequence. Our study of outcrops throughout the region has recognised that the progression of deformation is represented by four regionally-significant structural stages (layer-parallel shortening, folding-and-thrusting, extension and renewed thrusting). The first stage of deformation includes several sub-stages (layer-parallel shortening, bed-parallel simple shear and fold nucleation). Deformation continued in a second stage, where thrusting was coupled by fold amplification and tightening. Kinematic evolution is provided by a third stage, where dominantly negative inversion of previous weakened zones and mechanical discontinuities occurred, coupled by normal faults activation. Out-of-sequence thrusting follows the chain thinning phase, as the late orogenic deformation phase of the contractional tectonics which affected Sicily. Each stage is defined as a discrete phase of deformation, characterised by the development of a characteristic set of structures, such as cleavage, folds, faults and veins. Each deformative step may be sequentially framed in a kinematic history, where a continuous shortening process, halted by an extension episode due to chain overthickening, in a tectonic setting dominated by collisional tectonics.

  16. Identification and comparative expression analysis of interleukin 2/15 receptor B chain in chickens infected with E. tenella

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Interleukin (IL) 2 and IL15 receptor beta chain (IL2/15Receptor beta, CD122) play critical roles in signal transduction for the biological activities of IL2 and IL15. Increased knowledge of non-mammalian IL2/15Receptor beta will enhance the understanding of IL2 and IL15 functions. Meth...

  17. Characterization of contact structures for the spread of infectious diseases in a pork supply chain in northern Germany by dynamic network analysis of yearly and monthly networks.

    PubMed

    Büttner, K; Krieter, J; Traulsen, I

    2015-04-01

    A major risk factor in the spread of diseases between holdings is the transport of live animals. This study analysed the animal movements of the pork supply chain of a producer group in Northern Germany. The parameters in-degree and out-degree, ingoing and outgoing infection chain, betweenness and ingoing and outgoing closeness were measured using dynamic network analysis to identify holdings with central positions in the network and to characterize the overall network topology. The potential maximum epidemic size was also estimated. All parameters were calculated for three time periods: the 3-yearly network, the yearly and the monthly networks. The yearly and the monthly networks were more fragmented than the 3-yearly network. On average, one-third of the holdings were isolated in the yearly networks and almost three quarters in the monthly networks. This represented an immense reduction in the number of holdings participating in the trade of the monthly networks. The overall network topology showed right-skewed distributions for all calculated centrality parameters indicating that network resilience was high concerning the random removal of holdings. However, for a targeted removal of holdings according to their centrality, a rapid fragmentation of the trade network could be expected. Furthermore, to capture the real importance of holdings for disease transmission, indirect trade contacts (infection chain) should be considered. In contrast to the parameters regarding direct trade contacts (degree), the infection chain parameter did not underestimate the potential risk of disease transmission. This became more obvious, the longer the observed time period was. For all three time periods, the results for the estimation of the potential maximum epidemic size illustrated that the outgoing infection chain should be chosen. It considers the chronological order and the directed nature of the contacts and has no restrictions such as the strongly connected components of a

  18. Identification of the significant factors in food safety using global sensitivity analysis and the accept-and-reject algorithm: application to the cold chain of ham.

    PubMed

    Duret, Steven; Guillier, Laurent; Hoang, Hong-Minh; Flick, Denis; Laguerre, Onrawee

    2014-06-16

    Deterministic models describing heat transfer and microbial growth in the cold chain are widely studied. However, it is difficult to apply them in practice because of several variable parameters in the logistic supply chain (e.g., ambient temperature varying due to season and product residence time in refrigeration equipment), the product's characteristics (e.g., pH and water activity) and the microbial characteristics (e.g., initial microbial load and lag time). This variability can lead to different bacterial growth rates in food products and has to be considered to properly predict the consumer's exposure and identify the key parameters of the cold chain. This study proposes a new approach that combines deterministic (heat transfer) and stochastic (Monte Carlo) modeling to account for the variability in the logistic supply chain and the product's characteristics. The model generates a realistic time-temperature product history , contrary to existing modeling whose describe time-temperature profile Contrary to existing approaches that use directly a time-temperature profile, the proposed model predicts product temperature evolution from the thermostat setting and the ambient temperature. The developed methodology was applied to the cold chain of cooked ham including, the display cabinet, transport by the consumer and the domestic refrigerator, to predict the evolution of state variables, such as the temperature and the growth of Listeria monocytogenes. The impacts of the input factors were calculated and ranked. It was found that the product's time-temperature history and the initial contamination level are the main causes of consumers' exposure. Then, a refined analysis was applied, revealing the importance of consumer behaviors on Listeria monocytogenes exposure. PMID:24786551

  19. Identification of the significant factors in food safety using global sensitivity analysis and the accept-and-reject algorithm: application to the cold chain of ham.

    PubMed

    Duret, Steven; Guillier, Laurent; Hoang, Hong-Minh; Flick, Denis; Laguerre, Onrawee

    2014-06-16

    Deterministic models describing heat transfer and microbial growth in the cold chain are widely studied. However, it is difficult to apply them in practice because of several variable parameters in the logistic supply chain (e.g., ambient temperature varying due to season and product residence time in refrigeration equipment), the product's characteristics (e.g., pH and water activity) and the microbial characteristics (e.g., initial microbial load and lag time). This variability can lead to different bacterial growth rates in food products and has to be considered to properly predict the consumer's exposure and identify the key parameters of the cold chain. This study proposes a new approach that combines deterministic (heat transfer) and stochastic (Monte Carlo) modeling to account for the variability in the logistic supply chain and the product's characteristics. The model generates a realistic time-temperature product history , contrary to existing modeling whose describe time-temperature profile Contrary to existing approaches that use directly a time-temperature profile, the proposed model predicts product temperature evolution from the thermostat setting and the ambient temperature. The developed methodology was applied to the cold chain of cooked ham including, the display cabinet, transport by the consumer and the domestic refrigerator, to predict the evolution of state variables, such as the temperature and the growth of Listeria monocytogenes. The impacts of the input factors were calculated and ranked. It was found that the product's time-temperature history and the initial contamination level are the main causes of consumers' exposure. Then, a refined analysis was applied, revealing the importance of consumer behaviors on Listeria monocytogenes exposure.

  20. Positive Mode LC-MS/MS Analysis of Chondroitin Sulfate Modified Glycopeptides Derived from Light and Heavy Chains of The Human Inter-α-Trypsin Inhibitor Complex.

    PubMed

    Gomez Toledo, Alejandro; Nilsson, Jonas; Noborn, Fredrik; Sihlbom, Carina; Larson, Göran

    2015-12-01

    The inter-α-trypsin inhibitor complex is a macromolecular arrangement of structurally related heavy chain proteins covalently cross-linked to the chondroitin sulfate (CS) chain of the proteoglycan bikunin. The inter-α-trypsin inhibitor complex is abundant in plasma and associated with inflammation, kidney diseases, cancer and diabetes. Bikunin is modified at Ser-10 by a single low-sulfated CS chain of 23-55 monosaccharides with 4-9 sulfate groups. The innermost four monosaccharides (GlcAβ3Galβ3Galβ4Xylβ-O-) compose the linkage region, believed to be uniform with a 4-O-sulfation to the outer Gal. The cross-linkage region of the bikunin CS chain is located in the nonsulfated nonreducing end, (GalNAcβ4GlcAβ3)(n), to which heavy chains (H1-H3) may be bound in GalNAc to Asp ester linkages. In this study we employed a glycoproteomics protocol to enrich and analyze light and heavy chain linkage and cross-linkage region CS glycopeptides derived from the IαI complex of human plasma, urine and cerebrospinal fluid samples. The samples were trypsinized, enriched by strong anion exchange chromatography, partially depolymerized with chondroitinase ABC and analyzed by LC-MS/MS using higher-energy collisional dissociation. The analyses demonstrated that the CS linkage region of bikunin is highly heterogeneous. In addition to sulfation of the Gal residue, Xyl phosphorylation was observed although exclusively in urinary samples. We also identified novel Neu5Ac and Fuc modifications of the linkage region as well as the presence of mono- and disialylated core 1 O-linked glycans on Thr-17. Heavy chains H1 and H2 were identified cross-linked to GalNAc residues one or two GlcA residues apart and H1 was found linked to either the terminal or subterminal GalNAc residues. The fragmentation behavior of CS glycopeptides under variable higher-energy collisional dissociation conditions displays an energy dependence that may be used to obtain complementary structural details. Finally

  1. Human laminin B2 chain

    SciTech Connect

    Pikkarainen, T.; Kallunki, T.; Tryggvason, K.

    1988-05-15

    The complete amino acid sequence of the human laminin B2 chains has been determined by sequencing of cDNA clones. The six overlapping clones studied cover approximately 7.5 kilobases of which 5312 nucleotides were sequenced from the 5' end. The open reading frame codes for a 33-residue signal peptide and a 1576-residue B2 chain proper, which is 189 residues less than in the highly homologous B1 chain. Computer analysis revealed that the B2 chain consists of distinct domains that contain helical structures, cysteine-rich repeats, and globular regions, as does the B1 chain. However, domain ..cap alpha.. and domain ..beta.. of the B1 chain have no counterpart in B2, and the number of cysteine-rich repeats is 12, or 1 less than in the B1 chain. The degree of homology between the two chains is highest in the cysteine repeat-containing domains III and V where 40% of the residues match. However, in helical domains I/II only 16% of residues match. The results demonstrate that the B1 and B2 chains of laminin are highly homologous proteins that are probably the products of related genes.

  2. Transcription analysis of class II human leukocyte antigen genes from normal and immunodeficient B lymphocytes, using polymerase chain reaction.

    PubMed Central

    Bull, M; van Hoef, A; Gorski, J

    1990-01-01

    The RNA transcript levels of all human leukocyte antigen class II loci were determined from class II congenital immunodeficient B cells by polymerase chain reaction amplification of cDNA. No mRNA was observed under conditions in which 0.01% normal levels could be visualized. Pre-mRNA could be amplified from normal B cells but not from immunodeficient B cells, indicating a transcription defect. Images PMID:2113177

  3. Finding starting points for Markov chain Monte Carlo analysis of genetic data from large and complex pedigrees.

    PubMed

    Luo, Yuqun; Lin, Shili

    2003-07-01

    Genetic data from founder populations are advantageous for studies of complex traits that are often plagued by the problem of genetic heterogeneity. However, the desire to analyze large and complex pedigrees that often arise from such populations, coupled with the need to handle many linked and highly polymorphic loci simultaneously, poses challenges to current standard approaches. A viable alternative to solving such problems is via Markov chain Monte Carlo (MCMC) procedures, where a Markov chain, defined on the state space of a latent variable (e.g., genotypic configuration or inheritance vector), is constructed. However, finding starting points for the Markov chains is a difficult problem when the pedigree is not single-locus peelable; methods proposed in the literature have not yielded completely satisfactory solutions. We propose a generalization of the heated Gibbs sampler with relaxed penetrances (HGRP) of Lin et al., ([1993] IMA J. Math. Appl. Med. Biol. 10:1-17) to search for starting points. HGRP guarantees that a starting point will be found if there is no error in the data, but the chain usually needs to be run for a long time if the pedigree is extremely large and complex. By introducing a forcing step, the current algorithm substantially reduces the state space, and hence effectively speeds up the process of finding a starting point. Our algorithm also has a built-in preprocessing procedure for Mendelian error detection. The algorithm has been applied to both simulated and real data on two large and complex Hutterite pedigrees under many settings, and good results are obtained. The algorithm has been implemented in a user-friendly package called START. PMID:12813723

  4. Kinetic analysis of a monoclonal therapeutic antibody and its single-chain homolog by surface plasmon resonance.

    PubMed

    Patel, Rekha; Andrien, Bruce A

    2010-01-01

    Monoclonal antibodies (mAbs) and antibody fragments have become an emerging class of therapeutics since 1986. Their versatility enables them to be engineered for optimal efficiency and decreased immunogenicity, and the path to market has been set by recent regulatory approvals. One of the initial criteria for success of any protein or antibody therapeutic is to understand its binding characteristics to the target antigen. Surface plasmon resonance (SPR) has been widely used and is an important tool for ligand-antigen binding characterization. In this work, the binding kinetics of a recombinant mAb and its single-chain antibody homolog, single-chain variable fragment (scFv), was analyzed by SPR. These two proteins target the same antigen. The binding kinetics of the mAb (bivalent antibody) and scFv (monovalent scFv) for this antigen was analyzed along with an assessment of the thermodynamics of the binding interactions. Alternative binding configurations were investigated to evaluate potential experimental bias because theoretically experimental binding configuration should have no impact on binding kinetics. Self-association binding kinetics in the proteins' respective formulation solutions and antigen epitope mapping were also evaluated. Functional characterization of monoclonal and single-chain antibodies has become just as important as structural characterization in the biotechnology field. PMID:19720041

  5. The dynamic excitation of a granular chain for biomedical ultrasound applications: contact mechanics finite element analysis and validation

    NASA Astrophysics Data System (ADS)

    Gélat, P.; Yang, J.; Thomas, P. J.; Hutchins, D. A.; Akanji, O.; Davis, L. A. J.; Freear, S.; Harput, S.; Saffari, N.

    2016-01-01

    There has been recent interest in the transmission of acoustic signals along granular chains of spherical beads to produce waveforms of relevance to biomedical ultrasound applications. Hertzian contact between adjacent beads can introduce different harmonic content into the signal as it propagates. This transduction mechanism has the potential to be of use in both diagnostic and therapeutic ultrasound applications, and is the object of the study presented here. Although discrete dynamics models of this behaviour exist, a more comprehensive solution must be sought if changes in shape and deformation of individual beads are to be considered. Thus, the finite element method was used to investigate the dynamics of a granular chain of six, 1 mm diameter chrome steel spherical beads excited at one end using a sinusoidal displacement signal at 73 kHz. Output from this model was compared with the solution provided by the discrete dynamics model, and good overall agreement obtained. In addition, it was able to resolve the complex dynamics of the granular chain, including the multiple collisions which occur. It was demonstrated that under dynamic excitation conditions, the inability of discrete mechanics models to account for elastic deformation of the beads when these lose contact, could lead to discrepancies with experimental observations.

  6. Type analysis of the oligosaccharide chains on microheterogeneous components of bovine pancreatic DNAase by the lectin-nitrocellulose sheet method.

    PubMed Central

    Kijimoto-Ochiai, S; Katagiri, Y U; Hatae, T; Okuyama, H

    1989-01-01

    The oligosaccharide chains of microheterogeneous bovine pancreatic DNAases were characterized by the lectin-nitrocellulose sheet method. The active fractions of the DNAases from column chromatography showed four major and several minor spots on a two-dimensional polyacrylamide gel. They were transferred on to nitrocellulose sheets and treated with glycosidases (neuraminidase, endo-beta-N-acetyl glucosaminidase H or F, or peptide N-glycosidase F) and treated with peroxidase-coupled lectins (concanavalin A, Ricinus communis agglutinin or wheat-germ agglutinin). From the results, the most probable oligosaccharide types were proposed to be as follows: the four major spots contained components which had high-mannose type or hybrid-type oligosaccharides, such as those susceptible to endo-beta-N-acetylglucosaminidase H. In addition, spot 1 contained a complex-type biantennary oligosaccharide without sialic acid and spot 3 contained a tri- or tetra-antennary complex-type oligosaccharide with sialic acid. The component corresponding to spot 2 had a hybrid-type oligosaccharide chain with a 'bisecting' acetylglucosamine, linked 1-4 to the beta-mannose residue of the trimannosyl core, and the component corresponding to spot 4 had a high-mannose-type oligosaccharide chain. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. PMID:2920025

  7. A Value Chain Analysis of ghost nets in the Arafura Sea: identifying trans-boundary stakeholders, intervention points and livelihood trade-offs.

    PubMed

    Butler, J R A; Gunn, R; Berry, H L; Wagey, G A; Hardesty, B D; Wilcox, C

    2013-07-15

    Lost or discarded fishing nets are a significant component of marine debris which has trans-boundary impacts in large marine ecosystems. Such 'ghost nets' cause the by-catch of marine fauna and require retrieval from coastlines where they wash up. Identifying the causes of discarded nets and feasible intervention points requires analysis of a complex value chain and the stakeholders within it, yet no studies have attempted this. In this paper we combine Value Chain Analysis, commonly applied to understand value-adding for a commodity, with elements of Life Cycle Assessment and social network analysis to examine the drivers, stakeholders, economic, environmental and social costs and benefits in the life of a trawl net. We use the Arafura Sea as a case study, which is shared by Indonesia, Papua New Guinea and Australia, and is the focus of a Trans-boundary Diagnostic Assessment (TDA) within the Arafura-Timor Seas Ecosystem Action program (ATSEA). We follow a trawl net through four sub-systems: manufacture of webbing in South Korea, fishing and loss by an Indonesian vessel, retrieval as ghost net on the northern Australian coastline by Indigenous rangers, and disposal or re-cycling as 'GhostNet Art' by Indigenous artists. Primary stakeholders along the value chain incur economic and social benefits, and economic and environmental costs. There is an anomaly in the chain between Indonesian fishermen and Indigenous rangers, artists and communities due to the lack of market linkages between these primary stakeholders. The first 'nexus of influence' where reductions in net losses and environmental costs can be achieved is through interactions between GhostNets Australia, the World Wide Fund for Nature and the Australian Government, which can influence Indonesian fishery management institutions and fishing crews. The second nexus is via the international art market which by publicising GhostNet Art can raise awareness amongst fish consumers about the impacts of ghost nets

  8. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis--a case report of corneal ulcer.

    PubMed

    Chen, K H; Sheu, M M; Lin, S R

    1997-09-01

    We report a case of corneal ulcer caused by nontuberculous mycobacteria which was confirmed by smear and culture. We attempted a new method for the rapid identification of mycobacteria to the species level on the basis of evaluation by the polymerase chain reaction of the gene encoding. The method is involved with restriction enzyme analysis of PCR product obtained with primers common to all mycobacteria. Using the restriction enzyme Bst EII and Hae III, clinically relevant and other frequent laboratory isolates were differentiated to the species or subspecies level by PCR-restriction enzyme analysis. The main prevalence of pattern analysis is Mycobacterium chelonae subsp. abscessus in this case. The outcome suggests that PCR-restriction enzyme analysis should be a useful method for early diagnosis concerning nontuberculous mycobacterial keratitis. PMID:9348738

  9. Total Proteome Analysis Identifies Migration Defects as a Major Pathogenetic Factor in Immunoglobulin Heavy Chain Variable Region (IGHV)-unmutated Chronic Lymphocytic Leukemia*

    PubMed Central

    Eagle, Gina L.; Zhuang, Jianguo; Jenkins, Rosalind E.; Till, Kathleen J.; Jithesh, Puthen V.; Lin, Ke; Johnson, Gillian G.; Oates, Melanie; Park, Kevin; Kitteringham, Neil R.; Pettitt, Andrew R.

    2015-01-01

    The mutational status of the immunoglobulin heavy chain variable region defines two clinically distinct forms of chronic lymphocytic leukemia (CLL) known as mutated (M-CLL) and unmutated (UM-CLL). To elucidate the molecular mechanisms underlying the adverse clinical outcome associated with UM-CLL, total proteomes from nine UM-CLL and nine M-CLL samples were analyzed by isobaric tags for relative and absolute quantification (iTRAQ)-based mass spectrometry. Based on the expression of 3521 identified proteins, principal component analysis separated CLL samples into two groups corresponding to immunoglobulin heavy chain variable region mutational status. Computational analysis showed that 43 cell migration/adhesion pathways were significantly enriched by 39 differentially expressed proteins, 35 of which were expressed at significantly lower levels in UM-CLL samples. Furthermore, UM-CLL cells underexpressed proteins associated with cytoskeletal remodeling and overexpressed proteins associated with transcriptional and translational activity. Taken together, our findings indicate that UM-CLL cells are less migratory and more adhesive than M-CLL cells, resulting in their retention in lymph nodes, where they are exposed to proliferative stimuli. In keeping with this hypothesis, analysis of an extended cohort of 120 CLL patients revealed a strong and specific association between UM-CLL and lymphadenopathy. Our study illustrates the potential of total proteome analysis to elucidate pathogenetic mechanisms in cancer. PMID:25645933

  10. Exploration Supply Chain Simulation

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Exploration Supply Chain Simulation project was chartered by the NASA Exploration Systems Mission Directorate to develop a software tool, with proper data, to quantitatively analyze supply chains for future program planning. This tool is a discrete-event simulation that uses the basic supply chain concepts of planning, sourcing, making, delivering, and returning. This supply chain perspective is combined with other discrete or continuous simulation factors. Discrete resource events (such as launch or delivery reviews) are represented as organizational functional units. Continuous resources (such as civil service or contractor program functions) are defined as enabling functional units. Concepts of fixed and variable costs are included in the model to allow the discrete events to interact with cost calculations. The definition file is intrinsic to the model, but a blank start can be initiated at any time. The current definition file is an Orion Ares I crew launch vehicle. Parameters stretch from Kennedy Space Center across and into other program entities (Michaud Assembly Facility, Aliant Techsystems, Stennis Space Center, Johnson Space Center, etc.) though these will only gain detail as the file continues to evolve. The Orion Ares I file definition in the tool continues to evolve, and analysis from this tool is expected in 2008. This is the first application of such business-driven modeling to a NASA/government-- aerospace contractor endeavor.

  11. A quantitative analysis of Propionibacterium acnes in lesional and non-lesional skin of patients with progressive macular hypomelanosis by real-time polymerase chain reaction

    PubMed Central

    de Morais Cavalcanti, Silvana Maria; de França, Emmanuel Rodrigues; Magalhães, Marcelo; Lins, Ana Kelly; Brandão, Laura Costa; Magalhães, Vera

    2011-01-01

    Little is known about the etiology of progressive macular hypomelanosis, although it has been suggested that Propionibacterium acnes plays an important role. While microbiological culture is commonly employed to identify Propionibacterium acnes, new identification methods have been under investigation, amongst them polymerase chain reaction. To determine the cut-off point for the number of genome copies of Propionibacterium acnes in the lesional skin of patients with progressive macular hypomelanosis as a positive marker, employing quantitative real-time polymerase chain reaction and anaerobic culture, considered gold standard. An observational study with a comparison group, included 35 patients with dermatosis, attended at the Oswaldo Cruz University Hospital, Pernambuco, Brazil, between March and May 2008. Lesional skin was compared to non-lesional skin through positive testing with real-time polymerase chain reaction and culture. The Statistical Package for Social Sciences, version 12.0, was employed for the association analysis with the McNemar test, and the cut-off point with the ROC curve for maximum values. Propionibacterium acnes was most frequently encountered in lesional areas (p<0,025). The cut-off point of Propionibacterium acnes in lesional skin was 1,333 genome copies, with a sensitivity of 87,9% and a specificity of 100,0%. Since Propionibacterium acnes is a saprophyte, identifying the cut-off point may assist in determining its positivity in lesional skin in patients suffering with this dermatosis. PMID:24031649

  12. Quantitative proteomic analysis reveals metabolic alterations, calcium dysregulation, and increased expression of extracellular matrix proteins in laminin α2 chain-deficient muscle.

    PubMed

    de Oliveira, Bruno Menezes; Matsumura, Cintia Y; Fontes-Oliveira, Cibely C; Gawlik, Kinga I; Acosta, Helena; Wernhoff, Patrik; Durbeej, Madeleine

    2014-11-01

    Congenital muscular dystrophy with laminin α2 chain deficiency (MDC1A) is one of the most severe forms of muscular disease and is characterized by severe muscle weakness and delayed motor milestones. The genetic basis of MDC1A is well known, yet the secondary mechanisms ultimately leading to muscle degeneration and subsequent connective tissue infiltration are not fully understood. In order to obtain new insights into the molecular mechanisms underlying MDC1A, we performed a comparative proteomic analysis of affected muscles (diaphragm and gastrocnemius) from laminin α2 chain-deficient dy(3K)/dy(3K) mice, using multidimensional protein identification technology combined with tandem mass tags. Out of the approximately 700 identified proteins, 113 and 101 proteins, respectively, were differentially expressed in the diseased gastrocnemius and diaphragm muscles compared with normal muscles. A large portion of these proteins are involved in different metabolic processes, bind calcium, or are expressed in the extracellular matrix. Our findings suggest that metabolic alterations and calcium dysregulation could be novel mechanisms that underlie MDC1A and might be targets that should be explored for therapy. Also, detailed knowledge of the composition of fibrotic tissue, rich in extracellular matrix proteins, in laminin α2 chain-deficient muscle might help in the design of future anti-fibrotic treatments. All MS data have been deposited in the ProteomeXchange with identifier PXD000978 (http://proteomecentral.proteomexchange.org/dataset/PXD000978).

  13. Calibration chain design based on integrating sphere transfer radiometer for SI-traceable on-orbit spectral radiometric calibration and its uncertainty analysis

    NASA Astrophysics Data System (ADS)

    Zhao, Wei-Ning; Fang, Wei; Sun, Li-Wei; Cui, Li-Hong; Wang, Yu-Peng

    2016-09-01

    In order to satisfy the requirement of SI-traceable on-orbit absolute radiation calibration transfer with high accuracy for satellite remote sensors, a transfer chain consisting of a fiber coupling monochromator (FBM) and an integrating sphere transfer radiometer (ISTR) was designed in this paper. Depending on the Sun, this chain based on detectors provides precise spectral radiometric calibration and measurement to spectrometers in the reflective solar band (RSB) covering 300-2500 nm with a spectral bandwidth of 0.5-6 nm. It shortens the traditional chain based on lamp source and reduces the calibration uncertainty from 5% to 0.5% by using the cryogenic radiometer in space as a radiometric benchmark and trap detectors as secondary standard. This paper also gives a detailed uncertainty budget with reasonable distribution of each impact factor, including the weak spectral signal measurement with uncertainty of 0.28%. According to the peculiar design and comprehensive uncertainty analysis, it illustrates that the spectral radiance measurement uncertainty of the ISTR system can reach to 0.48%. The result satisfies the requirements of SI-traceable on-orbit calibration and has wider significance for expanding the application of the remote sensing data with high-quality. Project supported by the National Natural Science Foundation of China (Grant No. 41474161) and the National High-Technology Program of China (Grant No. 2015AA123703).

  14. Semiquantitative reverse transcription-polymerase chain reaction analysis of mRNA for growth factors and growth factor receptors from normal and healing rabbit medial collateral ligament tissue.

    PubMed

    Sciore, P; Boykiw, R; Hart, D A

    1998-07-01

    Growth factors and their receptors play an essential role in the development, maturation, and response to injury of all tissues. A number of studies have explored the possibility of improving ligament healing with exogenous growth factors. However, limited data is available regarding the endogenous growth factor network in ligaments on which any exogenous growth factors must impact. The purpose of this study was to assess the endogenous growth factor network with molecular techniques. By the sensitive reverse transcription-polymerase chain reaction technique, transcripts for a number of growth factors and receptors were detected with RNA isolated from normal and healing rabbit medial collateral ligament tissues. These include transforming growth factor-beta1, insulin-like growth factors I and II, basic fibroblast growth factor, endothelin-1, and the receptors for insulin and insulin-like growth factor II. Semiquantitative reverse transcription-polymerase chain reaction analysis of RNA from normal and scar tissues from the medial collateral ligament revealed that the levels of several transcripts were elevated in the scar tissue. It was not possible to confirm biological activity because of the hypocellularity of the tissues; however, the results obtained indicate that the reverse transcription-polymerase chain reaction approach to defining the endogenous growth factor-receptor phenotype is feasible, and further definition should contribute to the development of rational approaches to exogenous therapy to improve healing.

  15. Calibration chain design based on integrating sphere transfer radiometer for SI-traceable on-orbit spectral radiometric calibration and its uncertainty analysis

    NASA Astrophysics Data System (ADS)

    Zhao, Wei-Ning; Fang, Wei; Sun, Li-Wei; Cui, Li-Hong; Wang, Yu-Peng

    2016-09-01

    In order to satisfy the requirement of SI-traceable on-orbit absolute radiation calibration transfer with high accuracy for satellite remote sensors, a transfer chain consisting of a fiber coupling monochromator (FBM) and an integrating sphere transfer radiometer (ISTR) was designed in this paper. Depending on the Sun, this chain based on detectors provides precise spectral radiometric calibration and measurement to spectrometers in the reflective solar band (RSB) covering 300–2500 nm with a spectral bandwidth of 0.5–6 nm. It shortens the traditional chain based on lamp source and reduces the calibration uncertainty from 5% to 0.5% by using the cryogenic radiometer in space as a radiometric benchmark and trap detectors as secondary standard. This paper also gives a detailed uncertainty budget with reasonable distribution of each impact factor, including the weak spectral signal measurement with uncertainty of 0.28%. According to the peculiar design and comprehensive uncertainty analysis, it illustrates that the spectral radiance measurement uncertainty of the ISTR system can reach to 0.48%. The result satisfies the requirements of SI-traceable on-orbit calibration and has wider significance for expanding the application of the remote sensing data with high-quality. Project supported by the National Natural Science Foundation of China (Grant No. 41474161) and the National High-Technology Program of China (Grant No. 2015AA123703).

  16. Exploratory Analysis of Fast-Food Chain Restaurant Menus Before and After Implementation of Local Calorie-Labeling Policies, 2005–2011

    PubMed Central

    Namba, Alexa; Leonberg, Beth L.; Wootan, Margo G.

    2013-01-01

    Introduction Since 2008, several states and municipalities have implemented regulations requiring provision of nutrition information at chain restaurants to address obesity. Although early research into the effect of such labels on consumer decisions has shown mixed results, little information exists on the restaurant industry’s response to labeling. The objective of this exploratory study was to evaluate the effect of menu labeling on fast-food menu offerings over 7 years, from 2005 through 2011. Methods Menus from 5 fast-food chains that had outlets in jurisdictions subject to menu-labeling laws (cases) were compared with menus from 4 fast-food chains operating in jurisdictions not requiring labeling (controls). A trend analysis assessed whether case restaurants improved the healthfulness of their menus relative to the control restaurants. Results Although the overall prevalence of “healthier” food options remained low, a noteworthy increase was seen after 2008 in locations with menu-labeling laws relative to those without such laws. Healthier food options increased from 13% to 20% at case locations while remaining static at 8% at control locations (test for difference in the trend, P = .02). Since 2005, the average calories for an à la carte entrée remained moderately high (approximately 450 kilocalories), with less than 25% of all entrées and sides qualifying as healthier and no clear systematic differences in the trend between chain restaurants in case versus control areas (P ≥ .50). Conclusion These findings suggest that menu labeling has thus far not affected the average nutritional content of fast-food menu items, but it may motivate restaurants to increase the availability of healthier options. PMID:23786908

  17. Static network analysis of a pork supply chain in Northern Germany-Characterisation of the potential spread of infectious diseases via animal movements.

