Applying activity-based costing in long-term care.

PubMed

Wodchis, W P

1998-01-01

As greater numbers of the elderly use health services, and as health care costs climb, effective financial tracking is essential. Cost management in health care can benefit if costs are linked to the care activities where they are incurred. Activity-based costing (ABC) provides a useful approach. The framework aligns costs (inputs), through activities (process), to outputs and outcomes. It allocates costs based on client care needs rather than management structure. The ABC framework was tested in a residential care facility and in supportive housing apartments. The results demonstrate the feasibility and advantages of ABC for long term care agencies, including community-based care.

Parameter Estimation for a Turbulent Buoyant Jet Using Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Christopher, Jason D.; Wimer, Nicholas T.; Hayden, Torrey R. S.; Lapointe, Caelan; Grooms, Ian; Rieker, Gregory B.; Hamlington, Peter E.

2016-11-01

Approximate Bayesian Computation (ABC) is a powerful tool that allows sparse experimental or other "truth" data to be used for the prediction of unknown model parameters in numerical simulations of real-world engineering systems. In this presentation, we introduce the ABC approach and then use ABC to predict unknown inflow conditions in simulations of a two-dimensional (2D) turbulent, high-temperature buoyant jet. For this test case, truth data are obtained from a simulation with known boundary conditions and problem parameters. Using spatially-sparse temperature statistics from the 2D buoyant jet truth simulation, we show that the ABC method provides accurate predictions of the true jet inflow temperature. The success of the ABC approach in the present test suggests that ABC is a useful and versatile tool for engineering fluid dynamics research.

Modified artificial bee colony for the vehicle routing problems with time windows.

PubMed

Alzaqebah, Malek; Abdullah, Salwani; Jawarneh, Sana

2016-01-01

The natural behaviour of the honeybee has attracted the attention of researchers in recent years and several algorithms have been developed that mimic swarm behaviour to solve optimisation problems. This paper introduces an artificial bee colony (ABC) algorithm for the vehicle routing problem with time windows (VRPTW). A Modified ABC algorithm is proposed to improve the solution quality of the original ABC. The high exploration ability of the ABC slows-down its convergence speed, which may due to the mechanism used by scout bees in replacing abandoned (unimproved) solutions with new ones. In the Modified ABC a list of abandoned solutions is used by the scout bees to memorise the abandoned solutions, then the scout bees select a solution from the list based on roulette wheel selection and replace by a new solution with random routs selected from the best solution. The performance of the Modified ABC is evaluated on Solomon benchmark datasets and compared with the original ABC. The computational results demonstrate that the Modified ABC outperforms the original ABC also produce good solutions when compared with the best-known results in the literature. Computational investigations show that the proposed algorithm is a good and promising approach for the VRPTW.

Parameter Estimation for a Pulsating Turbulent Buoyant Jet Using Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Christopher, Jason; Wimer, Nicholas; Lapointe, Caelan; Hayden, Torrey; Grooms, Ian; Rieker, Greg; Hamlington, Peter

2017-11-01

Approximate Bayesian Computation (ABC) is a powerful tool that allows sparse experimental or other ``truth'' data to be used for the prediction of unknown parameters, such as flow properties and boundary conditions, in numerical simulations of real-world engineering systems. Here we introduce the ABC approach and then use ABC to predict unknown inflow conditions in simulations of a two-dimensional (2D) turbulent, high-temperature buoyant jet. For this test case, truth data are obtained from a direct numerical simulation (DNS) with known boundary conditions and problem parameters, while the ABC procedure utilizes lower fidelity large eddy simulations. Using spatially-sparse statistics from the 2D buoyant jet DNS, we show that the ABC method provides accurate predictions of true jet inflow parameters. The success of the ABC approach in the present test suggests that ABC is a useful and versatile tool for predicting flow information, such as boundary conditions, that can be difficult to determine experimentally.

Artificial Boundary Conditions Based on the Difference Potentials Method

NASA Technical Reports Server (NTRS)

Tsynkov, Semyon V.

1996-01-01

While numerically solving a problem initially formulated on an unbounded domain, one typically truncates this domain, which necessitates setting the artificial boundary conditions (ABC's) at the newly formed external boundary. The issue of setting the ABC's appears to be most significant in many areas of scientific computing, for example, in problems originating from acoustics, electrodynamics, solid mechanics, and fluid dynamics. In particular, in computational fluid dynamics (where external problems present a wide class of practically important formulations) the proper treatment of external boundaries may have a profound impact on the overall quality and performance of numerical algorithms. Most of the currently used techniques for setting the ABC's can basically be classified into two groups. The methods from the first group (global ABC's) usually provide high accuracy and robustness of the numerical procedure but often appear to be fairly cumbersome and (computationally) expensive. The methods from the second group (local ABC's) are, as a rule, algorithmically simple, numerically cheap, and geometrically universal; however, they usually lack accuracy of computations. In this paper we first present a survey and provide a comparative assessment of different existing methods for constructing the ABC's. Then, we describe a relatively new ABC's technique of ours and review the corresponding results. This new technique, in our opinion, is currently one of the most promising in the field. It enables one to construct such ABC's that combine the advantages relevant to the two aforementioned classes of existing methods. Our approach is based on application of the difference potentials method attributable to V. S. Ryaben'kii. This approach allows us to obtain highly accurate ABC's in the form of certain (nonlocal) boundary operator equations. The operators involved are analogous to the pseudodifferential boundary projections first introduced by A. P. Calderon and then also studied by R. T. Seeley. The apparatus of the boundary pseudodifferential equations, which has formerly been used mostly in the qualitative theory of integral equations and PDE'S, is now effectively employed for developing numerical methods in the different fields of scientific computing.

cosmoabc: Likelihood-free inference for cosmology

NASA Astrophysics Data System (ADS)

Ishida, Emille E. O.; Vitenti, Sandro D. P.; Penna-Lima, Mariana; Trindade, Arlindo M.; Cisewski, Jessi; M.; de Souza, Rafael; Cameron, Ewan; Busti, Vinicius C.

2015-05-01

Approximate Bayesian Computation (ABC) enables parameter inference for complex physical systems in cases where the true likelihood function is unknown, unavailable, or computationally too expensive. It relies on the forward simulation of mock data and comparison between observed and synthetic catalogs. cosmoabc is a Python Approximate Bayesian Computation (ABC) sampler featuring a Population Monte Carlo variation of the original ABC algorithm, which uses an adaptive importance sampling scheme. The code can be coupled to an external simulator to allow incorporation of arbitrary distance and prior functions. When coupled with the numcosmo library, it has been used to estimate posterior probability distributions over cosmological parameters based on measurements of galaxy clusters number counts without computing the likelihood function.

Taking error into account when fitting models using Approximate Bayesian Computation.

PubMed

van der Vaart, Elske; Prangle, Dennis; Sibly, Richard M

2018-03-01

Stochastic computer simulations are often the only practical way of answering questions relating to ecological management. However, due to their complexity, such models are difficult to calibrate and evaluate. Approximate Bayesian Computation (ABC) offers an increasingly popular approach to this problem, widely applied across a variety of fields. However, ensuring the accuracy of ABC's estimates has been difficult. Here, we obtain more accurate estimates by incorporating estimation of error into the ABC protocol. We show how this can be done where the data consist of repeated measures of the same quantity and errors may be assumed to be normally distributed and independent. We then derive the correct acceptance probabilities for a probabilistic ABC algorithm, and update the coverage test with which accuracy is assessed. We apply this method, which we call error-calibrated ABC, to a toy example and a realistic 14-parameter simulation model of earthworms that is used in environmental risk assessment. A comparison with exact methods and the diagnostic coverage test show that our approach improves estimation of parameter values and their credible intervals for both models. © 2017 by the Ecological Society of America.

ABrox-A user-friendly Python module for approximate Bayesian computation with a focus on model comparison.

PubMed

Mertens, Ulf Kai; Voss, Andreas; Radev, Stefan

2018-01-01

We give an overview of the basic principles of approximate Bayesian computation (ABC), a class of stochastic methods that enable flexible and likelihood-free model comparison and parameter estimation. Our new open-source software called ABrox is used to illustrate ABC for model comparison on two prominent statistical tests, the two-sample t-test and the Levene-Test. We further highlight the flexibility of ABC compared to classical Bayesian hypothesis testing by computing an approximate Bayes factor for two multinomial processing tree models. Last but not least, throughout the paper, we introduce ABrox using the accompanied graphical user interface.

Deciphering the Routes of invasion of Drosophila suzukii by Means of ABC Random Forest.

PubMed

Fraimout, Antoine; Debat, Vincent; Fellous, Simon; Hufbauer, Ruth A; Foucaud, Julien; Pudlo, Pierre; Marin, Jean-Michel; Price, Donald K; Cattel, Julien; Chen, Xiao; Deprá, Marindia; François Duyck, Pierre; Guedot, Christelle; Kenis, Marc; Kimura, Masahito T; Loeb, Gregory; Loiseau, Anne; Martinez-Sañudo, Isabel; Pascual, Marta; Polihronakis Richmond, Maxi; Shearer, Peter; Singh, Nadia; Tamura, Koichiro; Xuéreb, Anne; Zhang, Jinping; Estoup, Arnaud

2017-04-01

Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 loci on 23 worldwide sampling locations). To do this, we use approximate Bayesian computation (ABC), which has improved the reconstruction of invasion routes, but can be computationally expensive. We use our study to illustrate the use of a new, more efficient, ABC method, ABC random forest (ABC-RF) and compare it to a standard ABC method (ABC-LDA). We find that Japan emerges as the most probable source of the earliest recorded invasion into Hawaii. Southeast China and Hawaii together are the most probable sources of populations in western North America, which then in turn served as sources for those in eastern North America. European populations are genetically more homogeneous than North American populations, and their most probable source is northeast China, with evidence of limited gene flow from the eastern US as well. All introduced populations passed through bottlenecks, and analyses reveal five distinct admixture events. These findings can inform hypotheses concerning how this species evolved between different and independent source and invasive populations. Methodological comparisons indicate that ABC-RF and ABC-LDA show concordant results if ABC-LDA is based on a large number of simulated datasets but that ABC-RF out-performs ABC-LDA when using a comparable and more manageable number of simulated datasets, especially when analyzing complex introduction scenarios. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Artificial Boundary Conditions for Computation of Oscillating External Flows

NASA Technical Reports Server (NTRS)

Tsynkov, S. V.

1996-01-01

In this paper, we propose a new technique for the numerical treatment of external flow problems with oscillatory behavior of the solution in time. Specifically, we consider the case of unbounded compressible viscous plane flow past a finite body (airfoil). Oscillations of the flow in time may be caused by the time-periodic injection of fluid into the boundary layer, which in accordance with experimental data, may essentially increase the performance of the airfoil. To conduct the actual computations, we have to somehow restrict the original unbounded domain, that is, to introduce an artificial (external) boundary and to further consider only a finite computational domain. Consequently, we will need to formulate some artificial boundary conditions (ABC's) at the introduced external boundary. The ABC's we are aiming to obtain must meet a fundamental requirement. One should be able to uniquely complement the solution calculated inside the finite computational domain to its infinite exterior so that the original problem is solved within the desired accuracy. Our construction of such ABC's for oscillating flows is based on an essential assumption: the Navier-Stokes equations can be linearized in the far field against the free-stream back- ground. To actually compute the ABC's, we represent the far-field solution as a Fourier series in time and then apply the Difference Potentials Method (DPM) of V. S. Ryaben'kii. This paper contains a general theoretical description of the algorithm for setting the DPM-based ABC's for time-periodic external flows. Based on our experience in implementing analogous ABC's for steady-state problems (a simpler case), we expect that these boundary conditions will become an effective tool for constructing robust numerical methods to calculate oscillatory flows.

Digest: Demographic inferences accounting for selection at linked sites†.

PubMed

Simon, Alexis; Duranton, Maud

2018-05-16

Complex demography and selection at linked sites can generate spurious signatures of divergent selection. Unfortunately, many attempts at demographic inference consider overly simple models and neglect the effect of selection at linked sites. In this issue, Rougemont and Bernatchez (2018) applied an approximate Bayesian computation (ABC) framework that accounts for indirect selection to reveal a complex history of secondary contacts in Atlantic salmon (Salmo salar) that might explain a high rate of latitudinal clines in this species. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Volume Quantification of Acute Infratentorial Hemorrhage with Computed Tomography: Validation of the Formula 1/2ABC and 2/3SH

PubMed Central

Zhang, Yunyun; Yan, Jing; Fu, Yi; Chen, Shengdi

2013-01-01

Objective To compare the accuracy of formula 1/2ABC with 2/3SH on volume estimation for hypertensive infratentorial hematoma. Methods One hundred and forty-seven CT scans diagnosed as hypertensive infratentorial hemorrhage were reviewed. Based on the shape, hematomas were categorized as regular or irregular. Multilobular was defined as a special shape of irregular. Hematoma volume was calculated employing computer-assisted volumetric analysis (CAVA), 1/2ABC and 2/3SH, respectively. Results The correlation coefficients between 1/2ABC (or 2/3SH) and CAVA were greater than 0.900 in all subgroups. There were neither significant differences in absolute values of volume deviation nor percentage deviation between 1/2ABC and 2/3SH for regular hemorrhage (P>0.05). While for cerebellar, brainstem and irregular hemorrhages, the absolute values of volume deviation and percentage deviation by formula 1/2ABC were greater than 2/3SH (P<0.05). 1/2ABC and 2/3SH underestimated hematoma volume each by 10% and 5% for cerebellar hemorrhage, 14% and 9% for brainstem hemorrhage, 19% and 16% for regular hemorrhage, 9% and 3% for irregular hemorrhage, respectively. In addition, for the multilobular hemorrhage, 1/2ABC underestimated the volume by 9% while 2/3SH overestimated it by 2%. Conclusions For regular hemorrhage volume calculation, the accuracy of 2/3SH is similar to 1/2ABC. While for cerebellar, brainstem or irregular hemorrhages (including multilobular), 2/3SH is more accurate than 1/2ABC. PMID:23638025

Creating an iPhone Application for Collecting Continuous ABC Data

ERIC Educational Resources Information Center

Whiting, Seth W.; Dixon, Mark R.

2012-01-01

This paper provides an overview and task analysis for creating a continuous ABC data- collection application using Xcode on a Mac computer. Behavior analysts can program an ABC data collection system, complete with a customized list of target clients, antecedents, behaviors, and consequences to be recorded, and have the data automatically sent to…

Approximate Bayesian computation in large-scale structure: constraining the galaxy-halo connection

NASA Astrophysics Data System (ADS)

Hahn, ChangHoon; Vakili, Mohammadjavad; Walsh, Kilian; Hearin, Andrew P.; Hogg, David W.; Campbell, Duncan

2017-08-01

Standard approaches to Bayesian parameter inference in large-scale structure assume a Gaussian functional form (chi-squared form) for the likelihood. This assumption, in detail, cannot be correct. Likelihood free inferences such as approximate Bayesian computation (ABC) relax these restrictions and make inference possible without making any assumptions on the likelihood. Instead ABC relies on a forward generative model of the data and a metric for measuring the distance between the model and data. In this work, we demonstrate that ABC is feasible for LSS parameter inference by using it to constrain parameters of the halo occupation distribution (HOD) model for populating dark matter haloes with galaxies. Using specific implementation of ABC supplemented with population Monte Carlo importance sampling, a generative forward model using HOD and a distance metric based on galaxy number density, two-point correlation function and galaxy group multiplicity function, we constrain the HOD parameters of mock observation generated from selected 'true' HOD parameters. The parameter constraints we obtain from ABC are consistent with the 'true' HOD parameters, demonstrating that ABC can be reliably used for parameter inference in LSS. Furthermore, we compare our ABC constraints to constraints we obtain using a pseudo-likelihood function of Gaussian form with MCMC and find consistent HOD parameter constraints. Ultimately, our results suggest that ABC can and should be applied in parameter inference for LSS analyses.

An ABC Literacy Journey: Anchoring in Texts, Bridging Language, and Creating Stories

ERIC Educational Resources Information Center

Evers, Amy J.; Lang, Lisa F.; Smith, Sharon V.

2009-01-01

The authors describe how alphabet books teach so much more than just the ABCs. They provide excellent resources, allowing teachers to link and integrate the reciprocal processes of reading and writing. Encapsulated within the writing workshop framework, the authors use multigenre and multicultural alphabet books as anchor texts for a literacy…

50 CFR 648.96 - FMP review, specification, and framework adjustment process.

Code of Federal Regulations, 2012 CFR

2012-10-01

... and ACLs. (1) The Councils or the PDT may develop options for setting ABC, ACL, and OFL for each.... The Councils or the PDT may recommend to the SSC that ABC, ACL, and OFL are specified for each.... (ii) ACL recommendations. The Councils shall establish ACLs for each management area that are...

50 CFR 648.96 - FMP review, specification, and framework adjustment process.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Councils or the PDT may develop options for setting ABC, ACL, and OFL for each monkfish stock, as necessary... recommend to the SSC that ABC, ACL, and OFL are specified for each monkfish stock for multiple years as... not limited to, OFLs, ACLs, and management uncertainty. (ii) ACL recommendations. The Councils shall...

50 CFR 648.96 - FMP review, specification, and framework adjustment process.

Code of Federal Regulations, 2013 CFR

2013-10-01

... and ACLs. (1) The Councils or the PDT may develop options for setting ABC, ACL, and OFL for each.... The Councils or the PDT may recommend to the SSC that ABC, ACL, and OFL are specified for each.... (ii) ACL recommendations. The Councils shall establish ACLs for each management area that are...

50 CFR 648.96 - FMP review, specification, and framework adjustment process.

Code of Federal Regulations, 2014 CFR

2014-10-01

... and ACLs. (1) The Councils or the PDT may develop options for setting ABC, ACL, and OFL for each.... The Councils or the PDT may recommend to the SSC that ABC, ACL, and OFL are specified for each.... (ii) ACL recommendations. The Councils shall establish ACLs for each management area that are...

Preclinical properties and human in vivo assessment of 123 I-ABC577 as a novel SPECT agent for imaging amyloid-β

PubMed Central

Okumura, Yuki; Kobayashi, Ryohei; Onishi, Takako; Shoyama, Yoshinari; Barret, Olivier; Alagille, David; Jennings, Danna; Marek, Kenneth; Seibyl, John; Tamagnan, Gilles; Tanaka, Akihiro; Shirakami, Yoshifumi

2016-01-01

Abstract Non-invasive imaging of amyloid-β in the brain, a hallmark of Alzheimer’s disease, may support earlier and more accurate diagnosis of the disease. In this study, we assessed the novel single photon emission computed tomography tracer 123 I-ABC577 as a potential imaging biomarker for amyloid-β in the brain. The radio-iodinated imidazopyridine derivative 123 I-ABC577 was designed as a candidate for a novel amyloid-β imaging agent. The binding affinity of 123 I-ABC577 for amyloid-β was evaluated by saturation binding assay and in vitro autoradiography using post-mortem Alzheimer’s disease brain tissue. Biodistribution experiments using normal rats were performed to evaluate the biokinetics of 123 I-ABC577. Furthermore, to validate 123 I-ABC577 as a biomarker for Alzheimer’s disease, we performed a clinical study to compare the brain uptake of 123 I-ABC577 in three patients with Alzheimer’s disease and three healthy control subjects. 123 I-ABC577 binding was quantified by use of the standardized uptake value ratio, which was calculated for the cortex using the cerebellum as a reference region. Standardized uptake value ratio images were visually scored as positive or negative. As a result, 123 I-ABC577 showed high binding affinity for amyloid-β and desirable pharmacokinetics in the preclinical studies. In the clinical study, 123 I-ABC577 was an effective marker for discriminating patients with Alzheimer’s disease from healthy control subjects based on visual images or the ratio of cortical-to-cerebellar binding. In patients with Alzheimer’s disease, 123 I-ABC577 demonstrated clear retention in cortical regions known to accumulate amyloid, such as the frontal cortex, temporal cortex, and posterior cingulate. In contrast, less, more diffuse, and non-specific uptake without localization to these key regions was observed in healthy controls. At 150 min after injection, the cortical standardized uptake value ratio increased by ∼60% in patients with Alzheimer’s disease relative to healthy control subjects. Both healthy control subjects and patients with Alzheimer’s disease showed minimal 123 I-ABC577 retention in the white matter. These observations indicate that 123 I-ABC577 may be a useful single photon emission computed tomography imaging maker to identify amyloid-β in the human brain. The availability of an amyloid-β tracer for single photon emission computed tomography might increase the accessibility of diagnostic imaging for Alzheimer’s disease. PMID:26490333

From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli

PubMed Central

2011-01-01

Background Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. These are crucial for their survival, which requires them to react to extracellular stresses such as heat shock, ethanol treatment or phage infection. Here we focus on studying the phage shock protein (Psp) stress response in Escherichia coli induced by a phage infection or other damage to the bacterial membrane. This system has not yet been theoretically modelled or analysed in silico. Results We develop a model of the Psp response system, and illustrate how such models can be constructed and analyzed in light of available sparse and qualitative information in order to generate novel biological hypotheses about their dynamical behaviour. We analyze this model using tools from Petri-net theory and study its dynamical range that is consistent with currently available knowledge by conditioning model parameters on the available data in an approximate Bayesian computation (ABC) framework. Within this ABC approach we analyze stochastic and deterministic dynamics. This analysis allows us to identify different types of behaviour and these mechanistic insights can in turn be used to design new, more detailed and time-resolved experiments. Conclusions We have developed the first mechanistic model of the Psp response in E. coli. This model allows us to predict the possible qualitative stochastic and deterministic dynamic behaviours of key molecular players in the stress response. Our inferential approach can be applied to stress response and signalling systems more generally: in the ABC framework we can condition mathematical models on qualitative data in order to delimit e.g. parameter ranges or the qualitative system dynamics in light of available end-point or qualitative information. PMID:21569396

CREATING AN IPHONE APPLICATION FOR COLLECTING CONTINUOUS ABC DATA

PubMed Central

Whiting, Seth W; Dixon, Mark R

2012-01-01

This paper provides an overview and task analysis for creating a continuous ABC data-collection application using Xcode on a Mac computer. Behavior analysts can program an ABC data collection system, complete with a customized list of target clients, antecedents, behaviors, and consequences to be recorded, and have the data automatically sent to an e-mail account after observations have concluded. Further suggestions are provided to customize the ABC data- collection system for individual preferences and clinical needs. PMID:23060682

Creating an iPhone application for collecting continuous ABC data.

PubMed

Whiting, Seth W; Dixon, Mark R

2012-01-01

This paper provides an overview and task analysis for creating a continuous ABC data-collection application using Xcode on a Mac computer. Behavior analysts can program an ABC data collection system, complete with a customized list of target clients, antecedents, behaviors, and consequences to be recorded, and have the data automatically sent to an e-mail account after observations have concluded. Further suggestions are provided to customize the ABC data- collection system for individual preferences and clinical needs.

Bayesian experimental design for models with intractable likelihoods.

PubMed

Drovandi, Christopher C; Pettitt, Anthony N

2013-12-01

In this paper we present a methodology for designing experiments for efficiently estimating the parameters of models with computationally intractable likelihoods. The approach combines a commonly used methodology for robust experimental design, based on Markov chain Monte Carlo sampling, with approximate Bayesian computation (ABC) to ensure that no likelihood evaluations are required. The utility function considered for precise parameter estimation is based upon the precision of the ABC posterior distribution, which we form efficiently via the ABC rejection algorithm based on pre-computed model simulations. Our focus is on stochastic models and, in particular, we investigate the methodology for Markov process models of epidemics and macroparasite population evolution. The macroparasite example involves a multivariate process and we assess the loss of information from not observing all variables. © 2013, The International Biometric Society.

JPRS Report, West Europe, Reference Aid, Glossary of Acronyms and Abbreviations of Norway

DTIC Science & Technology

1989-04-04

nuclear-biological- chemical [use NBC] ABC/S Forsvarets ABC-sekretariat Defense NBC Secretariat adj . adjutant adm administrasj on adm...institusj onens regneanlegg kjem kjemi(sk) kj. st. kj^restilling Kjeller Institute Computing Facility chemical driving position kjt kj...National Federation of the Chemical Mineral Industry Air Commander, North Norway LKR lett kontrollrom LKS Luftkommandor S0r-Norge LK-sjef

Our bodies are our own: resistance to ABC-based HIV-prevention programmes in northern Tanzanian conservation organisations.

PubMed

Reid-Hresko, John

2014-01-01

ABC-based HIV-prevention programmes have been widely employed in northern Tanzanian wildlife conservation settings in an attempt to (re)shape the sexual behaviours of conservation actors. Utilising findings from 66 semi-structured interviews conducted in 2009-2010, this paper examines ABC prevention as a form of Foucauldian governmentality--circulating technologies of power that mobilise disciplinary technologies and attempt to transform such efforts into technologies of the self--and explores how individuals understand and respond to attempts to govern their behaviour. ABC regimes attempt to rework subjectivity, positioning HIV-related behaviours within a risk-based neoliberal rationality. However, efforts to use ABC as a technology to govern populations and individual bodies are largely incommensurate with existing Tanzanian sociocultural formations, including economic and gendered inequalities, and local understandings of sexuality. The language research participants used to talk about ABC and the justifications they offered for non-compliance illuminate this discrepancy. Data reveal that the recipients of ABC campaigns are active producers of understandings that work for them in their lives, but may not produce the behavioural shifts envisioned by programme goals. These findings corroborate previous research, which questions the continued plausibility of ABC as a stand-alone HIV- prevention framework.

Model selection and parameter estimation in structural dynamics using approximate Bayesian computation

NASA Astrophysics Data System (ADS)

Ben Abdessalem, Anis; Dervilis, Nikolaos; Wagg, David; Worden, Keith

2018-01-01

This paper will introduce the use of the approximate Bayesian computation (ABC) algorithm for model selection and parameter estimation in structural dynamics. ABC is a likelihood-free method typically used when the likelihood function is either intractable or cannot be approached in a closed form. To circumvent the evaluation of the likelihood function, simulation from a forward model is at the core of the ABC algorithm. The algorithm offers the possibility to use different metrics and summary statistics representative of the data to carry out Bayesian inference. The efficacy of the algorithm in structural dynamics is demonstrated through three different illustrative examples of nonlinear system identification: cubic and cubic-quintic models, the Bouc-Wen model and the Duffing oscillator. The obtained results suggest that ABC is a promising alternative to deal with model selection and parameter estimation issues, specifically for systems with complex behaviours.

A Novel Artificial Bee Colony Approach of Live Virtual Machine Migration Policy Using Bayes Theorem

PubMed Central

Xu, Gaochao; Hu, Liang; Fu, Xiaodong

2013-01-01

Green cloud data center has become a research hotspot of virtualized cloud computing architecture. Since live virtual machine (VM) migration technology is widely used and studied in cloud computing, we have focused on the VM placement selection of live migration for power saving. We present a novel heuristic approach which is called PS-ABC. Its algorithm includes two parts. One is that it combines the artificial bee colony (ABC) idea with the uniform random initialization idea, the binary search idea, and Boltzmann selection policy to achieve an improved ABC-based approach with better global exploration's ability and local exploitation's ability. The other one is that it uses the Bayes theorem to further optimize the improved ABC-based process to faster get the final optimal solution. As a result, the whole approach achieves a longer-term efficient optimization for power saving. The experimental results demonstrate that PS-ABC evidently reduces the total incremental power consumption and better protects the performance of VM running and migrating compared with the existing research. It makes the result of live VM migration more high-effective and meaningful. PMID:24385877

A novel artificial bee colony approach of live virtual machine migration policy using Bayes theorem.

PubMed

Xu, Gaochao; Ding, Yan; Zhao, Jia; Hu, Liang; Fu, Xiaodong

2013-01-01

Green cloud data center has become a research hotspot of virtualized cloud computing architecture. Since live virtual machine (VM) migration technology is widely used and studied in cloud computing, we have focused on the VM placement selection of live migration for power saving. We present a novel heuristic approach which is called PS-ABC. Its algorithm includes two parts. One is that it combines the artificial bee colony (ABC) idea with the uniform random initialization idea, the binary search idea, and Boltzmann selection policy to achieve an improved ABC-based approach with better global exploration's ability and local exploitation's ability. The other one is that it uses the Bayes theorem to further optimize the improved ABC-based process to faster get the final optimal solution. As a result, the whole approach achieves a longer-term efficient optimization for power saving. The experimental results demonstrate that PS-ABC evidently reduces the total incremental power consumption and better protects the performance of VM running and migrating compared with the existing research. It makes the result of live VM migration more high-effective and meaningful.

Simulation-based estimation of mean and standard deviation for meta-analysis via Approximate Bayesian Computation (ABC).

PubMed

Kwon, Deukwoo; Reis, Isildinha M

2015-08-12

When conducting a meta-analysis of a continuous outcome, estimated means and standard deviations from the selected studies are required in order to obtain an overall estimate of the mean effect and its confidence interval. If these quantities are not directly reported in the publications, they must be estimated from other reported summary statistics, such as the median, the minimum, the maximum, and quartiles. We propose a simulation-based estimation approach using the Approximate Bayesian Computation (ABC) technique for estimating mean and standard deviation based on various sets of summary statistics found in published studies. We conduct a simulation study to compare the proposed ABC method with the existing methods of Hozo et al. (2005), Bland (2015), and Wan et al. (2014). In the estimation of the standard deviation, our ABC method performs better than the other methods when data are generated from skewed or heavy-tailed distributions. The corresponding average relative error (ARE) approaches zero as sample size increases. In data generated from the normal distribution, our ABC performs well. However, the Wan et al. method is best for estimating standard deviation under normal distribution. In the estimation of the mean, our ABC method is best regardless of assumed distribution. ABC is a flexible method for estimating the study-specific mean and standard deviation for meta-analysis, especially with underlying skewed or heavy-tailed distributions. The ABC method can be applied using other reported summary statistics such as the posterior mean and 95 % credible interval when Bayesian analysis has been employed.

Accelerating Approximate Bayesian Computation with Quantile Regression: application to cosmological redshift distributions

NASA Astrophysics Data System (ADS)

Kacprzak, T.; Herbel, J.; Amara, A.; Réfrégier, A.

2018-02-01

Approximate Bayesian Computation (ABC) is a method to obtain a posterior distribution without a likelihood function, using simulations and a set of distance metrics. For that reason, it has recently been gaining popularity as an analysis tool in cosmology and astrophysics. Its drawback, however, is a slow convergence rate. We propose a novel method, which we call qABC, to accelerate ABC with Quantile Regression. In this method, we create a model of quantiles of distance measure as a function of input parameters. This model is trained on a small number of simulations and estimates which regions of the prior space are likely to be accepted into the posterior. Other regions are then immediately rejected. This procedure is then repeated as more simulations are available. We apply it to the practical problem of estimation of redshift distribution of cosmological samples, using forward modelling developed in previous work. The qABC method converges to nearly same posterior as the basic ABC. It uses, however, only 20% of the number of simulations compared to basic ABC, achieving a fivefold gain in execution time for our problem. For other problems the acceleration rate may vary; it depends on how close the prior is to the final posterior. We discuss possible improvements and extensions to this method.

Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.

PubMed

Chan, Yvonne L; Schanzenbach, David; Hickerson, Michael J

2014-09-01

Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Statistical Hypothesis Testing in Intraspecific Phylogeography: NCPA versus ABC

PubMed Central

Templeton, Alan R.

2009-01-01

Nested clade phylogeographic analysis (NCPA) and approximate Bayesian computation (ABC) have been used to test phylogeographic hypotheses. Multilocus NCPA tests null hypotheses, whereas ABC discriminates among a finite set of alternatives. The interpretive criteria of NCPA are explicit and allow complex models to be built from simple components. The interpretive criteria of ABC are ad hoc and require the specification of a complete phylogeographic model. The conclusions from ABC are often influenced by implicit assumptions arising from the many parameters needed to specify a complex model. These complex models confound many assumptions so that biological interpretations are difficult. Sampling error is accounted for in NCPA, but ABC ignores important sources of sampling error that creates pseudo-statistical power. NCPA generates the full sampling distribution of its statistics, but ABC only yields local probabilities, which in turn make it impossible to distinguish between a good fitting model, a non-informative model, and an over-determined model. Both NCPA and ABC use approximations, but convergences of the approximations used in NCPA are well defined whereas those in ABC are not. NCPA can analyze a large number of locations, but ABC cannot. Finally, the dimensionality of tested hypothesis is known in NCPA, but not for ABC. As a consequence, the “probabilities” generated by ABC are not true probabilities and are statistically non-interpretable. Accordingly, ABC should not be used for hypothesis testing, but simulation approaches are valuable when used in conjunction with NCPA or other methods that do not rely on highly parameterized models. PMID:19192182

First MRI application of an active breathing coordinator

NASA Astrophysics Data System (ADS)

Kaza, E.; Symonds-Tayler, R.; Collins, D. J.; McDonald, F.; McNair, H. A.; Scurr, E.; Koh, D.-M.; Leach, M. O.

2015-02-01

A commercial active breathing coordinator (ABC) device, employed to hold respiration at a specific level for a predefined duration, was successfully adapted for magnetic resonance imaging (MRI) use for the first time. Potential effects of the necessary modifications were assessed and taken into account. Automatic MR acquisition during ABC breath holding was achieved. The feasibility of MR-ABC thoracic and abdominal examinations together with the advantages of imaging in repeated ABC-controlled breath holds were demonstrated on healthy volunteers. Five lung cancer patients were imaged under MR-ABC, visually confirming the very good intra-session reproducibility of organ position in images acquired with the same patient positioning as used for computed tomography (CT). Using identical ABC settings, good MR-CT inter-modality registration was achieved. This demonstrates the value of ABC, since application of T1, T2 and diffusion weighted MR sequences provides a wider range of contrast mechanisms and additional diagnostic information compared to CT, thus improving radiotherapy treatment planning and assessment.

First MRI application of an active breathing coordinator.

PubMed

Kaza, E; Symonds-Tayler, R; Collins, D J; McDonald, F; McNair, H A; Scurr, E; Koh, D-M; Leach, M O

2015-02-21

A commercial active breathing coordinator (ABC) device, employed to hold respiration at a specific level for a predefined duration, was successfully adapted for magnetic resonance imaging (MRI) use for the first time. Potential effects of the necessary modifications were assessed and taken into account. Automatic MR acquisition during ABC breath holding was achieved. The feasibility of MR-ABC thoracic and abdominal examinations together with the advantages of imaging in repeated ABC-controlled breath holds were demonstrated on healthy volunteers. Five lung cancer patients were imaged under MR-ABC, visually confirming the very good intra-session reproducibility of organ position in images acquired with the same patient positioning as used for computed tomography (CT). Using identical ABC settings, good MR-CT inter-modality registration was achieved. This demonstrates the value of ABC, since application of T1, T2 and diffusion weighted MR sequences provides a wider range of contrast mechanisms and additional diagnostic information compared to CT, thus improving radiotherapy treatment planning and assessment.

First MRI application of an active breathing coordinator

PubMed Central

Kaza, E; Symonds-Tayler, R; Collins, D J; McDonald, F; McNair, H A; Scurr, E; Koh, D-M; Leach, M O

2015-01-01

Abstract A commercial active breathing coordinator (ABC) device, employed to hold respiration at a specific level for a predefined duration, was successfully adapted for magnetic resonance imaging (MRI) use for the first time. Potential effects of the necessary modifications were assessed and taken into account. Automatic MR acquisition during ABC breath holding was achieved. The feasibility of MR-ABC thoracic and abdominal examinations together with the advantages of imaging in repeated ABC-controlled breath holds were demonstrated on healthy volunteers. Five lung cancer patients were imaged under MR-ABC, visually confirming the very good intra-session reproducibility of organ position in images acquired with the same patient positioning as used for computed tomography (CT). Using identical ABC settings, good MR-CT inter-modality registration was achieved. This demonstrates the value of ABC, since application of T1, T2 and diffusion weighted MR sequences provides a wider range of contrast mechanisms and additional diagnostic information compared to CT, thus improving radiotherapy treatment planning and assessment. PMID:25633183

COSMOABC: Likelihood-free inference via Population Monte Carlo Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Ishida, E. E. O.; Vitenti, S. D. P.; Penna-Lima, M.; Cisewski, J.; de Souza, R. S.; Trindade, A. M. M.; Cameron, E.; Busti, V. C.; COIN Collaboration

2015-11-01

Approximate Bayesian Computation (ABC) enables parameter inference for complex physical systems in cases where the true likelihood function is unknown, unavailable, or computationally too expensive. It relies on the forward simulation of mock data and comparison between observed and synthetic catalogues. Here we present COSMOABC, a Python ABC sampler featuring a Population Monte Carlo variation of the original ABC algorithm, which uses an adaptive importance sampling scheme. The code is very flexible and can be easily coupled to an external simulator, while allowing to incorporate arbitrary distance and prior functions. As an example of practical application, we coupled COSMOABC with the NUMCOSMO library and demonstrate how it can be used to estimate posterior probability distributions over cosmological parameters based on measurements of galaxy clusters number counts without computing the likelihood function. COSMOABC is published under the GPLv3 license on PyPI and GitHub and documentation is available at http://goo.gl/SmB8EX.

Selecting Summary Statistics in Approximate Bayesian Computation for Calibrating Stochastic Models

PubMed Central

Burr, Tom

2013-01-01

Approximate Bayesian computation (ABC) is an approach for using measurement data to calibrate stochastic computer models, which are common in biology applications. ABC is becoming the “go-to” option when the data and/or parameter dimension is large because it relies on user-chosen summary statistics rather than the full data and is therefore computationally feasible. One technical challenge with ABC is that the quality of the approximation to the posterior distribution of model parameters depends on the user-chosen summary statistics. In this paper, the user requirement to choose effective summary statistics in order to accurately estimate the posterior distribution of model parameters is investigated and illustrated by example, using a model and corresponding real data of mitochondrial DNA population dynamics. We show that for some choices of summary statistics, the posterior distribution of model parameters is closely approximated and for other choices of summary statistics, the posterior distribution is not closely approximated. A strategy to choose effective summary statistics is suggested in cases where the stochastic computer model can be run at many trial parameter settings, as in the example. PMID:24288668

Selecting summary statistics in approximate Bayesian computation for calibrating stochastic models.

PubMed

Burr, Tom; Skurikhin, Alexei

2013-01-01

Approximate Bayesian computation (ABC) is an approach for using measurement data to calibrate stochastic computer models, which are common in biology applications. ABC is becoming the "go-to" option when the data and/or parameter dimension is large because it relies on user-chosen summary statistics rather than the full data and is therefore computationally feasible. One technical challenge with ABC is that the quality of the approximation to the posterior distribution of model parameters depends on the user-chosen summary statistics. In this paper, the user requirement to choose effective summary statistics in order to accurately estimate the posterior distribution of model parameters is investigated and illustrated by example, using a model and corresponding real data of mitochondrial DNA population dynamics. We show that for some choices of summary statistics, the posterior distribution of model parameters is closely approximated and for other choices of summary statistics, the posterior distribution is not closely approximated. A strategy to choose effective summary statistics is suggested in cases where the stochastic computer model can be run at many trial parameter settings, as in the example.

Approximate Bayesian computation for forward modeling in cosmology

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

Akeret, Joël; Refregier, Alexandre; Amara, Adam

Bayesian inference is often used in cosmology and astrophysics to derive constraints on model parameters from observations. This approach relies on the ability to compute the likelihood of the data given a choice of model parameters. In many practical situations, the likelihood function may however be unavailable or intractable due to non-gaussian errors, non-linear measurements processes, or complex data formats such as catalogs and maps. In these cases, the simulation of mock data sets can often be made through forward modeling. We discuss how Approximate Bayesian Computation (ABC) can be used in these cases to derive an approximation to themore » posterior constraints using simulated data sets. This technique relies on the sampling of the parameter set, a distance metric to quantify the difference between the observation and the simulations and summary statistics to compress the information in the data. We first review the principles of ABC and discuss its implementation using a Population Monte-Carlo (PMC) algorithm and the Mahalanobis distance metric. We test the performance of the implementation using a Gaussian toy model. We then apply the ABC technique to the practical case of the calibration of image simulations for wide field cosmological surveys. We find that the ABC analysis is able to provide reliable parameter constraints for this problem and is therefore a promising technique for other applications in cosmology and astrophysics. Our implementation of the ABC PMC method is made available via a public code release.« less

Automating approximate Bayesian computation by local linear regression.

PubMed

Thornton, Kevin R

2009-07-07

In several biological contexts, parameter inference often relies on computationally-intensive techniques. "Approximate Bayesian Computation", or ABC, methods based on summary statistics have become increasingly popular. A particular flavor of ABC based on using a linear regression to approximate the posterior distribution of the parameters, conditional on the summary statistics, is computationally appealing, yet no standalone tool exists to automate the procedure. Here, I describe a program to implement the method. The software package ABCreg implements the local linear-regression approach to ABC. The advantages are: 1. The code is standalone, and fully-documented. 2. The program will automatically process multiple data sets, and create unique output files for each (which may be processed immediately in R), facilitating the testing of inference procedures on simulated data, or the analysis of multiple data sets. 3. The program implements two different transformation methods for the regression step. 4. Analysis options are controlled on the command line by the user, and the program is designed to output warnings for cases where the regression fails. 5. The program does not depend on any particular simulation machinery (coalescent, forward-time, etc.), and therefore is a general tool for processing the results from any simulation. 6. The code is open-source, and modular.Examples of applying the software to empirical data from Drosophila melanogaster, and testing the procedure on simulated data, are shown. In practice, the ABCreg simplifies implementing ABC based on local-linear regression.

An Enhanced Artificial Bee Colony Algorithm with Solution Acceptance Rule and Probabilistic Multisearch.

PubMed

Yurtkuran, Alkın; Emel, Erdal

2016-01-01

The artificial bee colony (ABC) algorithm is a popular swarm based technique, which is inspired from the intelligent foraging behavior of honeybee swarms. This paper proposes a new variant of ABC algorithm, namely, enhanced ABC with solution acceptance rule and probabilistic multisearch (ABC-SA) to address global optimization problems. A new solution acceptance rule is proposed where, instead of greedy selection between old solution and new candidate solution, worse candidate solutions have a probability to be accepted. Additionally, the acceptance probability of worse candidates is nonlinearly decreased throughout the search process adaptively. Moreover, in order to improve the performance of the ABC and balance the intensification and diversification, a probabilistic multisearch strategy is presented. Three different search equations with distinctive characters are employed using predetermined search probabilities. By implementing a new solution acceptance rule and a probabilistic multisearch approach, the intensification and diversification performance of the ABC algorithm is improved. The proposed algorithm has been tested on well-known benchmark functions of varying dimensions by comparing against novel ABC variants, as well as several recent state-of-the-art algorithms. Computational results show that the proposed ABC-SA outperforms other ABC variants and is superior to state-of-the-art algorithms proposed in the literature.

ABC estimation of unit costs for emergency department services.

PubMed

Holmes, R L; Schroeder, R E

1996-04-01

Rapid evolution of the health care industry forces managers to make cost-effective decisions. Typical hospital cost accounting systems do not provide emergency department managers with the information needed, but emergency department settings are so complex and dynamic as to make the more accurate activity-based costing (ABC) system prohibitively expensive. Through judicious use of the available traditional cost accounting information and simple computer spreadsheets. managers may approximate the decision-guiding information that would result from the much more costly and time-consuming implementation of ABC.

Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path–Force Matching QM/MM Method

PubMed Central

Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Pu, J.

2016-01-01

Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path–force matching (RP–FM) has been developed. In RP–FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP–FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters. PMID:27498639

76 FR 47533 - Fisheries of the Northeastern United States; Monkfish; Framework Adjustment 7

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-05

... FMP). The New England Fishery Management Council and Mid- Atlantic Fishery Management Council (Councils) developed Framework 7 to adjust the annual catch target (ACT) for the Northern Fishery Management... catch (ABC) for monkfish. The New England Council's Scientific and Statistical Committee (SSC) has...

On Certain Topological Indices of Boron Triangular Nanotubes

NASA Astrophysics Data System (ADS)

Aslam, Adnan; Ahmad, Safyan; Gao, Wei

2017-08-01

The topological index gives information about the whole structure of a chemical graph, especially degree-based topological indices that are very useful. Boron triangular nanotubes are now replacing usual carbon nanotubes due to their excellent properties. We have computed general Randić (Rα), first Zagreb (M1) and second Zagreb (M2), atom-bond connectivity (ABC), and geometric-arithmetic (GA) indices of boron triangular nanotubes. Also, we have computed the fourth version of atom-bond connectivity (ABC4) and the fifth version of geometric-arithmetic (GA5) indices of boron triangular nanotubes.

Amoeba-based computing for traveling salesman problem: long-term correlations between spatially separated individual cells of Physarum polycephalum.

PubMed

Zhu, Liping; Aono, Masashi; Kim, Song-Ju; Hara, Masahiko

2013-04-01

A single-celled, multi-nucleated amoeboid organism, a plasmodium of the true slime mold Physarum polycephalum, can perform sophisticated computing by exhibiting complex spatiotemporal oscillatory dynamics while deforming its amorphous body. We previously devised an "amoeba-based computer (ABC)" to quantitatively evaluate the optimization capability of the amoeboid organism in searching for a solution to the traveling salesman problem (TSP) under optical feedback control. In ABC, the organism changes its shape to find a high quality solution (a relatively shorter TSP route) by alternately expanding and contracting its pseudopod-like branches that exhibit local photoavoidance behavior. The quality of the solution serves as a measure of the optimality of which the organism maximizes its global body area (nutrient absorption) while minimizing the risk of being illuminated (exposure to aversive stimuli). ABC found a high quality solution for the 8-city TSP with a high probability. However, it remains unclear whether intracellular communication among the branches of the organism is essential for computing. In this study, we conducted a series of control experiments using two individual cells (two single-celled organisms) to perform parallel searches in the absence of intercellular communication. We found that ABC drastically lost its ability to find a solution when it used two independent individuals. However, interestingly, when two individuals were prepared by dividing one individual, they found a solution for a few tens of minutes. That is, the two divided individuals remained correlated even though they were spatially separated. These results suggest the presence of a long-term memory in the intrinsic dynamics of this organism and its significance in performing sophisticated computing. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics.

PubMed

Madec, Morgan; Pecheux, François; Gendrault, Yves; Rosati, Elise; Lallement, Christophe; Haiech, Jacques

2016-10-01

The topic of this article is the development of an open-source automated design framework for synthetic biology, specifically for the design of artificial gene regulatory networks based on a digital approach. In opposition to other tools, GeNeDA is an open-source online software based on existing tools used in microelectronics that have proven their efficiency over the last 30 years. The complete framework is composed of a computation core directly adapted from an Electronic Design Automation tool, input and output interfaces, a library of elementary parts that can be achieved with gene regulatory networks, and an interface with an electrical circuit simulator. Each of these modules is an extension of microelectronics tools and concepts: ODIN II, ABC, the Verilog language, SPICE simulator, and SystemC-AMS. GeNeDA is first validated on a benchmark of several combinatorial circuits. The results highlight the importance of the part library. Then, this framework is used for the design of a sequential circuit including a biological state machine.

The jABC Approach to Rigorous Collaborative Development of SCM Applications

NASA Astrophysics Data System (ADS)

Hörmann, Martina; Margaria, Tiziana; Mender, Thomas; Nagel, Ralf; Steffen, Bernhard; Trinh, Hong

Our approach to the model-driven collaborative design of IKEA's P3 Delivery Management Process uses the jABC [9] for model driven mediation and choreography to complement a RUP-based (Rational Unified Process) development process. jABC is a framework for service development based on Lightweight Process Coordination. Users (product developers and system/software designers) easily develop services and applications by composing reusable building-blocks into (flow-) graph structures that can be animated, analyzed, simulated, verified, executed, and compiled. This way of handling the collaborative design of complex embedded systems has proven to be effective and adequate for the cooperation of non-programmers and non-technical people, which is the focus of this contribution, and it is now being rolled out in the operative practice.

Using Approximate Bayesian Computation to Probe Multiple Transiting Planet Systems

NASA Astrophysics Data System (ADS)

Morehead, Robert C.

2015-08-01

The large number of multiple transiting planet systems (MTPS) uncovered with Kepler suggest a population of well-aligned planetary systems. Previously, the distribution of transit duration ratios in MTPSs has been used to place constraints on the distributions of mutual orbital inclinations and orbital eccentricities in these systems. However, degeneracies with the underlying number of planets in these systems pose added challenges and make explicit likelihood functions intractable. Approximate Bayesian computation (ABC) offers an intriguing path forward. In its simplest form, ABC proposes from a prior on the population parameters to produce synthetic datasets via a physically-motivated model. Samples are accepted or rejected based on how close they come to reproducing the actual observed dataset to some tolerance. The accepted samples then form a robust and useful approximation of the true posterior distribution of the underlying population parameters. We will demonstrate the utility of ABC in exoplanet populations by presenting new constraints on the mutual inclination and eccentricity distributions in the Kepler MTPSs. We will also introduce Simple-ABC, a new open-source Python package designed for ease of use and rapid specification of general models, suitable for use in a wide variety of applications in both exoplanet science and astrophysics as a whole.

Approximate Bayesian Computation by Subset Simulation using hierarchical state-space models

NASA Astrophysics Data System (ADS)

Vakilzadeh, Majid K.; Huang, Yong; Beck, James L.; Abrahamsson, Thomas

2017-02-01

A new multi-level Markov Chain Monte Carlo algorithm for Approximate Bayesian Computation, ABC-SubSim, has recently appeared that exploits the Subset Simulation method for efficient rare-event simulation. ABC-SubSim adaptively creates a nested decreasing sequence of data-approximating regions in the output space that correspond to increasingly closer approximations of the observed output vector in this output space. At each level, multiple samples of the model parameter vector are generated by a component-wise Metropolis algorithm so that the predicted output corresponding to each parameter value falls in the current data-approximating region. Theoretically, if continued to the limit, the sequence of data-approximating regions would converge on to the observed output vector and the approximate posterior distributions, which are conditional on the data-approximation region, would become exact, but this is not practically feasible. In this paper we study the performance of the ABC-SubSim algorithm for Bayesian updating of the parameters of dynamical systems using a general hierarchical state-space model. We note that the ABC methodology gives an approximate posterior distribution that actually corresponds to an exact posterior where a uniformly distributed combined measurement and modeling error is added. We also note that ABC algorithms have a problem with learning the uncertain error variances in a stochastic state-space model and so we treat them as nuisance parameters and analytically integrate them out of the posterior distribution. In addition, the statistical efficiency of the original ABC-SubSim algorithm is improved by developing a novel strategy to regulate the proposal variance for the component-wise Metropolis algorithm at each level. We demonstrate that Self-regulated ABC-SubSim is well suited for Bayesian system identification by first applying it successfully to model updating of a two degree-of-freedom linear structure for three cases: globally, locally and un-identifiable model classes, and then to model updating of a two degree-of-freedom nonlinear structure with Duffing nonlinearities in its interstory force-deflection relationship.

Active Breathing Control for Hodgkin's Disease in Childhood and Adolescence: Feasibility, Advantages, and Limits

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

Claude, Line; Malet, Claude Phys.; Pommier, Pascal

2007-04-01

Purpose: The challenge in early Hodgkin's disease (HD) in children is to maintain good survival rates while sparing organs at risk. This study assesses the feasibility of active breathing control (ABC) in children, and compares normal tissue irradiation with and without ABC. Methods and Materials: Between May 2003 and June 2004, seven children with HD with mediastinal involvement, median age 15, were treated by chemotherapy and involved-field radiation therapy. A free-breathing computed tomography simulation scan and one additional scan during deep inspiration using ABC were performed. A comparison between planning treatment with clinical target volume including supraclavicular regions, mediastinum, andmore » hila was performed, both in free breathing and using ABC. Results: For a prescription of 36 Gy, pulmonary dose-volume histograms revealed a mean reduction in lung volume irradiated at more than 20 Gy (V20) and 30 Gy (V30) of 25% and 26%, respectively, using ABC (p = 0.016). The mean volume of heart irradiated at 30 Gy or more decreased from 15% to 12% (nonsignificant). The mean dose delivered to breasts in girls was small in both situations (less than 2 Gy) and stable with or without ABC. Considering axillary irradiation, the mean dose delivered to breasts remained low (<9 Gy), without significant difference using ABC or not. The mean radiation dose delivered to thyroid was stable using ABC or not. Conclusions: Using ABC is feasible in childhood. The use of ABC decreases normal lung tissue irradiation. Concerning heart irradiation, a minimal gain is also shown. No significant change has been demonstrated concerning breast and thyroid irradiation.« less

Online information and support needs of women with advanced breast cancer: a qualitative analysis.

PubMed

Kemp, Emma; Koczwara, Bogda; Butow, Phyllis; Turner, Jane; Girgis, Afaf; Schofield, Penelope; Hulbert-Williams, Nicholas; Levesque, Janelle; Spence, Danielle; Vatandoust, Sina; Kichenadasse, Ganessan; Roy, Amitesh; Sukumaran, Shawgi; Karapetis, Christos S; Richards, Caroline; Fitzgerald, Michael; Beatty, Lisa

2018-04-24

Women with advanced breast cancer (ABC) face significant adjustment challenges, yet few resources provide them with information and support, and attendance barriers can preclude access to face-to-face psychosocial support. This paper reports on two qualitative studies examining (i) whether information and support-seeking preferences of women with ABC could be addressed in an online intervention, and (ii) how an existing intervention for patients with early stage cancer could be adapted for women with ABC. Women with ABC participated in telephone interviews about their information and support-seeking preferences (N = 21) and evaluated an online intervention focused on early-stage cancer (N = 15). Interviews were transcribed and underwent thematic analysis using the framework method to identify salient themes. Participants most commonly sought medical, lifestyle-related, and practical information/support; however, when presented with an online intervention, participants most commonly gave positive feedback on content on coping with emotional distress. Difficulty finding information and barriers to using common sources of information/support including health professionals, family and friends, and peers were reported; however, some women also reported not wanting information or support. All participants evaluating the existing intervention gave positive feedback on various components, with results suggesting an online intervention could be an effective means of providing information/support to women with ABC, given improved specificity/relevance to ABC and increased tailoring to individual circumstances and preferences. Adaptation of an existing online intervention for early stage cancer appears to be a promising avenue to address the information and support needs of women with ABC.

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study

PubMed Central

Gascuel, Olivier

2017-01-01

Inferring epidemiological parameters such as the R0 from time-scaled phylogenies is a timely challenge. Most current approaches rely on likelihood functions, which raise specific issues that range from computing these functions to finding their maxima numerically. Here, we present a new regression-based Approximate Bayesian Computation (ABC) approach, which we base on a large variety of summary statistics intended to capture the information contained in the phylogeny and its corresponding lineage-through-time plot. The regression step involves the Least Absolute Shrinkage and Selection Operator (LASSO) method, which is a robust machine learning technique. It allows us to readily deal with the large number of summary statistics, while avoiding resorting to Markov Chain Monte Carlo (MCMC) techniques. To compare our approach to existing ones, we simulated target trees under a variety of epidemiological models and settings, and inferred parameters of interest using the same priors. We found that, for large phylogenies, the accuracy of our regression-ABC is comparable to that of likelihood-based approaches involving birth-death processes implemented in BEAST2. Our approach even outperformed these when inferring the host population size with a Susceptible-Infected-Removed epidemiological model. It also clearly outperformed a recent kernel-ABC approach when assuming a Susceptible-Infected epidemiological model with two host types. Lastly, by re-analyzing data from the early stages of the recent Ebola epidemic in Sierra Leone, we showed that regression-ABC provides more realistic estimates for the duration parameters (latency and infectiousness) than the likelihood-based method. Overall, ABC based on a large variety of summary statistics and a regression method able to perform variable selection and avoid overfitting is a promising approach to analyze large phylogenies. PMID:28263987

A user-centred methodology for designing an online social network to motivate health behaviour change.

PubMed

Kamal, Noreen; Fels, Sidney

2013-01-01

Positive health behaviour is critical to preventing illness and managing chronic conditions. A user-centred methodology was employed to design an online social network to motivate health behaviour change. The methodology was augmented by utilizing the Appeal, Belonging, Commitment (ABC) Framework, which is based on theoretical models for health behaviour change and use of online social networks. The user-centred methodology included four phases: 1) initial user inquiry on health behaviour and use of online social networks; 2) interview feedback on paper prototypes; 2) laboratory study on medium fidelity prototype; and 4) a field study on the high fidelity prototype. The points of inquiry through these phases were based on the ABC Framework. This yielded an online social network system that linked to external third party databases to deploy to users via an interactive website.

Comparison of mechanistic transport cycle models of ABC exporters.

PubMed

Szöllősi, Dániel; Rose-Sperling, Dania; Hellmich, Ute A; Stockner, Thomas

2018-04-01

ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. "This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain." Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Evolutionary Trajectories of Entomopathogenic Fungi ABC Transporters.

PubMed

Baral, Bikash

2017-01-01

The ABC protein superfamily-also called traffic ATPases-are energy-dependent ubiquitous proteins, representing one of the crucial and the largest family in the fungal genomes. The ATP-binding cassette endows a characteristic 200-250 amino acids and is omnipresent in all organisms ranging from prokaryotes to eukaryotes. Unlike in bacteria with nutrient import functions, ABC transporters in fungal entomopathogens serve as effective efflux pumps that are largely involved in the shuttle of metabolites across the biological membranes. Thus, the search for ABC proteins may prove of immense importance in elucidating the functional and molecular mechanism at the host-pathogen (insect-fungus) interface. Their sequence homology, domain topology, and functional traits led to the actual identification of nine different families in fungal entomopathogens. Evolutionary relationships within the ABC superfamily are discussed, concentrating on computational approaches for comparative identification of ABC transporters in insect-pathogenic fungi (entomopathogens) with those of animals, plants, and their bacterial orthologs. Ancestors of some fungal candidates have duplicated extensively in some phyla, while others were lost in one lineage or the other, and predictions for the cause of their duplications and/or loss in some phyla are made. ABC transporters of fungal insect-pathogens serve both defensive and offensive functions effective against land-dwelling and ground foraging voracious insects. This study may help to unravel the molecular cascades of ABC proteins to illuminate the means through which insects cope with fungal infection and fungal-related diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Applying activity-based costing to the nuclear medicine unit.

PubMed

Suthummanon, Sakesun; Omachonu, Vincent K; Akcin, Mehmet

2005-08-01

Previous studies have shown the feasibility of using activity-based costing (ABC) in hospital environments. However, many of these studies discuss the general applications of ABC in health-care organizations. This research explores the potential application of ABC to the nuclear medicine unit (NMU) at a teaching hospital. The finding indicates that the current cost averages 236.11 US dollars for all procedures, which is quite different from the costs computed by using ABC. The difference is most significant with positron emission tomography scan, 463 US dollars (an increase of 96%), as well as bone scan and thyroid scan, 114 US dollars (a decrease of 52%). The result of ABC analysis demonstrates that the operational time (machine time and direct labour time) and the cost of drugs have the most influence on cost per procedure. Clearly, to reduce the cost per procedure for the NMU, the reduction in operational time and cost of drugs should be analysed. The result also indicates that ABC can be used to improve resource allocation and management. It can be an important aid in making management decisions, particularly for improving pricing practices by making costing more accurate. It also facilitates the identification of underutilized resources and related costs, leading to cost reduction. The ABC system will also help hospitals control costs, improve the quality and efficiency of the care they provide, and manage their resources better.

SPECT Analysis of Cardiac Perfusion Changes After Whole-Breast/Chest Wall Radiation Therapy With or Without Active Breathing Coordinator: Results of a Randomized Phase 3 Trial

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

Zellars, Richard, E-mail: zellari@jhmi.edu; Bravo, Paco E.; Tryggestad, Erik

2014-03-15

Purpose: Cardiac muscle perfusion, as determined by single-photon emission computed tomography (SPECT), decreases after breast and/or chest wall (BCW) irradiation. The active breathing coordinator (ABC) enables radiation delivery when the BCW is farther from the heart, thereby decreasing cardiac exposure. We hypothesized that ABC would prevent radiation-induced cardiac toxicity and conducted a randomized controlled trial evaluating myocardial perfusion changes after radiation for left-sided breast cancer with or without ABC. Methods and Materials: Stages I to III left breast cancer patients requiring adjuvant radiation therapy (XRT) were randomized to ABC or No-ABC. Myocardial perfusion was evaluated by SPECT scans (before andmore » 6 months after BCW radiation) using 2 methods: (1) fully automated quantitative polar mapping; and (2) semiquantitative visual assessment. The left ventricle was divided into 20 segments for the polar map and 17 segments for the visual method. Segments were grouped by anatomical rings (apical, mid, basal) or by coronary artery distribution. For the visual method, 2 nuclear medicine physicians, blinded to treatment groups, scored each segment's perfusion. Scores were analyzed with nonparametric tests and linear regression. Results: Between 2006 and 2010, 57 patients were enrolled and 43 were available for analysis. The cohorts were well matched. The apical and left anterior descending coronary artery segments had significant decreases in perfusion on SPECT scans in both ABC and No-ABC cohorts. In unadjusted and adjusted analyses, controlling for pretreatment perfusion score, age, and chemotherapy, ABC was not significantly associated with prevention of perfusion deficits. Conclusions: In this randomized controlled trial, ABC does not appear to prevent radiation-induced cardiac perfusion deficits.« less

Inference of Transmission Network Structure from HIV Phylogenetic Trees

DOE PAGES

Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan; ...

2017-01-13

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic.more » Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.« less

Inference of Transmission Network Structure from HIV Phylogenetic Trees

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

Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic.more » Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.« less

Agent Based Computing Machine

DTIC Science & Technology

2005-12-09

decision making logic that respond to the environment (concentration of operands - the state vector), and bias or "mood" as established by its history of...mentioned in the chart, there is no need for file management in a ABC Machine. Information is distributed, no history is maintained. The instruction set... Postgresql ) for collection of cluster samples/snapshots over intervals of time. An prototypical example of an XML file to configure and launch the ABC

A novel method for landslide displacement prediction by integrating advanced computational intelligence algorithms.