    PubMed

    Büttner, Kathrin; Krieter, Joachim; Traulsen, Arne; Traulsen, Imke

    2013-07-01

    Transport of live animals is a major risk factor in the spread of infectious diseases between holdings. The present study analysed the pork supply chain of a producer community in Northern Germany. The structure of trade networks can be characterised by carrying out a network analysis. To identify holdings with a central position in this directed network of pig production, several parameters describing these properties were measured (in-degree, out-degree, ingoing and outgoing infection chain, betweenness centrality and ingoing and outgoing closeness centrality). To obtain the importance of the different holding types (multiplier, farrowing farms, finishing farms and farrow-to-finishing farms) within the pyramidal structure of the pork supply chain, centrality parameters were calculated for the entire network as well as for the individual holding types. Using these centrality parameters, two types of holdings could be identified. In the network studied, finishing and farrow-to-finishing farms were more likely to be infected due to the high number of ingoing trade contacts. Due to the high number of outgoing trade contacts multipliers and farrowing farms had an increased risk to spread a disease to other holdings. However, the results of the centrality parameters degree and infection chain were not always consistent, such that the indirect trade contacts should be taken into consideration to understand the real importance of a holding in spreading or contracting an infection. Furthermore, all calculated parameters showed a highly right-skewed distribution. Networks with such a degree distribution are considered to be highly resistant concerning the random removal of nodes. But by strategic removal of the most central holdings, e.g. by trade restrictions or selective vaccination or culling, the network structure can be changed efficiently and thus decompose into fragments. Such a fragmentation of the trade networks is of particular importance from an epidemiological

  18. A Comparison of Bayesian Monte Carlo Markov Chain and Maximum Likelihood Estimation Methods for the Statistical Analysis of Geodetic Time Series

    NASA Astrophysics Data System (ADS)

    Olivares, G.; Teferle, F. N.

    2013-12-01

    Geodetic time series provide information which helps to constrain theoretical models of geophysical processes. It is well established that such time series, for example from GPS, superconducting gravity or mean sea level (MSL), contain time-correlated noise which is usually assumed to be a combination of a long-term stochastic process (characterized by a power-law spectrum) and random noise. Therefore, when fitting a model to geodetic time series it is essential to also estimate the stochastic parameters beside the deterministic ones. Often the stochastic parameters include the power amplitudes of both time-correlated and random noise, as well as, the spectral index of the power-law process. To date, the most widely used method for obtaining these parameter estimates is based on maximum likelihood estimation (MLE). We present an integration method, the Bayesian Monte Carlo Markov Chain (MCMC) method, which, by using Markov chains, provides a sample of the posteriori distribution of all parameters and, thereby, using Monte Carlo integration, all parameters and their uncertainties are estimated simultaneously. This algorithm automatically optimizes the Markov chain step size and estimates the convergence state by spectral analysis of the chain. We assess the MCMC method through comparison with MLE, using the recently released GPS position time series from JPL and apply it also to the MSL time series from the Revised Local Reference data base of the PSMSL. Although the parameter estimates for both methods are fairly equivalent, they suggest that the MCMC method has some advantages over MLE, for example, without further computations it provides the spectral index uncertainty, is computationally stable and detects multimodality.

  19. Static network analysis of a pork supply chain in Northern Germany-Characterisation of the potential spread of infectious diseases via animal movements.

    PubMed

    Büttner, Kathrin; Krieter, Joachim; Traulsen, Arne; Traulsen, Imke

    2013-07-01

    Transport of live animals is a major risk factor in the spread of infectious diseases between holdings. The present study analysed the pork supply chain of a producer community in Northern Germany. The structure of trade networks can be characterised by carrying out a network analysis. To identify holdings with a central position in this directed network of pig production, several parameters describing these properties were measured (in-degree, out-degree, ingoing and outgoing infection chain, betweenness centrality and ingoing and outgoing closeness centrality). To obtain the importance of the different holding types (multiplier, farrowing farms, finishing farms and farrow-to-finishing farms) within the pyramidal structure of the pork supply chain, centrality parameters were calculated for the entire network as well as for the individual holding types. Using these centrality parameters, two types of holdings could be identified. In the network studied, finishing and farrow-to-finishing farms were more likely to be infected due to the high number of ingoing trade contacts. Due to the high number of outgoing trade contacts multipliers and farrowing farms had an increased risk to spread a disease to other holdings. However, the results of the centrality parameters degree and infection chain were not always consistent, such that the indirect trade contacts should be taken into consideration to understand the real importance of a holding in spreading or contracting an infection. Furthermore, all calculated parameters showed a highly right-skewed distribution. Networks with such a degree distribution are considered to be highly resistant concerning the random removal of nodes. But by strategic removal of the most central holdings, e.g. by trade restrictions or selective vaccination or culling, the network structure can be changed efficiently and thus decompose into fragments. Such a fragmentation of the trade networks is of particular importance from an epidemiological

  20. Identification of 'carbon hot-spots' and quantification of GHG intensities in the biodiesel supply chain using hybrid LCA and structural path analysis.

    PubMed

    Acquaye, Adolf A; Wiedmann, Thomas; Feng, Kuishang; Crawford, Robert H; Barrett, John; Kuylenstierna, Johan; Duffy, Aidan P; Koh, S C Lenny; McQueen-Mason, Simon

    2011-03-15

    It is expected that biodiesel production in the EU will remain the dominant contributor as part of a 10% minimum binding target for biofuel in transportation fuel by 2020 within the 20% renewable energy target in the overall EU energy mix. Life cycle assessments (LCA) of biodiesel to evaluate its environmental impacts have, however, remained questionable, mainly because of the adoption of a traditional process analysis approach resulting in system boundary truncation and because of issues regarding the impacts of land use change and N(2)O emissions from fertilizer application. In this study, a hybrid LCA methodology is used to evaluate the life cycle CO(2) equivalent emissions of rape methyl ester (RME) biodiesel. The methodology uses input-output analysis to estimate upstream indirect emissions in order to complement traditional process LCA in a hybrid framework. It was estimated that traditional LCA accounted for 2.7 kg CO(2)-eq per kg of RME or 36.6% of total life cycle emissions of the RME supply chin. Further to the inclusion of upstream indirect impacts in the LCA system (which accounted for 23% of the total life cycle emissions), emissions due to direct land use change (6%) and indirect land use change (16.5%) and N(2)O emissions from fertilizer applications (17.9%) were also calculated. Structural path analysis is used to decompose upstream indirect emissions paths of the biodiesel supply chain in order to identify, quantify, and rank high carbon emissions paths or 'hot-spots' in the biodiesel supply chain. It was shown, for instance, that inputs from the 'Other Chemical Products' sector (identified as phosphoric acid, H(3)PO(4)) into the biodiesel production process represented the highest carbon emission path (or hot-spot) with 5.35% of total upstream indirect emissions of the RME biodiesel supply chain. PMID:21319814

  1. Application of a bi-stable chain model for the analysis of jerky twin boundary motion in NiMnGa

    NASA Astrophysics Data System (ADS)

    Benichou, Itamar; Faran, Eilon; Shilo, Doron; Givli, Sefi

    2013-01-01

    The "jerky" motion of a twin boundary in the ferromagnetic shape memory alloy NiMnGa is studied experimentally and theoretically. We employ a bi-stable chain model in order to interpret macroscopic stress-strain experiments and extract important micro-level properties. The analysis reveals the existence of a periodic barrier for type I twin boundary motion with an average distance of 19 μm and amplitude of 0.16 J/m2. Further, we show that the macroscopic mechanical response depends on the length of the crystal and predict a significant decrease of the hysteresis in sub-mm length specimens.

  2. Integrated Markov Chain Monte Carlo (MCMC) analysis of primordial non-Gaussianity (f{sub NL}) in the recent CMB data

    SciTech Connect

    Kim, Jaiseung

    2011-04-01

    We have made a Markov Chain Monte Carlo (MCMC) analysis of primordial non-Gaussianity (f{sub NL}) using the WMAP bispectrum and power spectrum. In our analysis, we have simultaneously constrained f{sub NL} and cosmological parameters so that the uncertainties of cosmological parameters can properly propagate into the f{sub NL} estimation. Investigating the parameter likelihoods deduced from MCMC samples, we find slight deviation from Gaussian shape, which makes a Fisher matrix estimation less accurate. Therefore, we have estimated the confidence interval of f{sub NL} by exploring the parameter likelihood without using the Fisher matrix. We find that the best-fit values of our analysis make a good agreement with other results, but the confidence interval is slightly different.

  3. [Species identification of grouper and snapper in Taiwan Strait using polymerase chain reaction-restriction fragment length polymorphism analysis and lab-on-a-chip system].

    PubMed

    Chen, Shuangya; Zhang, Jin; Chen, Weiling; Xu, Dunming; Zhou, Yu

    2011-07-01

    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis and lab-on-a-chip system were used to identify grouper and snapper species in Taiwan Strait. A fragment of 464 bp length of mitochondrial cytochrome b gene was amplified by PCR and the products were digested with restriction enzymes Dde I , Hae III and NLa III, individually. The fragments generated after digestion were further resolved on the DNA Chip. Eight grouper species and five snapper species were successfully identified. The results demonstrated that PCR-RFLP analysis and lab-on-a-chip system provide a fast, easy, automated, and reliable analysis approach. This approach is potential for the purpose of fish adulteration control.

  4. Backcountry Adventure as Spiritual Development: A Means-End Study

    ERIC Educational Resources Information Center

    Marsh, Paul E.

    2008-01-01

    What do people mean when they describe backcountry adventure experiences as being "spiritual"? Spiritual aspects of adventure experiences in the wilderness have been recounted anecdotally and recognized in research. This body of research, however, has left the definition of the term spiritual to the individual participants, and has not yet…

  5. Performance of Polymerase Chain Reaction Analysis of the Amniotic Fluid of Pregnant Women for Diagnosis of Congenital Toxoplasmosis: A Systematic Review and Meta-Analysis

    PubMed Central

    2016-01-01

    Introduction Congenital infection caused by Toxoplasma gondii can cause serious damage that can be diagnosed in utero or at birth, although most infants are asymptomatic at birth. Prenatal diagnosis of congenital toxoplasmosis considerably improves the prognosis and outcome for infected infants. For this reason, an assay for the quick, sensitive, and safe diagnosis of fetal toxoplasmosis is desirable. Goal To systematically review the performance of polymerase chain reaction (PCR) analysis of the amniotic fluid of pregnant women with recent serological toxoplasmosis diagnoses for the diagnosis of fetal toxoplasmosis. Method A systematic literature review was conducted via a search of electronic databases; the literature included primary studies of the diagnostic accuracy of PCR analysis of amniotic fluid from pregnant women who seroconverted during pregnancy. The PCR test was compared to a gold standard for diagnosis. Results A total of 1.269 summaries were obtained from the electronic database and reviewed, and 20 studies, comprising 4.171 samples, met the established inclusion criteria and were included in the review. The following results were obtained: studies about PCR assays for fetal toxoplasmosis are generally susceptible to bias; reports of the tests’ use lack critical information; the protocols varied among studies; the heterogeneity among studies was concentrated in the tests’ sensitivity; there was evidence that the sensitivity of the tests increases with time, as represented by the trimester; and there was more heterogeneity among studies in which there was more time between maternal diagnosis and fetal testing. The sensitivity of the method, if performed up to five weeks after maternal diagnosis, was 87% and specificity was 99%. Conclusion The global sensitivity heterogeneity of the PCR test in this review was 66.5% (I2). The tests show low evidence of heterogeneity with a sensitivity of 87% and specificity of 99% when performed up to five weeks

  6. Immunogenetic analysis of the heavy chain variable regions of IgE from patients allergic to peanuts.

    PubMed

    Janezic, A; Chapman, C J; Snow, R E; Hourihane, J O; Warner, J O; Stevenson, F K

    1998-03-01

    Peanuts are one of the most allergenic of the foods, and hypersensitivity responses to peanut allergens can be fatal. Although the nature of the antigenic components of peanuts is being defined at the molecular level, there is little information on the induced IgE antibodies, which are central to the allergic reaction. Recognition sites of IgE antibody molecules arise from the variable regions of heavy and light chains (VH and VL). By using nested polymerase chain reactions with specific primers for the available repertoire of VH genes, together with primers in the constant epsilon region, we have amplified VH sequences of IgE from blood lymphocytes of two patients with peanut allergy. After cloning and sequencing the products, we found a predominance of VH1 family use in both patients, which was not found in control IgM-specific primers. The IgE VH sequences were highly somatically mutated, but in only six of 17 cases was there clear evidence for clustering of amino acids indicative of antigen selection. Previous results from patients with allergy to house dust mites have indicated predominance of VH5 use and little evidence for antigen selection. Although results from two patients allergic to peanuts must be regarded as preliminary, they do suggest that the IgE response to peanuts may have a different VH bias, with a similar mutational pattern.

  7. Resonance Assignments and Secondary Structure Analysis of Dynein Light Chain 8 by Magic-angle Spinning NMR Spectroscopy

    SciTech Connect

    Sun, Shangjin; Butterworth, Andrew H.; Paramasivam, Sivakumar; Yan, Si; Lightcap, Christine M.; Williams, John C.; Polenova, Tatyana E.

    2011-08-04

    Dynein light chain LC8 is the smallest subunit of the dynein motor complex and has been shown to play important roles in both dynein-dependent and dynein-independent physiological functions via its interaction with a number of its binding partners. It has also been linked to pathogenesis including roles in viral infections and tumorigenesis. Structural information for LC8-target proteins is critical to understanding the underlying function of LC8 in these complexes. However, some LC8-target interactions are not amenable to structural characterization by conventional structural biology techniques owing to their large size, low solubility, and crystallization difficulties. Here, we report magic-angle spinning (MAS) NMR studies of the homodimeric apo-LC8 protein as a first effort in addressing more complex, multi-partner, LC8-based protein assemblies. We have established site-specific backbone and side-chain resonance assignments for the majority of the residues of LC8, and show TALOS+-predicted torsion angles ø and ψ in close agreement with most residues in the published LC8 crystal structure. Data obtained through these studies will provide the first step toward using MAS NMR to examine the LC8 structure, which will eventually be used to investigate protein–protein interactions in larger systems that cannot be determined by conventional structural studies.

  8. A novel multiplexing, polymerase chain reaction-based assay for the analysis of chromosome 18q status in colorectal cancer.

    PubMed

    Erill, Nadina; Colomer, Anna; Calvo, Miquel; Vidal, August; Román, Ruth; Verdú, Montse; Cordón-Cardó, Carlos; Puig, Xavier

    2005-10-01

    Chromosome 18q allelic loss has been reported to have prognostic significance in stage II colorectal carcinoma. We have developed a fluorescent multiplex polymerase chain reaction assay to analyze five microsatellite markers (D18S55, D18S58, D18S61, D18S64, and D18S69) for allelic loss at the long arm of chromosome 18. Amplicon detection and evaluation was accomplished by capillary electrophoresis using an ABI 310 genetic analyzer. Robustness of the assay when performed on DNA extracted from formalin-fixed, paraffin-embedded tissue sections was confirmed by analyzing its repeatability and reproducibility. Allelic loss was assessed in 61 stage II colorectal tumors and was detected in 58% (31 of 53) of tumors not showing instability. As part of the study, results of 207 previous polymerase chain reaction/polyacrylamide-based assays were re-evaluated by two independent observers to determine the degree of concordance of visual evaluation. In the case of stage II colorectal tumors, when electropherogram results were compared with those obtained from visual evaluation of the same markers after polyacrylamide gel electrophoresis, discrepancies between observers were detected in 16.4% of determinations. In conclusion, we have developed a robust and reliable assay for multiplexed loss of heterozygosity determination that improves assessment of chromosome 18q allelic loss in colorectal tumors processed as routine formalin-fixed, paraffin-embedded specimens.

  9. Resonance Assignments and Secondary Structure Analysis of Dynein Light Chain 8 by Magic Angle Spinning NMR Spectroscopy

    PubMed Central

    Sun, Shangjin; Butterworth, Andrew H.; Paramasivam, Sivakumar; Yan, Si; Lightcap, Christine M.; Williams, John C.; Polenova, Tatyana

    2012-01-01

    Dynein light chain LC8 is the smallest subunit of the dynein motor complex and has been shown to play important roles in both dynein dependent and dynein independent physiological functions via its interaction with a number of its binding partners. It has also been linked to pathogenesis including roles in viral infections and tumorigenesis. Structural information for LC8-target proteins is critical to understanding the underlying function of LC8 in these complexes. However, some LC8-target interactions are not amenable for structural characterization by conventional structural biology techniques due to their large size, low solubility and crystallization difficulties. Here, we report magic angle spinning (MAS) NMR studies of the homodimeric apo-LC8 protein as a first effort in addressing more complex, multi-partner LC8-based protein assemblies. We have established site-specific backbone and side chain resonance assignments for the majority of the residues of LC8, and show TALOS+ predicted torsion angles ϕ and ψ in close agreement with most residues in the published LC8 crystal structure. Data obtained through these studies will provide the first step toward using MAS NMR to examine the LC8 structure, which will eventually be used to investigate protein-protein interactions in larger systems, which cannot be determined by conventional structural studies. PMID:23243318

  10. A novel multiplexing, polymerase chain reaction-based assay for the analysis of chromosome 18q status in colorectal cancer.

    PubMed

    Erill, Nadina; Colomer, Anna; Calvo, Miquel; Vidal, August; Román, Ruth; Verdú, Montse; Cordón-Cardó, Carlos; Puig, Xavier

    2005-10-01

    Chromosome 18q allelic loss has been reported to have prognostic significance in stage II colorectal carcinoma. We have developed a fluorescent multiplex polymerase chain reaction assay to analyze five microsatellite markers (D18S55, D18S58, D18S61, D18S64, and D18S69) for allelic loss at the long arm of chromosome 18. Amplicon detection and evaluation was accomplished by capillary electrophoresis using an ABI 310 genetic analyzer. Robustness of the assay when performed on DNA extracted from formalin-fixed, paraffin-embedded tissue sections was confirmed by analyzing its repeatability and reproducibility. Allelic loss was assessed in 61 stage II colorectal tumors and was detected in 58% (31 of 53) of tumors not showing instability. As part of the study, results of 207 previous polymerase chain reaction/polyacrylamide-based assays were re-evaluated by two independent observers to determine the degree of concordance of visual evaluation. In the case of stage II colorectal tumors, when electropherogram results were compared with those obtained from visual evaluation of the same markers after polyacrylamide gel electrophoresis, discrepancies between observers were detected in 16.4% of determinations. In conclusion, we have developed a robust and reliable assay for multiplexed loss of heterozygosity determination that improves assessment of chromosome 18q allelic loss in colorectal tumors processed as routine formalin-fixed, paraffin-embedded specimens. PMID:16237217

  11. Food Chain Security and Vulnerability

    NASA Astrophysics Data System (ADS)

    Brunet, Sébastien; Delvenne, Pierre; Claisse, Frédéric

    In our contemporary societies, the food chain could be defined as a macro-technical system, which depends on a wide variety of actors and risks analysis methods. In this contribution, risks related to the food chain are defined in terms of "modern risks" (Beck 1992). The whole national economic sector of food production/distribution is vulnerable to a local accident, which can affect the functioning of food chain, the export programs and even the political system. Such a complex socio-technical environment is undoubtedly vulnerable to intentional act such as terrorism.

  12. Application of principal component analysis in the pollution assessment with heavy metals of vegetable food chain in the old mining areas

    PubMed Central

    2012-01-01

    Background The aim of the paper is to assess by the principal components analysis (PCA) the heavy metal contamination of soil and vegetables widely used as food for people who live in areas contaminated by heavy metals (HMs) due to long-lasting mining activities. This chemometric technique allowed us to select the best model for determining the risk of HMs on the food chain as well as on people's health. Results Many PCA models were computed with different variables: heavy metals contents and some agro-chemical parameters which characterize the soil samples from contaminated and uncontaminated areas, HMs contents of different types of vegetables grown and consumed in these areas, and the complex parameter target hazard quotients (THQ). Results were discussed in terms of principal component analysis. Conclusion There were two major benefits in processing the data PCA: firstly, it helped in optimizing the number and type of data that are best in rendering the HMs contamination of the soil and vegetables. Secondly, it was valuable for selecting the vegetable species which present the highest/minimum risk of a negative impact on the food chain and human health. PMID:23234365

  13. Mitochondrial DNA variation in chinook salmon and chum salmon detected by restriction enzyme analysis of polymerase chain reaction products

    USGS Publications Warehouse

    Cronin, M.; Spearman, R.; Wilmot, R.; Patton, J.; Bickman, J.

    1993-01-01

    We analyze intraspecific mitochondrial DNA variation in chinook salmon from drainages in the Yukon River, the Kenai River, and Oregon and California rivers; and chum salmon from the Yukon River and vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified seperately using the polymerase chain reaction and then digested with at least 19 restrictions enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base subsitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (8) occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rviers and four occured in the Oregon/California, with only one haplotype shared between the regions. Sample sizes were too small to quantify the degree of stock seperation among drainages, but the patterns of variation that we observed suggest utility of the technique in genetic stock identification.

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

    PubMed

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

    2013-01-01

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

  15. Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach.

    PubMed

    Iñiguez, Alena M; Araújo, Adauto; Ferreira, Luiz Fernando; Vicente, Ana Carolina P

    2003-01-01

    The aim of this work was to determine approaches that would improve the quality of ancient DNA (aDNA) present in coprolites to enhance the possibility of success in retrieving specific sequence targets. We worked with coprolites from South American archaeological sites in Brazil and Chile dating up to 7,000 years ago. Using established protocols for aDNA extraction we obtained samples showing high degradation as usually happens with this kind of material. The reconstructive polymerization pretreatment was essential to overcome the DNA degradation and the serial dilutions helped with to prevent polymerase chain reaction (PCR) inhibitors. Moreover, the random amplified polymorphic DNA-PCR has been shown to be a reliable technique for further experiments to recover specific aDNA sequences.

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

    PubMed

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

    2013-01-01

    A novel real-time polymerase chain reaction (PCR)-based quantitative screening method was developed for three genetically modified soybeans: RRS, A2704-12, and MON89788. The 35S promoter (P35S) of cauliflower mosaic virus is introduced into RRS and A2704-12 but not MON89788. We then designed a screening method comprised of the combination of the quantification of P35S and the event-specific quantification of MON89788. The conversion factor (Cf) required to convert the amount of a genetically modified organism (GMO) from a copy number ratio to a weight ratio was determined experimentally. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDR), respectively. The determined RSDR values for the method were less than 25% for both targets. We consider that the developed method would be suitable for the simple detection and approximate quantification of GMO. PMID:23302646

  17. Crystal structure analysis of auromomycin apoprotein (macromomycin) shows importance of protein side chains to chromophore binding selectivity.

    PubMed

    Van Roey, P; Beerman, T A

    1989-09-01

    The crystal structure of macromomycin, the apoprotein of the antitumor antibiotic auromomycin, has been determined and refined at 1.6-A resolution. The overall structure is composed of a flattened seven-stranded antiparallel beta-barrel and two antiparallel beta-sheet ribbons. The barrel and the ribbons define a deep cleft that is the chromophore binding site. The cleft is very accessible and in this structure is occupied by two 2-methyl-2,4-pentanediol and two water molecules. The overall shape of the binding site is similar to that of the analogue actinoxanthin. Highly specific side chains that are not conserved between different analogues extend into the binding site and may be important to the chromophore binding specificity.

  18. A Markov chain analysis of the movements of juvenile salmonids in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the information collected at McNary Dam was in the form of three-dimensional tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and test configurations of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting three-dimensional results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we investigated the feasibility of using a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis is one way that can be used to summarize numerically the behavior of fish in the forebay. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, proportions of yearling and subyearling Chinook salmon passing the three powerhouse areas was often greater in the southern and middle areas, compared to the northern area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to confirm and quantify the extent of milling behavior that had been observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the

  19. Engineered Ionizable Side Chains.

    PubMed

    Cymes, Gisela D; Grosman, Claudio

    2015-01-01

    One of the great challenges of mechanistic ion-channel biology is to obtain structural information from well-defined functional states. In the case of neurotransmitter-gated ion channels, the open-channel conformation is particularly elusive owing to its transient nature and brief mean lifetime. In this Chapter, we show how the analysis of single-channel currents recorded from mutants engineered to contain single ionizable side chains in the transmembrane region can provide specific information about the open-channel conformation without any interference from the closed or desensitized conformations. The method takes advantage of the fact that the alternate binding and unbinding of protons to and from an ionizable side chain causes the charge of the protein to fluctuate by 1 unit. We show that, in mutant muscle acetylcholine nicotinic receptors (AChRs), this fluctuating charge affects the rate of ion conduction in such a way that individual proton-transfer events can be identified in a most straightforward manner. From the extent to which the single-channel current amplitude is reduced every time a proton binds, we can learn about the proximity of the engineered side chain to the lumen of the pore. And from the kinetics of proton binding and unbinding, we can calculate the side-chain's affinity for protons (pK a), and hence, we can learn about the electrostatic properties of the microenvironment around the introduced ionizable group. The application of this method to systematically mutated AChRs allowed us to identify unambiguously the stripes of the M1, M2 and M3 transmembrane α-helices that face the pore's lumen in the open-channel conformation in the context of a native membrane. PMID:26381938

  20. In vivo analysis of fibroin heavy chain signal peptide of silkworm Bombyx mori using recombinant baculovirus as vector

    SciTech Connect

    Wang Shengpeng; Guo Tingqing; Guo Xiuyang; Huang Junting; Lu Changde . E-mail: cdlu@sibs.ac.cn

    2006-03-24

    In order to investigate the functional signal peptide of silkworm fibroin heavy chain (FibH) and the effect of N- and C-terminal parts of FibH on the secretion of FibH in vivo, N- and C-terminal segments of fibh gene were fused with enhanced green fluorescent protein (EGFP) gene. The fused gene was then introduced into silkworm larvae and expressed in silk gland using recombinant AcMNPV (Autographa californica multiple nuclear polyhedrosis virus) as vector. The fluorescence of EGFP was observed with fluorescence microscope. FibH-EGFP fusion proteins extracted from silk gland were analyzed by Western blot. Results showed that the two alpha helices within N-terminal 163 amino acid residues and the C-terminal 61 amino acid residues were not necessary for cleavage of signal peptide and secretion of the fusion protein into silk gland. Then the C-terminal 61 amino acid residues were substituted with a His-tag in the fusion protein to facilitate the purification. N-terminal sequencing of the purified protein showed that the signal cleavage site is between position 21 and 22 amino acid residues.

  1. From nucleotides to DNA analysis by a SERS substrate of a self similar chain of silver nanospheres

    NASA Astrophysics Data System (ADS)

    Coluccio, M. L.; Gentile, F.; Das, G.; Perozziello, G.; Malara, N.; Alrasheed, S.; Candeloro, P.; Di Fabrizio, E.

    2015-11-01

    In this work we realized a device of silver nanostructures designed so that they have a great ability to sustain the surface-enhanced Raman scattering effect. The nanostructures were silver self-similar chains of three nanospheres, having constant ratios between their diameters and between their reciprocal distances. They were realized by electron beam lithography, to write the pattern, and by silver electroless deposition technique, to fill it with the metal. The obtained device showed the capability to increase the Raman signal coming from the gap between the two smallest nanospheres (whose size is around 10 nm) and so it allows the detection of biomolecules fallen into this hot spot. In particular, oligonucleotides with 6 DNA bases, deposited on these devices with a drop coating method, gave a Raman spectrum characterized by a clear fingerprint coming from the hot spot and, with the help of a fitting method, also oligonucleotides of 9 bases, which are less than 3 nm long, were resolved. In conclusion the silver nanolens results in a SERS device able to measure all the molecules, or part of them, held into the hot spot of the nanolenses, and thus it could be a future instrument with which to analyze DNA portions.

  2. Analysis of DNA damage and repair in murine leukemia L1210 cells using a quantitative polymerase chain reaction assay.

    PubMed Central

    Kalinowski, D P; Illenye, S; Van Houten, B

    1992-01-01

    The polymerase chain reaction (PCR) represents an alternative to the current methods for investigating DNA damage and repair in specific genomic segments. In theory, any DNA lesion which blocks Taq polymerase can be measured by this assay. We used quantitative PCR (QPCR) to determine the lesion frequencies produced by cisplatin and ultraviolet light (UV) in a 2.3 kilobase (kb) segment of mitochondrial DNA and a 2.6 kb segment of the DHFR gene in mouse leukemia L1210 cells. The frequency of UV-induced lesions increased linearly with dose, and was 0.58 lesions/10 kb/10 J/m2 in the mitochondrial DNA, and 0.37 lesions/10 kb/10 J/m2 in the DHFR gene. With cisplatin, the lesion frequency also increased linearly with dose, and was 0.17 lesions/10 kb/10 microM in the DHFR gene, and 0.07 lesions/10 kb/10 microM in mitochondrial DNA. This result is contrary to that of Murata et al., 1990 (1), in which mitochondrial DNA received greater cisplatin damage than did nuclear DNA. Using PCR to measure the repair of UV-induced lesions in the DHFR gene segment, we observed that less than 10% of the lesions were removed by 4 h, but over 70% of the lesions were removed by 8 h. Repair of 43% of UV-induced lesions in mitochondrial DNA was also observed during a 24 h period. Images PMID:1630919

  3. An analysis of the efficacy of serial screening for familial nasopharyngeal carcinoma based on Markov chain models.

    PubMed

    Choi, Cheuk Wai; Lee, Michael C H; Ng, Wai Tong; Law, Lai Yau; Yau, Tsz Kok; Lee, Anne W M

    2011-03-01

    Treatment of nasopharyngeal carcinoma (NPC) can be improved by early detection of the disease as treatment outcome worsens with disease's progression. This can be achieved with a mass screening program using Epstein Barr virus (EBV) serology and nasopharyngoscopy. The efficacy of any screening strategy should be evaluated before putting it into practice. Such evaluation is ideally performed with simulation as time and cost often preclude the evaluation by randomized trial. This study simulated and compared the outcomes of 4 screening strategies over a period of 12 years: (A) Annual screening, (B) biennial screening, (C) triennial screening, and (D) triennial screening for participants tested EBV negative and annual screening once the participants are tested EBV positive. Progression of the disease was divided into 4 phases and calculated by applying Markov chain model. Parameters of the transition matrix and probabilities were estimated using data from previous screening results of 1,072 family members of NPC patients. The early detection rates with strategies A, B, C and D are 88, 79, 71 and 87% respectively. The 5-year overall survival with screening is 10-12% higher than that without and is the highest with strategies A and D. Strategy D, however, requires only 64% screening tests compared with strategy A and has almost identical resultant disease stage distribution to strategy A. We concluded that strategy D offered the highest efficacy for NPC screening of family members of NPC patients among the four strategies studied. PMID:21052850

  4. Application of spatial Markov chains to the analysis of the temporal-spatial evolution of soil erosion.

    PubMed

    Liu, Ruimin; Men, Cong; Wang, Xiujuan; Xu, Fei; Yu, Wenwen

    2016-01-01

    Soil and water conservation in the Three Gorges Reservoir Area of China is important, and soil erosion is a significant issue. In the present study, spatial Markov chains were applied to explore the impacts of the regional context on soil erosion in the Xiangxi River watershed, and Thematic Mapper remote sensing data from 1999 and 2007 were employed. The results indicated that the observed changes in soil erosion were closely related to the soil erosion levels of the surrounding areas. When neighboring regions were not considered, the probability that moderate erosion transformed into slight and severe erosion was 0.8330 and 0.0049, respectively. However, when neighboring regions that displayed intensive erosion were considered, the probabilities were 0.2454 and 0.7513, respectively. Moreover, the different levels of soil erosion in neighboring regions played different roles in soil erosion. If the erosion levels in the neighboring region were lower, the probability of a high erosion class transferring to a lower level was relatively high. In contrast, if erosion levels in the neighboring region were higher, the probability was lower. The results of the present study provide important information for the planning and implementation of soil conservation measures in the study area. PMID:27642824

  5. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

    USGS Publications Warehouse

    Chase, D.M.; Elliott, D.G.; Pascho, R.J.