PubMed

Zhou, Chao; Yin, Kunlong; Cao, Ying; Ahmed, Bayes; Fu, Xiaolin

2018-05-08

Landslide displacement prediction is considered as an essential component for developing early warning systems. The modelling of conventional forecast methods requires enormous monitoring data that limit its application. To conduct accurate displacement prediction with limited data, a novel method is proposed and applied by integrating three computational intelligence algorithms namely: the wavelet transform (WT), the artificial bees colony (ABC), and the kernel-based extreme learning machine (KELM). At first, the total displacement was decomposed into several sub-sequences with different frequencies using the WT. Next each sub-sequence was predicted separately by the KELM whose parameters were optimized by the ABC. Finally the predicted total displacement was obtained by adding all the predicted sub-sequences. The Shuping landslide in the Three Gorges Reservoir area in China was taken as a case study. The performance of the new method was compared with the WT-ELM, ABC-KELM, ELM, and the support vector machine (SVM) methods. Results show that the prediction accuracy can be improved by decomposing the total displacement into sub-sequences with various frequencies and by predicting them separately. The ABC-KELM algorithm shows the highest prediction capacity followed by the ELM and SVM. Overall, the proposed method achieved excellent performance both in terms of accuracy and stability.

An Application of the Difference Potentials Method to Solving External Problems in CFD

NASA Technical Reports Server (NTRS)

Ryaben 'Kii, Victor S.; Tsynkov, Semyon V.

1997-01-01

Numerical solution of infinite-domain boundary-value problems requires some special techniques that would make the problem available for treatment on the computer. Indeed, the problem must be discretized in a way that the computer operates with only finite amount of information. Therefore, the original infinite-domain formulation must be altered and/or augmented so that on one hand the solution is not changed (or changed slightly) and on the other hand the finite discrete formulation becomes available. One widely used approach to constructing such discretizations consists of truncating the unbounded original domain and then setting the artificial boundary conditions (ABC's) at the newly formed external boundary. The role of the ABC's is to close the truncated problem and at the same time to ensure that the solution found inside the finite computational domain would be maximally close to (in the ideal case, exactly the same as) the corresponding fragment of the original infinite-domain solution. Let us emphasize that the proper treatment of artificial boundaries may have a profound impact on the overall quality and performance of numerical algorithms. The latter statement is corroborated by the numerous computational experiments and especially concerns the area of CFD, in which external problems present a wide class of practically important formulations. In this paper, we review some work that has been done over the recent years on constructing highly accurate nonlocal ABC's for calculation of compressible external flows. The approach is based on implementation of the generalized potentials and pseudodifferential boundary projection operators analogous to those proposed first by Calderon. The difference potentials method (DPM) by Ryaben'kii is used for the effective computation of the generalized potentials and projections. The resulting ABC's clearly outperform the existing methods from the standpoints of accuracy and robustness, in many cases noticeably speed up the multigrid convergence, and at the same time are quite comparable to other methods from the standpoints of geometric universality and simplicity of implementation.

A PhoPQ-Regulated ABC Transporter System Exports Tetracycline in Pseudomonas aeruginosa.

PubMed

Chen, Lin; Duan, Kangmin

2016-05-01

Pseudomonas aeruginosa is an important human pathogen whose infections are difficult to treat due to its high intrinsic resistance to many antibiotics. Here, we show that the disruption of PA4456, encoding the ATP binding component of a putative ATP-binding cassette (ABC) transporter, increased the bacterium's susceptible to tetracycline and other antibiotics or toxic chemicals. Fluorescence spectroscopy and antibiotic accumulation tests showed that the interruption of the ABC transporter caused increased intracellular accumulation of tetracycline, demonstrating a role of the ABC transporter in tetracycline expulsion. Site-directed mutagenesis proved that the conserved residues of E170 in the Walker B motif and H203 in the H-loop, which are important for ATP hydrolysis, were essential for the function of PA4456. Through a genome-wide search, the PhoPQ two-component system was identified as a regulator of the computationally predicted PA4456-4452 operon that encodes the ABC transporter system. A >5-fold increase of the expression of this operon was observed in the phoQ mutant. The results obtained also show that the expression of the phzA1B1C1D1E1 operon and the production of pyocyanin were significantly higher in the ABC transporter mutant, signifying a connection between the ABC transporter and pyocyanin production. These results indicated that the PhoPQ-regulated ABC transporter is associated with intrinsic resistance to antibiotics and other adverse compounds in P. aeruginosa, probably by extruding them out of the cell. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Time-dependent density functional theory with twist-averaged boundary conditions

NASA Astrophysics Data System (ADS)

Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.

2016-05-01

Background: Time-dependent density functional theory is widely used to describe excitations of many-fermion systems. In its many applications, three-dimensional (3D) coordinate-space representation is used, and infinite-domain calculations are limited to a finite volume represented by a spatial box. For finite quantum systems (atoms, molecules, nuclei, hadrons), the commonly used periodic or reflecting boundary conditions introduce spurious quantization of the continuum states and artificial reflections from boundary; hence, an incorrect treatment of evaporated particles. Purpose: The finite-volume artifacts for finite systems can be practically cured by invoking an absorbing potential in a certain boundary region sufficiently far from the described system. However, such absorption cannot be applied in the calculations of infinite matter (crystal electrons, quantum fluids, neutron star crust), which suffer from unphysical effects stemming from a finite computational box used. Here, twist-averaged boundary conditions (TABC) have been used successfully to diminish the finite-volume effects. In this work, we extend TABC to time-dependent modes. Method: We use the 3D time-dependent density functional framework with the Skyrme energy density functional. The practical calculations are carried out for small- and large-amplitude electric dipole and quadrupole oscillations of 16O. We apply and compare three kinds of boundary conditions: periodic, absorbing, and twist-averaged. Results: Calculations employing absorbing boundary conditions (ABC) and TABC are superior to those based on periodic boundary conditions. For low-energy excitations, TABC and ABC variants yield very similar results. With only four twist phases per spatial direction in TABC, one obtains an excellent reduction of spurious fluctuations. In the nonlinear regime, one has to deal with evaporated particles. In TABC, the floating nucleon gas remains in the box; the amount of nucleons in the gas is found to be roughly the same as the number of absorbed particles in ABC. Conclusion: We demonstrate that by using TABC, one can reduce finite-volume effects drastically without adding any additional parameters associated with absorption at large distances. Moreover, TABC are an obvious choice for time-dependent calculations for infinite systems. Since TABC calculations for different twists can be performed independently, the method is trivially adapted to parallel computing.

Approximate Bayesian computation for spatial SEIR(S) epidemic models.

PubMed

Brown, Grant D; Porter, Aaron T; Oleson, Jacob J; Hinman, Jessica A

2018-02-01

Approximate Bayesia n Computation (ABC) provides an attractive approach to estimation in complex Bayesian inferential problems for which evaluation of the kernel of the posterior distribution is impossible or computationally expensive. These highly parallelizable techniques have been successfully applied to many fields, particularly in cases where more traditional approaches such as Markov chain Monte Carlo (MCMC) are impractical. In this work, we demonstrate the application of approximate Bayesian inference to spatially heterogeneous Susceptible-Exposed-Infectious-Removed (SEIR) stochastic epidemic models. These models have a tractable posterior distribution, however MCMC techniques nevertheless become computationally infeasible for moderately sized problems. We discuss the practical implementation of these techniques via the open source ABSEIR package for R. The performance of ABC relative to traditional MCMC methods in a small problem is explored under simulation, as well as in the spatially heterogeneous context of the 2014 epidemic of Chikungunya in the Americas. Copyright © 2017 Elsevier Ltd. All rights reserved.

The aggregate site frequency spectrum for comparative population genomic inference.

PubMed

Xue, Alexander T; Hickerson, Michael J

2015-12-01

Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent postglacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multilevel statistical frameworks to test models involving assemblages and/or communities, and as large-scale SNP data from nonmodel species become routine, the aSFS expands the potential for powerful next-generation comparative population genomic inference. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

A MULTIPLE TESTING OF THE ABC METHOD AND THE DEVELOPMENT OF A SECOND GENERATION MODEL. PART I, PRELIMINARY DISCUSSIONS OF METHODOLOGY. SUPPLEMENT, COMPUTER PROGRAMS OF THE HDL INFORMATION SYSTEMS.

ERIC Educational Resources Information Center

ALTMANN, BERTHOLD; BROWN, WILLIAM G.

THE FIRST-GENERATION APPROACH BY CONCEPT (ABC) STORAGE AND RETRIEVAL METHOD, A METHOD WHICH UTILIZES AS A SUBJECT APPROACH APPROPRIATE STANDARDIZED ENGLISH-LANGUAGE STATEMENTS PROCESSED AND PRINTED IN A PERMUTED INDEX FORMAT, UNDERWENT A PERFORMANCE TEST, THE PRIMARY OBJECTIVE OF WHICH WAS TO SPOT DEFICIENCIES AND TO DEVELOP A SECOND-GENERATION…

Multidrug resistance in parasites: ABC transporters, P-glycoproteins and molecular modelling.

PubMed

Jones, P M; George, A M

2005-04-30

Parasitic diseases, caused by protozoa, helminths and arthropods, rank among the most important problems in human and veterinary medicine, and in agriculture, leading to debilitating sicknesses and loss of life. In the absence of vaccines and with the general failure of vector eradication programs, drugs are the main line of defence, but the newest drugs are being tracked by the emergence of resistance in parasites, sharing ominous parallels with multidrug resistance in bacterial pathogens. Any of a number of mechanisms will elicit a drug resistance phenotype in parasites, including: active efflux, reduced uptake, target modification, drug modification, drug sequestration, by-pass shunting, or substrate competition. The role of ABC transporters in parasitic multidrug resistance mechanisms is being subjected to more scrutiny, due in part to the established roles of certain ABC transporters in human diseases, and also to an increasing portfolio of ABC transporters from parasite genome sequencing projects. For example, over 100 ABC transporters have been identified in the Escherichia coli genome, but to date only about 65 in all parasitic genomes. Long established laboratory investigations are now being assisted by molecular biology, bioinformatics, and computational modelling, and it is in these areas that the role of ABC transporters in parasitic multidrug resistance mechanisms may be defined and put in perspective with that of other proteins. We discuss ABC transporters in parasites, and conclude with an example of molecular modelling that identifies a new interaction between the structural domains of a parasite P-glycoprotein.

Artificial bee colony in neuro - Symbolic integration

NASA Astrophysics Data System (ADS)

Kasihmuddin, Mohd Shareduwan Mohd; Sathasivam, Saratha; Mansor, Mohd. Asyraf

2017-08-01

Swarm intelligence is a research area that models the population of the swarm based on natural computation. Artificial bee colony (ABC) algorithm is a swarm based metaheuristic algorithm introduced by Karaboga to optimize numerical problem. Pattern-SAT is a pattern reconstruction paradigm that utilized 2SAT logical rule in representing the behavior of the desired pattern. The information of the desired pattern in terms of 2SAT logic is embedded to Hopfield neural network (HNN-P2SAT) and the desired pattern is reconstructed during the retrieval phase. Since the performance of HNN-P2SAT in Pattern-SAT deteriorates when the number of 2SAT clause increased, newly improved ABC is used to reduce the computation burden during the learning phase of HNN-P2SAT (HNN-P2SATABC). The aim of this study is to investigate the performance of Pattern-SAT produced by ABC incorporated with HNN-P2SAT and compare it with conventional standalone HNN. The comparison is examined by using Microsoft Visual Basic C++ 2013 software. The detailed comparison in doing Pattern-SAT is discussed based on global Pattern-SAT, ratio of activated clauses and computation time. The result obtained from computer simulation indicates the beneficial features of HNN-P2SATABC in doing Pattern-SAT. This finding is expected to result in a significant implication on the choice of searching method used to do Pattern-SAT.

An Asymmetric Birdcage Coil for Small-animal MR Imaging at 7T

PubMed Central

Kim, Kyoung-Nam; Han, Sang-Doc; Seo, Jeung-Hoon; Heo, Phil; Yoo, Dongkyeom; Im, Geun Ho; Lee, Jung Hee

2017-01-01

The birdcage (BC) coil is currently being utilized for uniform radiofrequency (RF) transmit/receive (Tx/Rx) or Tx-only configuration in many magnetic resonance (MR) imaging applications, but insufficient magnetic flux (|B1|) density and their non-uniform distribution still exists in high-field (HF) environments. We demonstrate that the asymmetric birdcage (ABC) transmit/receive (Tx/Rx) volume coil, which is a modified standard birdcage (SBC) coil with the end ring split into two halves, is suitable for improving the |B1| sensitivity in 7T small-animal MR imaging. Cylindrical SBC and ABC coils with 35 mm diameter were constructed and bench tested for mouse body MR imaging at 300 MHz using a 7T scanner. To assess the ABC coil performance, computational electromagnetic (EM) simulation and 7T MR experiment were performed by using a cylindrical phantom and in vivo mouse body and quantitatively compared with the SBC coil in terms of |B1| distribution, RF transmit (|B1+|) field, and signal-to-noise ratio (SNR). The bench measurements of the two BC coils are similar, yielding a quality value (Q-value) of 74.42 for the SBC coil and 77.06 for the ABC coil. The computational calculation results clearly show that the proposed ABC coil offers superior |B1| field and |B1+| field sensitivity in the central axial slice compared with the SBC coil. There was also high SNR and uniformly distributed flip angle (FA) under the loaded condition of mouse body in the 7T experiment. Although ABC geometry allows a further increase in the |B1| field and |B1+| field sensitivity in only the central axial slice, the geometrical modification of the SBC coil can make a high performance RF coil feasible in the central axial slice and also make target imaging possible in the diagonal direction. PMID:27725573

A Large Animal Model that Recapitulates the Spectrum of Human Intervertebral Disc Degeneration

PubMed Central

Gullbrand, Sarah E.; Malhotra, Neil R.; Schaer, Thomas P.; Zawacki, Zosia; Martin, John T.; Bendigo, Justin R.; Milby, Andrew H.; Dodge, George R.; Vresilovic, Edward J.; Elliott, Dawn M.; Mauck, Robert L.; Smith, Lachlan J.

2016-01-01

Objective The objective of this study was to establish a large animal model that recapitulates the spectrum of intervertebral disc degeneration that occurs in humans and which is suitable for pre-clinical evaluation of a wide range of experimental therapeutics. Design Degeneration was induced in the lumbar intervertebral discs of large frame goats by either intradiscal injection of chondroitinase ABC (ChABC) over a range of dosages (0.1U, 1U or 5U) or subtotal nucleotomy. Radiographs were used to assess disc height changes over 12 weeks. Degenerative changes to the discs and endplates were assessed via magnetic resonance imaging (MRI), semi-quantitative histological grading, micro-computed tomography (µCT), and measurement of disc biomechanical properties. Results Degenerative changes were observed for all interventions that ranged from mild (0.1U ChABC) to moderate (1U ChABC and nucleotomy) to severe (5U ChABC). All groups showed progressive reductions in disc height over 12 weeks. Histological scores were significantly increased in the 1U and 5U ChABC groups. Reductions in T2 and T1ρ, and increased Pfirrmann grade were observed on MRI. Resorption and remodeling of the cortical boney endplate adjacent to ChABC injected discs also occurred. Spine segment range of motion was greater and compressive modulus was lower in 1U ChABC and nucleotomy discs compared to intact. Conclusions A large animal model of disc degeneration was established that recapitulates the spectrum of structural, compositional and biomechanical features of human disc degeneration. This model may serve as a robust platform for evaluating the efficacy of therapeutics targeted towards varying degrees of disc degeneration. PMID:27568573

Architectures of Kepler Planet Systems with Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Morehead, Robert C.; Ford, Eric B.

2015-12-01

The distribution of period normalized transit duration ratios among Kepler’s multiple transiting planet systems constrains the distributions of mutual orbital inclinations and orbital eccentricities. However, degeneracies in these parameters tied to the underlying number of planets in these systems complicate their interpretation. To untangle the true architecture of planet systems, the mutual inclination, eccentricity, and underlying planet number distributions must be considered simultaneously. The complexities of target selection, transit probability, detection biases, vetting, and follow-up observations make it impractical to write an explicit likelihood function. Approximate Bayesian computation (ABC) offers an intriguing path forward. In its simplest form, ABC generates a sample of trial population parameters from a prior distribution to produce synthetic datasets via a physically-motivated forward model. Samples are then accepted or rejected based on how close they come to reproducing the actual observed dataset to some tolerance. The accepted samples form a robust and useful approximation of the true posterior distribution of the underlying population parameters. We build on the considerable progress from the field of statistics to develop sequential algorithms for performing ABC in an efficient and flexible manner. We demonstrate the utility of ABC in exoplanet populations and present new constraints on the distributions of mutual orbital inclinations, eccentricities, and the relative number of short-period planets per star. We conclude with a discussion of the implications for other planet occurrence rate calculations, such as eta-Earth.

High order local absorbing boundary conditions for acoustic waves in terms of farfield expansions

NASA Astrophysics Data System (ADS)

Villamizar, Vianey; Acosta, Sebastian; Dastrup, Blake

2017-03-01

We devise a new high order local absorbing boundary condition (ABC) for radiating problems and scattering of time-harmonic acoustic waves from obstacles of arbitrary shape. By introducing an artificial boundary S enclosing the scatterer, the original unbounded domain Ω is decomposed into a bounded computational domain Ω- and an exterior unbounded domain Ω+. Then, we define interface conditions at the artificial boundary S, from truncated versions of the well-known Wilcox and Karp farfield expansion representations of the exact solution in the exterior region Ω+. As a result, we obtain a new local absorbing boundary condition (ABC) for a bounded problem on Ω-, which effectively accounts for the outgoing behavior of the scattered field. Contrary to the low order absorbing conditions previously defined, the error at the artificial boundary induced by this novel ABC can be easily reduced to reach any accuracy within the limits of the computational resources. We accomplish this by simply adding as many terms as needed to the truncated farfield expansions of Wilcox or Karp. The convergence of these expansions guarantees that the order of approximation of the new ABC can be increased arbitrarily without having to enlarge the radius of the artificial boundary. We include numerical results in two and three dimensions which demonstrate the improved accuracy and simplicity of this new formulation when compared to other absorbing boundary conditions.

Frequency domain finite-element and spectral-element acoustic wave modeling using absorbing boundaries and perfectly matched layer

NASA Astrophysics Data System (ADS)

Rahimi Dalkhani, Amin; Javaherian, Abdolrahim; Mahdavi Basir, Hadi

2018-04-01

Wave propagation modeling as a vital tool in seismology can be done via several different numerical methods among them are finite-difference, finite-element, and spectral-element methods (FDM, FEM and SEM). Some advanced applications in seismic exploration benefit the frequency domain modeling. Regarding flexibility in complex geological models and dealing with the free surface boundary condition, we studied the frequency domain acoustic wave equation using FEM and SEM. The results demonstrated that the frequency domain FEM and SEM have a good accuracy and numerical efficiency with the second order interpolation polynomials. Furthermore, we developed the second order Clayton and Engquist absorbing boundary condition (CE-ABC2) and compared it with the perfectly matched layer (PML) for the frequency domain FEM and SEM. In spite of PML method, CE-ABC2 does not add any additional computational cost to the modeling except assembling boundary matrices. As a result, considering CE-ABC2 is more efficient than PML for the frequency domain acoustic wave propagation modeling especially when computational cost is high and high-level absorbing performance is unnecessary.

Autonomic Closure for Turbulent Flows Using Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Doronina, Olga; Christopher, Jason; Hamlington, Peter; Dahm, Werner

2017-11-01

Autonomic closure is a new technique for achieving fully adaptive and physically accurate closure of coarse-grained turbulent flow governing equations, such as those solved in large eddy simulations (LES). Although autonomic closure has been shown in recent a priori tests to more accurately represent unclosed terms than do dynamic versions of traditional LES models, the computational cost of the approach makes it challenging to implement for simulations of practical turbulent flows at realistically high Reynolds numbers. The optimization step used in the approach introduces large matrices that must be inverted and is highly memory intensive. In order to reduce memory requirements, here we propose to use approximate Bayesian computation (ABC) in place of the optimization step, thereby yielding a computationally-efficient implementation of autonomic closure that trades memory-intensive for processor-intensive computations. The latter challenge can be overcome as co-processors such as general purpose graphical processing units become increasingly available on current generation petascale and exascale supercomputers. In this work, we outline the formulation of ABC-enabled autonomic closure and present initial results demonstrating the accuracy and computational cost of the approach.

Approximate Bayesian Computation in the estimation of the parameters of the Forbush decrease model

NASA Astrophysics Data System (ADS)

Wawrzynczak, A.; Kopka, P.

2017-12-01

Realistic modeling of the complicated phenomena as Forbush decrease of the galactic cosmic ray intensity is a quite challenging task. One aspect is a numerical solution of the Fokker-Planck equation in five-dimensional space (three spatial variables, the time and particles energy). The second difficulty arises from a lack of detailed knowledge about the spatial and time profiles of the parameters responsible for the creation of the Forbush decrease. Among these parameters, the central role plays a diffusion coefficient. Assessment of the correctness of the proposed model can be done only by comparison of the model output with the experimental observations of the galactic cosmic ray intensity. We apply the Approximate Bayesian Computation (ABC) methodology to match the Forbush decrease model to experimental data. The ABC method is becoming increasing exploited for dynamic complex problems in which the likelihood function is costly to compute. The main idea of all ABC methods is to accept samples as an approximate posterior draw if its associated modeled data are close enough to the observed one. In this paper, we present application of the Sequential Monte Carlo Approximate Bayesian Computation algorithm scanning the space of the diffusion coefficient parameters. The proposed algorithm is adopted to create the model of the Forbush decrease observed by the neutron monitors at the Earth in March 2002. The model of the Forbush decrease is based on the stochastic approach to the solution of the Fokker-Planck equation.

Global Artificial Boundary Conditions for Computation of External Flow Problems with Propulsive Jets

NASA Technical Reports Server (NTRS)

Tsynkov, Semyon; Abarbanel, Saul; Nordstrom, Jan; Ryabenkii, Viktor; Vatsa, Veer

1998-01-01

We propose new global artificial boundary conditions (ABC's) for computation of flows with propulsive jets. The algorithm is based on application of the difference potentials method (DPM). Previously, similar boundary conditions have been implemented for calculation of external compressible viscous flows around finite bodies. The proposed modification substantially extends the applicability range of the DPM-based algorithm. In the paper, we present the general formulation of the problem, describe our numerical methodology, and discuss the corresponding computational results. The particular configuration that we analyze is a slender three-dimensional body with boat-tail geometry and supersonic jet exhaust in a subsonic external flow under zero angle of attack. Similarly to the results obtained earlier for the flows around airfoils and wings, current results for the jet flow case corroborate the superiority of the DPM-based ABC's over standard local methodologies from the standpoints of accuracy, overall numerical performance, and robustness.

75 FR 2488 - Mid-Atlantic Fishery Management Council; Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-15

... Mid-Atlantic Fishery Management Council's (MAFMC) Scientific and Statistical Committee (SSC) will hold... include new member orientation (overview of Council process and role of the SSC), review and adoption of SSC Standard Operating Practices and Procedures, ABC Control Rule Framework and Council Risk Policy...

ABCs of SLEEPING: A review of the evidence behind pediatric sleep practice recommendations.

PubMed

Allen, Stephanie L; Howlett, Melissa D; Coulombe, J Aimée; Corkum, Penny V

2016-10-01

The ABCs of SLEEPING mnemonic was developed to serve as an organizing framework for common pediatric sleep recommendations. The mnemonic stands for 1) age appropriate bedtimes and wake-times with consistency, 2) schedules and routines, 3) location, 4) exercise and diet, 5) no electronics in the bedroom or before bed, 6) positivity 7) independence when falling asleep and 8) needs of child met during the day, 9) equal great sleep. This review examines the empirical evidence behind the practices and recommendations captured by the ABCs of SLEEPING mnemonic for children aged 1 to 12. A search was conducted of key electronic databases (PubMed, PsycINFO, CINAHL, & EMBASE) to identify English articles that included the concepts of sleep, insomnia, and/or bedtime. 77 articles were eligible for inclusion and were coded to extract key details and findings regarding the relations between sleep practices identified in the ABCs of SLEEPING mnemonic and sleep outcomes. Findings provided preliminary support for many of the recommendations that are commonly made to families regarding healthy sleep practices. However, more robust investigations are needed to better understand the causal contributions of healthy sleep practices to the onset and maintenance of children's sleep problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimal Medical Equipment Maintenance Service Proposal Decision Support System combining Activity Based Costing (ABC) and the Analytic Hierarchy Process (AHP).

PubMed

da Rocha, Leticia; Sloane, Elliot; M Bassani, Jose

2005-01-01

This study describes a framework to support the choice of the maintenance service (in-house or third party contract) for each category of medical equipment based on: a) the real medical equipment maintenance management system currently used by the biomedical engineering group of the public health system of the Universidade Estadual de Campinas located in Brazil to control the medical equipment maintenance service, b) the Activity Based Costing (ABC) method, and c) the Analytic Hierarchy Process (AHP) method. Results show the cost and performance related to each type of maintenance service. Decision-makers can use these results to evaluate possible strategies for the categories of equipment.

Development of the Assessment of Burden of COPD tool: an integrated tool to measure the burden of COPD.

PubMed

Slok, Annerika H M; in 't Veen, Johannes C C M; Chavannes, Niels H; van der Molen, Thys; Rutten-van Mölken, Maureen P M H; Kerstjens, Huib A M; Salomé, Philippe L; Holverda, Sebastiaan; Dekhuijzen, P N Richard; Schuiten, Denise; Asijee, Guus M; van Schayck, Onno C P

2014-07-10

In deciding on the treatment plan for patients with chronic obstructive pulmonary disease (COPD), the burden of COPD as experienced by patients should be the core focus. It is therefore important for daily practice to develop a tool that can both assess the burden of COPD and facilitate communication with patients in clinical practice. This paper describes the development of an integrated tool to assess the burden of COPD in daily practice. A definition of the burden of COPD was formulated by a Dutch expert team. Interviews showed that patients and health-care providers agreed on this definition. We found no existing instruments that fully measured burden of disease according to this definition. However, the Clinical COPD Questionnaire meets most requirements, and was therefore used and adapted. The adapted questionnaire is called the Assessment of Burden of COPD (ABC) scale. In addition, the ABC tool was developed, of which the ABC scale is the core part. The ABC tool is a computer program with an algorithm that visualises outcomes and provides treatment advice. The next step in the development of the tool is to test the validity and effectiveness of both the ABC scale and tool in daily practice.

Development of the Assessment of Burden of COPD tool: an integrated tool to measure the burden of COPD

PubMed Central

Slok, Annerika H M; in ’t Veen, Johannes C C M; Chavannes, Niels H; van der Molen, Thys; Rutten-van Mölken, Maureen P M H; Kerstjens, Huib A M; Salomé, Philippe L; Holverda, Sebastiaan; Dekhuijzen, PN Richard; Schuiten, Denise; Asijee, Guus M; van Schayck, Onno C P

2014-01-01

In deciding on the treatment plan for patients with chronic obstructive pulmonary disease (COPD), the burden of COPD as experienced by patients should be the core focus. It is therefore important for daily practice to develop a tool that can both assess the burden of COPD and facilitate communication with patients in clinical practice. This paper describes the development of an integrated tool to assess the burden of COPD in daily practice. A definition of the burden of COPD was formulated by a Dutch expert team. Interviews showed that patients and health-care providers agreed on this definition. We found no existing instruments that fully measured burden of disease according to this definition. However, the Clinical COPD Questionnaire meets most requirements, and was therefore used and adapted. The adapted questionnaire is called the Assessment of Burden of COPD (ABC) scale. In addition, the ABC tool was developed, of which the ABC scale is the core part. The ABC tool is a computer program with an algorithm that visualises outcomes and provides treatment advice. The next step in the development of the tool is to test the validity and effectiveness of both the ABC scale and tool in daily practice. PMID:25010353

A hybrid artificial bee colony algorithm and pattern search method for inversion of particle size distribution from spectral extinction data

NASA Astrophysics Data System (ADS)

Wang, Li; Li, Feng; Xing, Jian

2017-10-01

In this paper, a hybrid artificial bee colony (ABC) algorithm and pattern search (PS) method is proposed and applied for recovery of particle size distribution (PSD) from spectral extinction data. To be more useful and practical, size distribution function is modelled as the general Johnson's ? function that can overcome the difficulty of not knowing the exact type beforehand encountered in many real circumstances. The proposed hybrid algorithm is evaluated through simulated examples involving unimodal, bimodal and trimodal PSDs with different widths and mean particle diameters. For comparison, all examples are additionally validated by the single ABC algorithm. In addition, the performance of the proposed algorithm is further tested by actual extinction measurements with real standard polystyrene samples immersed in water. Simulation and experimental results illustrate that the hybrid algorithm can be used as an effective technique to retrieve the PSDs with high reliability and accuracy. Compared with the single ABC algorithm, our proposed algorithm can produce more accurate and robust inversion results while taking almost comparative CPU time over ABC algorithm alone. The superiority of ABC and PS hybridization strategy in terms of reaching a better balance of estimation accuracy and computation effort increases its potentials as an excellent inversion technique for reliable and efficient actual measurement of PSD.

A Multiuser Detector Based on Artificial Bee Colony Algorithm for DS-UWB Systems

PubMed Central

Liu, Xiaohui

2013-01-01

Artificial Bee Colony (ABC) algorithm is an optimization algorithm based on the intelligent behavior of honey bee swarm. The ABC algorithm was developed to solve optimizing numerical problems and revealed premising results in processing time and solution quality. In ABC, a colony of artificial bees search for rich artificial food sources; the optimizing numerical problems are converted to the problem of finding the best parameter which minimizes an objective function. Then, the artificial bees randomly discover a population of initial solutions and then iteratively improve them by employing the behavior: moving towards better solutions by means of a neighbor search mechanism while abandoning poor solutions. In this paper, an efficient multiuser detector based on a suboptimal code mapping multiuser detector and artificial bee colony algorithm (SCM-ABC-MUD) is proposed and implemented in direct-sequence ultra-wideband (DS-UWB) systems under the additive white Gaussian noise (AWGN) channel. The simulation results demonstrate that the BER and the near-far effect resistance performances of this proposed algorithm are quite close to those of the optimum multiuser detector (OMD) while its computational complexity is much lower than that of OMD. Furthermore, the BER performance of SCM-ABC-MUD is not sensitive to the number of active users and can obtain a large system capacity. PMID:23983638

[Simple evaluation of numbers of asbestos bodies in bronchoalveolar lavage fluid under light microscopy: analysis of 35 pulmonary nodular lesions].

PubMed

Kawahara, Kunimitsu; Kawasumi, Hiromi; Nagano, Teruaki; Sasada, Shinji; Okamoto, Norio

2008-04-01

More than 1 asbestos body (AB) per ml of bronchoalveolar lavage fluid (BALF) under light microscopy was defined as AB positive (ABP) and suggests an occupational asbestos exposure. We microscopically evaluated the AB number per one ml of BALF, which we defined as the AB concentration (ABC), using bronchoalveolar lavage (BAL) cytocentrifuge slides obtained from 35 patients having pulmonary nodular lesions (20 carcinoma and 15 nonneoplastic disease) and examined the correlation between ABC and clinicopathological data including findings on Helical computed tomography scan (HCTS) and occupational history of asbestos exposure (OHAE). BAL was performed by the standard technique without removing mucous with a gauze filter. AB was microscopically defined as a structure consisting of a core of transparent asbestos surrounded by an iron-protein coat. Twenty of 35 patients were ABP (ABP rate; 57%) and ABC ranged from 0 to 207.98/ml (mean ABC; 11.33/ml). Mean ABC was significantly higher in patients with OHAE (15.04/ml) compared to that in patients without OHAE (3.23/ml). Twenty-two of 35 patients (63%) lacked abnormality on HCTS and among these, 12 patients (55%) were ABP. In 20 pulmonary carcinoma patients, the ABP rate was 85% and ABC ranged from 0 to 31.1/ml (Mean ABC; 2.99/ml). The ABP rate of pulmonary carcinoma patients was 40% (8 patients) and among these, 5 patients (63%) did not show any abnormality on HCTS. In conclusion, our method was simple and useful and should be applied to patients with pulmonary nodular lesions and OHAE, even if there are no abnormalities on HCTS.

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red.

PubMed

Bray, T C; Hall, S J G; Bruford, M W

2014-02-01

Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well-documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree-based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario. © 2013 Blackwell Verlag GmbH.

ABC Tracker: Increasing Teacher Capacity for Assessing Student Behavior

ERIC Educational Resources Information Center

Borgmeier, Chris; Loman, Sheldon L.; Strickland-Cohen, M. Kathleen

2017-01-01

Students with persistent challenging behavior are present in nearly every classroom. Teachers need the knowledge and skills to understand student behavior and intervene effectively. This article presents a framework to guide teachers in understanding student behavior and feasible tools for collecting data about the function of student behavior.…

Framework for Mapping of Receiver Interference Tolerance Masks to Tolerable Effective Isotropic Radiated Power Levels : GPS ABC Workshop V RTCA Washington, DC October 14, 2016.

DOT National Transportation Integrated Search

2016-10-14

Outline : : Interference Tolerance Mask (ITM) to Effective Isotropic Radiated Power (IRP) for the particular case of a single transmitter : : ITM() to IRP() for the general case of multiple transmitters : : Input parameters needed to solv...

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

PubMed

Lopes, J S; Arenas, M; Posada, D; Beaumont, M A

2014-03-01

The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

Reduction of dark-band-like metal artifacts caused by dental implant bodies using hypothetical monoenergetic imaging after dual-energy computed tomography.

PubMed

Tanaka, Ray; Hayashi, Takafumi; Ike, Makiko; Noto, Yoshiyuki; Goto, Tazuko K

2013-06-01

The aim of this study was to evaluate the usefulness of hypothetical monoenergetic images after dual-energy computed tomography (DECT) for assessment of the bone encircling dental implant bodies. Seventy-two axial images of implantation sites clipped out from image data scanned using DECT in dual-energy mode were used. Subjective assessment on reduction of dark-band-like artifacts (R-DBAs) and diagnosability of adjacent bone condition (D-ABC) in 3 sets of DECT images-a fused image set (DE120) and 2 sets of hypothetical monoenergetic images (ME100, ME190)-was performed and the results were statistically analyzed. With regards to R-DBAs and D-ABC, significant differences among DE120, ME100, and ME190 were observed. The ME100 and ME190 images revealed more artifact reduction and diagnosability than those of DE120. DECT imaging followed by hypothetical monoenergetic image construction can cause R-DBAs and increase D-ABC and may be potentially used for the evaluation of postoperative changes in the bone encircling implant bodies. Copyright © 2013 Elsevier Inc. All rights reserved.

The Approximate Bayesian Computation methods in the localization of the atmospheric contamination source

NASA Astrophysics Data System (ADS)

Kopka, P.; Wawrzynczak, A.; Borysiewicz, M.

2015-09-01

In many areas of application, a central problem is a solution to the inverse problem, especially estimation of the unknown model parameters to model the underlying dynamics of a physical system precisely. In this situation, the Bayesian inference is a powerful tool to combine observed data with prior knowledge to gain the probability distribution of searched parameters. We have applied the modern methodology named Sequential Approximate Bayesian Computation (S-ABC) to the problem of tracing the atmospheric contaminant source. The ABC is technique commonly used in the Bayesian analysis of complex models and dynamic system. Sequential methods can significantly increase the efficiency of the ABC. In the presented algorithm, the input data are the on-line arriving concentrations of released substance registered by distributed sensor network from OVER-LAND ATMOSPHERIC DISPERSION (OLAD) experiment. The algorithm output are the probability distributions of a contamination source parameters i.e. its particular location, release rate, speed and direction of the movement, start time and duration. The stochastic approach presented in this paper is completely general and can be used in other fields where the parameters of the model bet fitted to the observable data should be found.

An ABC estimate of pedigree error rate: application in dog, sheep and cattle breeds.

PubMed

Leroy, G; Danchin-Burge, C; Palhiere, I; Baumung, R; Fritz, S; Mériaux, J C; Gautier, M

2012-06-01

On the basis of correlations between pairwise individual genealogical kinship coefficients and allele sharing distances computed from genotyping data, we propose an approximate Bayesian computation (ABC) approach to assess pedigree file reliability through gene-dropping simulations. We explore the features of the method using simulated data sets and show precision increases with the number of markers. An application is further made with five dog breeds, four sheep breeds and one cattle breed raised in France and displaying various characteristics and population sizes, using microsatellite or SNP markers. Depending on the breeds, pedigree error estimations range between 1% and 9% in dog breeds, 1% and 10% in sheep breeds and 4% in cattle breeds. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Multiple sequence alignment using multi-objective based bacterial foraging optimization algorithm.

PubMed

Rani, R Ranjani; Ramyachitra, D

2016-12-01

Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution. It employs Multi-objective, such as: Maximization of Similarity, Non-gap percentage, Conserved blocks and Minimization of gap penalty. BAliBASE 3.0 benchmark database was utilized to examine the proposed algorithm against other methods In this paper, two algorithms have been proposed: Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC) and Bacterial Foraging Optimization Algorithm. It was found that Hybrid Genetic Algorithm with Artificial Bee Colony performed better than the existing optimization algorithms. But still the conserved blocks were not obtained using GA-ABC. Then BFO was used for the alignment and the conserved blocks were obtained. The proposed Multi-Objective Bacterial Foraging Optimization Algorithm (MO-BFO) was compared with widely used MSA methods Clustal Omega, Kalign, MUSCLE, MAFFT, Genetic Algorithm (GA), Ant Colony Optimization (ACO), Artificial Bee Colony (ABC), Particle Swarm Optimization (PSO) and Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC). The final results show that the proposed MO-BFO algorithm yields better alignment than most widely used methods. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Self-Handicapping and Irrational Beliefs about Approval in a Sample of Teacher Candidates

ERIC Educational Resources Information Center

Kaya, Çinar; Ugur, Erol; Sar, Ali Haydar; Ercengiz, Mustafa

2017-01-01

The main objective of the current study is to examine the relationships between self-handicapping, and irrational beliefs about approval, irrational beliefs about interpersonal relationships, irrational beliefs about self and the overall level of irrational beliefs by reference to the " ABC " framework. Participants of the study were 263…

Arnold Diffusion of Charged Particles in ABC Magnetic Fields

NASA Astrophysics Data System (ADS)

Luque, Alejandro; Peralta-Salas, Daniel

2017-06-01

We prove the existence of diffusing solutions in the motion of a charged particle in the presence of ABC magnetic fields. The equations of motion are modeled by a 3DOF Hamiltonian system depending on two parameters. For small values of these parameters, we obtain a normally hyperbolic invariant manifold and we apply the so-called geometric methods for a priori unstable systems developed by A. Delshams, R. de la Llave and T.M. Seara. We characterize explicitly sufficient conditions for the existence of a transition chain of invariant tori having heteroclinic connections, thus obtaining global instability (Arnold diffusion). We also check the obtained conditions in a computer-assisted proof. ABC magnetic fields are the simplest force-free-type solutions of the magnetohydrodynamics equations with periodic boundary conditions, and can be considered as an elementary model for the motion of plasma-charged particles in a tokamak.

Performance advantages of CPML over UPML absorbing boundary conditions in FDTD algorithm

NASA Astrophysics Data System (ADS)

Gvozdic, Branko D.; Djurdjevic, Dusan Z.

2017-01-01

Implementation of absorbing boundary condition (ABC) has a very important role in simulation performance and accuracy in finite difference time domain (FDTD) method. The perfectly matched layer (PML) is the most efficient type of ABC. The aim of this paper is to give detailed insight in and discussion of boundary conditions and hence to simplify the choice of PML used for termination of computational domain in FDTD method. In particular, we demonstrate that using the convolutional PML (CPML) has significant advantages in terms of implementation in FDTD method and reducing computer resources than using uniaxial PML (UPML). An extensive number of numerical experiments has been performed and results have shown that CPML is more efficient in electromagnetic waves absorption. Numerical code is prepared, several problems are analyzed and relative error is calculated and presented.

Drift of Phase Fluctuations in the ABC Model

NASA Astrophysics Data System (ADS)

Bertini, Lorenzo; Buttà, Paolo

2013-07-01

In a recent work, Bodineau and Derrida analyzed the phase fluctuations in the ABC model. In particular, they computed the asymptotic variance and, on the basis of numerical simulations, they conjectured the presence of a drift, which they guessed to be an antisymmetric function of the three densities. By assuming the validity of the fluctuating hydrodynamic approximation, we prove the presence of such a drift, providing an analytical expression for it. This expression is then shown to be an antisymmetric function of the three densities. The antisymmetry of the drift can also be inferred from a symmetry property of the underlying microscopic dynamics.

Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

PubMed

Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

2014-10-01

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus. © 2014 John Wiley & Sons Ltd.

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.

PubMed

Slater, Graham J; Harmon, Luke J; Wegmann, Daniel; Joyce, Paul; Revell, Liam J; Alfaro, Michael E

2012-03-01

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

High-order Two-way Artificial Boundary Conditions for Nonlinear Wave Propagation with Backscattering

NASA Technical Reports Server (NTRS)

Fibich, Gadi; Tsynkov, Semyon

2000-01-01

When solving linear scattering problems, one typically first solves for the impinging wave in the absence of obstacles. Then, by linear superposition, the original problem is reduced to one that involves only the scattered waves driven by the values of the impinging field at the surface of the obstacles. In addition, when the original domain is unbounded, special artificial boundary conditions (ABCs) that would guarantee the reflectionless propagation of waves have to be set at the outer boundary of the finite computational domain. The situation becomes conceptually different when the propagation equation is nonlinear. In this case the impinging and scattered waves can no longer be separated, and the problem has to be solved in its entirety. In particular, the boundary on which the incoming field values are prescribed, should transmit the given incoming waves in one direction and simultaneously be transparent to all the outgoing waves that travel in the opposite direction. We call this type of boundary conditions two-way ABCs. In the paper, we construct the two-way ABCs for the nonlinear Helmholtz equation that models the laser beam propagation in a medium with nonlinear index of refraction. In this case, the forward propagation is accompanied by backscattering, i.e., generation of waves in the direction opposite to that of the incoming signal. Our two-way ABCs generate no reflection of the backscattered waves and at the same time impose the correct values of the incoming wave. The ABCs are obtained for a fourth-order accurate discretization to the Helmholtz operator; the fourth-order grid convergence is corroborated experimentally by solving linear model problems. We also present solutions in the nonlinear case using the two-way ABC which, unlike the traditional Dirichlet boundary condition, allows for direct calculation of the magnitude of backscattering.

Sexism in School Textbooks Prepared under Education Reform in Turkey

ERIC Educational Resources Information Center

Esen, Yasemin

2007-01-01

The objective of this study is to analyze the new textbooks prepared under the framework of the "curriculum reform" realized in Turkey , as part of the EU harmonization process, in terms of gender representation. For this purpose, illustrations in the new ABC, Life Studies and Social Studies textbooks prepared under the new program were…

Assessments Used to Diagnose Developmental Coordination Disorder: Do Their Underlying Constructs Match the Diagnostic Criteria?

ERIC Educational Resources Information Center

Darsaklis, Vasiliki; Snider, Laurie M.; Majnemer, Annette; Mazer, Barbara

2013-01-01

This study examined the constructs underlying the Movement Assessment Battery for Children-2 (M-ABC-2), Bruninks-Oseretsky Test of Motor Proficiency (BOTMP) and Vineland Adaptive Behavior Scale-2 (VABS-2) using the framework of the International Classification of Functioning Disability and Health--Child Youth version (ICF-CY) and the diagnostic…

Computer Simulation of the Virulome of Bacillus anthracis Using Proteomics

DTIC Science & Technology

2006-07-31

hypothetical protein gi|47526566 spermidine /putrescine ABC transporter, spermidine /putrescine-binding protein gi|47526625 oligoendopeptidase F, putative gi...glutamyl-trna(gln) amidotransferase, a subunit x gi|50196927 aspartate aminotransferase x gi|50196970 spermidine synthase x

The ABC's of Delivering A Research-Driven Adventure Learning Program From the Field

NASA Astrophysics Data System (ADS)

Pregont, P.; Porsild, M.

2008-12-01

A is for anchoring the delivery of your research to your audience in a standard-aligned curriculum. B is for BGAN Satellite Communication System assisting in delivering real-time authentic media. C is for a collaborative online learning environment to engage learners" Z is for the peaceful sleep you will get once your program is up and running! As part of Team GoNorth! (http://www.PolarHusky.com) it is our job to deliver adventure learning. We set out to do this back when the computer was a 4-foot, 50-lb box powered by a hand-crank where one would have a window of ten minutes in a 24-hour period to catch the satellite (before Al Gore created the Internet!). Every year we review the quantum leaps in what is now possible from the field and in the classroom, and over the years we have wrestled technical issues, solutions and numerous re-structures in the process of our of curriculum development. With this presentation we will provide some basic ABC's on how you can remained focused on your research, yet deliver an adventure learning program for learners to investigate real-world issues within your scientific research. Our scales are most likely different. The volume of our curriculum is an annual production of 4-500 pages to be used from Kindergarden through 12th grade around the world. The framework of our online learning environment must be able to supports millions of users at a time. "In the field" means on a a 3-4 month dogsled expedition - so sending out our live updates involve thawing out the computers and setting up the satellite communication system to work in a ground blizzard! But regardless of the scope and location of your field research, you can probably build on some of our experiences in the planning of an upcoming adventure learning program to engage learners of all or any ages in your scientific explorations!

Standardized reporting of bleeding complications for clinical investigations in acute coronary syndromes: a proposal from the academic bleeding consensus (ABC) multidisciplinary working group.

PubMed

Rao, Sunil V; Eikelboom, John; Steg, Ph Gabriel; Lincoff, A Michael; Weintraub, William S; Bassand, Jean-Pierre; Rao, A Koneti; Gibson, C Michael; Petersen, John L; Mehran, Roxana; Manoukian, Steven V; Charnigo, Richard; Lee, Kerry L; Moscucci, Mauro; Harrington, Robert A

2009-12-01

Clinical trials of antithrombotic agents for the treatment of ACS routinely assess bleeding as a safety endpoint, but variation in bleeding definitions makes comparison of the relative safety of these agents difficult. The ABC Multidisciplinary Working Group, an informal working group comprising clinical researchers and representatives from the US Food and Drug Administration, the National Institutes of Health, and the pharmaceutical industry, sought to develop a consensus approach to measuring the incidence and severity of bleeding complications during clinical trials of acute coronary syndromes (ACS). A meeting of the ABC was convened in April 2008 in Washington, DC, with the goal of developing a consensus approach to measuring the incidence and severity of hemorrhagic complications during clinical trials of ACS. Relevant literature on bleeding was reviewed through a series of short lectures and intensive group discussion. Using existing evidence on bleeding and outcomes as well as clinical judgment, criteria for the assessment of bleeding were developed through expert consensus. This consensus statement divides bleeding-related data elements into three categories: essential, recommended, and optional. The ABC Group recommendations for collection and reporting of bleeding complications provide a framework for consistency in the collection of information on hemorrhagic complications in trials of ACS. Widespread adoption of the statement recommendations will facilitate understanding of the mechanisms of adverse outcomes after bleeding and comparisons of the relative safety of antithrombotic agents, as well as the interpretation of safety results from future studies.

Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters.

PubMed

Tieleman, D Peter

2006-10-01

A key function of biological membranes is to provide mechanisms for the controlled transport of ions, nutrients, metabolites, peptides and proteins between a cell and its environment. We are using computer simulations to study several processes involved in transport. In model membranes, the distribution of small molecules can be accurately calculated; we are making progress towards understanding the factors that determine the partitioning behaviour in the inhomogeneous lipid environment, with implications for drug distribution, membrane protein folding and the energetics of voltage gating. Lipid bilayers can be simulated at a scale that is sufficiently large to study significant defects, such as those caused by electroporation. Computer simulations of complex membrane proteins, such as potassium channels and ATP-binding cassette (ABC) transporters, can give detailed information about the atomistic dynamics that form the basis of ion transport, selectivity, conformational change and the molecular mechanism of ATP-driven transport. This is illustrated in the present review with recent simulation studies of the voltage-gated potassium channel KvAP and the ABC transporter BtuCD.

Skull removal in MR images using a modified artificial bee colony optimization algorithm.

PubMed

Taherdangkoo, Mohammad

2014-01-01

Removal of the skull from brain Magnetic Resonance (MR) images is an important preprocessing step required for other image analysis techniques such as brain tissue segmentation. In this paper, we propose a new algorithm based on the Artificial Bee Colony (ABC) optimization algorithm to remove the skull region from brain MR images. We modify the ABC algorithm using a different strategy for initializing the coordinates of scout bees and their direction of search. Moreover, we impose an additional constraint to the ABC algorithm to avoid the creation of discontinuous regions. We found that our algorithm successfully removed all bony skull from a sample of de-identified MR brain images acquired from different model scanners. The obtained results of the proposed algorithm compared with those of previously introduced well known optimization algorithms such as Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO) demonstrate the superior results and computational performance of our algorithm, suggesting its potential for clinical applications.

Analysis of cylindrical wrap-around and doubly conformal patch antennas by way of the finite element-artificial absorber method

NASA Technical Reports Server (NTRS)

Volakis, J. L.; Kempel, L. C.; Sliva, R.; Wang, H. T. G.; Woo, A. G.

1994-01-01

The goal of this project was to develop analysis codes for computing the scattering and radiation of antennas on cylindrically and doubly conformal platforms. The finite element-boundary integral (FE-BI) method has been shown to accurately model the scattering and radiation of cavity-backed patch antennas. Unfortunately extension of this rigorous technique to coated or doubly curved platforms is cumbersome and inefficient. An alternative approximate approach is to employ an absorbing boundary condition (ABC) for terminating the finite element mesh thus avoiding use of a Green's function. A FE-ABC method is used to calculate the radar cross section (RCS) and radiation pattern of a cavity-backed patch antenna which is recessed within a metallic surface. It is shown that this approach is accurate for RCS and antenna pattern calculations with an ABC surface displaced as little as 0.3 lambda from the cavity aperture. These patch antennas may have a dielectric overlay which may also be modeled with this technique.

The ABC's of Screen Design: What Teachers Should Know To Teach Students To Author in Hypermedia.

ERIC Educational Resources Information Center

Dana, Ann S.; Handler, Marianne G.

The alphabet can be used as a framework for identifying key issues, ideas, and factors that teachers and students need to consider in developing hypermedia projects. Rather than in alphabetical order, the terms are introduced as they apply to the discussion on the teaching of multimedia skills. The following terms and concepts are highlighted:…

[Polymorphisms of killer cell immunoglobulin-like receptor and its ligand HLA-I gene among northern Chinese Han population].

PubMed

Wu, Lingyan; Xie, Zhengde; Liu, Yali; Ai, Junhong; Liu, Chunyan; Shen, Kunling

2015-10-01

OBJECTIVE To investigate the distribution of killer cell immunoglobulin-like receptors (KIR) and their specific ligands human leukocyte antigen-I (HLA-I) gene in northern China. METHODS One hundred and eighty-four unrelated northern Chinese Han individuals were recruited. Genotypes of the KIR and HLA-ABC genes were studied by sequence-specific primer polymerase chain reaction (SSP-PCR). RESULTS Sixteen KIR genes were detected among the 184 unrelated individuals. In all individuals, the four framework genes were present. The frequencies for those carrying the remaining 12 KIR genes have ranged from 16.3% to 99.5%. Twenty-four KIR genotypes were identified, for which half were detected in a single individual. A new genotype comprised of KIR2DL3, 3DL1, 2DP1 and the framework genes was detected in one subject. Respectively, 12, 27 and 11 specificities of HLA alleles were identified on the HLA-A, B, C loci. CONCLUSION The distribution of polymorphisms of KIR and its ligand HLA-ABC genes among northern Chinese Han population have been ascertained. The frequencies of 9 KIR/HLA combinations in the above population have been determined for the first time.

Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius

PubMed Central

FOUNTAIN, TOBY; DUVAUX, LUDOVIC; HORSBURGH, GAVIN; REINHARDT, KLAUS; BUTLIN, ROGER K

2014-01-01

The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonization, that is, to metapopulation dynamics. Pest control limits the lifespan of subpopulations, causing frequent local extinctions, and human-facilitated dispersal allows the colonization of empty patches. Founder events often result in drastic reductions in diversity and an increased influence of genetic drift. Coupled with restricted migration, this can lead to rapid population differentiation. We therefore predicted strong population structuring. Here, using 21 newly characterized microsatellite markers and approximate Bayesian computation (ABC), we investigate simplified versions of two classical models of metapopulation dynamics, in a coalescent framework, to estimate the number and genetic composition of founders in the common bed bug. We found very limited diversity within infestations but high degrees of structuring across the city of London, with extreme levels of genetic differentiation between infestations (FST = 0.59). ABC results suggest a common origin of all founders of a given subpopulation and that the numbers of colonists were low, implying that even a single mated female is enough to found a new infestation successfully. These patterns of colonization are close to the predictions of the propagule pool model, where all founders originate from the same parental infestation. These results show that aspects of metapopulation dynamics can be captured in simple models and provide insights that are valuable for the future targeted control of bed bug infestations. PMID:24446663

Evolutionary algorithms for the optimal management of coastal groundwater: A comparative study toward future challenges

NASA Astrophysics Data System (ADS)

Ketabchi, Hamed; Ataie-Ashtiani, Behzad

2015-01-01

This paper surveys the literature associated with the application of evolutionary algorithms (EAs) in coastal groundwater management problems (CGMPs). This review demonstrates that previous studies were mostly relied on the application of limited and particular EAs, mainly genetic algorithm (GA) and its variants, to a number of specific problems. The exclusive investigation of these problems is often not the representation of the variety of feasible processes may be occurred in coastal aquifers. In this study, eight EAs are evaluated for CGMPs. The considered EAs are: GA, continuous ant colony optimization (CACO), particle swarm optimization (PSO), differential evolution (DE), artificial bee colony optimization (ABC), harmony search (HS), shuffled complex evolution (SCE), and simplex simulated annealing (SIMPSA). The first application of PSO, ABC, HS, and SCE in CGMPs is reported here. Moreover, the four benchmark problems with different degree of difficulty and variety are considered to address the important issues of groundwater resources in coastal regions. Hence, the wide ranges of popular objective functions and constraints with the number of decision variables ranging from 4 to 15 are included. These benchmark problems are applied in the combined simulation-optimization model to examine the optimization scenarios. Some preliminary experiments are performed to select the most efficient parameters values for EAs to set a fair comparison. The specific capabilities of each EA toward CGMPs in terms of results quality and required computational time are compared. The evaluation of the results highlights EA's applicability in CGMPs, besides the remarkable strengths and weaknesses of them. The comparisons show that SCE, CACO, and PSO yield superior solutions among the EAs according to the quality of solutions whereas ABC presents the poor performance. CACO provides the better solutions (up to 17%) than the worst EA (ABC) for the problem with the highest decision variables and more complexity. In terms of computational time, PSO and SIMPSA are the fastest. SCE needs the highest computational time, even up to four times in comparison to the fastest EAs. CACO and PSO can be recommended for application in CGMPs, in terms of both abovementioned criteria.

Phase behavior of model ABC triblock copolymers

NASA Astrophysics Data System (ADS)

Chatterjee, Joon

The phase behavior of poly(isoprene-b-styrene- b-ethylene oxide) (ISO), a model ABC triblock copolymer has been studied. This class of materials exhibit self-assembly, forming a large array of ordered morphologies at length scales of 5-100 nm. The formation of stable three-dimensionally continuous network morphologies is of special interest in this study. Since these nanostructures considerably impact the material properties, fundamental knowledge for designing ABC systems have high technological importance for realizing applications in the areas of nanofabrication, nanoporous media, separation membranes, drug delivery and high surface area catalysts. A comprehensive framework was developed to describe the phase behavior of the ISO triblock copolymers at weak to intermediate segregation strengths spanning a wide range of composition. Phases were characterized through a combination of characterization techniques, including small angle x-ray scattering, dynamic mechanical spectroscopy, transmission electron microscopy, and birefringence measurements. Combined with previous investigations on ISO, six different stable ordered state symmetries have been identified: lamellae (LAM), Fddd orthorhombic network (O70), double gyroid (Q230), alternating gyroid (Q214), hexagonal (HEX), and body-centered cubic (BCC). The phase map was found to be somewhat asymmetric around the fI = fO isopleth. This work provides a guide for theoretical studies and gives insight into the intricate effects of various parameters on the self-assembly of ABC triblock copolymers. Experimental SAXS data evaluated with a simple scattering intensity model show that local mixing varies continuously across the phase map between states of two- and three-domain segregation. Strategies of blending homopolymers with ISO triblock copolymer were employed for studying the swelling properties of a lamellar state. Results demonstrate that lamellar domains swell or shrink depending upon the type of homopolymer that was mixed. The results provide insight into the chain conformation of ABC triblock copolymers, where the B blocks are completely bridged across the adjacent A and C domains. In the final part of the thesis, the swelling properties were used to study the directed assembly of ABC triblock copolymers on chemically nanopatterned surfaces.

ATP-induced conformational changes of nucleotide-binding domains in an ABC transporter. Importance of the water-mediated entropic force.

PubMed

Hayashi, Tomohiko; Chiba, Shuntaro; Kaneta, Yusuke; Furuta, Tadaomi; Sakurai, Minoru

2014-11-06

ATP binding cassette (ABC) proteins belong to a superfamily of active transporters. Recent experimental and computational studies have shown that binding of ATP to the nucleotide binding domains (NBDs) of ABC proteins drives the dimerization of NBDs, which, in turn, causes large conformational changes within the transmembrane domains (TMDs). To elucidate the active substrate transport mechanism of ABC proteins, it is first necessary to understand how the NBD dimerization is driven by ATP binding. In this study, we selected MalKs (NBDs of a maltose transporter) as a representative NBD and calculated the free-energy change upon dimerization using molecular mechanics calculations combined with a statistical thermodynamic theory of liquids, as well as a method to calculate the translational, rotational, and vibrational entropy change. This combined method is applied to a large number of snapshot structures obtained from molecular dynamics simulations containing explicit water molecules. The results suggest that the NBD dimerization proceeds with a large gain of water entropy when ATP molecules bind to the NBDs. The energetic gain arising from direct NBD-NBD interactions is canceled by the dehydration penalty and the configurational-entropy loss. ATP hydrolysis induces a loss of the shape complementarity between the NBDs, which leads to the dissociation of the dimer, due to a decrease in the water-entropy gain and an increase in the configurational-entropy loss. This interpretation of the NBD dimerization mechanism in concert with ATP, especially focused on the water-mediated entropy force, is potentially applicable to a wide variety of the ABC transporters.

Inferring the mode of origin of polyploid species from next-generation sequence data.

PubMed

Roux, Camille; Pannell, John R

2015-03-01

Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels. © 2015 John Wiley & Sons Ltd.

Results of cement augmentation and curettage in aneurysmal bone cyst of spine

PubMed Central

Basu, Saumyajit; Patel, Dharmesh R; Dhakal, Gaurav; Sarangi, T

2016-01-01

Aneurysmal bone cyst (ABC) is a vascular tumor of the spine. Management of spinal ABC still remains controversial because of its location, vascular nature and incidence of recurrence. In this manuscript, we hereby describe two cases of ABC spine treated by curettage, vertebral cement augmentation for control of bleeding and internal stabilization with two years followup. To the best of our knowledge, this is the first case report in the literature describing the role of cement augmentation in spinal ABC in controlling vascular bleeding in curettage of ABC of spine. Case 1: A 22 year old male patient presented with chronic back pain. On radiological investigation, there were multiple, osteolytic septite lesions at L3 vertebral body without neural compression or instability. Percutaneous transpedicular biopsy of L3 from involved pedicle was done. This was followed by cement augmentation through the uninvolved pedicle. Next, transpedicular complete curettage was done through involved pedicle. Case 2: A 15-year-old female presented with nonradiating back pain and progressive myelopathy. On radiological investigation, there was an osteolytic lesion at D9. At surgery, decompression, pedicle screw-rod fixation and posterolateral fusion from D7 to D11 was done. At D9 level, through normal pedicle cement augmentation was added to provide anterior column support and to control the expected bleeding following curettage. Transpedicular complete curettage was done through the involved pedicle with controlled bleeding at the surgical field. Cement augmentation was providing controlled bleeding at surgical field during curettage, internal stabilization and control of pain. On 2 years followup, pain was relieved and there was a stable spinal segment with well filled cement without any sign of recurrence in computed tomography scan. In selected cases of spinal ABC with single vertebral, single pedicle involvement; cement augmentation of vertebra through normal pedicle has an important role in surgery aimed for curettage of vertebra. PMID:26955184

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

Cheung, Y; Rahimi, A; Sawant, A

Purpose: Active breathing control (ABC) has been used to reduce treatment margin due to respiratory organ motion by enforcing temporary breath-holds. However, in practice, even if the ABC device indicates constant lung volume during breath-hold, the patient may still exhibit minor chest motion. Consequently, therapists are given a false sense of security that the patient is immobilized. This study aims at quantifying such motion during ABC breath-holds by monitoring the patient chest motion using a surface photogrammetry system, VisionRT. Methods: A female patient with breast cancer was selected to evaluate chest motion during ABC breath-holds. During the entire course ofmore » treatment, the patient’s chest surface was monitored by a surface photogrammetry system, VisionRT. Specifically, a user-defined region-of-interest (ROI) on the chest surface was selected for the system to track at a rate of ∼3Hz. The surface motion was estimated by rigid image registration between the current ROI image captured and a reference image. The translational and rotational displacements computed were saved in a log file. Results: A total of 20 fractions of radiation treatment were monitored by VisionRT. After removing noisy data, we obtained chest motion of 79 breath-hold sessions. Mean chest motion in AP direction during breath-holds is 1.31mm with 0.62mm standard deviation. Of the 79 sessions, the patient exhibited motion ranging from 0–1 mm (30 sessions), 1–2 mm (37 sessions), 2–3 mm (11 sessions) and >3 mm (1 session). Conclusion: Contrary to popular assumptions, the patient is not completely still during ABC breath-hold sessions. In this particular case studied, the patient exhibited chest motion over 2mm in 14 out of 79 breath-holds. Underestimating treatment margin for radiation therapy with ABC could reduce treatment effectiveness due to geometric miss or overdose of critical organs. The senior author receives research funding from NIH, VisionRT, Varian Medical Systems and Elekta.« less

Artificial blood circulation: stabilization, physiological control, and optimization.

PubMed

Lerner, A Y

1990-04-01

The requirements for creating an efficient Artificial Blood Circulation System (ABCS) have been determined. A hierarchical three-level adaptive control system is suggested for ABCS to solve the following problems: stabilization of the circulation conditions, left and right pump coordination, physiological control for maintaining a proper relation between the cardiac output and the level of gas exchange required for metabolism, and optimization of the system behavior. The adaptations to varying load and body parameters will be accomplished using the signals which characterize the real-time computer-processed values of correlations between the changes in hydraulic resistance of blood vessels, or the changes in aortic pressure, and the oxygen (or carbon dioxide) concentration.

On Topological Indices of Certain Dendrimer Structures

NASA Astrophysics Data System (ADS)

Aslam, Adnan; Bashir, Yasir; Ahmad, Safyan; Gao, Wei

2017-05-01

A topological index can be considered as transformation of chemical structure in to real number. In QSAR/QSPR study, physicochemical properties and topological indices such as Randić, Zagreb, atom-bond connectivity ABC, and geometric-arithmetic GA index are used to predict the bioactivity of chemical compounds. Dendrimers are highly branched, star-shaped macromolecules with nanometer-scale dimensions. Dendrimers are defined by three components: a central core, an interior dendritic structure (the branches), and an exterior surface with functional surface groups. In this paper we determine generalised Randić, general Zagreb, general sum-connectivity indices of poly(propyl) ether imine, porphyrin, and zinc-Porphyrin dendrimers. We also compute ABC and GA indices of these families of dendrimers.

DFT study of the polarization behaviors of various distorted barium titanate crystals: The role of atomic displacements

NASA Astrophysics Data System (ADS)

Mirseraji, Mojtaba; Shahraki, Mehran Gholipour

2018-06-01

A Local Density Approximation (LDA) was employed to investigate the influence of applied strains on valence charge distributions, atomic displacements, Tisbnd O (3) bond distances and the total polarizations in barium titanate (BaTiO3). Four types of various strains were imposed on perfect tetragonal BaTiO3 along the a, c, ab and abc axial directions. Electromechanical properties of BaTiO3 were evaluated in LDA framework and a good agreement with previous results was achieved. The results show that, in the cases of a, ab strains, the values of polarization are almost constant in negative strains and increased by gradual increasing of the positive strains after a sudden enhancement at about +0.1% strain. In the case of c-strain, axial oxygen and Ti atoms underwent the highest displacements and the polarization linearly increased by applied strain. The case of abc-strain, represent the both types of features. In negative abc-strain show a similar polarization behavior like c-strain case and in positive region, polarization behavior is the same as a- and ab-strain cases. In the abc-strains of -0.3% and +0.1%, an abrupt jump in total polarization curve and a small change, are observed due to abnormal atomic displacements. In the most cases a direct relation between polarization and Tisbnd O (3) bond distance was also beheld. Finally, the effects of valence charge distributions on the atomic displacements and total polarizations are studied. It is found that there is a direct relation between polarization and Valence Charge Asymmetry of 3d -orbitals.

The short version of the Activities-specific Balance Confidence (ABC) scale: its validity, reliability, and relationship to balance impairment and falls in older adults.

PubMed

Schepens, Stacey; Goldberg, Allon; Wallace, Melissa

2010-01-01

A shortened version of the ABC 16-item scale (ABC-16), the ABC-6, has been proposed as an alternative balance confidence measure. We investigated whether the ABC-6 is a valid and reliable measure of balance confidence and examined its relationship to balance impairment and falls in older adults. Thirty-five community-dwelling older adults completed the ABC-16, including the 6 questions of the ABC-6. They also completed the following clinical balance tests: unipedal stance time (UST), functional reach (FR), Timed Up and Go (TUG), and maximum step length (MSL). Participants reported 12-month falls history. Balance confidence on the ABC-6 was significantly lower than on the ABC-16, however scores were highly correlated. Fallers reported lower balance confidence than non-fallers as measured by the ABC-6 scale, but confidence did not differ between the groups with the ABC-16. The ABC-6 significantly correlated with all balance tests assessed and number of falls. The ABC-16 significantly correlated with all balance tests assessed, but not with number of falls. Test-retest reliability for the ABC-16 and ABC-6 was good to excellent. The ABC-6 is a valid and reliable measure of balance confidence in community-dwelling older adults, and shows stronger relationships to falls than does the ABC-16. The ABC-6 may be a more useful balance confidence assessment tool than the ABC-16. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

Image steganalysis using Artificial Bee Colony algorithm

NASA Astrophysics Data System (ADS)

Sajedi, Hedieh

2017-09-01

Steganography is the science of secure communication where the presence of the communication cannot be detected while steganalysis is the art of discovering the existence of the secret communication. Processing a huge amount of information takes extensive execution time and computational sources most of the time. As a result, it is needed to employ a phase of preprocessing, which can moderate the execution time and computational sources. In this paper, we propose a new feature-based blind steganalysis method for detecting stego images from the cover (clean) images with JPEG format. In this regard, we present a feature selection technique based on an improved Artificial Bee Colony (ABC). ABC algorithm is inspired by honeybees' social behaviour in their search for perfect food sources. In the proposed method, classifier performance and the dimension of the selected feature vector depend on using wrapper-based methods. The experiments are performed using two large data-sets of JPEG images. Experimental results demonstrate the effectiveness of the proposed steganalysis technique compared to the other existing techniques.

Hematoma Shape, Hematoma Size, Glasgow Coma Scale Score and ICH Score: Which Predicts the 30-Day Mortality Better for Intracerebral Hematoma?

PubMed Central

Wang, Chih-Wei; Liu, Yi-Jui; Lee, Yi-Hsiung; Hueng, Dueng-Yuan; Fan, Hueng-Chuen; Yang, Fu-Chi; Hsueh, Chun-Jen; Kao, Hung-Wen; Juan, Chun-Jung; Hsu, Hsian-He

2014-01-01

Purpose To investigate the performance of hematoma shape, hematoma size, Glasgow coma scale (GCS) score, and intracerebral hematoma (ICH) score in predicting the 30-day mortality for ICH patients. To examine the influence of the estimation error of hematoma size on the prediction of 30-day mortality. Materials and Methods This retrospective study, approved by a local institutional review board with written informed consent waived, recruited 106 patients diagnosed as ICH by non-enhanced computed tomography study. The hemorrhagic shape, hematoma size measured by computer-assisted volumetric analysis (CAVA) and estimated by ABC/2 formula, ICH score and GCS score was examined. The predicting performance of 30-day mortality of the aforementioned variables was evaluated. Statistical analysis was performed using Kolmogorov-Smirnov tests, paired t test, nonparametric test, linear regression analysis, and binary logistic regression. The receiver operating characteristics curves were plotted and areas under curve (AUC) were calculated for 30-day mortality. A P value less than 0.05 was considered as statistically significant. Results The overall 30-day mortality rate was 15.1% of ICH patients. The hematoma shape, hematoma size, ICH score, and GCS score all significantly predict the 30-day mortality for ICH patients, with an AUC of 0.692 (P = 0.0018), 0.715 (P = 0.0008) (by ABC/2) to 0.738 (P = 0.0002) (by CAVA), 0.877 (P<0.0001) (by ABC/2) to 0.882 (P<0.0001) (by CAVA), and 0.912 (P<0.0001), respectively. Conclusion Our study shows that hematoma shape, hematoma size, ICH scores and GCS score all significantly predict the 30-day mortality in an increasing order of AUC. The effect of overestimation of hematoma size by ABC/2 formula in predicting the 30-day mortality could be remedied by using ICH score. PMID:25029592

A New Approach for Obtaining Cosmological Constraints from Type Ia Supernovae using Approximate Bayesian Computation

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

Jennings, Elise; Wolf, Rachel; Sako, Masao

2016-11-09

Cosmological parameter estimation techniques that robustly account for systematic measurement uncertainties will be crucial for the next generation of cosmological surveys. We present a new analysis method, superABC, for obtaining cosmological constraints from Type Ia supernova (SN Ia) light curves using Approximate Bayesian Computation (ABC) without any likelihood assumptions. The ABC method works by using a forward model simulation of the data where systematic uncertainties can be simulated and marginalized over. A key feature of the method presented here is the use of two distinct metrics, the `Tripp' and `Light Curve' metrics, which allow us to compare the simulated data to the observed data set. The Tripp metric takes as input the parameters of models fit to each light curve with the SALT-II method, whereas the Light Curve metric uses the measured fluxes directly without model fitting. We apply the superABC sampler to a simulated data set ofmore » $$\\sim$$1000 SNe corresponding to the first season of the Dark Energy Survey Supernova Program. Varying $$\\Omega_m, w_0, \\alpha$$ and $$\\beta$$ and a magnitude offset parameter, with no systematics we obtain $$\\Delta(w_0) = w_0^{\\rm true} - w_0^{\\rm best \\, fit} = -0.036\\pm0.109$$ (a $$\\sim11$$% 1$$\\sigma$$ uncertainty) using the Tripp metric and $$\\Delta(w_0) = -0.055\\pm0.068$$ (a $$\\sim7$$% 1$$\\sigma$$ uncertainty) using the Light Curve metric. Including 1% calibration uncertainties in four passbands, adding 4 more parameters, we obtain $$\\Delta(w_0) = -0.062\\pm0.132$$ (a $$\\sim14$$% 1$$\\sigma$$ uncertainty) using the Tripp metric. Overall we find a $17$% increase in the uncertainty on $$w_0$$ with systematics compared to without. We contrast this with a MCMC approach where systematic effects are approximately included. We find that the MCMC method slightly underestimates the impact of calibration uncertainties for this simulated data set.« less

Loss of plastoglobule kinases ABC1K1 and ABC1K3 causes conditional degreening, modified prenyl-lipids, and recruitment of the jasmonic acid pathway

USDA-ARS?s Scientific Manuscript database

Plastoglobules (PGs) are plastid lipid-protein particles. This study examines the function of PG-localized kinases ABC1K1 and ABC1K3 in Arabidopsis thaliana. Several lines of evidence suggested that ABC1K1 and ABC1K3 form a protein complex. Null mutants for both genes (abc1k1 and abc1k3) and the dou...

Teaching with Technology: Literature and Software.

ERIC Educational Resources Information Center

Allen, Denise

1994-01-01

Reviews five computer programs and compact disc-read only memory (CD-ROM) products designed to improve students' reading and problem-solving skills: (1) "Reading Realities" (Teacher Support Software); (2) "Kid Rhymes" (Creative Pursuits); (3) "First-Start Biographies" (Troll Associates); (4) "My Silly CD of ABCs" (Discis Classroom Editions); and…

Complementarity of statistical treatments to reconstruct worldwide routes of invasion: The case of the Asian ladybird Harmonia axyridis

USDA-ARS?s Scientific Manuscript database

Technical Abstract. Molecular markers can provide clear insight into the introduction history of invasive species. However, inferences about recent introduction histories remain challenging, because of the stochastic demographic processes often involved. Approximate Bayesian computation (ABC) can he...

The ABCs of Writing a Technical Glossary.

ERIC Educational Resources Information Center

Gray, Evie; Ingram, William; Bodson, Dennis

1998-01-01

Explains format, style rules, and lexicographic conventions that improve clarity and precision in a technical glossary. Discusses general rules, rules of style, rules of grammar and syntax, and rules for figures. Describes the computer display techniques and file management system used to develop such a glossary. (SR)

[The ABC transporters of Saccharomyces cerevisiae].

PubMed

Wawrzycka, Donata

2011-01-01

The ABC transporters (ATP Binding Cassette) compose one of the bigest protein family with the great medical, industrial and economical impact. They are found in all organism from bacteria to man. ABC proteins are responsible for resistance of microorganism to antibiotics and fungicides and multidrug resistance of cancer cells. Mutations in ABC transporters genes cause seriuos deseases like cystic fibrosis, adrenoleucodystrophy or ataxia. Transport catalized by ABC proteins is charged with energy from the ATP hydrolysis. The ABC superfamily contains transporters, canals, receptors. Analysis of the Saccharomyces cerevisiae genome allowed to distinguish 30 potential ABC proteins which are classified into 6 subfamilies. The structural and functional similarity of the yeast and human ABC proteins allowes to use the S. cerevisiae as a model organism for ABC transporters characterisation. In this work the present state of knowleadge on yeast S. cerevisiae ABC proteins was summarised.

Identification of ABC Transporter Genes of Fusarium graminearum with Roles in Azole Tolerance and/or Virulence

PubMed Central

Döll, Katharina; Karlovsky, Petr; Deising, Holger B.; Wirsel, Stefan G. R.

2013-01-01

Fusarium graminearum is a plant pathogen infecting several important cereals, resulting in substantial yield losses and mycotoxin contamination of the grain. Triazole fungicides are used to control diseases caused by this fungus on a worldwide scale. Our previous microarray study indicated that 15 ABC transporter genes were transcriptionally upregulated in response to tebuconazole treatment. Here, we deleted four ABC transporter genes in two genetic backgrounds of F. graminearum representing the DON (deoxynivalenol) and the NIV (nivalenol) trichothecene chemotypes. Deletion of FgABC3 and FgABC4 belonging to group I of ABC-G and to group V of ABC-C subfamilies of ABC transporters, respectively, considerably increased the sensitivity to the class I sterol biosynthesis inhibitors triazoles and fenarimol. Such effects were specific since they did not occur with any other fungicide class tested. Assessing the contribution of the four ABC transporters to virulence of F. graminearum revealed that, irrespective of their chemotypes, deletion mutants of FgABC1 (ABC-C subfamily group V) and FgABC3 were impeded in virulence on wheat, barley and maize. Phylogenetic context and analyses of mycotoxin production suggests that FgABC3 may encode a transporter protecting the fungus from host-derived antifungal molecules. In contrast, FgABC1 may encode a transporter responsible for the secretion of fungal secondary metabolites alleviating defence of the host. Our results show that ABC transporters play important and diverse roles in both fungicide resistance and pathogenesis of F. graminearum. PMID:24244413

26 CFR 1.6655-6 - Methods of accounting.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of accounting method. Corporation ABC, a calendar year taxpayer, uses an accrual method of accounting... 26 Internal Revenue 13 2010-04-01 2010-04-01 false Methods of accounting. 1.6655-6 Section 1.6655... Methods of accounting. (a) In general. In computing any required installment, a corporation must use the...

Regulation of Expression of abcA and Its Response to Environmental Conditions

PubMed Central

Villet, Regis A.; Truong-Bolduc, Que Chi; Wang, Yin; Estabrooks, Zoe; Medeiros, Heidi

2014-01-01

The ATP-dependent transporter gene abcA in Staphylococcus aureus confers resistance to hydrophobic β-lactams. In strain ISP794, abcA is regulated by the transcriptional regulators MgrA and NorG and shares a 420-nucleotide intercistronic region with the divergently transcribed pbp4 gene, which encodes the transpeptidase Pbp4. Exposure of exponentially growing cells to iron-limited media, oxidative stress, and acidic pH (5.5) for 0.5 to 2 h had no effect on abcA expression. In contrast, nutrient limitation produced a significant increase in abcA transcripts. We identified three additional regulators (SarA, SarZ, and Rot) that bind to the overlapping promoter region of abcA and pbp4 in strain MW2 and investigated their role in the regulation of abcA expression. Expression of abcA is decreased by 10.0-fold in vivo in a subcutaneous abscess model. In vitro, abcA expression depends on rot and sarZ regulators. Moenomycin A exposure of strain MW2 produced an increase in abcA transcripts. Relative to MW2, the MIC of moenomycin was decreased 8-fold for MW2ΔabcA and increased 10-fold for the MW2 abcA overexpresser, suggesting that moenomycin is a substrate of AbcA. PMID:24509312

Lévy flight artificial bee colony algorithm

NASA Astrophysics Data System (ADS)

Sharma, Harish; Bansal, Jagdish Chand; Arya, K. V.; Yang, Xin-She

2016-08-01

Artificial bee colony (ABC) optimisation algorithm is a relatively simple and recent population-based probabilistic approach for global optimisation. The solution search equation of ABC is significantly influenced by a random quantity which helps in exploration at the cost of exploitation of the search space. In the ABC, there is a high chance to skip the true solution due to its large step sizes. In order to balance between diversity and convergence in the ABC, a Lévy flight inspired search strategy is proposed and integrated with ABC. The proposed strategy is named as Lévy Flight ABC (LFABC) has both the local and global search capability simultaneously and can be achieved by tuning the Lévy flight parameters and thus automatically tuning the step sizes. In the LFABC, new solutions are generated around the best solution and it helps to enhance the exploitation capability of ABC. Furthermore, to improve the exploration capability, the numbers of scout bees are increased. The experiments on 20 test problems of different complexities and five real-world engineering optimisation problems show that the proposed strategy outperforms the basic ABC and recent variants of ABC, namely, Gbest-guided ABC, best-so-far ABC and modified ABC in most of the experiments.

Genome-Wide Identification, Characterization and Phylogenetic Analysis of ATP-Binding Cassette (ABC) Transporter Genes in Common Carp (Cyprinus carpio).

PubMed

Liu, Xiang; Li, Shangqi; Peng, Wenzhu; Feng, Shuaisheng; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A; Xu, Peng

2016-01-01

The ATP-binding cassette (ABC) gene family is considered to be one of the largest gene families in all forms of prokaryotic and eukaryotic life. Although the ABC transporter genes have been annotated in some species, detailed information about the ABC superfamily and the evolutionary characterization of ABC genes in common carp (Cyprinus carpio) are still unclear. In this research, we identified 61 ABC transporter genes in the common carp genome. Phylogenetic analysis revealed that they could be classified into seven subfamilies, namely 11 ABCAs, six ABCBs, 19 ABCCs, eight ABCDs, two ABCEs, four ABCFs, and 11 ABCGs. Comparative analysis of the ABC genes in seven vertebrate species including common carp, showed that at least 10 common carp genes were retained from the third round of whole genome duplication, while 12 duplicated ABC genes may have come from the fourth round of whole genome duplication. Gene losses were also observed for 14 ABC genes. Expression profiles of the 61 ABC genes in six common carp tissues (brain, heart, spleen, kidney, intestine, and gill) revealed extensive functional divergence among the ABC genes. Different copies of some genes had tissue-specific expression patterns, which may indicate some gene function specialization. This study provides essential genomic resources for future studies in common carp.

Genome-Wide Identification, Characterization and Phylogenetic Analysis of ATP-Binding Cassette (ABC) Transporter Genes in Common Carp (Cyprinus carpio)

PubMed Central

Peng, Wenzhu; Feng, Shuaisheng; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A.

2016-01-01

The ATP-binding cassette (ABC) gene family is considered to be one of the largest gene families in all forms of prokaryotic and eukaryotic life. Although the ABC transporter genes have been annotated in some species, detailed information about the ABC superfamily and the evolutionary characterization of ABC genes in common carp (Cyprinus carpio) are still unclear. In this research, we identified 61 ABC transporter genes in the common carp genome. Phylogenetic analysis revealed that they could be classified into seven subfamilies, namely 11 ABCAs, six ABCBs, 19 ABCCs, eight ABCDs, two ABCEs, four ABCFs, and 11 ABCGs. Comparative analysis of the ABC genes in seven vertebrate species including common carp, showed that at least 10 common carp genes were retained from the third round of whole genome duplication, while 12 duplicated ABC genes may have come from the fourth round of whole genome duplication. Gene losses were also observed for 14 ABC genes. Expression profiles of the 61 ABC genes in six common carp tissues (brain, heart, spleen, kidney, intestine, and gill) revealed extensive functional divergence among the ABC genes. Different copies of some genes had tissue-specific expression patterns, which may indicate some gene function specialization. This study provides essential genomic resources for future studies in common carp. PMID:27058731

A novel approach for choosing summary statistics in approximate Bayesian computation.

PubMed

Aeschbacher, Simon; Beaumont, Mark A; Futschik, Andreas

2012-11-01

The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine-learning literature. We consider different types of boosting and compare them to partial least-squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the reintroduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θ(anc) = 4N(e)u) and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L(2)-loss performs best. Applying that method to the ibex data, we estimate θ(anc)≈ 1.288 and find that most of the variation across loci of the ancestral mutation rate u is between 7.7 × 10(-4) and 3.5 × 10(-3) per locus per generation. The proportion of males with access to matings is estimated as ω≈ 0.21, which is in good agreement with recent independent estimates.

A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation

PubMed Central

Aeschbacher, Simon; Beaumont, Mark A.; Futschik, Andreas

2012-01-01

The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine-learning literature. We consider different types of boosting and compare them to partial least-squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the reintroduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4Neu) and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θ^anc≈1.288 and find that most of the variation across loci of the ancestral mutation rate u is between 7.7 × 10−4 and 3.5 × 10−3 per locus per generation. The proportion of males with access to matings is estimated as ω^≈0.21, which is in good agreement with recent independent estimates. PMID:22960215

Travel in Time: Tradition to Technology. Proceedings of the 1985 ABC International Convention (Chicago, Illinois, October 1985).

ERIC Educational Resources Information Center

Bruno, Sam J., Ed.; Pettit, John D., Jr., Ed.

These conference proceedings contain the following 23 presentations: "Development of a Communication Skill Model Using Interpretive Structural Modeling" (Karen S. Nantz and Linda Gammill); "The Coincidence of Needs: An Inventional Model for Audience Analysis" (Gina Burchard); "A Computer Algorithm for Measuring Readability" (Terry D. Lundgren);…

Application of the Approximate Bayesian Computation methods in the stochastic estimation of atmospheric contamination parameters for mobile sources

NASA Astrophysics Data System (ADS)

Kopka, Piotr; Wawrzynczak, Anna; Borysiewicz, Mieczyslaw

2016-11-01

In this paper the Bayesian methodology, known as Approximate Bayesian Computation (ABC), is applied to the problem of the atmospheric contamination source identification. The algorithm input data are on-line arriving concentrations of the released substance registered by the distributed sensors network. This paper presents the Sequential ABC algorithm in detail and tests its efficiency in estimation of probabilistic distributions of atmospheric release parameters of a mobile contamination source. The developed algorithms are tested using the data from Over-Land Atmospheric Diffusion (OLAD) field tracer experiment. The paper demonstrates estimation of seven parameters characterizing the contamination source, i.e.: contamination source starting position (x,y), the direction of the motion of the source (d), its velocity (v), release rate (q), start time of release (ts) and its duration (td). The online-arriving new concentrations dynamically update the probability distributions of search parameters. The atmospheric dispersion Second-order Closure Integrated PUFF (SCIPUFF) Model is used as the forward model to predict the concentrations at the sensors locations.

In defence of model-based inference in phylogeography

PubMed Central

Beaumont, Mark A.; Nielsen, Rasmus; Robert, Christian; Hey, Jody; Gaggiotti, Oscar; Knowles, Lacey; Estoup, Arnaud; Panchal, Mahesh; Corander, Jukka; Hickerson, Mike; Sisson, Scott A.; Fagundes, Nelson; Chikhi, Lounès; Beerli, Peter; Vitalis, Renaud; Cornuet, Jean-Marie; Huelsenbeck, John; Foll, Matthieu; Yang, Ziheng; Rousset, Francois; Balding, David; Excoffier, Laurent

2017-01-01

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics. PMID:29284924

Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations.

PubMed

Schiffmann, Christoph; Sebastiani, Daniel

2011-05-10

We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules.

Mutations in the Arabidopsis Peroxisomal ABC Transporter COMATOSE Allow Differentiation between Multiple Functions In Planta: Insights from an Allelic Series

PubMed Central

Dietrich, Daniela; Schmuths, Heike; Lousa, Carine De Marcos; Baldwin, Jocelyn M.; Baldwin, Stephen A.; Baker, Alison; Holdsworth, Michael J.

2009-01-01

COMATOSE (CTS), the Arabidopsis homologue of human Adrenoleukodystrophy protein (ALDP), is required for import of substrates for peroxisomal β-oxidation. A new allelic series and a homology model based on the bacterial ABC transporter, Sav1866, provide novel insights into structure-function relations of ABC subfamily D proteins. In contrast to ALDP, where the majority of mutations result in protein absence from the peroxisomal membrane, all CTS mutants produced stable protein. Mutation of conserved residues in the Walker A and B motifs in CTS nucleotide-binding domain (NBD) 1 resulted in a null phenotype but had little effect in NBD2, indicating that the NBDs are functionally distinct in vivo. Two alleles containing mutations in NBD1 outside the Walker motifs (E617K and C631Y) exhibited resistance to auxin precursors 2,4-dichlorophenoxybutyric acid (2,4-DB) and indole butyric acid (IBA) but were wild type in all other tests. The homology model predicted that the transmission interfaces are domain-swapped in CTS, and the differential effects of mutations in the conserved “EAA motif” of coupling helix 2 supported this prediction, consistent with distinct roles for each NBD. Our findings demonstrate that CTS functions can be separated by mutagenesis and the structural model provides a framework for interpretation of phenotypic data. PMID:19019987

Aneurysmal Bone Cyst: An Analysis of 38 Cases and Report of Four Unusual Surface Ones

PubMed Central

Shooshtarizadeh, Tina; Movahedinia, Sajjadeh; Mostafavi, Hassan; Jamshidi, Khodamorad; Sami, Sam Hajialiloo

2016-01-01

Aneurysmal bone cyst (ABC) is a benign expansile bone tumor, most commonly involving the medulla of long bones. ABC rarely arises within the cortex or in the subperiosteal region, radiographically mimicking other conditions, in particular surface osteosarcomathat is low-grade in nature and may go secondary ABC changes, and telangiectatic osteosarcoma. Both of these are sometimes mistaken microscopically for primary ABC. We review the characteristics of ABC cases in our center and report four unusualsurface ABCs arising in the subperiosteal or cortical region of long bones, identified among 38 histologically proven ABCs during a four-year period in our center. The surface ABCs occurred at an older agewith a predilection for diaphysis of femur, tibia, and humerus. PMID:27200397

Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti.

PubMed

Torres-Quesada, Omar; Millán, Vicenta; Nisa-Martínez, Rafael; Bardou, Florian; Crespi, Martín; Toro, Nicolás; Jiménez-Zurdo, José I

2013-01-01

The legume symbiont Sinorhizobium meliloti expresses a plethora of small noncoding RNAs (sRNAs) whose function is mostly unknown. Here, we have functionally characterized two tandemly encoded S. meliloti Rm1021 sRNAs that are similar in sequence and structure. Homologous sRNAs (designated AbcR1 and AbcR2) have been shown to regulate several ABC transporters in the related α-proteobacteria Agrobacterium tumefaciens and Brucella abortus. In Rm1021, AbcR1 and AbcR2 exhibit divergent unlinked regulation and are stabilized by the RNA chaperone Hfq. AbcR1 is transcribed in actively dividing bacteria, either in culture, rhizosphere or within the invasion zone of mature alfalfa nodules. Conversely, AbcR2 expression is induced upon entry into stationary phase and under abiotic stress. Only deletion of AbcR1 resulted into a discrete growth delay in rich medium, but both are dispensable for symbiosis. Periplasmic proteome profiling revealed down-regulation of the branched-chain amino acid binding protein LivK by AbcR1, but not by AbcR2. A double-plasmid reporter assay confirmed the predicted specific targeting of the 5'-untranslated region of the livK mRNA by AbcR1 in vivo. Our findings provide evidences of independent regulatory functions of these sRNAs, probably to fine-tune nutrient uptake in free-living and undifferentiated symbiotic rhizobia.

Independent Activity of the Homologous Small Regulatory RNAs AbcR1 and AbcR2 in the Legume Symbiont Sinorhizobium meliloti

PubMed Central

Torres-Quesada, Omar; Millán, Vicenta; Nisa-Martínez, Rafael; Bardou, Florian; Crespi, Martín; Toro, Nicolás; Jiménez-Zurdo, José I.

2013-01-01

The legume symbiont Sinorhizobium meliloti expresses a plethora of small noncoding RNAs (sRNAs) whose function is mostly unknown. Here, we have functionally characterized two tandemly encoded S. meliloti Rm1021 sRNAs that are similar in sequence and structure. Homologous sRNAs (designated AbcR1 and AbcR2) have been shown to regulate several ABC transporters in the related α-proteobacteria Agrobacterium tumefaciens and Brucella abortus. In Rm1021, AbcR1 and AbcR2 exhibit divergent unlinked regulation and are stabilized by the RNA chaperone Hfq. AbcR1 is transcribed in actively dividing bacteria, either in culture, rhizosphere or within the invasion zone of mature alfalfa nodules. Conversely, AbcR2 expression is induced upon entry into stationary phase and under abiotic stress. Only deletion of AbcR1 resulted into a discrete growth delay in rich medium, but both are dispensable for symbiosis. Periplasmic proteome profiling revealed down-regulation of the branched-chain amino acid binding protein LivK by AbcR1, but not by AbcR2. A double-plasmid reporter assay confirmed the predicted specific targeting of the 5′-untranslated region of the livK mRNA by AbcR1 in vivo. Our findings provide evidences of independent regulatory functions of these sRNAs, probably to fine-tune nutrient uptake in free-living and undifferentiated symbiotic rhizobia. PMID:23869210

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

Wu, J; Hill, G; Spiegel, J

Purpose: To investigate the clinical and dosimetric benefits of automatic gating of left breast mixed with breath-hold technique. Methods: Two Active Breathing Control systems, ABC2.0 and ABC3.0, were used during simulation and treatment delivery. The two systems are different such that ABC2.0 is a breath-hold system without beam control capability, while ABC3.0 has capability in both breath-hold and beam gating. At simulation, each patient was scanned twice: one with free breathing (FB) and one with breath hold through ABC. Treatment plan was generated on the CT with ABC. The same plan was also recalculated on the CT with FB. Thesemore » two plans were compared to assess plan quality. For treatments with ABC2.0, beams with MU > 55 were manually split into multiple subfields. All subfields were identical and shared the total MU. For treatment with ABC3.0, beam splitting was unnecessary. Instead, treatment was delivered in gating mode mixed with breath-hold technique. Treatment delivery efficiency using the two systems was compared. Results: The prescribed dose was 50.4Gy at 1.8Gy/fraction. The maximum heart dose averaged over 10 patients was 46.0±2.5Gy and 24.5±12.2Gy for treatments with FB and with ABC respectively. The corresponding heart V10 was 13.2±3.6% and 1.0±1.6% respectively. The averaged MUs were 99.8±7.5 for LMT, 99.2±9.4 for LLT. For treatment with ABC2.0, normally the original beam was split into 2 subfields. The averaged total time to delivery all beams was 4.3±0.4min for treatments with ABC2.0 and 3.3±0.6min for treatments with ABC3.0 in gating mode. Conclusion: Treatment with ABC tremendously reduced heart dose. Compared to treatments with ABC2.0, gating with ABC3.0 reduced the total treatment time by 23%. Use of ABC3.0 improved the delivery efficiency, and eliminated the possibility of mistreatments. The latter may happen with ABC2.0 where beam is not terminated when breath signal falls outside of the treatment window.« less

Back to BaySICS: a user-friendly program for Bayesian Statistical Inference from Coalescent Simulations.

PubMed

Sandoval-Castellanos, Edson; Palkopoulou, Eleftheria; Dalén, Love

2014-01-01

Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.

Catalytic and transport cycles of ABC exporters.

PubMed

Al-Shawi, Marwan K

2011-09-07

ABC (ATP-binding cassette) transporters are arguably the most important family of ATP-driven transporters in biology. Despite considerable effort and advances in determining the structures and physiology of these transporters, their fundamental molecular mechanisms remain elusive and highly controversial. How does ATP hydrolysis by ABC transporters drive their transport function? Part of the problem in answering this question appears to be a perceived need to formulate a universal mechanism. Although it has been generally hoped and assumed that the whole superfamily of ABC transporters would exhibit similar conserved mechanisms, this is proving not to be the case. Structural considerations alone suggest that there are three overall types of coupling mechanisms related to ABC exporters, small ABC importers and large ABC importers. Biochemical and biophysical characterization leads us to the conclusion that, even within these three classes, the catalytic and transport mechanisms are not fully conserved, but continue to evolve. ABC transporters also exhibit unusual characteristics not observed in other primary transporters, such as uncoupled basal ATPase activity, that severely complicate mechanistic studies by established methods. In this chapter, I review these issues as related to ABC exporters in particular. A consensus view has emerged that ABC exporters follow alternating-access switch transport mechanisms. However, some biochemical data suggest that alternating catalytic site transport mechanisms are more appropriate for fully symmetrical ABC exporters. Heterodimeric and asymmetrical ABC exporters appear to conform to simple alternating-access-type mechanisms.

A Bayesian Approach to Genome/Linguistic Relationships in Native South Americans

PubMed Central

Amorim, Carlos Eduardo Guerra; Bisso-Machado, Rafael; Ramallo, Virginia; Bortolini, Maria Cátira; Bonatto, Sandro Luis; Salzano, Francisco Mauro; Hünemeier, Tábita

2013-01-01

The relationship between the evolution of genes and languages has been studied for over three decades. These studies rely on the assumption that languages, as many other cultural traits, evolve in a gene-like manner, accumulating heritable diversity through time and being subjected to evolutionary mechanisms of change. In the present work we used genetic data to evaluate South American linguistic classifications. We compared discordant models of language classifications to the current Native American genome-wide variation using realistic demographic models analyzed under an Approximate Bayesian Computation (ABC) framework. Data on 381 STRs spread along the autosomes were gathered from the literature for populations representing the five main South Amerindian linguistic groups: Andean, Arawakan, Chibchan-Paezan, Macro-Jê, and Tupí. The results indicated a higher posterior probability for the classification proposed by J.H. Greenberg in 1987, although L. Campbell's 1997 classification cannot be ruled out. Based on Greenberg's classification, it was possible to date the time of Tupí-Arawakan divergence (2.8 kya), and the time of emergence of the structure between present day major language groups in South America (3.1 kya). PMID:23696865

A bayesian approach to genome/linguistic relationships in native South Americans.

PubMed

Amorim, Carlos Eduardo Guerra; Bisso-Machado, Rafael; Ramallo, Virginia; Bortolini, Maria Cátira; Bonatto, Sandro Luis; Salzano, Francisco Mauro; Hünemeier, Tábita

2013-01-01

The relationship between the evolution of genes and languages has been studied for over three decades. These studies rely on the assumption that languages, as many other cultural traits, evolve in a gene-like manner, accumulating heritable diversity through time and being subjected to evolutionary mechanisms of change. In the present work we used genetic data to evaluate South American linguistic classifications. We compared discordant models of language classifications to the current Native American genome-wide variation using realistic demographic models analyzed under an Approximate Bayesian Computation (ABC) framework. Data on 381 STRs spread along the autosomes were gathered from the literature for populations representing the five main South Amerindian linguistic groups: Andean, Arawakan, Chibchan-Paezan, Macro-Jê, and Tupí. The results indicated a higher posterior probability for the classification proposed by J.H. Greenberg in 1987, although L. Campbell's 1997 classification cannot be ruled out. Based on Greenberg's classification, it was possible to date the time of Tupí-Arawakan divergence (2.8 kya), and the time of emergence of the structure between present day major language groups in South America (3.1 kya).

Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

PubMed Central

Peter, Benjamin M.; Huerta-Sanchez, Emilia; Nielsen, Rasmus

2012-01-01

An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. We use simulations to assess the power and accuracy of our method and apply it to seven of the strongest sweeps currently known in humans. We identify two genes, ASPM and PSCA, that are most likely affected by selection on standing variation; and we find three genes, ADH1B, LCT, and EDAR, in which the adaptive alleles seem to have swept from a new mutation. We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection. PMID:23071458

An ATP-driven efflux pump is a novel pathogenicity factor in rice blast disease.

PubMed Central

Urban, M; Bhargava, T; Hamer, J E

1999-01-01

Cells tolerate exposure to cytotoxic compounds through the action of ATP-driven efflux pumps belonging to the ATP-binding cassette (ABC) superfamily of membrane transporters. Phytopathogenic fungi encounter toxic environments during plant invasion as a result of the plant defense response. Here we demonstrate the requirement for an ABC transporter during host infection by the fungal plant pathogen Magnaporthe grisea. The ABC1 gene was identified in an insertional mutagenesis screen for pathogenicity mutants. The ABC1 insertional mutant and a gene-replacement mutant arrest growth and die shortly after penetrating either rice or barley epidermal cells. The ABC1-encoded protein is similar to yeast ABC transporters implicated in multidrug resistance, and ABC1 gene transcripts are inducible by toxic drugs and a rice phytoalexin. However, abc1 mutants are not hypersensitive to antifungal compounds. The non-pathogenic, insertional mutation in ABC1 occurs in the promoter region and dramatically reduces transcript induction by metabolic poisons. These data strongly suggest that M.grisea requires the up-regulation of specific ABC transporters for pathogenesis; most likely to protect itself against plant defense mechanisms. PMID:9927411

4th International Consensus Conference on Advanced Breast Cancer (ABC4), Lisbon, November 4, 2017 : ABC4 Consensus: Assessment by a Panel of German Experts.

PubMed

Untch, Michael; Würstlein, Rachel; Marschner, Norbert; Lüftner, Diana; Augustin, Doris; Briest, Susanne; Ettl, Johannes; Haidinger, Renate; Müller, Lothar; Müller, Volkmar; Ruckhäberle, Eugen; Harbeck, Nadia; Thomssen, Christoph

2018-05-01

The fourth international advanced breast cancer consensus conference (ABC4) on the diagnosis and treatment of advanced breast cancer (ABC) headed by Professor Fatima Cardoso was once again held in Lisbon on November 2 - 4, 2017. To simplify matters, the abbreviation ABC will be used hereinafter in the text. In clinical practice, the abbreviation corresponds to metastatic breast cancer or locally far-advanced disease. This year the focus was on new developments in the treatment of ABC. Topics discussed included the importance of CDK4/6 inhibition in hormone receptor (HR)-positive ABC, the use of dual antibody blockade to treat HER2-positive ABC, PARP inhibition in triple-negative ABC and the potential therapeutic outcomes. Another major area discussed at the conference was BRCA-associated breast cancer, the treatment of cerebral metastasis, and individualized treatment decisions based on molecular testing (so-called precision medicine). As in previous years, close cooperation with representatives from patient organizations from around the world is an important aspect of the ABC conference. This cooperation was reinforced and expanded at the ABC4 conference. A global alliance was founded at the conclusion of the consensus conference, which aims to promote and coordinate the measures considered necessary by patient advocates worldwide. Because the panel of experts was composed of specialists from all over the world, it was inevitable that the ABC consensus also reflected country-specific features. As in previous years, a team of German breast cancer specialists who closely followed the consensus voting of the ABC panelists in Lisbon and intensively discussed the votes has therefore commented on the consensus in the context of the current German guidelines on the diagnosis and treatment of breast cancer 1 ,  2 used in clinical practice in Germany. The ABC consensus is based on the votes of the ABC panelists in Lisbon.

Determinants of fast food consumption among Iranian high school students based on planned behavior theory.

PubMed

Sharifirad, Gholamreza; Yarmohammadi, Parastoo; Azadbakht, Leila; Morowatisharifabad, Mohammad Ali; Hassanzadeh, Akbar

2013-01-01

This study was conducted to identify some factors (beliefs and norms) which are related to fast food consumption among high school students in Isfahan, Iran. We used the framework of the theory planned behavior (TPB) to predict this behavior. Cross-sectional data were available from high school students (n = 521) who were recruited by cluster randomized sampling. All of the students completed a questionnaire assessing variables of standard TPB model including attitude, subjective norms, perceived behavior control (PBC), and the additional variables past behavior, actual behavior control (ABC). The TPB variables explained 25.7% of the variance in intentions with positive attitude as the strongest (β = 0.31, P < 0.001) and subjective norms as the weakest (β = 0.29, P < 0.001) determinant. Concurrently, intentions accounted for 6% of the variance for fast food consumption. Past behavior and ABC accounted for an additional amount of 20.4% of the variance in fast food consumption. Overall, the present study suggests that the TPB model is useful in predicting related beliefs and norms to the fast food consumption among adolescents. Subjective norms in TPB model and past behavior in TPB model with additional variables (past behavior and actual behavior control) were the most powerful predictors of fast food consumption. Therefore, TPB model may be a useful framework for planning intervention programs to reduce fast food consumption by students.

Sustained delivery of thermostabilized chABC enhances axonal sprouting and functional recovery after spinal cord injury.

PubMed

Lee, Hyunjung; McKeon, Robert J; Bellamkonda, Ravi V

2010-02-23

Chondroitin sulfate proteoglycans (CSPGs) are a major class of axon growth inhibitors that are up-regulated after spinal cord injury (SCI) and contribute to regenerative failure. Chondroitinase ABC (chABC) digests glycosaminoglycan chains on CSPGs and can thereby overcome CSPG-mediated inhibition. But chABC loses its enzymatic activity rapidly at 37 degrees C, necessitating the use of repeated injections or local infusions for a period of days to weeks. These infusion systems are invasive, infection-prone, and clinically problematic. To overcome this limitation, we have thermostabilized chABC and developed a system for its sustained local delivery in vivo, obviating the need for chronically implanted catheters and pumps. Thermostabilized chABC remained active at 37 degrees C in vitro for up to 4 weeks. CSPG levels remained low in vivo up to 6 weeks post-SCI when thermostabilized chABC was delivered by a hydrogel-microtube scaffold system. Axonal growth and functional recovery following the sustained local release of thermostabilized chABC versus a single treatment of unstabilized chABC demonstrated significant differences in CSPG digestion. Animals treated with thermostabilized chABC in combination with sustained neurotrophin-3 delivery showed significant improvement in locomotor function and enhanced growth of cholera toxin B subunit-positive sensory axons and sprouting of serotonergic fibers. Therefore, improving chABC thermostability facilitates minimally invasive, sustained, local delivery of chABC that is potentially effective in overcoming CSPG-mediated regenerative failure. Combination therapy with thermostabilized chABC with neurotrophic factors enhances axonal regrowth, sprouting, and functional recovery after SCI.

The mitochondrial transporter ABC-me (ABCB10), a downstream target of GATA-1, is essential for erythropoiesis in vivo.

PubMed

Hyde, B B; Liesa, M; Elorza, A A; Qiu, W; Haigh, S E; Richey, L; Mikkola, H K; Schlaeger, T M; Shirihai, O S

2012-07-01

The mitochondrial transporter ATP binding cassette mitochondrial erythroid (ABC-me/ABCB10) is highly induced during erythroid differentiation by GATA-1 and its overexpression increases hemoglobin production rates in vitro. However, the role of ABC-me in erythropoiesis in vivo is unknown. Here we report for the first time that erythrocyte development in mice requires ABC-me. ABC-me-/- mice die at day 12.5 of gestation, showing nearly complete eradication of primitive erythropoiesis and lack of hemoglobinized cells at day 10.5. ABC-me-/- erythroid cells fail to differentiate because they exhibit a marked increase in apoptosis, both in vivo and ex vivo. Erythroid precursors are particularly sensitive to oxidative stress and ABC-me in the heart and its yeast ortholog multidrug resistance-like 1 have been shown to protect against oxidative stress. Thus, we hypothesized that increased apoptosis in ABC-me-/- erythroid precursors was caused by oxidative stress. Within this context, ABC-me deletion causes an increase in mitochondrial superoxide production and protein carbonylation in erythroid precursors. Furthermore, treatment of ABC-me-/- erythroid progenitors with the mitochondrial antioxidant MnTBAP (superoxide dismutase 2 mimetic) supports survival, ex vivo differentiation and increased hemoglobin production. Altogether, our findings demonstrate that ABC-me is essential for erythropoiesis in vivo.

75 FR 49549 - ABC & D Recycling, Inc.-Lease and Operation Exemption-a Line of Railroad in Ware, MA

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-13

... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. FD 35397] ABC & D Recycling, Inc.--Lease and Operation Exemption--a Line of Railroad in Ware, MA ABC & D Recycling, Inc. (ABC & D..., ABC & D Recycling, Inc.--Lease and Operation Exemption--a Line of Railroad in Ware, Massachusetts (STB...

Accurate Black Hole Spin Measurements using ABC

NASA Astrophysics Data System (ADS)

Connolly, Andrew

Measuring the spin of black holes provides important insights into the supernova formation mechanism of stellar-mass black holes, galaxy merger scenarios for supermassive black holes, and the launching mechanisms of ballistic jets. It is therefore of crucial importance to measure black hole spins to a high degree of accuracy. Stellar-mass black holes in binary systems (BHBs) have two major advantages over Active Galactic Nuclei (AGN): (1) owing to their proximity and brightness, observations of BHBs are not as limited by counting statistics as their supermassive counter-parts; (2) unlike in AGN, one can use two largely independent methods to measure the spin in BHBs, providing a check on spin measurements. However, the high flux that makes BHBs such excellent targets for spin measurements also proves to be their Achilles heel: modern CCD cameras are optimized for observing faint sources. Consequently, observations of bright BHBs with CCD cameras are subject to non-linear instrumental effects among them pile-up and grade migration that strongly distort the spectrum. Since spin measurements rely on a very precise model of both the continuum X-ray flux and disc reflection signatures superimposed on top of the former, these instrumental effects may cause inferred spin measurements to differ by a factor of two or more. Current mitigation strategies are aimed at removing instrumental effects either during the observations themselves, by requiring simultaneous observations with multiple telescopes, or in post-processing. Even when these techniques are employed, pile-up may remain unrecognized and still distort results, whereas mitigation strategies may introduce additional systematic biases, e.g. due to increased (cross-)calibration uncertainties. Advances in modern statistical methodology allow for efficient modeling of instrumental effects during the analysis stage, largely eliminating the requirements for observations with multiple instruments or increased observation time. In particular, a class of methods col- lectively called Approximate Bayesian Computation (ABC) is capable of exploiting the fact that it is possible to simulate instrumental effects to a high degree of accuracy in order to build reliable statistical models incorporating pile-up and related effects. With the loss of the Hitomi spacecraft, it is more important than ever to make full use of the data we collect with current instruments. We propose an ambitious program to estimate the spins of 13 black holes in X-ray binaries using observations with XMMNewton s EPIC MOS and pn, Suzaku s XIS and Chandra s ACIS and HETG instruments. We will build a general framework for dealing with pile-up in spectral modeling using ABC and refine current instrumental simulators for inclusion in this framework. Coupled with state-of-the- art sampling methods, this will allow us to take advantage of dozens of observations in the archives of all three instruments. We will be able to estimate spins to much bet- ter accuracy than ever before and test current models for black hole formation as well as jet launching mechanisms. The program will deliver a considerable legacy, because the statistical and methodological framework will be general. Application to other instruments suffering from photon pile-up, e.g. Swift/XRT, Fermi/GBM, ASCA/SIS, and GALEX, will only require is a model capable of simulating the relevant instrumental effects. This will enable other science cases beyond that proposed here which rely on precise spectral measurements or cases where pile-up cannot be avoided, e.g. high-precision radius measurements in neutron stars, understanding X-ray dust scattering, and stellar evolution studies of globular clusters.

Use of a Short-Form Balance Confidence Scale to Predict Future Recurrent Falls in People With Parkinson Disease.

PubMed

Cole, Michael H; Rippey, Jodi; Naughton, Geraldine A; Silburn, Peter A

2016-01-01

To assess whether the 16-item Activities-specific Balance Confidence scale (ABC-16) and short-form 6-item Activities-specific Balance Confidence scale (ABC-6) could predict future recurrent falls in people with Parkinson disease (PD) and to validate the robustness of their predictive capacities. Twelve-month prospective cohort study. General community. People with idiopathic PD (N=79). Clinical tests were conducted to assess symptom severity, balance confidence, and medical history. Over the subsequent 12 months, participants recorded any falls on daily fall calendars, which they returned monthly by reply paid post. Logistic regression and receiver operating characteristic analyses estimated the sensitivities and specificities of the ABC-16 and ABC-6 for predicting future recurrent falls in this cohort, and "leave-one-out" validation was used to assess their robustness. Of the 79 patients who completed follow-up, 28 (35.4%) fell more than once during the 12-month period. Both the ABC-16 and ABC-6 were significant predictors of future recurrent falls, and moderate sensitivities (ABC-16: 75.0%; ABC-6: 71.4%) and specificities (ABC-16: 76.5%; ABC-6: 74.5%) were reported for each tool for a cutoff score of 77.5 and 65.8, respectively. The results have significant implications and demonstrate that the ABC-16 and ABC-6 independently identify patients with PD at risk of future recurrent falls. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Whole-Genome Survey of the Putative ATP-Binding Cassette Transporter Family Genes in Vitis vinifera

PubMed Central

Çakır, Birsen; Kılıçkaya, Ozan

2013-01-01

The ATP-binding cassette (ABC) protein superfamily constitutes one of the largest protein families known in plants. In this report, we performed a complete inventory of ABC protein genes in Vitis vinifera, the whole genome of which has been sequenced. By comparison with ABC protein members of Arabidopsis thaliana, we identified 135 putative ABC proteins with 1 or 2 NBDs in V. vinifera. Of these, 120 encode intrinsic membrane proteins, and 15 encode proteins missing TMDs. V. vinifera ABC proteins can be divided into 13 subfamilies with 79 “full-size,” 41 “half-size,” and 15 “soluble” putative ABC proteins. The main feature of the Vitis ABC superfamily is the presence of 2 large subfamilies, ABCG (pleiotropic drug resistance and white-brown complex homolog) and ABCC (multidrug resistance-associated protein). We identified orthologs of V. vinifera putative ABC transporters in different species. This work represents the first complete inventory of ABC transporters in V. vinifera. The identification of Vitis ABC transporters and their comparative analysis with the Arabidopsis counterparts revealed a strong conservation between the 2 species. This inventory could help elucidate the biological and physiological functions of these transporters in V. vinifera. PMID:24244377

What does an MRI scan cost?

PubMed

Young, David W

2015-11-01

Historically, hospital departments have computed the costs of individual tests or procedures using the ratio of cost to charges (RCC) method, which can produce inaccurate results. To determine a more accurate cost of a test or procedure, the activity-based costing (ABC) method must be used. Accurate cost calculations will ensure reliable information about the profitability of a hospital's DRGs.

PubMed Central

Untch, Michael; Würstlein, Rachel; Marschner, Norbert; Lüftner, Diana; Augustin, Doris; Briest, Susanne; Ettl, Johannes; Haidinger, Renate; Müller, Lothar; Müller, Volkmar; Ruckhäberle, Eugen; Harbeck, Nadia; Thomssen, Christoph

2018-01-01

The fourth international advanced breast cancer consensus conference (ABC4) on the diagnosis and treatment of advanced breast cancer (ABC) headed by Professor Fatima Cardoso was once again held in Lisbon on November 2 – 4, 2017. To simplify matters, the abbreviation ABC will be used hereinafter in the text. In clinical practice, the abbreviation corresponds to metastatic breast cancer or locally far-advanced disease. This year the focus was on new developments in the treatment of ABC. Topics discussed included the importance of CDK4/6 inhibition in hormone receptor (HR)-positive ABC, the use of dual antibody blockade to treat HER2-positive ABC, PARP inhibition in triple-negative ABC and the potential therapeutic outcomes. Another major area discussed at the conference was BRCA-associated breast cancer, the treatment of cerebral metastasis, and individualized treatment decisions based on molecular testing (so-called precision medicine). As in previous years, close cooperation with representatives from patient organizations from around the world is an important aspect of the ABC conference. This cooperation was reinforced and expanded at the ABC4 conference. A global alliance was founded at the conclusion of the consensus conference, which aims to promote and coordinate the measures considered necessary by patient advocates worldwide. Because the panel of experts was composed of specialists from all over the world, it was inevitable that the ABC consensus also reflected country-specific features. As in previous years, a team of German breast cancer specialists who closely followed the consensus voting of the ABC panelists in Lisbon and intensively discussed the votes has therefore commented on the consensus in the context of the current German guidelines on the diagnosis and treatment of breast cancer 1 ,  2 used in clinical practice in Germany. The ABC consensus is based on the votes of the ABC panelists in Lisbon. PMID:29880982

Genome-wide identification, phylogenetic analysis, and expression profiles of ATP-binding cassette transporter genes in the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae).

PubMed

Xiao, Lin-Fan; Zhang, Wei; Jing, Tian-Xing; Zhang, Meng-Yi; Miao, Ze-Qing; Wei, Dan-Dan; Yuan, Guo-Rui; Wang, Jin-Jun

2018-03-01

The ATP-binding cassette (ABC) is the largest transporter gene family and the genes play key roles in xenobiotic resistance, metabolism, and development of all phyla. However, the specific functions of ABC gene families in insects is unclear. We report a genome-wide identification, phylogenetic, and transcriptional analysis of the ABC genes in the oriental fruit fly, Bactrocera dorsalis (Hendel). We identified a total of 47 ABC genes (BdABCs) from the transcriptomic and genomic databases of B. dorsalis and classified these genes into eight subfamilies (A-H), including 7 ABCAs, 7 ABCBs, 9 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 15 ABCGs, and 3 ABCHs. Comparative phylogenetic analysis of the ABCs suggests an orthologous relationship between B. dorsalis and other insect species in which these genes have been related to pesticide resistance and essential biological processes. Comparison of transcriptome and relative expression patterns of BdABCs indicated diverse multifunctions within different B. dorsalis tissues. The expression of 4, 10, and 14 BdABCs from 18 BdABCs was significantly upregulated after exposure to LD 50 s of malathion, avermectin, and beta-cypermethrin, respectively. The maximum expression level of most BdABCs (including BdABCFs, BdABCGs, and BdABCHs) occurred at 48h post exposures, whereas BdABCEs peaked at 24h after treatment. Furthermore, RNA interference-mediated suppression of BdABCB7 resulted in increased toxicity of malathion against B. dorsalis. These data suggest that ABC transporter genes might play key roles in xenobiotic metabolism and biosynthesis in B. dorsalis. Copyright © 2017 Elsevier Inc. All rights reserved.

Regulation of the ATPase activity of ABCE1 from Pyrococcus abyssi by Fe-S cluster status and Mg²⁺: implication for ribosomal function.

PubMed

Sims, Lynn M; Igarashi, Robert Y

2012-08-15

Ribosomal function is dependent on multiple proteins. The ABCE1 ATPase, a unique ABC superfamily member that bears two Fe₄S₄ clusters, is crucial for ribosomal biogenesis and recycling. Here, the ATPase activity of the Pyrococcus abyssi ABCE1 (PabABCE1) was studied using both apo- (without reconstituted Fe-S clusters) and holo- (with full complement of Fe-S clusters reconstituted post-purification) forms, and is shown to be jointly regulated by the status of Fe-S clusters and Mg²⁺. Typically ATPases require Mg²⁺, as is true for PabABCE1, but Mg²⁺ also acts as a negative allosteric effector that modulates ATP affinity of PabABCE1. Physiological [Mg²⁺] inhibits the PabABCE1 ATPase (K(i) of ∼1 μM) for both apo- and holo-PabABCE1. Comparative kinetic analysis of Mg²⁺ inhibition shows differences in degree of allosteric regulation between the apo- and holo-PabABCE1 where the apparent ATP K(m) of apo-PabABCE1 increases >30-fold from ∼30 μM to over 1 mM with M²⁺. This effect would significantly convert the ATPase activity of PabABCE1 from being independent of cellular energy charge (φ) to being dependent on φ with cellular [Mg²⁺]. These findings uncover intricate overlapping effects by both [Mg²⁺] and the status of Fe-S clusters that regulate ABCE1's ATPase activity with implications to ribosomal function. Copyright © 2012 Elsevier Inc. All rights reserved.

Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach.

PubMed

Koutroumpas, Konstantinos; Ballarini, Paolo; Votsi, Irene; Cournède, Paul-Henry

2016-09-01

Likelihood-free methods, like Approximate Bayesian Computation (ABC), have been extensively used in model-based statistical inference with intractable likelihood functions. When combined with Sequential Monte Carlo (SMC) algorithms they constitute a powerful approach for parameter estimation and model selection of mathematical models of complex biological systems. A crucial step in the ABC-SMC algorithms, significantly affecting their performance, is the propagation of a set of parameter vectors through a sequence of intermediate distributions using Markov kernels. In this article, we employ Dirichlet process mixtures (DPMs) to design optimal transition kernels and we present an ABC-SMC algorithm with DPM kernels. We illustrate the use of the proposed methodology using real data for the canonical Wnt signaling pathway. A multi-compartment model of the pathway is developed and it is compared to an existing model. The results indicate that DPMs are more efficient in the exploration of the parameter space and can significantly improve ABC-SMC performance. In comparison to alternative sampling schemes that are commonly used, the proposed approach can bring potential benefits in the estimation of complex multimodal distributions. The method is used to estimate the parameters and the initial state of two models of the Wnt pathway and it is shown that the multi-compartment model fits better the experimental data. Python scripts for the Dirichlet Process Gaussian Mixture model and the Gibbs sampler are available at https://sites.google.com/site/kkoutroumpas/software konstantinos.koutroumpas@ecp.fr. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Silent ABC Transporter Isolated from Streptomyces rochei F20 Induces Multidrug Resistance

PubMed Central

Fernández-Moreno, Miguel A.; Carbó, Lázaro; Cuesta, Trinidad; Vallín, Carlos; Malpartida, Francisco

1998-01-01

In the search for heterologous activators for actinorhodin production in Streptomyces lividans, 3.4 kb of DNA from Streptomyces rochei F20 (a streptothricin producer) were characterized. Subcloning experiments showed that the minimal DNA fragment required for activation was 0.4 kb in size. The activation is mediated by increasing the levels of transcription of the actII-ORF4 gene. Sequencing of the minimal activating fragment did not reveal any clues about its mechanism; nevertheless, it was shown to overlap the 3′ end of two convergent genes, one of whose translated products (ORF2) strongly resembles that of other genes belonging to the ABC transporter superfamily. Computer-assisted analysis of the 3.4-kb DNA sequence showed the 3′ terminus of an open reading frame (ORF), i.e., ORFA, and three complete ORFs (ORF1, ORF2, and ORFB). Searches in the databases with their respective gene products revealed similarities for ORF1 and ORF2 with ATP-binding proteins and transmembrane proteins, respectively, which are found in members of the ABC transporter superfamily. No similarities for ORFA and ORFB were found in the databases. Insertional inactivation of ORF1 and ORF2, their transcription analysis, and their cloning in heterologous hosts suggested that these genes were not expressed under our experimental conditions; however, cloning of ORF1 and ORF2 together (but not separately) under the control of an expressing promoter induced resistance to several chemically different drugs: oleandomycin, erythromycin, spiramycin, doxorubicin, and tetracycline. Thus, this genetic system, named msr, is a new bacterial multidrug ABC transporter. PMID:9696745

The mitochondrial transporter ABC-me (ABCB10), a downstream target of GATA-1, is essential for erythropoiesis in vivo

PubMed Central

Hyde, B B; Liesa, M; Elorza, A A; Qiu, W; Haigh, S E; Richey, L; Mikkola, H K; Schlaeger, T M; Shirihai, O S

2012-01-01

The mitochondrial transporter ATP binding cassette mitochondrial erythroid (ABC-me/ABCB10) is highly induced during erythroid differentiation by GATA-1 and its overexpression increases hemoglobin production rates in vitro. However, the role of ABC-me in erythropoiesis in vivo is unknown. Here we report for the first time that erythrocyte development in mice requires ABC-me. ABC-me−/− mice die at day 12.5 of gestation, showing nearly complete eradication of primitive erythropoiesis and lack of hemoglobinized cells at day 10.5. ABC-me−/− erythroid cells fail to differentiate because they exhibit a marked increase in apoptosis, both in vivo and ex vivo. Erythroid precursors are particularly sensitive to oxidative stress and ABC-me in the heart and its yeast ortholog multidrug resistance-like 1 have been shown to protect against oxidative stress. Thus, we hypothesized that increased apoptosis in ABC-me−/− erythroid precursors was caused by oxidative stress. Within this context, ABC-me deletion causes an increase in mitochondrial superoxide production and protein carbonylation in erythroid precursors. Furthermore, treatment of ABC-me−/− erythroid progenitors with the mitochondrial antioxidant MnTBAP (superoxide dismutase 2 mimetic) supports survival, ex vivo differentiation and increased hemoglobin production. Altogether, our findings demonstrate that ABC-me is essential for erythropoiesis in vivo. PMID:22240895

On the Huygens absorbing boundary conditions for electromagnetics

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

Berenger, Jean-Pierre

A new absorbing boundary condition (ABC) is presented for the solution of Maxwell equations in unbounded spaces. Called the Huygens ABC, this condition is a generalization of two previously published ABCs, namely the multiple absorbing surfaces (MAS) and the re-radiating boundary condition (rRBC). The properties of the Huygens ABC are derived theoretically in continuous spaces and in the finite-difference (FDTD) discretized space. A solution is proposed to render the Huygens ABC effective for the absorption of evanescent waves. Numerical experiments with the FDTD method show that the effectiveness of the Huygens ABC is close to that of the PML ABCmore » in some realistic problems of numerical electromagnetics. It is also shown in the paper that a combination of the Huygens ABC with the PML ABC is very well suited to the solution of some particular problems.« less

Investigating the compatibility of the biocontrol agent Clonostachys rosea IK726 with prodigiosin-producing Serratia rubidaea S55 and phenazine-producing Pseudomonas chlororaphis ToZa7.