    2006-01-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

  6. Haplotyping using a combination of polymerase chain reaction-single-strand conformational polymorphism analysis and haplotype-specific PCR amplification.

    PubMed

    Zhou, Huitong; Li, Shaobin; Liu, Xiu; Wang, Jiqing; Luo, Yuzhu; Hickford, Jon G H

    2014-12-01

    A single nucleotide polymorphism (SNP) may have an impact on phenotype, but it may also be influenced by multiple SNPs within a gene; hence, the haplotype or phase of multiple SNPs needs to be known. Various methods for haplotyping SNPs have been proposed, but a simple and cost-effective method is currently unavailable. Here we describe a haplotyping approach using two simple techniques: polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and haplotype-specific PCR. In this approach, individual regions of a gene are analyzed by PCR-SSCP to identify variation that defines sub-haplotypes, and then extended haplotypes are assembled from the sub-haplotypes either directly or with the additional use of haplotype-specific PCR amplification. We demonstrate the utility of this approach by haplotyping ovine FABP4 across two variable regions that contain seven SNPs and one indel. The simplicity of this approach makes it suitable for large-scale studies and/or diagnostic screening.

  7. Application of spatial Markov chains to the analysis of the temporal-spatial evolution of soil erosion.

    PubMed

    Liu, Ruimin; Men, Cong; Wang, Xiujuan; Xu, Fei; Yu, Wenwen

    2016-01-01

    Soil and water conservation in the Three Gorges Reservoir Area of China is important, and soil erosion is a significant issue. In the present study, spatial Markov chains were applied to explore the impacts of the regional context on soil erosion in the Xiangxi River watershed, and Thematic Mapper remote sensing data from 1999 and 2007 were employed. The results indicated that the observed changes in soil erosion were closely related to the soil erosion levels of the surrounding areas. When neighboring regions were not considered, the probability that moderate erosion transformed into slight and severe erosion was 0.8330 and 0.0049, respectively. However, when neighboring regions that displayed intensive erosion were considered, the probabilities were 0.2454 and 0.7513, respectively. Moreover, the different levels of soil erosion in neighboring regions played different roles in soil erosion. If the erosion levels in the neighboring region were lower, the probability of a high erosion class transferring to a lower level was relatively high. In contrast, if erosion levels in the neighboring region were higher, the probability was lower. The results of the present study provide important information for the planning and implementation of soil conservation measures in the study area.

  8. LC-MS/MS-based analysis of coenzyme A and short-chain acyl-coenzyme A thioesters.

    PubMed

    Neubauer, Stefan; Chu, Dinh Binh; Marx, Hans; Sauer, Michael; Hann, Stephan; Koellensperger, Gunda

    2015-09-01

    Absolute quantification of intracellular coenzyme A (CoA), coenzyme A disulfide, and short-chain acyl-coenzyme A thioesters was addressed by developing a tailored metabolite profiling method based on liquid chromatography in combination with tandem mass spectrometric detection (LC-MS/MS). A reversed phase chromatographic separation was established which is capable of separating a broad spectrum of CoA, its corresponding derivatives, and their isomers despite the fact that no ion-pairing reagent was used (which was considered as a key advantage of the method). Excellent analytical figures of merit such as high sensitivity (LODs in the nM to sub-nM range) and high repeatability (routinely 4 %; N = 15) were obtained. Method validation comprised a study on standard purity, stability, and recoveries during sample preparation. Uniformly labeled U(13)C yeast cell extracts offered ideal internal standards for validation purposes and for a quantification exercise in the rumen bacterium Megasphaera elsdenii.

  9. Leishmania spp. identification by polymerase chain reaction-restriction fragment length polymorphism analysis and its applications in French Guiana.

    PubMed

    Simon, Stéphane; Veron, Vincent; Carme, Bernard

    2010-02-01

    Leishmania (Viannia) guyanensis was for many years the only species commonly identified in French Guiana, but precise species identifications were quite rare. We describe a new restriction fragment length polymorphism-polymerase chain reaction technique using a 615-bp fragment of the RNA polymerase II gene and 2 restriction enzymes, TspRI and HgaI. Seven reference strains (Leishmania (Leishmania) amazonensis, Leishmania (Viannia) lainsoni, Leishmania (Viannia) braziliensis, L. (V.) guyanensis, Leishmania (Viannia) naiffi, Leishmania (Leishmania) major, Leishmania (Leishmania) infantum) and 112 clinical samples from positive lesions were used for the development of the technique. The rates of positive species identification were 85.7% for punch skin biopsy specimens, 93.1% for positive Giemsa-stained smears, and 100% for positive culture supernatants. In the framework of cutaneous leishmaniasis species surveillance for the 2006 to 2008 period, parasite identification was carried out for 199 samples from different patients. The prevalence of the various Leishmania spp. was 84.4% for L. (V.) guyanensis, 8.0% for L. (V.) braziliensis, 5.0% for L. (L.) amazonensis, and 2.6% for L. (V.) lainsoni. L. (V.) braziliensis seems to be locally an emerging pathogen.

  10. A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species.

    PubMed

    Wang, Xifeng; Cheng, Gang; Lu, Yan; Zhang, Chenglin; Wu, Xiaobing; Han, Haitang; Zhao, Yaofeng; Ren, Liming

    2016-01-01

    Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates.

  11. Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: A systematic expression analysis

    PubMed Central

    Hamm, Alexander; Veeck, Juergen; Bektas, Nuran; Wild, Peter J; Hartmann, Arndt; Heindrichs, Uwe; Kristiansen, Glen; Werbowetski-Ogilvie, Tamra; Del Maestro, Rolando; Knuechel, Ruth; Dahl, Edgar

    2008-01-01

    Background The inter-alpha-trypsin inhibitors (ITI) are a family of plasma protease inhibitors, assembled from a light chain – bikunin, encoded by AMBP – and five homologous heavy chains (encoded by ITIH1, ITIH2, ITIH3, ITIH4, and ITIH5), contributing to extracellular matrix stability by covalent linkage to hyaluronan. So far, ITIH molecules have been shown to play a particularly important role in inflammation and carcinogenesis. Methods We systematically investigated differential gene expression of the ITIH gene family, as well as AMBP and the interacting partner TNFAIP6 in 13 different human tumor entities (of breast, endometrium, ovary, cervix, stomach, small intestine, colon, rectum, lung, thyroid, prostate, kidney, and pancreas) using cDNA dot blot analysis (Cancer Profiling Array, CPA), semiquantitative RT-PCR and immunohistochemistry. Results We found that ITIH genes are clearly downregulated in multiple human solid tumors, including breast, colon and lung cancer. Thus, ITIH genes may represent a family of putative tumor suppressor genes that should be analyzed in greater detail in the future. For an initial detailed analysis we chose ITIH2 expression in human breast cancer. Loss of ITIH2 expression in 70% of cases (n = 50, CPA) could be confirmed by real-time PCR in an additional set of breast cancers (n = 36). Next we studied ITIH2 expression on the protein level by analyzing a comprehensive tissue micro array including 185 invasive breast cancer specimens. We found a strong correlation (p < 0.001) between ITIH2 expression and estrogen receptor (ER) expression indicating that ER may be involved in the regulation of this ECM molecule. Conclusion Altogether, this is the first systematic analysis on the differential expression of ITIH genes in human cancer, showing frequent downregulation that may be associated with initiation and/or progression of these malignancies. PMID:18226209

  12. A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species

    PubMed Central

    Lu, Yan; Zhang, Chenglin; Wu, Xiaobing; Han, Haitang; Zhao, Yaofeng; Ren, Liming

    2016-01-01

    Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates. PMID:26901135

  13. A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species.

    PubMed

    Wang, Xifeng; Cheng, Gang; Lu, Yan; Zhang, Chenglin; Wu, Xiaobing; Han, Haitang; Zhao, Yaofeng; Ren, Liming

    2016-01-01

    Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates. PMID:26901135

  14. Temporal relation between the ADC and DC potential responses to transient focal ischemia in the rat: a Markov chain Monte Carlo simulation analysis.

    PubMed

    King, Martin D; Crowder, Martin J; Hand, David J; Harris, Neil G; Williams, Stephen R; Obrenovitch, Tihomir P; Gadian, David G

    2003-06-01

    Markov chain Monte Carlo simulation was used in a reanalysis of the longitudinal data obtained by Harris et al. (J Cereb Blood Flow Metab 20:28-36) in a study of the direct current (DC) potential and apparent diffusion coefficient (ADC) responses to focal ischemia. The main purpose was to provide a formal analysis of the temporal relationship between the ADC and DC responses, to explore the possible involvement of a common latent (driving) process. A Bayesian nonlinear hierarchical random coefficients model was adopted. DC and ADC transition parameter posterior probability distributions were generated using three parallel Markov chains created using the Metropolis algorithm. Particular attention was paid to the within-subject differences between the DC and ADC time course characteristics. The results show that the DC response is biphasic, whereas the ADC exhibits monophasic behavior, and that the two DC components are each distinguishable from the ADC response in their time dependencies. The DC and ADC changes are not, therefore, driven by a common latent process. This work demonstrates a general analytical approach to the multivariate, longitudinal data-processing problem that commonly arises in stroke and other biomedical research. PMID:12796716

  15. Polarization analysis of VLF/ELF waves observed at subauroral latitudes during the VLF-CHAIN campaign

    NASA Astrophysics Data System (ADS)

    Martinez-Calderon, Claudia; Shiokawa, Kazuo; Miyoshi, Yoshizumi; Ozaki, Mitsunori; Schofield, Ian; Connors, Martin

    2015-02-01

    Chorus wave emissions are one of the most intense naturally occurring phenomena in the very low (VLF) and extremely low frequency (ELF) ranges. They are believed to be one of the major contributors to acceleration and loss of electrons in the radiation belts. During the VLF Campaign observation with High-resolution Aurora Imaging Network (VLF-CHAIN) from 17 to 25 February 2012, several types of VLF/ELF emissions, including chorus, were observed at subauroral latitudes in Athabasca, Canada. To our knowledge, there has not been any comprehensive study of the physical properties of such emissions at these latitudes. In this study, we calculate spectral and polarization parameters of VLF/ELF waves with high temporal resolution. We found that the polarization angle of several emissions depended on both frequency and time. We suggest that the frequency-dependent events, which usually last several tens of minutes, might be the consequence of the broadening of the ray path that the waves follow from their generation region to the ground. Furthermore, time-dependent events, also lasting tens of minutes, have a polarization angle that changes from negative to positive values (or vice versa) every few minutes. We suggest that this could be due to variations of the wave duct, either near the generation region or along the wave propagation path. Using another ground station in Fort Vermillion, Canada, about 450 km northwest of Athabasca, we tracked the movements of the ionospheric exit point of three chorus emissions observed simultaneously at both stations. Although we found that movement of the ionospheric exit point does not follow a general direction, it is subject to hovering motion, suggesting that the exit point can be affected by small-scale plasma processes.

  16. Avian haemosporidian parasites (Haemosporida): A comparative analysis of different polymerase chain reaction assays in detection of mixed infections.

    PubMed

    Bernotienė, Rasa; Palinauskas, Vaidas; Iezhova, Tatjana; Murauskaitė, Dovilė; Valkiūnas, Gediminas

    2016-04-01

    Mixed infections of different species and genetic lineages of haemosporidian parasites (Haemosporida) predominate in wildlife, and such infections are particularly virulent. However, currently used polymerase chain reaction (PCR)-based detection methods often do not read mixed infections. Sensitivity of different PCR assays in detection of mixed infections has been insufficiently tested, but this knowledge is essential in studies addressing parasite diversity in wildlife. Here, we applied five different PCR assays, which are broadly used in wildlife avian haemosporidian research, and compared their sensitivity in detection of experimentally designed mixed infections of Haemoproteus and Plasmodium parasites. Three of these PCR assays use primer sets that amplify fragments of cytochrome b gene (cyt b), one of cytochrome oxidase subunit I (COI) gene, and one target apicoplast genome. We collected blood from wild-caught birds and, using microscopic and PCR-based methods applied in parallel, identified single infections of ten haemosporidian species with similar parasitemia. Then, we prepared 15 experimental mixes of different haemosporidian parasites, which often are present simultaneously in wild birds. Similar concentration of total DNA was used in each parasite lineage during preparation of mixes. Positive amplifications were sequenced, and the presence of mixed infections was reported by visualising double-base calling in sequence electropherograms. This study shows that the use of each single PCR assay markedly underestimates biodiversity of haemosporidian parasites. The application of at least 3 PCR assays in parallel detected the majority, but still not all lineages present in mixed infections. We determined preferences of different primers in detection of parasites belonging to different genera of haemosporidians during mixed infections.

  17. Molecular cloning, characterisation and mRNA expression analysis of the sheep myosin light chain 1 gene.

    PubMed

    Zhang, Chunlan; Wang, Guizhi; Ji, Zhibin; Liu, Zhaohua; Hou, Lei; Liu, Guanqing; Wang, Jianmin

    2015-09-10

    The complete cDNA sequence of the sheep MYL1 (Myosin light chain 1) gene was cloned using RT-PCR, 5' RACE and 3' RACE. We obtained two alternatively spliced isoforms of the MYL1 gene, MYL1a and MYL1b, which are 849 and 1046bp in length and encode proteins composed of 150 and 192 amino acid residues, respectively. And the GenBank accession numbers of MYL1a and MYL1b full-length cDNA sequences that we cloned are KJ700419 and KJ710701, respectively. Neither protein was predicted to have a signal peptide, but both were predicted to have several N-glycosylation and phosphorylation sites. More than half of the secondary structure of these proteins was predicted to be α-helical. The human MYL2 protein (1m8q.1.C) is the most similar in tertiary structure. Sequence alignment showed that the sheep MYL1a protein shares more than 92% amino acid sequence similar with Mus musculus, Homo sapiens, Rattus norvegicus, Sus scrofa and Gallus gallus and that the MYL1b protein shares more than 93% amino acid sequence similar with M. musculus, H. sapiens, R. norvegicus, Bos taurus and Oryctolagus cuniculus. Transcription profile analyses of various tissues indicated that the sheep MYL1a and MYL1b mRNAs were highly but differentially expressed in the longissimus dorsi. Moreover, the expression levels of these genes in the longissimus dorsi differed between Dorper and Small-tailed Han sheep. These results serve as a foundation for further investigations of the function of the sheep MYL1 gene. PMID:25911560

  18. Chemical genetics analysis of an aniline mustard anticancer agent reveals complex I of the electron transport chain as a target.

    PubMed

    Fedeles, Bogdan I; Zhu, Angela Y; Young, Kellie S; Hillier, Shawn M; Proffitt, Kyle D; Essigmann, John M; Croy, Robert G

    2011-09-30

    The antitumor agent 11β (CAS 865070-37-7), consisting of a DNA-damaging aniline mustard linked to an androgen receptor (AR) ligand, is known to form covalent DNA adducts and to induce apoptosis potently in AR-positive prostate cancer cells in vitro; it also strongly prevents growth of LNCaP xenografts in mice. The present study describes the unexpectedly strong activity of 11β against the AR-negative HeLa cells, both in cell culture and tumor xenografts, and uncovers a new mechanism of action that likely explains this activity. Cellular fractionation experiments indicated that mitochondria are the major intracellular sink for 11β; flow cytometry studies showed that 11β exposure rapidly induced oxidative stress, mitochondria being an important source of reactive oxygen species (ROS). Additionally, 11β inhibited oxygen consumption both in intact HeLa cells and in isolated mitochondria. Specifically, 11β blocked uncoupled oxygen consumption when mitochondria were incubated with complex I substrates, but it had no effect on oxygen consumption driven by substrates acting downstream of complex I in the mitochondrial electron transport chain. Moreover, 11β enhanced ROS generation in isolated mitochondria, suggesting that complex I inhibition is responsible for ROS production. At the cellular level, the presence of antioxidants (N-acetylcysteine or vitamin E) significantly reduced the toxicity of 11β, implicating ROS production as an important contributor to cytotoxicity. Collectively, our findings establish complex I inhibition and ROS generation as a new mechanism of action for 11β, which supplements conventional DNA adduct formation to promote cancer cell death.

  19. Transient and Transgenic Analysis of the Zebrafish Ventricular Myosin Heavy Chain (vmhc) Promoter: An Inhibitory Mechanism of Ventricle-Specific Gene Expression

    PubMed Central

    Zhang, Ruilin; Xu, Xiaolei

    2009-01-01

    The zebrafish ventricular myosin heavy chain (vmhc) gene exhibits restricted expression in the ventricle. However, the molecular mechanism underlying this chamber-specific expression is unclear. Here, we exploited both transient and transgenic technologies to dissect the zebrafish vmhc promoter. We demonstrated that a combination of two transient assays in this animal model quickly identified chamber-specific cis-elements, isolating a 2.2 kb fragment upstream from the vmhc gene that can drive ventricle-specific expression. Furthermore, deletion analysis identified multiple cis-elements that exhibited cardiac-specific expression. To achieve chamber specificity, a distal element was required to coordinate with and suppress a proximal enhancer element. Finally, we discovered that Nkx2.5-binding sites (NKE) were essential for this repressive function. In summary, our study of the zebrafish vmhc promoter suggests that ventricle-specific expression is achieved through an inhibitory mechanism that suppresses expression in the atrium. PMID:19322764

  20. The Medium-Chain Dehydrogenase/Reductase Engineering Database: A systematic analysis of a diverse protein family to understand sequence–structure–function relationship

    PubMed Central

    Knoll, Michael; Pleiss, Jürgen

    2008-01-01

    The Medium-Chain Dehydrogenase/Reductase Engineering Database (MDRED, http://www.mdred.uni-stuttgart.de) has been established to serve as an analysis tool for a systematic investigation of sequence–structure–function relationships. It includes sequence and structure information of 2684 and 42 medium-chain dehydrogenases/reductases (MDRs), respectively. Although MDRs are very diverse in sequence, they have a conserved tertiary structure. MDRs are assigned to 199 homologous families and 29 superfamilies. For each family, annotated multiple sequence alignments are provided, and functionally relevant residues are annotated. Twenty-five superfamilies were classified as zinc-containing MDRs, four as non-zinc-containing MDRs. For the zinc-containing MDRs, three subclasses were identified by systematic analysis of a variable loop region, the quaternary structure determining loop (QSDL): the class of short, medium, and long QSDL, which include 11, 3, and 5 superfamilies, respectively. The length of the QSDL is predictive for tetramer (short QSDL) and dimer (long QSDL) formation. The class of medium QSDL includes both tetrameric and dimeric MDRs. The shape of the substrate-binding site is highly conserved in all zinc-containing MDRs with the exception of two variable regions, the substrate recognition sites (SRS): two residues located on the QSDL (SRS1) and, for the class of long QSDL, one residue located in the catalytic domain (SRS2). The MDRED is the first online-accessible resource of MDRs that integrates information on sequence, structure, and function. Annotation of functionally relevant residues assist the understanding of sequence–structure–function relationships. Thus, the MDRED serves as a valuable tool to identify potential hotspots for engineering properties such as substrate specificity. PMID:18614751

  1. Antibiotic resistance and molecular typing among cockle (Anadara granosa) strains of Vibrio parahaemolyticus by polymerase chain reaction (PCR)-based analysis.

    PubMed

    Sahilah, A M; Laila, R A S; Sallehuddin, H Mohd; Osman, H; Aminah, A; Ahmad Azuhairi, A

    2014-02-01

    Genomic DNA of Vibrio parahaemolyticus were characterized by antibiotic resistance, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis. These isolates originated from 3 distantly locations of Selangor, Negeri Sembilan and Melaka (East coastal areas), Malaysia. A total of 44 (n = 44) of tentatively V. parahaemolyticus were also examined for the presence of toxR, tdh and trh gene. Of 44 isolates, 37 were positive towards toxR gene; while, none were positive to tdh and trh gene. Antibiotic resistance analysis showed the V. parahaemolyticus isolates were highly resistant to bacitracin (92%, 34/37) and penicillin (89%, 33/37) followed by resistance towards ampicillin (68%, 25/37), cefuroxime (38%, 14/37), amikacin (6%, 2/37) and ceftazidime (14%, 5/37). None of the V. parahaemolyticus isolates were resistant towards chloramphenicol, ciprofloxacin, ceftriaxone, enrofloxacin, norfloxacin, streptomycin and vancomycin. Antibiogram patterns exhibited, 9 patterns and phenotypically less heterogenous when compared to PCR-based techniques using ERIC- and RAPD-PCR. The results of the ERIC- and RAPD-PCR were analyzed using GelCompare software. ERIC-PCR with primers ERIC1R and ERIC2 discriminated the V. parahaemolyticus isolates into 6 clusters and 21 single isolates at a similarity level of 80%. While, RAPD-PCR with primer Gen8 discriminated the V. parahaemolyticus isolates into 11 clusters and 10 single isolates and Gen9 into 8 clusters and 16 single isolates at the same similarity level examined. Results in the presence study demonstrated combination of phenotypically and genotypically methods show a wide heterogeneity among cockle isolates of V. parahaemolyticus.

  2. Antibiotic resistance and molecular typing among cockle (Anadara granosa) strains of Vibrio parahaemolyticus by polymerase chain reaction (PCR)-based analysis.

    PubMed

    Sahilah, A M; Laila, R A S; Sallehuddin, H Mohd; Osman, H; Aminah, A; Ahmad Azuhairi, A

    2014-02-01

    Genomic DNA of Vibrio parahaemolyticus were characterized by antibiotic resistance, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis. These isolates originated from 3 distantly locations of Selangor, Negeri Sembilan and Melaka (East coastal areas), Malaysia. A total of 44 (n = 44) of tentatively V. parahaemolyticus were also examined for the presence of toxR, tdh and trh gene. Of 44 isolates, 37 were positive towards toxR gene; while, none were positive to tdh and trh gene. Antibiotic resistance analysis showed the V. parahaemolyticus isolates were highly resistant to bacitracin (92%, 34/37) and penicillin (89%, 33/37) followed by resistance towards ampicillin (68%, 25/37), cefuroxime (38%, 14/37), amikacin (6%, 2/37) and ceftazidime (14%, 5/37). None of the V. parahaemolyticus isolates were resistant towards chloramphenicol, ciprofloxacin, ceftriaxone, enrofloxacin, norfloxacin, streptomycin and vancomycin. Antibiogram patterns exhibited, 9 patterns and phenotypically less heterogenous when compared to PCR-based techniques using ERIC- and RAPD-PCR. The results of the ERIC- and RAPD-PCR were analyzed using GelCompare software. ERIC-PCR with primers ERIC1R and ERIC2 discriminated the V. parahaemolyticus isolates into 6 clusters and 21 single isolates at a similarity level of 80%. While, RAPD-PCR with primer Gen8 discriminated the V. parahaemolyticus isolates into 11 clusters and 10 single isolates and Gen9 into 8 clusters and 16 single isolates at the same similarity level examined. Results in the presence study demonstrated combination of phenotypically and genotypically methods show a wide heterogeneity among cockle isolates of V. parahaemolyticus. PMID:24068534

  3. Field application of a combined pig and poultry market chain and risk pathway analysis within the Pacific Islands region as a tool for targeted disease surveillance and biosecurity.

    PubMed

    Brioudes, Aurélie; Gummow, Bruce

    2016-07-01

    Limited resources are one of the major constraints in effective disease monitoring and control in developing countries. This paper examines the pig and poultry market chains of four targeted Pacific Island countries and territories (PICTs): Fiji, Papua New Guinea, Solomon Islands and Vanuatu and combines them with a risk pathway analysis to identify the highest risk areas (risk hotspots) and risky practices and behaviours (risk factors) of animal disease introduction and/or spread, using highly pathogenic avian influenza (HPAI) and foot-and-mouth disease (FMD) as model diseases because of their importance in the region. The results show that combining a market chain analysis with risk pathways is a practical way of communicating risk to animal health officials and improving biosecurity. It provides a participatory approach that helps officials to better understand the trading regulations in place in their country and to better evaluate their role as part of the control system. Common risk patterns were found to play a role in all four PICTs. Legal trade pathways rely essentially on preventive measures put in place in the exporting countries while no or only limited control measures are undertaken by the importing countries. Legal importations of animals and animal products are done mainly by commercial farms which then supply local smallholders. Targeting surveillance on these potential hotspots would limit the risk of introduction and spread of animal diseases within the pig and poultry industry and better rationalize use of skilled manpower. Swill feeding is identified as a common practice in the region that represents a recognized risk factor for dissemination of pathogens to susceptible species. Illegal introduction of animals and animal products is suspected, but appears restricted to small holder farms in remote areas, limiting the risk of spread of transboundary animal diseases along the market chain. Introduction of undeclared goods hidden within a legal

  4. Field application of a combined pig and poultry market chain and risk pathway analysis within the Pacific Islands region as a tool for targeted disease surveillance and biosecurity.

    PubMed

    Brioudes, Aurélie; Gummow, Bruce

    2016-07-01

    Limited resources are one of the major constraints in effective disease monitoring and control in developing countries. This paper examines the pig and poultry market chains of four targeted Pacific Island countries and territories (PICTs): Fiji, Papua New Guinea, Solomon Islands and Vanuatu and combines them with a risk pathway analysis to identify the highest risk areas (risk hotspots) and risky practices and behaviours (risk factors) of animal disease introduction and/or spread, using highly pathogenic avian influenza (HPAI) and foot-and-mouth disease (FMD) as model diseases because of their importance in the region. The results show that combining a market chain analysis with risk pathways is a practical way of communicating risk to animal health officials and improving biosecurity. It provides a participatory approach that helps officials to better understand the trading regulations in place in their country and to better evaluate their role as part of the control system. Common risk patterns were found to play a role in all four PICTs. Legal trade pathways rely essentially on preventive measures put in place in the exporting countries while no or only limited control measures are undertaken by the importing countries. Legal importations of animals and animal products are done mainly by commercial farms which then supply local smallholders. Targeting surveillance on these potential hotspots would limit the risk of introduction and spread of animal diseases within the pig and poultry industry and better rationalize use of skilled manpower. Swill feeding is identified as a common practice in the region that represents a recognized risk factor for dissemination of pathogens to susceptible species. Illegal introduction of animals and animal products is suspected, but appears restricted to small holder farms in remote areas, limiting the risk of spread of transboundary animal diseases along the market chain. Introduction of undeclared goods hidden within a legal

  5. FECAL INDICATOR BACTERIA MEASUREMENTS BY QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) ANALYSIS IN FRESH ARCHIVED DNA EXTRACT OF WATER SAMPLE FILTRATES

    EPA Science Inventory

    The U.S. EPA has initiated a new recreational water study to evaluate the correlation between illness rates in swimmers and Enterococcus concentrations determined by the mEI agar membrane filter (MF) method and several new technologies including QPCR analysis. Results of this stu...

  6. COMPARISON OF ENTEROCOCCUS MEASUREMENTS IN FRESHWATER AT TWO RECREATIONAL BEACHES BY QUANTITATIVE POLYMERASE CHAIN REACTION AND MEMBRANE FILER CULTURE ANALYSIS

    EPA Science Inventory

    Cell densities of the fecal pollution indicator genus, Enterococcus, were determined by a rapid (2-3 hr) quantitative PCR (QPCR) analysis based method in 100 ml water samples collected from recreational beaches on Lake Michigan and Lake Erie during the summer of 2003. Enumeration...

  7. A Markov chain analysis of the movements of juvenile salmonids, including sockeye salmon, in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the valuable information collected at McNary Dam was in the form of three-dimensional (hereafter referred to as 3-D) tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and testing of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting 3-D results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we used a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis allowed us to numerically summarize the behavior of fish in the forebay. This report is the second report published in 2012 that uses this analytical method. The first report included only fish released as part of the annual studies conducted at McNary Dam. This second report includes sockeye salmon that were released as part of studies conducted by the Chelan and Grant County Public Utility Districts at mid-Columbia River dams. The studies conducted in the mid-Columbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width was different between studies. Additionally, no passive integrated transponder tags were implanted in sockeye salmon. Differences in transmitter pulse width resulted in lower detection probabilities for sockeye salmon at McNary Dam. The absence of passive integrated transponder tags prevented us from determining if fish passed the powerhouse through the juvenile bypass system (JBS) or turbines. To

  8. Genome shuffling of Saccharomyces cerevisiae for enhanced glutathione yield and relative gene expression analysis using fluorescent quantitation reverse transcription polymerase chain reaction.

    PubMed

    Yin, Hua; Ma, Yanlin; Deng, Yang; Xu, Zhenbo; Liu, Junyan; Zhao, Junfeng; Dong, Jianjun; Yu, Junhong; Chang, Zongming

    2016-08-01

    Genome shuffling is an efficient and promising approach for the rapid improvement of microbial phenotypes. In this study, genome shuffling was applied to enhance the yield of glutathione produced by Saccharomyces cerevisiae YS86. Six isolates with subtle improvements in glutathione yield were obtained from populations generated by ultraviolet (UV) irradiation and nitrosoguanidine (NTG) mutagenesis. These yeast strains were then subjected to recursive pool-wise protoplast fusion. A strain library that was likely to yield positive colonies was created by fusing the lethal protoplasts obtained from both UV irradiation and heat treatments. After two rounds of genome shuffling, a high-yield recombinant YSF2-19 strain that exhibited 3.2- and 3.3-fold increases in glutathione production in shake flask and fermenter respectively was obtained. Comparative analysis of synthetase gene expression was conducted between the initial and shuffled strains using FQ (fluorescent quantitation) RT-PCR (reverse transcription polymerase chain reaction). Delta CT (threshold cycle) relative quantitation analysis revealed that glutathione synthetase gene (GSH-I) expression at the transcriptional level in the YSF2-19 strain was 9.9-fold greater than in the initial YS86. The shuffled yeast strain has a potential application in brewing, other food, and pharmaceutical industries. Simultaneously, the analysis of improved phenotypes will provide more valuable data for inverse metabolic engineering. PMID:27302037

  9. Application of near-infrared spectroscopy as an alternative to chemical and color analysis to discriminate the production chains of Asiago d'Allevo cheese.