PubMed

Kamou, Nathalie N; Dubey, Mukesh; Tzelepis, Georgios; Menexes, Georgios; Papadakis, Emmanouil N; Karlsson, Magnus; Lagopodi, Anastasia L; Jensen, Dan Funck

2016-05-01

This study was carried out to assess the compatibility of the biocontrol fungus Clonostachys rosea IK726 with the phenazine-producing Pseudomonas chlororaphis ToZa7 or with the prodigiosin-producing Serratia rubidaea S55 against Fusarium oxysporum f. sp. radicis-lycopersici. The pathogen was inhibited by both strains in vitro, whereas C. rosea displayed high tolerance to S. rubidaea but not to P. chlororaphis. We hypothesized that this could be attributed to the ATP-binding cassette (ABC) proteins. The results of the reverse transcription quantitative PCR showed an induction of seven genes (abcB1, abcB20, abcB26, abcC12, abcC12, abcG8 and abcG25) from subfamilies B, C and G. In planta experiments showed a significant reduction in foot and root rot on tomato plants inoculated with C. rosea and P. chlororaphis. This study demonstrates the potential for combining different biocontrol agents and suggests an involvement of ABC transporters in secondary metabolite tolerance in C. rosea.

Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation

PubMed Central

Vo, Brenda N.; Drovandi, Christopher C.; Pettitt, Anthony N.; Pettet, Graeme J.

2015-01-01

In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2–12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226–268 µm2h−1, 311–351 µm2h−1 and 0.23–0.39, 0.32–0.61 for the experimental periods of 0–24 h and 24–48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ. PMID:26642072

The Computational Infrastructure for Geodynamics: An Example of Software Curation and Citation in the Geodynamics Community

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2017-12-01

Curation of software promotes discoverability and accessibility and works hand in hand with scholarly citation to ascribe value to, and provide recognition for software development. To meet this challenge, the Computational Infrastructure for Geodynamics (CIG) maintains a community repository built on custom and open tools to promote discovery, access, identification, credit, and provenance of research software for the geodynamics community. CIG (geodynamics.org) originated from recognition of the tremendous effort required to develop sound software and the need to reduce duplication of effort and to sustain community codes. CIG curates software across 6 domains and has developed and follows software best practices that include establishing test cases, documentation, and a citable publication for each software package. CIG software landing web pages provide access to current and past releases; many are also accessible through the CIG community repository on github. CIG has now developed abc - attribution builder for citation to enable software users to give credit to software developers. abc uses zenodo as an archive and as the mechanism to obtain a unique identifier (DOI) for scientific software. To assemble the metadata, we searched the software's documentation and research publications and then requested the primary developers to verify. In this process, we have learned that each development community approaches software attribution differently. The metadata gathered is based on guidelines established by groups such as FORCE11 and OntoSoft. The rollout of abc is gradual as developers are forward-looking, rarely willing to go back and archive prior releases in zenodo. Going forward all actively developed packages will utilize the zenodo and github integration to automate the archival process when a new release is issued. How to handle legacy software, multi-authored libraries, and assigning roles to software remain open issues.

Approximate Bayesian estimation of extinction rate in the Finnish Daphnia magna metapopulation.

PubMed

Robinson, John D; Hall, David W; Wares, John P

2013-05-01

Approximate Bayesian computation (ABC) is useful for parameterizing complex models in population genetics. In this study, ABC was applied to simultaneously estimate parameter values for a model of metapopulation coalescence and test two alternatives to a strict metapopulation model in the well-studied network of Daphnia magna populations in Finland. The models shared four free parameters: the subpopulation genetic diversity (θS), the rate of gene flow among patches (4Nm), the founding population size (N0) and the metapopulation extinction rate (e) but differed in the distribution of extinction rates across habitat patches in the system. The three models had either a constant extinction rate in all populations (strict metapopulation), one population that was protected from local extinction (i.e. a persistent source), or habitat-specific extinction rates drawn from a distribution with specified mean and variance. Our model selection analysis favoured the model including a persistent source population over the two alternative models. Of the closest 750,000 data sets in Euclidean space, 78% were simulated under the persistent source model (estimated posterior probability = 0.769). This fraction increased to more than 85% when only the closest 150,000 data sets were considered (estimated posterior probability = 0.774). Approximate Bayesian computation was then used to estimate parameter values that might produce the observed set of summary statistics. Our analysis provided posterior distributions for e that included the point estimate obtained from previous data from the Finnish D. magna metapopulation. Our results support the use of ABC and population genetic data for testing the strict metapopulation model and parameterizing complex models of demography. © 2013 Blackwell Publishing Ltd.

Air pollution, greenhouse gases and climate change: Global and regional perspectives

NASA Astrophysics Data System (ADS)

Ramanathan, V.; Feng, Y.

Greenhouse gases (GHGs) warm the surface and the atmosphere with significant implications for rainfall, retreat of glaciers and sea ice, sea level, among other factors. About 30 years ago, it was recognized that the increase in tropospheric ozone from air pollution (NO x, CO and others) is an important greenhouse forcing term. In addition, the recognition of chlorofluorocarbons (CFCs) on stratospheric ozone and its climate effects linked chemistry and climate strongly. What is less recognized, however, is a comparably major global problem dealing with air pollution. Until about ten years ago, air pollution was thought to be just an urban or a local problem. But new data have revealed that air pollution is transported across continents and ocean basins due to fast long-range transport, resulting in trans-oceanic and trans-continental plumes of atmospheric brown clouds (ABCs) containing sub micron size particles, i.e., aerosols. ABCs intercept sunlight by absorbing as well as reflecting it, both of which lead to a large surface dimming. The dimming effect is enhanced further because aerosols may nucleate more cloud droplets, which makes the clouds reflect more solar radiation. The dimming has a surface cooling effect and decreases evaporation of moisture from the surface, thus slows down the hydrological cycle. On the other hand, absorption of solar radiation by black carbon and some organics increase atmospheric heating and tend to amplify greenhouse warming of the atmosphere. ABCs are concentrated in regional and mega-city hot spots. Long-range transport from these hot spots causes widespread plumes over the adjacent oceans. Such a pattern of regionally concentrated surface dimming and atmospheric solar heating, accompanied by widespread dimming over the oceans, gives rise to large regional effects. Only during the last decade, we have begun to comprehend the surprisingly large regional impacts. In S. Asia and N. Africa, the large north-south gradient in the ABC dimming has altered both the north-south gradients in sea surface temperatures and land-ocean contrast in surface temperatures, which in turn slow down the monsoon circulation and decrease rainfall over the continents. On the other hand, heating by black carbon warms the atmosphere at elevated levels from 2 to 6 km, where most tropical glaciers are located, thus strengthening the effect of GHGs on retreat of snow packs and glaciers in the Hindu Kush-Himalaya-Tibetan glaciers. Globally, the surface cooling effect of ABCs may have masked as much 47% of the global warming by greenhouse gases, with an uncertainty range of 20-80%. This presents a dilemma since efforts to curb air pollution may unmask the ABC cooling effect and enhance the surface warming. Thus efforts to reduce GHGs and air pollution should be done under one common framework. The uncertainties in our understanding of the ABC effects are large, but we are discovering new ways in which human activities are changing the climate and the environment.

50 CFR 622.60 - Adjustment of management measures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... markings and identification, allowable biological catch (ABC) and ABC control rules, rebuilding plans, sale... harvested shrimp (maintaining shrimp in whole condition, use as bait), target effort and fishing mortality... identification, vessel markings and identification, ABC and ABC control rules, rebuilding plans, sale and...

50 CFR 622.60 - Adjustment of management measures.

Code of Federal Regulations, 2014 CFR

2014-10-01

... markings and identification, allowable biological catch (ABC) and ABC control rules, rebuilding plans, sale... harvested shrimp (maintaining shrimp in whole condition, use as bait), target effort and fishing mortality... identification, vessel markings and identification, ABC and ABC control rules, rebuilding plans, sale and...

Developing a high-performance team training framework for internal medicine residents: the ABC'S of teamwork.

PubMed

Carbo, Alexander R; Tess, Anjala V; Roy, Christopher; Weingart, Saul N

2011-06-01

Effective teamwork and communication can prevent error and mitigate harm. High-performance team training was developed in the aviation industry for flight crews and is being incorporated in health care settings, such as emergency departments, operating rooms, and labor and delivery suites. We translated and adapted high-performance teamwork and communication principles from other industries and other disciplines to an inpatient internal medicine environment. We selected key principles from aviation and anesthesia crew training programs in 2004 and organized them into the ABC'S of teamwork. These included appropriate Assertiveness, effective Briefings, Callback and verification, Situational awareness, and Shared mental models. Based on this content, we developed a training session for internal medicine residents and faculty, and evaluated learners' patient safety attitudes and knowledge before and after training with a written survey. More than 50 residents participated in the module. The percentage of correct answers on a question related to key teamwork principles increased from 35% before training to 67% after training (P = 0.03). Before training, 65% of the residents reported that they "would feel comfortable telling a senior clinician his/her plan was unsafe"; this increased to 94% after training (P = 0.005). After the training session, residents were able to provide examples from their clinical practice that emphasized all of the ABC'S of teamwork. Teamwork principles can be adapted from other disciplines and applied to internal medicine. After a single session, residents displayed greater knowledge of teamwork principles and reported changed attitudes toward key teamwork behaviors.

Development of a practical costing method for hospitals.

PubMed

Cao, Pengyu; Toyabe, Shin-Ichi; Akazawa, Kouhei

2006-03-01

To realize an effective cost control, a practical and accurate cost accounting system is indispensable in hospitals. In traditional cost accounting systems, the volume-based costing (VBC) is the most popular cost accounting method. In this method, the indirect costs are allocated to each cost object (services or units of a hospital) using a single indicator named a cost driver (e.g., Labor hours, revenues or the number of patients). However, this method often results in rough and inaccurate results. The activity based costing (ABC) method introduced in the mid 1990s can prove more accurate results. With the ABC method, all events or transactions that cause costs are recognized as "activities", and a specific cost driver is prepared for each activity. Finally, the costs of activities are allocated to cost objects by the corresponding cost driver. However, it is much more complex and costly than other traditional cost accounting methods because the data collection for cost drivers is not always easy. In this study, we developed a simplified ABC (S-ABC) costing method to reduce the workload of ABC costing by reducing the number of cost drivers used in the ABC method. Using the S-ABC method, we estimated the cost of the laboratory tests, and as a result, similarly accurate results were obtained with the ABC method (largest difference was 2.64%). Simultaneously, this new method reduces the seven cost drivers used in the ABC method to four. Moreover, we performed an evaluation using other sample data from physiological laboratory department to certify the effectiveness of this new method. In conclusion, the S-ABC method provides two advantages in comparison to the VBC and ABC methods: (1) it can obtain accurate results, and (2) it is simpler to perform. Once we reduce the number of cost drivers by applying the proposed S-ABC method to the data for the ABC method, we can easily perform the cost accounting using few cost drivers after the second round of costing.

Thermo-responsive magnetic liposomes for hyperthermia-triggered local drug delivery.

PubMed

Dai, Min; Wu, Cong; Fang, Hong-Ming; Li, Li; Yan, Jia-Bao; Zeng, Dan-Lin; Zou, Tao

2017-06-01

We prepared and characterised thermo-responsive magnetic liposomes, which were designed to combine features of magnetic targeting and thermo-responsive control release for hyperthermia-triggered local drug delivery. The particle size and zeta-potential of the thermo-responsive magnetic ammonium bicarbonate (MagABC) liposomes were about 210 nm and -14 mV, respectively. The MagABC liposomes showed encapsulation efficiencies of about 15% and 82% for magnetic nanoparticles (mean crystallite size 12 nm) and doxorubicin (DOX), respectively. The morphology of the MagABC liposomes was visualised using transmission electron microscope (TEM). The MagABC liposomes showed desired thermo-responsive release. The MagABC liposomes, when physically targeted to tumour cells in culture by a permanent magnetic field yielded a substantial increase in intracellular accumulation of DOX as compared to non-magnetic ammonium bicarbonate (ABC) liposomes. This resulted in a parallel increase in cytotoxicity for DOX loaded MagABC liposomes over DOX loaded ABC liposomes in tumour cells.

The Centre of High-Performance Scientific Computing, Geoverbund, ABC/J - Geosciences enabled by HPSC

NASA Astrophysics Data System (ADS)

Kollet, Stefan; Görgen, Klaus; Vereecken, Harry; Gasper, Fabian; Hendricks-Franssen, Harrie-Jan; Keune, Jessica; Kulkarni, Ketan; Kurtz, Wolfgang; Sharples, Wendy; Shrestha, Prabhakar; Simmer, Clemens; Sulis, Mauro; Vanderborght, Jan

2016-04-01

The Centre of High-Performance Scientific Computing (HPSC TerrSys) was founded 2011 to establish a centre of competence in high-performance scientific computing in terrestrial systems and the geosciences enabling fundamental and applied geoscientific research in the Geoverbund ABC/J (geoscientfic research alliance of the Universities of Aachen, Cologne, Bonn and the Research Centre Jülich, Germany). The specific goals of HPSC TerrSys are to achieve relevance at the national and international level in (i) the development and application of HPSC technologies in the geoscientific community; (ii) student education; (iii) HPSC services and support also to the wider geoscientific community; and in (iv) the industry and public sectors via e.g., useful applications and data products. A key feature of HPSC TerrSys is the Simulation Laboratory Terrestrial Systems, which is located at the Jülich Supercomputing Centre (JSC) and provides extensive capabilities with respect to porting, profiling, tuning and performance monitoring of geoscientific software in JSC's supercomputing environment. We will present a summary of success stories of HPSC applications including integrated terrestrial model development, parallel profiling and its application from watersheds to the continent; massively parallel data assimilation using physics-based models and ensemble methods; quasi-operational terrestrial water and energy monitoring; and convection permitting climate simulations over Europe. The success stories stress the need for a formalized education of students in the application of HPSC technologies in future.

Methods for modeling cytoskeletal and DNA filaments

NASA Astrophysics Data System (ADS)

Andrews, Steven S.

2014-02-01

This review summarizes the models that researchers use to represent the conformations and dynamics of cytoskeletal and DNA filaments. It focuses on models that address individual filaments in continuous space. Conformation models include the freely jointed, Gaussian, angle-biased chain (ABC), and wormlike chain (WLC) models, of which the first three bend at discrete joints and the last bends continuously. Predictions from the WLC model generally agree well with experiment. Dynamics models include the Rouse, Zimm, stiff rod, dynamic WLC, and reptation models, of which the first four apply to isolated filaments and the last to entangled filaments. Experiments show that the dynamic WLC and reptation models are most accurate. They also show that biological filaments typically experience strong hydrodynamic coupling and/or constrained motion. Computer simulation methods that address filament dynamics typically compute filament segment velocities from local forces using the Langevin equation and then integrate these velocities with explicit or implicit methods; the former are more versatile and the latter are more efficient. Much remains to be discovered in biological filament modeling. In particular, filament dynamics in living cells are not well understood, and current computational methods are too slow and not sufficiently versatile. Although primarily a review, this paper also presents new statistical calculations for the ABC and WLC models. Additionally, it corrects several discrepancies in the literature about bending and torsional persistence length definitions, and their relations to flexural and torsional rigidities.

The A [plus] B [double arrow] C of Chemical Thermodynamics.

ERIC Educational Resources Information Center

Gerhartl, F. J.

1994-01-01

Basic chemical thermodynamics usually treats non-p,T reactions in a stepmotherly fashion. This paper covers the main aspects of the theoretical principles of reactions (p,T; V,T; p,H; and V,U) and offers results from the ABC computer program, which was designed to show the validity of the equilibrium theory to all types of reaction modes. (PVD)

Beyond Transitional Probability Computations: Extracting Word-Like Units when Only Statistical Information Is Available

ERIC Educational Resources Information Center

Perruchet, Pierre; Poulin-Charronnat, Benedicte

2012-01-01

Endress and Mehler (2009) reported that when adult subjects are exposed to an unsegmented artificial language composed from trisyllabic words such as ABX, YBC, and AZC, they are unable to distinguish between these words and what they coined as the "phantom-word" ABC in a subsequent test. This suggests that statistical learning generates knowledge…

A Neisseria meningitidis fbpABC mutant is incapable of using nonheme iron for growth.

PubMed

Khun, H H; Kirby, S D; Lee, B C

1998-05-01

The neisserial fbpABC locus has been proposed to act as an iron-specific ABC transporter system. To confirm this assigned function, we constructed an fbpABC mutant in Neisseria meningitidis by insertional inactivation of fbpABC with a selectable antibiotic marker. The mutant was unable to use iron supplied from human transferrin, human lactoferrin, or iron chelates. However, the use of iron from heme and human hemoglobin was unimpaired. These results support the obligatory participation of fbpABC in neisserial periplasmic iron transport and do not indicate a role for this genetic locus in the heme iron pathway.

A Neisseria meningitidis fbpABC Mutant Is Incapable of Using Nonheme Iron for Growth

PubMed Central

Khun, Heng H.; Kirby, Shane D.; Lee, B. Craig

1998-01-01

The neisserial fbpABC locus has been proposed to act as an iron-specific ABC transporter system. To confirm this assigned function, we constructed an fbpABC mutant in Neisseria meningitidis by insertional inactivation of fbpABC with a selectable antibiotic marker. The mutant was unable to use iron supplied from human transferrin, human lactoferrin, or iron chelates. However, the use of iron from heme and human hemoglobin was unimpaired. These results support the obligatory participation of fbpABC in neisserial periplasmic iron transport and do not indicate a role for this genetic locus in the heme iron pathway. PMID:9573125

Object Detection Based on Template Matching through Use of Best-So-Far ABC

PubMed Central

2014-01-01

Best-so-far ABC is a modified version of the artificial bee colony (ABC) algorithm used for optimization tasks. This algorithm is one of the swarm intelligence (SI) algorithms proposed in recent literature, in which the results demonstrated that the best-so-far ABC can produce higher quality solutions with faster convergence than either the ordinary ABC or the current state-of-the-art ABC-based algorithm. In this work, we aim to apply the best-so-far ABC-based approach for object detection based on template matching by using the difference between the RGB level histograms corresponding to the target object and the template object as the objective function. Results confirm that the proposed method was successful in both detecting objects and optimizing the time used to reach the solution. PMID:24812556

Generative inference for cultural evolution.

PubMed

Kandler, Anne; Powell, Adam

2018-04-05

One of the major challenges in cultural evolution is to understand why and how various forms of social learning are used in human populations, both now and in the past. To date, much of the theoretical work on social learning has been done in isolation of data, and consequently many insights focus on revealing the learning processes or the distributions of cultural variants that are expected to have evolved in human populations. In population genetics, recent methodological advances have allowed a greater understanding of the explicit demographic and/or selection mechanisms that underlie observed allele frequency distributions across the globe, and their change through time. In particular, generative frameworks-often using coalescent-based simulation coupled with approximate Bayesian computation (ABC)-have provided robust inferences on the human past, with no reliance on a priori assumptions of equilibrium. Here, we demonstrate the applicability and utility of generative inference approaches to the field of cultural evolution. The framework advocated here uses observed population-level frequency data directly to establish the likely presence or absence of particular hypothesized learning strategies. In this context, we discuss the problem of equifinality and argue that, in the light of sparse cultural data and the multiplicity of possible social learning processes, the exclusion of those processes inconsistent with the observed data might be the most instructive outcome. Finally, we summarize the findings of generative inference approaches applied to a number of case studies.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Requirements for Information/Education Programs on Hypothermia.

DTIC Science & Technology

1979-10-23

NY (NBC) WEZF - Burlington, VT (ABC) Bangor, ME: 112,800 WLBZ - Bangor, ME (NBC) WABI - Bangor, ME (CBS) WVII - Bangor, ME (ABC) Presque Isle , ME...28,700 WAGM - Presque Isle , ME CBS(ABC-NBC) A-2 MID-ATLANTIC: 18,885,600 New York, NY: 6,375,500 Raleigh-Durham, NC: 451,800 WCBS - New York, NY (CBS...NY (ABC) WICZ - Binghamton, NY (NBC) WilingonNC: 135,300 WWAY -IWilmington, NC (ABC) WECT - Wilmington, NC NBC (CBS) Erie , PA: 132,600 WICU - Erie , PA

Determinants of Fast Food Consumption among Iranian High School Students Based on Planned Behavior Theory

PubMed Central

Sharifirad, Gholamreza; Yarmohammadi, Parastoo; Azadbakht, Leila; Morowatisharifabad, Mohammad Ali; Hassanzadeh, Akbar

2013-01-01

Objective. This study was conducted to identify some factors (beliefs and norms) which are related to fast food consumption among high school students in Isfahan, Iran. We used the framework of the theory planned behavior (TPB) to predict this behavior. Subjects & Methods. Cross-sectional data were available from high school students (n = 521) who were recruited by cluster randomized sampling. All of the students completed a questionnaire assessing variables of standard TPB model including attitude, subjective norms, perceived behavior control (PBC), and the additional variables past behavior, actual behavior control (ABC). Results. The TPB variables explained 25.7% of the variance in intentions with positive attitude as the strongest (β = 0.31, P < 0.001) and subjective norms as the weakest (β = 0.29, P < 0.001) determinant. Concurrently, intentions accounted for 6% of the variance for fast food consumption. Past behavior and ABC accounted for an additional amount of 20.4% of the variance in fast food consumption. Conclusion. Overall, the present study suggests that the TPB model is useful in predicting related beliefs and norms to the fast food consumption among adolescents. Subjective norms in TPB model and past behavior in TPB model with additional variables (past behavior and actual behavior control) were the most powerful predictors of fast food consumption. Therefore, TPB model may be a useful framework for planning intervention programs to reduce fast food consumption by students. PMID:23936635

Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil.

PubMed

Gehara, Marcelo; Garda, Adrian A; Werneck, Fernanda P; Oliveira, Eliana F; da Fonseca, Emanuel M; Camurugi, Felipe; Magalhães, Felipe de M; Lanna, Flávia M; Sites, Jack W; Marques, Ricardo; Silveira-Filho, Ricardo; São Pedro, Vinícius A; Colli, Guarino R; Costa, Gabriel C; Burbrink, Frank T

2017-09-01

Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data, we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest. © 2017 John Wiley & Sons Ltd.

Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes

NASA Astrophysics Data System (ADS)

Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M.; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

2015-10-01

Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03884g

Building Self-Esteem of Children and Adolescents through Adventure-Based Counseling.

ERIC Educational Resources Information Center

Nassar-McMillan, Sylvia C.; Cashwell, Craig S.

1997-01-01

Explores ways in which communities and school counselors can foster self-esteem in children and adolescents through adventure-based counseling (ABC). Discusses the importance of self-esteem, the philosophy and tenets of ABC, the effectiveness of ABC, and ways to integrate ABC concepts into groups. Focuses on prevention and intervention. (RJM)

Finite-difference time-domain simulation of GPR data

NASA Astrophysics Data System (ADS)

Chen, How-Wei; Huang, Tai-Min

1998-10-01

Simulation of digital ground penetrating radar (GPR) wave propagation in two-dimensional (2-D) media is developed, tested, implemented, and applied using a time-domain staggered-grid finite-difference (FD) numerical method. Three types of numerical algorithms for constructing synthetic common-shot, constant-offset radar profiles based on an actual transmitter-to-receiver configuration and based on the exploding reflector concept are demonstrated to mimic different types of radar survey geometries. Frequency-dependent attenuation is also incorporated to account for amplitude decay and time shift in the recorded responses. The algorithms are based on an explicit FD solution to Maxwell's curl equations. In addition, the first-order TE mode responses of wave propagation phenomena are considered due to the operating frequency of current GPR instruments. The staggered-grid technique is used to sample the fields and approximate the spatial derivatives with fourth-order FDs. The temporal derivatives are approximated by an explicit second-order difference time-marching scheme. By combining paraxial approximation of the one-way wave equation ( A2) and the damping mechanisms (sponge filter), we propose a new composite absorbing boundary conditions (ABC) algorithm that effectively absorb both incoming and outgoing waves. To overcome the angle- and frequency-dependent characteristic of the absorbing behaviors, each ABC has two types of absorption mechanism. The first ABC uses a modified Clayton and Enquist's A2 condition. Moreover, a fixed and a floating A2 ABC that operates at one grid point is proposed. The second ABC uses a damping mechanism. By superimposing artificial damping and by alternating the physical attenuation properties and impedance contrast of the media within the absorbing region, those waves impinging on the boundary can be effectively attenuated and can prevent waves from reflecting back into the grid. The frequency-dependent characteristic of the damping mechanism can be used to adjust the width of the absorbing zone around the computational domain. By applying any combination of absorbing mechanism, non-physical reflections from the computation domain boundary can be effectively minimized. The algorithm enables us to use very thin absorbing boundaries. The model can be parameterized through velocity, relative electrical permittivity (dielectric constants), electrical conductivity, magnetic permeability, loss tangent, Q values, and attenuation. According to this scheme, widely varying electrical properties of near-surface earth materials can be modeled. The capability of simulating common-source, constant-offset and zero-offset gathers is also demonstrated through various synthetic examples. The synthetic cases for typical GPR applications include buried objects such as pipes of different materials, AVO analysis for ground water exploration, archaeological site investigation, and stratigraphy studies. The algorithms are also applied to iterative modeling of GPR data acquired over a gymnasium construction site on the NCCU campus.

ABCE1 is essential for S phase progression in human cells

PubMed Central

Toompuu, Marina; Kärblane, Kairi; Pata, Pille; Truve, Erkki; Sarmiento, Cecilia

2016-01-01

ABSTRACT ABCE1 is a highly conserved protein universally present in eukaryotes and archaea, which is crucial for the viability of different organisms. First identified as RNase L inhibitor, ABCE1 is currently recognized as an essential translation factor involved in several stages of eukaryotic translation and ribosome biogenesis. The nature of vital functions of ABCE1, however, remains unexplained. Here, we study the role of ABCE1 in human cell proliferation and its possible connection to translation. We show that ABCE1 depletion by siRNA results in a decreased rate of cell growth due to accumulation of cells in S phase, which is accompanied by inefficient DNA synthesis and reduced histone mRNA and protein levels. We infer that in addition to the role in general translation, ABCE1 is involved in histone biosynthesis and DNA replication and therefore is essential for normal S phase progression. In addition, we analyze whether ABCE1 is implicated in transcript-specific translation via its association with the eIF3 complex subunits known to control the synthesis of cell proliferation-related proteins. The expression levels of a few such targets regulated by eIF3A, however, were not consistently affected by ABCE1 depletion. PMID:26985706

A novel approach for dimension reduction of microarray.

PubMed

Aziz, Rabia; Verma, C K; Srivastava, Namita

2017-12-01

This paper proposes a new hybrid search technique for feature (gene) selection (FS) using Independent component analysis (ICA) and Artificial Bee Colony (ABC) called ICA+ABC, to select informative genes based on a Naïve Bayes (NB) algorithm. An important trait of this technique is the optimization of ICA feature vector using ABC. ICA+ABC is a hybrid search algorithm that combines the benefits of extraction approach, to reduce the size of data and wrapper approach, to optimize the reduced feature vectors. This hybrid search technique is facilitated by evaluating the performance of ICA+ABC on six standard gene expression datasets of classification. Extensive experiments were conducted to compare the performance of ICA+ABC with the results obtained from recently published Minimum Redundancy Maximum Relevance (mRMR) +ABC algorithm for NB classifier. Also to check the performance that how ICA+ABC works as feature selection with NB classifier, compared the combination of ICA with popular filter techniques and with other similar bio inspired algorithm such as Genetic Algorithm (GA) and Particle Swarm Optimization (PSO). The result shows that ICA+ABC has a significant ability to generate small subsets of genes from the ICA feature vector, that significantly improve the classification accuracy of NB classifier compared to other previously suggested methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

Caenorhabditis elegans ABCRNAi transporters interact genetically with rde-2 and mut-7.

PubMed

Sundaram, Prema; Han, Wang; Cohen, Nancy; Echalier, Benjamin; Albin, John; Timmons, Lisa

2008-02-01

RNA interference (RNAi) mechanisms are conserved and consist of an interrelated network of activities that not only respond to exogenous dsRNA, but also perform endogenous functions required in the fine tuning of gene expression and in maintaining genome integrity. Not surprisingly, RNAi functions have widespread influences on cellular function and organismal development. Previously, we observed a reduced capacity to mount an RNAi response in nine Caenorhabditis elegans mutants that are defective in ABC transporter genes (ABC(RNAi) mutants). Here, we report an exhaustive study of mutants, collectively defective in 49 different ABC transporter genes, that allowed for the categorization of one additional transporter into the ABC(RNAi) gene class. Genetic complementation tests reveal functions for ABC(RNAi) transporters in the mut-7/rde-2 branch of the RNAi pathway. These second-site noncomplementation interactions suggest that ABC(RNAi) proteins and MUT-7/RDE-2 function together in parallel pathways and/or as multiprotein complexes. Like mut-7 and rde-2, some ABC(RNAi) mutants display transposon silencing defects. Finally, our analyses reveal a genetic interaction network of ABC(RNAi) gene function with respect to this part of the RNAi pathway. From our results, we speculate that the coordinated activities of ABC(RNAi) transporters, through their effects on endogenous RNAi-related mechanisms, ultimately affect chromosome function and integrity.

Antitumor effect of the novel sphingosine kinase 2 inhibitor ABC294640 is enhanced by inhibition of autophagy and by sorafenib in human cholangiocarcinoma cells.

PubMed

Ding, Xiwei; Chaiteerakij, Roongruedee; Moser, Catherine D; Shaleh, Hassan; Boakye, Jeffrey; Chen, Gang; Ndzengue, Albert; Li, Ying; Zhou, Yanling; Huang, Shengbing; Sinicrope, Frank A; Zou, Xiaoping; Thomas, Melanie B; Smith, Charles D; Roberts, Lewis R

2016-04-12

Sphingosine kinase 2 (Sphk2) has an oncogenic role in cancer. A recently developed first-in-class Sphk2 specific inhibitor ABC294640 displays antitumor activity in many cancer models. However, the role of Sphk2 and the antitumor activity of its inhibitor ABC294640 are not known in cholangiocarcinoma. We investigated the potential of targeting Sphk2 for the treatment of cholangiocarcinoma. We found that Sphk2 is overexpressed in five established human cholangiocarcinoma cell lines (WITT, HuCCT1, EGI-1, OZ and HuH28) and a new patient-derived cholangiocarcinoma cell line (LIV27) compared to H69 normal cholangiocytes. Inhibition of Sphk2 by ABC294640 inhibited proliferation and induced caspase-dependent apoptosis. Furthermore, we found that ABC294640 inhibited STAT3 phosphorylation, one of the key signaling pathways regulating cholangiocarcinoma cell proliferation and survival. ABC294640 also induced autophagy. Inhibition of autophagy by bafilomycin A1 or chloroquine potentiated ABC294640-induced cytotoxicity and apoptosis. In addition, ABC294640 in combination with sorafenib synergistically inhibited cell proliferation of cholangiocarcinoma cells. Strong decreases in STAT3 phosphorylation were observed in WITT and HuCCT1 cells exposed to the ABC294640 and sorafenib combination. These findings provide novel evidence that Sphk2 may be a rational therapeutic target in cholangiocarcinoma. Combinations of ABC294640 with sorafenib and/or autophagy inhibitors may provide novel strategies for the treatment of cholangiocarcinoma.

A novel artificial bee colony algorithm based on modified search equation and orthogonal learning.

PubMed

Gao, Wei-feng; Liu, San-yang; Huang, Ling-ling

2013-06-01

The artificial bee colony (ABC) algorithm is a relatively new optimization technique which has been shown to be competitive to other population-based algorithms. However, ABC has an insufficiency regarding its solution search equation, which is good at exploration but poor at exploitation. To address this concerning issue, we first propose an improved ABC method called as CABC where a modified search equation is applied to generate a candidate solution to improve the search ability of ABC. Furthermore, we use the orthogonal experimental design (OED) to form an orthogonal learning (OL) strategy for variant ABCs to discover more useful information from the search experiences. Owing to OED's good character of sampling a small number of well representative combinations for testing, the OL strategy can construct a more promising and efficient candidate solution. In this paper, the OL strategy is applied to three versions of ABC, i.e., the standard ABC, global-best-guided ABC (GABC), and CABC, which yields OABC, OGABC, and OCABC, respectively. The experimental results on a set of 22 benchmark functions demonstrate the effectiveness and efficiency of the modified search equation and the OL strategy. The comparisons with some other ABCs and several state-of-the-art algorithms show that the proposed algorithms significantly improve the performance of ABC. Moreover, OCABC offers the highest solution quality, fastest global convergence, and strongest robustness among all the contenders on almost all the test functions.

Expression, purification and characterization of GAPDH-ChSase ABC I from Proteus vulgaris in Escherichia coli.

PubMed

Li, Ye; Chen, Zhenya; Zhou, Zhao; Yuan, Qipeng

2016-12-01

Chondroitinases (ChSases) are a family of polysaccharide lyases that can depolymerize high molecular weight chondroitin sulfate (CS) and dermatan sulfate (DS). In this study, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is stably expressed in different cells like normal cells and cancer cells and the expression is relatively insensitive to experimental conditions, was expressed as a fusion protein with ChSase ABC I. Results showed that the expression level and enzyme activity of GAPDH-ChSase ABC I were about 2.2 and 3.0 times higher than those of ChSase ABC I. By optimization of fermentation conditions, higher productivity of ChSase ABC I was achieved as 880 ± 61 IU/g wet cell weight compared with the reported ones. The optimal temperature and pH of GAPDH-ChSase ABC I were 40 °C and 7.5, respectively. GAPDH-ChSase ABC I had a kcat/Km of 131 ± 4.1 L/μmol s and the catalytic efficiency was decreased as compared to ChSase ABC I. The relative activity of GAPDH-ChSase ABC I remained 89% after being incubated at 30 °C for 180 min and the thermostability of ChSase ABC I was enhanced by GAPDH when it was incubated at 30, 35, 40 and 45 °C. Copyright © 2016 Elsevier Inc. All rights reserved.

Application of activity-based costing (ABC) for a Peruvian NGO healthcare provider.

PubMed

Waters, H; Abdallah, H; Santillán, D

2001-01-01

This article describes the application of activity-based costing (ABC) to calculate the unit costs of the services for a health care provider in Peru. While traditional costing allocates overhead and indirect costs in proportion to production volume or to direct costs, ABC assigns costs through activities within an organization. ABC uses personnel interviews to determine principal activities and the distribution of individual's time among these activities. Indirect costs are linked to services through time allocation and other tracing methods, and the result is a more accurate estimate of unit costs. The study concludes that applying ABC in a developing country setting is feasible, yielding results that are directly applicable to pricing and management. ABC determines costs for individual clinics, departments and services according to the activities that originate these costs, showing where an organization spends its money. With this information, it is possible to identify services that are generating extra revenue and those operating at a loss, and to calculate cross subsidies across services. ABC also highlights areas in the health care process where efficiency improvements are possible. Conclusions about the ultimate impact of the methodology are not drawn here, since the study was not repeated and changes in utilization patterns and the addition of new clinics affected applicability of the results. A potential constraint to implementing ABC is the availability and organization of cost information. Applying ABC efficiently requires information to be readily available, by cost category and department, since the greatest benefits of ABC come from frequent, systematic application of the methodology in order to monitor efficiency and provide feedback for management. The article concludes with a discussion of the potential applications of ABC in the health sector in developing countries.

Abacavir induces platelet-endothelium interactions by interfering with purinergic signalling: A step from inflammation to thrombosis.

PubMed

Alvarez, Angeles; Rios-Navarro, Cesar; Blanch-Ruiz, Maria Amparo; Collado-Diaz, Victor; Andujar, Isabel; Martinez-Cuesta, Maria Angeles; Orden, Samuel; Esplugues, Juan V

2017-05-01

The controversy connecting Abacavir (ABC) with cardiovascular disease has been fuelled by the lack of a credible mechanism of action. ABC shares structural similarities with endogenous purines, signalling molecules capable of triggering prothrombotic/proinflammatory programmes. Platelets are leading actors in the process of thrombosis. Our study addresses the effects of ABC on interactions between platelets and other vascular cells, while exploring the adhesion molecules implicated and the potential interference with the purinergic signalling pathway. The effects of ABC on platelet aggregation and platelet-endothelium interactions were evaluated, respectively, with an aggregometer and a flow chamber system that reproduced conditions in vivo. The role of adhesion molecules and purinergic receptors in endothelial and platelet populations was assessed by selective pre-incubation with specific antagonists and antibodies. ABC and carbovir triphosphate (CBT) levels were evaluated by HPLC. The results showed that ABC promoted the adherence of platelets to endothelial cells, a crucial step for the formation of thrombi. This was not a consequence of a direct effect of ABC on platelets, but resulted from activation of the endothelium via purinergic ATP-P2X 7 receptors, which subsequently triggered an interplay between P-selectin and ICAM-1 on endothelial cells with constitutively expressed GPIIb/IIIa and GPIbα on platelets. ABC did not induce platelet activation (P-selectin expression or Ca 2+ mobilization) or aggregation, even at high concentrations. CBT levels in endothelial cells were lower than those required to induce platelet-endothelium interactions. Thus, ABC interference with endothelial purinergic signalling leads to platelet recruitment. This highlights the endothelium as the main cell target of ABC in this interaction, which is in line with previous experimental evidence that ABC induces manifestations of vascular inflammation. Copyright © 2017 Elsevier B.V. All rights reserved.

SU-E-T-401: Feasibility Study of Using ABC to Gate Lung SBRT Treatment

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

Cao, D; Xie, X; Shepard, D

2014-06-01

Purpose: The current SBRT treatment techniques include free breathing (FB) SBRT and gated FB SBRT. Gated FB SBRT has smaller target and less lung toxicity with longer treatment time. The recent development of direct connectivity between the ABC and linac allowing for automated beam gating. In this study, we have examined the feasibility of using ABC system to gate the lung SBRT treatment. Methods: A CIRS lung phantom with a 3cm sphere-insert and a moving chest plate was used in this study. Sinusoidal motion was used for the FB pattern. An ABC signal was imported to simulate breath holds. 4D-CTmore » was taken in FB mode and average-intensity-projection (AIP) was used to create FB and 50% gated FB SBRT planning CT. A manually gated 3D CT scan was acquired for ABC gated SBRT planning.An SBRT plan was created for each treatment option. A surface-mapping system was used for 50% gating and ABC system was used for ABC gating. A manually gated CBCT scan was also performed to verify setup. Results: Among three options, the ABC gated plan has the smallest PTV of 35.94cc, which is 35% smaller comparing to that of the FB plan. Consequently, the V20 of the left lung reduced by 15% and 23% comparing to the 50% gated FB and FB plans, respectively. The FB plan took 4.7 minutes to deliver, while the 50% gated FB plan took 18.5 minutes. The ABC gated plan delivery took only 10.6 minutes. A stationary target with 3cm diameter was also obtained from the manually gated CBCT scan. Conclusion: A strategy for ABC gated lung SBRT was developed. ABC gating can significantly reduce the lung toxicity while maintaining the target coverage. Comparing to the 50% gated FB SBRT, ABC gated treatment can also provide less lung toxicity as well as improved delivery efficiency. This research is funded by Elekta.« less

ABC transporters are involved in defense against permethrin insecticide in the malaria vector Anopheles stephensi.

PubMed

Epis, Sara; Porretta, Daniele; Mastrantonio, Valentina; Comandatore, Francesco; Sassera, Davide; Rossi, Paolo; Cafarchia, Claudia; Otranto, Domenico; Favia, Guido; Genchi, Claudio; Bandi, Claudio; Urbanelli, Sandra

2014-07-29

Proteins from the ABC family (ATP-binding cassette) represent the largest known group of efflux pumps, responsible for transporting specific molecules across lipid membranes in both prokaryotic and eukaryotic organisms. In arthropods they have been shown to play a role in insecticide defense/resistance. The presence of ABC transporters and their possible association with insecticide transport have not yet been investigated in the mosquito Anopheles stephensi, the major vector of human malaria in the Middle East and South Asian regions. Here we investigated the presence and role of ABCs in transport of permethrin insecticide in a susceptible strain of this mosquito species. To identify ABC transporter genes we obtained a transcriptome from untreated larvae of An. stephensi and then compared it with the annotated transcriptome of Anopheles gambiae. To analyse the association between ABC transporters and permethrin we conducted bioassays with permethrin alone and in combination with an ABC inhibitor, and then we investigated expression profiles of the identified genes in larvae exposed to permethrin. Bioassays showed an increased mortality of mosquitoes when permethrin was used in combination with the ABC-transporter inhibitor. Genes for ABC transporters were detected in the transcriptome, and five were selected (AnstABCB2, AnstABCB3, AnstABCB4, AnstABCmember6 and AnstABCG4). An increased expression in one of them (AnstABCG4) was observed in larvae exposed to the LD50 dose of permethrin. Contrary to what was found in other insect species, no up-regulation was observed in the AnstABCB genes. Our results show for the first time the involvement of ABC transporters in larval defense against permethrin in An. stephensi and, more in general, confirm the role of ABC transporters in insecticide defense. The differences observed with previous studies highlight the need of further research as, despite the growing number of studies on ABC transporters in insects, the heterogeneity of the results available at present does not allow us to infer general trends in ABC transporter-insecticide interactions.

Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

PubMed Central

Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric

2016-01-01

Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927

Critical Problems in Very Large Scale Computer Systems

DTIC Science & Technology

1989-09-30

N Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Anant Agarwal (617) 253-1448 William J. Dally (617) 253-6043 Srinivas Devadas ...rapidly switched between the ports. Labelling the terminal voltages ab.c. d. this attempts to enforce a constraint a - b = c - d. This is a reciprocal...Srinivas Devadas and his students have been focusing on the optimization ofcomibinational and sequen- tial circuits specified at the register

Transforming System Engineering through Model-Centric Engineering

DTIC Science & Technology

2015-11-18

best practices and provide computational technologies for real-time training within digital engineering environments  Multidisciplinary System...MBSE well due to continued training and practicing . While MBSE is a part of the MCE it does not encompass the full idea and enabling technologies of... practices against other Industry contractors and it was believed that ABC was trailing the others in the use of MDAO capabilities. They decided that

Audio-Visual Biofeedback Does Not Improve the Reliability of Target Delineation Using Maximum Intensity Projection in 4-Dimensional Computed Tomography Radiation Therapy Planning

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

Lu, Wei, E-mail: wlu@umm.edu; Neuner, Geoffrey A.; George, Rohini

2014-01-01

Purpose: To investigate whether coaching patients' breathing would improve the match between ITV{sub MIP} (internal target volume generated by contouring in the maximum intensity projection scan) and ITV{sub 10} (generated by combining the gross tumor volumes contoured in 10 phases of a 4-dimensional CT [4DCT] scan). Methods and Materials: Eight patients with a thoracic tumor and 5 patients with an abdominal tumor were included in an institutional review board-approved prospective study. Patients underwent 3 4DCT scans with: (1) free breathing (FB); (2) coaching using audio-visual (AV) biofeedback via the Real-Time Position Management system; and (3) coaching via a spirometer systemmore » (Active Breathing Coordinator or ABC). One physician contoured all scans to generate the ITV{sub 10} and ITV{sub MIP}. The match between ITV{sub MIP} and ITV{sub 10} was quantitatively assessed with volume ratio, centroid distance, root mean squared distance, and overlap/Dice coefficient. We investigated whether coaching (AV or ABC) or uniform expansions (1, 2, 3, or 5 mm) of ITV{sub MIP} improved the match. Results: Although both AV and ABC coaching techniques improved frequency reproducibility and ABC improved displacement regularity, neither improved the match between ITV{sub MIP} and ITV{sub 10} over FB. On average, ITV{sub MIP} underestimated ITV{sub 10} by 19%, 19%, and 21%, with centroid distance of 1.9, 2.3, and 1.7 mm and Dice coefficient of 0.87, 0.86, and 0.88 for FB, AV, and ABC, respectively. Separate analyses indicated a better match for lung cancers or tumors not adjacent to high-intensity tissues. Uniform expansions of ITV{sub MIP} did not correct for the mismatch between ITV{sub MIP} and ITV{sub 10}. Conclusions: In this pilot study, audio-visual biofeedback did not improve the match between ITV{sub MIP} and ITV{sub 10}. In general, ITV{sub MIP} should be limited to lung cancers, and modification of ITV{sub MIP} in each phase of the 4DCT data set is recommended.« less

ABC versus CAB for cardiopulmonary resuscitation: a prospective, randomized simulator-based trial.

PubMed

Marsch, Stephan; Tschan, Franziska; Semmer, Norbert K; Zobrist, Roger; Hunziker, Patrick R; Hunziker, Sabina

2013-09-06

After years of advocating ABC (Airway-Breathing-Circulation), current guidelines of cardiopulmonary resuscitation (CPR) recommend CAB (Circulation-Airway-Breathing). This trial compared ABC with CAB as initial approach to CPR from the arrival of rescuers until the completion of the first resuscitation cycle. 108 teams, consisting of two physicians each, were randomized to receive a graphical display of either the ABC algorithm or the CAB algorithm. Subsequently teams had to treat a simulated cardiac arrest. Data analysis was performed using video recordings obtained during simulations. The primary endpoint was the time to completion of the first resuscitation cycle of 30 compressions and two ventilations. The time to execution of the first resuscitation measure was 32 ± 12 seconds in ABC teams and 25 ± 10 seconds in CAB teams (P = 0.002). 18/53 ABC teams (34%) and none of the 55 CAB teams (P = 0.006) applied more than the recommended two initial rescue breaths which caused a longer duration of the first cycle of 30 compressions and two ventilations in ABC teams (31 ± 13 vs.23 ± 6 sec; P = 0.001). Overall, the time to completion of the first resuscitation cycle was longer in ABC teams (63 ± 17 vs. 48 ± 10 sec; P <0.0001). This randomized controlled trial found CAB superior to ABC with an earlier start of CPR and a shorter time to completion of the first 30:2 resuscitation cycle. These findings endorse the change from ABC to CAB in international resuscitation guidelines.

Diagnosing and discriminating between primary and secondary aneurysmal bone cysts

PubMed Central

Sasaki, Hiromi; Nagano, Satoshi; Shimada, Hirofumi; Yokouchi, Masahiro; Setoguchi, Takao; Ishidou, Yasuhiro; Kunigou, Osamu; Maehara, Kosuke; Komiya, Setsuro

2017-01-01

Aneurysmal bone cysts (ABCs) are benign bony lesions frequently accompanied by multiple cystic lesions and aggressive bone destruction. They are relatively rare lesions, representing only 1% of bone tumors. The pathogenesis of ABCs has yet to be elucidated. In the present study, a series of 22 cases of primary and secondary ABC from patients treated in Department of Orthopedic Surgery, Kagoshima University Hospital (Kagoshima, Japan) from 2001–2015 were retrospectively analyzed. The average age at the time of diagnosis of primary ABC was 17.9 years. Intralesional curettage and artificial bone grafting were performed in the majority of the patients with primary ABC. The local recurrence rate following curettage for primary ABC was 18%, and the cause of local recurrence was considered to be insufficient curettage. Although no adjuvant therapy was administered during the surgeries, it may assist the prevention of local recurrence in certain cases. The cases of secondary ABC were preceded by benign bone tumors, including fibrous dysplasia, giant cell tumors, chondroblastoma and non-ossifying fibroma. The features of the secondary ABC typically reflected those of the preceding bone tumor. In the majority of cases, distinguishing the primary ABC from the secondary ABC was possible based on characteristic features, including age of the patient at diagnosis and the tumor location. In cases that exhibit ambiguous features, including a soft tissue mass or a thick septal enhancement on the preoperative magnetic resonance images, a biopsy must be obtained in order to exclude other types of aggressive bone tumors, including giant cell tumor, osteosarcoma and telangiectatic osteosarcoma. PMID:28454393

Anticipated Benefits of Care (ABC): psychometrics and predictive value in psychiatric disorders.

PubMed

Warden, D; Trivedi, M H; Carmody, T J; Gollan, J K; Kashner, T M; Lind, L; Crismon, M L; Rush, A J

2010-06-01

Attitudes and expectations about treatment have been associated with symptomatic outcomes, adherence and utilization in patients with psychiatric disorders. No measure of patients' anticipated benefits of treatment on domains of everyday functioning has previously been available. The Anticipated Benefits of Care (ABC) is a new, 10-item questionnaire used to measure patient expectations about the impact of treatment on domains of everyday functioning. The ABC was collected at baseline in adult out-patients with major depressive disorder (MDD) (n=528), bipolar disorder (n=395) and schizophrenia (n=447) in the Texas Medication Algorithm Project (TMAP). Psychometric properties of the ABC were assessed, and the association of ABC scores with treatment response at 3 months was evaluated. Evaluation of the ABC's internal consistency yielded Cronbach's alpha of 0.90-0.92 for patients across disorders. Factor analysis showed that the ABC was unidimensional for all patients and for patients with each disorder. For patients with MDD, lower anticipated benefits of treatment was associated with less symptom improvement and lower odds of treatment response [odds ratio (OR) 0.72, 95% confidence interval (CI) 0.57-0.87, p=0.0011]. There was no association between ABC and symptom improvement or treatment response for patients with bipolar disorder or schizophrenia, possibly because these patients had modest benefits with treatment. The ABC is the first self-report that measures patient expectations about the benefits of treatment on everyday functioning, filling an important gap in available assessments of attitudes and expectations about treatment. The ABC is simple, easy to use, and has acceptable psychometric properties for use in research or clinical settings.

mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling

PubMed Central

Alshamlan, Hala; Badr, Ghada; Alohali, Yousef

2015-01-01

An artificial bee colony (ABC) is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR), and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM) algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA) and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO). The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems. PMID:25961028

mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling.

PubMed

Alshamlan, Hala; Badr, Ghada; Alohali, Yousef

2015-01-01

An artificial bee colony (ABC) is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR), and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM) algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA) and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO). The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.

75 FR 11991 - ABC & D Recycling, Inc.-Lease and Operation Exemption-a Line of Railroad in Ware, MA

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [STB Finance Docket No. 35356] ABC & D Recycling, Inc.--Lease and Operation Exemption--a Line of Railroad in Ware, MA ABC & D Recycling, Inc. (ABC & D), a noncarrier, has filed a verified notice of exemption under 49 CFR 1150.31 to lease from O...

ABCE1 Is a Highly Conserved RNA Silencing Suppressor

PubMed Central

Kärblane, Kairi; Gerassimenko, Jelena; Nigul, Lenne; Piirsoo, Alla; Smialowska, Agata; Vinkel, Kadri; Kylsten, Per; Ekwall, Karl; Swoboda, Peter; Truve, Erkki; Sarmiento, Cecilia

2015-01-01

ATP-binding cassette sub-family E member 1 (ABCE1) is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference. PMID:25659154

Simple heuristics and rules of thumb: where psychologists and behavioural biologists might meet.

PubMed

Hutchinson, John M C; Gigerenzer, Gerd

2005-05-31

The Centre for Adaptive Behaviour and Cognition (ABC) has hypothesised that much human decision-making can be described by simple algorithmic process models (heuristics). This paper explains this approach and relates it to research in biology on rules of thumb, which we also review. As an example of a simple heuristic, consider the lexicographic strategy of Take The Best for choosing between two alternatives: cues are searched in turn until one discriminates, then search stops and all other cues are ignored. Heuristics consist of building blocks, and building blocks exploit evolved or learned abilities such as recognition memory; it is the complexity of these abilities that allows the heuristics to be simple. Simple heuristics have an advantage in making decisions fast and with little information, and in avoiding overfitting. Furthermore, humans are observed to use simple heuristics. Simulations show that the statistical structures of different environments affect which heuristics perform better, a relationship referred to as ecological rationality. We contrast ecological rationality with the stronger claim of adaptation. Rules of thumb from biology provide clearer examples of adaptation because animals can be studied in the environments in which they evolved. The range of examples is also much more diverse. To investigate them, biologists have sometimes used similar simulation techniques to ABC, but many examples depend on empirically driven approaches. ABC's theoretical framework can be useful in connecting some of these examples, particularly the scattered literature on how information from different cues is integrated. Optimality modelling is usually used to explain less detailed aspects of behaviour but might more often be redirected to investigate rules of thumb.

Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.

PubMed

Lane, Thomas S; Rempe, Caroline S; Davitt, Jack; Staton, Margaret E; Peng, Yanhui; Soltis, Douglas Edward; Melkonian, Michael; Deyholos, Michael; Leebens-Mack, James H; Chase, Mark; Rothfels, Carl J; Stevenson, Dennis; Graham, Sean W; Yu, Jun; Liu, Tao; Pires, J Chris; Edger, Patrick P; Zhang, Yong; Xie, Yinlong; Zhu, Ying; Carpenter, Eric; Wong, Gane Ka-Shu; Stewart, C Neal

2016-05-31

The ATP-binding cassette (ABC) transporter gene superfamily is ubiquitous among extant organisms and prominently represented in plants. ABC transporters act to transport compounds across cellular membranes and are involved in a diverse range of biological processes. Thus, the applicability to biotechnology is vast, including cancer resistance in humans, drug resistance among vertebrates, and herbicide and other xenobiotic resistance in plants. In addition, plants appear to harbor the highest diversity of ABC transporter genes compared with any other group of organisms. This study applied transcriptome analysis to survey the kingdom-wide ABC transporter diversity in plants and suggest biotechnology applications of this diversity. We utilized sequence similarity-based informatics techniques to infer the identity of ABC transporter gene candidates from 1295 phylogenetically-diverse plant transcriptomes. A total of 97,149 putative (approximately 25 % were full-length) ABC transporter gene members were identified; each RNA-Seq library (plant sample) had 88 ± 30 gene members. As expected, simpler organisms, such as algae, had fewer unique members than vascular land plants. Differences were also noted in the richness of certain ABC transporter subfamilies. Land plants had more unique ABCB, ABCC, and ABCG transporter gene members on average (p < 0.005), and green algae, red algae, and bryophytes had significantly more ABCF transporter gene members (p < 0.005). Ferns had significantly fewer ABCA transporter gene members than all other plant groups (p < 0.005). We present a transcriptomic overview of ABC transporter gene members across all major plant groups. An increase in the number of gene family members present in the ABCB, ABCC, and ABCD transporter subfamilies may indicate an expansion of the ABC transporter superfamily among green land plants, which include all crop species. The striking difference between the number of ABCA subfamily transporter gene members between ferns and other plant taxa is surprising and merits further investigation. Discussed is the potential exploitation of ABC transporters in plant biotechnology, with an emphasis on crops.

ABC transporters affect the elimination and toxicity of CdTe quantum dots in liver and kidney cells

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

Chen, Mingli; Yin, Huancai; Bai, Pengli

This paper aimed to investigate the role of adenosine triphosphate-binding cassette (ABC) transporters on the efflux and the toxicity of nanoparticles in liver and kidney cells. In this study, we synthesized CdTe quantum dots (QDs) that were monodispersed and emitted green fluorescence (maximum peak at 530 nm). Such QDs tended to accumulate in human hepatocellular carcinoma cells (HepG2), human kidney cells 2 (HK-2), and Madin-Darby canine kidney (MDCK) cells, and cause significant toxicity in all the three cell lines. Using specific inhibitors and inducers of P-glycoprotein (Pgp) and multidrug resistance associated proteins (Mrps), the cellular accumulation and subsequent toxicity ofmore » QDs in HepG2 and HK-2 cells were significantly affected, while only slight changes appeared in MDCK cells, corresponding well with the functional expressions of ABC transporters in cells. Moreover, treatment of QDs caused concentration- and time- dependent induction of ABC transporters in HepG2 and HK-2 cells, but such phenomenon was barely found in MDCK cells. Furthermore, the effects of CdTe QDs on ABC transporters were found to be greater than those of CdCl{sub 2} at equivalent concentrations of cadmium, indicating that the effects of QDs should be a combination of free Cd{sup 2+} and specific properties of QDs. Overall, these results indicated a strong dependence between the functional expressions of ABC transporters and the efflux of QDs, which could be an important reason for the modulation of QDs toxicity by ABC transporters. - Highlights: • ABC transporters contributed actively to the cellular efflux of CdTe quantum dots. • ABC transporters affected the cellular toxicity of CdTe quantum dots. • Treatment of CdTe quantum dots induced the gene expression of ABC transporters. • Free Cd{sup 2+} should be partially involved in the effects of QDs on ABC transporters. • Cellular efflux of quantum dots could be an important modulator for its toxicity.« less

Falls and confidence related quality of life outcome measures in an older British cohort

PubMed Central

Parry, S; Steen, N; Galloway, S; Kenny, R; Bond, J

2001-01-01

Falls are common in older subjects and result in loss of confidence and independence. The Falls Efficacy Scale (FES) and the Activities-specific Balance Confidence scale (ABC) were developed in North America to quantify these entities, but contain idiom unfamiliar to an older British population. Neither has been validated in the UK. The FES and the ABC were modified for use within British culture and the internal consistency and test-retest reliability of the modified scales (FES-UK and ABC-UK) assessed. A total of 193 consecutive, ambulant, new, and return patients (n=119; 62%) and their friends and relatives ("visitors", n=74; 38%) were tested on both scales, while the last 60 subjects were retested within one week. Internal reliability was excellent for both scales (Cronbach's alpha 0.97 (FES-UK), and 0.98 (ABC-UK)). Test-retest reliability was good for both scales, though superior for the ABC-UK (intraclass correlation coefficient 0.58 (FES-UK), 0.89 (ABC-UK)). There was evidence to suggest that the ABC-UK was better than the FES-UK at distinguishing between older patients and younger patients (|tABC| = 4.4; |tFES| = 2.3); and between fallers and non-fallers (|tABC| = 8.7; |tFES| = 5.0) where the t statistics are based on the comparison of two independent samples. The ABC-UK and FES-UK are both reliable and valid measures for the assessment of falls and balance related confidence in older adults. However, better test-retest reliability and more robust differentiation of subgroups in whom falls related quality of life would be expected to be different make the ABC-UK the current instrument of choice in assessing this entity in older British subjects.


Keywords: quality of life; falls; elderly; health status measurement PMID:11161077

Sensitive and Specific Fluorescent Probes for Functional Analysis of the Three Major Types of Mammalian ABC Transporters

PubMed Central

Lebedeva, Irina V.; Pande, Praveen; Patton, Wayne F.

2011-01-01

An underlying mechanism for multi drug resistance (MDR) is up-regulation of the transmembrane ATP-binding cassette (ABC) transporter proteins. ABC transporters also determine the general fate and effect of pharmaceutical agents in the body. The three major types of ABC transporters are MDR1 (P-gp, P-glycoprotein, ABCB1), MRP1/2 (ABCC1/2) and BCRP/MXR (ABCG2) proteins. Flow cytometry (FCM) allows determination of the functional expression levels of ABC transporters in live cells, but most dyes used as indicators (rhodamine 123, DiOC2(3), calcein-AM) have limited applicability as they do not detect all three major types of ABC transporters. Dyes with broad coverage (such as doxorubicin, daunorubicin and mitoxantrone) lack sensitivity due to overall dimness and thus may yield a significant percentage of false negative results. We describe two novel fluorescent probes that are substrates for all three common types of ABC transporters and can serve as indicators of MDR in flow cytometry assays using live cells. The probes exhibit fast internalization, favorable uptake/efflux kinetics and high sensitivity of MDR detection, as established by multidrug resistance activity factor (MAF) values and Kolmogorov-Smirnov statistical analysis. Used in combination with general or specific inhibitors of ABC transporters, both dyes readily identify functional efflux and are capable of detecting small levels of efflux as well as defining the type of multidrug resistance. The assay can be applied to the screening of putative modulators of ABC transporters, facilitating rapid, reproducible, specific and relatively simple functional detection of ABC transporter activity, and ready implementation on widely available instruments. PMID:21799851

Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm.

PubMed

Li, Bai; Lin, Mu; Liu, Qiao; Li, Ya; Zhou, Changjun

2015-10-01

Protein folding is a fundamental topic in molecular biology. Conventional experimental techniques for protein structure identification or protein folding recognition require strict laboratory requirements and heavy operating burdens, which have largely limited their applications. Alternatively, computer-aided techniques have been developed to optimize protein structures or to predict the protein folding process. In this paper, we utilize a 3D off-lattice model to describe the original protein folding scheme as a simplified energy-optimal numerical problem, where all types of amino acid residues are binarized into hydrophobic and hydrophilic ones. We apply a balance-evolution artificial bee colony (BE-ABC) algorithm as the minimization solver, which is featured by the adaptive adjustment of search intensity to cater for the varying needs during the entire optimization process. In this work, we establish a benchmark case set with 13 real protein sequences from the Protein Data Bank database and evaluate the convergence performance of BE-ABC algorithm through strict comparisons with several state-of-the-art ABC variants in short-term numerical experiments. Besides that, our obtained best-so-far protein structures are compared to the ones in comprehensive previous literature. This study also provides preliminary insights into how artificial intelligence techniques can be applied to reveal the dynamics of protein folding. Graphical Abstract Protein folding optimization using 3D off-lattice model and advanced optimization techniques.

Decision-making ability of Physarum polycephalum enhanced by its coordinated spatiotemporal oscillatory dynamics.

PubMed

Iwayama, Koji; Zhu, Liping; Hirata, Yoshito; Aono, Masashi; Hara, Masahiko; Aihara, Kazuyuki

2016-04-12

An amoeboid unicellular organism, a plasmodium of the true slime mold Physarum polycephalum, exhibits complex spatiotemporal oscillatory dynamics and sophisticated information processing capabilities while deforming its amorphous body. We previously devised an 'amoeba-based computer (ABC),' that implemented optical feedback control to lead this amoeboid organism to search for a solution to the traveling salesman problem (TSP). In the ABC, the shortest TSP route (the optimal solution) is represented by the shape of the organism in which the body area (nutrient absorption) is maximized while the risk of being exposed to aversive light stimuli is minimized. The shortness of the TSP route found by ABC, therefore, serves as a quantitative measure of the optimality of the decision made by the organism. However, it remains unclear how the decision-making ability of the organism originates from the oscillatory dynamics of the organism. We investigated the number of coexisting traveling waves in the spatiotemporal patterns of the oscillatory dynamics of the organism. We show that a shorter TSP route can be found when the organism exhibits a lower number of traveling waves. The results imply that the oscillatory dynamics are highly coordinated throughout the global body. Based on the results, we discuss the fact that the decision-making ability of the organism can be enhanced not by uncorrelated random fluctuations, but by its highly coordinated oscillatory dynamics.

Temporal dynamics of the ABC transporter response to insecticide treatment: insights from the malaria vector Anopheles stephensi

NASA Astrophysics Data System (ADS)

Epis, Sara; Porretta, Daniele; Mastrantonio, Valentina; Urbanelli, Sandra; Sassera, Davide; De Marco, Leone; Mereghetti, Valeria; Montagna, Matteo; Ricci, Irene; Favia, Guido; Bandi, Claudio

2014-12-01

In insects, ABC transporters have been shown to contribute to defence/resistance to insecticides by reducing toxic concentrations in cells/tissues. Despite the extensive studies about this detoxifying mechanism, the temporal patterns of ABC transporter activation have been poorly investigated. Using the malaria vector Anopheles stephensi as a study system, we investigated the expression profile of ABC genes belonging to different subfamilies in permethrin-treated larvae at different time points (30 min to 48 h). Our results showed that the expression of ABCB and ABCG subfamily genes was upregulated at 1 h after treatment, with the highest expression observed at 6 h. Therefore, future investigations on the temporal dynamics of ABC gene expression will allow a better implementation of insecticide treatment regimens, including the use of specific inhibitors of ABC efflux pumps.

LhnR and upstream operon LhnABC in Agrobacterium vitis regulate the induction of tobacco hypersensitive responses, grape necrosis and swarming motility.

PubMed

Zheng, Desen; Hao, Guixia; Cursino, Luciana; Zhang, Hongsheng; Burr, Thomas J

2012-09-01

The characterization of Tn5 transposon insertional mutants of Agrobacterium vitis strain F2/5 revealed a gene encoding a predicted LysR-type transcriptional regulator, lhnR (for 'LysR-type regulator associated with HR and necrosis'), and an immediate upstream operon consisting of three open reading frames (lhnABC) required for swarming motility, surfactant production and the induction of a hypersensitive response (HR) on tobacco and necrosis on grape. The operon lhnABC is unique to A. vitis among the sequenced members in Rhizobiaceae. Mutagenesis of lhnR and lhnABC by gene disruption and complementation of ΔlhnR and ΔlhnABC confirmed their roles in the expression of these phenotypes. Mutation of lhnR resulted in complete loss of HR, swarming motility, surfactant production and reduced necrosis, whereas mutation of lhnABC resulted in loss of swarming motility, delayed and reduced HR development and reduced surfactant production and necrosis. The data from promoter-green fluorescent protein (gfp) fusions showed that lhnR suppresses the expression of lhnABC and negatively autoregulates its own expression. It was also shown that lhnABC negatively affects its own expression and positively affects the transcription of lhnR. lhnR and lhnABC constitute a regulatory circuit that coordinates the transcription level of lhnR, resulting in the expression of swarming, surfactant, HR and necrosis phenotypes. © 2012 THE AUTHORS. MOLECULAR PLANT PATHOLOGY © 2012 BSPP AND BLACKWELL PUBLISHING LTD.

Model criticism based on likelihood-free inference, with an application to protein network evolution.

PubMed

Ratmann, Oliver; Andrieu, Christophe; Wiuf, Carsten; Richardson, Sylvia

2009-06-30

Mathematical models are an important tool to explain and comprehend complex phenomena, and unparalleled computational advances enable us to easily explore them without any or little understanding of their global properties. In fact, the likelihood of the data under complex stochastic models is often analytically or numerically intractable in many areas of sciences. This makes it even more important to simultaneously investigate the adequacy of these models-in absolute terms, against the data, rather than relative to the performance of other models-but no such procedure has been formally discussed when the likelihood is intractable. We provide a statistical interpretation to current developments in likelihood-free Bayesian inference that explicitly accounts for discrepancies between the model and the data, termed Approximate Bayesian Computation under model uncertainty (ABCmicro). We augment the likelihood of the data with unknown error terms that correspond to freely chosen checking functions, and provide Monte Carlo strategies for sampling from the associated joint posterior distribution without the need of evaluating the likelihood. We discuss the benefit of incorporating model diagnostics within an ABC framework, and demonstrate how this method diagnoses model mismatch and guides model refinement by contrasting three qualitative models of protein network evolution to the protein interaction datasets of Helicobacter pylori and Treponema pallidum. Our results make a number of model deficiencies explicit, and suggest that the T. pallidum network topology is inconsistent with evolution dominated by link turnover or lateral gene transfer alone.

The Military Applications of Cloud Computing Technologies

DTIC Science & Technology

2013-05-23

tactical networks will potentially cause some unique issues when implementing the JIE. Tactical networks are temporary in nature , and are utilized...connected ABCS clients will receive software updates and security patches as they are published over the network , rather than catching up after an extended...approach from the previous JNN network model, in that it introduces a limited, wireless capability to a unit’s LAN that will enable limited, on-the

Applying Activity Based Costing (ABC) Method to Calculate Cost Price in Hospital and Remedy Services

PubMed Central

Rajabi, A; Dabiri, A

2012-01-01

Background Activity Based Costing (ABC) is one of the new methods began appearing as a costing methodology in the 1990’s. It calculates cost price by determining the usage of resources. In this study, ABC method was used for calculating cost price of remedial services in hospitals. Methods: To apply ABC method, Shahid Faghihi Hospital was selected. First, hospital units were divided into three main departments: administrative, diagnostic, and hospitalized. Second, activity centers were defined by the activity analysis method. Third, costs of administrative activity centers were allocated into diagnostic and operational departments based on the cost driver. Finally, with regard to the usage of cost objectives from services of activity centers, the cost price of medical services was calculated. Results: The cost price from ABC method significantly differs from tariff method. In addition, high amount of indirect costs in the hospital indicates that capacities of resources are not used properly. Conclusion: Cost price of remedial services with tariff method is not properly calculated when compared with ABC method. ABC calculates cost price by applying suitable mechanisms but tariff method is based on the fixed price. In addition, ABC represents useful information about the amount and combination of cost price services. PMID:23113171

MetaABC--an integrated metagenomics platform for data adjustment, binning and clustering.

PubMed

Su, Chien-Hao; Hsu, Ming-Tsung; Wang, Tse-Yi; Chiang, Sufeng; Cheng, Jen-Hao; Weng, Francis C; Kao, Cheng-Yan; Wang, Daryi; Tsai, Huai-Kuang

2011-08-15

MetaABC is a metagenomic platform that integrates several binning tools coupled with methods for removing artifacts, analyzing unassigned reads and controlling sampling biases. It allows users to arrive at a better interpretation via series of distinct combinations of analysis tools. After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams. MetaABC source code and documentation are available at http://bits2.iis.sinica.edu.tw/MetaABC/ CONTACT: dywang@gate.sinica.edu.tw; hktsai@iis.sinica.edu.tw Supplementary data are available at Bioinformatics online.

Understanding exoplanet populations with simulation-based methods

NASA Astrophysics Data System (ADS)

Morehead, Robert Charles

The Kepler candidate catalog represents an unprecedented sample of exoplanet host stars. This dataset is ideal for probing the populations of exoplanet systems and exploring their architectures. Confirming transiting exoplanets candidates through traditional follow-up methods is challenging, especially for faint host stars. Most of Kepler's validated planets relied on statistical methods to separate true planets from false-positives. Multiple transiting planet systems (MTPS) have been previously shown to have low false-positive rates and over 850 planets in MTPSs have been statistically validated so far. We show that the period-normalized transit duration ratio (xi) offers additional information that can be used to establish the planetary nature of these systems. We briefly discuss the observed distribution of xi for the Q1-Q17 Kepler Candidate Search. We also use xi to develop a Bayesian statistical framework combined with Monte Carlo methods to determine which pairs of planet candidates in an MTPS are consistent with the planet hypothesis for a sample of 862 MTPSs that include candidate planets, confirmed planets, and known false-positives. This analysis proves to be efficient and advantageous in that it only requires catalog-level bulk candidate properties and galactic population modeling to compute the probabilities of a myriad of feasible scenarios composed of background and companion stellar blends in the photometric aperture, without needing additional observational follow-up. Our results agree with the previous results of a low false-positive rate in the Kepler MTPSs. This implies, independently of any other estimates, that most of the MTPSs detected by Kepler are planetary in nature, but that a substantial fraction could be orbiting stars other than then the putative target star, and therefore may be subject to significant error in the inferred planet parameters resulting from unknown or mismeasured stellar host attributes. We also apply approximate Bayesian computation (ABC) using forward simulations of the Kepler planet catalog to simultaneously constrain the distributions of mutual inclination between the planets, orbital eccentricity, the underlying number of planets per planetary system, and the fraction of stars that host planet systems in a subsample of Kepler candidate planets using SimpleABC, a Python package we developed that is a general-purpose framework for ABC analysis. For our investigation into planet architectures, we limit our investigation to candidates in orbits from 10 to 320 days, where the false-positive contamination rate is expected to be low. We test two models, the first is an independent eccentricity ( e) model where mutual inclination and e are drawn from Rayleigh distributions with dispersions sigmaim and sigmae, planets per planetary system is drawn from a Poisson distribution with mean lambda, and the fraction of stars with planetary systems is drawn from two-state categorical distribution parameterized by etap. We also test an Equipartition Model identical to the Independent e Model, except that sigmae is linked to sigmaim by a scaling factor gammae. For the Independent e Model, we find sigmaim = 5.51° +8.00-3.35, sigmae = 0.03+0.05-0.01, lambda = 6.62+7.74 -3.36, and etap = 0.20 +0.18-0.11. For the Equipartition Model, we find sigmaim = 1.15°+0.56-0.33 , gammae = 1.38+1.89 -0.93, lambda = 2.25+0.56-0.29, and etap = 0.56+0.08-0.11 . These results, especially the Equipartition Model, are in good agreement with previous studies. However, deficiencies in our single population models suggest that at least one additional subpopulation of planet systems is needed to explain the Kepler sample, providing more confirmation of the so-called "Kepler Dichotomy".

Characterisation of single domain ATP-binding cassette protien homologues of Theileria parva.

PubMed

Kibe, M K; Macklin, M; Gobright, E; Bishop, R; Urakawa, T; ole-MoiYoi, O K

2001-09-01

Two distinct genes encoding single domain, ATP-binding cassette transport protein homologues of Theileria parva were cloned and sequenced. Neither of the genes is tandemly duplicated. One gene, TpABC1, encodes a predicted protein of 593 amino acids with an N-terminal hydrophobic domain containing six potential membrane-spanning segments. A single discontinuous ATP-binding element was located in the C-terminal region of TpABC1. The second gene, TpABC2, also contains a single C-terminal ATP-binding motif. Copies of TpABC2 were present at four loci in the T. parva genome on three different chromosomes. TpABC1 exhibited allelic polymorphism between stocks of the parasite. Comparison of cDNA and genomic sequences revealed that TpABC1 contained seven short introns, between 29 and 84 bp in length. The full-length TpABC1 protein was expressed in insect cells using the baculovirus system. Application of antibodies raised against the recombinant antigen to western blots of T. parva piroplasm lysates detected an 85 kDa protein in this life-cycle stage.

Sulfadiazine resistance in Toxoplasma gondii: no involvement of overexpression or polymorphisms in genes of therapeutic targets and ABC transporters

PubMed Central

Doliwa, Christelle; Escotte-Binet, Sandie; Aubert, Dominique; Sauvage, Virginie; Velard, Frédéric; Schmid, Aline; Villena, Isabelle

2013-01-01

Several treatment failures have been reported for the treatment of toxoplasmic encephalitis, chorioretinitis, and congenital toxoplasmosis. Recently we found three Toxoplasma gondii strains naturally resistant to sulfadiazine and we developed in vitro two sulfadiazine resistant strains, RH-RSDZ and ME-49-RSDZ, by gradual pressure. In Plasmodium, common mechanisms of drug resistance involve, among others, mutations and/or amplification within genes encoding the therapeutic targets dhps and dhfr and/or the ABC transporter genes family. To identify genotypic and/or phenotypic markers of resistance in T. gondii, we sequenced and analyzed the expression levels of therapeutic targets dhps and dhfr, three ABC genes, two Pgp, TgABC.B1 and TgABC.B2, and one MRP, TgABC.C1, on sensitive strains compared to sulfadiazine resistant strains. Neither polymorphism nor overexpression was identified. Contrary to Plasmodium, in which mutations and/or overexpression within gene targets and ABC transporters are involved in antimalarial resistance, T. gondii sulfadiazine resistance is not related to these toxoplasmic genes studied. PMID:23707894

Optimization of Straight Cylindrical Turning Using Artificial Bee Colony (ABC) Algorithm

NASA Astrophysics Data System (ADS)

Prasanth, Rajanampalli Seshasai Srinivasa; Hans Raj, Kandikonda

2017-04-01

Artificial bee colony (ABC) algorithm, that mimics the intelligent foraging behavior of honey bees, is increasingly gaining acceptance in the field of process optimization, as it is capable of handling nonlinearity, complexity and uncertainty. Straight cylindrical turning is a complex and nonlinear machining process which involves the selection of appropriate cutting parameters that affect the quality of the workpiece. This paper presents the estimation of optimal cutting parameters of the straight cylindrical turning process using the ABC algorithm. The ABC algorithm is first tested on four benchmark problems of numerical optimization and its performance is compared with genetic algorithm (GA) and ant colony optimization (ACO) algorithm. Results indicate that, the rate of convergence of ABC algorithm is better than GA and ACO. Then, the ABC algorithm is used to predict optimal cutting parameters such as cutting speed, feed rate, depth of cut and tool nose radius to achieve good surface finish. Results indicate that, the ABC algorithm estimated a comparable surface finish when compared with real coded genetic algorithm and differential evolution algorithm.

ABC1 Consensus Conference - a German Perspective: First International Consensus Conference on Advanced Breast Cancer (ABC1), Lisbon, November 5, 2011.

PubMed

Thomssen, Christoph; Marschner, Norbert; Untch, Michael; Decker, Thomas; Hegewisch-Becker, Susanna; Jackisch, Christian; Janni, Wolfgang; Hans-Joachim, Lück; von Minckwitz, Gunter; Scharl, Anton; Schneeweiss, Andreas; Tesch, Hans; Welt, Anja; Harbeck, Nadia

2012-02-01

A group of German breast cancer experts (medical oncologists and gynaecologists) reviewed and commented on the results of the first international 'Advanced Breast Cancer First Consensus Conference' (ABC1) for the diagnosis and treatment of advanced breast cancer. The ABC1 Conference is an initiative of the European School of Oncology (ESO) Metastatic Breast Cancer Task Force in cooperation with the EBCC (European Breast Cancer Conference), ESMO (European Society of Medical Oncology) and the American JNCI (Journal of the National Cancer Institute). The main focus of the ABC1 Conference was metastatic breast cancer (stage IV). The ABC1 consensus is based on the vote of 33 breast cancer experts from different countries and has been specified as a guideline for therapeutic practice by the German expert group. It is the objective of the ABC1 consensus as well as of the German comments to provide an internationally standardized and evidence-based foundation for qualified decision-making in the treatment of metastatic breast cancer.

Implementation and comparative analysis of the optimisations produced by evolutionary algorithms for the parameter extraction of PSP MOSFET model

NASA Astrophysics Data System (ADS)

Hadia, Sarman K.; Thakker, R. A.; Bhatt, Kirit R.

2016-05-01

The study proposes an application of evolutionary algorithms, specifically an artificial bee colony (ABC), variant ABC and particle swarm optimisation (PSO), to extract the parameters of metal oxide semiconductor field effect transistor (MOSFET) model. These algorithms are applied for the MOSFET parameter extraction problem using a Pennsylvania surface potential model. MOSFET parameter extraction procedures involve reducing the error between measured and modelled data. This study shows that ABC algorithm optimises the parameter values based on intelligent activities of honey bee swarms. Some modifications have also been applied to the basic ABC algorithm. Particle swarm optimisation is a population-based stochastic optimisation method that is based on bird flocking activities. The performances of these algorithms are compared with respect to the quality of the solutions. The simulation results of this study show that the PSO algorithm performs better than the variant ABC and basic ABC algorithm for the parameter extraction of the MOSFET model; also the implementation of the ABC algorithm is shown to be simpler than that of the PSO algorithm.

Iowa ABC connections : [tech transfer summary].

DOT National Transportation Integrated Search

2015-06-01

The Iowa Department of Transportation (DOT) and other organizations have : been developing accelerated bridge construction (ABC) concepts, details, and : processes, and Iowa has come to be viewed as a national leader in the area of : ABC. However, th...

Rhombohedral Multilayer Graphene: A Magneto-Raman Scattering Study.

PubMed

Henni, Younes; Ojeda Collado, Hector Pablo; Nogajewski, Karol; Molas, Maciej R; Usaj, Gonzalo; Balseiro, Carlos A; Orlita, Milan; Potemski, Marek; Faugeras, Clement

2016-06-08

Graphene layers are known to stack in two stable configurations, namely, ABA or ABC stacking, with drastically distinct electronic properties. Unlike the ABA stacking, little has been done to experimentally investigate the electronic properties of ABC graphene multilayers. Here, we report on the first magneto optical study of a large ABC domain in a graphene multilayer flake, with ABC sequences exceeding 17 graphene sheets. ABC-stacked multilayers can be fingerprinted with a characteristic electronic Raman scattering response, which persists even at room temperatures. Tracing the magnetic field evolution of the inter Landau level excitations from this domain gives strong evidence for the existence of a dispersionless electronic band near the Fermi level, characteristic of such stacking. Our findings present a simple yet powerful approach to probe ABC stacking in graphene multilayer flakes, where this highly degenerated band appears as an appealing candidate to host strongly correlated states.

Modified artificial bee colony algorithm for reactive power optimization

NASA Astrophysics Data System (ADS)

Sulaiman, Noorazliza; Mohamad-Saleh, Junita; Abro, Abdul Ghani

2015-05-01

Bio-inspired algorithms (BIAs) implemented to solve various optimization problems have shown promising results which are very important in this severely complex real-world. Artificial Bee Colony (ABC) algorithm, a kind of BIAs has demonstrated tremendous results as compared to other optimization algorithms. This paper presents a new modified ABC algorithm referred to as JA-ABC3 with the aim to enhance convergence speed and avoid premature convergence. The proposed algorithm has been simulated on ten commonly used benchmarks functions. Its performance has also been compared with other existing ABC variants. To justify its robust applicability, the proposed algorithm has been tested to solve Reactive Power Optimization problem. The results have shown that the proposed algorithm has superior performance to other existing ABC variants e.g. GABC, BABC1, BABC2, BsfABC dan IABC in terms of convergence speed. Furthermore, the proposed algorithm has also demonstrated excellence performance in solving Reactive Power Optimization problem.

Aggressive aneurysmal bone cyst of the maxilla confused with telangiectatic osteosarcoma.

PubMed

Lee, Hyun-Min; Cho, Kyu-Sup; Choi, Kyung-Un; Roh, Hwan-Jung

2012-06-01

Aneurysmal bone cyst (ABC) is a benign, expansile lesion typically affecting the long bones and vertebrae of patients younger than 20 years. Approximately 2% of ABCs occur in the head and neck region, most commonly affecting the mandible. Although the most common co-existing lesion associated with ABCs is the giant cell tumor, ABCs can be radiologically confused with telangiectatic osteosarcoma in cases of aggressive behavior and rapid growth. Here, we report a case of an aggressive ABC of the maxilla confused with telangiectatic osteosarcoma in a patient who underwent several operations for an osteoblastoma that was diagnosed histopathologically. This case highlights the need for a differential diagnosis both radiologically and histopathologically, because ABCs can easily be interpreted as a giant cell tumor or an osteoblastoma, and, on occasion, can be mistaken for osteogenic malignancies. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

PubMed Central

Romero-Severson, Ethan O.; Bulla, Ingo; Hengartner, Nick; Bártolo, Inês; Abecasis, Ana; Azevedo-Pereira, José M.; Taveira, Nuno; Leitner, Thomas

2017-01-01

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission. PMID:28912340

Using Approximate Bayesian Computation to infer sex ratios from acoustic data.

PubMed

Lehnen, Lisa; Schorcht, Wigbert; Karst, Inken; Biedermann, Martin; Kerth, Gerald; Puechmaille, Sebastien J

2018-01-01

Population sex ratios are of high ecological relevance, but are challenging to determine in species lacking conspicuous external cues indicating their sex. Acoustic sexing is an option if vocalizations differ between sexes, but is precluded by overlapping distributions of the values of male and female vocalizations in many species. A method allowing the inference of sex ratios despite such an overlap will therefore greatly increase the information extractable from acoustic data. To meet this demand, we developed a novel approach using Approximate Bayesian Computation (ABC) to infer the sex ratio of populations from acoustic data. Additionally, parameters characterizing the male and female distribution of acoustic values (mean and standard deviation) are inferred. This information is then used to probabilistically assign a sex to a single acoustic signal. We furthermore develop a simpler means of sex ratio estimation based on the exclusion of calls from the overlap zone. Applying our methods to simulated data demonstrates that sex ratio and acoustic parameter characteristics of males and females are reliably inferred by the ABC approach. Applying both the ABC and the exclusion method to empirical datasets (echolocation calls recorded in colonies of lesser horseshoe bats, Rhinolophus hipposideros) provides similar sex ratios as molecular sexing. Our methods aim to facilitate evidence-based conservation, and to benefit scientists investigating ecological or conservation questions related to sex- or group specific behaviour across a wide range of organisms emitting acoustic signals. The developed methodology is non-invasive, low-cost and time-efficient, thus allowing the study of many sites and individuals. We provide an R-script for the easy application of the method and discuss potential future extensions and fields of applications. The script can be easily adapted to account for numerous biological systems by adjusting the type and number of groups to be distinguished (e.g. age, social rank, cryptic species) and the acoustic parameters investigated.

Technical note: real-time web-based wireless visual guidance system for radiotherapy.

PubMed

Lee, Danny; Kim, Siyong; Palta, Jatinder R; Kim, Taeho

2017-06-01

Describe a Web-based wireless visual guidance system that mitigates issues associated with hard-wired audio-visual aided patient interactive motion management systems that are cumbersome to use in routine clinical practice. Web-based wireless visual display duplicates an existing visual display of a respiratory-motion management system for visual guidance. The visual display of the existing system is sent to legacy Web clients over a private wireless network, thereby allowing a wireless setting for real-time visual guidance. In this study, active breathing coordinator (ABC) trace was used as an input for visual display, which captured and transmitted to Web clients. Virtual reality goggles require two (left and right eye view) images for visual display. We investigated the performance of Web-based wireless visual guidance by quantifying (1) the network latency of visual displays between an ABC computer display and Web clients of a laptop, an iPad mini 2 and an iPhone 6, and (2) the frame rate of visual display on the Web clients in frames per second (fps). The network latency of visual display between the ABC computer and Web clients was about 100 ms and the frame rate was 14.0 fps (laptop), 9.2 fps (iPad mini 2) and 11.2 fps (iPhone 6). In addition, visual display for virtual reality goggles was successfully shown on the iPhone 6 with 100 ms and 11.2 fps. A high network security was maintained by utilizing the private network configuration. This study demonstrated that a Web-based wireless visual guidance can be a promising technique for clinical motion management systems, which require real-time visual display of their outputs. Based on the results of this study, our approach has the potential to reduce clutter associated with wired-systems, reduce space requirements, and extend the use of medical devices from static usage to interactive and dynamic usage in a radiotherapy treatment vault.

Expressing Constitutively Active Rheb in Adult Dorsal Root Ganglion Neurons Enhances the Integration of Sensory Axons that Regenerate Across a Chondroitinase-Treated Dorsal Root Entry Zone Following Dorsal Root Crush

PubMed Central

Wu, Di; Klaw, Michelle C.; Kholodilov, Nikolai; Burke, Robert E.; Detloff, Megan R.; Côté, Marie-Pascale; Tom, Veronica J.

2016-01-01

While the peripheral branch of dorsal root ganglion neurons (DRG) can successfully regenerate after injury, lesioned central branch axons fail to regrow across the dorsal root entry zone (DREZ), the interface between the dorsal root and the spinal cord. This lack of regeneration is due to the limited regenerative capacity of adult sensory axons and the growth-inhibitory environment at the DREZ, which is similar to that found in the glial scar after a central nervous system (CNS) injury. We hypothesized that transduction of adult DRG neurons using adeno-associated virus (AAV) to express a constitutively-active form of the GTPase Rheb (caRheb) will increase their intrinsic growth potential after a dorsal root crush. Additionally, we posited that if we combined that approach with digestion of upregulated chondroitin sulfate proteoglycans (CSPG) at the DREZ with chondroitinase ABC (ChABC), we would promote regeneration of sensory axons across the DREZ into the spinal cord. We first assessed if this strategy promotes neuritic growth in an in vitro model of the glial scar containing CSPG. ChABC allowed for some regeneration across the once potently inhibitory substrate. Combining ChABC treatment with expression of caRheb in DRG significantly improved this growth. We then determined if this combination strategy also enhanced regeneration through the DREZ after dorsal root crush in adult rats in vivo. After unilaterally crushing C4-T1 dorsal roots, we injected AAV5-caRheb or AAV5-GFP into the ipsilateral C5-C8 DRGs. ChABC or PBS was injected into the ipsilateral dorsal horn at C5-C8 to digest CSPG, for a total of four animal groups (caRheb + ChABC, caRheb + PBS, GFP + ChABC, GFP + PBS). Regeneration was rarely observed in PBS-treated animals, whereas short-distance regrowth across the DREZ was observed in ChABC-treated animals. No difference in axon number or length between the ChABC groups was observed, which may be related to intraganglionic inflammation induced by the injection. ChABC-mediated regeneration is functional, as stimulation of ipsilateral median and ulnar nerves induced neuronal c-Fos expression in deafferented dorsal horn in both ChABC groups. Interestingly, caRheb + ChABC animals had significantly more c-Fos+ nuclei indicating that caRheb expression in DRGs promoted functional synaptogenesis of their axons that regenerated beyond a ChABC-treated DREZ. PMID:27458339

ABC-B transporter genes in Dirofilaria immitis.

PubMed

Bourguinat, Catherine; Che, Hua; Mani, Thangadurai; Keller, Kathy; Prichard, Roger K

2016-08-01

Dirofilaria immitis is a filarial nematode causing infection and heartworm disease in dogs and other canids, cats, and occasionally in humans. Prevention with macrocyclic lactones (ML) is recommended during the mosquito transmission season. Recently, ML resistance has been reported. ABC-B transporter genes are thought to be involved in the mechanism of ML resistance in other nematodes. This study aimed to identify all the ABC-B transporter genes in D. immitis using as a reference the nDi.2.2 D. immitis whole genome, which is not completely annotated. Using bioinformatic tools and PCR amplification on pooled D. immitis genomic DNA and on pooled cDNA, nine ABC transporter genes including one pseudogene were characterized. Bioinformatic and phylogenetic analyses allowed identification of three P-glycoproteins (Pgps) (Dim-pgp-3 Dim-pgp-10, Dim-pgp-11), of two ABC-B half transporter genes (one ortholog of Cel-haf-4 and Cel-haf-9; and one ortholog of Cel-haf-1 and Cel-haf-3), of one ABC half transporter gene (ortholog of Cel-haf-5) that contained an ABC-C motif, and of one additional half transporter that would require functional study for characterization. The number of ABC-B transporter genes identified was lower than in Caenorhabditis elegans and Haemonchus contortus. Further studies are needed to understand their possible role in ML resistance in D. immitis. These ABC transporters constitute a base for ML resistance investigation in D. immitis and advance our understanding of the molecular biology of this parasite. Copyright © 2016. Published by Elsevier Ltd.

Downregulation of miR-29a/b/c in placenta accreta inhibits apoptosis of implantation site intermediate trophoblast cells by targeting MCL1.

PubMed

Gu, Yongzhong; Bian, Yuehong; Xu, Xiaofei; Wang, Xietong; Zuo, Changting; Meng, Jinlai; Li, Hongyan; Zhao, Shigang; Ning, Yunnan; Cao, Yongzhi; Huang, Tao; Yan, Junhao; Chen, Zi-Jiang

2016-12-01

Placenta accreta is defined as abnormal adhesion of placental villi to the uterine myometrium. Although this condition has become more common as a result of the increasing rate of cesarean sections, the underlying causative mechanism(s) remain elusive. Because microRNA-29a/b/c (miR-29a/b/c) have been shown to play important roles in placental development, this study evaluated the roles of these microRNAs in placenta accreta. Expression of miR-29a/b/c and myeloid cell leukemia-1 (MCL1) were quantified in patient tissues and HTR8/SVneo trophoblast cells using the real-time quantitative polymerase chain reaction. Western blotting was used to analyze expression of the MCL1 protein in HTR8/SVneo trophoblast cells with altered expression of miR-29a/b/c. To determine their role in apoptosis, miR-29a/b/c were overexpressed in HTR-8/SVneo cells, and levels of apoptosis were analyzed by flow cytometry. Luciferase activity assays were used to determine whether MCL1 is a target gene of miR-29a/b/c. Expression of miR-29a/b/c was significantly lower in creta sites compared to noncreta sites (p = 0.018, 0.041, and 0.022, respectively), but expression of MCL1 was upregulated in creta sites (p = 0.039). MCL1 expression was significantly downregulated in HTR-8/SVneo cells overexpressing miR-29a/b/c (p = 0.002, 0.008, and 0.013, respectively). Luciferase activity assays revealed that miR-29a/b/c directly target the 3' untranslated region of MCL1 in 293T cells. Over-expression of miR-29a/b/c induced apoptosis in the HTR-8/SVneo trophoblast cell line. Moreover, histopathological evaluation revealed that the number of implantation site intermediate trophoblast (ISIT) cells was increased in creta sites and that these cells were positive for MCL1. Our results demonstrate that in placenta accreta, miR-29a/b/c inhibits apoptosis of ISIT cells by targeting MCL1. These findings provide new insights into the pathogenesis of placenta accreta. Copyright © 2016 Elsevier Ltd. All rights reserved.

The minimal-ABC trees with B1-branches.

PubMed

Dimitrov, Darko; Du, Zhibin; Fonseca, Carlos M da

2018-01-01

The atom-bond connectivity index (or, for short, ABC index) is a molecular structure descriptor bridging chemistry to graph theory. It is probably the most studied topological index among all numerical parameters of a graph that characterize its topology. For a given graph G = (V, E), the ABC index of G is defined as [Formula: see text], where di denotes the degree of the vertex i, and ij is the edge incident to the vertices i and j. A combination of physicochemical and the ABC index properties are commonly used to foresee the bioactivity of different chemical composites. Additionally, the applicability of the ABC index in chemical thermodynamics and other areas of chemistry, such as in dendrimer nanostars, benzenoid systems, fluoranthene congeners, and phenylenes is well studied in the literature. While finding of the graphs with the greatest ABC-value is a straightforward assignment, the characterization of the tree(s) with minimal ABC index is a problem largely open and has recently given rise to numerous studies and conjectures. A B1-branch of a graph is a pendent path of order 2. In this paper, we provide an important step forward to the full characterization of these minimal trees. Namely, we show that a minimal-ABC tree contains neither 4 nor 3 B1-branches. The case when the number of B1-branches is 2 is also considered.

Use of an autologous bioengineered composite skin in extensive burns: Clinical and functional outcomes. A multicentric study.

PubMed

Gómez, C; Galán, J M; Torrero, V; Ferreiro, I; Pérez, D; Palao, R; Martínez, E; Llames, S; Meana, A; Holguín, P

2011-06-01

We report clinical and functional outcomes obtained after application of an autologous bioengineered composite skin (ABCS) produced in a single Spanish tissue-engineering unit. Twenty-five burned patients treated with ABCS from 1999 to 2007 in five burn centres were included in the study. Mean age was 29 years (SD 11), with mean total body surface area (TBSA) burned being 74% (SD 17) and mean full-thickness injury of 61% (SD 19) of TBSA. The mean area initially engrafted with ABCS was 24% (SD 13) of TBSA, with a final take of 49% (SD 30, range 0-100%). ABCS achieved permanent coverage of a mean of 11% (SD 8) of TBSA. In subset analyses, lack of pre- and post-application wound bed infection and lack of serious acute systemic complications at the time of engraftment were significantly associated with better ABCS take. Final take obtained with ABCS could be improved with the use of non-cytotoxic topical antibiotics following engraftment. The use of plasma to prepare ABCS reduces production costs: cost-effectiveness ratio is not a limitation for its use. In terms of patient satisfaction, cosmetic/functional outcomes (general appearance, texture, flexibility, sensitivity and colour) of ABCS and split-thickness autografts are not different statistically. Copyright © 2010 Elsevier Ltd and ISBI. All rights reserved.

Design, Synthesis and Biological Evaluation of Novel Phosphorylated Abacavir Derivatives as Antiviral Agents Against Newcastle Disease Virus Infection in Chicken.

PubMed

K A, Suresh; Venkata Subbaiah, Kadiam C; Lavanya, Rayapu; Chandrasekhar, Kuruva; Chamarti, Naga Raju; Kumar, M Suresh; Wudayagiri, Rajendra; Valluru, Lokanatha

2016-09-01

Newcastle disease virus is the most devastating virus in poultry industry. It can eradicate the entire poultry flocks once infected. This study is aimed to investigate the antiviral efficacy of novel phosphorylated analogues of the drug abacavir (ABC) against Newcastle disease virus (NDV). About 16 analogues of ABC were designed and docking was performed against fusion protein of NDV. Three compounds were identified and selected for synthesis and biological evaluation based on binding affinity and docking scores. The compounds were synthesized and characterized by IR, (1)H, (13)C, (31)P and CHN analysis and mass spectra. These compounds were tested for antiviral efficacy against NDV-infected DF-1 cells. Compound ABC-1 had shown potent antiviral activity as evidenced by significant reduction in plaque units and cytopathic effect. Therefore, ABC-1 was selected to test for NDV-infected chicken survival rate. Effective dose50 concentrations were determined for ABC-1. Antioxidant enzyme levels in brain, liver and lung tissues were estimated. Superoxide dismutase and catalase were significantly raised and lipid peroxidation and HA titer levels were decreased upon treatment with 2 mg/kg body weight ABC-1. Histopathological modifications were also restored in the ABC-1-treated group. These findings demonstrated ABC-1 as a potential antiviral agent against NDV in chicken.

The ABC and AUSSAT.

ERIC Educational Resources Information Center

McGarritty, Ian

1985-01-01

Discusses the Australian Broadcasting Corporation's (ABC) utilization of the AUSSAT telecommunications satellite to extend its television and radio transmission range to reach remote Australian audiences; the satellite's program gathering and interchange capabilities; and ABC's generation of other benefits to offset cost of satellite services.…

Activities-specific balance confidence scale for predicting future falls in Indian older adults.

PubMed

Moiz, Jamal Ali; Bansal, Vishal; Noohu, Majumi M; Gaur, Shailendra Nath; Hussain, Mohammad Ejaz; Anwer, Shahnawaz; Alghadir, Ahmad

2017-01-01

Activities-specific balance confidence (ABC) scale is a subjective measure of confidence in performing various ambulatory activities without falling or experiencing a sense of unsteadiness. This study aimed to examine the ability of the Hindi version of the ABC scale (ABC-H scale) to discriminate between fallers and non-fallers and to examine its predictive validity for prospective falls. This was a prospective cohort study. A total of 125 community-dwelling older adults (88 were men) completed the ABC-H scale. The occurrence of falls over the follow-up period of 12 months was recorded. Discriminative validity was analyzed by comparing the total ABC-H scale scores between the faller and non-faller groups. A receiver operating characteristic curve analysis and a logistic regression analysis were used to examine the predictive accuracy of the ABC-H scale. The mean ABC-H scale score of the faller group was significantly lower than that of the non-faller group (52.6±8.1 vs 73.1±12.2; P <0.001). The optimal cutoff value for distinguishing faller and non-faller adults was ≤58.13. The sensitivity, specificity, area under the curve, and positive and negative likelihood ratios of the cutoff score were 86.3%, 87.3%, 0.91 ( P <0.001), 6.84, and 0.16, respectively. The percentage test accuracy and false-positive and false-negative rates were 86.87%, 12.2%, and 13.6%, respectively. A dichotomized total ABC-H scale score of ≤58.13% (adjusted odds ratio =0.032, 95% confidence interval =0.004-0.25, P =0.001) was significantly related with future falls. The ABC-H scores were significantly and independently related with future falls in the community-dwelling Indian older adults. The ability of the ABC-H scale to predict future falls was adequate with high sensitivity and specificity values.

High absolute basophil count is a powerful independent predictor of inferior overall survival in patients with primary myelofibrosis.

PubMed

Lucijanic, Marko; Livun, Ana; Stoos-Veic, Tajana; Pejsa, Vlatko; Jaksic, Ozren; Cicic, David; Lucijanic, Jelena; Romic, Zeljko; Orehovec, Biserka; Aralica, Gorana; Miletic, Marko; Kusec, Rajko

2018-05-01

To investigate the clinical and prognostic significance of absolute basophil count (ABC) in patients with primary myelofibrosis (PMF). We retrospectively investigated 58 patients with PMF treated in our institution in the period from 2006 to 2017. ABC was obtained in addition to other hematological and clinical parameters. Patients were separated into high and low ABC groups using the Receiver operating characteristic curve analysis. ABC was higher in PMF patients than in healthy controls (P < 0.001). Patients with high ABC had higher white blood cells (P < 0.001), higher red cell distribution width (P = 0.035), higher lactate dehydrogenase (P < 0.001), more frequently had circulatory blasts (P < 0.001), constitutional symptoms (P = 0.030) and massive splenomegaly (P = 0.014). ABC was also positively correlated with absolute monocyte count (AMC) (P < 0.001) and other components of differential blood count. There was no difference in ABC regarding driver mutations or degree of bone marrow fibrosis. Univariately, high ABC was significantly associated with inferior overall survival (hazard ratio (HR) 4.79, P < 0.001). This effect remained statistically significant (HR 4.27, P = 0.009) in a multivariate Cox regression model adjusted for age, gender, Dynamic International Prognostic Scoring System (HR 2.6, P = 0.001) and AMC (HR 8.45, P = 0.002). High ABC reflects higher disease activity and stronger proliferative potential of disease. ABC and AMC independently predict survival and therefore seem to reflect different underlying pathophysiologic processes. Hence, both have a potential for improvement of current prognostic scores. Basophils represent a part of malignant clone in PMF and are associated with unfavorable disease features and poor prognosis which is independent of currently established prognostic scoring system and monocytosis.

Aberrant immunoglobulin class switch recombination and switch translocations in activated B cell-like diffuse large B cell lymphoma.

PubMed

Lenz, Georg; Nagel, Inga; Siebert, Reiner; Roschke, Anna V; Sanger, Warren; Wright, George W; Dave, Sandeep S; Tan, Bruce; Zhao, Hong; Rosenwald, Andreas; Muller-Hermelink, Hans Konrad; Gascoyne, Randy D; Campo, Elias; Jaffe, Elaine S; Smeland, Erlend B; Fisher, Richard I; Kuehl, W Michael; Chan, Wing C; Staudt, Louis M

2007-03-19

To elucidate the mechanisms underlying chromosomal translocations in diffuse large B cell lymphoma (DLBCL), we investigated the nature and extent of immunoglobulin class switch recombination (CSR) in these tumors. We used Southern blotting to detect legitimate and illegitimate CSR events in tumor samples of the activated B cell-like (ABC), germinal center B cell-like (GCB), and primary mediastinal B cell lymphoma (PMBL) subgroups of DLBCL. The frequency of legitimate CSR was lower in ABC DLBCL than in GCB DLBCL and PMBL. In contrast, ABC DLBCL had a higher frequency of internal deletions within the switch mu (Smu) region compared with GCB DLBCL and PMBL. ABC DLBCLs also had frequent deletions within Sgamma and other illegitimate switch recombinations. Sequence analysis revealed ongoing Smu deletions within ABC DLBCL tumor clones, which were accompanied by ongoing duplications and activation-induced cytidine deaminase-dependent somatic mutations. Unexpectedly, short fragments derived from multiple chromosomes were interspersed within Smu in one case. These findings suggest that ABC DLBCLs have abnormalities in the regulation of CSR that could predispose to chromosomal translocations. Accordingly, aberrant switch recombination was responsible for translocations in ABC DLBCLs involving BCL6, MYC, and a novel translocation partner, SPIB.

Interaction of ABC multidrug transporters with anticancer protein kinase inhibitors: substrates and/or inhibitors?

PubMed

Hegedus, Csilla; Ozvegy-Laczka, Csilla; Szakács, Gergely; Sarkadi, Balázs

2009-05-01

Protein kinase inhibitors (PKI) are becoming key agents in modern cancer chemotherapy, and combination of PKIs with classical chemotherapeutic drugs may help to overcome currently untreatable metastatic cancers. Since chemotherapy resistance is a recurrent problem, mechanisms of resistance should be clarified in order to help further drug development. Here we suggest that in addition to PKI resistance based on altered target structures, the active removal of these therapeutic agents by the MDR-ABC transporters should also be considered as a major cause of clinical resistance. We discuss the occurring systemic and cellular mechanisms, which may hamper PKI efficiency, and document the role of selected MDR-ABC transporters in these phenomena through their interactions with these anticancer agents. Moreover, we suggest that PKI interactions with ABC transporters may modulate overall drug metabolism, including the fate of diverse, chemically or target-wise unrelated drugs. These effects are based on multiple forms of MDR-ABC transporter interaction with PKIs, as these compounds may be both substrates and/or inhibitors of an ABC transporter. We propose that these interactions should be carefully considered in clinical application, and a combined MDR-ABC transporter and PKI effect may bring a major advantage in future drug development.

Computing Finite-Time Lyapunov Exponents with Optimally Time Dependent Reduction

NASA Astrophysics Data System (ADS)

Babaee, Hessam; Farazmand, Mohammad; Sapsis, Themis; Haller, George

2016-11-01

We present a method to compute Finite-Time Lyapunov Exponents (FTLE) of a dynamical system using Optimally Time-Dependent (OTD) reduction recently introduced by H. Babaee and T. P. Sapsis. The OTD modes are a set of finite-dimensional, time-dependent, orthonormal basis {ui (x , t) } |i=1N that capture the directions associated with transient instabilities. The evolution equation of the OTD modes is derived from a minimization principle that optimally approximates the most unstable directions over finite times. To compute the FTLE, we evolve a single OTD mode along with the nonlinear dynamics. We approximate the FTLE from the reduced system obtained from projecting the instantaneous linearized dynamics onto the OTD mode. This results in a significant reduction in the computational cost compared to conventional methods for computing FTLE. We demonstrate the efficiency of our method for double Gyre and ABC flows. ARO project 66710-EG-YIP.

Laboratory investigation of grouted coupler connection details for ABC bridge projects.

DOT National Transportation Integrated Search

2015-08-01

With an ever increasing desire to utilize accelerated bridge construction (ABC) techniques, it is becoming critical that bridge : designers and contractors have confidence in typical details. The Keg Creek Bridge on US 6 in Iowa was a recent ABC exam...

The ABC protein turned chloride channel whose failure causes cystic fibrosis

NASA Astrophysics Data System (ADS)

Gadsby, David C.; Vergani, Paola; Csanády, László

2006-03-01

CFTR chloride channels are encoded by the gene mutated in patients with cystic fibrosis. These channels belong to the superfamily of ABC transporter ATPases. ATP-driven conformational changes, which in other ABC proteins fuel uphill substrate transport across cellular membranes, in CFTR open and close a gate to allow transmembrane flow of anions down their electrochemical gradient. New structural and biochemical information from prokaryotic ABC proteins and functional information from CFTR channels has led to a unifying mechanism explaining those ATP-driven conformational changes.

ArgR is an essential local transcriptional regulator of the arcABC operon in Streptococcus suis and is crucial for biological fitness in an acidic environment.

PubMed

Fulde, Marcus; Willenborg, Joerg; de Greeff, Astrid; Benga, Laurentiu; Smith, Hilde E; Valentin-Weigand, Peter; Goethe, Ralph

2011-02-01

Streptococcus suis is one of the most important pathogens in pigs and can also cause severe infections in humans. Despite its clinical relevance, very little is known about the factors that contribute to its virulence. Recently, we identified a new putative virulence factor in S. suis, the arginine deiminase system (ADS), an arginine catabolic enzyme system encoded by the arcABC operon, which enables S. suis to survive in an acidic environment. In this study, we focused on ArgR, an ADS-associated regulator belonging to the ArgR/AhrC arginine repressor family. Using an argR knockout strain we were able to show that ArgR is essential for arcABC operon expression and necessary for the biological fitness of S. suis. By cDNA expression microarray analyses and quantitative real-time RT-PCR we found that the arcABC operon is the only gene cluster regulated by ArgR, which is in contrast to the situation in many other bacteria. Reporter gene analysis with gfp under the control of the arcABC promoter demonstrated that ArgR is able to activate the arcABC promoter. Electrophoretic mobility shift assays with fragments of the arcABC promoter and recombinant ArgR, and chromatin immunoprecipitation with antibodies directed against ArgR, revealed that ArgR interacts with the arcABC promoter in vitro and in vivo by binding to a region from -147 to -72 bp upstream of the transcriptional start point. Overall, our results show that in S. suis, ArgR is an essential, system-specific transcriptional regulator of the ADS that interacts directly with the arcABC promoter in vivo.

Transcriptome-Based Identification of ABC Transporters in the Western Tarnished Plant Bug Lygus hesperus

PubMed Central

Hull, J. Joe; Chaney, Kendrick; Geib, Scott M.; Fabrick, Jeffrey A.; Brent, Colin S.; Walsh, Douglas; Lavine, Laura Corley

2014-01-01

ATP-binding cassette (ABC) transporters are a large superfamily of proteins that mediate diverse physiological functions by coupling ATP hydrolysis with substrate transport across lipid membranes. In insects, these proteins play roles in metabolism, development, eye pigmentation, and xenobiotic clearance. While ABC transporters have been extensively studied in vertebrates, less is known concerning this superfamily in insects, particularly hemipteran pests. We used RNA-Seq transcriptome sequencing to identify 65 putative ABC transporter sequences (including 36 full-length sequences) from the eight ABC subfamilies in the western tarnished plant bug (Lygus hesperus), a polyphagous agricultural pest. Phylogenetic analyses revealed clear orthologous relationships with ABC transporters linked to insecticide/xenobiotic clearance and indicated lineage specific expansion of the L. hesperus ABCG and ABCH subfamilies. The transcriptional profile of 13 LhABCs representative of the ABCA, ABCB, ABCC, ABCG, and ABCH subfamilies was examined across L. hesperus development and within sex-specific adult tissues. All of the transcripts were amplified from both reproductively immature and mature adults and all but LhABCA8 were expressed to some degree in eggs. Expression of LhABCA8 was spatially localized to the testis and temporally timed with male reproductive development, suggesting a potential role in sexual maturation and/or spermatozoa protection. Elevated expression of LhABCC5 in Malpighian tubules suggests a possible role in xenobiotic clearance. Our results provide the first transcriptome-wide analysis of ABC transporters in an agriculturally important hemipteran pest and, because ABC transporters are known to be important mediators of insecticidal resistance, will provide the basis for future biochemical and toxicological studies on the role of this protein family in insecticide resistance in Lygus species. PMID:25401762

Targeting receptor-activator of nuclear kappaB ligand in aneurysmal bone cysts: verification of target and therapeutic response.

PubMed

Pelle, Dominic W; Ringler, Jonathan W; Peacock, Jacqueline D; Kampfschulte, Kevin; Scholten, Donald J; Davis, Mary M; Mitchell, Deanna S; Steensma, Matthew R

2014-08-01

Aneurysmal bone cyst (ABC) is a benign tumor of bone presenting as a cystic, expansile lesion in both the axial and appendicular skeleton. Axial lesions demand special consideration, because treatment-related morbidity can be devastating. In similar lesions, such as giant cell tumor of bone (GCTB), the receptor-activator of nuclear kappaB ligand (RANKL)-receptor-activator of nuclear kappaB (RANK) signaling axis is essential to tumor progression. Although ABC and GCTB are distinct entities, they both contain abundant multinucleated giant cells and are osteolytic characteristically. We hypothesize that ABCs express both RANKL and RANK similarly in a cell-type specific manner, and that targeted RANKL therapy will mitigate ABC tumor progression. Cellular expression of RANKL and RANK was determined in freshly harvested ABC samples using laser confocal microscopy. A consistent cell-type-specific pattern was observed: fibroblastlike stromal cells expressed RANKL strongly whereas monocyte/macrophage precursor and multinucleated giant cells expressed RANK. Relative RANKL expression was determined by quantitative real-time polymerase chain reaction in ABC and GCTB tissue samples; no difference in relative expression was observed (P > 0.05). In addition, we review the case of a 5-year-old boy with a large, aggressive sacral ABC. After 3 months of targeted RANKL inhibition with denosumab, magnetic resonance imaging demonstrated tumor shrinkage, bone reconstitution, and healing of a pathologic fracture. Ambulation, and bowel and bladder function were restored at 6 months. Denosumab treatment was well tolerated. Post hoc analysis demonstrated strong RANKL expression in the pretreatment tumor sample. These findings demonstrate that RANKL-RANK signal activation is essential to ABC tumor progression. RANKL-targeted therapy may be an effective alternative to surgery in select ABC presentations. Copyright © 2014 Mosby, Inc. All rights reserved.

Embracing equifinality with efficiency: Limits of Acceptability sampling using the DREAM(LOA) algorithm

NASA Astrophysics Data System (ADS)

Vrugt, Jasper A.; Beven, Keith J.

2018-04-01

This essay illustrates some recent developments to the DiffeRential Evolution Adaptive Metropolis (DREAM) MATLAB toolbox of Vrugt (2016) to delineate and sample the behavioural solution space of set-theoretic likelihood functions used within the GLUE (Limits of Acceptability) framework (Beven and Binley, 1992, 2014; Beven and Freer, 2001; Beven, 2006). This work builds on the DREAM(ABC) algorithm of Sadegh and Vrugt (2014) and enhances significantly the accuracy and CPU-efficiency of Bayesian inference with GLUE. In particular it is shown how lack of adequate sampling in the model space might lead to unjustified model rejection.

Yang-Mills theory and the ABC conjecture

NASA Astrophysics Data System (ADS)

He, Yang-Hui; Hu, Zhi; Probst, Malte; Read, James

2018-05-01

We establish a precise correspondence between the ABC Conjecture and 𝒩 = 4 super-Yang-Mills theory. This is achieved by combining three ingredients: (i) Elkies’ method of mapping ABC-triples to elliptic curves in his demonstration that ABC implies Mordell/Faltings; (ii) an explicit pair of elliptic curve and associated Belyi map given by Khadjavi-Scharaschkin; and (iii) the fact that the bipartite brane-tiling/dimer model for a gauge theory with toric moduli space is a particular dessin d’enfant in the sense of Grothendieck. We explore this correspondence for the highest quality ABC-triples as well as large samples of random triples. The conjecture itself is mapped to a statement about the fundamental domain of the toroidal compactification of the string realization of 𝒩 = 4 SYM.

Compact high order schemes with gradient-direction derivatives for absorbing boundary conditions

NASA Astrophysics Data System (ADS)

Gordon, Dan; Gordon, Rachel; Turkel, Eli

2015-09-01

We consider several compact high order absorbing boundary conditions (ABCs) for the Helmholtz equation in three dimensions. A technique called "the gradient method" (GM) for ABCs is also introduced and combined with the high order ABCs. GM is based on the principle of using directional derivatives in the direction of the wavefront propagation. The new ABCs are used together with the recently introduced compact sixth order finite difference scheme for variable wave numbers. Experiments on problems with known analytic solutions produced very accurate results, demonstrating the efficacy of the high order schemes, particularly when combined with GM. The new ABCs are then applied to the SEG/EAGE Salt model, showing the advantages of the new schemes.

Lifestyle segmentation of US food shoppers to examine organic and local food consumption.

PubMed

Nie, Cong; Zepeda, Lydia

2011-08-01

The food related lifestyle (FRL) model, widely used on European data, is applied to US data using a modified survey instrument to examine organic and local food consumption. Since empirical studies indicate these shoppers are motivated by environmental and health concerns and limited by access, the conceptual framework employs an environmental behavior model, Attitude Behavior Context (ABC), which is consistent with means-end chain theory, the Health Belief (HB) model, and the FRL model. ABC theory incorporates contextual factors that may limit consumers' ability to act on their intentions. US food shopper data was collected in 2003 (n=956) utilizing an instrument with variables adapted from the FRL, ABC, and HB models. Cluster analysis segmented food shoppers into four FRL groups: rational, adventurous, careless, and a fourth segment that had some characteristics of both conservative and uninvolved consumers. The segments exhibited significant differences in organic and local food consumption. These were correlated with consumers' environmental concerns, knowledge and practices, health concerns and practices, as well as some demographic characteristics (race, gender, age, education), income, and variables that measured access to these foods. Implications for marketing and public policy strategies to promote organic and local foods include: emphasizing taste, nutrition, value, children, and enjoyment of cooking for rational consumers; and emphasizing health, fitness, and freshness, and providing ethnic foods for adventurous consumers. While both careless and conservative/uninvolved consumers valued convenience, the former tended to be in the highest income group, while the latter were in the lowest, were more likely to be either in the youngest or oldest age groups, and were very concerned about food safety and health. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Functional Network of the Arabidopsis Plastoglobule Proteome Based on Quantitative Proteomics and Genome-Wide Coexpression Analysis1[C][W][OA

PubMed Central

Lundquist, Peter K.; Poliakov, Anton; Bhuiyan, Nazmul H.; Zybailov, Boris; Sun, Qi; van Wijk, Klaas J.

2012-01-01

Plastoglobules (PGs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions. An integrated view of the role of the PG is lacking. Here, we better define the PG proteome and provide a conceptual framework for further studies. The PG proteome from Arabidopsis (Arabidopsis thaliana) leaf chloroplasts was determined by mass spectrometry of isolated PGs and quantitative comparison with the proteomes of unfractionated leaves, thylakoids, and stroma. Scanning electron microscopy showed the purity and size distribution of the isolated PGs. Compared with previous PG proteome analyses, we excluded several proteins and identified six new PG proteins, including an M48 metallopeptidase and two Absence of bc1 complex (ABC1) atypical kinases, confirmed by immunoblotting. This refined PG proteome consisted of 30 proteins, including six ABC1 kinases and seven fibrillins together comprising more than 70% of the PG protein mass. Other fibrillins were located predominantly in the stroma or thylakoid and not in PGs; we discovered that this partitioning can be predicted by their isoelectric point and hydrophobicity. A genome-wide coexpression network for the PG genes was then constructed from mRNA expression data. This revealed a modular network with four distinct modules that each contained at least one ABC1K and/or fibrillin gene. Each module showed clear enrichment in specific functions, including chlorophyll degradation/senescence, isoprenoid biosynthesis, plastid proteolysis, and redox regulators and phosphoregulators of electron flow. We propose a new testable model for the PGs, in which sets of genes are associated with specific PG functions. PMID:22274653

Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica

PubMed Central

Kimura, Megumi K.; Uchiyama, Kentaro; Nakao, Katsuhiro; Moriguchi, Yoshinari; San Jose-Maldia, Lerma; Tsumura, Yoshihiko

2014-01-01

Background and Aims Distribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM). Methods Genetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis. Key Results STRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia. Conclusions The combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis. PMID:25355521

Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

NASA Astrophysics Data System (ADS)

Flechsig, Holger

2016-02-01

ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter. Possible explanations are discussed in the light of currently debated transport scenarios of ABC transporters.

The Cost of Library Services: Activity-Based Costing in an Australian Academic Library.

ERIC Educational Resources Information Center

Robinson, Peter; Ellis-Newman, Jennifer

1998-01-01

Explains activity-based costing (ABC), discusses the benefits of ABC to library managers, and describes the steps involved in implementing ABC in an Australian academic library. Discusses the budgeting process in universities, and considers benefits to the library. (Author/LRW)

Effect of SOS-induced levels of imuABC on spontaneous and damage-induced mutagenesis in Caulobacter crescentus.

PubMed

Alves, Ingrid R; Lima-Noronha, Marco A; Silva, Larissa G; Fernández-Silva, Frank S; Freitas, Aline Luiza D; Marques, Marilis V; Galhardo, Rodrigo S

2017-11-01

imuABC (imuAB dnaE2) genes are responsible for SOS-mutagenesis in Caulobacter crescentus and other bacterial species devoid of umuDC. In this work, we have constructed operator-constitutive mutants of the imuABC operon. We used this genetic tool to investigate the effect of SOS-induced levels of these genes upon both spontaneous and damage-induced mutagenesis. We showed that constitutive expression of imuABC does not increase spontaneous or damage-induced mutagenesis, nor increases cellular resistance to DNA-damaging agents. Nevertheless, the presence of the operator-constitutive mutation rescues mutagenesis in a recA background, indicating that imuABC are the only genes required at SOS-induced levels for translesion synthesis (TLS) in C. crescentus. Furthermore, these data also show that TLS mediated by ImuABC does not require RecA, unlike umuDC-dependent mutagenesis in E. coli. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of steam activation of biochar produced from a giant Miscanthus on copper sorption and toxicity.

PubMed

Shim, Taeyong; Yoo, Jisu; Ryu, Changkook; Park, Yong-Kwon; Jung, Jinho

2015-12-01

This study aims to evaluate the physiochemical properties, sorption characteristics, and toxicity effects of biochar (BC) produced from Miscanthus sacchariflorus via slow pyrolysis at 500°C and its steam activation product (ABC). Although BC has a much lower surface area than ABC (181 and 322m(2)g(-1), respectively), the Cu sorption capacities of BC and ABC are not significantly different (p>0.05). A two-compartment model successfully explains the sorption of BC and ABC as being dominated by fast and slow sorption processes, respectively. In addition, both BC and ABC efficiently eliminate the toxicity of Cu towards Daphnia magna. However, ABC itself induced acute toxicity to D. magna, which is possibly due to increased aromaticity upon steam activation. These findings suggest that activation of BC produced from M. sacchariflorus at a pyrolytic temperature of 500°C may not be appropriate in terms of Cu sorption and toxicity reduction. Copyright © 2015 Elsevier Ltd. All rights reserved.

Implication of RuvABC and RecG in homologous recombination in Streptomyces ambofaciens.

PubMed

Hoff, Grégory; Bertrand, Claire; Piotrowski, Emilie; Thibessard, Annabelle; Leblond, Pierre

2017-01-01

Most bacterial organisms rely on homologous recombination to repair DNA double-strand breaks and for the post-replicative repair of DNA single-strand gaps. Homologous recombination can be divided into three steps: (i) a pre-synaptic step in which the DNA 3'-OH ends are processed, (ii) a recA-dependent synaptic step allowing the invasion of an intact copy and the formation of Holliday junctions, and (iii) a post-synaptic step consisting of migration and resolution of these junctions. Currently, little is known about factors involved in homologous recombination, especially for the post-synaptic step. In Escherichia coli, branch migration and resolution are performed by the RuvABC complex, but could also rely on the RecG helicase in a redundant manner. In this study, we show that recG and ruvABC are well-conserved among Streptomyces. ΔruvABC, ΔrecG and ΔruvABC ΔrecG mutant strains were constructed. ΔruvABC ΔrecG is only slightly affected by exposure to DNA damage (UV). We also show that conjugational recombination decreases in the absence of RuvABC and RecG, but that intra-chromosomal recombination is not affected. These data suggest that RuvABC and RecG are indeed involved in homologous recombination in Streptomyces ambofaciens and that alternative factors are able to take over Holliday junction in Streptomyces. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

EggLib: processing, analysis and simulation tools for population genetics and genomics

PubMed Central

2012-01-01

Background With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. Results In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. Conclusions EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded. PMID:22494792

EggLib: processing, analysis and simulation tools for population genetics and genomics.

PubMed

De Mita, Stéphane; Siol, Mathieu

2012-04-11

With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded.

Effect of β-elemene on the kinetics of intracellular transport of d-luciferin potassium salt (ABC substrate) in doxorubicin-resistant breast cancer cells and the associated molecular mechanism.

PubMed

Tang, Chao-Yuan; Zhu, Li-Xin; Yu, Jian-Dong; Chen, Zhi; Gu, Man-Cang; Mu, Chao-Feng; Liu, Qi; Xiong, Yang

2018-07-30

In order to explore the mechanism of the reversing multidrug resistance (MDR) phenotypes by β-elemene (β-ELE) in doxorubicin (DOX)-resistant breast cancer cells (MCF-7/DOX), both the functionality and quantity of the ABC transporters in MCF-7/DOX were studied. Bioluminescence imaging (BLI) was used to study the efflux of d-luciferin potassium salt, the substrate of ATP-binding cassette transporters (ABC transporters), in MCF-7/DOX cells treated by β-ELE. At the same time three major ABC transport proteins and genes-related MDR, P-glycoprotein (P-gp, ABCB1) and multidrug resistance-associated protein 1 (MRP, ABCC1) as well as breast cancer resistance protein (BCRP, ABCG2) were analyzed by q-PCR and Western blot. To investigate the efflux functionality of ABC transporters, MCF-7/DOX Fluc cell line with stably-overexpressed luciferase was established. BLI was then used to real-time monitor the efflux kinetics of d-luciferin potassium salt before and after MCF-7/DOX Fluc cells being treated with β-ELE or not. The results showed that the efflux of d-luciferin potassium salt from MCF-7/DOX Fluc was lessened when pretreated with β-ELE, which means that β-ELE may dampen the functionality of ABC transporters, thus decrease the efflux of d-fluorescein potassium or other chemotherapies which also serve as the substrates of ABC transporters. As the effect of β-ELE on the expression of ABC transporters, the results of q-PCR and Western blot showed that gene and protein expression of ABC transporters such as P-gp, MRP, and BCRP were down-regulated after the treatment of β-ELE. To verify the efficacy of β-ELE on reversing MDR, MCF-7/DOX cells were treated with the combination of DOX and β-ELE. MTT assay showed that β-ELE increased the inhibitory effect of DOX on the proliferation of MCF-7/DOX, and the IC 50 of the combination group was much lower than that of the single DOX or β-ELE treatment. In all, β-ELE may reverse MDR through the substrates of ABC transporters by two ways, to lessen the ABC protein efflux by weakening their functionality, or to reduce the quantity of ABC gene and protein expression. Copyright © 2018. Published by Elsevier B.V.