    PubMed

    Cozzi, Giulio; Ferlito, Jacopo; Pasini, Gabriella; Contiero, Barbara; Gottardo, Flaviana

    2009-12-23

    A near-infrared spectroscopy (NIRS) application was developed to discriminate Asiago d'Allevo cheese coming from different production chains (alpine farms, mountain and lowland factories). One hundred wheels were collected in different seasons from all productive sites of Asiago d'Allevo: 14 alpine farms and 8 mountain and 13 lowland factories. Samples were analyzed for chemical composition and color and scanned by NIRS (1100-2500 nm). A factorial discriminant analysis based on chemical and color data showed a clear separation between alpine and factory products due to their different fatty acids profile and color. However, cheeses from lowland and mountain factories were undistinguishable. A discriminant analysis using NIRS spectra alone or combined with chemical and color data showed similar results. A final calibration based on NIRS spectra was developed and validated by a set of 7 external samples to discriminate alpine from factory products. This real-time analysis is a reliable alternative to expensive and time-consuming lab determinations.

  10. Rapid deoxyribonucleic acid analysis by allele-specific polymerase chain reaction for detection of mutations in the steroid 21-hydroxylase gene

    SciTech Connect

    Wilson, R.C.; Wei, J.Q.; Cheng, K.C.

    1995-05-01

    Rapid DNA analysis based on allele-specific polymerase chain reaction (PCR) using mutation site-specific primers was developed to detect mutations in the CYP21 gene known to cause steroid 21-hydroxylase deficiency. In contrast to the previous method, in which PCR of genomic DNA was followed by dot blot analysis with radio active probes and multiple rounds of stripping and reprobing for each of the 8 most common mutation sites, the results using this new method were immediately visualized after the PCR run by ethidium bromide-stained agarose gel electrophoresis. Using allele-specific PCR, mutation(s) were identified on 148 affected chromosomes out of 160 tested. Although mutation(s) were identified on only one chromosome of 11 of these patients, their parents showed a consistent pattern on DNA analysis. The only exception was that in one family, in which the parents each had a detectable mutation, a mutation was detected on only one allele of the patient. Most likely there is a mutation in the patient`s other allele that could have arisen de novo or was inherited from the parent and was not evident in the transmitting parent`s phenotype. When compared with the dot blot procedure, allele-specific PCR is more rapid, less labor-intensive, and avoids the use of radioactivity. 26 refs., 3 figs., 2 tabs.

  11. Bioactive Glass S53P4 versus Chlorhexidine Gluconate as Intracanal Medicament in Primary Teeth: An In-vivo Study Using Polymerase Chain Reaction Analysis

    PubMed Central

    Goel, Ankit; Sinha, Abhishek; Khandeparker, Rakshit Vijay Sinai; Mehrotra, Rachit; Vashisth, Pallavi; Garg, Anuj

    2015-01-01

    Background: Bacteria have long been recognized as the primary etiology for pulpal and periapical lesions, which necessitates the elimination of bacteria from the root canal system. In primary teeth, irrigation and debridement is the main protocol required to disinfect the canal. Biomechanical preparation cannot be vigorously done on the primary teeth due to anatomical barrier such as thin and flared roots. This calls for the use of an effective intracanal medication that will assist disinfection of root canal system. Aim of the study was to examine the in-vivo susceptibility of root canal bacteria to chlorhexidine (CHX) gluconate-1% gel and bioactive glass (BAG) S53P4 when used as intracanal medicaments using polymerase chain reaction (PCR). Methodology: PCR (analysis used oligonucleotide primers of Escherichia coli) was used to detect and compare the microbial load reduction after medication of 14 teeth for a week with either CHX gel - 1% or BAG S53P4. The pre and post microbial load was checked in the form of colony forming units. When analysis was done, a statistically significant difference was observed between the two groups. Results: The study revealed that both medicaments caused a considerable amount of microbial load reduction. BAG S53P4 caused much more reduction than CHX 1% gel. Statistical analysis showed a significant difference between the two groups. Conclusion: BAG S53P4 has superior antibacterial property as compared to CHX 1% gel. PMID:26464542

  12. A Markov chain analysis of the movements of juvenile salmonids in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the information collected at McNary Dam was in the form of three-dimensional tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and test configurations of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting three-dimensional results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we investigated the feasibility of using a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis is one way that can be used to summarize numerically the behavior of fish in the forebay. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, proportions of yearling and subyearling Chinook salmon passing the three powerhouse areas was often greater in the southern and middle areas, compared to the northern area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to confirm and quantify the extent of milling behavior that had been observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the

  13. Application of an immunoaffinity-based preconcentration method for mass spectrometric analysis of the O-chain polysaccharide of Aeromonas salmonicida from in vitro- and in vivo-grown cells.

    PubMed

    Wang, Zhan; Liu, Xin; Garduño, Elizabeth; Garduño, Rafael A; Li, Jianjun; Altman, Eleonora

    2009-06-01

    In this study, application of magnetic beads (Dynabeads) coated with Aeromonas salmonicida lipopolysaccharide-specific polyclonal antisera to MS-based characterization of bacterial lipopolysaccharides has been evaluated. The results showed that the affinity-based preconcentration strategy resulted in at least a 100-fold increase in the detection of sensitivity, affording direct capillary electrophoresis (CE)-MS analysis of A. salmonicida lipopolysaccharide O-chain polysaccharide from in vitro-cultured cells. Subsequent CE-MS analysis of in vivo-grown cells of A. salmonicida confirmed significant changes in the structure of the lipopolysaccharide O-chain polysaccharide as a result of in vivo cultivation. PMID:19456871

  14. Laser amplifier chain

    DOEpatents

    Hackel, R.P.

    1992-10-20

    A laser amplifier chain has a plurality of laser amplifiers arranged in a chain to sequentially amplify a low-power signal beam to produce a significantly higher-power output beam. Overall efficiency of such a chain is improved if high-gain, low efficiency amplifiers are placed on the upstream side of the chain where only a very small fraction of the total pumped power is received by the chain and low-gain, high-efficiency amplifiers are placed on the downstream side where a majority of pumping energy is received by the chain. 6 figs.

  15. Laser amplifier chain

    DOEpatents

    Hackel, Richard P.

    1992-01-01

    A laser amplifier chain has a plurality of laser amplifiers arranged in a chain to sequentially amplify a low-power signal beam to produce a significantly higher-power output beam. Overall efficiency of such a chain is improved if high-gain, low efficiency amplifiers are placed on the upstream side of the chain where only a very small fraction of the total pumped power is received by the chain and low-gain, high-efficiency amplifiers are placed on the downstream side where a majority of pumping energy is received by the chain.

  16. The Collaborative Study on the Enzymatic Analysis of Positional Distribution of Short- and Medium-chain Fatty Acids in Milk Fat Using Immobilized Candida antarctica Lipase B.

    PubMed

    Yoshinaga, Kazuaki; Sato, Shinichi; Sasaki, Ryo; Asada, Mihoko; Hori, Ryuji; Imagi, Jun; Miyazaki, Yosuke; Nagai, Toshiharu; Saito, Katsuyoshi; Sano, Takashi; Sasaki, Akiko; Sato, Chiemi; Tsukahara, Yuki; Yamashita, Atsushi; Watanabe, Shimpei; Watanabe, Yomi

    2016-01-01

    The positional distributions of fatty acids (FAs) in milk fat containing short- and medium-chain FAs were analyzed by sn-1(3)-selective transesterification of triacylglycerols (TAGs) with ethanol using immobilized Candida antarctica lipase B (CALB), in a collaborative study conducted by 10 laboratories. The mean C4:0, C6:0, and C8:0 FA contents, when analyzed as propyl esters (PEs) using gas chromatography (GC) with a DB-23 capillary column, were found to be 3.0, 2.0, and, 1.3 area%, respectively. Their reproducibility standard deviations were 0.33, 0.18, and 0.19, respectively. The mean C4:0, C6:0, and C8:0 contents at the sn-2 position were 0.3, 0.4, and 1.0 area%, respectively. Their reproducibility standard deviations were 0.17, 0.11, and 0.19, respectively. The reproducibility standard deviations of C4:0, C6:0, and C8:0 FAs at the sn-2 position were either the same as or smaller than those for milk fat, although the FA contents at the sn-2 position were smaller than those in the milk fat. Therefore, it was concluded that the CALB method for estimating the regiospecific distribution is applicable to TAGs containing short- and medium-chain FAs. When estimating the short-chain (SC) FA contents in fats and oils by GC, it is better to analyze SCFAs as PEs or butyl esters, and not as methyl esters, in order to prevent loss of SCFAs during the experimental procedure because of their volatility and water solubility. This study also revealed that the stationary phase of the GC capillary column affected the flame ionization detector (FID) response of SCFAs. The theoretical FID correction factor (MWFA / active carbon number / atomic weight of carbon) fitted well with the actual FID responses of C4:0-C12:0 FAs when they were analyzed as PEs using a DB-23 column; however, this was not the case when the GC analysis was performed using wax-type columns. PMID:26972465

  17. Quantitative polymerase chain reaction analysis with allele-specific oligonucleotide primers for individual IgH VDJ regions to evaluate tumor burden in myeloma patients.

    PubMed

    Sata, Hiroshi; Shibayama, Hirohiko; Maeda, Ikuhiro; Habuchi, Yoko; Nakatani, Eiji; Fukushima, Kentaro; Fujita, Jiro; Ezoe, Sachiko; Tadokoro, Seiji; Maeda, Tetsuo; Mizuki, Masao; Kosugi, Satoru; Nakagawa, Masashi; Ueda, Shuji; Iida, Masato; Tokumine, Yukihiro; Azenishi, Yasuhiko; Mitsui, Hideki; Oritani, Kenji; Kanakura, Yuzuru

    2015-05-01

    Quantitative polymerase chain reaction (PCR) with patient-specific, allele-specific oligonucleotide (ASO) primers for individual immunoglobulin H VDJ region (ASO-PCR) amplification was performed using several sources of clinical material, including mRNA from peripheral blood cells (PBMNCs), whole bone marrow cells (BMMNCs), and the CD20+ CD38- B-cell population in bone marrow, as well as cell-free DNA from the sera of patients with multiple myeloma (MM). We designed the ASO primers and produced sufficient PCR fragments to evaluate tumor burden in 20 of 30 bone marrow samples at diagnosis. Polymerase chain reaction amplification efficiency depended on primer sequences because the production of ASO-PCR fragments did not correlate with serum M-protein levels. However, the ASO-PCR levels in BMMNCs showed statistically significant correlations with those in PBMNCs and CD20+ CD38- B-cells. The good association between the BMMNC and PBMNC data indicated that PBMNCs could be a suitable source for monitoring minimal residual disease (MRD). In the case of cell-free DNA, ASO-PCR levels showed a unique pattern and remained high even after treatment. Because the sequence information for each ASO-PCR product was identical to the original, the cell-free DNA might also be useful for evaluating MRD. Moreover, the ASO-PCR products were clearly detected in 17 of 22 mRNA samples from CD20+ CD38- populations, suggesting that MM clones might exist in relatively earlier stages of B cells than in plasma cells. Thus, ASO-PCR analysis using various clinical materials is useful for detecting MRD in MM patients as well as for clarifying MM pathogenesis. PMID:25591497

  18. Quantitative polymerase chain reaction analysis with allele-specific oligonucleotide primers for individual IgH VDJ regions to evaluate tumor burden in myeloma patients.

    PubMed

    Sata, Hiroshi; Shibayama, Hirohiko; Maeda, Ikuhiro; Habuchi, Yoko; Nakatani, Eiji; Fukushima, Kentaro; Fujita, Jiro; Ezoe, Sachiko; Tadokoro, Seiji; Maeda, Tetsuo; Mizuki, Masao; Kosugi, Satoru; Nakagawa, Masashi; Ueda, Shuji; Iida, Masato; Tokumine, Yukihiro; Azenishi, Yasuhiko; Mitsui, Hideki; Oritani, Kenji; Kanakura, Yuzuru

    2015-05-01

    Quantitative polymerase chain reaction (PCR) with patient-specific, allele-specific oligonucleotide (ASO) primers for individual immunoglobulin H VDJ region (ASO-PCR) amplification was performed using several sources of clinical material, including mRNA from peripheral blood cells (PBMNCs), whole bone marrow cells (BMMNCs), and the CD20+ CD38- B-cell population in bone marrow, as well as cell-free DNA from the sera of patients with multiple myeloma (MM). We designed the ASO primers and produced sufficient PCR fragments to evaluate tumor burden in 20 of 30 bone marrow samples at diagnosis. Polymerase chain reaction amplification efficiency depended on primer sequences because the production of ASO-PCR fragments did not correlate with serum M-protein levels. However, the ASO-PCR levels in BMMNCs showed statistically significant correlations with those in PBMNCs and CD20+ CD38- B-cells. The good association between the BMMNC and PBMNC data indicated that PBMNCs could be a suitable source for monitoring minimal residual disease (MRD). In the case of cell-free DNA, ASO-PCR levels showed a unique pattern and remained high even after treatment. Because the sequence information for each ASO-PCR product was identical to the original, the cell-free DNA might also be useful for evaluating MRD. Moreover, the ASO-PCR products were clearly detected in 17 of 22 mRNA samples from CD20+ CD38- populations, suggesting that MM clones might exist in relatively earlier stages of B cells than in plasma cells. Thus, ASO-PCR analysis using various clinical materials is useful for detecting MRD in MM patients as well as for clarifying MM pathogenesis.

  19. Molecular cloning and sequence analysis of complementary DNA encoding rat mammary gland medium-chain S-acyl fatty acid synthetase thio ester hydrolase

    SciTech Connect

    Safford, R.; de Silva, J.; Lucas, C.; Windust, J.H.C.; Shedden, J.; James, C.M.; Sidebottom, C.M.; Slabas, A.R.; Tombs, M.P.; Hughes, S.G.

    1987-03-10

    Poly(A) + RNA from pregnant rat mammary glands was size-fractionated by sucrose gradient centrifugation, and fractions enriched in medium-chain S-acyl fatty acid synthetase thio ester hydrolase (MCH) were identified by in vitro translation and immunoprecipitation. A cDNA library was constructed, in pBR322, from enriched poly(A) + RNA and screened with two oligonucleotide probes deduced from rat MCH amino acid sequence data. Cross-hybridizing clones were isolated and found to contain cDNA inserts ranging from approx. 1100 to 1550 base pairs (bp). A 1550-bp cDNA insert, from clone 43H09, was confirmed to encode MCH by hybrid-select translation/immunoprecipitation studies and by comparison of the amino acid sequence deduced from the DNA sequence of the clone to the amino acid sequence of the MCH peptides. Northern blot analysis revealed the size of the MCH mRNA to be 1500 nucleotides, and it is therefore concluded that the 1550-bp insert (including G x C tails) of clone 43H09 represents a full- or near-full-length copy of the MCH gene. The rat MCH sequence is the first reported sequence of a thioesterase from a mammalian source, but comparison of the deduced amino acid sequences of MCH and the recently published mallard duck medium-chain S-acyl fatty acid synthetase thioesterase reveals significant homology. In particular, a seven amino acid sequence containing the proposed active serine of the duck thioesterase is found to be perfectly conserved in rat MCH.

  20. Multiscale and Fractal Analysis of Silicon Content Time Series Observed in Blast Furnace Hot Metal Using Hurst Exponent Chain

    NASA Astrophysics Data System (ADS)

    Luo, Shihua; Guo, Fan; Lai, Dejian; Yan, Fang; Tang, Feilai

    2015-09-01

    Hurst exponent is an important measure of nonlinearity of dynamical time series. In this paper, using rescaled-range (R/S) analysis, multi-fractal detrended fluctuation analysis (MF-DFA) methods, the multiscale Hurst exponent (MHE) and the multiscale generalized Hurst exponent (MGHE) of coarse-grained silicon content ([Si]) time series in blast furnace (BF) hot metal were calculated. First, we collected these [Si] time series from No. 1 BF of Nanchang Iron and Steel Co. and No. 10 BF of Xinyu Iron and Steel Co. in Jiangxi Province, China. Then, we analyzed and compared the estimated Hurst exponents and the generalized Hurst exponent of these observed time series with some simulated time series. Our results show that the observed time series from these BFs have negative correlation with the Hurst exponent less than 0.5, the generalized Hurst exponent H(q) is a nonlinear function of q, and such negative correlation and local various structure persist in their moving averages of the observed time series up to lag 5 or 10.

  1. Quality assurance of temporal variability of natural decay chain and neutron induced background for low-level NORM analysis

    DOE PAGES

    Yoho, Michael; Porterfield, Donivan R.; Landsberger, Sheldon

    2015-09-22

    In this study, twenty-one high purity germanium (HPGe) background spectra were collected over 2 years at Los Alamos National Laboratory. A quality assurance methodology was developed to monitor spectral background levels from thermal and fast neutron flux levels and naturally occurring radioactive material decay series radionuclides. 238U decay products above 222Rn demonstrated minimal temporal variability beyond that expected from counting statistics. 238U and 232Th progeny below Rn gas displayed at most twice the expected variability. Further, an analysis of the 139 keV 74Ge(n, γ) and 691 keV 72Ge(n, n') spectral features demonstrated temporal stability for both thermal and fast neutronmore » fluxes.« less

  2. Quality assurance of temporal variability of natural decay chain and neutron induced background for low-level NORM analysis

    SciTech Connect

    Yoho, Michael; Porterfield, Donivan R.; Landsberger, Sheldon

    2015-09-22

    In this study, twenty-one high purity germanium (HPGe) background spectra were collected over 2 years at Los Alamos National Laboratory. A quality assurance methodology was developed to monitor spectral background levels from thermal and fast neutron flux levels and naturally occurring radioactive material decay series radionuclides. 238U decay products above 222Rn demonstrated minimal temporal variability beyond that expected from counting statistics. 238U and 232Th progeny below Rn gas displayed at most twice the expected variability. Further, an analysis of the 139 keV 74Ge(n, γ) and 691 keV 72Ge(n, n') spectral features demonstrated temporal stability for both thermal and fast neutron fluxes.

  3. Structure–Function Analysis of the Non-Muscle Myosin Light Chain Kinase (nmMLCK) Isoform by NMR Spectroscopy and Molecular Modeling: Influence of MYLK Variants

    PubMed Central

    Shen, Kui; Ramirez, Benjamin; Mapes, Brandon; Shen, Grace R.; Gokhale, Vijay; Brown, Mary E.; Santarsiero, Bernard; Ishii, Yoshitaka; Dudek, Steven M.; Wang, Ting; Garcia, Joe G. N.

    2015-01-01

    The MYLK gene encodes the multifunctional enzyme, myosin light chain kinase (MLCK), involved in isoform-specific non-muscle and smooth muscle contraction and regulation of vascular permeability during inflammation. Three MYLK SNPs (P21H, S147P, V261A) alter the N-terminal amino acid sequence of the non-muscle isoform of MLCK (nmMLCK) and are highly associated with susceptibility to acute lung injury (ALI) and asthma, especially in individuals of African descent. To understand the functional effects of SNP associations, we examined the N-terminal segments of nmMLCK by 1H-15N heteronuclear single quantum correlation (HSQC) spectroscopy, a 2-D NMR technique, and by in silico molecular modeling. Both NMR analysis and molecular modeling indicated SNP localization to loops that connect the immunoglobulin-like domains of nmMLCK, consistent with minimal structural changes evoked by these SNPs. Molecular modeling analysis identified protein-protein interaction motifs adversely affected by these MYLK SNPs including binding by the scaffold protein 14-3-3, results confirmed by immunoprecipitation and western blot studies. These structure-function studies suggest novel mechanisms for nmMLCK regulation, which may confirm MYLK as a candidate gene in inflammatory lung disease and advance knowledge of the genetic underpinning of lung-related health disparities. PMID:26111161

  4. Market surveillance on non-halal additives incorporated in surimi based products using polymerase chain reaction (PCR)-southern hybridization analysis

    NASA Astrophysics Data System (ADS)

    Aravindran, S.; Sahilah, A. M.; Aminah, A.

    2014-09-01

    Halal surveillance on halal ingredients incorporated in surimi based products were studied using polymerase chain reaction (PCR)-southern hybridization on chip analysis. The primers used in this technique were targeted on mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence which able to differentiate 7 type (beef, chicken, duck, goat, buffalo, lamb and pork) of species on a single chip. 17 (n = 17*3) different brands of surimi-based product were purchased randomly from Selangor local market in January 2013. Of 17 brands, 3 (n = 3*3) brands were positive for chicken DNA, 1 (n = 1*3) brand was positive for goat DNA, and the remainder 13 brands (n = 13*3) have no DNA species detected. The sensitivity of PCR-southern hybridization primers to detect each meat species was 0.1 ng. In the present study, it is evidence that PCR-Southern Hybridization analysis offered a reliable result due to its highly specific and sensitive properties in detecting non-halal additive such as plasma protein incorporation in surimi-based product.

  5. Identification of blood meal sources of Lutzomyia longipalpis using polymerase chain reaction-restriction fragment length polymorphism analysis of the cytochrome B gene.

    PubMed

    Soares, Vítor Yamashiro Rocha; Silva, Jailthon Carlos da; Silva, Kleverton Ribeiro da; Pires e Cruz, Maria do Socorro; Santos, Marcos Pérsio Dantas; Ribolla, Paulo Eduardo Martins; Alonso, Diego Peres; Coelho, Luiz Felipe Leomil; Costa, Dorcas Lamounier; Costa, Carlos Henrique Nery

    2014-06-01

    An analysis of the dietary content of haematophagous insects can provide important information about the transmission networks of certain zoonoses. The present study evaluated the potential of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome B (cytb) gene to differentiate between vertebrate species that were identified as possible sources of sandfly meals. The complete cytb gene sequences of 11 vertebrate species available in the National Center for Biotechnology Information database were digested with Aci I, Alu I, Hae III and Rsa I restriction enzymes in silico using Restriction Mapper software. The cytb gene fragment (358 bp) was amplified from tissue samples of vertebrate species and the dietary contents of sandflies and digested with restriction enzymes. Vertebrate species presented a restriction fragment profile that differed from that of other species, with the exception of Canis familiaris and Cerdocyon thous. The 358 bp fragment was identified in 76 sandflies. Of these, 10 were evaluated using the restriction enzymes and the food sources were predicted for four: Homo sapiens (1), Bos taurus (1) and Equus caballus (2). Thus, the PCR-RFLP technique could be a potential method for identifying the food sources of arthropods. However, some points must be clarified regarding the applicability of the method, such as the extent of DNA degradation through intestinal digestion, the potential for multiple sources of blood meals and the need for greater knowledge regarding intraspecific variations in mtDNA.

  6. Analytical Detection of Immunoglobulin Heavy Chain Gene Rearrangements in Gastric Lymphoid Infiltrates by Peak Area Analysis of the Melting Curve in the LightCycler System

    PubMed Central

    Retamales, Eduardo; Rodriguez, Luis; Guzman, Leda; Aguayo, Francisco; Palma, Mariana; Backhouse, Claudia; Argandona, Jorge; Riquelme, Erick; Corvalan, Alejandro

    2007-01-01

    Because it is difficult to differentiate gastric mucosa-associated lymphoid tissue (MALT) lymphoma from chronic gastritis in gastric lymphoid infiltrates, molecular detection of monoclonality through immunoglobulin heavy chain (IgH) gene rearrangements is commonly performed. However, heterogeneity in the performance and results obtained from IgH gene rearrangements has been reported. To improve the accuracy in the diagnosis of gastric lymphoid infiltrates, we developed an analytical approach based on one-peak area analysis of the melting curve in the LightCycler System. Using a training-testing approach, the likelihood ratio method was selected to find a discriminative function of 4.64 in the training set (10 gastric MALT lymphomas and 10 chronic gastritis cases). This discriminative function was validated in the testing set (five gastric MALT lymphomas, six abnormal lymphocytic infiltrates with subsequently demonstrated gastric MALT lymphomas, and six cases of chronic gastritis). All but one case of gastric MALT lymphoma, as well as abnormal lymphocytic infiltrates, clustered under 4.64, and all chronic gastritis cases clustered above 4.64. These results were validated by conventional electrophoreses confirming one or two sharp bands in cases of gastric MALT lymphomas and a smear of multiple bands in cases of chronic gastritis. Analytical detection of IgH gene rearrangement in gastric lymphoid infiltrates by one-peak area analysis correctly distinguishes gastric MALT lymphomas from chronic gastritis, even in cases with diagnosis of abnormal lymphocytic infiltrates. PMID:17591935

  7. Markov chains-cellular automata modeling and multicriteria analysis of land cover change in the Lower Nhecolândia subregion of the Brazilian Pantanal wetland

    NASA Astrophysics Data System (ADS)

    Bacani, Vitor Matheus; Sakamoto, Arnaldo Yoso; Quénol, Hervé; Vannier, Clémence; Corgne, Samuel

    2016-01-01

    The dynamics of land use/land cover change in the Lower Nhecolândia wetland are marked by deforestation for pasture expansion, resulting in a real threat to the ecological stability. The aim of our work was to analyze the spatial distribution of land cover changes in the Lower Nhecolândia from 1985 to 2013 and to predict changes in trends for 2040. The mapping of land cover changes was developed using Landsat satellite images of 1985, 1999, 2007, and 2013, based on geographic object-based image analysis approach. This study uses integrated Markov chains and cellular automata modeling and multicriteria evaluation techniques to produce transition probability maps and describe the trajectory analysis methodology to construct a continuity of spatial and temporal changes for the wetland. The results of the multitemporal change detection classification show that, from 1985 to 2013, the forest woodland decreased by 6.89% and the grassland class increased by 18.29%. On the other hand, all water bodies showed a reducing trend, while the bare soil class increased compared to 1985, but did not present a regular trend of increase or decrease. From the present day, the trend for the future is a reduction of almost 6.4% by 2040. We found that deforestation actions will be concentrated in the areas with the highest concentration of saline lakes, constituting a serious threat to the natural functioning of this environmental system.

  8. Comparative quantitative analysis of 14 types of human papillomavirus by real-time polymerase chain reaction monitoring Invader reaction (Q-Invader assay).

    PubMed

    Tadokoro, Kenichi; Akutsu, Yuki; Tanaka, Kazuya; Saito, Tsuyoshi; Yamaguchi, Toshikazu; Egashira, Toru; Ishiwata, Isamu; Hara, Takashi

    2010-01-01

    Human papillomavirus (HPV) is associated with several cervical diseases. A simple, rapid, cost-effective assay for identifying viral genotypes would greatly aid efforts for early detection and disease prevention. A real-time polymerase chain reaction monitoring Invader reaction assay (Q-Invader assay) was developed for genotyping and comparative quantitative analysis of 14 high-risk HPV genotypes (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 67, and 68). A total of 131 cervical samples containing HPV in Japan were examined by Q-Invader assay, and the results were compared with those from sequencing with consensus and genotype-specific primers. Genotypes determined by Q-Invader agreed with those of sequencing in all samples. Coinfections with multiple high-risk genotypes were correctly identified by Q-Invader assay in 27 samples. In addition, the relative ratios of the genotypes were determined. Thus, Q-Invader assay is a useful tool for genotyping and comparative quantitative analysis of high-risk HPV types. PMID:19733028

  9. Structure-Function Analysis of the Non-Muscle Myosin Light Chain Kinase (nmMLCK) Isoform by NMR Spectroscopy and Molecular Modeling: Influence of MYLK Variants.

    PubMed

    Shen, Kui; Ramirez, Benjamin; Mapes, Brandon; Shen, Grace R; Gokhale, Vijay; Brown, Mary E; Santarsiero, Bernard; Ishii, Yoshitaka; Dudek, Steven M; Wang, Ting; Garcia, Joe G N

    2015-01-01

    The MYLK gene encodes the multifunctional enzyme, myosin light chain kinase (MLCK), involved in isoform-specific non-muscle and smooth muscle contraction and regulation of vascular permeability during inflammation. Three MYLK SNPs (P21H, S147P, V261A) alter the N-terminal amino acid sequence of the non-muscle isoform of MLCK (nmMLCK) and are highly associated with susceptibility to acute lung injury (ALI) and asthma, especially in individuals of African descent. To understand the functional effects of SNP associations, we examined the N-terminal segments of nmMLCK by 1H-15N heteronuclear single quantum correlation (HSQC) spectroscopy, a 2-D NMR technique, and by in silico molecular modeling. Both NMR analysis and molecular modeling indicated SNP localization to loops that connect the immunoglobulin-like domains of nmMLCK, consistent with minimal structural changes evoked by these SNPs. Molecular modeling analysis identified protein-protein interaction motifs adversely affected by these MYLK SNPs including binding by the scaffold protein 14-3-3, results confirmed by immunoprecipitation and western blot studies. These structure-function studies suggest novel mechanisms for nmMLCK regulation, which may confirm MYLK as a candidate gene in inflammatory lung disease and advance knowledge of the genetic underpinning of lung-related health disparities.

  10. An analysis of Staphylococcus aureus infections at a military medical center using the PLEX-ID combined polymerase chain reaction-mass spectrometry system.

    PubMed

    Washington, Michael A; Agee, Willie A; Kajiura, Lauren; Staege, Catherine M; Uyehara, Catherine Ft; Barnhill, Jason C

    2014-04-01

    Staphylococcus aureus (S. aureus) is a major cause of morbidity in the military health care setting. Culture-based methods are the most common means of identifying infections caused by this agent. However, culture-based methods lack sensitivity and specificity. The Abbott PLEX-ID instrument uses a combination of the polymerase chain reaction and mass spectrometry for the identification of bacterial isolates. We investigated whether the Abbott PLEX-ID system could identify S. aureus in clinical material and facilitate the epidemiological analysis of individual isolates. The PLEX-ID system positively identified 100% of isolates previously found to be methicillin resistant S. aureus by culture. In addition, analysis using the PLEX-ID software revealed that the majority of S. aureus isolates at Tripler Army Medical Center derive from clonal complex 8 and nearly 100% of these strains express the R-variant of the Panton-Valentine leukocidin virulence factor. These results demonstrate the utility of the PLEX-ID system in identifying clinical isolates and reveal an unexpected level of homogeneity among clinical S. aureus isolates recovered at Tripler Army Medical Center. These results also demonstrate the utility of the PLEX-ID system in identifying the resistance patterns, predicting the virulence properties, and tracking the migration of bacterial pathogens in the clinical setting.

  11. Molecular design of boronic acid-functionalized squarylium cyanine dyes for multiple discriminant analysis of sialic acid in biological samples: selectivity toward monosaccharides controlled by different alkyl side chain lengths.

    PubMed

    Ouchi, Kazuki; Colyer, Christa L; Sebaiy, Mahmoud; Zhou, Jin; Maeda, Takeshi; Nakazumi, Hiroyuki; Shibukawa, Masami; Saito, Shingo

    2015-02-01

    We designed a new series of boronic acid-functionalized squarylium cyanine dyes (SQ-BA) with different lengths of alkyl chain residues, suitable for multiple discriminant analysis (MDA) of sialic acid (Neu5Ac) in biological samples. The SQ-BA dyes form aggregates based on hydrophobic interactions, which result in quenched fluorescence in aqueous solutions. When the boronic acid binds with saccharides, the fluorescence intensity increases as a result of dissociation to the emissive monomeric complex. We inferred that different dye aggregate structures (H-aggregates and J-aggregates) were induced depending on the alkyl chain length, so that monosaccharides would be recognized in different ways (especially, multipoint interaction with J-aggregates). A distinctive emission enhancement of SQ-BA dyes with shorter-alkyl-chains in the presence of Neu5Ac was observed (2.4-fold fluorescence enhancement; with formation constant 10(1.7) M(-1)), with no such enhancement for SQ-BA dyes with longer-alkyl-chain. In addition, various enhancement factors for other monosaccharides were observed depending on the alkyl chain length. Detailed thermodynamic and NMR studies of the SQ-BA complexes revealed the unique recognition mechanism: the dye aggregate with a shorter-alkyl-chain causes the slipped parallel structure and forms a stable 2:1 complex with Neu5Ac, as distinct from longer-alkyl-chain dyes, which form a 1:1 monomeric complex. MDA using the four SQ-BA dyes was performed for human urine samples, resulting in the successful discrimination between normal and abnormal Neu5Ac levels characteristic of disease. Thus, we successfully controlled various responses to similar monosaccharides with a novel approach that chemically modified not the boronic acid moiety itself but the length of the alkyl chain residue attached to the dye in order to generate specificity.

  12. Functional analysis, a resilience improvement tool applied to a waste management system - application to the "household waste management chain"

    NASA Astrophysics Data System (ADS)

    Beraud, H.; Barroca, B.; Hubert, G.

    2012-12-01

    A waste management system plays a leading role in the capacity of an area to restart after flooding, as their impact on post-crisis management can be very considerable. Improving resilience, i.e. enabling it to maintain or recover acceptable operating levels after flooding is primordial. To achieve this, we must understand how the system works for bringing any potential dysfunctions to light and taking preventive measures. Functional analysis has been used for understanding the complexity of this type of system. The purpose of this article is to show the interest behind this type of method and the limits in its use for improving resilience of waste management system as well as other urban technical systems1, by means of theoretical modelling and its application on a study site. 1In a systemic vision of the city, urban technical systems combine all the user service systems that are essential for the city to operate (electricity, water supplies, transport, sewerage, etc.). These systems are generally organised in the form of networks (Coutard, 2010; CERTU, 2005).

  13. Analysis of side chain rotational restrictions of membrane-embedded proteins by spin-label ESR spectroscopy

    NASA Astrophysics Data System (ADS)

    Štrancar, Janez; Kavalenka, Aleh; Ziherl, Primož; Stopar, David; Hemminga, Marcus A.

    2009-04-01

    Site-directed spin-labeling electron spin resonance (SDSL-ESR) is a promising tool for membrane protein structure determination. Here we propose a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the restrictions of the local conformational spaces of the spin label attached at different protein sites along the primary structure of the membrane-embedded protein. We test the sensitivity of this approach for membrane-embedded M13 major coat protein decorated with a limited number of strategically placed spin labels employing high-throughput site-directed mutagenesis. We find a reasonably good agreement of the simulated and the experimental data taking a protein conformation close to the one determined by fluorescence resonance energy transfer analysis [P.V. Nazarov, R.B.M. Koehorst, W.L. Vos, V.V. Apanasovich, M.A. Hemminga, FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein, Biophys. J. 92 (2007) 1296-1305].

  14. Analysis of side chain rotational restrictions of membrane-embedded proteins by spin-label ESR spectroscopy.

    PubMed

    Strancar, Janez; Kavalenka, Aleh; Ziherl, Primoz; Stopar, David; Hemminga, Marcus A

    2009-04-01

    Site-directed spin-labeling electron spin resonance (SDSL-ESR) is a promising tool for membrane protein structure determination. Here we propose a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the restrictions of the local conformational spaces of the spin label attached at different protein sites along the primary structure of the membrane-embedded protein. We test the sensitivity of this approach for membrane-embedded M13 major coat protein decorated with a limited number of strategically placed spin labels employing high-throughput site-directed mutagenesis. We find a reasonably good agreement of the simulated and the experimental data taking a protein conformation close to the one determined by fluorescence resonance energy transfer analysis [P.V. Nazarov, R.B.M. Koehorst, W.L. Vos, V.V. Apanasovich, M.A. Hemminga, FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein, Biophys. J. 92 (2007) 1296-1305]. PMID:19138542

  15. Molecular Analysis of Oral Bacteria in Heart Valve of Patients With Cardiovascular Disease by Real-Time Polymerase Chain Reaction

    PubMed Central

    Oliveira, Francisco Artur Forte; Forte, Clarissa Pessoa Fernandes; Silva, Paulo Goberlânio de Barros; Lopes, Camile B.; Montenegro, Raquel Carvalho; dos Santos, Ândrea Kely Campos Ribeiro; Sobrinho, Carlos Roberto Martins Rodrigues; Mota, Mário Rogério Lima; Sousa, Fabrício Bitu; Alves, Ana Paula Negreiros Nunes

    2015-01-01

    Abstract Structural deficiencies and functional abnormalities of heart valves represent an important cause of cardiovascular morbidity and mortality, and a number of diseases, such as aortic stenosis, have been recently associated with infectious agents. This study aimed to analyze oral bacteria in dental plaque, saliva, and cardiac valves of patients with cardiovascular disease. Samples of supragingival plaque, subgingival plaque, saliva, and cardiac valve tissue were collected from 42 patients with heart valve disease. Molecular analysis of Streptococcus mutans, Prevotella intermedia, Porphyromonas gingivalis, and Treponema denticola was performed through real-time PCR. The micro-organism most frequently detected in heart valve samples was the S. mutans (89.3%), followed by P. intermedia (19.1%), P. gingivalis (4.2%), and T. denticola (2.1%). The mean decayed, missing, filled teeth (DMFT) was 26.4 ± 6.9 (mean ± SD), and according to the highest score of periodontal disease observed for each patient, periodontal pockets > 4 mm and dental calculus were detected in 43.4% and 34.7% of patients, respectively. In conclusion, oral bacteria, especially S. mutans, were found in the cardiac valve samples of patients with a high rate of caries and gingivitis/periodontitis. PMID:26632711

  16. Molecular Analysis of Oral Bacteria in Heart Valve of Patients With Cardiovascular Disease by Real-Time Polymerase Chain Reaction.

    PubMed

    Oliveira, Francisco Artur Forte; Forte, Clarissa Pessoa Fernandes; Silva, Paulo Goberlânio de Barros; Lopes, Camile B; Montenegro, Raquel Carvalho; Santos, Ândrea Kely Campos Ribeiro Dos; Sobrinho, Carlos Roberto Martins Rodrigues; Mota, Mário Rogério Lima; Sousa, Fabrício Bitu; Alves, Ana Paula Negreiros Nunes

    2015-11-01

    Structural deficiencies and functional abnormalities of heart valves represent an important cause of cardiovascular morbidity and mortality, and a number of diseases, such as aortic stenosis, have been recently associated with infectious agents. This study aimed to analyze oral bacteria in dental plaque, saliva, and cardiac valves of patients with cardiovascular disease. Samples of supragingival plaque, subgingival plaque, saliva, and cardiac valve tissue were collected from 42 patients with heart valve disease. Molecular analysis of Streptococcus mutans, Prevotella intermedia, Porphyromonas gingivalis, and Treponema denticola was performed through real-time PCR. The micro-organism most frequently detected in heart valve samples was the S. mutans (89.3%), followed by P. intermedia (19.1%), P. gingivalis (4.2%), and T. denticola (2.1%). The mean decayed, missing, filled teeth (DMFT) was 26.4 ± 6.9 (mean ± SD), and according to the highest score of periodontal disease observed for each patient, periodontal pockets > 4 mm and dental calculus were detected in 43.4% and 34.7% of patients, respectively. In conclusion, oral bacteria, especially S. mutans, were found in the cardiac valve samples of patients with a high rate of caries and gingivitis/periodontitis. PMID:26632711

  17. Molecular Analysis of Oral Bacteria in Heart Valve of Patients With Cardiovascular Disease by Real-Time Polymerase Chain Reaction.

    PubMed

    Oliveira, Francisco Artur Forte; Forte, Clarissa Pessoa Fernandes; Silva, Paulo Goberlânio de Barros; Lopes, Camile B; Montenegro, Raquel Carvalho; Santos, Ândrea Kely Campos Ribeiro Dos; Sobrinho, Carlos Roberto Martins Rodrigues; Mota, Mário Rogério Lima; Sousa, Fabrício Bitu; Alves, Ana Paula Negreiros Nunes

    2015-11-01

    Structural deficiencies and functional abnormalities of heart valves represent an important cause of cardiovascular morbidity and mortality, and a number of diseases, such as aortic stenosis, have been recently associated with infectious agents. This study aimed to analyze oral bacteria in dental plaque, saliva, and cardiac valves of patients with cardiovascular disease. Samples of supragingival plaque, subgingival plaque, saliva, and cardiac valve tissue were collected from 42 patients with heart valve disease. Molecular analysis of Streptococcus mutans, Prevotella intermedia, Porphyromonas gingivalis, and Treponema denticola was performed through real-time PCR. The micro-organism most frequently detected in heart valve samples was the S. mutans (89.3%), followed by P. intermedia (19.1%), P. gingivalis (4.2%), and T. denticola (2.1%). The mean decayed, missing, filled teeth (DMFT) was 26.4 ± 6.9 (mean ± SD), and according to the highest score of periodontal disease observed for each patient, periodontal pockets > 4 mm and dental calculus were detected in 43.4% and 34.7% of patients, respectively. In conclusion, oral bacteria, especially S. mutans, were found in the cardiac valve samples of patients with a high rate of caries and gingivitis/periodontitis.

  18. Sequencing and expression analysis of CD3γ/δ and CD3ɛ chains in mandarin fish, Siniperca chuatsi

    NASA Astrophysics Data System (ADS)

    Guo, Zheng; Nie, Pin

    2013-01-01

    The genomic and cDNA sequences of the CD3γ/δ and CD3ɛ homologues in the mandarin fish, Siniperca chuats i, were determined. As in other vertebrate CD3 molecules, the deduced amino acid sequences of mandarin fish CD3γ/δ and CD3ɛ contained conserved residues and motifs, such as cysteine residues and CXXC and immunoreceptor tyrosine-based activation motifs. However, mandarin fish CD3γ/δ and CD3ɛ showed some differences to their mammalian counterparts, specifically the absence of a negatively charged residue in the transmembrane region of CD3γ/δ. Additionally, while an N -glycosylation site was present in CD3ɛ, the site was not observed in CD3γ/δ. The CD3γ/δ and CD3ɛ subunit sequences contain six and five exons, respectively, consistent with homologues from Atlantic salmon, Salmo salar. Phylogenetic analysis also revealed that CD3γ/δ and CD3ɛ in mandarin fish are closely related to their counterparts in Acanthopterygian fish. Real-time PCR showed CD3γ/δ and CD3ɛ were expressed mainly in the thymus and spleen in normal healthy fish and, to a lesser extent, in mucosal-associated lymphoid tissues, such as the intestine and gills. When lymphocytes isolated from head kidney were treated with the mitogens phytohemagglutinin, concanavalin, and polyriboinosinic polyribocytidylic acid, mRNA expression levels of CD3γ/δ and CD3ɛ were significantly elevated within 12 h of treatment. This indicated the presence of T lymphocytes in the head kidney of teleost fish, and also the recognition of mitogens by the lymphocytes. Mandarin fish infected with the bacterial pathogen Flavobacterium columnare also showed an increase in the expression of CD3γ/δ and CD3ɛ mRNA, indicating that CD3γ/δ and CD3ɛ lymphocytes are involved in the immune response of this species.

  19. Multiplex SILAC Analysis of a Cellular TDP-43 Proteinopathy Model Reveals Protein Inclusions Associated with SUMOylation and Diverse Polyubiquitin Chains*

    PubMed Central

    Seyfried, Nicholas T.; Gozal, Yair M.; Dammer, Eric B.; Xia, Qiangwei; Duong, Duc M.; Cheng, Dongmei; Lah, James J.; Levey, Allan I.; Peng, Junmin

    2010-01-01

    Transactive response (TAR) DNA-binding protein 43 (TDP-43) is a major protein component within ubiquitin-positive inclusions of frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Although TDP-43 is a nuclear DNA/RNA-binding protein, in pathological conditions, TDP-43 has been reported to redistribute to the cytoplasm where it is cleaved and forms insoluble, ubiquitinated, and phosphorylated inclusions. Here we present a cellular model in which full-length human TDP-43 or a splicing isoform (TDP-S6) that lacks the C terminus is overexpressed in a human cell line and mouse primary neurons. Whereas recombinant and endogenous TDP-43 was primarily localized in the nucleus, the shorter TDP-S6 formed highly insoluble cytoplasmic and nuclear inclusions reminiscent of disease-specific pathology. Western blot analysis of detergent-insoluble extracts showed an increase in high molecular weight immunoreactive species for TDP-S6 compared with TDP-43, consistent with ubiquitination or ubiquitin-like modifications. We used a multiplex stable isotope labeling with amino acids in cell culture approach to compare the detergent-insoluble proteome from mock-, TDP-43-, and TDP-S6-transfected cells. TDP-S6 overexpression caused a concomitant increase in both ubiquitin (Ub) and the small Ub-like modifier-2/3 (SUMO-2/3) within the insoluble proteome. Similarly, full-length TDP-43 overexpression also resulted in the elevation of SUMO-2/3. Immunofluorescence showed strong co-localization of endogenous Ub with both cytoplasmic and nuclear TDP-S6 inclusions, whereas SUMO-2/3 was co-localized mainly with the nuclear inclusions. Quantitative mass spectrometry further revealed that mixed Lys-48 and Lys-63 polyUb linkages were associated with the TDP insoluble fractions. Together our data indicate that expression of a TDP-43 splice variant lacking a C terminus recapitulates many of the cellular and biochemical features associated with disease pathology and that the interplay of

  20. Jetfighter: An Experiential Value Chain Exercise

    ERIC Educational Resources Information Center

    Sheehan, Norman T.; Gamble, Edward N.

    2010-01-01

    Value chain analysis is widely taught in business schools and applied by practitioners to improve business performance. Despite its ubiquity, many students struggle to understand and apply value chain concepts in practice. JetFighter uses a complex manufacturing process (making intricate paper planes) to provide students an opportunity to enhance…

  1. Use of length heterogeneity polymerase chain reaction (LH-PCR) as non-invasive approach for dietary analysis of Svalbard reindeer, Rangifer tarandus platyrhynchus.

    PubMed

    Joo, Sungbae; Han, Donguk; Lee, Eun Ju; Park, Sangkyu

    2014-01-01

    To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components.

  2. Analysis of p53 gene mutations in human gliomas by polymerase chain reaction-based single-strand conformation polymorphism and DNA sequencing.

    PubMed

    Sarkar, F H; Kupsky, W J; Li, Y W; Sreepathi, P

    1994-03-01

    Mutations in the p53 gene have been recognized in brain tumors, and clonal expansion of p53 mutant cells has been shown to be associated with glioma progression. However, studies on the p53 gene have been limited by the need for frozen tissues. We have developed a method utilizing polymerase chain reaction (PCR) for the direct analysis of p53 mutation by single-strand conformation polymorphism (SSCP) and by direct DNA sequencing of the p53 gene using a single 10-microns paraffin-embedded tissue section. We applied this method to screen for p53 gene mutations in exons 5-8 in human gliomas utilizing paraffin-embedded tissues. Twenty paraffin blocks containing tumor were selected from surgical specimens from 17 different adult patients. Tumors included six anaplastic astrocytomas (AAs), nine glioblastomas (GBs), and two mixed malignant gliomas (MMGs). The tissue section on the stained glass slide was used to guide microdissection of an unstained adjacent tissue section to ensure > 90% of the tumor cell population for p53 mutational analysis. Simultaneously, microdissection of the tissue was also carried out to obtain normal tissue from adjacent areas as a control. Mutations in the p53 gene were identified in 3 of 17 (18%) patients by PCR-SSCP analysis and subsequently confirmed by PCR-based DNA sequencing. Mutations in exon 5 resulting in amino acid substitution were found in one thalamic AA (codon 158, CGC > CTT: Arg > Leu) and one cerebral hemispheric GB (codon 151, CCG > CTG: Pro > Leu).(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Analysis of T cell receptor AV and BV chain gene expression by infiltrating lymphocytes in Spitz naevi and in halo naevi.

    PubMed

    Birck, A; thor Straten, P; Li, L; Hou-Jensen, K; Sugár, J; Zeuthen, J

    1997-02-01

    Spitz naevi and halo naevi are benign melanocytic lesions that share many histological features with malignant melanoma. All lesions are characterized by a brisk infiltration of lymphocytes, mainly of the T cell subtype, and halo naevi are known to undergo spontaneous regression. Since the benign nature of Spitz naevi and halo naevi might therefore be caused by specific T cell responses against tumour-associated antigens, it was found of interest to characterize this T cell response in detail. A reverse transcriptase-polymerase chain reaction (RT-PCR)-based method adapted for analysis of paraffin-embedded material combined with Southern blot analysis has been used to analyse the T cell receptor (TCR) AV and BV repertoires of infiltrating lymphocytes in 14 different melanocytic lesions. The results have shown that only a few particular TCRAV and TCRBV regions are expressed in each lesion. To evaluate the T cell response, it is of interest to know the HLA-type of the analysed lesions, since most melanoma-specific effector lymphocytes are CD8+ cytotoxic T cells and therefore HLA class I-restricted. As blood samples were not available from any of these patients, an RT-PCR method using HLA-A2-specific primers was used to analyse for the presence of this allele. The preferentially expressed TCRAV genes were sequenced, and this analysis showed that the high expression of these TCRAV genes was due to a clonal or oligocional expansion of T cells. In summary, the expression of relatively few TCR variable regions indicates a clonal expansion of T cells. PMID:9067965

  4. Comparing the Southern blot method and polymerase chain reaction product analysis for chimeric RCCX detection in CYP21A2 deficiency.

    PubMed

    Lee, Hsien-Hsiung; Lee, Yann-Jinn; Chao, Mei-Chyn

    2010-04-15

    The 3.2-kb TaqI-produced fragment of the CYP21A1P pseudogene and the 3.7-kb TaqI-produced fragment of the functional CYP21A2 gene exist on chromosome 6p21.3. We used the polymerase chain reaction (PCR) product and Southern blot method with TaqI endonuclease digestion to identify a chimeric RCCX module in two unrelated patients with congenital adrenal hyperplasia (CAH). After TaqI cleavage, the PCR product analysis revealed that patient 1 with the chimeric CYP21A1P/CYP21A2 gene in one allele and IVS2-12A/C>G in combination with the 707-714del mutation in the other allele produced a configuration of 3.2- and 2.4-kb fragments. Patient 2, who carried IVS2-12A/C>G in combination with the 707-714del mutation in one allele and the chimeric TNXA/TNXB gene in the other allele, presented with 3.2- and 2.3-kb fragments. However, Southern blot analysis showed that patients 1 and 2 produced 3.2-, 2.4-, and 2.5-kb fragments. We conclude that the chimeric CYP21A1P/CYP21A2 gene, IVS2-12A/C>G in combination with the 707-714del mutation, and the chimeric TNXA/TNXB gene cannot be distinguished by the Southern blot method. Conversely, the chimeric TNXA/TNXB gene was identified in the PCR product analysis due to the appearance of the 2.37-kb fragment, which indicates the occurrence of the chimeric TNXA/TNXB formation extending to the boundary of TNXA in the RCCX region. PMID:19961824

  5. Use of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) as Non-Invasive Approach for Dietary Analysis of Svalbard Reindeer, Rangifer tarandus platyrhynchus

    PubMed Central

    Joo, Sungbae; Han, Donguk; Lee, Eun Ju; Park, Sangkyu

    2014-01-01

    To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components. PMID:24618847

  6. Use of Markov Chain Monte Carlo analysis with a physiologically-based pharmacokinetic model of methylmercury to estimate exposures in US women of childbearing age.

    PubMed

    Allen, Bruce C; Hack, C Eric; Clewell, Harvey J

    2007-08-01

    A Bayesian approach, implemented using Markov Chain Monte Carlo (MCMC) analysis, was applied with a physiologically-based pharmacokinetic (PBPK) model of methylmercury (MeHg) to evaluate the variability of MeHg exposure in women of childbearing age in the U.S. population. The analysis made use of the newly available National Health and Nutrition Survey (NHANES) blood and hair mercury concentration data for women of age 16-49 years (sample size, 1,582). Bayesian analysis was performed to estimate the population variability in MeHg exposure (daily ingestion rate) implied by the variation in blood and hair concentrations of mercury in the NHANES database. The measured variability in the NHANES blood and hair data represents the result of a process that includes interindividual variation in exposure to MeHg and interindividual variation in the pharmacokinetics (distribution, clearance) of MeHg. The PBPK model includes a number of pharmacokinetic parameters (e.g., tissue volumes, partition coefficients, rate constants for metabolism and elimination) that can vary from individual to individual within the subpopulation of interest. Using MCMC analysis, it was possible to combine prior distributions of the PBPK model parameters with the NHANES blood and hair data, as well as with kinetic data from controlled human exposures to MeHg, to derive posterior distributions that refine the estimates of both the population exposure distribution and the pharmacokinetic parameters. In general, based on the populations surveyed by NHANES, the results of the MCMC analysis indicate that a small fraction, less than 1%, of the U.S. population of women of childbearing age may have mercury exposures greater than the EPA RfD for MeHg of 0.1 microg/kg/day, and that there are few, if any, exposures greater than the ATSDR MRL of 0.3 microg/kg/day. The analysis also indicates that typical exposures may be greater than previously estimated from food consumption surveys, but that the variability

  7. A Markov chain analysis of the movements of juvenile salmonids, including sockeye salmon, in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the valuable information collected at McNary Dam was in the form of three-dimensional (hereafter referred to as 3-D) tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and testing of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting 3-D results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we used a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis allowed us to numerically summarize the behavior of fish in the forebay. This report is the second report published in 2012 that uses this analytical method. The first report included only fish released as part of the annual studies conducted at McNary Dam. This second report includes sockeye salmon that were released as part of studies conducted by the Chelan and Grant County Public Utility Districts at mid-Columbia River dams. The studies conducted in the mid-Columbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width was different between studies. Additionally, no passive integrated transponder tags were implanted in sockeye salmon. Differences in transmitter pulse width resulted in lower detection probabilities for sockeye salmon at McNary Dam. The absence of passive integrated transponder tags prevented us from determining if fish passed the powerhouse through the juvenile bypass system (JBS) or turbines. To

  8. Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

    PubMed Central

    Zarrin, Majid; Erfaninejad, Maryam

    2016-01-01

    Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates. PMID:27588085

  9. Analysis of the rDNA internal transcribed spacer region of the Fusarium species by polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    ZARRIN, MAJID; GANJ, FARZANEH; FARAMARZI, SAMA

    2016-01-01

    The Fusarium species are a widely spread phytopathogen identified in an extensive variety of hosts. The Fusarium genus is one of the most heterogeneous fungi and is difficult to classify. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis is a useful method in detection of DNA polymorphism in objective sequences. The aim of the present study was to identify the phylogenetic associations and usefulness of the internal transcribed spacer (ITS) region as a genetic marker within the most clinically important strain of the Fusarium species. A total of 50 strains of Fusarium spp. were used in the study, including environmental, clinical and reference isolates. The primers ITS1 and ITS4 were used in the study. Two restriction enzymes, HaeIII and SmaI, were assessed for the digestion of PCR products. A PCR product of ~550-base pairs was generated for each Fusarium species. The digested products with HaeIII and SmaI demonstrated that the bands generated for the medically significant Fusarium species, including F. solani, F. oxysporum, F. verticillidea, F. proliferatum and F. fujikuri, have different restriction enzyme patterns. In conclusion, it appears that the PCR-RFLP method used in the present study produces a sufficient restriction profile for differentiation of the most medically significant Fusarium species. PMID:27073635

  10. Bulk and Compound-Specific Isotope Analysis of Long-Chain, n-alkanes From a 85-kyr Core From Lake Peten Itza, Guatemala

    NASA Astrophysics Data System (ADS)

    Mays, J. L.; Brenner, M.; Bush, M. B.; Correa, A.; Curtis, J. H.; Hodell, D. A.

    2007-12-01

    Drill cores obtained from Lake Petén Itzá, Guatemala, contain a ~85-kyr record of terrestrial climate from lowland Central America. Variations in sediment lithology suggest rapid changes in precipitation during the last glacial and deglacial periods. Previous work in nearby Lake Quexil demonstrated the utility of using the carbon isotopic compositions of leaf wax n-alkanes to infer changes in terrestrial vegetation (Huang et al., 2001). Here we report carbon isotopes of bulk organic and long-chain n-alkanes in 60 samples to reconstruct changes in the relative proportion of C3 and C4 biomass in the watershed under changing climate and atmospheric CO2 conditions during the past 85 kyrs. Compound-specific carbon isotope results are compared directly with pollen analysis from the same samples. Huang, Y., F.A. Street-Perrott, S.E. Metcalfe, M. Brenner, M. Moreland, and K.H. Freeman. 2001. Climate change as the dominant control on glacial-interglacial variations in C3 and C4 plant abundance. Science 293:1647-1651.

  11. Commercial enzyme-linked immunosorbent assay versuspolymerase chain reaction for the diagnosis of chronic Chagas disease: a systematic review and meta-analysis.

    PubMed

    Brasil, Pedro Emmanuel Alvarenga Americano do; Castro, Rodolfo; Castro, Liane de

    2016-01-01

    Chronic Chagas disease diagnosis relies on laboratory tests due to its clinical characteristics. The aim of this research was to review commercial enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) diagnostic test performance. Performance of commercial ELISA or PCR for the diagnosis of chronic Chagas disease were systematically searched in PubMed, Scopus, Embase, ISI Web, and LILACS through the bibliography from 1980-2014 and by contact with the manufacturers. The risk of bias was assessed with QUADAS-2. Heterogeneity was estimated with the I2 statistic. Accuracies provided by the manufacturers usually overestimate the accuracy provided by academia. The risk of bias is high in most tests and in most QUADAS dimensions. Heterogeneity is high in either sensitivity, specificity, or both. The evidence regarding commercial ELISA and ELISA-rec sensitivity and specificity indicates that there is overestimation. The current recommendation to use two simultaneous serological tests can be supported by the risk of bias analysis and the amount of heterogeneity but not by the observed accuracies. The usefulness of PCR tests are debatable and health care providers should not order them on a routine basis. PCR may be used in selected cases due to its potential to detect seronegative subjects.

  12. Hybrid metabolic flux analysis and recombinant protein prediction in Pichia pastoris X-33 cultures expressing a single-chain antibody fragment.

    PubMed

    Isidro, Inês A; Portela, Rui M; Clemente, João J; Cunha, António E; Oliveira, Rui

    2016-09-01

    Despite the growing importance of the Pichia pastoris expression system as industrial workhorse, the literature is almost absent in systematic studies on how culture medium composition affects central carbon fluxes and heterologous protein expression. In this study we investigate how 26 variations of the BSM+PTM1 medium impact central carbon fluxes and protein expression in a P. pastoris X-33 strain expressing a single-chain antibody fragment. To achieve this goal, we adopted a hybrid metabolic flux analysis (MFA) methodology, which is a modification of standard MFA to predict the rate of synthesis of recombinant proteins. Hybrid MFA combines the traditional parametric estimation of central carbon fluxes with non-parametric statistical modeling of product-related quantitative or qualitative measurements as a function of central carbon fluxes. It was observed that protein yield variability was 53.6 % (relative standard deviation) among the different experiments. Protein yield is much more sensitive to medium composition than biomass growth, which is mainly determined by the carbon source availability and main salts. Hybrid MFA was able to describe accurately the protein yield with normalized RMSE of 6.3 % over 5 independent experiments. The metabolic state that promotes high protein yields is characterized by high overall metabolic rates through main central carbon pathways concomitantly with a relative shift of carbon flux from biosynthetic towards energy generating pathways. PMID:27129458

  13. Analysis of transtheoretical model of health behavioral changes in a nutrition intervention study--a continuous time Markov chain model with Bayesian approach.

    PubMed

    Ma, Junsheng; Chan, Wenyaw; Tsai, Chu-Lin; Xiong, Momiao; Tilley, Barbara C

    2015-11-30

    Continuous time Markov chain (CTMC) models are often used to study the progression of chronic diseases in medical research but rarely applied to studies of the process of behavioral change. In studies of interventions to modify behaviors, a widely used psychosocial model is based on the transtheoretical model that often has more than three states (representing stages of change) and conceptually permits all possible instantaneous transitions. Very little attention is given to the study of the relationships between a CTMC model and associated covariates under the framework of transtheoretical model. We developed a Bayesian approach to evaluate the covariate effects on a CTMC model through a log-linear regression link. A simulation study of this approach showed that model parameters were accurately and precisely estimated. We analyzed an existing data set on stages of change in dietary intake from the Next Step Trial using the proposed method and the generalized multinomial logit model. We found that the generalized multinomial logit model was not suitable for these data because it ignores the unbalanced data structure and temporal correlation between successive measurements. Our analysis not only confirms that the nutrition intervention was effective but also provides information on how the intervention affected the transitions among the stages of change. We found that, compared with the control group, subjects in the intervention group, on average, spent substantively less time in the precontemplation stage and were more/less likely to move from an unhealthy/healthy state to a healthy/unhealthy state. PMID:26123093

  14. A resilience assessment framework for infrastructure and economic systems : quantitative and qualitative resilience analysis of petrochemical supply chains to a hurricane.

    SciTech Connect

    Ehlen, Mark Andrew; Vugrin, Eric D.; Warren, Drake E.

    2010-03-01

    In recent years, the nation has recognized that critical infrastructure protection should consider not only the prevention of disruptive events, but also the processes that infrastructure systems undergo to maintain functionality following disruptions. This more comprehensive approach has been termed critical infrastructure resilience (CIR). Given the occurrence of a particular disruptive event, the resilience of a system to that event is the system's ability to efficiently reduce both the magnitude and duration of the deviation from targeted system performance levels. Sandia National Laboratories (Sandia) has developed a comprehensive resilience assessment framework for evaluating the resilience of infrastructure and economic systems. The framework includes a quantitative methodology that measures resilience costs that result from a disruption to infrastructure function. The framework also includes a qualitative analysis methodology that assesses system characteristics that affect resilience in order to provide insight and direction for potential improvements to resilience. This paper describes the resilience assessment framework. This paper further demonstrates the utility of the assessment framework through application to a hypothetical scenario involving the disruption of a petrochemical supply chain by a hurricane.