Is there continued evidence for an association between abacavir usage and myocardial infarction risk in individuals with HIV? A cohort collaboration.

PubMed

Sabin, Caroline A; Reiss, Peter; Ryom, Lene; Phillips, Andrew N; Weber, Rainer; Law, Matthew; Fontas, Eric; Mocroft, Amanda; de Wit, Stephane; Smith, Colette; Dabis, Francois; d'Arminio Monforte, Antonella; El-Sadr, Wafaa; Lundgren, Jens D

2016-03-31

In March 2008, the D:A:D study published results demonstrating an increased risk of myocardial infarction (MI) for patients on abacavir (ABC). We describe changes to the use of ABC since this date, and investigate changes to the association between ABC and MI with subsequent follow-up. A total of 49,717 D:A:D participants were followed from study entry until the first of an MI, death, 1 February 2013 or 6 months after last visit. Associations between a person's 10-year cardiovascular disease (CVD) risk and the likelihood of initiating or discontinuing ABC were assessed using multivariable logistic/Poisson regression. Poisson regression was used to assess the association between current ABC use and MI risk, adjusting for potential confounders, and a test of interaction was performed to assess whether the association had changed in the post-March 2008 period. Use of ABC increased from 10 % of the cohort in 2000 to 20 % in 2008, before stabilising at 18-19 %. Increases in use pre-March 2008, and subsequent decreases, were greatest in those at moderate and high CVD risk. Post-March 2008, those on ABC at moderate/high CVD risk were more likely to discontinue ABC than those at low/unknown CVD risk, regardless of viral load (≤1,000 copies/ml: relative rate 1.49 [95 % confidence interval 1.34-1.65]; >1,000 copies/ml: 1.23 [1.02-1.48]); no such associations were seen pre-March 2008. There was some evidence that antiretroviral therapy (ART)-naïve persons at moderate/high CVD risk post-March 2008 were less likely to initiate ABC than those at low/unknown CVD risk (odds ratio 0.74 [0.48-1.13]). By 1 February 2013, 941 MI events had occurred in 367,559 person-years. Current ABC use was associated with a 98 % increase in MI rate (RR 1.98 [1.72-2.29]) with no difference in the pre- (1.97 [1.68-2.33]) or post- (1.97 [1.43-2.72]) March 2008 periods (interaction P = 0.74). Despite a reduction in the channelling of ABC for patients at higher CVD risk since 2008, we continue to observe an association between ABC use and MI risk. Whilst confounding cannot be fully ruled out, this further diminishes channelling bias as an explanation for our findings.

Linear and nonlinear dynamo properties of time-dependent ABC flows

NASA Astrophysics Data System (ADS)

Brummell, N. H.; Cattaneo, F.; Tobias, S. M.

2001-04-01

The linear and nonlinear dynamo properties of a class of periodically forced flows is considered. The forcing functions are chosen to drive, in the absence of magnetic effects (kinematic regime), a time-dependent version of the ABC flow with A= B= C=1. The time-dependence consists of a harmonic displacement of the origin along the line x= y= z=1 with amplitude ɛ and frequency Ω. The finite-time Lyapunov exponents are computed for several values of ɛ and Ω. It is found that for values of these parameters near unity chaotic streamlines occupy most of the volume. In this parameter range, and for moderate kinetic and magnetic Reynolds numbers, the basic flow is both hydrodynamically and hydromagnetically unstable. However, the dynamo instability has a higher growth rate than the hydrodynamic one, so that the nonlinear regime can be reached with negligible departures from the basic ABC flow. In the nonlinear regime, two distinct classes of behaviour are observed. In one, the exponential growth of the magnetic field saturates and the dynamo settles to a stationary state whereby the magnetic energy is maintained indefinitely. In the other the velocity field evolves to a nondynamo state and the magnetic field, following an initial amplification, decays to zero. The transition from the dynamo to the nondynamo state can be mediated by the hydrodynamic instability or by magnetic perturbations. The properties of the ensuing nonlinear dynamo states are investigated for different parameter values. The implications for a general theory of nonlinear dynamos are discussed.

Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes.

PubMed

Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

2015-11-14

Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.

A novel cloning template designing method by using an artificial bee colony algorithm for edge detection of CNN based imaging sensors.

PubMed

Parmaksızoğlu, Selami; Alçı, Mustafa

2011-01-01

Cellular Neural Networks (CNNs) have been widely used recently in applications such as edge detection, noise reduction and object detection, which are among the main computer imaging processes. They can also be realized as hardware based imaging sensors. The fact that hardware CNN models produce robust and effective results has attracted the attention of researchers using these structures within image sensors. Realization of desired CNN behavior such as edge detection can be achieved by correctly setting a cloning template without changing the structure of the CNN. To achieve different behaviors effectively, designing a cloning template is one of the most important research topics in this field. In this study, the edge detecting process that is used as a preliminary process for segmentation, identification and coding applications is conducted by using CNN structures. In order to design the cloning template of goal-oriented CNN architecture, an Artificial Bee Colony (ABC) algorithm which is inspired from the foraging behavior of honeybees is used and the performance analysis of ABC for this application is examined with multiple runs. The CNN template generated by the ABC algorithm is tested by using artificial and real test images. The results are subjectively and quantitatively compared with well-known classical edge detection methods, and other CNN based edge detector cloning templates available in the imaging literature. The results show that the proposed method is more successful than other methods.

A Novel Cloning Template Designing Method by Using an Artificial Bee Colony Algorithm for Edge Detection of CNN Based Imaging Sensors

PubMed Central

Parmaksızoğlu, Selami; Alçı, Mustafa

2011-01-01

Cellular Neural Networks (CNNs) have been widely used recently in applications such as edge detection, noise reduction and object detection, which are among the main computer imaging processes. They can also be realized as hardware based imaging sensors. The fact that hardware CNN models produce robust and effective results has attracted the attention of researchers using these structures within image sensors. Realization of desired CNN behavior such as edge detection can be achieved by correctly setting a cloning template without changing the structure of the CNN. To achieve different behaviors effectively, designing a cloning template is one of the most important research topics in this field. In this study, the edge detecting process that is used as a preliminary process for segmentation, identification and coding applications is conducted by using CNN structures. In order to design the cloning template of goal-oriented CNN architecture, an Artificial Bee Colony (ABC) algorithm which is inspired from the foraging behavior of honeybees is used and the performance analysis of ABC for this application is examined with multiple runs. The CNN template generated by the ABC algorithm is tested by using artificial and real test images. The results are subjectively and quantitatively compared with well-known classical edge detection methods, and other CNN based edge detector cloning templates available in the imaging literature. The results show that the proposed method is more successful than other methods. PMID:22163903

Plane wave packet formulation of atom-plus-diatom quantum reactive scattering.

PubMed

Althorpe, Stuart C

2004-07-15

We recently interpreted several reactive scattering experiments using a plane wave packet (PWP) formulation of quantum scattering theory [see, e.g., S. C. Althorpe, F. Fernandez-Alonso, B. D. Bean, J. D. Ayers, A. E. Pomerantz, R. N. Zare, and E. Wrede, Nature (London) 416, 67 (2002)]. This paper presents the first derivation of this formulation for atom-plus-diatom reactive scattering, and explains its relation to conventional time-independent reactive scattering. We generalize recent results for spherical-particle scattering [S. C. Althorpe, Phys. Rev. A 69, 042702 (2004)] to atom-rigid-rotor scattering in the space-fixed frame, atom-rigid-rotor scattering in the body-fixed frame, and finally A+BC rearrangement scattering. The reactive scattering is initiated by a plane wave packet, describing the A+BC reagents in center-of-mass scattering coordinates, and is detected by projecting onto a series of AC+B (or AB+C) plane wave "probe" packets. The plane wave packets are localized at the closest distance from the scattering center at which the interaction potential can be neglected. The time evolution of the initial plane wave packet provides a clear visualization of the scattering into space of the reaction products. The projection onto the probe packets yields the time-independent, state-to-state scattering amplitude, and hence the differential cross section. We explain how best to implement the PWP approach in a numerical computation, and illustrate this with a detailed application to the H+D2 reaction. (c) 2004 American Institute of Physics

76 FR 42710 - Statement of Organization, Functions, and Delegations of Authority

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-19

..., Functions, and Delegations of Authority Part A, Office of the Secretary, Statement of Organization, Functions, and Delegations of Authority for the Department of Health and Human Services is being amended at... (ABC1). V. Under Chapter ABC, Section ABC.20 Functions, 2nd paragraph, replace ``State, tribal, and...

ABCs of Being Smart: S Is for Supporting

ERIC Educational Resources Information Center

Foster, Joanne

2014-01-01

Joanne Foster's article "R We There Yet?" was first published in "Parenting for High Potential" ("PHP") in 2006, which became the springboard for the "ABCs of Being Smart" series of columns. At that time, Foster invited "PHP" readers to think about their own versions of the "ABCs of Being…

75 FR 6706 - In the Matter of Certain Foldable Stools; Notice of Commission Decision Not To Review an Initial...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-10

... Distributing and Crate & Barrel with ``LTD Commodities, LLC, d/b/a abc Distributing'' and ``Euromarket Designs... of investigation named several respondents including the following: abc Distributing Inc. (``abc Distributing'') of Bannockburn, Illinois; Crate & Barrel, Inc. (``Crate & Barrel'') of Northbrook, Illinois...

ABC's of Construction. Final Report.

ERIC Educational Resources Information Center

Greater Baton Rouge Chamber of Commerce, LA.

The ABC's of Construction project was a demonstration project designed to integrate basic skills training with an industry-developed vocational-craft training program. The program was located at the central training facility of the Pelican Chapter of Associated Builders and Contractors (ABC), an organization made up of nearly 300 member companies…

The ABCs of Activity-Based Costing: A Cost Containment and Reallocation Tool.

ERIC Educational Resources Information Center

Turk, Frederick J.

1992-01-01

This article describes activity-based costing (ABC) and how this tool may help management understand the costs of major activities and identify possible alternatives. Also discussed are the traditional costing systems used by higher education and ways of applying ABC to higher education. (GLR)

Do You Know Your ABC?

ERIC Educational Resources Information Center

Neale, Claire

2013-01-01

Within primary schools, the core subjects of literacy and numeracy are highly regarded, and rightly so, as children need to learn to read, write and be numerically literate. This means that all children learn their ABCs at an early age, But, what about the "other ABC"--"Airway, Breathing and Circulation?" Accidents and medical…

Meta-Analysis of the Validation Studies of the Kaufman Assessment Battery for Children.

ERIC Educational Resources Information Center

Ochieng, Charles O.

2003-01-01

Conducted a meta-analysis of the Kaufman Assessment Battery for Children (K-ABC) to ascertain the numbers of factors in the mental processing subtest of the K-ABC. Analyses yielded sequential and simultaneous processing factors, suggesting that the original K-ABC theory was not supported. (SLD)

GPS-ABC radiated chamber testing overview and results : GPS-ABC Workshop VI : RTCA Washington, DC, March 30, 2017.

DOT National Transportation Integrated Search

2017-03-30

This presentation, which was given during the GPS-ABC Workshop VI in Washington, DC on March 30, 2017 details the authors' radiated testing protocols and results. GPS receiver testing was carried out April 25-29, 2016 at the Army : Research Laborator...

fbpABC gene cluster in Neisseria meningitidis is transcribed as an operon.

PubMed

Khun, H H; Deved, V; Wong, H; Lee, B C

2000-12-01

The neisserial fbpABC locus has been proposed to constitute a single transcriptional unit. To confirm this operonic arrangement, transcription assays using reverse transcriptase PCR amplification were conducted with Neisseria meningitidis. The presence of fbpAB and fbpBC transcripts obtained by priming cDNA synthesis with an fbpC-sequence-specific oligonucleotide indicates that fbpABC is organized as a single expression unit. The ratio of fbpA to fbpABC mRNA was approximately between 10- to 20-fold, as determined by real-time quantitative PCR.

fbpABC Gene Cluster in Neisseria meningitidis Is Transcribed as an Operon

PubMed Central

Khun, Heng H.; Deved, Vinay; Wong, Howard; Lee, B. Craig

2000-01-01

The neisserial fbpABC locus has been proposed to constitute a single transcriptional unit. To confirm this operonic arrangement, transcription assays using reverse transcriptase PCR amplification were conducted with Neisseria meningitidis. The presence of fbpAB and fbpBC transcripts obtained by priming cDNA synthesis with an fbpC-sequence-specific oligonucleotide indicates that fbpABC is organized as a single expression unit. The ratio of fbpA to fbpABC mRNA was approximately between 10- to 20-fold, as determined by real-time quantitative PCR. PMID:11083849

Placental ABC Transporters: Biological Impact and Pharmaceutical Significance.

PubMed

Joshi, Anand A; Vaidya, Soniya S; St-Pierre, Marie V; Mikheev, Andrei M; Desino, Kelly E; Nyandege, Abner N; Audus, Kenneth L; Unadkat, Jashvant D; Gerk, Phillip M

2016-12-01

The human placenta fulfills a variety of essential functions during prenatal life. Several ABC transporters are expressed in the human placenta, where they play a role in the transport of endogenous compounds and may protect the fetus from exogenous compounds such as therapeutic agents, drugs of abuse, and other xenobiotics. To date, considerable progress has been made toward understanding ABC transporters in the placenta. Recent studies on the expression and functional activities are discussed. This review discusses the placental expression and functional roles of several members of ABC transporter subfamilies B, C, and G including MDR1/P-glycoprotein, the MRPs, and BCRP, respectively. Since placental ABC transporters modulate fetal exposure to various compounds, an understanding of their functional and regulatory mechanisms will lead to more optimal medication use when necessary in pregnancy.

Placental ABC Transporters: Biological Impact and Pharmaceutical Significance

PubMed Central

Joshi, Anand A.; Vaidya, Soniya S.; St-Pierre, Marie V.; Mikheev, Andrei M.; Desino, Kelly E.; Nyandege, Abner N.; Audus, Kenneth L.; Unadkat, Jashvant D.; Gerk, Phillip M.

2017-01-01

The human placenta fulfills a variety of essential functions during prenatal life. Several ABC transporters are expressed in the human placenta, where they play a role in the transport of endogenous compounds and may protect the fetus from exogenous compounds such as therapeutic agents, drugs of abuse, and other xenobiotics. To date, considerable progress has been made toward understanding ABC transporters in the placenta. Recent studies on the expression and functional activities are discussed. This review discusses the placental expression and functional roles of several members of ABC transporter subfamilies B, C, and G including MDR1/P-glycoprotein, the MRPs, and BCRP, respectively. Since placental ABC transporters modulate fetal exposure to various compounds, an understanding of their functional and regulatory mechanisms will lead to more optimal medication use when necessary in pregnancy. PMID:27644937

Purification and characterization of chondroitinase ABC from Acinetobacter sp. C26.

PubMed

Zhu, Changliang; Zhang, Jingliang; Zhang, Jing; Jiang, Yanhui; Shen, Zhaopeng; Guan, Huashi; Jiang, Xiaolu

2017-02-01

An extracellular chondroitinase ABC (ChSase ABC, EC 4.2.2.4) produced by cultivating Acinetobacter sp. C26, was purified to homogeneity from the supernatant by ammonium sulfate fractionation, Q-Sepharose Fast Flow and Sephadex G-100 chromatography. The 76kDa enzyme was purified 48.09-fold to homogeneity with specific activity of 348.64U/mg, Using the chondroitin sulfate A (CS-A) as substrate, the maximal reaction rate (Vmax) and Michaelis-Menten constant (Km) of ChSase ABC were found to be 10.471μmol/min/ml and 0.105mg/ml, respectively. The enzyme showed the highest activity at the optimal conditions of pH 6.0 and 42 ∘C, respectively. This enzyme was stable at pH 5-10, 5-9 and 5-7 at 4°C, 37°C and 42°C, respectively. Investigation about thermal stability of ChSase ABC displayed that it was stable at 37°C. ChSase ABC activity was increased in presence of Na + , K + , Mn 2+ , 1,10-phenanthrolin and strongly inhibited by Cu 2+ , Hg 2+ , Al 3+ and SDS. These properties suggested that ChSase ABC from Acinetobacter sp. C26 bring promising prospects in medical and industry applications. Copyright © 2016 Elsevier B.V. All rights reserved.

The ABC transporter Rv1272c of Mycobacterium tuberculosis enhances the import of long-chain fatty acids in Escherichia coli.

PubMed

Martin, Audrey; Daniel, Jaiyanth

2018-02-05

Mycobacterium tuberculosis (Mtb), which causes tuberculosis, is capable of accumulating triacylglycerol (TAG) by utilizing fatty acids from host cells. ATP-binding cassette (ABC) transporters are involved in transport processes in all organisms. Among the classical ABC transporters in Mtb none have been implicated in fatty acid import. Since the transport of fatty acids from the host cell is important for dormancy-associated TAG synthesis in the pathogen, mycobacterial ABC transporter(s) could potentially be involved in this process. Based on sequence identities with a bacterial ABC transporter that mediates fatty acid import for TAG synthesis, we identified Rv1272c, a hitherto uncharacterized ABC-transporter in Mtb that also shows sequence identities with a plant ABC transporter involved in fatty acid transport. We expressed Rv1272c in E. coli and show that it enhances the import of radiolabeled fatty acids. We also show that Rv1272c causes a significant increase in the metabolic incorporation of radiolabeled long-chain fatty acids into cardiolipin, a tetra-acylated phospholipid, and phosphatidylglycerol in E. coli. This is the first report on the function of Rv1272c showing that it displays a long-chain fatty acid transport function. Copyright © 2018 Elsevier Inc. All rights reserved.

Abc Amino Acids: Design, Synthesis, and Properties of New Photoelastic Amino Acids

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

Standaert, Robert F; Park, Dr Seung Bum

2006-01-01

Photoisomerizable amino acids provide a direct avenue to the experimental manipulation of bioactive polypeptides, potentially allowing real-time, remote control of biological systems and enabling useful applications in nanobiotechnology. Herein, we report a new class of photoisomerizable amino acids intended to cause pronounced expansion and contraction in the polypeptide backbone, i.e., to be photoelastic. These compounds, termed Abc amino acids, employ a photoisomerizable azobiphenyl chromophore to control the relative disposition of aminomethyl and carboxyl substituents. Molecular modeling of nine Abc isomers led to the identification of one with particularly attractive properties, including the ability to induce contractions up to 13A inmore » the backbone upon transa?cis photoisomerization. This isomer, designated mpAbc, has substituents at meta and para positions on the inner (azo-linked) and outer rings, respectively. An efficient synthesis of Fmoc-protected mpAbc was executed in which the biaryl components were formed via Suzuki couplings and the azo linkage was formed via amine/nitroso condensation; protected forms of three other Abc isomers were prepared similarly. A decapeptide incorporating mpAbc was synthesized by conventional solid-phase methods and displayed characteristic azobenzene photochemical behavior with optimal conversion to the cis isomer at 360 nm and a thermal cisa?trans half life of 100 min. at 80 AoC.« less

A lightweight distributed framework for computational offloading in mobile cloud computing.

PubMed

Shiraz, Muhammad; Gani, Abdullah; Ahmad, Raja Wasim; Adeel Ali Shah, Syed; Karim, Ahmad; Rahman, Zulkanain Abdul

2014-01-01

The latest developments in mobile computing technology have enabled intensive applications on the modern Smartphones. However, such applications are still constrained by limitations in processing potentials, storage capacity and battery lifetime of the Smart Mobile Devices (SMDs). Therefore, Mobile Cloud Computing (MCC) leverages the application processing services of computational clouds for mitigating resources limitations in SMDs. Currently, a number of computational offloading frameworks are proposed for MCC wherein the intensive components of the application are outsourced to computational clouds. Nevertheless, such frameworks focus on runtime partitioning of the application for computational offloading, which is time consuming and resources intensive. The resource constraint nature of SMDs require lightweight procedures for leveraging computational clouds. Therefore, this paper presents a lightweight framework which focuses on minimizing additional resources utilization in computational offloading for MCC. The framework employs features of centralized monitoring, high availability and on demand access services of computational clouds for computational offloading. As a result, the turnaround time and execution cost of the application are reduced. The framework is evaluated by testing prototype application in the real MCC environment. The lightweight nature of the proposed framework is validated by employing computational offloading for the proposed framework and the latest existing frameworks. Analysis shows that by employing the proposed framework for computational offloading, the size of data transmission is reduced by 91%, energy consumption cost is minimized by 81% and turnaround time of the application is decreased by 83.5% as compared to the existing offloading frameworks. Hence, the proposed framework minimizes additional resources utilization and therefore offers lightweight solution for computational offloading in MCC.

A Lightweight Distributed Framework for Computational Offloading in Mobile Cloud Computing

PubMed Central

Shiraz, Muhammad; Gani, Abdullah; Ahmad, Raja Wasim; Adeel Ali Shah, Syed; Karim, Ahmad; Rahman, Zulkanain Abdul

2014-01-01

The latest developments in mobile computing technology have enabled intensive applications on the modern Smartphones. However, such applications are still constrained by limitations in processing potentials, storage capacity and battery lifetime of the Smart Mobile Devices (SMDs). Therefore, Mobile Cloud Computing (MCC) leverages the application processing services of computational clouds for mitigating resources limitations in SMDs. Currently, a number of computational offloading frameworks are proposed for MCC wherein the intensive components of the application are outsourced to computational clouds. Nevertheless, such frameworks focus on runtime partitioning of the application for computational offloading, which is time consuming and resources intensive. The resource constraint nature of SMDs require lightweight procedures for leveraging computational clouds. Therefore, this paper presents a lightweight framework which focuses on minimizing additional resources utilization in computational offloading for MCC. The framework employs features of centralized monitoring, high availability and on demand access services of computational clouds for computational offloading. As a result, the turnaround time and execution cost of the application are reduced. The framework is evaluated by testing prototype application in the real MCC environment. The lightweight nature of the proposed framework is validated by employing computational offloading for the proposed framework and the latest existing frameworks. Analysis shows that by employing the proposed framework for computational offloading, the size of data transmission is reduced by 91%, energy consumption cost is minimized by 81% and turnaround time of the application is decreased by 83.5% as compared to the existing offloading frameworks. Hence, the proposed framework minimizes additional resources utilization and therefore offers lightweight solution for computational offloading in MCC. PMID:25127245

Quantum dynamics of tunneling dominated reactions at low temperatures

NASA Astrophysics Data System (ADS)

Hazra, Jisha; Balakrishnan, N.

2015-05-01

We report a quantum dynamics study of the Li + HF → LiF + H reaction at low temperatures of interest to cooling and trapping experiments. Contributions from non-zero partial waves are analyzed and results show narrow resonances in the energy dependence of the cross section that survive partial wave summation. The computations are performed using the ABC code and a simple modification of the ABC code that enables separate energy cutoffs for the reactant and product rovibrational energy levels is found to dramatically reduce the basis set size and computational expense. Results obtained using two ab initio electronic potential energy surfaces for the LiHF system show strong sensitivity to the choice of the potential. In particular, small differences in the barrier heights of the two potential surfaces are found to dramatically influence the reaction cross sections at low energies. Comparison with recent measurements of the reaction cross section (Bobbenkamp et al 2011 J. Chem. Phys. 135 204306) shows similar energy dependence in the threshold regime and an overall good agreement with experimental data compared to previous theoretical results. Also, usefulness of a recently introduced method for ultracold reactions that employ the quantum close-coupling method at short-range and the multichannel quantum defect theory at long-range, is demonstrated in accurately evaluating product state-resolved cross sections for D + H2 and H + D2 reactions.

The impact of active breathing control on internal mammary lymph node coverage and normal tissue exposure in breast cancer patients planned for left-sided postmastectomy radiation therapy.

PubMed

Barry, Aisling; Rock, Kathy; Sole, Claudio; Rahman, Mohammad; Pintilie, Melania; Lee, Grace; Fyles, Anthony; Koch, C Anne

The purpose of this study was to evaluate the impact of the active breathing control (ABC) technique on IMN coverage and organs at risk in patients planned for postmastectomy radiation therapy (PMRT), with the inclusion of the internal mammary lymph nodes (IMNs). The effect of body mass index (BMI) on recorded dosimetric parameters was examined in the same patient cohort. Fifty left-sided postmastectomy patients with breast cancer who underwent free-breathing (FB) and ABC-Elekta CT simulation scans were selected at random from an institutional breast cancer database between 2008 and 2014. The ABC plans were directly compared with FB plans from the same patient. The IMN planning target volume coverage met dosimetric criteria for coverage of receiving more than 90% of the prescribed dose (V90) >90%, although it decreased with ABC compared with FB (94.5% vs 98%, P < .001). Overall, ABC significantly reduced doses to all measured heart and left anterior descending coronary artery parameters, ipsilateral lung V20, and mean lung dose compared with FB (P < .001). There was no difference seen between the ABC and FB plans with respect to the dose to contralateral lung or contralateral breast. There was no correlation identified between BMI and any of the dosimetric parameters recorded from the ABC and FB plans. Our results suggest that ABC reduces IMN coverage in left-sided breast cancer patients planned for PMRT; however, dosimetric criteria for IMN coverage were still met, suggesting that this is not likely to be clinically significant. ABC led to significant sparing of organs at risk compared with FB conditions and was not affected by BMI. Collectively, the results support the use of ABC for breast cancer patients undergoing left-sided PMRT requiring regional nodal irradiation that includes the IMNs. Further prospective clinical studies are required to determine the impact of these results on late normal tissue effects. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

ATP-binding cassette transporters in reproduction: a new frontier

PubMed Central

Bloise, E.; Ortiga-Carvalho, T.M.; Reis, F.M.; Lye, S.J.; Gibb, W.; Matthews, S.G.

2016-01-01

BACKGROUND The transmembrane ATP-binding cassette (ABC) transporters actively efflux an array of clinically relevant compounds across biological barriers, and modulate biodistribution of many physiological and pharmacological factors. To date, over 48 ABC transporters have been identified and shown to be directly and indirectly involved in peri-implantation events and fetal/placental development. They efflux cholesterol, steroid hormones, vitamins, cytokines, chemokines, prostaglandins, diverse xenobiotics and environmental toxins, playing a critical role in regulating drug disposition, immunological responses and lipid trafficking, as well as preventing fetal accumulation of drugs and environmental toxins. METHODS This review examines ABC transporters as important mediators of placental barrier functions and key reproductive processes. Expression, localization and function of all identified ABC transporters were systematically reviewed using PubMed and Google Scholar websites to identify relevant studies examining ABC transporters in reproductive tissues in physiological and pathophysiological states. Only reports written in English were incorporated with no restriction on year of publication. While a major focus has been placed on the human, extensive evidence from animal studies is utilized to describe current understanding of the regulation and function of ABC transporters relevant to human reproduction. RESULTS ABC transporters are modulators of steroidogenesis, fertilization, implantation, nutrient transport and immunological responses, and function as ‘gatekeepers’ at various barrier sites (i.e. blood-testes barrier and placenta) against potentially harmful xenobiotic factors, including drugs and environmental toxins. These roles appear to be species dependent and change as a function of gestation and development. The best-described ABC transporters in reproductive tissues (primarily in the placenta) are the multidrug transporters p-glycoprotein and breast cancer-related protein, the multidrug resistance proteins 1 through 5 and the cholesterol transporters ABCA1 and ABCG1. CONCLUSIONS The ABC transporters have various roles across multiple reproductive tissues. Knowledge of efflux direction, tissue distribution, substrate specificity and regulation of the ABC transporters in the placenta and other reproductive tissues is rapidly expanding. This will allow better understanding of the disposition of specific substrates within reproductive tissues, and facilitate development of novel treatments for reproductive disorders as well as improved approaches to protecting the developing fetus. PMID:26545808

Long-term bleeding risk prediction in 'real world' patients with atrial fibrillation: Comparison of the HAS-BLED and ABC-Bleeding risk scores. The Murcia Atrial Fibrillation Project.

PubMed

Esteve-Pastor, María Asunción; Rivera-Caravaca, José Miguel; Roldan, Vanessa; Vicente, Vicente; Valdés, Mariano; Marín, Francisco; Lip, Gregory Y H

2017-10-05

Risk scores in patients with atrial fibrillation (AF) based on clinical factors alone generally have only modest predictive value for predicting high risk patients that sustain events. Biomarkers might be an attractive prognostic tool to improve bleeding risk prediction. The new ABC-Bleeding score performed better than HAS-BLED score in a clinical trial cohort but has not been externally validated. The aim of this study was to analyze the predictive performance of the ABC-Bleeding score compared to HAS-BLED score in an independent "real-world" anticoagulated AF patients with long-term follow-up. We enrolled 1,120 patients stable on vitamin K antagonist treatment. The HAS-BLED and ABC-Bleeding scores were quantified. Predictive values were compared by c-indexes, IDI, NRI, as well as decision curve analysis (DCA). Median HAS-BLED score was 2 (IQR 2-3) and median ABC-Bleeding was 16.5 (IQR 14.3-18.6). After 6.5 years of follow-up, 207 (2.84 %/year) patients had major bleeding events, of which 65 (0.89 %/year) had intracranial haemorrhage (ICH) and 85 (1.17 %/year) had gastrointestinal bleeding events (GIB). The c-index of HAS-BLED was significantly higher than ABC-Bleeding for major bleeding (0.583 vs 0.518; p=0.025), GIB (0.596 vs 0.519; p=0.017) and for the composite of ICH-GIB (0.593 vs 0.527; p=0.030). NRI showed a significant negative reclassification for major bleeding and for the composite of ICH-GIB with the ABC-Bleeding score compared to HAS-BLED. Using DCAs, the use of HAS-BLED score gave an approximate net benefit of 4 % over the ABC-Bleeding score. In conclusion, in the first "real-world" validation of the ABC-Bleeding score, HAS-BLED performed significantly better than the ABC-Bleeding score in predicting major bleeding, GIB and the composite of GIB and ICH.

TaABC1, a member of the activity of bc1 complex protein kinase family from common wheat, confers enhanced tolerance to abiotic stresses in Arabidopsis

PubMed Central

Wang, Caixiang; Jing, Ruilian; Mao, Xinguo; Chang, Xiaoping; Li, Ang

2011-01-01

Abiotic stresses such as drought, salinity, and low temperature have drastic effects on plant growth and development. However, the molecular mechanisms regulating biochemical and physiological changes in response to stresses are not well understood. Protein kinases are major signal transduction factors among the reported molecular mechanisms mediating acclimation to environmental changes. Protein kinase ABC1 (activity of bc1 complex) is involved in regulating coenzyme Q biosynthesis in mitochondria in yeast (Saccharomyces cersvisiae), and in balancing oxidative stress in chloroplasts in Arabidopsis thaliana. In the current study, TaABC1 (Triticum aestivum L. activity of bc1 complex) protein kinase was localized to the cell membrane, cytoplasm, and nucleus. The effects of overexpressing TaABC1 in transgenic Arabidopsis plants on responses to drought, salt, and cold stress were further investigated. Transgenic Arabidopsis overexpressing the TaABC1 protein showed lower water loss and higher osmotic potential, photochemistry efficiency, and chlorophyll content, while cell membrane stability and controlled reactive oxygen species homeostasis were maintained. In addition, overexpression of TaABC1 increased the expression of stress-responsive genes, such as DREB1A, DREB2A, RD29A, ABF3, KIN1, CBF1, LEA, and P5CS, detected by real-time PCR analysis. The results suggest that TaABC1 overexpression enhances drought, salt, and cold stress tolerance in Arabidopsis, and imply that TaABC1 may act as a regulatory factor involved in a multiple stress response pathways. PMID:21115661

The feoABC Locus of Yersinia pestis Likely Has Two Promoters Causing Unique Iron Regulation

PubMed Central

O'Connor, Lauren; Fetherston, Jacqueline D.; Perry, Robert D.

2017-01-01

The FeoABC ferrous transporter is a wide-spread bacterial system. While the feoABC locus is regulated by a number of factors in the bacteria studied, we have previously found that regulation of feoABC in Yersinia pestis appears to be unique. None of the non-iron responsive transcriptional regulators that control expression of feoABC in other bacteria do so in Y. pestis. Another unique factor is the iron and Fur regulation of the Y. pestis feoABC locus occurs during microaerobic but not aerobic growth. Here we show that this unique iron-regulation is not due to a unique aspect of the Y. pestis Fur protein but to DNA sequences that regulate transcription. We have used truncations, alterations, and deletions of the feoA::lacZ reporter to assess the mechanism behind the failure of iron to repress transcription under aerobic conditions. These studies plus EMSAs and DNA sequence analysis have led to our proposal that the feoABC locus has two promoters: an upstream P1 promoter whose expression is relatively iron-independent but repressed under microaerobic conditions and the known downstream Fur-regulated P2 promoter. In addition, we have identified two regions that bind Y. pestis protein(s), although we have not identified these protein(s) or their function. Finally we used iron uptake assays to demonstrate that both FeoABC and YfeABCD transport ferrous iron in an energy-dependent manner and also use ferric iron as a substrate for uptake. PMID:28785546

The systems biology of uric acid transporters: the role of remote sensing and signaling.

PubMed

Nigam, Sanjay K; Bhatnagar, Vibha

2018-07-01

Uric acid homeostasis in the body is mediated by a number of SLC and ABC transporters in the kidney and intestine, including several multispecific 'drug' transporters (e.g., OAT1, OAT3, and ABCG2). Optimization of uric acid levels can be viewed as a 'systems biology' problem. Here, we consider uric acid transporters from a systems physiology perspective using the framework of the 'Remote Sensing and Signaling Hypothesis.' This hypothesis explains how SLC and ABC 'drug' and other transporters mediate interorgan and interorganismal communication (e.g., gut microbiome and host) via small molecules (e.g., metabolites, antioxidants signaling molecules) through transporters expressed in tissues lining body fluid compartments (e.g., blood, urine, cerebrospinal fluid). The list of uric acid transporters includes: SLC2A9, ABCG2, URAT1 (SLC22A12), OAT1 (SLC22A6), OAT3 (SLC22A8), OAT4 (SLC22A11), OAT10 (SLC22A13), NPT1 (SLC17A1), NPT4 (SLC17A3), MRP2 (ABCC2), MRP4 (ABCC4). Normally, SLC2A9, - along with URAT1, OAT1 and OAT3, - appear to be the main transporters regulating renal urate handling, while ABCG2 appears to regulate intestinal transport. In chronic kidney disease (CKD), intestinal ABCG2 becomes much more important, suggesting remote organ communication between the injured kidney and the intestine. The remote sensing and signaling hypothesis provides a useful systems-level framework for understanding the complex interplay of uric acid transporters expressed in different tissues involved in optimizing uric acid levels under normal and diseased (e.g., CKD, gut microflora dysbiosis) conditions.

A Manual for Implementation of ABC Video Duplication Projects.

ERIC Educational Resources Information Center

Hill, Joseph, Ed.

The ABC (Appalachian BOCES Consortium) consists of 10 BOCES (Boards of Cooperative Educational Services) which serve the 14 southern counties of New York State designated as Appalachia. Each year since 1974, the ABC has participated in regional video duplication projects, which have yielded a total of nearly 4,000 video titles. The complexity of…

Abrasive wear behavior of heat-treated ABC-silicon carbide

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

Zhang, Xiao Feng; Lee, Gun Y.; Chen, Da

2002-06-17

Hot-pressed silicon carbide, containing aluminum, boron, and carbon additives (ABC-SiC), was subjected to three-body and two-body wear testing using diamond abrasives over a range of sizes. In general, the wear resistance of ABC-SiC, with suitable heat treatment, was superior to that of commercial SiC.

75 FR 42069 - Fisheries of the South Atlantic and Gulf of Mexico; South Atlantic Fishery Management Council...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-20

...) will hold a meeting of its Scientific and Statistical Committee (SSC) to discuss Acceptable Biological Catch (ABC) Control Rules, and recommend ABC values for South Atlantic managed species. See... discuss ABC control rules for stocks which do not have peer reviewed quantitative stock assessments and...

Parents' Perspectives on Braille Literacy: Results from the ABC Braille Study

ERIC Educational Resources Information Center

Kamei-Hannan, Cheryl; Sacks, Sharon Zell

2012-01-01

Introduction: Parents who were the primary caretakers of children in the Alphabetic and Contracted Braille Study (ABC Braille Study) revealed their perspectives about braille literacy. Methods: A 30-item questionnaire was constructed by the ABC Braille research team, and researchers conducted telephone interviews with 31 parents who were the…

Association of Serotonin Concentration to Behavior and IQ in Autistic Children.

ERIC Educational Resources Information Center

Kuperman, Samuel; And Others

1987-01-01

The IQ and behavior patterns on the Autism Behavior Checklist (ABC) of 25 boys were compared to blood concentrations of platelet rich plasma (PRP) serotonin. Although no correlations were found between serotonin levels and IQ or ABC scales, four individual ABC items did correlate with serotonin concentrations. (Author/DB)

Confirmatory Factor Analysis of the Kaufman Assessment Battery for Children: A Reevaluation.

ERIC Educational Resources Information Center

Strommen, Erik

1988-01-01

Performed confirmatory factor analyses of Kaufman Assessment Battery for Children (K-ABC) using subtest correlations for standardization samples provided in manuals to test hypothesis that factors underlying K-ABC are substantially intercorrelated at all age levels for two- and three-factor models. Findings suggest K-ABC cannot distinguish between…

78 FR 48860 - New England Fishery Management Council; Public Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-12

... ABC Control Rule Working Group (ABC WG) and Electronic Monitoring Working Group (EM WG). DATES: The first meeting of the ABC Control Rule Working Group will be on Tuesday, September 3, 2013. The meeting..., times and places for the meetings will be posted on the Council's Web site, http://nefmc.org/ . FOR...

School-Based Management and Accountability Procedures Manual

ERIC Educational Resources Information Center

North Carolina Department of Public Instruction, 2004

2004-01-01

From the mission, several principles were developed to guide the School-Based Management and Accountability Program (the ABCs). (1) The ABCs sets standards for student performance and growth in the basics that are the foundation for further learning and achievement; (2) The accountability system in the ABCs plan is designed to result in improved…

Molecular analysis of imipenem-resistant Acinetobacter baumannii isolated from US service members wounded in Iraq, 2003–2008

USDA-ARS?s Scientific Manuscript database

Clonal spread and global dissemination of imipenem resistant (IR) A. baumannii-A. calcoaceticus complex (ABC) have been reported in recent years. However, the epidemiological features of the IR-ABCs in military treatment facilities (MTFs) have not been systematically studied. In this study, 298 ABC...

Escalated convergent artificial bee colony

NASA Astrophysics Data System (ADS)

Jadon, Shimpi Singh; Bansal, Jagdish Chand; Tiwari, Ritu

2016-03-01

Artificial bee colony (ABC) optimisation algorithm is a recent, fast and easy-to-implement population-based meta heuristic for optimisation. ABC has been proved a rival algorithm with some popular swarm intelligence-based algorithms such as particle swarm optimisation, firefly algorithm and ant colony optimisation. The solution search equation of ABC is influenced by a random quantity which helps its search process in exploration at the cost of exploitation. In order to find a fast convergent behaviour of ABC while exploitation capability is maintained, in this paper basic ABC is modified in two ways. First, to improve exploitation capability, two local search strategies, namely classical unidimensional local search and levy flight random walk-based local search are incorporated with ABC. Furthermore, a new solution search strategy, namely stochastic diffusion scout search is proposed and incorporated into the scout bee phase to provide more chance to abandon solution to improve itself. Efficiency of the proposed algorithm is tested on 20 benchmark test functions of different complexities and characteristics. Results are very promising and they prove it to be a competitive algorithm in the field of swarm intelligence-based algorithms.

Enhanced High-Rate Shockwave Lithotripsy Stone Comminution in an In Vivo Porcine Model Using Acoustic Bubble Coalescence.

PubMed

Alavi Tamaddoni, Hedieh; Roberts, William W; Duryea, Alexander P; Cain, Charles A; Hall, Timothy L

2016-12-01

Cavitation plays a significant role in the efficacy of stone comminution during shockwave lithotripsy (SWL). Although cavitation on the surface of urinary stones helps to improve fragmentation, cavitation bubbles along the propagation path may shield or block subsequent shockwaves (SWs) and potentially induce collateral tissue damage. Previous in vitro work has shown that applying low-amplitude acoustic waves after each SW can force bubbles to consolidate and enhance SWL efficacy. In this study, the feasibility of applying acoustic bubble coalescence (ABC) in vivo was tested. Model stones were percutaneously implanted and treated with 2500 lithotripsy SWs at 120 SW/minute with or without ABC. Comparing the results of stone comminution, a significant improvement was observed in the stone fragmentation process when ABC was used. Without ABC, only 25% of the mass of the stone was fragmented to particles <2 mm in size. With ABC, 75% of the mass was fragmented to particles <2 mm in size. These results suggest that ABC can reduce the shielding effect of residual bubble nuclei, resulting in a more efficient SWL treatment.

ATP-binding cassette (ABC) proteins in aquatic invertebrates: Evolutionary significance and application in marine ecotoxicology.

PubMed

Jeong, Chang-Bum; Kim, Hui-Su; Kang, Hye-Min; Lee, Jae-Seong

2017-04-01

The ATP-binding cassette (ABC) protein superfamily is known to play a fundamental role in biological processes and is highly conserved across animal taxa. The ABC proteins function as active transporters for multiple substrates across the cellular membrane by ATP hydrolysis. As this superfamily is derived from a common ancestor, ABC genes have evolved via lineage-specific duplications through the process of adaptation. In this review, we summarized information about the ABC gene families in aquatic invertebrates, considering their evolution and putative functions in defense mechanisms. Phylogenetic analysis was conducted to examine the evolutionary significance of ABC gene families in aquatic invertebrates. Particularly, a massive expansion of multixenobiotic resistance (MXR)-mediated efflux transporters was identified in the absence of the ABCG2 (BCRP) gene in Ecdysozoa and Platyzoa, suggesting that a loss of Abcg2 gene occurred sporadically in these species during divergence of Protostome to Lophotrochozoa. Furthermore, in aquatic invertebrates, the ecotoxicological significance of MXR is discussed while considering the role of MXR-mediated efflux transporters in response to various environmental pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome-wide identification of ATP-binding cassette (ABC) transporters and their roles in response to polycyclic aromatic hydrocarbons (PAHs) in the copepod Paracyclopina nana.

PubMed

Jeong, Chang-Bum; Kim, Duck-Hyun; Kang, Hye-Min; Lee, Young Hwan; Kim, Hui-Su; Kim, Il-Chan; Lee, Jae-Seong

2017-02-01

The ATP-binding cassette (ABC) protein superfamily is one of the largest gene families and is highly conserved in all domains. The ABC proteins play roles in several biological processes, including multi-xenobiotic resistance (MXR), by functioning as transporters in the cellular membrane. They also mediate the cellular efflux of a wide range of substrates against concentration gradients. In this study, 37 ABC genes belonging to eight distinct subfamilies were identified in the marine copepod Paracyclopina nana and annotated based on a phylogenetic analysis. Also, the functions of P-glycoproteins (P-gp) and multidrug resistance-associated proteins (MRPs), conferring MXR, were verified using fluorescent substrates and specific inhibitors. The activities of MXR-mediated ABC proteins and their transcriptional level were examined in response to polyaromatic hydrocarbons (PAHs), main components of the water-accommodated fraction. This study increases the understanding of the protective role of MXR in response to PAHs over the comparative evolution of ABC gene families. Copyright © 2016 Elsevier B.V. All rights reserved.

A hybrid artificial bee colony algorithm for numerical function optimization

NASA Astrophysics Data System (ADS)

Alqattan, Zakaria N.; Abdullah, Rosni

2015-02-01

Artificial Bee Colony (ABC) algorithm is one of the swarm intelligence algorithms; it has been introduced by Karaboga in 2005. It is a meta-heuristic optimization search algorithm inspired from the intelligent foraging behavior of the honey bees in nature. Its unique search process made it as one of the most competitive algorithm with some other search algorithms in the area of optimization, such as Genetic algorithm (GA) and Particle Swarm Optimization (PSO). However, the ABC performance of the local search process and the bee movement or the solution improvement equation still has some weaknesses. The ABC is good in avoiding trapping at the local optimum but it spends its time searching around unpromising random selected solutions. Inspired by the PSO, we propose a Hybrid Particle-movement ABC algorithm called HPABC, which adapts the particle movement process to improve the exploration of the original ABC algorithm. Numerical benchmark functions were used in order to experimentally test the HPABC algorithm. The results illustrate that the HPABC algorithm can outperform the ABC algorithm in most of the experiments (75% better in accuracy and over 3 times faster).

Factor validity and norms for the aberrant behavior checklist in a community sample of children with mental retardation.

PubMed

Marshburn, E C; Aman, M G

1992-09-01

The Aberrant Behavior Checklist (ABC) is a 58-item rating scale that was developed primarily to measure the effects of pharmacological intervention in individuals living in residential facilities. This study investigated the use of the ABC in a sample of community children with mental retardation. Teacher ratings on the ABC were collected on 666 students attending special classes. The data were factor analyzed and compared with other studies using the ABC. In addition, subscales were analyzed as a function of age, sex, and classroom placement, and preliminary norms were derived. A four-factor solution of the ABC was obtained. Congruence between the four derived factors and corresponding factors from the original ABC was high (congruence coefficients ranged between .87 and .96). Classroom placement and age had significant effects on subscale scores, whereas sex failed to affect ratings. The current results are sufficiently close to the original factor solution that the original scoring method can be used with community samples, although further studies are needed to look at this in more detail.

Brassboard Astrometric Beam Combiner (ABC) Development for the Space Interferometry Mission (SIM)

NASA Technical Reports Server (NTRS)

Jeganathan, Muthu; Kuan, Gary; Rud, Mike; Lin, Sean; Sutherland, Kristen; Moore, James; An, Xin

2008-01-01

The Astrometric Beam Combiner (ABC) is a critical element of the Space Interferometry Mission (SIM) that performs three key functions: coherently combine starlight from two siderostats; individually detect starlight for angle tracking; and disperse and detect the interferometric fringes. In addition, the ABC contains: a stimulus, cornercubes and shutters for in-orbit calibration; several tip/tilt mirror mechanisms for in-orbit alignment; and internal metrology beam launcher for pathlength monitoring. The detailed design of the brassboard ABC (which has the form, fit and function of the flight unit) is complete, procurement of long-lead items is underway, and assembly and testing is expected to be completed in Spring 2009. In this paper, we present the key requirements for the ABC, details of the completed optical and mechanical design as well as plans for assembly and alignment.

Structure, function, and evolution of bacterial ATP-binding cassette systems

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

Davidson, A.L.; Dassa, E.; Orelle, C.

2010-07-27

The ATP-binding cassette (ABC) systems constitute one of the largest superfamilies of paralogous sequences. All ABC systems share a highly conserved ATP-hydrolyzing domain or protein (the ABC; also referred to as a nucleotide-binding domain [NBD]) that is unequivocally characterized by three short sequence motifs (Fig. 1): these are the Walker A and Walker B motifs, indicative of the presence of a nucleotide-binding site, and the signature motif, unique to ABC proteins, located upstream of the Walker B motif (426). Other motifs diagnostic of ABC proteins are also indicated in Fig. 1. The biological significance of these motifs is discussed inmore » Structure, Function, and Dynamics of the ABC. ABC systems are widespread among living organisms and have been detected in all genera of the three kingdoms of life, with remarkable conservation in the primary sequence of the cassette and in the organization of the constitutive domains or subunits (203, 420). ABC systems couple the energy of ATP hydrolysis to an impressively large variety of essential biological phenomena, comprising not only transmembrane (TM) transport, for which they are best known, but also several non-transport-related processes, such as translation elongation (62) and DNA repair (174). Although ABC systems deserve much attention because they are involved in severe human inherited diseases (107), they were first discovered and characterized in detail in prokaryotes, as early as the 1970s (13, 148, 238, 468). The most extensively analyzed systems were the high-affinity histidine and maltose uptake systems of Salmonella enterica serovar Typhimurium and Escherichia coli. Over 2 decades ago, after the completion of the nucleotide sequences encoding these transporters in the respective laboratories of Giovanna Ames and Maurice Hofnung, Hiroshi Nikaido and colleagues noticed that the two systems displayed a global similarity in the nature of their components and, moreover, that the primary sequences of MalK and HisP, the proteins suspected to energize these transporters, shared as much as 32% identity in amino acid residues when their sequences were aligned (171). Later, it was found that several bacterial proteins involved in uptake of nutrients, export of toxins, cell division, bacterial nodulation of plants, and DNA repair displayed the same similarity in their sequences (127, 196). This led to the notion that the conserved protein, which had been shown to bind ATP (198, 201), would probably energize the systems mentioned above by coupling the energy of ATP hydrolysis to transport. The latter was demonstrated with the maltose and histidine transporters by use of isolated membrane vesicles (105, 379) and purified transporters reconstituted into proteoliposomes (30, 98). The determination of the sequence of the first eukaryotic protein strongly similar to these bacterial transporters (the P-glycoprotein, involved in resistance of cancer cells to multiple drugs) (169, 179) demonstrated that these proteins were not restricted to prokaryotes. Two names, 'traffic ATPases' (15) and the more accepted name 'ABC transporters' (193, 218), were proposed for members of this new superfamily. ABC systems can be divided into three main functional categories, as follows. Importers mediate the uptake of nutrients in prokaryotes. The nature of the substrates that are transported is very wide, including mono- and oligosaccharides, organic and inorganic ions, amino acids, peptides, ironsiderophores, metals, polyamine cations, opines, and vitamins. Exporters are involved in the secretion of various molecules, such as peptides, lipids, hydrophobic drugs, polysaccharides, and proteins, including toxins such as hemolysin. The third category of systems is apparently not involved in transport, with some members being involved in translation of mRNA and in DNA repair. Despite the large, diverse population of substrates handled and the difference in the polarity of transport, importers and exporters share a common organization made of two hydrophobic membrane-spanning or integral membrane (IM) domains and two hydrophilic domains carrying the ABC peripherally associated with the IM domains on the cytosolic side of the membrane (26). In importers, these four domains are almost always independent polypeptide chains that come together to form a multimeric complex. In most exporters, including the E. coli hemolysin exporter HlyB, the N-terminal IM and the C-terminal ABC domains are fused as a single polypeptide chain (IM-ABC). An inverted organization in which the IM domain is C-terminal with respect to the ABC domain (ABC-IM) exists, such as in the MacB protein, involved in macrolide resistance in E. coli. No IM domain partners have been identified for ABC proteins falling into the third category, and these proteins consist of two ABCs fused together (ABC2).« less

ATP binding cassette (ABC) transporters: expression and clinical value in glioblastoma.

PubMed

Dréan, Antonin; Rosenberg, Shai; Lejeune, François-Xavier; Goli, Larissa; Nadaradjane, Aravindan Arun; Guehennec, Jérémy; Schmitt, Charlotte; Verreault, Maïté; Bielle, Franck; Mokhtari, Karima; Sanson, Marc; Carpentier, Alexandre; Delattre, Jean-Yves; Idbaih, Ahmed

2018-03-08

ATP-binding cassette transporters (ABC transporters) regulate traffic of multiple compounds, including chemotherapeutic agents, through biological membranes. They are expressed by multiple cell types and have been implicated in the drug resistance of some cancer cells. Despite significant research in ABC transporters in the context of many diseases, little is known about their expression and clinical value in glioblastoma (GBM). We analyzed expression of 49 ABC transporters in both commercial and patient-derived GBM cell lines as well as from 51 human GBM tumor biopsies. Using The Cancer Genome Atlas (TCGA) cohort as a training dataset and our cohort as a validation dataset, we also investigated the prognostic value of these ABC transporters in newly diagnosed GBM patients, treated with the standard of care. In contrast to commercial GBM cell lines, GBM-patient derived cell lines (PDCL), grown as neurospheres in a serum-free medium, express ABC transporters similarly to parental tumors. Serum appeared to slightly increase resistance to temozolomide correlating with a tendency for an increased expression of ABCB1. Some differences were observed mainly due to expression of ABC transporters by microenvironmental cells. Together, our data suggest that the efficacy of chemotherapeutic agents may be misestimated in vitro if they are the targets of efflux pumps whose expression can be modulated by serum. Interestingly, several ABC transporters have prognostic value in the TCGA dataset. In our cohort of 51 GBM patients treated with radiation therapy with concurrent and adjuvant temozolomide, ABCA13 overexpression is associated with a decreased progression free survival in univariate (p < 0.01) and multivariate analyses including MGMT promoter methylation (p = 0.05) suggesting reduced sensitivity to temozolomide in ABCA13 overexpressing GBM. Expression of ABC transporters is: (i) detected in GBM and microenvironmental cells and (ii) better reproduced in GBM-PDCL. ABCA13 expression is an independent prognostic factor in newly diagnosed GBM patients. Further prospective studies are warranted to investigate whether ABCA13 expression can be used to further personalize treatments for GBM.

Retrospective Methods Analysis of Semiautomated Intracerebral Hemorrhage Volume Quantification From a Selection of the STICH II Cohort (Early Surgery Versus Initial Conservative Treatment in Patients With Spontaneous Supratentorial Lobar Intracerebral Haematomas).

PubMed

Haley, Mark D; Gregson, Barbara A; Mould, W Andrew; Hanley, Daniel F; Mendelow, Alexander David

2018-02-01

The ABC/2 method for calculating intracerebral hemorrhage (ICH) volume has been well validated. However, the formula, derived from the volume of an ellipse, assumes the shape of ICH is elliptical. We sought to compare the agreement of the ABC/2 formula with other methods through retrospective analysis of a selection of the STICH II cohort (Early Surgery Versus Initial Conservative Treatment in Patients With Spontaneous Supratentorial Lobar Intracerebral Haematomas). From 390 patients, 739 scans were selected from the STICH II image archive based on the availability of a CT scan compatible with OsiriX DICOM viewer. ICH volumes were calculated by the reference standard semiautomatic segmentation in OsiriX software and compared with calculated arithmetic methods (ABC/2, ABC/2.4, ABC/3, and 2/3SC) volumes. Volumes were compared by difference plots for specific groups: randomization ICH (n=374), 3- to 7-day postsurgical ICH (n=206), antithrombotic-associated ICH (n=79), irregular-shape ICH (n=703) and irregular-density ICH (n=650). Density and shape were measured by the Barras ordinal shape and density groups (1-5). The ABC/2.4 method had the closest agreement to the semiautomatic segmentation volume in all groups, except for the 3- to 7-day postsurgical ICH group where the ABC/3 method was superior. Although the ABC/2 formula for calculating elliptical ICH is well validated, it must be used with caution in ICH scans where the elliptical shape of ICH is a false assumption. We validated the adjustment of the ABC/2.4 method in randomization, antithrombotic-associated, heterogeneous-density, and irregular-shape ICH. URL: http://www.isrctn.com/ISRCTN22153967. Unique identifier: ISRCTN22153967. © 2018 American Heart Association, Inc.

Reproducibility of lung tumor position and reduction of lung mass within the planning target volume using active breathing control (ABC).

PubMed

Cheung, Patrick C F; Sixel, Katharina E; Tirona, Romeo; Ung, Yee C

2003-12-01

The active breathing control (ABC) device allows for temporary immobilization of respiratory motion by implementing a breath hold at a predefined relative lung volume and air flow direction. The purpose of this study was to quantitatively evaluate the ability of the ABC device to immobilize peripheral lung tumors at a reproducible position, increase total lung volume, and thereby reduce lung mass within the planning target volume (PTV). Ten patients with peripheral non-small-cell lung cancer tumors undergoing radiotherapy had CT scans of their thorax with and without ABC inspiration breath hold during the first 5 days of treatment. Total lung volumes were determined from the CT data sets. Each peripheral lung tumor was contoured by one physician on all CT scans to generate gross tumor volumes (GTVs). The lung density and mass contained within a 1.5-cm PTV margin around each peripheral tumor was calculated using CT numbers. Using the center of the GTV from the Day 1 ABC scan as the reference, the displacement of subsequent GTV centers on Days 2 to 5 for each patient with ABC applied was calculated in three dimensions. With the use of ABC inspiration breath hold, total lung volumes increased by an average of 42%. This resulted in an average decrease in lung mass of 18% within a standard 1.5-cm PTV margin around the GTV. The average (+/- standard deviation) displacement of GTV centers with ABC breath hold applied was 0.3 mm (+/- 1.8 mm), 1.2 mm (+/- 2.3 mm), and 1.1 mm (+/- 3.5 mm) in the lateral direction, anterior-posterior direction, and superior-inferior direction, respectively. Results from this study indicate that there remains some inter-breath hold variability in peripheral lung tumor position with the use of ABC inspiration breath hold, which prevents significant PTV margin reduction. However, lung volumes can significantly increase, thereby decreasing the mass of lung within a standard PTV.

The ABC transporter ABCG29 is involved in H2O2 tolerance and biocontrol traits in the fungus Clonostachys rosea.

PubMed

Dubey, Mukesh; Jensen, Dan Funck; Karlsson, Magnus

2016-04-01

For successful biocontrol interactions, biological control organisms must tolerate toxic metabolites produced by themselves or plant pathogens during mycoparasitic/antagonistic interactions, by host plant during colonization of the plant, and xenobiotics present in the environment. ATP-binding cassette (ABC) transporters can play a significant role in tolerance of toxic compounds by mediating active transport across the cellular membrane. This paper reports on functional characterization of an ABC transporter ABCG29 in the biocontrol fungus Clonostachys rosea strain IK726. Gene expression analysis showed induced expression of abcG29 during exposure to the Fusarium spp. mycotoxin zearalenone (ZEA) and the fungicides Cantus, Chipco Green and Apron. Expression of abcG29 in C. rosea was significantly higher during C. rosea-C. rosea (Cr-Cr) interaction or in exposure to C. rosea culture filtrate for 2 h, compared to interaction with Fusarium graminearum or 2 h exposure to F. graminearum culture filtrate. In contrast with gene expression data, ΔabcG29 strains did not display reduced tolerance towards ZEA, fungicides or chemical agents known for inducing oxidative, cell wall or osmotic stress, compared to C. rosea WT. The exception was a significant reduction in tolerance to H2O2 (10 mM) in ΔabcG29 strains when conidia were used as an inoculum. The antagonistic ability of ΔabcG29 strains towards F. graminearum, Fusarium oxysporum or Botrytis cinerea in dual plate assays were not different compared with WT. However, in biocontrol assays ΔabcG29 strains displayed reduced ability to protect Arabidopsis thaliana leaves from B. cinerea, and barley seedling from F. graminearum as measured by an A. thaliana detached leaf assay and a barley foot rot disease assay, respectively. These data show that the ABCG29 is dispensable for ZEA and fungicides tolerance, and antagonism but not H2O2 tolerance and biocontrol effects in C. rosea.

Support for the 2007 Meeting of the Society for Mathematical Psychology

DTIC Science & Technology

2007-12-10

Ballroom: Salons A,B,&C 1 1:45am-l:15pm Lunch (provided) Lakeside Area 1:15pm-4:00pm Symposia & Talk Sessions Ballroom: Salons A,B,&C 4:30pm-5:30pm Plenary...Symposia & Talk Sessions Ballroom: Salons A,B,&C 11:45am-1:15pm Lunch (provided) Lakeside Area 1:1 5pm-4:00pm Symposia & Talk Sessions Ballroom: Salons A,B...Sat 7:45am-8:45am Breakfast (provided) Lakeside Area 9:00am-1 1:45am Symposia & Talk Sessions Ballroom: Salons A,B,&C Program Overview Plenary

Hybrid artificial bee colony algorithm for parameter optimization of five-parameter bidirectional reflectance distribution function model.

PubMed

Wang, Qianqian; Zhao, Jing; Gong, Yong; Hao, Qun; Peng, Zhong

2017-11-20

A hybrid artificial bee colony (ABC) algorithm inspired by the best-so-far solution and bacterial chemotaxis was introduced to optimize the parameters of the five-parameter bidirectional reflectance distribution function (BRDF) model. To verify the performance of the hybrid ABC algorithm, we measured BRDF of three kinds of samples and simulated the undetermined parameters of the five-parameter BRDF model using the hybrid ABC algorithm and the genetic algorithm, respectively. The experimental results demonstrate that the hybrid ABC algorithm outperforms the genetic algorithm in convergence speed, accuracy, and time efficiency under the same conditions.

Factorial validity of the Movement Assessment Battery for Children-2 (age band 2).

PubMed

Wagner, Matthias Oliver; Kastner, Julia; Petermann, Franz; Bös, Klaus

2011-01-01

The Movement Assessment Battery for Children-2 (M-ABC-2) is one of the most commonly used tests for the diagnosis of specific developmental disorders of motor function (F82). The M-ABC-2 comprises eight subtests per age band (AB) that are assigned to three dimensions: manual dexterity, aiming and catching, and balance. However, while previous exploratory findings suggested the correctness of the assumption of factorial validity, there is no empirical evidence that the M-ABC-2 subtests allow for a valid reproduction of the postulated factorial structure. The purpose of this study was to empirically confirm the factorial validity of the M-ABC-2. The German normative sample of AB2 (7-10 years; N=323) was used as the study sample for the empirical analyses. Confirmatory factor analysis was used to verify the factorial validity of the M-ABC-2 (AB2). The incremental fit indices (χ2=28.675; df=17; Bollen-Stine p value=0.318; RMSEA=0.046 [0.011-0.075]; SRMR=0.038; CFI=0.960) provided evidence for the factorial validity of the M-ABC-2 (AB2). However, because of a lack of empirical verification for convergent and discriminant validity, there is still no evidence that F82 can be diagnosed using M-ABC-2 (AB2). Copyright © 2010 Elsevier Ltd. All rights reserved.