  15. Commercial enzyme-linked immunosorbent assay versus polymerase chain reaction for the diagnosis of chronic Chagas disease: a systematic review and meta-analysis

    PubMed Central

    do Brasil, Pedro Emmanuel Alvarenga Americano; Castro, Rodolfo; de Castro, Liane

    2016-01-01

    Chronic Chagas disease diagnosis relies on laboratory tests due to its clinical characteristics. The aim of this research was to review commercial enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) diagnostic test performance. Performance of commercial ELISA or PCR for the diagnosis of chronic Chagas disease were systematically searched in PubMed, Scopus, Embase, ISI Web, and LILACS through the bibliography from 1980-2014 and by contact with the manufacturers. The risk of bias was assessed with QUADAS-2. Heterogeneity was estimated with the I2 statistic. Accuracies provided by the manufacturers usually overestimate the accuracy provided by academia. The risk of bias is high in most tests and in most QUADAS dimensions. Heterogeneity is high in either sensitivity, specificity, or both. The evidence regarding commercial ELISA and ELISA-rec sensitivity and specificity indicates that there is overestimation. The current recommendation to use two simultaneous serological tests can be supported by the risk of bias analysis and the amount of heterogeneity but not by the observed accuracies. The usefulness of PCR tests are debatable and health care providers should not order them on a routine basis. PCR may be used in selected cases due to its potential to detect seronegative subjects. PMID:26814640

  16. Contribution to the modelling and analysis of logistics system performance by Petri nets and simulation models: Application in a supply chain

    NASA Astrophysics Data System (ADS)

    Azougagh, Yassine; Benhida, Khalid; Elfezazi, Said

    2016-02-01

    In this paper, the focus is on studying the performance of complex systems in a supply chain context by developing a structured modelling approach based on the methodology ASDI (Analysis, Specification, Design and Implementation) by combining the modelling by Petri nets and simulation using ARENA. The linear approach typically followed in conducting of this kind of problems has to cope with a difficulty of modelling due to the complexity and the number of parameters of concern. Therefore, the approach used in this work is able to structure modelling a way to cover all aspects of the performance study. The modelling structured approach is first introduced before being applied to the case of an industrial system in the field of phosphate. Results of the performance indicators obtained from the models developed, permitted to test the behaviour and fluctuations of this system and to develop improved models of the current situation. In addition, in this paper, it was shown how Arena software can be adopted to simulate complex systems effectively. The method in this research can be applied to investigate various improvements scenarios and their consequences before implementing them in reality.

  17. Crater chains on Mercury

    NASA Astrophysics Data System (ADS)

    Shevchenko, V.; Skobeleva, T.

    After discovery of disruption comet Shoemaker-Levy 9 into fragment train before it's collision with Jupiter there was proposed that linear crater chains on the large satellites of Jupiter and on the Moon are impact scars of past tidally disrupted comets.It's known that radar images have revealed the possible presence of water ice deposits in polar regions of Mercury. Impacts by a few large comets seem to provide the best explanation for both the amount and cleanliness of the ice deposits on Mercury because they have a larger volatile content that others external sources, for example, asteroid. A number of crater chains on the surface of Mercury are most likely the impact tracks of "fragment trains" of comets tidally disrupted by Sun or by Mercury and are not secondary craters. Mariner 10 image set (the three Mariner 10 flybys in 1974-1975) was used to recognize the crater chains these did not associate with secondary crater ejecta from observed impact structures. As example, it can be shown such crater chain located near crater Imhotep and crater Ibsen (The Kuiper Quadrangle of Mercury). Resolution of the Mariner 10 image is about 0.54 km/pixel. The crater chain is about 50 km long. It was found a similar crater chain inside large crater Sophocles (The Tolstoj Quadrangle of Mercury). The image resolution is about 1.46 km/pixel. The chain about 50 km long is located in northen part of the crater. Image resolution limits possibility to examine the form of craters strongly. It seems the craters in chains have roughly flat floor and smooth form. Most chain craters are approximately circular. It was examined many images from the Mariner 10 set and there were identified a total 15 crater chains and were unable to link any of these directly to any specific large crater associated with ejecta deposits. Chain craters are remarkably aligned. All distinguished crater chains are superposed on preexisting formations. A total of 127 craters were identified in the 15 recognized

  18. Vibrational analysis of amino acids and short peptides in hydrated media. VIII. Amino acids with aromatic side chains: L-phenylalanine, L-tyrosine, and L-tryptophan.

    PubMed

    Hernández, Belén; Pflüger, Fernando; Adenier, Alain; Kruglik, Sergei G; Ghomi, Mahmoud

    2010-11-25

    Four out of the 20 natural α-amino acids (α-AAs) contain aromatic rings in their side chains. In a recent paper (J. Phys. Chem. B 2010, 114, 9072-9083), we have analyzed the structural and vibrational features of l-histidine, one of the potent elements of this series. Here, we report on the three remaining members of this family, i.e., l-phenylalanine, l-tyrosine, and l-tryptophan. Their solution (H(2)O and D(2)O) Raman scattering and Fourier transform infrared absorption attenuated total reflection (FT-IR ATR) spectra were measured at room temperature from the species corresponding to those existing at physiological conditions. Because of the very low water solubility of tyrosine, special attention was paid to avoid any artifact concerning the report of the vibrational spectra corresponding to nondissolved powder of this AA in aqueous solution. Finally, we could obtain for the first time the Raman and FT-IR spectra of tyrosine at very low concentration (2.3 mM) upon long accumulation time. To clarify this point, those vibrational spectra of tyrosine recorded either in the solid phase or in a heterogeneous state, where dissolved and nondissolved species of this AA coexist in aqueous solution, are also provided as Supporting Information . To carry out a discussion on the general geometrical and vibrational behavior of these AAs, we resorted to quantum mechanical calculations at the DFT/B3LYP/6-31++G* level, allowing (i) determination of potential energy surfaces of these AAs in a continuum solvent as a function of the torsion angles χ(1) and χ(2), defining the conformation of each aromatic side chain around C(α)-C(β) and C(β)-C(γ) bonds, respectively; (ii) analysis of geometrical features of the AAs surrounded by clusters of n explicit (n = 5-7) water molecules interacting with the backbone and aromatic rings; and (iii) assignment of the observed vibrational modes by means of the theoretical data provided by the lowest energy conformers of explicitly

  19. Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models.

    PubMed

    Zhong, Yang; Patel, Sandeep

    2010-09-01

    Building upon the nonadditive electrostatic force field for alcohols based on the CHARMM charge equilibration (CHEQ) formalism, we introduce atom-pair specific solute-solvent Lennard-Jones (LJ) parameters for alcohol-water interaction force fields targeting improved agreement with experimental hydration free energies of a series of small molecule linear alcohols as well as ab initio water-alcohol geometries and energetics. We consider short-chain, linear alcohols from methanol to butanol as they are canonical small-molecule organic model compounds to represent the hydroxyl chemical functionality for parametrizing biomolecular force fields for proteins. We discuss molecular dynamics simulations of dilute aqueous solutions of methanol and ethanol in TIP4P-FQ water, with particular discussion of solution densities, structure defined in radial distribution functions, electrostatic properties (dipole moment distributions), hydrogen bonding patterns of water, as well as a Kirkwood-Buff (KB) integral analysis. Calculation of the latter provides an assessment of how well classical force fields parametrized to at least semiquantitatively match experimental hydration free energies capture the microscopic structures of dilute alcohol solutions; the latter translate into macroscopic thermodynamic properties through the application of KB analysis. We find that the CHEQ alcohol force fields of this work semiquantitatively match experimental KB integrals for methanol and ethanol mole fractions of 0.1 and 0.2. The force field combination qualitatively captures the concentration dependence of the alcohol-alcohol and water-water KB integrals, but due to inadequacies in the representation of the microscopic structures in such systems (which cannot be parametrized in any systematic fashion), a priori quantitative description of alcohol-water KB integrals remains elusive.

  20. N-3 long-chain polyunsaturated fatty acids and risk of all-cause mortality among general populations: a meta-analysis

    PubMed Central

    Chen, Guo-Chong; Yang, Jing; Eggersdorfer, Manfred; Zhang, Weiguo; Qin, Li-Qiang

    2016-01-01

    Prospective observational studies have shown inconsistent associations of dietary or circulating n-3 long-chain polyunsaturated fatty acids (LCPUFA) with risk of all-cause mortality. A meta-analysis was performed to evaluate the associations. Potentially eligible studies were identified by searching PubMed and EMBASE databases. The summary relative risks (RRs) with 95% confidence intervals (CIs) were calculated using the random-effects model. Eleven prospective studies involving 371 965 participants from general populations and 31 185 death events were included. The summary RR of all-cause mortality for high-versus-low n-3 LCPUFA intake was 0.91 (95% CI: 0.84–0.98). The summary RR for eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) intake was 0.83 (95% CI: 0.75–0.92) and 0.81 (95% CI: 0.74–0.95), respectively. In the dose-response analysis, each 0.3 g/d increment in n-3 LCPUFA intake was associated with 6% lower risk of all-cause mortality (RR = 0.94, 95% CI: 0.89–0.99); and each 1% increment in the proportions of circulating EPA and DHA in total fatty acids in blood was associated with 20% (RR = 0.80, 95% CI: 0.65–0.98) and 21% (RR = 0.79, 95% CI: 0.63–0.99) decreased risk of all-cause mortality, respectively. Moderate to high heterogeneity was observed across our anlayses. Our findings suggest that both dietary and circulating LCPUFA are inversely associated with all-cause mortality. PMID:27306836

  1. High Throughput Sequencing Analysis of the Immunoglobulin Heavy Chain Gene from Flow-Sorted B Cell Sub-Populations Define the Dynamics of Follicular Lymphoma Clonal Evolution.

    PubMed

    Carlotti, Emanuela; Wrench, David; Rosignoli, Guglielmo; Marzec, Jacek; Sangaralingam, Ajanthah; Hazanov, Lena; Michaeli, Miri; Hallam, Simon; Chaplin, Tracy; Iqbal, Sameena; Calaminici, Maria; Young, Bryan; Mehr, Ramit; Campbell, Peter; Fitzgibbon, Jude; Gribben, John G

    2015-01-01

    Understanding the dynamics of evolution of Follicular Lymphoma (FL) clones during disease progression is important for monitoring and targeting this tumor effectively. Genetic profiling of serial FL biopsies and examples of FL transmission following bone marrow transplant suggest that this disease may evolve by divergent evolution from a common ancestor cell. However where this ancestor cell resides and how it evolves is still unclear. The analysis of the pattern of somatic hypermutation of the immunoglobulin gene (Ig) is traditionally used for tracking the physiological clonal evolution of B cells within the germinal center and allows to discriminate those cells that have just entered the germinal center and display features of ancestor cells from those B cells that keep re-circulating across different lymphoid organs. Here we investigated the pattern of somatic hypermutation of the heavy chain of the immunoglobulin gene (IgH-VH) in 4 flow-sorted B cells subpopulations belonging to different stages of differentiation, from sequential lymph node biopsies of cases displaying diverse patterns of evolution, using the GS-FLX Titanium sequencing platform. We observed an unexpectedly high level of clonality, with hundreds of distinct tumor subclones in the different subpopulations from the same sample, the majority detected at a frequency <10-2. By using a lineage trees analysis we observed in all our FL and t-FL cases that the oligoclonal FL population was trapped in a narrow intermediate stage of maturation that maintains the capacity to undergo SHM, but was unable to further differentiate. The presence of such a complex architecture highlights challenges currently encountered in finding a cure for this disease. PMID:26325507

  2. Quantitation of Bt-176 maize genomic sequences by surface plasmon resonance-based biospecific interaction analysis of multiplex polymerase chain reaction (PCR).

    PubMed

    Feriotto, Giordana; Gardenghi, Sara; Bianchi, Nicoletta; Gambari, Roberto

    2003-07-30

    Surface plasmon resonance (SPR) based biosensors have been described for the identification of genetically modified organisms (GMO) by biospecific interaction analysis (BIA). This paper describes the design and testing of an SPR-based BIA protocol for quantitative determinations of GMOs. Biotinylated multiplex Polymerase Chain Reaction (PCR) products from nontransgenic maize as well as maize powders containing 0.5 and 2% genetically modified Bt-176 sequences were immobilized on different flow cells of a sensor chip. After immobilization, different oligonucleotide probes recognizing maize zein and Bt-176 sequences were injected. The results obtained were compared with Southern blot analysis and with quantitative real-time PCR assays. It was demonstrated that sequential injections of Bt-176 and zein probes to sensor chip flow cells containing multiplex PCR products allow discrimination between PCR performed using maize genomic DNA containing 0.5% Bt-176 sequences and that performed using maize genomic DNA containing 2% Bt-176 sequences. The efficiency of SPR-based BIA in discriminating material containing different amounts of Bt-176 maize is comparable to real-time quantitative PCR and much more reliable than Southern blotting, which in the past has been used for semiquantitative purposes. Furthermore, the approach allows the BIA assay to be repeated several times on the same multiplex PCR product immobilized on the sensor chip, after washing and regeneration of the flow cell. Finally, it is emphasized that the presented strategy to quantify GMOs could be proposed for all of the SPR-based, commercially available biosensors. Some of these optical SPR-based biosensors use, instead of flow-based sensor chips, stirred microcuvettes, reducing the costs of the experimentation.

  3. Monte Carlo Markov chains analysis of WMAP3 and SDSS data points to broken symmetry inflaton potentials and provides a lower bound on the tensor to scalar ratio

    SciTech Connect

    Destri, C.; Vega, H. J. de; Sanchez, N. G.

    2008-02-15

    We perform a Monte Carlo Markov chains (MCMC) analysis of the available cosmic microwave background (CMB) and large scale structure (LSS) data (including the three years WMAP data) with single field slow-roll new inflation and chaotic inflation models. We do this within our approach to inflation as an effective field theory in the Ginsburg-Landau spirit with fourth degree trinomial potentials in the inflaton field {phi}. We derive explicit formulae and study in detail the spectral index n{sub s} of the adiabatic fluctuations, the ratio r of tensor to scalar fluctuations, and the running index dn{sub s}/dlnk. We use these analytic formulas as hard constraints on n{sub s} and r in the MCMC analysis. Our analysis differs in this crucial aspect from previous MCMC studies in the literature involving the WMAP3 data. Our results are as follows: (i) The data strongly indicate the breaking (whether spontaneous or explicit) of the {phi}{yields}-{phi} symmetry of the inflaton potentials both for new and for chaotic inflation. (ii) Trinomial new inflation naturally satisfies this requirement and provides an excellent fit to the data. (iii) Trinomial chaotic inflation produces the best fit in a very narrow corner of the parameter space. (iv) The chaotic symmetric trinomial potential is almost certainly ruled out (at 95% C.L.). In trinomial chaotic inflation the MCMC runs go towards a potential in the boundary of the parameter space and which resembles a spontaneously symmetry broken potential of new inflation. (v) The above results and further physical analysis here lead us to conclude that new inflation gives the best description of the data. (vi) We find a lower bound for r within trinomial new inflation potentials: r>0.016(95%CL) and r>0.049(68%CL). (vii) The preferred new inflation trinomial potential is a double well, even function of the field with a moderate quartic coupling yielding as most probable values: n{sub s}{approx_equal}0.958, r{approx_equal}0.055. This value

  4. Chain entanglements. I. Theory

    NASA Astrophysics Data System (ADS)

    Fixman, Marshall

    1988-09-01

    A model of concentrated polymer solution dynamics is described. The forces in a linear generalized Langevin equation for the motion of a probe chain are derived on the assumption that all relaxation of the forces is due to motion of the surrounding matrix. Vicinal chain displacements are classified as viscoelastic deformation, reptation, and minor residual fluctuations. The latter provide a torsional relaxation of the primitive path that minimizes the significance of transverse forces on the probe chain. All displacements of vicinal segments are assumed proportional to the forces that they exert on the probe chain. In response to an external force, the displacement of the probe chain relative to a laboratory frame is increased by viscoelastic deformation of the matrix, but reptative diffusion relative to the deforming matrix is slowed down. The net effect on translational diffusion is negligible if the probe and vicinal chains have the same chain length N, but the friction constant for reptative motion is increased by a factor N1-xs. xs=1/2 if Gaussian conformational statistics applies during the disengagement process, while xs =0.6 if excluded volume statistics applies. The translational friction constant is βp ˜N2, as in reptation theory, but the viscosity is η˜N4-xs . The persistence of entanglements during the translational diffusion of the probe chain across many radii of gyration is rationalized pictorially in terms of correlated reptative motion of the probe and vicinal chains.

  5. Influence of molecular architecture on the entanglement network: topological analysis of linear, long- and short-chain branched polyethylene melts via Monte Carlo simulations.

    PubMed

    Jeong, Seung Heum; Kim, Jun Mo; Yoon, Jeongha; Tzoumanekas, Christos; Kröger, Martin; Baig, Chunggi

    2016-04-20

    We present detailed results on the effect of chain branching on the topological properties of entangled polymer melts via an advanced connectivity-altering Monte Carlo (MC) algorithm. Eleven representative model linear, short-chain branched (SCB), and long-chain branched (LCB) polyethylene (PE) melts were employed, based on the total chain length and/or the longest linear chain dimension. Directly analyzing the entanglement [or the primitive path (PP)] network of the system via the Z-code, we quantified several important topological measures: (a) the PP contour length Lpp, (b) the number of entanglements Zes per chain, (c) the end-to-end length of an entanglement strand des, (d) the number of carbon atoms per entanglement strand Nes, and (e) the probability distribution for each of these quantities. The results show that the SCB polymer melts have significantly more compact overall chain conformations compared to the linear polymers, exhibiting, relative to the corresponding linear analogues, (a) ∼20% smaller values of 〈Lpp〉 (the statistical average of Lpp), (b) ∼30% smaller values of 〈Zes〉, (c) ∼20% larger values of 〈des〉, and (d) ∼50% larger values of 〈Nes〉. In contrast, despite the intrinsically smaller overall chain dimensions than those of the linear analogues, the LCB (H-shaped and A3AA3 multiarm) PE melts exhibit relatively (a) 7-8% larger values of 〈Lpp〉, (b) 6-11% larger values of 〈Zes〉 for the H-shaped melt and ∼2% smaller values of 〈Zes〉 for the A3AA3 multiarm, (c) 2-5% smaller values of 〈des〉, and (d) 7-11% smaller values of 〈Nes〉. Several interesting features were also found in the results of the probability distribution functions P for each topological measure.

  6. Immunohistochemical analysis of the skin in junctional epidermolysis bullosa using laminin 5 chain specific antibodies is of limited value in predicting the underlying gene mutation.

    PubMed

    McMillan, J R; McGrath, J A; Pulkkinen, L; Kon, A; Burgeson, R E; Ortonne, J P; Meneguzzi, G; Uitto, J; Eady, R A

    1997-06-01

    The anchoring filament protein laminin 5 is composed of three polypeptide chains (alpha 3, beta 3 and gamma 2) each encoded by separate genes (LAMA3, LAMB3 and LAMC2, respectively). Mutations in any of these three genes may give rise to the autosomal recessive blistering skin disease, junctional epidermolysis bullosa. At present, there is no easy way of predicting which of these three genes might harbour the pathogenetic laminin 5 mutations in a case of junctional epidermolysis bullosa. In this study, we assessed whether immunohistochemistry might be helpful in this regard. We performed immunohistochemical labelling of the dermal-epidermal junction using alpha 3, beta 3 and gamma 2 chain-specific antibodies in 11 patients with junctional epidermolysis bullosa, in whom the laminin 5 mutations had been previously delineated. Although, labelling for the laminin 5 chain bearing the mutations was attenuated or undetectable in all cases, a complete absence of labelling or a reduction in the staining intensity for the other two chains was also seen in all cases. The results showed that immunohistochemical labelling of the dermal-epidermal junction using alpha 3, beta 3 and gamma 2 chain-specific antibodies is not a specific indicator for which of the laminin 5 chain genes contains the pathogenetic mutations, and is therefore unreliable in screening for individual laminin 5 gene mutations in cases of junctional epidermolysis bullosa. PMID:9217810

  7. Hepatic transcriptome analysis of inter-family variability in flesh n-3 long-chain polyunsaturated fatty acid content in Atlantic salmon

    PubMed Central

    2012-01-01

    Background Genetic selection of Atlantic salmon families better adapted to alternative feed formulations containing high levels of vegetable ingredients has been suggested to ensure sustainable growth of aquaculture. The present study aimed to identify molecular pathways that could underlie phenotypic differences in flesh n-3 long-chain polyunsaturated fatty acid (LC-PUFA) levels when fish are fed vegetable oil diets. Liver transcriptome was analyzed and compared in four families presenting higher or lower n-3 LC-PUFA contents at two contrasting flesh total lipid levels. Results The main effect of n-3 LC-PUFA contents was in the expression of immune response genes (38% of all significantly affected genes), broadly implicated in the modulation of inflammatory processes and innate immune response. Although genetic evaluations of traits used in the breeding program revealed that the chosen families were not balanced for viral disease resistance, this did not fully explain the preponderance of immune response genes in the transcriptomic analysis. Employing stringent statistical analysis no lipid metabolism genes were detected as being significantly altered in liver when comparing families with high and low n-3 LC-PUFA flesh contents. However, relaxing the statistical analysis enabled identification of potentially relevant effects, further studied by RT-qPCR, in cholesterol biosynthesis, lipoprotein metabolism and lipid transport, as well as eicosanoid metabolism particularly affecting the lipoxygenase pathway. Total lipid level in flesh also showed an important effect on immune response and 8% of significantly affected genes related to lipid metabolism, including a fatty acyl elongase (elovl2), an acyl carrier protein and stearoyl-CoA desaturase. Conclusions Inter-family differences in n-3 LC-PUFA content could not be related to effects on lipid metabolism, including transcriptional modulation of the LC-PUFA biosynthesis pathway. An association was found between flesh

  8. Systematic Analysis of Gene Expression Alterations and Clinical Outcomes for Long-Chain Acyl-Coenzyme A Synthetase Family in Cancer

    PubMed Central

    Chen, Wei-Ching; Wang, Chih-Yang; Hung, Yu-Hsuan; Weng, Tzu-Yang; Yen, Meng-Chi; Lai, Ming-Derg

    2016-01-01

    Dysregulated lipid metabolism contributes to cancer progression. Our previous study indicates that long-chain fatty acyl-Co A synthetase (ACSL) 3 is essential for lipid upregulation induced by endoplasmic reticulum stress. In this report, we aimed to identify the role of ACSL family in cancer with systematic analysis and in vitro experiment. We explored the ACSL expression using Oncomine database to determine the gene alteration during carcinogenesis and identified the association between ACSL expression and the survival of cancer patient using PrognoScan database. ACSL1 may play a potential oncogenic role in colorectal and breast cancer and play a potential tumor suppressor role in lung cancer. Co-expression analysis revealed that ACSL1 was coexpressed with MYBPH, PTPRE, PFKFB3, SOCS3 in colon cancer and with LRRFIP1, TSC22D1 in lung cancer. In accordance with PrognoScan analysis, downregulation of ACSL1 in colon and breast cancer cell line inhibited proliferation, migration, and anchorage-independent growth. In contrast, increase of oncogenic property was observed in lung cancer cell line by attenuating ACSL1. High ACSL3 expression predicted a better prognosis in ovarian cancer; in contrast, high ACSL3 predicted a worse prognosis in melanoma. ACSL3 was coexpressed with SNUPN, TRIP13, and SEMA5A in melanoma. High expression of ACSL4 predicted a worse prognosis in colorectal cancer, but predicted better prognosis in breast, brain and lung cancer. ACSL4 was coexpressed with SERPIN2, HNRNPCL1, ITIH2, PROCR, LRRFIP1. High expression of ACSL5 predicted good prognosis in breast, ovarian, and lung cancers. ACSL5 was coexpressed with TMEM140, TAPBPL, BIRC3, PTPRE, and SERPINB1. Low ACSL6 predicted a worse prognosis in acute myeloid leukemia. ACSL6 was coexpressed with SOX6 and DARC. Altogether, different members of ACSLs are implicated in diverse types of cancer development. ACSL-coexpressed molecules may be used to further investigate the role of ACSL family in

  9. Late Miocene to present-day exhumation and uplift of the Internal Zone of the Rif chain: Insights from low temperature thermochronometry and basin analysis

    NASA Astrophysics Data System (ADS)

    Romagny, A.; Ph. Münch; Cornée, J.-J.; Corsini, M.; Azdimousa, A.; Melinte-Dobrinescu, M. C.; Drinia, H.; Bonno, M.; Arnaud, N.; Monié, P.; Quillévéré, F.; Ben Moussa, A.

    2014-07-01

    Located on the margin of the west Alboran basin, the Gibraltar Arc (Betic-Rif mountain belt) displays post-Pliocene vertical movements evidenced by uplifted marine sedimentary basins and marine terraces. Quantification of vertical movements is an important clue to understand the origin of present-day relief generation in the Betic-Rif mountain chain together with the causes of the Messinian Salinity Crisis. In this paper, we present the results of a pluridisciplinary study combining an analysis of low temperature thermochronology and Pliocene basins evolution to constrain the exhumation history and surface uplift of internals units of the Rif belt (Northern Morocco). The mean (U-Th)/He apatite ages obtained from 11 samples are comprised between 14.1 and 17.8 Ma and display a wide dispersion, which could be explained by a great variability of apatite chemistries in the analyzed samples. No correlations between altitude and age have been found along altitudinal profile suggesting a rapid exhumation during this period. Thermal modeling using our (U-Th)/He apatite ages and geochronological data previously obtained in the same area (40Ar/39Ar and K/Ar data on biotite, zircon and apatite fission track) allow us to propose a cooling history. The rocks suffered a rapid cooling at 60-100 °C/Ma between 22.5 and 19 Ma, then cooled to temperatures around 40 °C between 19 and 18 Ma. They were re-heated at around 110 °C between 18 and 15 Ma then rapidly cooled and exhumed to reach the surface temperature at around 13 Ma. The re-heating could be related to a renewal in thrusting and burying of the inner zones. Between 15 and 13 Ma the cooling resumed at a rate of 50 °C/Ma indicating an exhumation rate of 0.8 mm/y considering an average 40 °C/km geothermal gradient. This exhumation may be linked to the extension in the Alboran Sea. Otherwise biostratigraphic and sedimentological analysis of Pliocene basins of the internal Rif provided informations on the more recent events

  10. Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

    PubMed Central

    Hadifar, Shima; Moghim, Sharareh; Fazeli, Hossein; GhasemianSafaei, Hajieh; Havaei, Seyed Asghar; Farid, Fariba; Esfahani, Bahram Nasr

    2015-01-01

    Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species. PMID:26380237

  11. Comparative quantitative analysis of BCR-ABL transcripts with the T315I mutant clone by polymerase chain reaction (PCR)-Invader method.

    PubMed

    Tadokoro, Kenichi; Ishikawa, Maho; Suzuki, Makoto; Saito, Tomoyoshi; Suzuki, Yoshie; Yamaguchi, Toshikazu; Yagasaki, Fumiharu

    2011-09-01

    Drug resistance is a serious complication in the treatment of chronic myeloid leukemia (CML). The most common and best-characterized mechanism of secondary imatinib resistance in CML is the development of kinase domain mutations in the BCR-ABL gene. Second-generation tyrosine kinase inhibitors, such as dasatinib or nilotinib, overcome most of these mutations, but they are not effective against the T315I mutant. To determine whether these mutations contribute to clinical resistance, it is necessary to monitor the ratio of the mutant and wild-type forms. Here, we developed a polymerase chain reaction (PCR)-Invader assay for comparative quantitative analysis (qPI assay) of BCR-ABL transcripts with the T315I mutant clone. T315I ratios were calculated for the wild-type and mutant fold-over-zero (FOZ) values. In examination with 2 kinds of plasmids containing wild-type or T315I mutant PCR amplicons, mutant FOZ values were detected down to 1% of the total. The results of 12 serial samples from 2 patients (case A: Philadelphia-positive acute lymphoblastic leukemia and case B: CML) with the T315I mutant clone were compared with those of direct sequencing or 2 kinds of allele-specific oligonucleotide (ASO)-PCR. All samples showed the T315I mutation by qPI assay and ASO-PCR, and 10 samples showed it by direct sequencing. Significant correlation (correlation coefficient; r2 = 0.951) was noted between the qPI assay and quantitative ASO-PCR to analyze T315I mutant ratios. Thus, the qPI assay is a useful method for evaluating the T315I mutant clone in BCR-ABL transcripts.

  12. High-Throughput Analysis of the T Cell Receptor Beta Chain Repertoire in PBMCs from Chronic Hepatitis B Patients with HBeAg Seroconversion

    PubMed Central

    Huang, Yong; Liu, Di; Huang, Yinuo; Zhang, Zhiyi

    2016-01-01

    T lymphocytes are the most important immune cells that affect both the development and treatment of hepatitis B. We used high-throughput sequencing to determine the diversity in the V and J regions of the TCRβ chain in 4 chronic hepatitis B patients before and after HBeAg seroconversion. Here, we demonstrate that the 4 patients expressed Vβ12-4 at the highest frequencies of 10.6%, 9.2%, 17.5%, and 7.5%, and Vβ28 was the second most common, with frequencies of 7.8%, 6.7%, 5.3%, and 10.9%, respectively. No significant changes were observed following seroconversion. With regard to the Jβ gene, Jβ2-1 was the most commonly expressed in the 4 patients at frequencies of 5.8%, 6.5%, 11.3%, and 7.3%, respectively. Analysis of the V-J region genes revealed several differences, including significant increases in the expression levels of V7-2-01-J2-1, V12-4-J1-1, and V28-1-J1-5 and a decrease in that of V19-01-J2-3. These results illustrate the presence of biased TCRVβ and Jβ gene expression in the chronic hepatitis B patients. TRBVβ12-4, Vβ28, Jβ2-1, V7-2-01-J2-1, V12-4-J1-1, and V28-1-J1-5 may be associated with the development and treatment of CHB.

  13. Comparative quantitative analysis of BCR-ABL transcripts with the T315I mutant clone by polymerase chain reaction (PCR)-Invader method.

    PubMed

    Tadokoro, Kenichi; Ishikawa, Maho; Suzuki, Makoto; Saito, Tomoyoshi; Suzuki, Yoshie; Yamaguchi, Toshikazu; Yagasaki, Fumiharu

    2011-09-01

    Drug resistance is a serious complication in the treatment of chronic myeloid leukemia (CML). The most common and best-characterized mechanism of secondary imatinib resistance in CML is the development of kinase domain mutations in the BCR-ABL gene. Second-generation tyrosine kinase inhibitors, such as dasatinib or nilotinib, overcome most of these mutations, but they are not effective against the T315I mutant. To determine whether these mutations contribute to clinical resistance, it is necessary to monitor the ratio of the mutant and wild-type forms. Here, we developed a polymerase chain reaction (PCR)-Invader assay for comparative quantitative analysis (qPI assay) of BCR-ABL transcripts with the T315I mutant clone. T315I ratios were calculated for the wild-type and mutant fold-over-zero (FOZ) values. In examination with 2 kinds of plasmids containing wild-type or T315I mutant PCR amplicons, mutant FOZ values were detected down to 1% of the total. The results of 12 serial samples from 2 patients (case A: Philadelphia-positive acute lymphoblastic leukemia and case B: CML) with the T315I mutant clone were compared with those of direct sequencing or 2 kinds of allele-specific oligonucleotide (ASO)-PCR. All samples showed the T315I mutation by qPI assay and ASO-PCR, and 10 samples showed it by direct sequencing. Significant correlation (correlation coefficient; r2 = 0.951) was noted between the qPI assay and quantitative ASO-PCR to analyze T315I mutant ratios. Thus, the qPI assay is a useful method for evaluating the T315I mutant clone in BCR-ABL transcripts. PMID:21867983

  14. Physiologically-based toxicokinetic model for cadmium using Markov-chain Monte Carlo analysis of concentrations in blood, urine, and kidney cortex from living kidney donors.