Mdr65 decreases toxicity of multiple insecticides in Drosophila melanogaster.

PubMed

Sun, Haina; Buchon, Nicolas; Scott, Jeffrey G

2017-10-01

ABC transporters are ubiquitous membrane-bound proteins, present in both prokaryotes and eukaryotes. The major function of eukaryotic ABC transporters is to mediate the efflux of a variety of substrates (including xenobiotics) out of cells. ABC transporters have been widely investigated in humans, particularly for their involvement in multidrug resistance (MDR). Considerably less is known about their roles in transport and/or excretion in insects. ABC transporters are only known to function as exporters in insects. Drosophila melanogaster has 56 ABC transporter genes, including eight which are phylogenetically most similar to the human Mdr genes (ABCB1 clade). We investigated the role of ABC transporters in the ABCB1 clade in modulating the susceptibility to insecticides. We took advantage of the GAL4/UAS system in D. melanogaster to knockdown the expression levels of Mdr65, Mdr50, Mdr49 and ABCB6 using transgenic UAS-RNAi lines and conditional driver lines. The most notable effects were increased sensitivities to nine different insecticides by silencing of Mdr65. Furthermore, a null mutation of Mdr65 decreased the malathion, malaoxon and fipronil LC 50 values by a factor of 1.9, 2.1 and 3.9, respectively. Altogether, this data demonstrates the critical role of ABC transporters, particularly Mdr65, in altering the toxicity of specific, structurally diverse, insecticides in D. melanogaster. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development

PubMed Central

Chen, Piaojuan; Li, Yi; Zhao, Lihua; Hou, Zhimin; Yan, Maokai; Hu, Bingyan; Liu, Yanhui; Azam, Syed Muhammad; Zhang, Ziyan; Rahman, Zia ur; Liu, Liping; Qin, Yuan

2017-01-01

Pineapple (Ananas comosus L.) cultivation commonly relies on asexual reproduction which is easily impeded by many factors in agriculture production. Sexual reproduction might be a novel approach to improve the pineapple planting. However, genes controlling pineapple sexual reproduction are still remain elusive. In different organisms a conserved superfamily proteins known as ATP binding cassette (ABC) participate in various biological processes. Whereas, till today the ABC gene family has not been identified in pineapple. Here 100 ABC genes were identified in the pineapple genome and grouped into eight subfamilies (5 ABCAs, 20 ABCBs, 16 ABCCs, 2 ABCDs, one ABCEs, 5 ABCFs, 42 ABCGs and 9 ABCIs). Gene expression profiling revealed the dynamic expression pattern of ABC gene family in various tissues and different developmental stages. AcABCA5, AcABCB6, AcABCC4, AcABCC7, AcABCC9, AcABCG26, AcABCG38 and AcABCG42 exhibited preferential expression in ovule and stamen. Over-expression of AcABCG38 in the Arabidopsis double mutant abcg1-2abcg16-2 partially restored its pollen abortion defects, indicating that AcABCG38 plays important roles in pollen development. Our study on ABC gene family in pineapple provides useful information for developing sexual pineapple plantation which could be utilized to improve pineapple agricultural production. PMID:29312399

Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development.

PubMed

Chen, Piaojuan; Li, Yi; Zhao, Lihua; Hou, Zhimin; Yan, Maokai; Hu, Bingyan; Liu, Yanhui; Azam, Syed Muhammad; Zhang, Ziyan; Rahman, Zia Ur; Liu, Liping; Qin, Yuan

2017-01-01

Pineapple ( Ananas comosus L .) cultivation commonly relies on asexual reproduction which is easily impeded by many factors in agriculture production. Sexual reproduction might be a novel approach to improve the pineapple planting. However, genes controlling pineapple sexual reproduction are still remain elusive. In different organisms a conserved superfamily proteins known as ATP binding cassette (ABC) participate in various biological processes. Whereas, till today the ABC gene family has not been identified in pineapple. Here 100 ABC genes were identified in the pineapple genome and grouped into eight subfamilies (5 ABCAs , 20 ABCB s, 16 ABCCs , 2 ABCDs , one ABCEs , 5 ABCFs , 42 ABCGs and 9 ABCIs ). Gene expression profiling revealed the dynamic expression pattern of ABC gene family in various tissues and different developmental stages. AcABCA5, AcABCB6, AcABCC4 , AcABCC7 , AcABCC9 , AcABCG26 , AcABCG38 and AcABCG42 exhibited preferential expression in ovule and stamen. Over-expression of AcABCG38 in the Arabidopsis double mutant abcg1-2abcg16-2 partially restored its pollen abortion defects, indicating that AcABCG38 plays important roles in pollen development. Our study on ABC gene family in pineapple provides useful information for developing sexual pineapple plantation which could be utilized to improve pineapple agricultural production.

Neuroprotective effect of chondroitinase ABC on primary and secondary brain injury after stroke in hypertensive rats.

PubMed

Chen, Xin-ran; Liao, Song-jie; Ye, Lan-xiang; Gong, Qiong; Ding, Qiao; Zeng, Jin-sheng; Yu, Jian

2014-01-16

Focal cerebral infarction causes secondary damage in the ipsilateral ventroposterior thalamic nucleus (VPN). Chondroitin sulfate proteoglycans (CSPGs) are a family of putative inhibitory components, and its degradation by chondroitinase ABC (ChABC) promotes post-injury neurogenesis. This study investigated the role of ChABC in the primary and secondary injury post stroke in hypertension. Renovascular hypertensive Sprague-Dawley rats underwent middle cerebral artery occlusion (MCAO), and were subjected to continuous intra-infarct infusion of ChABC (0.12 U/d for 7 days) 24 h later. Neurological function was evaluated by a modified neurologic severity score. Neurons were counted in the peri-infarct region and the ipsilateral VPN 8 and 14 days after MCAO by Nissl staining and NeuN labeling. The expressions of CSPGs, growth-associated protein-43 (GAP-43) and synaptophysin (SYN) were detected with immunofluorescence or Western blotting. The intra-infarct infusion of ChABC, by degrading accumulated CSPGs, rescued neuronal loss and increased the levels of GAP-43 and SYN in both the ipsilateral cortex and VPN, indicating enhancd neuron survival as well as augmented axonal growth and synaptic plasticity, eventually improving overall neurological function. The study demonstrated that intra-infarct ChABC infusion could salvage the brain from both primary and secondary injury by the intervention on the neuroinhibitory environment post focal cerebral infarction. © 2013 Published by Elsevier B.V.

A beamline systems model for Accelerator-Driven Transmutation Technology (ADTT) facilities

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

Todd, A.M.M.; Paulson, C.C.; Peacock, M.A.

1995-10-01

A beamline systems code, that is being developed for Accelerator-Driven Transmutation Technology (ADTT) facility trade studies, is described. The overall program is a joint Grumman, G.H. Gillespie Associates (GHGA) and Los Alamos National Laboratory effort. The GHGA Accelerator Systems Model (ASM) has been adopted as the framework on which this effort is based. Relevant accelerator and beam transport models from earlier Grumman systems codes are being adapted to this framework. Preliminary physics and engineering models for each ADTT beamline component have been constructed. Examples noted include a Bridge Coupled Drift Tube Linac (BCDTL) and the accelerator thermal system. A decisionmore » has been made to confine the ASM framework principally to beamline modeling, while detailed target/blanket, balance-of-plant and facility costing analysis will be performed externally. An interfacing external balance-of-plant and facility costing model, which will permit the performance of iterative facility trade studies, is under separate development. An ABC (Accelerator Based Conversion) example is used to highlight the present models and capabilities.« less

A beamline systems model for Accelerator-Driven Transmutation Technology (ADTT) facilities

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

Todd, Alan M. M.; Paulson, C. C.; Peacock, M. A.

1995-09-15

A beamline systems code, that is being developed for Accelerator-Driven Transmutation Technology (ADTT) facility trade studies, is described. The overall program is a joint Grumman, G. H. Gillespie Associates (GHGA) and Los Alamos National Laboratory effort. The GHGA Accelerator Systems Model (ASM) has been adopted as the framework on which this effort is based. Relevant accelerator and beam transport models from earlier Grumman systems codes are being adapted to this framework. Preliminary physics and engineering models for each ADTT beamline component have been constructed. Examples noted include a Bridge Coupled Drift Tube Linac (BCDTL) and the accelerator thermal system. Amore » decision has been made to confine the ASM framework principally to beamline modeling, while detailed target/blanket, balance-of-plant and facility costing analysis will be performed externally. An interfacing external balance-of-plant and facility costing model, which will permit the performance of iterative facility trade studies, is under separate development. An ABC (Accelerator Based Conversion) example is used to highlight the present models and capabilities.« less

The Asset-Based Context Matrix: A Tool for Assessing Children's Learning Opportunities and Participation in Natural Environments

ERIC Educational Resources Information Center

Wilson, Linda L.; Mott, Donald W.; Batman, Deb

2004-01-01

This article provides a description of the "Asset-Based Context Matrix" (ABC Matrix). The ABC Matrix is an assessment tool for designing interventions for children in natural learning environments. The tool is based on research evidence indicating that children's learning is enhanced in contextually meaningful learning environments. The ABC Matrix…

Applying the Post-Modern Double ABC-X Model to Family Food Insecurity

ERIC Educational Resources Information Center

Hutson, Samantha; Anderson, Melinda; Swafford, Melinda

2015-01-01

This paper develops the argument that using the Double ABC-X model in family and consumer sciences (FCS) curricula is a way to educate nutrition and dietetics students regarding a family's perceptions of food insecurity. The Double ABC-X model incorporates ecological theory as a basis to explain family stress and the resulting adjustment and…

The Role of Activity Based Costing (ABC) in Educational Support Services: A White Paper.

ERIC Educational Resources Information Center

Edds, Daniel B.

Many front-line managers who are assuming more financial responsibility for their organizations find traditional cost accounting inadequate for their needs and are turning to Activity Based Costing (ABC). ABC is not a financial reporting system to serve the needs of regulatory agencies, but a tool that tracks costs from the general ledger…

So, You Need To Justify Your Existing ABC Program (or Lobby for a New One).

ERIC Educational Resources Information Center

Walsh, Jean Terry; Gillis, Lee

1998-01-01

Advice for adventure-based counseling (ABC) programs seeking funding includes setting realistic goals, designing an evaluation that matches program resources, and keeping it simple. Low recidivism is most important to grantors. Published research on ABC is scarce, but on-site process research generates useful data, and local schools and agencies…

Enjoyment of Euclidean Planar Triangles

ERIC Educational Resources Information Center

Srinivasan, V. K.

2013-01-01

This article adopts the following classification for a Euclidean planar [triangle]ABC, purely based on angles alone. A Euclidean planar triangle is said to be acute angled if all the three angles of the Euclidean planar [triangle]ABC are acute angles. It is said to be right angled at a specific vertex, say B, if the angle ?ABC is a right angle…

Molecular characteristics of Multidrug Resistant Acinetobacter baumannii Isolates from US soldiers from Iraq at the National Naval Medical Center

USDA-ARS?s Scientific Manuscript database

Background: Infections with A. baumannii-calcoaceticus complex (ABC) have complicated the care of combat casualties, and the spread and global dissemination of imipenem resistant (IR) clones of ABC have been reported in recent years. However, the epidemiological features of the IR-ABCs in military t...

On the Certain Topological Indices of Titania Nanotube TiO2[m, n

NASA Astrophysics Data System (ADS)

Javaid, M.; Liu, Jia-Bao; Rehman, M. A.; Wang, Shaohui

2017-07-01

A numeric quantity that characterises the whole structure of a molecular graph is called the topological index that predicts the physical features, chemical reactivities, and boiling activities of the involved chemical compound in the molecular graph. In this article, we give new mathematical expressions for the multiple Zagreb indices, the generalised Zagreb index, the fourth version of atom-bond connectivity (ABC4) index, and the fifth version of geometric-arithmetic (GA5) index of TiO2[m, n]. In addition, we compute the latest developed topological index called by Sanskruti index. At the end, a comparison is also included to estimate the efficiency of the computed indices. Our results extended some known conclusions.

Application of the Activity-Based Costing Method for Unit-Cost Calculation in a Hospital

PubMed Central

Javid, Mahdi; Hadian, Mohammad; Ghaderi, Hossein; Ghaffari, Shahram; Salehi, Masoud

2016-01-01

Background: Choosing an appropriate accounting system for hospital has always been a challenge for hospital managers. Traditional cost system (TCS) causes cost distortions in hospital. Activity-based costing (ABC) method is a new and more effective cost system. Objective: This study aimed to compare ABC with TCS method in calculating the unit cost of medical services and to assess its applicability in Kashani Hospital, Shahrekord City, Iran. Methods: This cross-sectional study was performed on accounting data of Kashani Hospital in 2013. Data on accounting reports of 2012 and other relevant sources at the end of 2012 were included. To apply ABC method, the hospital was divided into several cost centers and five cost categories were defined: wage, equipment, space, material, and overhead costs. Then activity centers were defined. ABC method was performed into two phases. First, the total costs of cost centers were assigned to activities by using related cost factors. Then the costs of activities were divided to cost objects by using cost drivers. After determining the cost of objects, the cost price of medical services was calculated and compared with those obtained from TCS. Results: The Kashani Hospital had 81 physicians, 306 nurses, and 328 beds with the mean occupancy rate of 67.4% during 2012. Unit cost of medical services, cost price of occupancy bed per day, and cost per outpatient service were calculated. The total unit costs by ABC and TCS were respectively 187.95 and 137.70 USD, showing 50.34 USD more unit cost by ABC method. ABC method represented more accurate information on the major cost components. Conclusion: By utilizing ABC, hospital managers have a valuable accounting system that provides a true insight into the organizational costs of their department. PMID:26234974

Massive Transfusion: The Revised Assessment of Bleeding and Transfusion (RABT) Score.

PubMed

Joseph, Bellal; Khan, Muhammad; Truitt, Michael; Jehan, Faisal; Kulvatunyou, Narong; Azim, Asad; Jain, Arpana; Zeeshan, Muhammad; Tang, Andrew; O'Keeffe, Terence

2018-05-21

Massive transfusion (MT) is a lifesaving treatment for trauma patients with hemorrhagic shock, assessed by Assessment of Blood Consumption (ABC) Score based on mechanism of injury, systolic blood pressure (SBP), tachycardia, and FAST exam. The aim of this study was to assess the performance of ABC score by replacing hypotension and tachycardia; with Shock Index (SI) > 1.0 and including pelvic fractures. We performed a 2-year (2014-2015) analysis of all high-level trauma activations and excluded patients dead on arrival. The ABC score was calculated using the 4-point score [blunt (0)/penetrating trauma (1), HR ≥ 120 (1), SBP ≤ 90 mmHg (1), and FAST positive (1)]. The Revised Assessment of Bleeding and Transfusion (RABT) score also included 4 points, calculated by replacing HR and SBP with SI > 1.0 and including pelvic fracture. AUROC compared performances of the two scores. A total of 380 patients were included. The overall MT was 27%. Patients receiving MT had higher median ABC scores [1.1 (0-2) vs. 1 (0-2), p = 0.15] and RABT scores [2 (1-3) vs. 1 (0-2), p < 0.001]. The RABT score had better discriminative power (AUROC = 0.828) compared to ABC score (AUROC = 0.617) for predicting the need for MT. Cutoff of RABT score ≥ 2 had a sensitivity of 84% and specificity of 77% for predicting need for MT compared to ABC score with 39% sensitivity and 72% specificity. Replacement of hypotension and tachycardia with a SI > 1.0 and inclusion of pelvic fracture enhanced discrimination of ABC score for predicting the need for MT. The current ABC score would benefit from revision to more appropriately identify patients requiring MT.

Psychometric properties of the Activities-specific Balance Confidence Scale among individuals with a lower-limb amputation.

PubMed

Miller, William C; Deathe, A Barry; Speechley, Mark

2003-05-01

To evaluate the internal consistency, test-retest reliability, and construct validity of the Activities-specific Balance Confidence (ABC) Scale among people who have a lower-limb amputation. Retest design. A university-affiliated outpatient amputee clinic in Ontario. Two samples of individuals who have unilateral transtibial and transfemoral amputation. Sample 1 (n=54) was a consecutive and sample 2 (n=329) a convenience sample of all members of the clinic population. Not applicable. Repeated application of the ABC Scale, a 16-item questionnaire that assesses confidence in performing various mobility-related tasks. Correlation to test hypothesized relationships between the ABC Scale and the 2-minute walk (2MWT) and the timed up-and-go (TUG) tests; and assessment of the ability of the ABC Scale to discriminate among groups based on amputation cause, amputation level, mobility device use, automatic stepping ability, wearing time, stair climbing ability, and walking distance. Test-retest reliability (intraclass correlation coefficient) of the ABC Scale was .91 (95% confidence interval [CI], .84-.95) with individual item test-retest coefficients ranging from .53 to .87. Internal consistency, measured by Cronbach alpha, was .95. Hypothesized associations with the 2MWT and TUG test were observed with correlations of .72 (95% CI, .56-.84) and -.70 (95% CI, -.82 to -.53), respectively. The ABC Scale discriminated between all groups except those based on amputation level. Balance confidence, as measured by the ABC Scale, is a construct that provides unique information potentially useful to clinicians who provide amputee rehabilitation. The ABC Scale is reliable, with strong support for validity. Study of the scale's responsiveness is recommended.

Balance self-efficacy in older adults following inpatient rehabilitation.

PubMed

Kuys, Suzanne S; Donovan, Jacquelin; Mattin, Sarah; Low Choy, Nancy L

2015-06-01

Older adults discharging from inpatient rehabilitation were investigated to determine change in self-efficacy at 1 month after discharge, the relationship with discharge balance performance and physical function, and the influence of diagnosis. A prospective cohort of 101 adults older than 50 years of age, 43% men, average age 75.84 (SD 9.8) years, were recruited at discharge from inpatient rehabilitation. Balance self-efficacy was assessed using Activities-specific Balance Confidence (ABC) scale at discharge and 1 month following discharge. Balance and physical function were measured at discharge using the Functional Independence Measure, Balance Outcome Measure for Elder Rehabilitation, Modified Elderly Mobility Scale and gait speed. At discharge, balance self-efficacy was moderate (ABC score 62, SD 23) and did not change at follow-up. When grouped by discharge self-efficacy (ABC scores: low<50; moderate 51-80; high>80), significant between-group differences were found for balance (P=0.005) and physical function (P=0.035). At the 1-month follow-up, those with low discharge balance self-efficacy showed improvement (mean-change ABC score 12, 95% confidence interval 2-22) and those with high discharge balance self-efficacy had lower scores (mean-change ABC score 18, 95% confidence interval -8 to -28). Differences in ABC change scores were also found between diagnostic groups (F=3.740, P=0.03), with the orthopaedic group improving (ABC mean change=8) and the general frailty group showing a decrease in confidence (ABC mean change=10). The differences in balance self-efficacy change at 1 month following discharge were related to self-efficacy level at discharge and clinical group requiring rehabilitation. Clinicians need to be aware of these changes as patients are prepared for discharge.

Chemiluminescence Immunoassay for the Detection of Antibodies against the 2C and 3ABC Nonstructural Proteins Induced by Infecting Pigs with Foot-and-Mouth Disease Virus.

PubMed

Liu, Zezhong; Shao, Junjun; Zhao, Furong; Zhou, Guangqing; Gao, Shandian; Liu, Wei; Lv, Jianliang; Li, Xiumei; Li, Yangfan; Chang, Huiyun; Zhang, Yongguang

2017-08-01

The potential diagnostic value of chemiluminescence immunoassays (CLIAs) has been accepted in recent years, although their use for foot-and-mouth disease (FMD) diagnostics has not been reported. Full-length 3ABC and 2C proteins were expressed in bacteria and purified by affinity chromatography to develop a rapid and accurate approach to distinguish pigs infected with foot-and-mouth disease virus (FMDV) from vaccinated pigs. The recombinant proteins were then used as antigens to develop two CLIAs for the detection of antibodies against nonstructural viral proteins. The diagnostic performance of the two assays was compared by analyzing serum from pigs (naive pigs, n = 63; vaccinated, uninfected pigs, n = 532; naive, infected pigs, n = 117) with a known infection status. The 3ABC-2C CLIA had a higher accuracy rate, with a diagnostic sensitivity of 100% and a diagnostic specificity of 96.5%, than the 3ABC CLIA, which had a diagnostic sensitivity of 95.7% and a diagnostic specificity of 96.0%. The results of the 3ABC-2C CLIA also had a high rate of concordance with those of two commercial FMDV enzyme-linked immunosorbent assay (ELISA) kits used to assess serum collected from 962 pigs in the field (96.2% and 97.8%, respectively). The 3ABC-2C CLIA detected infection in serum samples from infected pigs earlier than the commercial ELISA kits. In addition, the 3ABC-2C CLIA produced results within 15 min. On the basis of these findings, the 3ABC-2C CLIA could serve as the foundation for the development of penside FMD diagnostics and offers an alternative method to detect FMDV infections. Copyright © 2017 American Society for Microbiology.

Inactivation and deficiency of core proteins of photosystems I and II caused by genetical phylloquinone and plastoquinone deficiency but retained lamellar structure in a T-DNA mutant of Arabidopsis.

PubMed

Shimada, Hiroshi; Ohno, Ryoichi; Shibata, Masaru; Ikegami, Isamu; Onai, Kiyoshi; Ohto, Masa-aki; Takamiya, Ken-ichiro

2005-02-01

Phylloquinone, a substituted 1,4-naphthoquinone with an 18-carbon-saturated phytyl tail, functions as a bound one-electron carrier cofactor at the A1 site of photosystem I (PSI). A Feldmann tag line mutant, no. 2755 (designated as abc4 hereafter), showed pale-green young leaves and white old leaves. The mutated nuclear gene encoded 1,4-dihydroxy-2-naphtoic acid phytyltransferase, an enzyme of phylloquinone biosynthesis, and high-performance liquid chromatography analysis revealed that the abc4 mutant contained no phylloquinone, and only about 3% plastoquinone. Photooxidation of P700 of PSI in the abc4 mutant was not observed, and reduced-versus-oxidized difference spectroscopy indicated that the abc4 mutant had no P700. The maximum quantum yield of photosystem II (PSII) in the abc4 mutant was much decreased, and the electron transfer from PSII to PSI in the abc4 mutant did not occur. For the pale-green leaves of the abc4 mutant plant, the ultrastructure of the chloroplasts was almost the same as that of the wild-type plant. However, the chloroplasts in the albino leaves of the mutant were smaller and had a lot of grana thylakoids and few stroma thylakoids. The amounts of PSI and PSII core subunits in the abc4 mutant were significantly decreased compared with those in the wild type. These results suggested that a deficiency of phylloquinone in PSI caused the abolishment of PSI and a partial defect of PSII due to a significant decrease of plastoquinone, but did not influence the ultrastructure of the chloroplasts in young leaves.

A cost management model for hospital food and nutrition in a public hospital.

PubMed

Neriz, Liliana; Núñez, Alicia; Ramis, Francisco

2014-11-13

In Chile, the use of costing systems in the public sector is limited. The Ministry of Health requires hospitals to manage themselves with the aim of decentralizing health care services and increasing their quality. However, self-management with a lack of accounting information is almost impossible. On the other hand, nutrition department costs have barely been studied before, and there are no studies specifically for activity based costing (ABC) systems. ABC focuses on the process and traces health care activities to gain a more accurate measurement of the object costs and the financial performance of an organization. This paper uses ABC in a nutrition unit of a public hospital of high complexity to determine costs associated with the different meals for inpatients. The paper also provides an activity based management (ABM) analysis for this unit. The results show positive effects on the reduction of costs for the nutrition department after implementing ABC/ABM. Therefore, there are opportunities to improve the profitability of the area and the results could also be replicated to other areas in the hospital. ABC shed light on the amount of nutritionist time devoted to completing paperwork, and as a result, system changes were introduced to reduce this burden and allow them to focus on more relevant activities. Additional efficiencies were achieved through the elimination of non-value adding activities and automation of reports. ABC reduced the cost of the nutrition department and could produce similar results in other areas of the hospital. This is a practical application of a financial management tool, ABC, which would be useful for hospital managers to reduce costs and improve the management of the unit. This paper takes ABC and examines its use in an area, which has had little exposure to the benefits of this tool.

Application of the Activity-Based Costing Method for Unit-Cost Calculation in a Hospital.

PubMed

Javid, Mahdi; Hadian, Mohammad; Ghaderi, Hossein; Ghaffari, Shahram; Salehi, Masoud

2015-05-17

Choosing an appropriate accounting system for hospital has always been a challenge for hospital managers. Traditional cost system (TCS) causes cost distortions in hospital. Activity-based costing (ABC) method is a new and more effective cost system. This study aimed to compare ABC with TCS method in calculating the unit cost of medical services and to assess its applicability in Kashani Hospital, Shahrekord City, Iran.‎ This cross-sectional study was performed on accounting data of Kashani Hospital in 2013. Data on accounting reports of 2012 and other relevant sources at the end of 2012 were included. To apply ABC method, the hospital was divided into several cost centers and five cost categories were defined: wage, equipment, space, material, and overhead costs. Then activity centers were defined. ABC method was performed into two phases. First, the total costs of cost centers were assigned to activities by using related cost factors. Then the costs of activities were divided to cost objects by using cost drivers. After determining the cost of objects, the cost price of medical services was calculated and compared with those obtained from TCS.‎ The Kashani Hospital had 81 physicians, 306 nurses, and 328 beds with the mean occupancy rate of 67.4% during 2012. Unit cost of medical services, cost price of occupancy bed per day, and cost per outpatient service were calculated. The total unit costs by ABC and TCS were respectively 187.95 and 137.70 USD, showing 50.34 USD more unit cost by ABC method. ABC method represented more accurate information on the major cost components. By utilizing ABC, hospital managers have a valuable accounting system that provides a true insight into the organizational costs of their department.

“ABC”—The Awareness-Body-Chart: A new tool assessing body awareness

PubMed Central

Avian, Alexander; Macheiner, Tanja; Salchinger, Beate; Dalkner, Nina; Fellendorf, Frederike T.; Birner, Armin; Bengesser, Susanne A.; Platzer, Martina; Kapfhammer, Hans-Peter; Probst, Michel; Reininghaus, Eva Z.

2017-01-01

Background Despite the importance of body awareness for health and well-being there is still a lack of valid assessment tools to scan proper body awareness. To respond to the limitations of questionnaires (reading/interpretation problems) the Awareness-Body-Chart (ABC) was designed to assess body awareness by colouring 51 regions according to their awareness. The objective of this study was to investigate the psychometric characteristics of the ABC. Methods In a questionnaire-study, 106 students in Graz (79 females, 27 males, age median 21 (IQR 20–23) years) filled in the ABC, furthermore a German body awareness questionnaire „KEKS”, and the Beck Depression Inventory II. Factor structure, internal consistency, and retest reliability of the ABC were investigated. Correlations of the ABC with the KEKS and the Beck Depression Inventory II and comparisons of subgroups were conducted. Results Through factor analyses, 14 factors with clear assignments to body parts could be categorized: cranium, face, cervical/lumbar region, chest/abdomen, back, shoulder, upper arm, lower arm/elbow, hand, genital area, thigh/hip, knee, lower leg, and foot. The 14 body parts and the total score showed acceptable to high Cronbach’s alphas (α = .64 - .97). The test-retest reliability showed values between ρ = .71 and ρ = .96. The correlation of the ABC and KEKS (r = .66, p < .001) confirmed validity. Further indications of validity could be seen in comparisons of subgroups and in correlations with the Beck Depression Inventory II. Conclusion The ABC proved good psychometric properties with acceptable to high internal consistency, acceptable to high retest reliability and high construct validity. It is an easy-to-use tool for clinical settings and research. The ABC opens new insights into body awareness-patterns of various subgroups. PMID:29036217

New Enhanced Artificial Bee Colony (JA-ABC5) Algorithm with Application for Reactive Power Optimization

PubMed Central

2015-01-01

The standard artificial bee colony (ABC) algorithm involves exploration and exploitation processes which need to be balanced for enhanced performance. This paper proposes a new modified ABC algorithm named JA-ABC5 to enhance convergence speed and improve the ability to reach the global optimum by balancing exploration and exploitation processes. New stages have been proposed at the earlier stages of the algorithm to increase the exploitation process. Besides that, modified mutation equations have also been introduced in the employed and onlooker-bees phases to balance the two processes. The performance of JA-ABC5 has been analyzed on 27 commonly used benchmark functions and tested to optimize the reactive power optimization problem. The performance results have clearly shown that the newly proposed algorithm has outperformed other compared algorithms in terms of convergence speed and global optimum achievement. PMID:25879054

New enhanced artificial bee colony (JA-ABC5) algorithm with application for reactive power optimization.

PubMed

Sulaiman, Noorazliza; Mohamad-Saleh, Junita; Abro, Abdul Ghani

2015-01-01

The standard artificial bee colony (ABC) algorithm involves exploration and exploitation processes which need to be balanced for enhanced performance. This paper proposes a new modified ABC algorithm named JA-ABC5 to enhance convergence speed and improve the ability to reach the global optimum by balancing exploration and exploitation processes. New stages have been proposed at the earlier stages of the algorithm to increase the exploitation process. Besides that, modified mutation equations have also been introduced in the employed and onlooker-bees phases to balance the two processes. The performance of JA-ABC5 has been analyzed on 27 commonly used benchmark functions and tested to optimize the reactive power optimization problem. The performance results have clearly shown that the newly proposed algorithm has outperformed other compared algorithms in terms of convergence speed and global optimum achievement.

Enhancing artificial bee colony algorithm with self-adaptive searching strategy and artificial immune network operators for global optimization.

PubMed

Chen, Tinggui; Xiao, Renbin

2014-01-01

Artificial bee colony (ABC) algorithm, inspired by the intelligent foraging behavior of honey bees, was proposed by Karaboga. It has been shown to be superior to some conventional intelligent algorithms such as genetic algorithm (GA), artificial colony optimization (ACO), and particle swarm optimization (PSO). However, the ABC still has some limitations. For example, ABC can easily get trapped in the local optimum when handing in functions that have a narrow curving valley, a high eccentric ellipse, or complex multimodal functions. As a result, we proposed an enhanced ABC algorithm called EABC by introducing self-adaptive searching strategy and artificial immune network operators to improve the exploitation and exploration. The simulation results tested on a suite of unimodal or multimodal benchmark functions illustrate that the EABC algorithm outperforms ACO, PSO, and the basic ABC in most of the experiments.

Enhancing Artificial Bee Colony Algorithm with Self-Adaptive Searching Strategy and Artificial Immune Network Operators for Global Optimization

PubMed Central

Chen, Tinggui; Xiao, Renbin

2014-01-01

Artificial bee colony (ABC) algorithm, inspired by the intelligent foraging behavior of honey bees, was proposed by Karaboga. It has been shown to be superior to some conventional intelligent algorithms such as genetic algorithm (GA), artificial colony optimization (ACO), and particle swarm optimization (PSO). However, the ABC still has some limitations. For example, ABC can easily get trapped in the local optimum when handing in functions that have a narrow curving valley, a high eccentric ellipse, or complex multimodal functions. As a result, we proposed an enhanced ABC algorithm called EABC by introducing self-adaptive searching strategy and artificial immune network operators to improve the exploitation and exploration. The simulation results tested on a suite of unimodal or multimodal benchmark functions illustrate that the EABC algorithm outperforms ACO, PSO, and the basic ABC in most of the experiments. PMID:24772023

Numerical Modelling of Electromagnetic Wave Propagation and Scattering: High-Order Schemes, Impedance Boundary Conditions and Cole-Cole Dielectrics

DTIC Science & Technology

2004-09-12

Time-Domain Reflectometry (TDR) experiment could serve as a means to determine the most appropriate frequency-domain model for the data at hand. Time...CO. Title: "A review of the perfectly matched layer ABC and some new results." August 2002: NASA Langley Research Center (ICASE), Hampton, VA. Title...ICASE, NASA Langley Research Center, Hamp- ton, VA. July-August 2002. 4. Organized a mini-symposium at the May 2004 Frontiers in Applied and Computational

An Image Processing Approach to Computing Distances Between RNA Secondary Structures Dot Plots (PREPRINT)

DTIC Science & Technology

2007-03-01

the P5abc subdomain of the tetrahymena thermophila ribozyme that was studied by Wu and Tinoco [24]. The results for the second sequence are found in...virus ribozyme that was studied by Lazinski et al. [25], for its regulation of self-cleavage activity. The results for the third sequence are found...mention the existence of eight possible mutations that provide the desired non-linear effect in the ribozyme structure, and this may explain the

A Study of the Communication Capabilities of the OPARS Flight Planning System for Various Levels of Demand.

DTIC Science & Technology

1980-03-01

Oceanography Center (FNOC) is currently testing and evaluating a computerized flight plan system, referred to, for short, as OPARS. This sytem , developed to...replace the Lockheed Jetplan flight plan sytem , provides users at remote sites with direct access to the FNOC computer via 11 telephone lines. The...validity, but only for format. For example, an entry of ABCE , as the four- letter identification code for the destination airfield, would be accepted

Starting with ABC and Finishing with XYZ: What Financial Reporting Model Best Fits a Faculty and Why?

ERIC Educational Resources Information Center

Berry, Prudence Jane

2014-01-01

This article looks at the range of financial reporting models available for use in the Australian higher education sector, the possible application of activity-based costing (ABC) in faculties and the eventual rejection of ABC in favour of a more qualitative model designed specifically for use in one institution, in a particular Faculty. The…

Use of the K-ABC with Children in Zaire, Africa: An Evaluation of the Sequential-Simultaneous Processing Distinction within an Intercultural Context.

ERIC Educational Resources Information Center

Giordani, Bruno; And Others

1996-01-01

Evaluation of the Kaufman Assessment Battery for Children (K-ABC) with 130 primary school children in Zaire revealed three findings: (1) the distinction between sequential processing and simultaneous processing was valid; (2) the K-ABC discriminated effectively among grade levels, health and family environment variables, and tribal membership; and…

The ABCs of School Choice: The Comprehensive Guide to Every Private School Choice Program in America. 2013 Edition

ERIC Educational Resources Information Center

Friedman Foundation for Educational Choice, 2013

2013-01-01

"The ABCs of School Choice" is the most comprehensive guide to every private school choice program in America, showcasing the voucher, tax-credit scholarship, education savings accounts, and individual tax credit/deduction programs currently operating in 21 states and Washington, D.C. "The ABCs of School Choice" provides policymakers, advocates,…

A rotor technology assessment of the advancing blade concept

NASA Technical Reports Server (NTRS)

Pleasants, W. A.

1983-01-01

A rotor technology assessment of the Advancing Blade Concept (ABC) was conducted in support of a preliminary design study. The analytical methodology modifications and inputs, the correlation, and the results of the assessment are documented. The primary emphasis was on the high-speed forward flight performance of the rotor. The correlation data base included both the wind tunnel and the flight test results. An advanced ABC rotor design was examined; the suitability of the ABC for a particular mission was not considered. The objective of this technology assessment was to provide estimates of the performance potential of an advanced ABC rotor designed for high speed forward flight.

A tutorial on activity-based costing of electronic health records.

PubMed

Federowicz, Marie H; Grossman, Mila N; Hayes, Bryant J; Riggs, Joseph

2010-01-01

As the American Recovery and Restoration Act of 2009 allocates $19 billion to health information technology, it will be useful for health care managers to project the true cost of implementing an electronic health record (EHR). This study presents a step-by-step guide for using activity-based costing (ABC) to estimate the cost of an EHR. ABC is a cost accounting method with a "top-down" approach for estimating the cost of a project or service within an organization. The total cost to implement an EHR includes obvious costs, such as licensing fees, and hidden costs, such as impact on productivity. Unlike other methods, ABC includes all of the organization's expenditures and is less likely to miss hidden costs. Although ABC is used considerably in manufacturing and other industries, it is a relatively new phenomenon in health care. ABC is a comprehensive approach that the health care field can use to analyze the cost-effectiveness of implementing EHRs. In this article, ABC is applied to a health clinic that recently implemented an EHR, and the clinic is found to be more productive after EHR implementation. This methodology can help health care administrators assess the impact of a stimulus investment on organizational performance.

Accelerator-based conversion (ABC) of weapons plutonium: Plant layout study and related design issues

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

Cowell, B.S.; Fontana, M.H.; Krakowski, R.A.

1995-04-01

In preparation for and in support of a detailed R and D Plan for the Accelerator-Based Conversion (ABC) of weapons plutonium, an ABC Plant Layout Study was conducted at the level of a pre-conceptual engineering design. The plant layout is based on an adaptation of the Molten-Salt Breeder Reactor (MSBR) detailed conceptual design that was completed in the early 1070s. Although the ABC Plant Layout Study included the Accelerator Equipment as an essential element, the engineering assessment focused primarily on the Target; Primary System (blanket and all systems containing plutonium-bearing fuel salt); the Heat-Removal System (secondary-coolant-salt and supercritical-steam systems); Chemicalmore » Processing; Operation and Maintenance; Containment and Safety; and Instrumentation and Control systems. Although constrained primarily to a reflection of an accelerator-driven (subcritical) variant of MSBR system, unique features and added flexibilities of the ABC suggest improved or alternative approaches to each of the above-listed subsystems; these, along with the key technical issues in need of resolution through a detailed R&D plan for ABC are described on the bases of the ``strawman`` or ``point-of-departure`` plant layout that resulted from this study.« less

Harnessing Drug Resistance: Using ABC Transporter Proteins To Target Cancer Cells

PubMed Central

Leitner, Heather M.; Kachadourian, Remy; Day, Brian J.

2007-01-01

The ATP-binding cassette (ABC) class of proteins is one of the most functionally diverse transporter families found in biological systems. Although the abundance of ABC proteins varies between species, they are highly conserved in sequence and often demonstrate similar functions across prokaryotic and eukaryotic organisms. Beginning with a brief summary of the events leading to our present day knowledge of ABC transporters, the purpose of this review is to discuss the potential for utilizing ABC transporters as a means for cellular glutathione (GSH) modulation. GSH is one of the most abundant thiol antioxidants in cells. It is involved in cellular division, protein and DNA synthesis, maintenance of cellular redox status and xenobiotic metabolism. Cellular GSH levels are often altered in many disease states including cancer. Over the past two decades there has been considerable emphasis on methods to sensitize cancer cells to chemotherapeutics and ionization radiation therapy by GSH depletion. We contend that ABC transporters, particularly multi-drug resistant proteins (MRPs), may be used as therapeutic targets for applications aimed at modulation of GSH levels. This review will emphasize MRP-mediated modulation of intracellular GSH levels as a potential alternative and adjunctive approach for cancer therapy. PMID:17585883

Characterization and regulation of the resistance-nodulation-cell division-type multidrug efflux pumps MdtABC and MdtUVW from the fire blight pathogen Erwinia amylovora.

PubMed

Pletzer, Daniel; Weingart, Helge

2014-07-11

The Gram-negative bacterium Erwinia amylovora is the causal agent of the devastating disease fire blight in rosaceous plants such as apple, pear, quince, raspberry, and cotoneaster. In order to survive and multiply in a host, microbes must be able to circumvent the toxic effects of antimicrobial plant compounds, such as flavonoids and tannins. E. amylovora uses multidrug efflux transporters that recognize and actively export toxic compounds out of the cells. Here, two heterotrimeric resistance-nodulation-cell division (RND)-type multidrug efflux pumps, MdtABC and MdtUVW, from E. amylovora were identified. These RND systems are unusual in that they contain two different RND proteins forming a functional pump. To find the substrate specificities of the two efflux systems, we overexpressed the transporters in a hypersensitive mutant lacking the major RND pump AcrB. Both transporters mediated resistance to several flavonoids, fusidic acid and novobiocin. Additionally, MdtABC mediated resistance towards josamycin, bile salts and silver nitrate, and MdtUVW towards clotrimazole. The ability of the mdtABC- and mdtUVW-deficient mutants to multiply in apple rootstock was reduced. Quantitative RT-PCR analyses revealed that the expression of the transporter genes was induced during infection of apple rootstock. The polyphenolic plant compound tannin, as well as the heavy metal salt tungstate was found to induce the expression of mdtABC. Finally, the expression of the mdtABC genes was shown to be regulated by BaeR, the response regulator of the two-component system BaeSR, a cell envelope stress response system that controls the adaptive responses to changes in the environment. The expression of MdtABC and MdtUVW is induced during growth of E. amylovora in planta. We identified the plant polyphenol tannin as inducer of mdtABC expression. The reduced ability of the mdtABC- and mdtUVW-deficient mutants to multiply in apple rootstock suggests that the efflux pumps are involved in resistance to plant antimicrobials, maybe including flavonoids, which were identified as substrates of both pumps. Furthermore, we found that the mdtABC operon belongs to the regulon of the two-component regulator BaeR suggesting a role of this RND transporter in the cell envelope stress response of E. amylovora.

Characterization and regulation of the Resistance-Nodulation-Cell Division-type multidrug efflux pumps MdtABC and MdtUVW from the fire blight pathogen Erwinia amylovora

PubMed Central

2014-01-01

Background The Gram-negative bacterium Erwinia amylovora is the causal agent of the devastating disease fire blight in rosaceous plants such as apple, pear, quince, raspberry, and cotoneaster. In order to survive and multiply in a host, microbes must be able to circumvent the toxic effects of antimicrobial plant compounds, such as flavonoids and tannins. E. amylovora uses multidrug efflux transporters that recognize and actively export toxic compounds out of the cells. Here, two heterotrimeric resistance-nodulation-cell division (RND)-type multidrug efflux pumps, MdtABC and MdtUVW, from E. amylovora were identified. These RND systems are unusual in that they contain two different RND proteins forming a functional pump. Results To find the substrate specificities of the two efflux systems, we overexpressed the transporters in a hypersensitive mutant lacking the major RND pump AcrB. Both transporters mediated resistance to several flavonoids, fusidic acid and novobiocin. Additionally, MdtABC mediated resistance towards josamycin, bile salts and silver nitrate, and MdtUVW towards clotrimazole. The ability of the mdtABC- and mdtUVW-deficient mutants to multiply in apple rootstock was reduced. Quantitative RT-PCR analyses revealed that the expression of the transporter genes was induced during infection of apple rootstock. The polyphenolic plant compound tannin, as well as the heavy metal salt tungstate was found to induce the expression of mdtABC. Finally, the expression of the mdtABC genes was shown to be regulated by BaeR, the response regulator of the two-component system BaeSR, a cell envelope stress response system that controls the adaptive responses to changes in the environment. Conclusions The expression of MdtABC and MdtUVW is induced during growth of E. amylovora in planta. We identified the plant polyphenol tannin as inducer of mdtABC expression. The reduced ability of the mdtABC- and mdtUVW-deficient mutants to multiply in apple rootstock suggests that the efflux pumps are involved in resistance to plant antimicrobials, maybe including flavonoids, which were identified as substrates of both pumps. Furthermore, we found that the mdtABC operon belongs to the regulon of the two-component regulator BaeR suggesting a role of this RND transporter in the cell envelope stress response of E. amylovora. PMID:25012600

Searching for the fastest dynamo: laminar ABC flows.

PubMed

Alexakis, Alexandros

2011-08-01

The growth rate of the dynamo instability as a function of the magnetic Reynolds number R(M) is investigated by means of numerical simulations for the family of the Arnold-Beltrami-Childress (ABC) flows and for two different forcing scales. For the ABC flows that are driven at the largest available length scale, it is found that, as the magnetic Reynolds number is increased: (a) The flow that results first in a dynamo is the 2 1/2-dimensional flow for which A=B and C=0 (and all permutations). (b) The second type of flow that results in a dynamo is the one for which A=B≃2C/5 (and permutations). (c) The most symmetric flow, A=B=C, is the third type of flow that results in a dynamo. (d) As R(M) is increased, the A=B=C flow stops being a dynamo and transitions from a local maximum to a third-order saddle point. (e) At larger R(M), the A=B=C flow reestablishes itself as a dynamo but remains a saddle point. (f) At the largest examined R(M), the growth rate of the 2 1/2-dimensional flows starts to decay, the A=B=C flow comes close to a local maximum again, and the flow A=B≃2C/5 (and permutations) results in the fastest dynamo with growth rate γ≃0.12 at the largest examined R(M). For the ABC flows that are driven at the second largest available length scale, it is found that (a) the 2 1/2-dimensional flows A=B,C=0 (and permutations) are again the first flows that result in a dynamo with a decreased onset. (b) The most symmetric flow, A=B=C, is the second type of flow that results in a dynamo. It is, and it remains, a local maximum. (c) At larger R(M), the flow A=B≃2C/5 (and permutations) appears as the third type of flow that results in a dynamo. As R(M) is increased, it becomes the flow with the largest growth rate. The growth rates appear to have some correlation with the Lyapunov exponents, but constructive refolding of the field lines appears equally important in determining the fastest dynamo flow.

Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation.

PubMed

Technow, Frank; Messina, Carlos D; Totir, L Radu; Cooper, Mark

2015-01-01

Genomic selection, enabled by whole genome prediction (WGP) methods, is revolutionizing plant breeding. Existing WGP methods have been shown to deliver accurate predictions in the most common settings, such as prediction of across environment performance for traits with additive gene effects. However, prediction of traits with non-additive gene effects and prediction of genotype by environment interaction (G×E), continues to be challenging. Previous attempts to increase prediction accuracy for these particularly difficult tasks employed prediction methods that are purely statistical in nature. Augmenting the statistical methods with biological knowledge has been largely overlooked thus far. Crop growth models (CGMs) attempt to represent the impact of functional relationships between plant physiology and the environment in the formation of yield and similar output traits of interest. Thus, they can explain the impact of G×E and certain types of non-additive gene effects on the expressed phenotype. Approximate Bayesian computation (ABC), a novel and powerful computational procedure, allows the incorporation of CGMs directly into the estimation of whole genome marker effects in WGP. Here we provide a proof of concept study for this novel approach and demonstrate its use with synthetic data sets. We show that this novel approach can be considerably more accurate than the benchmark WGP method GBLUP in predicting performance in environments represented in the estimation set as well as in previously unobserved environments for traits determined by non-additive gene effects. We conclude that this proof of concept demonstrates that using ABC for incorporating biological knowledge in the form of CGMs into WGP is a very promising and novel approach to improving prediction accuracy for some of the most challenging scenarios in plant breeding and applied genetics.

Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

PubMed Central

Technow, Frank; Messina, Carlos D.; Totir, L. Radu; Cooper, Mark

2015-01-01

Genomic selection, enabled by whole genome prediction (WGP) methods, is revolutionizing plant breeding. Existing WGP methods have been shown to deliver accurate predictions in the most common settings, such as prediction of across environment performance for traits with additive gene effects. However, prediction of traits with non-additive gene effects and prediction of genotype by environment interaction (G×E), continues to be challenging. Previous attempts to increase prediction accuracy for these particularly difficult tasks employed prediction methods that are purely statistical in nature. Augmenting the statistical methods with biological knowledge has been largely overlooked thus far. Crop growth models (CGMs) attempt to represent the impact of functional relationships between plant physiology and the environment in the formation of yield and similar output traits of interest. Thus, they can explain the impact of G×E and certain types of non-additive gene effects on the expressed phenotype. Approximate Bayesian computation (ABC), a novel and powerful computational procedure, allows the incorporation of CGMs directly into the estimation of whole genome marker effects in WGP. Here we provide a proof of concept study for this novel approach and demonstrate its use with synthetic data sets. We show that this novel approach can be considerably more accurate than the benchmark WGP method GBLUP in predicting performance in environments represented in the estimation set as well as in previously unobserved environments for traits determined by non-additive gene effects. We conclude that this proof of concept demonstrates that using ABC for incorporating biological knowledge in the form of CGMs into WGP is a very promising and novel approach to improving prediction accuracy for some of the most challenging scenarios in plant breeding and applied genetics. PMID:26121133

Rice Ferredoxin-Dependent Glutamate Synthase Regulates Nitrogen-Carbon Metabolomes and Is Genetically Differentiated between japonica and indica Subspecies.

PubMed

Yang, Xiaolu; Nian, Jinqiang; Xie, Qingjun; Feng, Jian; Zhang, Fengxia; Jing, Hongwei; Zhang, Jian; Dong, Guojun; Liang, Yan; Peng, Juli; Wang, Guodong; Qian, Qian; Zuo, Jianru

2016-11-07

Plants assimilate inorganic nitrogen absorbed from soil into organic forms as Gln and Glu through the glutamine synthetase/glutamine:2-oxoglutarate amidotransferase (GS/GOGAT) cycle. Whereas GS catalyzes the formation of Gln from Glu and ammonia, GOGAT catalyzes the transfer of an amide group from Gln to 2-oxoglutarate to produce two molecules of Glu. However, the regulatory role of the GS/GOGAT cycle in the carbon-nitrogen balance is not well understood. Here, we report the functional characterization of rice ABNORMAL CYTOKININ RESPONSE 1 (ABC1) gene that encodes a ferredoxin-dependent (Fd)-GOGAT. The weak mutant allele abc1-1 mutant shows a typical nitrogen-deficient syndrome, whereas the T-DNA insertional mutant abc1-2 is seedling lethal. Metabolomics analysis revealed the accumulation of an excessive amount of amino acids with high N/C ratio (Gln and Asn) and several intermediates in the tricarboxylic acid cycle in abc1-1, suggesting that ABC1 plays a critical role in nitrogen assimilation and carbon-nitrogen balance. Five non-synonymous single-nucleotide polymorphisms were identified in the ABC1 coding region and characterized as three distinct haplotypes, which have been highly and specifically differentiated between japonica and indica subspecies. Collectively, these results suggest that ABC1/OsFd-GOGAT is essential for plant growth and development by modulating nitrogen assimilation and the carbon-nitrogen balance. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

Transcriptomic insights on the ABC transporter gene family in the salmon louse Caligus rogercresseyi.

PubMed

Valenzuela-Muñoz, Valentina; Sturm, Armin; Gallardo-Escárate, Cristian

2015-04-09

ATP-binding cassette (ABC) protein family encode for membrane proteins involved in the transport of various biomolecules through the cellular membrane. These proteins have been identified in all taxa and present important physiological functions, including the process of insecticide detoxification in arthropods. For that reason the ectoparasite Caligus rogercresseyi represents a model species for understanding the molecular underpinnings involved in insecticide drug resistance. llumina sequencing was performed using sea lice exposed to 2 and 3 ppb of deltamethrin and azamethiphos. Contigs obtained from de novo assembly were annotated by Blastx. RNA-Seq analysis was performed and validated by qPCR analysis. From the transcriptome database of C. rogercresseyi, 57 putative members of ABC protein sequences were identified and phylogenetically classified into the eight subfamilies described for ABC transporters in arthropods. Transcriptomic profiles for ABC proteins subfamilies were evaluated throughout C. rogercresseyi development. Moreover, RNA-Seq analysis was performed for adult male and female salmon lice exposed to the delousing drugs azamethiphos and deltamethrin. High transcript levels of the ABCB and ABCC subfamilies were evidenced. Furthermore, SNPs mining was carried out for the ABC proteins sequences, revealing pivotal genomic information. The present study gives a comprehensive transcriptome analysis of ABC proteins from C. rogercresseyi, providing relevant information about transporter roles during ontogeny and in relation to delousing drug responses in salmon lice. This genomic information represents a valuable tool for pest management in the Chilean salmon aquaculture industry.

Computation of load performance and other parameters of extra high speed modified Lundell alternators from 3D-FE magnetic field solutions

NASA Technical Reports Server (NTRS)

Wang, R.; Demerdash, N. A.

1992-01-01

The combined magnetic vector potential - magnetic scalar potential method of computation of 3D magnetic fields by finite elements, introduced in a companion paper, in combination with state modeling in the abc-frame of reference, are used for global 3D magnetic field analysis and machine performance computation under rated load and overload condition in an example 14.3 kVA modified Lundell alternator. The results vividly demonstrate the 3D nature of the magnetic field in such machines, and show how this model can be used as an excellent tool for computation of flux density distributions, armature current and voltage waveform profiles and harmonic contents, as well as computation of torque profiles and ripples. Use of the model in gaining insight into locations of regions in the magnetic circuit with heavy degrees of saturation is demonstrated. Experimental results which correlate well with the simulations of the load case are given.

Ecological approach to resource survey and planning for environmentally significant Areas: The ABC method

NASA Astrophysics Data System (ADS)

Bastedo, Jamie D.; Nelson, J. Gordon; Theberge, John B.

1984-03-01

A resource survey and planning method for parks, reserves, and other environmentally significant areas (ESAs) is presented in the context of a holistic balanced approach to land use and environmental management. This method provides a framework for the acquisition, analysis, presentation, and application of diverse ecological data pertinent to land use planning and resource management within ESAs. Through the independent analysis and subsequent integration of abiotic, biotic, and cultural or ABC information, land areas within an ESA are identified in terms of their relative environmental significance and environmental constraints. The former term encompasses wildlife, historic, and other resource values, while the latter term reflects biophysical hazards and sensitivities, and land use conflicts. The method thus calls for a matching of an ESA's distinctive attributes with appropriate land use and institutional arrancements through an analysis of available acts, regulations, agencies, and other conservation and land use management mechanisms. The method culminates with a management proposal showing proposed park or reserve allocations, buffer areas, or other land use controls aimed at preserving an ESA's special ecological qualities, while providing for resource development. The authors suggest that all resource management decisions affecting ESA's should be governed by a philosophical stance that recognizes a spectrum of broad land use types, ranging from preservation to extractive use and rehabilitation.

Approximate Bayesian Computation Using Markov Chain Monte Carlo Simulation: Theory, Concepts, and Applications

NASA Astrophysics Data System (ADS)

Sadegh, M.; Vrugt, J. A.

2013-12-01

The ever increasing pace of computational power, along with continued advances in measurement technologies and improvements in process understanding has stimulated the development of increasingly complex hydrologic models that simulate soil moisture flow, groundwater recharge, surface runoff, root water uptake, and river discharge at increasingly finer spatial and temporal scales. Reconciling these system models with field and remote sensing data is a difficult task, particularly because average measures of model/data similarity inherently lack the power to provide a meaningful comparative evaluation of the consistency in model form and function. The very construction of the likelihood function - as a summary variable of the (usually averaged) properties of the error residuals - dilutes and mixes the available information into an index having little remaining correspondence to specific behaviors of the system (Gupta et al., 2008). The quest for a more powerful method for model evaluation has inspired Vrugt and Sadegh [2013] to introduce "likelihood-free" inference as vehicle for diagnostic model evaluation. This class of methods is also referred to as Approximate Bayesian Computation (ABC) and relaxes the need for an explicit likelihood function in favor of one or multiple different summary statistics rooted in hydrologic theory that together have a much stronger and compelling diagnostic power than some aggregated measure of the size of the error residuals. Here, we will introduce an efficient ABC sampling method that is orders of magnitude faster in exploring the posterior parameter distribution than commonly used rejection and Population Monte Carlo (PMC) samplers. Our methodology uses Markov Chain Monte Carlo simulation with DREAM, and takes advantage of a simple computational trick to resolve discontinuity problems with the application of set-theoretic summary statistics. We will also demonstrate a set of summary statistics that are rather insensitive to errors in the forcing data. This enhances prospects of detecting model structural deficiencies.

Applying activity-based costing to healthcare settings.

PubMed

Canby, J B

1995-02-01

Activity-based costing (ABC) focuses on processes that drive cost. By tracing healthcare activities back to events that generate cost, a more accurate measurement of financial performance is possible. This article uses ABC principles and techniques to determine costs associated with the x-ray process in a midsized outpatient clinic. The article also provides several tips for initiating an ABC cost system for an entire healthcare organization.

A MULTIPLE TESTING OF THE ABC METHOD AND THE DEVELOPMENT OF A SECOND-GENERATION MODEL. PART II, TEST RESULTS AND AN ANALYSIS OF RECALL RATIO.

ERIC Educational Resources Information Center

ALTMANN, BERTHOLD

AFTER A BRIEF SUMMARY OF THE TEST PROGRAM (DESCRIBED MORE FULLY IN LI 000 318), THE STATISTICAL RESULTS TABULATED AS OVERALL "ABC (APPROACH BY CONCEPT)-RELEVANCE RATIOS" AND "ABC-RECALL FIGURES" ARE PRESENTED AND REVIEWED. AN ABSTRACT MODEL DEVELOPED IN ACCORDANCE WITH MAX WEBER'S "IDEALTYPUS" ("DIE OBJEKTIVITAET…

75 FR 11749 - Fisheries of the Exclusive Economic Zone Off Alaska; Gulf of Alaska; Final 2010 and 2011 Harvest...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... TACs for 2010 and 2011 that are equal to ABCs for pollock, deep-water flatfish, rex sole, sablefish... recommended TACs for 2010 and 2011 that are less than the ABCs for Pacific cod, flathead sole, shallow-water... that the sum of all State and Federal water Pacific cod removals from the GOA not exceed ABC...

Alternative Basic Comprehensive Program (Project A.B.C.) Special Alternative Instructional Program. Final Evaluation Report 1992-93. OREA Report.

ERIC Educational Resources Information Center

Augustin, Marc A.

The Alternative Basic Comprehension Program (Project A.B.C.) for bilingual high school students was a special alternative instructional program funded by Title VII for the third year at two high schools in the Bronx. In the year under review, Project A.B.C. served 260 students of limited English proficiency (LEP). Participating students received…

Oncogenically active MYD88 mutations in human lymphoma.

PubMed

Ngo, Vu N; Young, Ryan M; Schmitz, Roland; Jhavar, Sameer; Xiao, Wenming; Lim, Kian-Huat; Kohlhammer, Holger; Xu, Weihong; Yang, Yandan; Zhao, Hong; Shaffer, Arthur L; Romesser, Paul; Wright, George; Powell, John; Rosenwald, Andreas; Muller-Hermelink, Hans Konrad; Ott, German; Gascoyne, Randy D; Connors, Joseph M; Rimsza, Lisa M; Campo, Elias; Jaffe, Elaine S; Delabie, Jan; Smeland, Erlend B; Fisher, Richard I; Braziel, Rita M; Tubbs, Raymond R; Cook, J R; Weisenburger, Denny D; Chan, Wing C; Staudt, Louis M

2011-02-03

The activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) remains the least curable form of this malignancy despite recent advances in therapy. Constitutive nuclear factor (NF)-κB and JAK kinase signalling promotes malignant cell survival in these lymphomas, but the genetic basis for this signalling is incompletely understood. Here we describe the dependence of ABC DLBCLs on MYD88, an adaptor protein that mediates toll and interleukin (IL)-1 receptor signalling, and the discovery of highly recurrent oncogenic mutations affecting MYD88 in ABC DLBCL tumours. RNA interference screening revealed that MYD88 and the associated kinases IRAK1 and IRAK4 are essential for ABC DLBCL survival. High-throughput RNA resequencing uncovered MYD88 mutations in ABC DLBCL lines. Notably, 29% of ABC DLBCL tumours harboured the same amino acid substitution, L265P, in the MYD88 Toll/IL-1 receptor (TIR) domain at an evolutionarily invariant residue in its hydrophobic core. This mutation was rare or absent in other DLBCL subtypes and Burkitt's lymphoma, but was observed in 9% of mucosa-associated lymphoid tissue lymphomas. At a lower frequency, additional mutations were observed in the MYD88 TIR domain, occurring in both the ABC and germinal centre B-cell-like (GCB) DLBCL subtypes. Survival of ABC DLBCL cells bearing the L265P mutation was sustained by the mutant but not the wild-type MYD88 isoform, demonstrating that L265P is a gain-of-function driver mutation. The L265P mutant promoted cell survival by spontaneously assembling a protein complex containing IRAK1 and IRAK4, leading to IRAK4 kinase activity, IRAK1 phosphorylation, NF-κB signalling, JAK kinase activation of STAT3, and secretion of IL-6, IL-10 and interferon-β. Hence, the MYD88 signalling pathway is integral to the pathogenesis of ABC DLBCL, supporting the development of inhibitors of IRAK4 kinase and other components of this pathway for the treatment of tumours bearing oncogenic MYD88 mutations.

ABC transporter activity linked to radiation resistance and molecular subtype in pediatric medulloblastoma

PubMed Central

2013-01-01

Background Resistance to radiation treatment remains a major clinical problem for patients with brain cancer. Medulloblastoma is the most common malignant brain tumor of childhood, and occurs in the cerebellum. Though radiation treatment has been critical in increasing survival rates in recent decades, the presence of resistant cells in a substantial number of medulloblastoma patients leads to relapse and death. Methods Using the established medulloblastoma cell lines UW228 and Daoy, we developed a novel model system to enrich for and study radiation tolerant cells early after radiation exposure. Using fluorescence-activated cell sorting, dead cells and cells that had initiated apoptosis were removed, allowing surviving cells to be investigated before extensive proliferation took place. Results Isolated surviving cells were tumorigenic in vivo and displayed elevated levels of ABCG2, an ABC transporter linked to stem cell behavior and drug resistance. Further investigation showed another family member, ABCA1, was also elevated in surviving cells in these lines, as well as in early passage cultures from pediatric medulloblastoma patients. We discovered that the multi-ABC transporter inhibitors verapamil and reserpine sensitized cells from particular patients to radiation, suggesting that ABC transporters have a functional role in cellular radiation protection. Additionally, verapamil had an intrinsic anti-proliferative effect, with transient exposure in vitro slowing subsequent in vivo tumor formation. When expression of key ABC transporter genes was assessed in medulloblastoma tissue from 34 patients, levels were frequently elevated compared with normal cerebellum. Analysis of microarray data from independent cohorts (n = 428 patients) showed expression of a number of ABC transporters to be strongly correlated with certain medulloblastoma subtypes, which in turn are associated with clinical outcome. Conclusions ABC transporter inhibitors are already being trialed clinically, with the aim of decreasing chemotherapy resistance. Our findings suggest that the inhibition of ABC transporters could also increase the efficacy of radiation treatment for medulloblastoma patients. Additionally, the finding that certain family members are associated with particular molecular subtypes (most notably high ABCA8 and ABCB4 expression in Sonic Hedgehog pathway driven tumors), along with cell membrane location, suggests ABC transporters are worthy of consideration for the diagnostic classification of medulloblastoma. PMID:24219920

The Asfora Bullet Cage System Shows Comparable Fusion Rate Success Versus Control Cage in Posterior Lumbar Interbody Fusion in a Randomized Clinical Trial.