    PubMed

    Fransson, Martin Niclas; Barregard, Lars; Sallsten, Gerd; Akerstrom, Magnus; Johanson, Gunnar

    2014-10-01

    The health effects of low-level chronic exposure to cadmium are increasingly recognized. To improve the risk assessment, it is essential to know the relation between cadmium intake, body burden, and biomarker levels of cadmium. We combined a physiologically-based toxicokinetic (PBTK) model for cadmium with a data set from healthy kidney donors to re-estimate the model parameters and to test the effects of gender and serum ferritin on systemic uptake. Cadmium levels in whole blood, blood plasma, kidney cortex, and urinary excretion from 82 men and women were used to calculate posterior distributions for model parameters using Markov-chain Monte Carlo analysis. For never- and ever-smokers combined, the daily systemic uptake was estimated at 0.0063 μg cadmium/kg body weight in men, with 35% increased uptake in women and a daily uptake of 1.2 μg for each pack-year per calendar year of smoking. The rate of urinary excretion from cadmium accumulated in the kidney was estimated at 0.000042 day(-1), corresponding to a half-life of 45 years in the kidneys. We have provided an improved model of cadmium kinetics. As the new parameter estimates derive from a single study with measurements in several compartments in each individual, these new estimates are likely to be more accurate than the previous ones where the data used originated from unrelated data sets. The estimated urinary excretion of cadmium accumulated in the kidneys was much lower than previous estimates, neglecting this finding may result in a marked under-prediction of the true kidney burden.

  15. Chain Reaction Polymerization.

    ERIC Educational Resources Information Center

    McGrath, James E.

    1981-01-01

    The salient features and importance of chain-reaction polymerization are discussed, including such topics as the thermodynamics of polymerization, free-radical polymerization kinetics, radical polymerization processes, copolymers, and free-radical chain, anionic, cationic, coordination, and ring-opening polymerizations. (JN)

  16. Critical Chain Exercises

    ERIC Educational Resources Information Center

    Doyle, John Kevin

    2010-01-01

    Critical Chains project management focuses on holding buffers at the project level vs. task level, and managing buffers as a project resource. A number of studies have shown that Critical Chain project management can significantly improve organizational schedule fidelity (i.e., improve the proportion of projects delivered on time) and reduce…

  17. Simultaneous confirmatory analysis of different transgenic maize (zea mays) lines using multiplex polymerase chain reaction-restriction analysis and capillary gel electrophoresis with laser induced fluorescence detection.

    PubMed

    García-Cañas, Virginia; Cifuentes, Alejandro

    2008-09-24

    A novel analytical procedure based on the combination of multiplex PCR, restriction analysis, and CGE-LIF to unambiguosly and simultaneously confirm the presence of multiple lines of genetically modified corn is proposed. This methodology is based on the amplification of event-specific DNA regions by multiplex PCR using 6-FAM-labeled primers. Subsequently, PCR products are digested by a mixture containing specific restriction endonucleases. Thus, restriction endonucleases selectively recognize DNA target sequences contained in the PCR products and cleave the double-stranded DNA at a given cleavage site. Next, the restriction digest is analyzed by CGE-LIF corroborating the length of the expected restriction fragments, confirming (or not) the existence of GMOs. For accurate size determination of the DNA fragments by CGE-LIF a special standard DNA mixture was produced in this laboratory for calibration. The suitability of this mixture for size determination of labeled DNA fragments is also demonstrated. The usefulness of the proposed methodology is demonstrated through the simultaneous detection and confirmatory analysis of samples containing 0.5% of GA21 and MON863 maize plus an endogenous gene of maize as control.

  18. Establishment of real-time quantitative reverse transcription polymerase chain reaction assay for transcriptional analysis of duck enteritis virus UL55 gene

    PubMed Central

    2011-01-01

    Background Real-time quantitative reverse transcription polymerase chain reaction assay (qRT-PCR) has become the benchmark for detection and quantification of target gene expression level and been utilized increasingly in detection of viral load and therapy monitoring. The dynamic transcription variation of duck enteritis virus UL55 gene during the life cycle of duck enteritis virus in infected cells has not been reported yet. Results The newly identified duck enteritis virus UL55 gene was amplified and cloned into pMD18-T vector after digestion to generate a recombinant plasmid pMD18-T/UL55 for the establishment of qRT-PCR as standard DNA. The results of agarose gel electrophoresis and melting curve analysis demonstrated the primers we designed for qRT-PCR were specific and available. We used β-actin as a reference gene for normalization and established two standard curves based on pMD18-T/UL55 and pMD18-T/β-actin successfully. Based on that, the transcriptional analysis of DEV UL55 gene was performed, and the result suggested the expression of UL55 mRNA was at a low level from 0 to 8 h post-infection(p.i.), then accumulated quickly since 12 h p.i. and peaked at 36 h p.i., it can be detected till 60 h p.i.. Nucleic acid inhibition test was carried out for analyzing a temporal regulation condition of DEV UL55 gene, result revealed that it was sensitive to ganciclovir. Synthesis procedures of DEV UL55 gene can be inhibited by ganciclovir. Conclusions The method we established in this paper can provide quantitative values reflecting the amounts of measured mRNA in samples. It's available for detection and quantification, also can be used in DEV diagnosis. The DEV UL55 gene was produced most abundantly during the late phase of replication in DEV-infected cells and the transcription of it depended on the synthesized DNA. DEV UL55 gene is a γ2 gene which occurs last and have a strict requirement for viral DNA synthesis. PMID:21631934

  19. Botswana's Beef Global Commodity Chain: Explaining the Resistance to Change

    ERIC Educational Resources Information Center

    Ransom, Elizabeth

    2011-01-01

    In an era of increasing global agricultural trade, many firms and farms seek to upgrade their agricultural commodity chains to become better integrated into global markets. Utilizing a global commodity chain (GCC) approach, this analysis unravels the challenges to and the potential consequences of upgrading Botswana's beef commodity chain.…

  20. Chain Effects: The Impact of Academy Chains on Low Income Students

    ERIC Educational Resources Information Center

    Hutchings, Merryn; Francis, Becky; De Vries, Robert

    2014-01-01

    The authors analysed school performance data to review how well disadvantaged pupils achieve in academy chains. They included chains only if they had at least three academies in 2013, and two sponsored secondary academies for the whole period from September 2010 to July 2013. This means that academies are included in our analysis only when there…

  1. SUMO Chain Formation by Plant Enzymes.

    PubMed

    Tomanov, Konstantin; Ziba, Ionida; Bachmair, Andreas

    2016-01-01

    SUMO conjugation is a conserved process of eukaryotes, and essential in metazoa. Different isoforms of SUMO are present in eukaryotic genomes. Saccharomyces cerevisiae has only one SUMO protein, humans have four and Arabidopsis thaliana has eight, the main isoforms being SUMO1 and SUMO2 with about 95 % identity. Functionally similar to human SUMO2 and SUMO3, Arabidopsis SUMO1 and 2 can form chains, even though they do not possess a consensus SUMOylation motif. The surprising finding that plants have dedicated enzymes for chain synthesis implies a specific role for SUMO chains in plants. By the cooperative action with SUMO chain recognizing ubiquitin ligases, chains might channel substrates into the ubiquitin-dependent degradation pathway.A method is described to generate SUMO chains, using plant enzymes produced in E. coli. In vitro SUMO chain formation may serve for further analysis of SUMO chain functions. It can also provide an easy-to-synthesize substrate for SUMO-specific proteases. PMID:27424748

  2. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    SciTech Connect

    Shi, Pan; Xi, Zhaoyong; Wang, Hu; Shi, Chaowei; Xiong, Ying; Tian, Changlin

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  3. Supramolecular buffering by ring-chain competition.

    PubMed

    Paffen, Tim F E; Ercolani, Gianfranco; de Greef, Tom F A; Meijer, E W

    2015-02-01

    Recently, we reported an organocatalytic system in which buffering of the molecular catalyst by supramolecular interactions results in a robust system displaying concentration-independent catalytic activity. Here, we demonstrate the design principles of the supramolecular buffering by ring-chain competition using a combined experimental and theoretical approach. Our analysis shows that supramolecular buffering of a molecule is caused by its participation as a chain stopper in supramolecular ring-chain equilibria, and we reveal here the influence of various thermodynamic parameters. Model predictions based on independently measured equilibrium constants corroborate experimental data of several molecular systems in which buffering occurs via competition between cyclization, growth of linear chains, and end-capping by the chain-stopper. Our analysis reveals that the effective molarity is the critical parameter in optimizing the broadness of the concentration regime in which supramolecular ring-chain buffering occurs as well as the maximum concentration of the buffered molecule. To conclude, a side-by-side comparison of supramolecular ring-chain buffering, pH buffering, and molecular titration is presented.

  4. Comparison of the accuracy of Hybrid Capture II and polymerase chain reaction in detecting clinically important cervical dysplasia: a systematic review and meta-analysis.

    PubMed

    Luu, Hung N; Dahlstrom, Kristina R; Mullen, Patricia Dolan; VonVille, Helena M; Scheurer, Michael E

    2013-06-01

    The effectiveness of screening programs for cervical cancer has benefited from the inclusion of Human papillomavirus (HPV) DNA assays; which assay to choose, however, is not clear based on previous reviews. Our review addressed test accuracy of Hybrid Capture II (HCII) and polymerase chain reaction (PCR) assays based on studies with stronger designs and with more clinically relevant outcomes. We searched OvidMedline, PubMed, and the Cochrane Library for English language studies comparing both tests, published 1985-2012, with cervical dysplasia defined by the Bethesda classification. Meta-analysis provided pooled sensitivity, specificity, and 95% confidence intervals (CIs); meta-regression identified sources of heterogeneity. From 29 reports, we found that the pooled sensitivity and specificity to detect high-grade squamous intraepithelial lesion (HSIL) was higher for HCII than PCR (0.89 [CI: 0.89-0.90] and 0.85 [CI: 0.84-0.86] vs. 0.73 [CI: 0.73-0.74] and 0.62 [CI: 0.62-0.64]). Both assays had higher accuracy to detect cervical dysplasia in Europe than in Asia-Pacific or North America (diagnostic odd ratio - dOR = 4.08 [CI: 1.39-11.91] and 4.56 [CI: 1.86-11.17] for HCII vs. 2.66 [CI: 1.16-6.53] and 3.78 [CI: 1.50-9.51] for PCR) and accuracy to detect HSIL than atypical squamous cells of undetermined significance (ASCUS)/ low-grade squamous intraepithelial lesion (LSIL) (HCII-dOR = 9.04 [CI: 4.12-19.86] and PCR-dOR = 5.60 [CI: 2.87-10.94]). For HCII, using histology as a gold standard results in higher accuracy than using cytology (dOR = 2.87 [CI: 1.31-6.29]). Based on higher test accuracy, our results support the use of HCII in cervical cancer screening programs. The role of HPV type distribution should be explored to determine the worldwide comparability of HPV test accuracy.

  5. Parameters optimization using experimental design for headspace solid phase micro-extraction analysis of short-chain chlorinated paraffins in waters under the European water framework directive.

    PubMed

    Gandolfi, F; Malleret, L; Sergent, M; Doumenq, P

    2015-08-01

    The water framework directives (WFD 2000/60/EC and 2013/39/EU) force European countries to monitor the quality of their aquatic environment. Among the priority hazardous substances targeted by the WFD, short chain chlorinated paraffins C10-C13 (SCCPs), still represent an analytical challenge, because few laboratories are nowadays able to analyze them. Moreover, an annual average quality standards as low as 0.4μgL(-1) was set for SCCPs in surface water. Therefore, to test for compliance, the implementation of sensitive and reliable analysis method of SCCPs in water are required. The aim of this work was to address this issue by evaluating automated solid phase micro-extraction (SPME) combined on line with gas chromatography-electron capture negative ionization mass spectrometry (GC/ECNI-MS). Fiber polymer, extraction mode, ionic strength, extraction temperature and time were the most significant thermodynamic and kinetic parameters studied. To determine the suitable factors working ranges, the study of the extraction conditions was first carried out by using a classical one factor-at-a-time approach. Then a mixed level factorial 3×2(3) design was performed, in order to give rise to the most influent parameters and to estimate potential interactions effects between them. The most influent factors, i.e. extraction temperature and duration, were optimized by using a second experimental design, in order to maximize the chromatographic response. At the close of the study, a method involving headspace SPME (HS-SPME) coupled to GC/ECNI-MS is proposed. The optimum extraction conditions were sample temperature 90°C, extraction time 80min, with the PDMS 100μm fiber and desorption at 250°C during 2min. Linear response from 0.2ngmL(-1) to 10ngmL(-1) with r(2)=0.99 and limits of detection and quantification, respectively of 4pgmL(-1) and 120pgmL(-1) in MilliQ water, were achieved. The method proved to be applicable in different types of waters and show key advantages, such

  6. Parameters optimization using experimental design for headspace solid phase micro-extraction analysis of short-chain chlorinated paraffins in waters under the European water framework directive.

    PubMed

    Gandolfi, F; Malleret, L; Sergent, M; Doumenq, P

    2015-08-01

    The water framework directives (WFD 2000/60/EC and 2013/39/EU) force European countries to monitor the quality of their aquatic environment. Among the priority hazardous substances targeted by the WFD, short chain chlorinated paraffins C10-C13 (SCCPs), still represent an analytical challenge, because few laboratories are nowadays able to analyze them. Moreover, an annual average quality standards as low as 0.4μgL(-1) was set for SCCPs in surface water. Therefore, to test for compliance, the implementation of sensitive and reliable analysis method of SCCPs in water are required. The aim of this work was to address this issue by evaluating automated solid phase micro-extraction (SPME) combined on line with gas chromatography-electron capture negative ionization mass spectrometry (GC/ECNI-MS). Fiber polymer, extraction mode, ionic strength, extraction temperature and time were the most significant thermodynamic and kinetic parameters studied. To determine the suitable factors working ranges, the study of the extraction conditions was first carried out by using a classical one factor-at-a-time approach. Then a mixed level factorial 3×2(3) design was performed, in order to give rise to the most influent parameters and to estimate potential interactions effects between them. The most influent factors, i.e. extraction temperature and duration, were optimized by using a second experimental design, in order to maximize the chromatographic response. At the close of the study, a method involving headspace SPME (HS-SPME) coupled to GC/ECNI-MS is proposed. The optimum extraction conditions were sample temperature 90°C, extraction time 80min, with the PDMS 100μm fiber and desorption at 250°C during 2min. Linear response from 0.2ngmL(-1) to 10ngmL(-1) with r(2)=0.99 and limits of detection and quantification, respectively of 4pgmL(-1) and 120pgmL(-1) in MilliQ water, were achieved. The method proved to be applicable in different types of waters and show key advantages, such

  7. Spectroscopy of element 115 decay chains

    SciTech Connect

    Rudolph, Dirk; Forsberg, U.; Golubev, P.; Sarmiento, L. G.; Yakushev, A.; Andersson, L.-L.; Di Nitto, A.; Duehllmann, Ch. E.; Gates, J. M.; Gregorich, K. E.; Gross, Carl J; Hessberger, F. P.; Herzberg, R.-D; Khuyagbaatar, J.; Kratz, J. V.; Rykaczewski, Krzysztof Piotr; Schaedel, M.; Aberg, S.; Ackermann, D.; Block, M.; Brand, H.; Carlsson, B. G.; Cox, D.; Derkx, X.; Eberhardt, K.; Even, J.; Fahlander, C.; Gerl, J.; Jaeger, E.; Kindler, B.; Krier, J.; Kojouharov, I.; Kurz, N.; Lommel, B.; Mistry, A.; Mokry, C.; Nitsche, H.; Omtvedt, J. P.; Papadakis, P.; Ragnarsson, I.; Runke, J.; Schaffner, H.; Schausten, B.; Thoerle-Pospiech, P.; Torres, T.; Traut, T.; Trautmann, N.; Tuerler, A.; Ward, A.; Ward, D. E.; Wiehl, N.

    2013-01-01

    A high-resolution a, X-ray and -ray coincidence spectroscopy experiment was conducted at the GSI Helmholtzzentrum fu r Schwerionenforschung. Thirty correlated a-decay chains were detected following the fusion-evaporation reaction 48Ca + 243Am. The observations are consistent with previous assignments of similar decay chains to originate from element Z = 115. The data includes first candidates of fingerprinting the decay step Mt --> Bh with characteristic X rays. For the first time, precise spectroscopy allows the derivation of excitation schemes of isotopes along the decay chains starting with elements Z > 112. Comprehensive Monte-Carlo simulations accompany the data analysis. Nuclear structure models provide a first level interpretation.

  8. Spectroscopy of element 115 decay chains.

    PubMed

    Rudolph, D; Forsberg, U; Golubev, P; Sarmiento, L G; Yakushev, A; Andersson, L-L; Di Nitto, A; Düllmann, Ch E; Gates, J M; Gregorich, K E; Gross, C J; Heßberger, F P; Herzberg, R-D; Khuyagbaatar, J; Kratz, J V; Rykaczewski, K; Schädel, M; Åberg, S; Ackermann, D; Block, M; Brand, H; Carlsson, B G; Cox, D; Derkx, X; Eberhardt, K; Even, J; Fahlander, C; Gerl, J; Jäger, E; Kindler, B; Krier, J; Kojouharov, I; Kurz, N; Lommel, B; Mistry, A; Mokry, C; Nitsche, H; Omtvedt, J P; Papadakis, P; Ragnarsson, I; Runke, J; Schaffner, H; Schausten, B; Thörle-Pospiech, P; Torres, T; Traut, T; Trautmann, N; Türler, A; Ward, A; Ward, D E; Wiehl, N

    2013-09-13

    A high-resolution α, x-ray, and γ-ray coincidence spectroscopy experiment was conducted at the GSI Helmholtzzentrum für Schwerionenforschung. Thirty correlated α-decay chains were detected following the fusion-evaporation reaction 48Ca + 243Am. The observations are consistent with previous assignments of similar decay chains to originate from element Z=115. For the first time, precise spectroscopy allows the derivation of excitation schemes of isotopes along the decay chains starting with elements Z>112. Comprehensive Monte Carlo simulations accompany the data analysis. Nuclear structure models provide a first level interpretation.

  9. Spectroscopy of element 115 decay chains.

    PubMed

    Rudolph, D; Forsberg, U; Golubev, P; Sarmiento, L G; Yakushev, A; Andersson, L-L; Di Nitto, A; Düllmann, Ch E; Gates, J M; Gregorich, K E; Gross, C J; Heßberger, F P; Herzberg, R-D; Khuyagbaatar, J; Kratz, J V; Rykaczewski, K; Schädel, M; Åberg, S; Ackermann, D; Block, M; Brand, H; Carlsson, B G; Cox, D; Derkx, X; Eberhardt, K; Even, J; Fahlander, C; Gerl, J; Jäger, E; Kindler, B; Krier, J; Kojouharov, I; Kurz, N; Lommel, B; Mistry, A; Mokry, C; Nitsche, H; Omtvedt, J P; Papadakis, P; Ragnarsson, I; Runke, J; Schaffner, H; Schausten, B; Thörle-Pospiech, P; Torres, T; Traut, T; Trautmann, N; Türler, A; Ward, A; Ward, D E; Wiehl, N

    2013-09-13

    A high-resolution α, x-ray, and γ-ray coincidence spectroscopy experiment was conducted at the GSI Helmholtzzentrum für Schwerionenforschung. Thirty correlated α-decay chains were detected following the fusion-evaporation reaction 48Ca + 243Am. The observations are consistent with previous assignments of similar decay chains to originate from element Z=115. For the first time, precise spectroscopy allows the derivation of excitation schemes of isotopes along the decay chains starting with elements Z>112. Comprehensive Monte Carlo simulations accompany the data analysis. Nuclear structure models provide a first level interpretation. PMID:24074079

  10. Comparison of Enterococcus quantitative polymerase chain reaction analysis results from midwest U.S. river samples using EPA Method 1611 and Method 1609 PCR reagents

    EPA Science Inventory

    The U.S. Environmental Protection Agency (EPA) has provided recommended beach advisory values in its 2012 recreational water quality criteria (RWQC) for states wishing to use quantitative polymerase chain reaction (qPCR) for the monitoring of Enterococcus fecal indicator bacteria...

  11. Structural and Biochemical Analysis of a Single Amino-Acid Mutant of WzzBSF That Alters Lipopolysaccharide O-Antigen Chain Length in Shigella flexneri

    PubMed Central

    Casey, Lachlan W.; Lonhienne, Thierry; Benning, Friederike; Morona, Renato; Kobe, Bostjan

    2015-01-01

    Lipopolysaccharide (LPS), a surface polymer of Gram-negative bacteria, helps bacteria survive in different environments and acts as a virulence determinant of host infection. The O-antigen (Oag) component of LPS exhibits a modal chain-length distribution that is controlled by polysaccharide co-polymerases (PCPs). The molecular basis of the regulation of Oag chain-lengths remains unclear, despite extensive mutagenesis and structural studies of PCPs from Escherichia coli and Shigella. Here, we identified a single mutation (A107P) of the Shigella flexneri WzzBSF, by a random mutagenesis approach, that causes a shortened Oag chain-length distribution in bacteria. We determined the crystal structures of the periplasmic domains of wild-type WzzBSF and the A107P mutant. Both structures form a highly similar open trimeric assembly in the crystals, and show a similar tendency to self-associate in solution. Binding studies by bio-layer interferometry reveal cooperative binding of very short (VS)-core-plus-O-antigen polysaccharide (COPS) to the periplasmic domains of both proteins, but with decreased affinity for the A107P mutant. Our studies reveal that subtle and localized structural differences in PCPs can have dramatic effects on LPS chain-length distribution in bacteria, for example by altering the affinity for the substrate, which supports the role of the structure of the growing Oag polymer in this process. PMID:26378781

  12. Atomic Chain Electronics

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige; Saini, Subhash (Technical Monitor)

    1998-01-01

    Adatom chains, precise structures artificially created on an atomically regulated surface, are the smallest possible candidates for future nanoelectronics. Since all the devices are created by combining adatom chains precisely prepared with atomic precision, device characteristics are predictable, and free from deviations due to accidental structural defects. In this atomic dimension, however, an analogy to the current semiconductor devices may not work. For example, Si structures are not always semiconducting. Adatom states do not always localize at the substrate surface when adatoms form chemical bonds to the substrate atoms. Transport properties are often determined for the entire system of the chain and electrodes, and not for chains only. These fundamental issues are discussed, which will be useful for future device considerations.

  13. New mooring chain designs

    SciTech Connect

    Canada, L.; Vicinay, J.; Sanz, A.; Lopez, E.

    1996-12-31

    The present work introduces the readers to the developments the high technology offshore chain industry has carried out in recent years, in an effort to offer products that meet the needs of petroleum exploration and production. In this manner the industry can continue to regard chain as a fundamental element in its moorings system, whether for projects with a 25 year life, or projects at depths of over 1,000 meters, or in such severe environments as those faced in the Sub-Arctic. Data are presented on Studless Chain and VGW or Variable Geometry and Weight chain. These will allow engineers designers to forget the needs for chains to be circumscribed to rigid guidelines of geometry or dimensions. Instead they can design mooring systems specific for the particular situations they face. No longer shall chain have to meet geometric standardization derived from the middle of the 19th century while meeting the requirements of the 2nd half of the 20th century.

  14. Rapid genotyping of human rotavirus using SYBR green real-time reverse transcription-polymerase chain reaction with melting curve analysis

    PubMed Central

    Tong, Yupin; Lee, Bonita E; Pang, Xiaoli L

    2015-01-01

    AIM: To develop a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay to genotype rotavirus (G and P) in Alberta from January 2012 to June 2013. METHODS: We developed and validated a different approach to perform rotavirus G and P genotyping using a two-step SYBR green RT-PCR (rt-gPCR) by selecting genotype-specific primers of published conventional RT nested PCR (cnRT-PCR) assay and optimizing the amplification conditions. cDNA was first synthesized from total RNA with SuperScript™ II reverse transcriptase kit followed by amplication step using monoplex SYBR green real-time PCR. After the PCR reaction, melting curve analysis was used to determine specific genotype. Sixteen samples previously genotyped using cnRT-PCR were tested using the new assay and the genotyping results were compared as sensitivity analysis. Assay specificity was evaluated by testing other gastroenteritis viruses with the new assay. The amplicon size of each available genotype was determined by gel-electrophoresis and DNA sequences were obtained using Sanger-sequencing method. After validation and optimization, the new assay was used to genotype 122 pediatric clinical stool samples previously tested positive for rotavirus using electron microscopy between January 2012 and June 2013. RESULTS: The new rt-gPCR assay was validated and optimized. The assay detected G1 to G4, G9, G12 and P[4] and P[8] that were available as positive controls in our laboratory. A single and clear peak of melting curve was generated for each of specific G and P genotypes with a Tm ranging from 80 °C to 82 °C. The sensitivity of rt-gPCR was comparable to cnRT-PCR with 100% correlation of the 16 samples with known G and P genotypes. No cross reaction was found with other gastroenteritis viruses. Using the new rt-gPCR assay, genotypes were obtained for 121 of the 122 pediatric clinical samples tested positive for rotavirus: G1P[8] (42.6%), G2P[4] (4.9%), G3P[8] (10.7%), G9P[8] (10.7%), G9P[4

  15. Neurofilament light chain

    PubMed Central

    Lu, Ching-Hua; Macdonald-Wallis, Corrie; Gray, Elizabeth; Pearce, Neil; Petzold, Axel; Norgren, Niklas; Giovannoni, Gavin; Fratta, Pietro; Sidle, Katie; Fish, Mark; Orrell, Richard; Howard, Robin; Talbot, Kevin; Greensmith, Linda; Kuhle, Jens

    2015-01-01

    Objective: To test blood and CSF neurofilament light chain (NfL) levels in relation to disease progression and survival in amyotrophic lateral sclerosis (ALS). Methods: Using an electrochemiluminescence immunoassay, NfL levels were measured in samples from 2 cohorts of patients with sporadic ALS and healthy controls, recruited in London (ALS/control, plasma: n = 103/42) and Oxford (ALS/control, serum: n = 64/36; paired CSF: n = 38/20). NfL levels in patients were measured at regular intervals for up to 3 years. Change in ALS Functional Rating Scale–Revised score was used to assess disease progression. Survival was evaluated using Cox regression and Kaplan–Meier analysis. Results: CSF, serum, and plasma NfL discriminated patients with ALS from healthy controls with high sensitivity (97%, 89%, 90%, respectively) and specificity (95%, 75%, 71%, respectively). CSF NfL was highly correlated with serum levels (r = 0.78, p < 0.0001). Blood NfL levels were approximately 4 times as high in patients with ALS compared with controls in both cohorts, and maintained a relatively constant expression during follow-up. Blood NfL levels at recruitment were strong, independent predictors of survival. The highest tertile of blood NfL at baseline had a mortality hazard ratio of 3.91 (95% confidence interval 1.98–7.94, p < 0.001). Conclusion: Blood-derived NfL level is an easily accessible biomarker with prognostic value in ALS. The individually relatively stable levels longitudinally offer potential for NfL as a pharmacodynamic biomarker in future therapeutic trials. Classification of evidence: This report provides Class III evidence that the NfL electrochemiluminescence immunoassay accurately distinguishes patients with sporadic ALS from healthy controls. PMID:25934855

  16. Impacts to the ethylene supply chain from a hurricane disruption.

    SciTech Connect

    Sun, Amy Cha-Tien; Downes, Paula Sue; Heinen, Russell; Welk, Margaret Ellen

    2010-03-01

    Analysis of chemical supply chains is an inherently complex task, given the dependence of these supply chains on multiple infrastructure systems (e.g., the petroleum sector, transportation, etc.). This effort requires data and information at various levels of resolution, ranging from network-level distribution systems to individual chemical reactions. Sandia National Laboratories (Sandia) has integrated its existing simulation and infrastructure analysis capabilities with chemical data models to analyze the chemical supply chains of several nationally critical chemical commodities. This paper describes how Sandia models the ethylene supply chain; that is, the supply chain for the most widely used raw material for plastics production including a description of the types of data and modeling capabilities that are required to represent the ethylene supply chain. The paper concludes with a description of Sandia's use the model to project how the supply chain would be affected by and adapt to a disruptive scenario hurricane.

  17. Phasic Triplet Markov Chains.

    PubMed

    El Yazid Boudaren, Mohamed; Monfrini, Emmanuel; Pieczynski, Wojciech; Aïssani, Amar

    2014-11-01

    Hidden Markov chains have been shown to be inadequate for data modeling under some complex conditions. In this work, we address the problem of statistical modeling of phenomena involving two heterogeneous system states. Such phenomena may arise in biology or communications, among other fields. Namely, we consider that a sequence of meaningful words is to be searched within a whole observation that also contains arbitrary one-by-one symbols. Moreover, a word may be interrupted at some site to be carried on later. Applying plain hidden Markov chains to such data, while ignoring their specificity, yields unsatisfactory results. The Phasic triplet Markov chain, proposed in this paper, overcomes this difficulty by means of an auxiliary underlying process in accordance with the triplet Markov chains theory. Related Bayesian restoration techniques and parameters estimation procedures according to the new model are then described. Finally, to assess the performance of the proposed model against the conventional hidden Markov chain model, experiments are conducted on synthetic and real data. PMID:26353069

  18. Prevalence and mutation analysis of short/branched chain acyl-CoA dehydrogenase deficiency (SBCADD) detected on newborn screening in Wisconsin.

    PubMed

    Van Calcar, Sandra C; Baker, Mei W; Williams, Phillip; Jones, Susan A; Xiong, Blia; Thao, Mai Choua; Lee, Sheng; Yang, Mai Khou; Rice, Greg M; Rhead, William; Vockley, Jerry; Hoffman, Gary; Durkin, Maureen S

    2013-01-01

    Short/branched chain acyl-CoA dehydrogenase deficiency (SBCADD), also called 2-methylbutyryl CoA dehydrogenase deficiency (2-MBCDD), is a disorder of l-isoleucine metabolism of uncertain clinical significance. SBCADD is inadvertently detected on expanded newborn screening by elevated 2-methylbutyrylcarnitine (C5), which has the same mass to charge (m/s) on tandem mass spectrometry (MS/MS) as isovalerylcarnitine (C5), an analyte that is elevated in isovaleric acidemia (IVA), a disorder in leucine metabolism. SBCADD cases identified in the Hmong-American population have been found in association with the c.1165 A>G mutation in the ACADSB gene. The purposes of this study were to: (a) estimate the prevalence of SBCADD and carrier frequency of the c.1165 A>G mutation in the Hmong ethnic group; (b) determine whether the c.1165 A>G mutation is common to all Hmong newborns screening positive for SBCADD; and (c) evaluate C5 acylcarnitine cut-off values to detect and distinguish between SBCADD and IVA diagnoses. During the first 10years of expanded newborn screening using MS/MS in Wisconsin (2001-2011), 97 infants had elevated C5 values (≥0.44μmol/L), of whom five were Caucasian infants confirmed to have IVA. Of the remaining 92 confirmed SBCADD cases, 90 were of Hmong descent. Mutation analysis was completed on an anonymous, random sample of newborn screening cards (n=1139) from Hmong infants. Fifteen infants, including nine who had screened positive for SBCADD based on a C5 acylcarnitine concentration ≥0.44μmol/L, were homozygous for the c.1165 A>G mutation. This corresponds to a prevalence in this ethnic group of being homozygous for the mutation of 1.3% (95% confidence interval 0.8-2.2%) and of being heterozygous for the mutation of 21.8% (95% confidence interval 19.4-24.3%), which is consistent with the Hardy-Weinberg equilibrium. Detection of homozygous individuals who were not identified on newborn screening suggests that the C5 screening cut-off would need to

  19. Prevalence and mutation analysis of short/branched chain acyl-CoA dehydrogenase deficiency (SBCADD) detected on newborn screening in Wisconsin

    PubMed Central

    Van Calcar, Sandra C.; Baker, Mei W.; Williams, Phillip; Jones, Susan A.; Xiong, Blia; Thao, Mai Choua; Lee, Sheng; Yang, Mai Khou; Rice, Greg M.; Rhead, William; Vockley, Jerry; Hoffman, Gary; Durkin, Maureen S.

    2015-01-01

    Short/branched chain acyl-CoA dehydrogenase deficiency (SBCADD), also called 2-methylbutyryl CoA dehydrogenase deficiency (2-MBCDD), is a disorder of L-isoleucine metabolism of uncertain clinical significance. SBCADD is inadvertently detected on expanded newborn screening by elevated 2-methylbutyrylcarnitine (C5), which has the same mass to charge (m/s) on tandem mass spectrometry (MS/MS) as isovalerylcarnitine (C5), an analyte that is elevated in isovaleric acidemia (IVA), a disorder in leucine metabolism. SBCADD cases identified in the Hmong-American population have been found in association with the c.1165 A>G mutation in the ACADSB gene. The purposes of this study were to: (a) estimate the prevalence of SBCADD and carrier frequency of the c.1165 A>G mutation in the Hmong ethnic group; (b) determine whether the c.1 165 A>G mutation is common to all Hmong newborns screening positive for SBCADD; and (c) evaluate C5 acylcarnitine cut-off values to detect and distinguish between SBCADD and IVA diagnoses. During the first 10 years of expanded newborn screening using MS/MS in Wisconsin (2001–2011), 97 infants had elevated C5 values (≥0.44 μmol/L), of whom five were Caucasian infants confirmed to have IVA Of the remaining 92 confirmed SBCADD cases, 90 were of Hmong descent. Mutation analysis was completed on an anonymous, random sample of newborn screening cards (n = 1139) from Hmong infants. Fifteen infants, including nine who had screened positive for SBCADD based on a C5 acylcarnitine concentrations ≥0.44 μmol/L, were homozygous for the c.1165 A>G mutation. This corresponds to a prevalence in this ethnic group of being homozygous for the mutation of 1.3% (95% confidence interval 0.8–2.2%) and of being heterozygous for the mutation of 21.8% (95% confidence interval 19.4–24.3%), which is consistent with the Hardy-Weinberg equilibrium. Detection of homozygous individuals who were not identified on newborn screening suggests that the C5 screening cut

  20. Spatial Data Supply Chains

    NASA Astrophysics Data System (ADS)

    Varadharajulu, P.; Azeem Saqiq, M.; Yu, F.; McMeekin, D. A.; West, G.; Arnold, L.; Moncrieff, S.

    2015-06-01

    This paper describes current research into the supply of spatial data to the end user in as close to real time as possible via the World Wide Web. The Spatial Data Infrastructure paradigm has been discussed since the early 1990s. The concept has evolved significantly since then but has almost always examined data from the perspective of the supplier. It has been a supplier driven focus rather than a user driven focus. The current research being conducted is making a paradigm shift and looking at the supply of spatial data as a supply chain, similar to a manufacturing supply chain in which users play a significant part. A comprehensive consultation process took place within Australia and New Zealand incorporating a large number of stakeholders. Three research projects that have arisen from this consultation process are examining Spatial Data Supply Chains within Australia and New Zealand and are discussed within this paper.

  1. Chain inflation revisited

    SciTech Connect

    Chialva, Diego; Danielsson, Ulf H E-mail: ulf.danielsson@fysast.uu.se

    2008-10-15

    This paper represents an in-depth treatment of the chain inflation scenario. We fully determine the evolution of the universe in the model, the conditions necessary in order to have a successful inflationary period, and the matching with the observational results regarding the cosmological perturbations. We study in great detail, and in general, the dynamics of the background, as well as the mechanism of generation of the perturbations. We also find an explicit formula for the spectrum of adiabatic perturbations. Our results prove that chain inflation is a viable model for solving the horizon, entropy and flatness problems of standard cosmology and for generating the right amount of adiabatic cosmological perturbations. The results are radically different from those found in previous works on the subject. Finally, we argue that there is a natural way to embed chain inflation into flux compactified string theory. We discuss the details of the implementation and how to fit observations.

  2. Supply-Chain Optimization Template

    NASA Technical Reports Server (NTRS)

    Quiett, William F.; Sealing, Scott L.

    2009-01-01

    The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

  3. Systemic lupus erythematosus: molecular cloning and analysis of 22 individual recombinant monoclonal kappa light chains specifically hydrolyzing human myelin basic protein.

    PubMed

    Timofeeva, Anna M; Buneva, Valentina N; Nevinsky, Georgy A

    2015-10-01

    Antibodies hydrolyzing myelin basic protein (MBP) can play an important role in the pathogenesis of multiple sclerosis (MS) and systemic lupus erythematosus (SLE). An immunoglobulin light chain phagemid library derived from peripheral blood lymphocytes of patients with SLE was used. Small pools of phage particles displaying light chains with different affinities for MBP were isolated by affinity chromatography on MBP-Sepharose, and the fraction eluted with 0.5 M NaCl was used for preparation of individual monoclonal light chains (MLChs, 26-27 kDa). Seventy-two of 440 individual colonies were randomly chosen, expressed in Escherichia coli in a soluble form, and MLChs were purified by metal chelating chromatography. Twenty-two of 72 MLChs have high affinity and efficiently hydrolyze only MBP (not other control proteins) demonstrating various pH optima in a 5.7-9.0 range and different substrate specificity in the hydrolysis of four different MBP oligopeptides. Four MLChs demonstrated serine protease-like and three thiol protease-like activities, while 11 MLChs were metalloproteases. The activity of three MLChs was inhibited by both phenylmethylsulfonyl fluoride (PMSF) and Ethylenediaminetetraacetic acid (EDTA), two other by EDTA and iodoacetamide, and one by PMSF, EDTA, and iodoacetamide. The ratio of relative activity in the presence of Ca(2+), Mg(2+), Mn(2+), Ni(2+), Zn(2+), Cu(2+), and Co(2+) was individual for each of 22 MLCh preparations. It is the first examples of human MLChs, which probably can possess two or even three different proteolytic activities. These observations suggest an extreme diversity of anti-MBP abzymes in SLE patients. The immune systems of individual SLE patients can generate a variety of anti-MBP abzymes, which can attack MBP of myelin-proteolipid sheath of axons and play an important role in MS and SLE pathogenesis.

  4. Supply chain optimization for pediatric perioperative departments.

    PubMed

    Davis, Janice L; Doyle, Robert

    2011-09-01

    Economic challenges compel pediatric perioperative departments to reduce nonlabor supply costs while maintaining the quality of patient care. Optimization of the supply chain introduces a framework for decision making that drives fiscally responsible decisions. The cost-effective supply chain is driven by implementing a value analysis process for product selection, being mindful of product sourcing decisions to reduce supply expense, creating logistical efficiency that will eliminate redundant processes, and managing inventory to ensure product availability. The value analysis approach is an analytical methodology for product selection that involves product evaluation and recommendation based on consideration of clinical benefit, overall financial impact, and revenue implications. PMID:21884843

  5. Supply chain optimization for pediatric perioperative departments.

    PubMed

    Davis, Janice L; Doyle, Robert

    2011-09-01

    Economic challenges compel pediatric perioperative departments to reduce nonlabor supply costs while maintaining the quality of patient care. Optimization of the supply chain introduces a framework for decision making that drives fiscally responsible decisions. The cost-effective supply chain is driven by implementing a value analysis process for product selection, being mindful of product sourcing decisions to reduce supply expense, creating logistical efficiency that will eliminate redundant processes, and managing inventory to ensure product availability. The value analysis approach is an analytical methodology for product selection that involves product evaluation and recommendation based on consideration of clinical benefit, overall financial impact, and revenue implications.

  6. Gamma-spectrometric analysis of high salinity fluids: how to analyze radionuclides of the thorium decay chain far from radioactive equilibrium?

    PubMed

    Degering, Detlev; Köhler, Matthias

    2011-11-01

    Highly saline brines from a geothermal plant in Neustadt-Glewe, Germany, were investigated with respect to their radionuclide concentrations. The natural decay series in these fluids are far from radioactive equilibrium with main activity contributions from the radium isotopes (226)Ra, (228)Ra and (224)Ra. A general mathematical formulation for the coupled radionuclide activities within one decay chain is applied on the system (228)Ra…(212)Pb and tested on real samples in order to evaluate several radionuclide concentrations at the moment of sampling.

  7. Secondary analysis of merged American Hospital Association data and U.S. Census data: beginning to understand the supply-demand chain in pediatric inpatient care.

    PubMed

    Lacey, Susan R; Kilgore, Meredith; Yun, Huifeng; Hughes, Ronda; Allison, Jeroan; Cox, Karen S

    2008-06-01

    Much attention has been focused on how the nursing shortage will impact the growing number of aging Americans. This study was conducted as a first step in understanding nursing supply relative to potential pediatric demand using merged data from the American Hospital Association's annual survey and Census data by state from the year 2000. Findings indicate that there is tremendous variability among reporting states related to estimated pediatric nurses (registered nurse full-time equivalents), potential pediatric demand (persons from birth to 18 years), and allocated pediatric beds. Future research will examine how this supply-demand chain impacts clinical and cost outcomes for pediatric patients.

  8. Supply chain quality.

    PubMed

    Feary, Simon

    2009-01-01

    As the development of complex manufacturing models and virtual companies become more prevalent in today's growing global markets, it is increasingly important to support the relationships between manufacturer and supplier. Utilising these relationships will ensure that supply chains operate more effectively and reduce costs, risks and time-to-market time frames, whilst maintaining product quality. PMID:20058652

  9. Supply chain management.

    PubMed

    Palevich, R F

    1999-02-01

    This article describes how Do It Best Corp. has used technology to improve its supply chain management. Among other topics it discusses the company's use of electronic data interchange, the Internet, electronic forecasting, and warehouse management systems to gain substantial savings and increase its competitiveness. PMID:10345634

  10. Breaking the Chains

    ERIC Educational Resources Information Center

    Stanistreet, Paul

    2007-01-01

    In 1792 more than 350,000 people in Britain signed a petition calling for an end to the slave trade. It was, writes historian Adam Hochschild in his book "Bury the Chains," "the first time in history that a large number of people became outraged, and stayed outraged for many years, over someone else's rights". In 1807--after 15 years of…

  11. Polymerase chain reaction system

    DOEpatents

    Benett, William J.; Richards, James B.; Stratton, Paul L.; Hadley, Dean R.; Milanovich, Fred P.; Belgrader, Phil; Meyer, Peter L.

    2004-03-02

    A portable polymerase chain reaction DNA amplification and detection system includes one or more chamber modules. Each module supports a duplex assay of a biological sample. Each module has two parallel interrogation ports with a linear optical system. The system is capable of being handheld.

  12. INTERACTING QUANTUM SPIN CHAINS

    SciTech Connect

    ZHELUDEV,A.

    2001-09-09

    A brief review of recent advances in neutron scattering studies of low-dimensional quantum magnets is followed by a particular example. The separation of single-particle and continuum states in the weakly-coupled S = l/2 chains system BaCu{sub 2}Si{sub 2}O{sub 7} is described in some detail.

  13. Heavy Chain Diseases

    MedlinePlus

    ... cells often prevents proper absorption of nutrients from food (malabsorption), resulting in severe diarrhea and weight loss. A rare form that affects the respiratory tract also exists. Blood tests are done when alpha heavy chain disease is suspected. Serum protein electrophoresis, measurement of ...

  14. Nodal-chain metals

    NASA Astrophysics Data System (ADS)

    Bzdušek, Tomáš; Wu, Quansheng; Rüegg, Andreas; Sigrist, Manfred; Soluyanov, Alexey A.

    2016-10-01

    The band theory of solids is arguably the most successful theory of condensed-matter physics, providing a description of the electronic energy levels in various materials. Electronic wavefunctions obtained from the band theory enable a topological characterization of metals for which the electronic spectrum may host robust, topologically protected, fermionic quasiparticles. Many of these quasiparticles are analogues of the elementary particles of the Standard Model, but others do not have a counterpart in relativistic high-energy theories. A complete list of possible quasiparticles in solids is lacking, even in the non-interacting case. Here we describe the possible existence of a hitherto unrecognized type of fermionic excitation in metals. This excitation forms a nodal chain—a chain of connected loops in momentum space—along which conduction and valence bands touch. We prove that the nodal chain is topologically distinct from previously reported excitations. We discuss the symmetry requirements for the appearance of this excitation and predict that it is realized in an existing material, iridium tetrafluoride (IrF4), as well as in other compounds of this class of materials. Using IrF4 as an example, we provide a discussion of the topological surface states associated with the nodal chain. We argue that the presence of the nodal-chain fermions will result in anomalous magnetotransport properties, distinct from those of materials exhibiting previously known excitations.

  15. Atwood's Heavy Chain

    ERIC Educational Resources Information Center

    Beeken, Paul

    2011-01-01

    While perusing various websites in search of a more challenging lab for my students, I came across a number of ideas where replacing the string in an Atwood's machine with a simple ball chain like the kind found in lamp pulls created an interesting system to investigate. The replacement of the string produced a nice nonuniform acceleration, but…

  16. Effect of chain architecture on the size, shape, and intrinsic viscosity of chains in polymer solutions: A molecular simulation study

    NASA Astrophysics Data System (ADS)

    Khabaz, Fardin; Khare, Rajesh

    2014-12-01

    Effect of chain architecture on the chain size, shape, and intrinsic viscosity was investigated by performing molecular dynamics simulations of polymer solutions in a good solvent. Four types of chains - linear, comb shaped, H-shaped, and star - were studied for this purpose using a model in which the solvent particles were considered explicitly. Results indicated that the chain length (N) dependence of the mean squared radius of gyration of the chains followed a power-law behavior < {R_g^2 } rangle ^{1/2} ˜ N^\\upsilon with scaling exponents of υ = 0.605, 0.642, 0.602, and 0.608, for the linear, comb shaped, H-shaped, and star shaped chains, respectively. The simulation results for the geometrical shrinking factor were higher than the prior theoretical predictions for comb shaped chains. Analysis of chain shape demonstrated that the star chains were significantly smaller and more spherical than the others, while the comb and H-shaped polymer chains showed a more cylindrical shape. It is shown that the intrinsic viscosity of the chains can be calculated by plotting the specific viscosity determined from simulations against the solution concentration. The intrinsic viscosity exhibited linear behavior with the reciprocal of the overlap concentration for all chain architectures studied. The molecular weight dependence of the intrinsic viscosity followed the Mark-Houwink relation, [η] = KMa, for all chain architectures. When comparing the calculated values of exponent a with the literature experimental values, agreement was found only for the H and star chains, and a disagreement for the linear and comb chains. The viscosity shrinking factor of the branched chains was compared with the available experimental data and the theoretical predictions and a general agreement was found.

  17. Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica

    SciTech Connect

    Harmer, Nicholas J.; King, Jerry D.; Palmer, Colin M.; Preston, Andrew; Maskell, Duncan J.; Blundell, Tom L.

    2007-08-01

    The expression, purification, and crystallisation of the short-chain dehydrogenases WbmF, WbmG and WbmH from B. bronchiseptica are described. Native diffraction data to 1.5, 2.0, and 2.2 Å were obtained for the three proteins, together with complexes with nucleotides. The short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica were cloned into Escherichia coli expression vectors, overexpressed and purified to homogeneity. Crystals of all three wild-type enzymes were obtained using vapour-diffusion crystallization with high-molecular-weight PEGs as a primary precipitant at alkaline pH. Some of the crystallization conditions permitted the soaking of crystals with cofactors and nucleotides or nucleotide sugars, which are possible substrate compounds, and further conditions provided co-complexes of two of the proteins with these compounds. The crystals diffracted to resolutions of between 1.50 and 2.40 Å at synchrotron X-ray sources. The synchrotron data obtained were sufficient to determine eight structures of the three enzymes in complex with a variety of cofactors and substrate molecules.

  18. Polymerase chain reaction and Southern blot-based analysis of the C9orf72 hexanucleotide repeat in different motor neuron diseases.

    PubMed

    Hübers, Annemarie; Marroquin, Nicolai; Schmoll, Birgit; Vielhaber, Stefan; Just, Marlies; Mayer, Benjamin; Högel, Josef; Dorst, Johannes; Mertens, Thomas; Just, Walter; Aulitzky, Anna; Wais, Verena; Ludolph, Albert C; Kubisch, Christian; Weishaupt, Jochen H; Volk, Alexander E

    2014-05-01

    The GGGGCC-hexanucleotide repeat expansion in C9orf72 is the most common genetic cause of familial amyotrophic lateral sclerosis and frontotemporal dementia. This study determined the frequency of C9orf72 repeat expansions in different motor neuron diseases (amyotrophic lateral sclerosis (ALS), motor neuron diseases affecting primarily the first or the second motor neuron and hereditary spastic paraplegia). Whereas most studies on C9orf72 repeat expansions published so far rely on a polymerase chain reaction-based screening, we applied both polymerase chain reaction-based techniques and Southern blotting. Furthermore, we determined the sensitivity and specificity of Southern blotting of the C9orf72 hexanucleotide repeat in DNA derived from lymphoblastoid cell lines. C9orf72 repeat expansions were found in 27.1% out of 166 familial ALS patients, only once in 68 sporadic ALS patients, and not in 61 hereditary spastic paraplegia patients or 52 patients with motor neuron diseases affecting clinically primarily either the first or the second motor neuron. We found hints for a correlation between C9orf72 repeat length and the age of onset. Somatic instability of the C9orf72 repeat was observed in lymphoblastoid cell lines compared with DNA derived from whole blood from the same patient and therefore caution is warranted for repeat length determination in immortalized cell lines.

  19. Isolated respiratory chain enzyme deficiency in patients with a mitochondrial (encephalo-) myopathy: Sequence analysis of the mitochondrial complex and IV genes

    SciTech Connect

    Vries, D. de; Coo, I. de; Buddiger, P.

    1994-09-01

    The mitochondrial respiratory chain consists of four enzyme complexes. Deficiencies of complex I (NADH dehydrogenase) and complex IV (cytochrome c oxidase) are frequently found in muscle biopsies from patients with a mitochondrial (encephalo-)myopathy. Mutations in the mitochondrial-encoded subunits have been observed in a number of different mitochondrial (encephalo-)myophathies. We screened eight mitochondrial (encephalo-)myopathy patients with an isolated complex I deficiency for mutations in the ND genes by direct sequencing. No abnormality was detected. We also studied 9 mitochondrial (encephalo-)myopathy patients and an isolated complex IV deficiency. In the muscle biopsy of one patient a novel heteroplasmic mutation (T {r_arrow} C) at nucleotide position 6681 was found in the mitochondrial COX I gene. This mutation led to the substitution of a conserved Tyr for His. As this mutation changed the secondary structure of the protein and was not found in the healthy mother, we consider it likely that this mutation is pathological. In the other patients no abnormality was detected. Therefore, mutations in the mitochondrially-encoded subunits are not a frequent cause of isolated respiratory chain enzyme deficiency.

  20. Flexible chains of ferromagnetic nanoparticles.

    PubMed

    Townsend, James; Burtovyy, Ruslan; Galabura, Yuriy; Luzinov, Igor

    2014-07-22

    We report the fabrication of flexible chains of ferromagnetic Ni nanoparticles that possess the ability to adapt other than the typically observed rigid (nearly) straight configurations in the absence of an external magnetic field. The dynamic mobility of the ferromagnetic chains originates from a layer of densely grafted polyethylene glycol macromolecules enveloping each nanoparticle in the chain. While ferromagnetic chains of unmodified Ni nanoparticles behave as stiff nickel nanorods, the chains made of the grafted nanoparticles demonstrate extreme flexibility. Upon changing the direction of the field, and inevitably going through a zero-field point, the shorter chains undergo chain-globule-chain transformation. The longer chains can bend to a high degree, attaining "snake-like" configurations.

  1. Markov Chain Monte Carlo and Irreversibility

    NASA Astrophysics Data System (ADS)

    Ottobre, Michela

    2016-06-01

    Markov Chain Monte Carlo (MCMC) methods are statistical methods designed to sample from a given measure π by constructing a Markov chain that has π as invariant measure and that converges to π. Most MCMC algorithms make use of chains that satisfy the detailed balance condition with respect to π; such chains are therefore reversible. On the other hand, recent work [18, 21, 28, 29] has stressed several advantages of using irreversible processes for sampling. Roughly speaking, irreversible diffusions converge to equilibrium faster (and lead to smaller asymptotic variance as well). In this paper we discuss some of the recent progress in the study of nonreversible MCMC methods. In particular: i) we explain some of the difficulties that arise in the analysis of nonreversible processes and we discuss some analytical methods to approach the study of continuous-time irreversible diffusions; ii) most of the rigorous results on irreversible diffusions are available for continuous-time processes; however, for computational purposes one needs to discretize such dynamics. It is well known that the resulting discretized chain will not, in general, retain all the good properties of the process that it is obtained from. In particular, if we want to preserve the invariance of the target measure, the chain might no longer be reversible. Therefore iii) we conclude by presenting an MCMC algorithm, the SOL-HMC algorithm [23], which results from a nonreversible discretization of a nonreversible dynamics.

  2. Perioperative supply chain management.

    PubMed

    Feistritzer, N R; Keck, B R

    2000-09-01

    Faced with declining revenues and increasing operating expenses, hospitals are evaluating numerous mechanisms designed to reduce costs while simultaneously maintaining quality care. Many facilities have targeted initial cost reduction efforts in the reduction of labor expenses. Once labor expenses have been "right sized," facilities have continued to focus on service delivery improvements by the optimization of the "supply chain" process. This report presents a case study of the efforts of Vanderbilt University Medical Center in the redesign of its supply chain management process in the department of Perioperative Services. Utilizing a multidisciplinary project management structure, 3 work teams were established to complete the redesign process. To date, the project has reduced costs by $2.3 million and enhanced quality patient care by enhancing the delivery of appropriate clinical supplies during the perioperative experience.

  3. Mobility chains analysis of technologies for passenger cars and light duty vehicles fueled with biofuels : application of the Greet model to project the role of biomass in America's energy future (RBAEF) project.

    SciTech Connect

    Wu, M.; Wu, Y.; Wang, M; Energy Systems

    2008-01-31

    The Role of Biomass in America's Energy Future (RBAEF) is a multi-institution, multiple-sponsor research project. The primary focus of the project is to analyze and assess the potential of transportation fuels derived from cellulosic biomass in the years 2015 to 2030. For this project, researchers at Dartmouth College and Princeton University designed and simulated an advanced fermentation process to produce fuel ethanol/protein, a thermochemical process to produce Fischer-Tropsch diesel (FTD) and dimethyl ether (DME), and a combined heat and power plant to co-produce steam and electricity using the ASPEN Plus{trademark} model. With support from the U.S. Department of Energy (DOE), Argonne National Laboratory (ANL) conducted, for the RBAEF project, a mobility chains or well-to-wheels (WTW) analysis using the Greenhouse gases, Regulated Emissions, and Energy use in Transportation (GREET) model developed at ANL. The mobility chains analysis was intended to estimate the energy consumption and emissions associated with the use of different production biofuels in light-duty vehicle technologies.

  4. Rapid identification of Bordetella pertussis pertactin gene variants using LightCycler real-time polymerase chain reaction combined with melting curve analysis and gel electrophoresis.

    PubMed Central

    Mäkinen, J.; Viljanen, M. K.; Mertsola, J.; Arvilommi, H.; He, Q.

    2001-01-01

    Recently, eight allelic variants of the pertactin gene (prn1-8) have been characterized in Bordetella pertussis strains isolated in Europe and the United States. It has been suggested that the divergence of the pertactin types of clinical isolates from those of the B. pertussis vaccine strains is a result of vaccine-driven evolution. Sequencing of the prn, which is relatively time-consuming, has so far been the only method for the differentiation of prn types. We have developed a rapid real-time polymerase chain reaction assay suitable for large-scale screening of the prn type of the circulating strains. This method correctly identified the prn type of all tested 41 clinical isolates and two Finnish vaccine strains. The method is simple and reliable and provides an alternative for sequencing in pertussis research. PMID:11747721

  5. Transcript analysis of CFTR frameshift mutations in lymphocytes using the reverse transcription-polymerase chain reaction technique and the protein truncation test.

    PubMed

    Romey, M C; Tuffery, S; Desgeorges, M; Bienvenu, T; Demaille, J; Claustres, M

    1996-09-01

    mRNA transcripts of the cystic fibrosis transmembrane conductance regulator (CFTR) gene were analyzed from lymphocytes of two cystic fibrosis compound heterozygotes (394delTT/3195del6 and 1215delG/ 2423delG), of five related carriers heterozygous for one of these mutations, and of five normal individuals. After reverse transcription of total RNA and amplification by the polymerase chain reaction, fragments were investigated by sequencing and by the protein truncation test (PTT). The three frameshift mutants were correctly detected by PTT, as they introduced a premature termination codon resulting in shortened protein products. The PTT approach thus provides a simple and reliable alternative method for detecting frameshift, nonsense, or splice site mutations, and for ascertaining their putative effect on the reading frame of the mRNA. In addition, we have identified 6 alternatively spliced forms of CFTR mRNA, two of which (transcripts lacking 4 + 5 or 17B) have not been described previously.

  6. Callisto Crater Chain Mosaic

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This mosaic of three images shows an area within the Valhalla region on Jupiter's moon, Callisto. North is to the top of the mosaic and the Sun illuminates the surface from the left. The smallest details that can be discerned in this picture are knobs and small impact craters about 160 meters (175 yards) across. The mosaic covers an area approximately 45 kilometers (28 miles) across. It shows part of a prominent crater chain located on the northern part of the Valhalla ring structure.

    Crater chains can form from the impact of material ejected from large impacts (forming secondary chains) or by the impact of a fragmented projectile, perhaps similar to the Shoemaker-Levy 9 cometary impacts into Jupiter in July 1994. It is believed this crater chain was formed by the impact of a fragmented projectile. The images which form this mosaic were obtained by the solid state imaging system aboard NASA's Galileo spacecraft on Nov. 4, 1996 (Universal Time).

    Launched in October 1989, Galileo entered orbit around Jupiter on December 7, 1995. The spacecraft's mission is to conduct detailed studies of the giant planet, its largest moons and the Jovian magnetic environment. The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.

    This image and other images and data received from Galileo are posted on the World Wide Web Galileo mission home page at http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at http:// www.jpl.nasa.gov/galileo/sepo.

  7. The innovation value chain.

    PubMed

    Hansen, Morten T; Birkinshaw, Julian

    2007-06-01

    The challenges of coming up with fresh ideas and realizing profits from them are different for every company. One firm may excel at finding good ideas but may have weak systems for bringing them to market. Another organization may have a terrific process for funding and rolling out new products and services but a shortage of concepts to develop. In this article, Hansen and Birkinshaw caution executives against using the latest and greatest innovation approaches and tools without understanding the unique deficiencies in their companies' innovation systems. They offer a framework for evaluating innovation performance: the innovation value chain. It comprises the three main phases of innovation (idea generation, conversion, and diffusion) as well as the critical activities performed during those phases (looking for ideas inside your unit; looking for them in other units; looking for them externally; selecting ideas; funding them; and promoting and spreading ideas companywide). Using this framework, managers get an end-to-end view of their innovation efforts. They can pinpoint their weakest links and tailor innovation best practices appropriately to strengthen those links. Companies typically succumb to one of three broad "weakest-link" scenarios. They are idea poor, conversion poor, or diffusion poor. The article looks at the ways smart companies - including Intuit, P&G, Sara Lee, Shell, and Siemens- modify the best innovation practices and apply them to address those organizations' individual needs and flaws. The authors warn that adopting the chain-based view of innovation requires new measures of what can be delivered by each link in the chain. The approach also entails new roles for employees "external scouts" and "internal evangelists," for example. Indeed, in their search for new hires, companies should seek out those candidates who can help address particular weaknesses in the innovation value chain. PMID:17580654

  8. The innovation value chain.

    PubMed

    Hansen, Morten T; Birkinshaw, Julian

    2007-06-01

    The challenges of coming up with fresh ideas and realizing profits from them are different for every company. One firm may excel at finding good ideas but may have weak systems for bringing them to market. Another organization may have a terrific process for funding and rolling out new products and services but a shortage of concepts to develop. In this article, Hansen and Birkinshaw caution executives against using the latest and greatest innovation approaches and tools without understanding the unique deficiencies in their companies' innovation systems. They offer a framework for evaluating innovation performance: the innovation value chain. It comprises the three main phases of innovation (idea generation, conversion, and diffusion) as well as the critical activities performed during those phases (looking for ideas inside your unit; looking for them in other units; looking for them externally; selecting ideas; funding them; and promoting and spreading ideas companywide). Using this framework, managers get an end-to-end view of their innovation efforts. They can pinpoint their weakest links and tailor innovation best practices appropriately to strengthen those links. Companies typically succumb to one of three broad "weakest-link" scenarios. They are idea poor, conversion poor, or diffusion poor. The article looks at the ways smart companies - including Intuit, P&G, Sara Lee, Shell, and Siemens- modify the best innovation practices and apply them to address those organizations' individual needs and flaws. The authors warn that adopting the chain-based view of innovation requires new measures of what can be delivered by each link in the chain. The approach also entails new roles for employees "external scouts" and "internal evangelists," for example. Indeed, in their search for new hires, companies should seek out those candidates who can help address particular weaknesses in the innovation value chain.

  9. Streamlining the supply chain.

    PubMed

    Neumann, Lydon

    2003-07-01

    Effective management of the supply chain requires attention to: Product management--formulary development and maintenance, compliance, clinical involvement, standardization, and demand-matchi