PubMed

Morgan, Jeremy P; Miller, Ashley L; Thompson, Paul A; Asfora, Wilson T

2016-04-01

Low back pain and degeneration of the intervertebral disc are an integrated malady that affects millions of Americans. Cage devices used in association with posterior lumbar interbody fusion (PLIF) have been shown to be an effective approach in the treatment of a number of lower spine disorders attributed to degenerative disc disease (DDD). This study was undertaken as part of a U.S. Food and Drug Administration (FDA) Investigational Device Exemption (IDE) study and compares the effectiveness of the Asfora Bullet Cage System (ABCS) to successfully fuse vertebra at one or two levels between L2 and S1 in patients with DDD to an FDA approved comparison device, the Medtronic-Sofamor Danek Inter Fix Threaded Fusion Device (MSDIFD). A total of 257 randomized participants were implanted with either the ABCS device (n = 132) or the MSDIFD device (n = 125) through an open posterior approach using autogenous local bone graft without the use of pedicle screws. Patients were evaluated prior to surgery and at the 24 month (24-M) visit for fusion status, deep tendon reflex status, sensory function, motor function, straight leg raise status, pain, disability, and device safety. Radiological evaluation and statistical analysis were performed by independent professionals. Evaluation of device success was performed at 24-M visit. From the original group of 257 patients, 59 were lost to follow-up. Primary measures of success at the 24-M visit involved pain and function, fusion, neurological status, and device-related adverse events measures. Pain and function improved in both (MSDIFD: 75.7 percent; ABCS: 82.6 percent). Fusion success with all radiographic points at 24-M visits was 79.4 percent MSDIFD and 88.2 percent ABCS. Neurological improvement was seen in both (MSDIFD: 77.0 percent; ABCS: 87.8 percent). One device-related grade 1 adverse event was reported in the MSDIFD group. Disc height preservation was equivalent for single level fusions (MSDIFD: 16.1 percent; ABCS: 20.0 percent) and second level fusions (MSDIFD: 10.7 percent; ABCS: 14.3 percent). General health and well-being improvement was the same (MSDIFD: 37.0 percent; ABCS: 40.0 percent). Subsequent fusion, up to 10 years, was equivalent (MSDIFD: 83.8 percent; ABCS: 91.2). Results for both devices were considered to be satisfactory, with a slight non-significant superiority for the ABCS. From the ABCS device FDA IDE sanctioned study and the review of the literature, we concluded that the Asfora Bullet Cage System is safe, effective and comparable to other interbody fusion devices which are used stand-alone or in conjunction with pedicle screws, rhBMP-2, or autogenous bone harvested from the iliac crest inserted through anterior, lateral or posterior approaches.

Bfr1p is responsible for tributyltin resistance in Schizosaccharomyces pombe.

PubMed

Akiyama, Koichi; Iwaki, Tomoko; Sugimoto, Naoko; Chardwiriyapreecha, Soracom; Kawano, Miyuki; Nishimoto, Sogo; Sugahara, Takuya; Sekito, Takayuki; Kakinuma, Yoshimi

2011-01-01

ATP-binding cassette (ABC) transporter plays an important role for resistance against xenobiotics. There are eleven ABC transporter genes in the genome of fission yeast Schizosaccharomyces pombe. We examined the role of ABC transporter against the toxicity of tributyltin chloride (TBT), a widespread environmental pollutant, in cell growth. Among individual ABC transporter mutants, the growth of a mutant deficient in Bfr1p, a plasma membrane-embedded transporter, was extremely sensitive to TBT. The lethal TBT concentration inducing 50% of cell death (LC(50)) was 25 µM for the parent strain and 10.2 µM for the bfr1∆ mutant. Thus, Bfr1p was responsible for TBT resistance in S. pombe.

Diversity in ABC transporters: Type I, II and III importers

PubMed Central

Rice, Austin J.; Park, Aekyung

2014-01-01

ATP-binding cassette transporters are multi-subunit membrane pumps that transport substrates across membranes. While significant in the transport process, transporter architecture exhibits a range of diversity that we are only beginning to recognize. This divergence may provide insight into the mechanisms of substrate transport and homeostasis. Until recently, ABC importers have been classified into two types, but with the emergence of energy-coupling factor (ECF) transporters there are potentially three types of ABC importers. In this review, we summarize an expansive body of research on the three types of importers with an emphasis on the basics that underlie ABC importers, such as structure, subunit composition and mechanism. PMID:25155087

Anger and the ABC model underlying Rational-Emotive Behavior Therapy.

PubMed

Ziegler, Daniel J; Smith, Phillip N

2004-06-01

The ABC model underlying Ellis's Rational-Emotive Behavior Therapy predicts that people who think more irrationally should display greater trait anger than do people who think less irrationally. This study tested this prediction regarding the ABC model. 186 college students were administered the Survey of Personal Beliefs and the State-Trait Anger Expression Inventory-Second Edition to measure irrational thinking and trait anger, respectively. Students who scored higher on Overall Irrational Thinking and Low Frustration Tolerance scored significantly higher on Trait Anger than did those who scored lower on Overall Irrational Thinking and Low Frustration Tolerance. This indicates support for the ABC model, especially Ellis's construct of irrational beliefs which is central to the model.

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data.

PubMed

Palero, Ferran; Lopes, Joao; Abelló, Pere; Macpherson, Enrique; Pascual, Marta; Beaumont, Mark A

2009-11-09

Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Protein complexes formed during the incision reaction catalyzed by the Escherichia coli UvrABC endonuclease.

PubMed Central

Yeung, A T; Mattes, W B; Grossman, L

1986-01-01

An examination has been made into the nature of the nucleoprotein complexes formed during the incision reaction catalyzed by the Escherichia coli UvrABC endonuclease when acting on a pyrimidine dimer-containing fd RF-I DNA species. The complexes of proteins and DNA form in unique stages. The first stage of binding involves an ATP-stimulated interaction of the UvrA protein with duplex DNA containing pyrimidine dimer sites. The UvrB protein significantly stabilizes the UvrA-pyrimidine dimer containing DNA complex which, in turn, provides a foundation for the binding of UvrC to activate the UvrABC endonuclease. The binding of one molecule of UvrC to each UvrAB-damaged DNA complex is needed to catalyze incision in the vicinity of pyrimidine dimer sites. The UvrABC-DNA complex persists after the incision event suggesting that the lack of UvrABC turnover may be linked to other activities in the excision-repair pathway beyond the initial incision reaction. PMID:3960727

Classification of E-Nose Aroma Data of Four Fruit Types by ABC-Based Neural Network

PubMed Central

Adak, M. Fatih; Yumusak, Nejat

2016-01-01

Electronic nose technology is used in many areas, and frequently in the beverage industry for classification and quality-control purposes. In this study, four different aroma data (strawberry, lemon, cherry, and melon) were obtained using a MOSES II electronic nose for the purpose of fruit classification. To improve the performance of the classification, the training phase of the neural network with two hidden layers was optimized using artificial bee colony algorithm (ABC), which is known to be successful in exploration. Test data were given to two different neural networks, each of which were trained separately with backpropagation (BP) and ABC, and average test performances were measured as 60% for the artificial neural network trained with BP and 76.39% for the artificial neural network trained with ABC. Training and test phases were repeated 30 times to obtain these average performance measurements. This level of performance shows that the artificial neural network trained with ABC is successful in classifying aroma data. PMID:26927124

Efficient extracellular production of type I secretion pathway-dependent Pseudomonas fluorescens lipase in recombinant Escherichia coli by heterologous ABC protein exporters.

PubMed

Eom, Gyeong Tae; Lee, Seung Hwan; Oh, Young Hoon; Choi, Ji Eun; Park, Si Jae; Song, Jae Kwang

2014-10-01

Heterologous ABC protein exporters, the apparatus of type I secretion pathway in Gram-negative bacteria, were used for extracellular production of Pseudomonas fluorescens lipase (TliA) in recombinant Escherichia coli. The effect of the expression of different ABC protein exporter gene clusters (P. fluorescens tliDEF, Pseudomonas aeruginosa aprDEF, Erwinia chrysanthemi prtDEF, and Serratia marcescens lipBCD genes) was examined on the secretion of TliA at growth temperatures of 20, 25, 30 and 35 °C. TliA secretion in recombinant E. coli XL10-Gold varied depending upon type of ABC protein exporter and culture temperature. E. coli expressing S. marcescens lipBCD genes showed the highest secretion level of TliA (122.8 U ml(-1)) when cultured at 25 °C. Thus, optimized culture conditions for efficient extracellular production of lipase in recombinant E. coli can be designed by changing the type of ABC protein exporter and the growth temperature.

Classification of E-Nose Aroma Data of Four Fruit Types by ABC-Based Neural Network.

PubMed

Adak, M Fatih; Yumusak, Nejat

2016-02-27

Electronic nose technology is used in many areas, and frequently in the beverage industry for classification and quality-control purposes. In this study, four different aroma data (strawberry, lemon, cherry, and melon) were obtained using a MOSES II electronic nose for the purpose of fruit classification. To improve the performance of the classification, the training phase of the neural network with two hidden layers was optimized using artificial bee colony algorithm (ABC), which is known to be successful in exploration. Test data were given to two different neural networks, each of which were trained separately with backpropagation (BP) and ABC, and average test performances were measured as 60% for the artificial neural network trained with BP and 76.39% for the artificial neural network trained with ABC. Training and test phases were repeated 30 times to obtain these average performance measurements. This level of performance shows that the artificial neural network trained with ABC is successful in classifying aroma data.

50 CFR Table 1a to Part 660... - 2013, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in metric tons)

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false 2013, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in metric tons) 1a Table 1a to Part 660, Subpart C... Part 660, Subpart C—2013, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights...

50 CFR Table 1a to Part 660... - 2013, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in metric tons)

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false 2013, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in metric tons) 1a Table 1a to Part 660, Subpart C... Part 660, Subpart C—2013, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights...

Structural Validity of the Movement ABC-2 Test: Factor Structure Comparisons across Three Age Groups

ERIC Educational Resources Information Center

Schulz, Joerg; Henderson, Sheila E.; Sugden, David A.; Barnett, Anna L.

2011-01-01

Background: The Movement ABC test is one of the most widely used assessments in the field of Developmental Coordination Disorder (DCD). Improvements to the 2nd edition of the test (M-ABC-2) include an extension of the age range and reduction in the number of age bands as well as revision of tasks. The total test score provides a measure of motor…

The ABCs of School Choice: The Comprehensive Guide to Every Private School Choice Program in America. 2016 Edition

ERIC Educational Resources Information Center

Friedman Foundation for Educational Choice, 2016

2016-01-01

"The ABCs of School Choice" is a comprehensive, data-rich guide to every private school choice program in America. The 2016 edition of "The ABCs of School Choice" is the best yet, not just because of the new look and the fantastic growth in the number of school choice programs, but also because it is now paired with a…

[German adaptation of the "Activities-Specific Balance Confidence (ABC) scale" for the assessment of falls-related self-efficacy].

PubMed

Schott, Nadja

2008-12-01

The present study investigates the psychometric properties and the factorial structure of the German adaptation of the Activities-Specific Balance Confidence (ABC) scale (Powell & Myers, 1995) for the evaluation of falls-related self-efficacy in community-dwelling older adults. The German adaptation of the ABC using a forward-backward procedure was administered to 113 older adults (age 68.9+/-8.5 years). The following internationally accepted instruments were used for validation: The Short Form Health Survey SF 36, the Geriatric Depression Scale (GDS), the Trail Making Test and the Letter Number Sequencing Test, and motor tests (balance, strength, mobility). The internal consistency (0.91-0.95) as well as the test-retest reliability of the subscales was excellent (0.94-0.98). The correlation coefficients with the validation instruments ranged between 0.33 and 0.58. Significant differences in the ABC-D scores were found in older adults with and without falls. Older adults with a recent fall history scored lower on the ABC-D than older adults without a recent fall history. To conclude, the German version of the ABC has properties analogous to the original English version and is apparently useful in assessing falls-related self-efficacy.

Expression, purification and thermostability of MBP-chondroitinase ABC I from Proteus vulgaris.

PubMed

Chen, Zhenya; Li, Ye; Yuan, Qipeng

2015-01-01

Chondroitinase ABC I (ChSase ABC I) which can degrade chondroitin sulfate (CS) and other glycosaminoglycan to oligosaccharide or unsaturated disaccharide, was fusionally expressed with maltose-binding protein (MBP) in Escherichia coli BL21(DE3) (E. coli BL21(DE3)) and purified for the first time in this study. The result showed that the productivity of recombinant MBP-ChSase ABC I was 3180 IU/(L fermentation liquor) with CS A as substrate, and the productivity might be the highest level when compared to the reported ones. The specific activity of recombinant MBP-ChSase ABC I was 76 IU/(mg protein) after purification. The Vmax, Km and kcat were 18.7 ± 0.3 μmol/Ls, 73.1 ± 4.1 μmol/L and 586.7 ± 10.8 s(-1), respectively. Enzyme activity of the purified enzyme remained about 78% after 210 min when the enzyme incubated at 30 °C. This study introduces a rapid method for highly expressing ChSase ABC I, and the method could be adopted in the process of industrial production. Furthermore the investigation of thermostability might lead to an important guide in clinical treatment. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison between the Movement ABC-2 and the Zurich Neuromotor Assessment in Preschool Children.

PubMed

Kakebeeke, Tanja H; Knaier, Elisa; Köchli, Sabrina; Chaouch, Aziz; Rousson, Valentin; Kriemler, Susi; Jenni, Oskar G

2016-12-01

An established test instrument for the assessment of motor performance in children between 3 and 16 years is the Movement Assessment Battery for Children - Second Edition (M-ABC-2). The Zurich Neuromotor Assessment (ZNA) is also widely used for the evaluation of children's motor performance but has not been compared with the M-ABC-2 for children below five years for the purpose of convergent validity. Forty-seven children (26 boys, 21 girls) between three and five years of age were assessed using the M-ABC-2 and the ZNA3-5. Rank correlations between scores of different test components were calculated. Only low-to-moderate correlations were observed when separate components of these tests were compared (.31 to .68, p < .05), especially when involving the associated movements from the ZNA3-5 (-.05 to -.13, p > .05). However, the correlation between summary scores of the two tests was .77 (p < .001), and it increased to .84 when associated movements were excluded, which was comparable in magnitude to the test-retest reliability of the M-ABC-2, supporting convergent validity between the two tests. Although the ZNA3-5 and M-ABC-2 measure different aspects of motor behavior, the two instruments may thus measure essentially the same construct. © The Author(s) 2016.

Use of novel chitosan hydrogels for chemical tissue bonding of autologous chondral transplants.

PubMed

Gittens, Jamila; Haleem, Amgad M; Grenier, Stephanie; Smyth, Niall A; Hannon, Charles P; Ross, Keir A; Torzilli, Peter A; Kennedy, John G

2016-07-01

The objective of this study was to evaluate the effect of chemical tissue bonding (CTB) on adhesion strength, fluid permeability, and cell viability across a cartilaginous graft-host interface in an in vitro autologous chondral transplant (ACT) model. Chitosan-based cross-linkers; Chitosan-Rose Bengal [Chi-RB (Ch-ABC)], Chitosan-Genipin [Chi-GP (Ch-ABC)], and Chitosan-Rose Bengal-Genipin [Chi-RB-GP (Ch-ABC)] were applied to bovine immature cartilage explants after pre-treatment with surface degrading enzyme, Chondroitinase-ABC (Ch-ABC). Adhesion strength, fluid permeability and cell viability were assessed via mechanical push-out shear testing, fluid transport and live/dead cell staining, respectively. All three chitosan-based cross-linkers significantly increased the adhesion strength at the graft-host interface, however, only a statistically significant decrease in fluid permeability was noted in Chi-GP (Ch-ABC) specimen compared to untreated controls. Cell viability was maintained for 7 days of culture across all three treatment groups. These results show the potential clinical relevance of novel chitosan-based hydrogels in enhancing tissue integration and reducing synovial fluid penetration after ACT procedures in diarthoidal joints such as the knee and ankle. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1139-1146, 2016. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

ABC Transporters Involved in Export of Cell Surface Glycoconjugates

PubMed Central

Cuthbertson, Leslie; Kos, Veronica; Whitfield, Chris

2010-01-01

Summary: Complex glycoconjugates play critical roles in the biology of microorganisms. Despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. One of the primary pathways involves representatives of the ATP-binding cassette (ABC) transporter superfamily. These proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both Gram-positive and Gram-negative bacteria. Recent investigations of the structure and function of ABC transporters involved in the export of lipopolysaccharide O antigens have revealed two fundamentally different strategies for coupling glycan polymerization to export. These mechanisms are distinguished by the presence (or absence) of characteristic nonreducing terminal modifications on the export substrates, which serve as chain termination and/or export signals, and by the presence (or absence) of a discrete substrate-binding domain in the nucleotide-binding domain polypeptide of the ABC transporter. A bioinformatic survey examining ABC exporters from known oligo- and polysaccharide biosynthesis loci identifies conserved nucleotide-binding domain protein families that correlate well with themes in the structures and assembly of glycans. The familial relationships among the ABC exporters generate hypotheses concerning the biosynthesis of structurally diverse oligo- and polysaccharides, which play important roles in the biology of bacteria with different lifestyles. PMID:20805402

Early Observations of the Type Ia Supernova iPTF 16abc

NASA Astrophysics Data System (ADS)

Miller, Adam; iPTF Collaboration

2018-01-01

Early observations of Type Ia supernovae (SNe) provide a unique probe of their progenitor systems and explosion physics. Here, we report the intermediate Palomar Transient Factory (iPTF) discovery of an extraordinarily young SN Ia, iPTF 16abc. By fitting a power law to our early light curve, we infer that first light for the SN only occurred 0.15 +0.15-0.07 d before our first detection. In the ~24 hr after discovery, iPTF 16abc rose by ~2 mag, following a near-linear rise in flux for ~3 d. Strong C II absorption is detected in the early spectra of iPTF 16abc, before disappearing after ~7 d. Unlike the extensively-observed Type Ia SN 2011fe, the (B-V)_0 colors of iPTF 16abc are blue and nearly constant in the days after explosion. We show that our early observations of iPTF 16abc cannot be explained by either SN shock breakout and the associated, subsequent cooling, or the SN ejecta colliding with a stellar companion. Instead, we argue that the early characteristics of iPTF 16abc, including: (i) the rapid, near-linear rise, (ii) the non-evolving blue colors, and (iii) the strong absorption from ionized carbon, are the result of either vigorous mixing of radioactive-Ni in the SN ejecta, or ejecta interaction with diffuse material, or a combination of the two. In the next few years, dozens of very young normal SNe Ia will be discovered, and observations similar to those presented here will constrain the white dwarf explosion mechanism.

Bone cysts: unicameral and aneurysmal bone cyst.

PubMed

Mascard, E; Gomez-Brouchet, A; Lambot, K

2015-02-01

Simple and aneurysmal bone cysts are benign lytic bone lesions, usually encountered in children and adolescents. Simple bone cyst is a cystic, fluid-filled lesion, which may be unicameral (UBC) or partially separated. UBC can involve all bones, but usually the long bone metaphysis and otherwise primarily the proximal humerus and proximal femur. The classic aneurysmal bone cyst (ABC) is an expansive and hemorrhagic tumor, usually showing characteristic translocation. About 30% of ABCs are secondary, without translocation; they occur in reaction to another, usually benign, bone lesion. ABCs are metaphyseal, excentric, bulging, fluid-filled and multicameral, and may develop in all bones of the skeleton. On MRI, the fluid level is evocative. It is mandatory to distinguish ABC from UBC, as prognosis and treatment are different. UBCs resolve spontaneously between adolescence and adulthood; the main concern is the risk of pathologic fracture. Treatment in non-threatening forms consists in intracystic injection of methylprednisolone. When there is a risk of fracture, especially of the femoral neck, surgery with curettage, filling with bone substitute or graft and osteosynthesis may be required. ABCs are potentially more aggressive, with a risk of bone destruction. Diagnosis must systematically be confirmed by biopsy, identifying soft-tissue parts, as telangiectatic sarcoma can mimic ABC. Intra-lesional sclerotherapy with alcohol is an effective treatment. In spinal ABC and in aggressive lesions with a risk of fracture, surgical treatment should be preferred, possibly after preoperative embolization. The risk of malignant transformation is very low, except in case of radiation therapy. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Sonothrombolysis is effective with recombinant tissue-type plasminogen activator, but not with Abciximab. Results from an in vitro study with whole blood clots and platelet-rich clots.

PubMed

Eggers, Jürgen; Ossadnik, Stefan; Hütten, Heiko; Seidel, Günter

2009-12-01

Transcranial "diagnostic" ultrasound (US) has been shown to accelerate thrombolysis related to recombinant tissue-type plasminogen activator (rt-PA). In this in vitro study, we evaluated the potential of US to increase clot dissolution mediated by Abciximab (Abc) compared to rt-PA. The effect of 1.8-MHz pulsed wave (PW) Doppler US on dissolution of whole venous blood clots (WBC) and platelet-rich clots (PRC) treated with Abc and rt-PA was investigated in an in vitro model. Clot dissolution was measured by weight loss. Abc-related WBC dissolution was enhanced by additional US, but the effect was not any more detectable when the US was attenuated by a human temporal bone (US-tb). In PRC there was no additional effect of US on the Abc-related clot lysis. Rt-PA-related clot dissolution was increased by US in WBC and PRC as well, however, US-tb was only effective in WBC. The effect of insonation on WBC dissolution treated with the combination of Abc plus rt-PA was lower compared with those treated with rt-PA. In this in vitro experiment, the additional effect of "diagnostic" US in combination with Abc was only present in WBC and less strong than with rt-PA. The results do not support the use of Abc for sonothrombolysis targeting both, fibrin-rich and platelet-rich clots. In contrast, US when combined with rt-PA increases dissolution in both, WBC and PRC as well.

The ABC of Biofilm Drug Tolerance: the MerR-Like Regulator BrlR Is an Activator of ABC Transport Systems, with PA1874-77 Contributing to the Tolerance of Pseudomonas aeruginosa Biofilms to Tobramycin.

PubMed

Poudyal, Bandita; Sauer, Karin

2018-02-01

A hallmark of biofilms is their tolerance to killing by antimicrobial agents. In Pseudomonas aeruginosa , biofilm drug tolerance requires the c-di-GMP-responsive MerR transcriptional regulator BrlR. However, the mechanism by which BrlR mediates biofilm drug tolerance has not been elucidated. Here, we demonstrate that BrlR activates the expression of at least 7 ABC transport systems, including the PA1874-PA1875-PA1876-PA1877 (PA1874-77) operon, with chromatin immunoprecipitation and DNA binding assays confirming BrlR binding to the promoter region of PA1874-77. Insertional inactivation of the 7 ABC transport systems rendered P. aeruginosa PAO1 biofilms susceptible to tobramycin or norfloxacin. Susceptibility was linked to drug accumulation, with BrlR contributing to norfloxacin accumulation in a manner dependent on multidrug efflux pumps and the PA1874-77 ABC transport system. Inactivation of the respective ABC transport system, furthermore, eliminated the recalcitrance of biofilms to killing by tobramycin but not norfloxacin, indicating that drug accumulation is not linked to biofilm drug tolerance. Our findings indicate for the first time that BrlR, a MerR-type transcriptional activator, activates genes encoding several ABC transport systems, in addition to multiple multidrug efflux pump genes. Moreover, our data confirm a BrlR target contributing to drug tolerance, likely countering the prevailing dogma that biofilm tolerance arises from a multiplicity of factors. Copyright © 2018 American Society for Microbiology.

A General Cross-Layer Cloud Scheduling Framework for Multiple IoT Computer Tasks.

PubMed

Wu, Guanlin; Bao, Weidong; Zhu, Xiaomin; Zhang, Xiongtao

2018-05-23

The diversity of IoT services and applications brings enormous challenges to improving the performance of multiple computer tasks' scheduling in cross-layer cloud computing systems. Unfortunately, the commonly-employed frameworks fail to adapt to the new patterns on the cross-layer cloud. To solve this issue, we design a new computer task scheduling framework for multiple IoT services in cross-layer cloud computing systems. Specifically, we first analyze the features of the cross-layer cloud and computer tasks. Then, we design the scheduling framework based on the analysis and present detailed models to illustrate the procedures of using the framework. With the proposed framework, the IoT services deployed in cross-layer cloud computing systems can dynamically select suitable algorithms and use resources more effectively to finish computer tasks with different objectives. Finally, the algorithms are given based on the framework, and extensive experiments are also given to validate its effectiveness, as well as its superiority.

Recent Abacavir Use Increases Risk of Type 1 and Type 2 Myocardial Infarctions Among Adults With HIV.

PubMed

Elion, Richard A; Althoff, Keri N; Zhang, Jinbing; Moore, Richard D; Gange, Stephen J; Kitahata, Mari M; Crane, Heidi M; Drozd, Daniel R; Stein, James H; Klein, Marina B; Eron, Joseph J; Silverberg, Michael J; Mathews, William C; Justice, Amy C; Sterling, Timothy R; Rabkin, Charles S; Mayor, Angel M; Klein, Daniel B; Horberg, Michael A; Bosch, Ronald J; Eyawo, Oghenowede; Palella, Frank J

2018-05-01

There is persistent confusion as to whether abacavir (ABC) increases the risk of myocardial infarction (MI), and whether such risk differs by type 1 (T1MI) or 2 (T2MI) MI in adults with HIV. Incident MIs in North American Cohort Collaboration on Research and Design participants were identified from 2001 to 2013. Discrete time marginal structural models addressed channeling biases and time-dependent confounding to estimate crude hazard ratio (HR) and adjusted hazard ratio (aHR) and 95% confidence intervals; analyses were performed for T1MI and T2MI separately. A sensitivity analysis evaluated whether Framingham risk score (FRS) modified the effect of ABC on MI occurrence. Eight thousand two hundred sixty-five adults who initiated antiretroviral therapy contributed 29,077 person-years and 123 MI events (65 T1MI and 58 T2MI). Median follow-up time was 2.9 (interquartile range 1.4-5.1) years. ABC initiators were more likely to have a history of injection drug use, hepatitis C virus infection, hypertension, diabetes, impaired kidney function, hyperlipidemia, low (<200 cells/mm) CD4 counts, and a history of AIDS. The risk of the combined MI outcome was greater for persons who used ABC in the previous 6 months [aHR = 1.84 (1.17-2.91)]; and persisted for T1MI (aHR = 1.62 [1.01]) and T2MI [aHR = 2.11 (1.08-4.29)]. FRS did not modify the effect of ABC on MI (P = 0.14) and inclusion of FRS in the MSM did not diminish the effect of recent ABC use on the combined outcome. Recent ABC use was associated with MI after adjustment for known risk factors and for FRS. However, screening for T1MI risks may not identify all or even most persons at risk of ABC use-associated MIs.

An alternative physiological role for the EmhABC efflux pump in Pseudomonas fluorescens cLP6a

PubMed Central

2011-01-01

Background Efflux pumps belonging to the resistance-nodulation-division (RND) superfamily in bacteria are involved in antibiotic resistance and solvent tolerance but have an unknown physiological role. EmhABC, a RND-type efflux pump in Pseudomonas fluorescens strain cLP6a, extrudes hydrophobic antibiotics, dyes and polycyclic aromatic hydrocarbons including phenanthrene. The effects of physico-chemical factors such as temperature or antibiotics on the activity and expression of EmhABC were determined in order to deduce its physiological role(s) in strain cLP6a in comparison to the emhB disruptant strain, cLP6a-1. Results Efflux assays conducted with 14C-phenanthrene showed that EmhABC activity is affected by incubation temperature. Increased phenanthrene efflux was measured in cLP6a cells grown at 10°C and decreased efflux was observed at 35°C compared with cells grown at the optimum temperature of 28°C. Membrane fatty acids in cLP6a cells were substantially altered by changes in growth temperature and in the presence of tetracycline. Changed membrane fatty acids and increased membrane permeability were associated with ~30-fold increased expression of emhABC in cLP6a cells grown at 35°C, and with increased extracellular free fatty acids. Growth of P. fluorescens cLP6a at supra-optimal temperature was enhanced by the presence of EmhABC compared to strain cLP6a-1. Conclusions Combined, these observations suggest that the EmhABC efflux pump may be involved in the management of membrane stress effects such as those due to unfavourable incubation temperatures. Efflux of fatty acids replaced as a result of membrane damage or phospholipid turnover may be the primary physiological role of the EmhABC efflux pump in P. fluorescens cLP6a. PMID:22085438

50 CFR Table 2a to Part 660... - 2012, and beyond, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in...

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false 2012, and beyond, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in metric tons) 2a Table 2a to Part 660, Subpart... Table 2a to Part 660, Subpart C—2012, and beyond, Specifications of OFL, ABC, ACL, ACT and Fishery...

50 CFR Table 2a to Part 660... - 2014, and Beyond, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in...

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false 2014, and Beyond, Specifications of OFL, ABC, ACL, ACT and Fishery Harvest guidelines (weights in metric tons) 2a Table 2a to Part 660, Subpart... Table 2a to Part 660, Subpart C—2014, and Beyond, Specifications of OFL, ABC, ACL, ACT and Fishery...

Psychological differentiation in Nigerian children.

PubMed

Jegede, R

1976-11-01

The human figure drawings of 646 male and female Nigerian primary school children were analyzed with the use of Witkin's Articulation of Body Concept (ABC) scale. There was a significant association between age and ABC scores for the Ss as a group. The correlation between age and ABC scores was significant with male Ss and almost so with female Ss. These findings are on the whole consistent with the results of previous research conducted in different sociocultural settings.

Electronic and magnetic properties of bare armchair BC2N nanoribbons

NASA Astrophysics Data System (ADS)

Li, Hong; Xiao, Xiang; Tie, Jun; Lu, Jing

2017-03-01

We present the electronic and magnetic properties of bare armchair BC2N nanoribbons (ABC2NNRs) in the view of density functional calculations. We consider three types of edge terminations with a width of 0.75 2.10 nm. All the investigated ribbons exhibit magnetic ground states with the magnetic moments mainly located on the edge C atoms. Room temperature accessible magnetic stabilities are obtained for ABC2NNRs with NC-NC and NC-BC edge alignments. We find the ABC2NNRs have various electronic structures, where half-metal, metal, and semiconductor are all acquired depend on the edge alignment and magnetic coupling state. The results show the ABC2NNRs can be a promising candidate material in nanoelectronics and nanospintronics.

Unicameral and aneurysmal bone cysts.

PubMed

Campanacci, M; Capanna, R; Picci, P

1986-03-01

One hundred and seventy-eight cases of unicameral bone cysts (UBC) treated with curettage and bone grafting were compared to 141 cases treated with cortisone injections. The end results were comparable in the two groups. Local recurrence risk factors in the surgical group were active cyst and previous operations. In the other group they were multilocation of the cyst, active cyst, and size of cyst. A new radiographic classification of aneurysmal bone cyst (ABC) is proposed in a report of 198 cases of ABC. The treatment of choice in ABC is surgical and the type (curettage, curettage plus phenole or cryosurgery, resection or hemiresection) is selected on the basis of the radiographic aspect and the rate of growth of the cyst. Radiotherapy is only indicated in inoperable ABC cases.

An internet based approach to improve general practitioners' knowledge and practices: the development and pilot testing of the "ABC's of vitamin D" program.

PubMed

Bonevski, B; Magin, P; Horton, G; Bryant, J; Randell, M; Kimlin, M G

2015-06-01

Online continuing medical education (CME) offers a number of advantages for physicians including flexibility with regards to location and timing of use. In order to effect physician practices and improve patient outcomes, it is important that the development of online CME is theory and evidence-based. This paper aims to describe the development of an online CME program for practising general practitioners (GPs) on vitamin D and sun health called "The ABC's of Vitamin D for GPs" using elements of design principles for physician-education web sites as a framework. The paper will also report the program's usability and acceptability pilot test results. The ABC's of Vitamin D program was developed following nine principles: needs assessment; evidence-based content development; multimodal program and modularisation; clinical cases; tailoring and interactivity; audit and feedback; credibility of the web site host; patient education materials; ease of use and navigation. Among the 20 GPs invited, acceptability and useability was tested with 12 GPs (60%) who agreed to participate and were interviewed following use of the program. The study was conducted between 2011 and 2013. An online CME program consisting of eight modules was constructed. Of the 12 participating GPs, most (n=11) reported that the program was clear and easy to understand, logical, easy to navigate, and took a reasonable amount of time (estimated between 1 and 3h) to complete. Eleven of 12 participants said they would use the program as an accredited CME activity and all participants indicated that the program was 'very or somewhat' likely to lead to changes in the advice patients are given. This study found that a theory and evidence based approach for the development of an online CME program for GPs was acceptable to users. Further research is needed to examine whether the online CME program is effective at changing GP practices and improving patient outcomes. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Properties of submicron particles in Atmospheric Brown Clouds

NASA Astrophysics Data System (ADS)

Adushkin, V. V.; Chen, B. B.; Dubovskoi, A. N.; Friedrich, F.; Pernik, L. M.; Popel, S. I.; Weidler, P. G.

2010-05-01

The Atmospheric Brown Clouds (ABC) is an important problem of this century. Investigations of last years and satellite data show that the ABC (or brown gas, smog, fog) cover extensive territories including the whole continents and oceans. The brown gas consists of a mixture of particles of anthropogenic sulfates, nitrates, organic origin, black carbon, dust, ashes, and also natural aerosols such as sea salt and mineral dust. The brown color is a result of absorption and scattering of solar radiation by the anthropogenic black carbon, ashes, the particles of salt dust, and nitrogen dioxide. The investigation of the ABC is a fundamental problem for prevention of degradation of the environment. At present in the CIS in-situ investigations of the ABC are carried out on Lidar Station Teplokluchenka (Kyrgyz Republic). Here, we present the results of experimental investigation of submicron (nanoscale) particles originating from the ABC and the properties of the particles. Samples of dust precipitating from the ABC were obtained at the area of Lidar Station Teplokluchenka as well as scientific station of the Russian Academy of Sciences near Bishkek. The data for determination of the grain composition were obtained with the aid of the scanning electron microscopes JEOL 6460 LV and Philips XL 30 FEG. Analysis of the properties of the particles was performed by means of the X-ray diffraction using diffractometer Siemens D5000. The images of the grains were mapped. The investigation allows us to get (after the image processing) the grain composition within the dust particle size range of 60 nm to 700 μm. Distributions of nano- and microscale particles in sizes were constructed using Rozin-Rammler coordinates. Analysis of the distributions shows that the ABC contain submicron (nanoscale) particles; 2) at higher altitudes the concentration of the submicron (nanoscale) particles in the ABC is higher than at lower altitudes. The chemical compositions of the particles are shown to be close to those typical for the ABC. We present also the results of the study of morphology and mineralogical composition of the obtained particles as well as their magnetic properties. This study was supported by the Division of Earth Sciences, Russian Academy of Sciences (research program "Nanoscale particles in nature and technogenic products: conditions of existence, physical and chemical properties, and mechanisms of formation") and by ISTC (project No. KR-1522).

Neuronal glycosylation differentials in normal, injured and chondroitinase-treated environments

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

Kilcoyne, Michelle; Sharma, Shashank; McDevitt, Niamh

2012-04-13

Highlights: Black-Right-Pointing-Pointer Carbohydrates are important in the CNS and ChABC has been used for spinal cord injury (SCI) treatment. Black-Right-Pointing-Pointer Neuronal glycosylation in injury and after ChABC treatment is unknown. Black-Right-Pointing-Pointer In silico mining verified that glyco-related genes were differentially regulated after SCI. Black-Right-Pointing-Pointer In vitro model system revealed abnormal sialylation in an injured environment. Black-Right-Pointing-Pointer The model indicated a return to normal neuronal glycosylation after ChABC treatment. -- Abstract: Glycosylation is found ubiquitously throughout the central nervous system (CNS). Chondroitin sulphate proteoglycans (CSPGs) are a group of molecules heavily substituted with glycosaminoglycans (GAGs) and are found in the extracellularmore » matrix (ECM) and cell surfaces. Upon CNS injury, a glial scar is formed, which is inhibitory for axon regeneration. Several CSPGs are up-regulated within the glial scar, including NG2, and these CSPGs are key inhibitory molecules of axonal regeneration. Treatment with chondroitinase ABC (ChABC) can neutralise the inhibitory nature of NG2. A gene expression dataset was mined in silico to verify differentially regulated glycosylation-related genes in neurons after spinal cord injury and identify potential targets for further investigation. To establish the glycosylation differential of neurons that grow in a healthy, inhibitory and ChABC-treated environment, we established an indirect co-culture system where PC12 neurons were grown with primary astrocytes, Neu7 astrocytes (which overexpress NG2) and Neu7 astrocytes treated with ChABC. After 1, 4 and 8 days culture, lectin cytochemistry of the neurons was performed using five fluorescently-labelled lectins (ECA MAA, PNA, SNA-I and WFA). Usually {alpha}-(2,6)-linked sialylation scarcely occurs in the CNS but this motif was observed on the neurons in the injured environment only at day 8. Treatment with ChABC was successful in returning neuronal glycosylation to normal conditions at all timepoints for MAA, PNA and SNA-I staining, and by day 8 in the case of WFA. This study demonstrated neuronal cell surface glycosylation changes in an inhibitory environment and indicated a return to normal glycosylation after treatment with ChABC, which may be promising for identifying potential therapies for neuronal regeneration strategies.« less

Computation of Nonlinear Backscattering Using a High-Order Numerical Method

NASA Technical Reports Server (NTRS)

Fibich, G.; Ilan, B.; Tsynkov, S.

2001-01-01

The nonlinear Schrodinger equation (NLS) is the standard model for propagation of intense laser beams in Kerr media. The NLS is derived from the nonlinear Helmholtz equation (NLH) by employing the paraxial approximation and neglecting the backscattered waves. In this study we use a fourth-order finite-difference method supplemented by special two-way artificial boundary conditions (ABCs) to solve the NLH as a boundary value problem. Our numerical methodology allows for a direct comparison of the NLH and NLS models and for an accurate quantitative assessment of the backscattered signal.

A new conformal absorbing boundary condition for finite element meshes and parallelization of FEMATS

NASA Technical Reports Server (NTRS)

Chatterjee, A.; Volakis, J. L.; Nguyen, J.; Nurnberger, M.; Ross, D.

1993-01-01

Some of the progress toward the development and parallelization of an improved version of the finite element code FEMATS is described. This is a finite element code for computing the scattering by arbitrarily shaped three dimensional surfaces composite scatterers. The following tasks were worked on during the report period: (1) new absorbing boundary conditions (ABC's) for truncating the finite element mesh; (2) mixed mesh termination schemes; (3) hierarchical elements and multigridding; (4) parallelization; and (5) various modeling enhancements (antenna feeds, anisotropy, and higher order GIBC).

Effect of body temperature on chondroitinase ABC's ability to cleave chondroitin sulfate glycosaminoglycans.

PubMed

Tester, Nicole J; Plaas, Anna H; Howland, Dena R

2007-04-01

Chondroitinase ABC (Ch'ase ABC) is a bacterial lyase that degrades chondroitin sulfate (CS), dermatan sulfate, and hyaluronan glycosaminoglycans (GAGs). This enzyme has received significant attention as a potential therapy for promoting central nervous system and peripheral nervous system repair based on its degradation of CS GAGs. Determination of the stability of Ch'ase ABC activity at temperatures equivalent to normal (37 degrees C) and elevated (39 degrees C) body temperatures is important for optimizing its clinical usage. We report here data obtained from examining enzymatic activity at these temperatures across nine lots of commercially available protease-free Ch'ase ABC. CS GAG degrading activity was assayed by using 1) immunohistochemical detection of unsaturated disaccharide stubs generated by digestion of proteoglycans in tissue sections and 2) fluorophore-assisted carbohydrate electrophoresis (FACE) and/or high-performance liquid chromatography (HPLC) to separate and quantify unsaturated disaccharide digestion products. Our results indicate that there is a significant effect of lot and time on enzymatic thermostability. Average enzymatic activity is significantly decreased at 1 and 3 days at 39 degrees C and 37 degrees C, respectively. Furthermore, the average activity seen after 1 day was significantly different between the two temperatures. Addition of bovine serum albumin as a stabilizer significantly preserved enzymatic activity at 1 day, but not 3 days, at 39 degrees C. These results show that the CS GAG degrading activity of Ch'ase ABC is significantly decreased with incubation at body temperature over time and that all lots do not show equal thermostability. These findings are important for the design and interpretation of experimental and potential clinical studies involving Ch'ase ABC. (c) 2007 Wiley-Liss, Inc.

ATP and AMP Mutually Influence Their Interaction with the ATP-binding Cassette (ABC) Adenylate Kinase Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) at Separate Binding Sites*

PubMed Central

Randak, Christoph O.; Dong, Qian; Ver Heul, Amanda R.; Elcock, Adrian H.; Welsh, Michael J.

2013-01-01

Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel in the ATP-binding cassette (ABC) transporter protein family. In the presence of ATP and physiologically relevant concentrations of AMP, CFTR exhibits adenylate kinase activity (ATP + AMP ⇆ 2 ADP). Previous studies suggested that the interaction of nucleotide triphosphate with CFTR at ATP-binding site 2 is required for this activity. Two other ABC proteins, Rad50 and a structural maintenance of chromosome protein, also have adenylate kinase activity. All three ABC adenylate kinases bind and hydrolyze ATP in the absence of other nucleotides. However, little is known about how an ABC adenylate kinase interacts with ATP and AMP when both are present. Based on data from non-ABC adenylate kinases, we hypothesized that ATP and AMP mutually influence their interaction with CFTR at separate binding sites. We further hypothesized that only one of the two CFTR ATP-binding sites is involved in the adenylate kinase reaction. We found that 8-azidoadenosine 5′-triphosphate (8-N3-ATP) and 8-azidoadenosine 5′-monophosphate (8-N3-AMP) photolabeled separate sites in CFTR. Labeling of the AMP-binding site with 8-N3-AMP required the presence of ATP. Conversely, AMP enhanced photolabeling with 8-N3-ATP at ATP-binding site 2. The adenylate kinase active center probe P1,P5-di(adenosine-5′) pentaphosphate interacted simultaneously with an AMP-binding site and ATP-binding site 2. These results show that ATP and AMP interact with separate binding sites but mutually influence their interaction with the ABC adenylate kinase CFTR. They further indicate that the active center of the adenylate kinase comprises ATP-binding site 2. PMID:23921386

Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides

PubMed Central

2011-01-01

Background Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene, ssrA. Results We targeted conserved positions in available genomic islands to amplify and sequence four additional vcrABC -containing genomic islands from previously-unsequenced vinyl chloride respiring Dehalococcoides enrichments. We identified a total of 31 ssrA-specific genomic islands from Dehalococcoides genomic data, accounting for 47 reductive dehalogenase homologous genes and many other non-core genes. Sixteen of these genomic islands contain a syntenic module of integration-associated genes located adjacent to the predicted site of integration, and among these islands, eight contain vcrABC as genetic 'cargo'. These eight vcrABC -containing genomic islands are syntenic across their ~12 kbp length, but have two phylogenetically discordant segments that unambiguously differentiate the integration module from the vcrABC cargo. Using available Dehalococcoides phylogenomic data we estimate that these ssrA-specific genomic islands are at least as old as the Dehalococcoides group itself, which in turn is much older than human civilization. Conclusions The vcrABC -containing genomic islands are a recently-acquired subset of a diverse collection of ssrA-specific mobile elements that are a major contributor to strain-level diversity in Dehalococcoides, and may have been throughout its evolution. The high similarity between vcrABC sequences is quantitatively consistent with recent horizontal acquisition driven by ~100 years of industrial pollution with chlorinated ethenes. PMID:21635780

Systemic treatment in advanced biliary cancers: A multicenter Australian analysis and review.

PubMed

Brungs, Daniel; Aghmesheh, Morteza; Sjoquist, Katrin; Goldstein, David

2017-10-01

While first-line palliative chemotherapy (CT1) improves survival and quality of life in advanced biliary cancer (ABC), there is no randomized evidence to support second-line chemotherapy (CT2) in ABC. We aim to explore to role of CT2 in ABC. We performed a retrospective review of all patients who received one or more lines of chemotherapy for ABC at four Australian cancer centers between 2008 and 2011. A Cox proportional hazard model was developed to determine the impact of clinicopathologic variables on overall survival (OS) from time of progression on CT1. We identified 73 patients who received palliative chemotherapy for ABC. Twenty-five patients (34%) received two or more lines of chemotherapy. Patients with a preserved performance status on progression on first-line chemotherapy (CT1) were more likely to receive second-line chemotherapy (CT2) (P < 0.001). Disease control rate with CT2 was 36%, and mean progression-free survival was 3.2 months (95% confidence interval 1.5-4.9 months). The following variables were significant in the univariate analysis of OS from time of progression on CT1: lines of chemotherapy (P = 0.0001), Eastern Cooperative Oncology Group performance status at progression on CT1 (P < 0.0001) and disease control with CT1 (P = 0.027). Lines of chemotherapy received and performance status remained significant in the multivariate analysis for OS from progression on CT1. Second-line chemotherapy is feasible in a subset of patients with ABC. Even after accounting for confounding variables, CT2 appears to increase OS in ABC, although we are unable to exclude other unmeasured factors such as tumor biology. These findings warrant further evaluation with prospective trials. © 2016 John Wiley & Sons Australia, Ltd.

Molecular mechanisms underlying origin and diversification of the angiosperm flower.

PubMed

Theissen, Guenter; Melzer, Rainer

2007-09-01

Understanding the mode and mechanisms of the evolution of the angiosperm flower is a long-standing and central problem of evolutionary biology and botany. It has essentially remained unsolved, however. In contrast, considerable progress has recently been made in our understanding of the genetic basis of flower development in some extant model species. The knowledge that accumulated this way has been pulled together in two major hypotheses, termed the 'ABC model' and the 'floral quartet model'. These models explain how the identity of the different types of floral organs is specified during flower development by homeotic selector genes encoding transcription factors. We intend to explain how the 'ABC model' and the 'floral quartet model' are now guiding investigations that help to understand the origin and diversification of the angiosperm flower. Investigation of orthologues of class B and class C floral homeotic genes in gymnosperms suggest that bisexuality was one of the first innovations during the origin of the flower. The transition from dimer to tetramer formation of floral homeotic proteins after establishment of class E proteins may have increased cooperativity of DNA binding of the transcription factors controlling reproductive growth. That way, we hypothesize, better 'developmental switches' originated that facilitated the early evolution of the flower. Expression studies of ABC genes in basally diverging angiosperm lineages, monocots and basal eudicots suggest that the 'classical' ABC system known from core eudicots originated from a more fuzzy system with fading borders of gene expression and gradual transitions in organ identity, by sharpening of ABC gene expression domains and organ borders. Shifting boundaries of ABC gene expression may have contributed to the diversification of the angiosperm flower many times independently, as may have changes in interactions between ABC genes and their target genes.

Molecular Mechanisms Underlying Origin and Diversification of the Angiosperm Flower

PubMed Central

Theissen, Guenter; Melzer, Rainer

2007-01-01

Background Understanding the mode and mechanisms of the evolution of the angiosperm flower is a long-standing and central problem of evolutionary biology and botany. It has essentially remained unsolved, however. In contrast, considerable progress has recently been made in our understanding of the genetic basis of flower development in some extant model species. The knowledge that accumulated this way has been pulled together in two major hypotheses, termed the ‘ABC model’ and the ‘floral quartet model’. These models explain how the identity of the different types of floral organs is specified during flower development by homeotic selector genes encoding transcription factors. Scope We intend to explain how the ‘ABC model’ and the ‘floral quartet model’ are now guiding investigations that help to understand the origin and diversification of the angiosperm flower. Conclusions Investigation of orthologues of class B and class C floral homeotic genes in gymnosperms suggest that bisexuality was one of the first innovations during the origin of the flower. The transition from dimer to tetramer formation of floral homeotic proteins after establishment of class E proteins may have increased cooperativity of DNA binding of the transcription factors controlling reproductive growth. That way, we hypothesize, better ‘developmental switches’ originated that facilitated the early evolution of the flower. Expression studies of ABC genes in basally diverging angiosperm lineages, monocots and basal eudicots suggest that the ‘classical’ ABC system known from core eudicots originated from a more fuzzy system with fading borders of gene expression and gradual transitions in organ identity, by sharpening of ABC gene expression domains and organ borders. Shifting boundaries of ABC gene expression may have contributed to the diversification of the angiosperm flower many times independently, as may have changes in interactions between ABC genes and their target genes. PMID:17670752

Effects of a switch from tenofovir- to abacavir-based antiretroviral therapy, with or without atazanavir, on renal function.

PubMed

Guillemi, Silvia A; Ling, Sean H; Dahlby, Julia S; Yip, Benita; Zhang, Wendy; Hull, Mark W; Lima, Viviane Dias; Hogg, Robert S; Werb, Ronald; Montaner, Julio S; Harris, Marianne

2016-01-01

Tenofovir disoproxil fumarate (TDF)-associated renal dysfunction may abate when TDF is replaced with abacavir (ABC). The extent to which the third drug atazanavir contributes to renal dysfunction is unclear. A retrospective analysis was conducted on adults who had plasma viral load (pVL)<200 copies/mL for≥six months while receiving TDF/lamivudine (3TC) - or TDF/emtricitabine (FTC)-based antiretroviral therapy (ART), then switched to ABC/3TC while retaining the third drug in the ART regimen. CD4, pVL, creatinine, estimated glomerular filtration rate (eGFR), serum phosphorus, urine albumin to creatinine ratio and serum lipids were compared between pre-switch baseline and 3, 6 and 12 months after the switch to ABC. A total of 286 patients switched from TDF to ABC between 2004 and 2014: 232 (81%) male, median age 48 years (interquartile range (IQR) 42, 56). The third drug was atazanavir (± ritonavir) in 141 (49%) cases. The pVL was<50 copies/mL in 93 to 96% at all time points. Median serum creatinine was 93 µmol/L (IQR 80-111) at baseline and decreased to 88 µmol/L (IQR 78-98) at 12 months after the switch to ABC. Median eGFR increased from 74 (IQR 60-88) mL/min at baseline to 80 mL/min (IQR 69-89) at 12 months. Results were not significantly different between patients on atazanavir versus those on another third drug. Viral suppression was maintained among patients who switched from TDF/3TC or TDF/FTC to ABC/3TC. Serum creatinine and eGFR improved up to 12 months after switching to ABC/3TC, irrespective of whether or not patients were also receiving atazanavir±ritonavir.

Use of patch testing for the diagnosis of abacavir-related hypersensitivity reaction in HIV patients.

PubMed

Giorgini, S; Martinelli, C; Tognetti, L; Carocci, A; Giuntini, R; Mastronardi, V; Torricelli, F; Leoncini, F; Lotti, T

2011-01-01

The use of antiretroviral drug abacavir (ABC) has been often associated with cutaneous hypersensitivity reactions, the majority being severe. The present study discusses the issues of patch testing associated with pharmacogenetic screening in light of the development of abacavir hypersensitivity reactions (HSRs). The present authors classified 100 patients into three groups: 20 patients (group A) had experienced a hypersensitivity reaction when treated with highly active antiretroviral therapy (HAART) including ABC; 60 HIV-positive patients (group B) were receiving HAART scheme including ABC; 20 HIV-negative patients acted as control group (group C). Patients of group A and B were patch tested with ABC as such, then with an ABC extract diluted to 1 and 10% in petrolatum. Group C patients underwent patches with petrolatum only. A biopsy of the lesion was performed in those patients who showed a positive skin reaction. All patients had been tested for HLA-B5701. A correlation between positive ABC-patch testing and HLA-B5701 was found in 50% of patients enrolled in group A, while in group B and C, all patients tested negative for both genetic marker and ABC-patch testing. Histopathology findings confirmed a vigorous CD4+ and CD8+ cellular response that is compatible with HSR. Patch testing is a safe and sensitive method that can be used for to confirm or exclude any correlation between abacavir and hypersensitivity skin reactions in patients who have been previously treated with abacavir during HAART. Correlation between patch test, immunohistochimical, and genetic tests results shows that genetic testing increases the possibility to identify patients with a true reaction. © 2012 Wiley Periodicals, Inc.

Abacavir/Lamivudine Versus Tenofovir DF/Emtricitabine as Part of Combination Regimens for Initial Treatment of HIV: Final Results

PubMed Central

Tierney, Camlin; Collier, Ann C.; Daar, Eric S.; Mollan, Katie; Budhathoki, Chakra; Godfrey, Catherine; Jahed, Nasreen C.; Myers, Laurie; Katzenstein, David; Farajallah, Awny; Rooney, James F.; Ha, Belinda; Woodward, William C.; Feinberg, Judith; Tashima, Karen; Murphy, Robert L.; Fischl, Margaret A.

2011-01-01

(See the editorial commentary by Hull and Montaner, on pages 1154–6.) Background. AIDS Clinical Trials Group A5202 compared blinded abacavir/lamivudine (ABC/3TC) to tenofovir DF/emtricitabine (TDF/FTC) with efavirenz (EFV) or atazanavir/ritonavir (ATV/r) in human immunodeficiency virus (HIV)-infected treatment-naive patients, stratified by screening HIV RNA (< or ≥105 copies/mL). Due to higher virologic failure with ABC/3TC in the high HIV RNA stratum, blinded treatment was stopped in this group, but study follow-up continued for all patients. Methods. Primary endpoints were times to virologic failure, regimen modification, and safety event. Results. In the low HIV RNA stratum, time to virologic failure was similar for ABC/3TC vs TDF/FTC with ATV/r (hazard ratio [HR] 1.25, 95% confidence interval [CI] 0.76, 2.05) or EFV (HR 1.23, 95% CI 0.77, 1.96), with significantly shorter times to regimen modification for ABC/3TC with EFV or ATV/r and to safety events with EFV. Prior to stopping blinded treatment in the high stratum, higher virologic failure rates were seen with ABC/3TC with EFV (HR 2.46, 95% CI 1.20, 5.05) or ATV/r (HR 2.22, 95% CI 1.19, 4.14). Conclusions. In the low HIV RNA stratum, times to virologic failure for ABC/3TC or TDF/FTC were not different with EFV or ATV/r. In the high stratum, virologic failure rate was significantly higher for ABC/3TC than for TDF/FTC when given with either EFV or ATV/r. PMID:21917892

An unexpected reaction pathway in the synthesis of the ABCE framework of strychnine-type alkaloids - A multidisciplinary study

NASA Astrophysics Data System (ADS)

Šoral, Michal; Markus, Jozef; Doháňošová, Jana; Šoralová, Stanislava; Dvoranová, Dana; Chyba, Andrej; Moncol, Ján; Berkeš, Dušan; Liptaj, Tibor

2017-01-01

Acid-catalyzed cyclization of spirocyclic 1‧-benzyl-2‧-(prop-2-en-1-yl)spiro[indole-3,3‧-pyrrolidine]-5‧-one (1) was performed. The pentacyclic product of Povarov-like imino-Diels-Alder reaction was isolated in high yield instead of expected tetracyclic aza-Prins intermediate. The unusual exotic alkaloid-type structure of the resulting molecule 2 was unambiguously confirmed by a detailed NMR analysis using a set of 2D NMR spectra including an INADEQUATE experiment. The relative configuration of 2 was predicted from the synthesis mechanism and DFT geometry calculations and independently confirmed using NOESY and residual dipolar coupling (RDC) assisted NMR analysis in stretched crosslinked polystyrene gels. The reversibility of the cycloaddition in aprotic solvents was observed. A new reaction pathway yielding a rare 6-5-5-5 tetracyclic spiroindoline 3 was suggested. The relative configuration within the tetracyclic framework was ultimately proved using Single-crystal X-ray diffraction analysis of compound 4.

Historical environmental change in Africa drives divergence and admixture of Aedes aegypti mosquitoes: a precursor to successful worldwide colonization?

PubMed

Bennett, Kelly Louise; Shija, Fortunate; Linton, Yvonne-Marie; Misinzo, Gerald; Kaddumukasa, Martha; Djouaka, Rousseau; Anyaele, Okorie; Harris, Angela; Irish, Seth; Hlaing, Thaung; Prakash, Anil; Lutwama, Julius; Walton, Catherine

2016-09-01

Increasing globalization has promoted the spread of exotic species, including disease vectors. Understanding the evolutionary processes involved in such colonizations is both of intrinsic biological interest and important to predict and mitigate future disease risks. The Aedes aegypti mosquito is a major vector of dengue, chikungunya and Zika, the worldwide spread of which has been facilitated by Ae. aegypti's adaption to human-modified environments. Understanding the evolutionary processes involved in this invasion requires characterization of the genetic make-up of the source population(s). The application of approximate Bayesian computation (ABC) to sequence data from four nuclear and one mitochondrial marker revealed that African populations of Ae. aegypti best fit a demographic model of lineage diversification, historical admixture and recent population structuring. As ancestral Ae. aegypti were dependent on forests, this population history is consistent with the effects of forest fragmentation and expansion driven by Pleistocene climatic change. Alternatively, or additionally, historical human movement across the continent may have facilitated their recent spread and mixing. ABC analysis and haplotype networks support earlier inferences of a single out-of-Africa colonization event, while a cline of decreasing genetic diversity indicates that Ae. aegypti moved first from Africa to the Americas and then to Asia. ABC analysis was unable to verify this colonization route, possibly because the genetic signal of admixture obscures the true colonization pathway. By increasing genetic diversity and forming novel allelic combinations, divergence and historical admixture within Africa could have provided the adaptive potential needed for the successful worldwide spread of Ae. aegypti. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Weight and lean body mass change with antiretroviral initiation and impact on bone mineral density.

PubMed

Erlandson, Kristine M; Kitch, Douglas; Tierney, Camlin; Sax, Paul E; Daar, Eric S; Tebas, Pablo; Melbourne, Kathleen; Ha, Belinda; Jahed, Nasreen C; McComsey, Grace A

2013-08-24

To compare the effect that initiating different antiretroviral therapy (ART) regimens has on weight, BMI, and lean body mass (LBM) and explore how changes in body composition are associated with bone mineral density (BMD). A5224s was a sub-study of A5202, a prospective trial of 1857 ART-naive participants randomized to blinded abacavir-lamivudine (ABC/3TC) or tenofovir DF-emtricitabine (TDF/FTC) with open-label efavirenz (EFV) or atazanavir-ritonavir (ATV/r). All participants underwent dual-energy absorptiometry (DXA) and abdominal computed tomography for body composition. Analyses used two-sample t-tests and linear regression. A5224s included 269 participants: 85% men, 47% white non-Hispanic, median age 38 years, HIV-1 RNA 4.6 log10 copies/ml, and CD4 cell count 233 cells/μl. Overall, significant gains occurred in weight, BMI, and LBM at 96 weeks post-randomization (all P<0.001). Assignment to ATV/r (vs. EFV) resulted in significantly greater weight (mean difference 3.35 kg) and BMI gain (0.88 kg/m; both P=0.02), but not LBM (0.67 kg; P=0.15), whereas ABC/3TC and TDF/FTC were not significantly different (P≥0.10). In multivariable analysis, only lower baseline CD4 cell count and higher HIV-1 RNA were associated with greater increase in weight, BMI, or LBM. In multivariable analyses, increased LBM was associated with an increased hip BMD. ABC/3TC vs. TDF/FTC did not differ in change in weight, BMI, or LBM; ATV/r vs. EFV resulted in greater weight and BMI gain but not LBM. A positive association between increased LBM and increased hip BMD should be further investigated through prospective interventional studies to verify the impact of increased LBM on hip BMD.

A new model to predict weak-lensing peak counts. II. Parameter constraint strategies

NASA Astrophysics Data System (ADS)

Lin, Chieh-An; Kilbinger, Martin

2015-11-01

Context. Peak counts have been shown to be an excellent tool for extracting the non-Gaussian part of the weak lensing signal. Recently, we developed a fast stochastic forward model to predict weak-lensing peak counts. Our model is able to reconstruct the underlying distribution of observables for analysis. Aims: In this work, we explore and compare various strategies for constraining a parameter using our model, focusing on the matter density Ωm and the density fluctuation amplitude σ8. Methods: First, we examine the impact from the cosmological dependency of covariances (CDC). Second, we perform the analysis with the copula likelihood, a technique that makes a weaker assumption than does the Gaussian likelihood. Third, direct, non-analytic parameter estimations are applied using the full information of the distribution. Fourth, we obtain constraints with approximate Bayesian computation (ABC), an efficient, robust, and likelihood-free algorithm based on accept-reject sampling. Results: We find that neglecting the CDC effect enlarges parameter contours by 22% and that the covariance-varying copula likelihood is a very good approximation to the true likelihood. The direct techniques work well in spite of noisier contours. Concerning ABC, the iterative process converges quickly to a posterior distribution that is in excellent agreement with results from our other analyses. The time cost for ABC is reduced by two orders of magnitude. Conclusions: The stochastic nature of our weak-lensing peak count model allows us to use various techniques that approach the true underlying probability distribution of observables, without making simplifying assumptions. Our work can be generalized to other observables where forward simulations provide samples of the underlying distribution.

The Yersinia pestis Siderophore, Yersiniabactin, and the ZnuABC system both contribute to Zinc acquisition and the development of lethal septicemic plague in mice

PubMed Central

Bobrov, Alexander G.; Kirillina, Olga; Fetherston, Jacqueline D.; Miller, M. Clarke; Burlison, Joseph A.; Perry, Robert D.

2014-01-01

Summary Bacterial pathogens must overcome host sequestration of zinc (Zn2+), an essential micronutrient, during the infectious disease process. While the mechanisms to acquire chelated Zn2+ by bacteria are largely undefined, many pathogens rely upon the ZnuABC family of ABC transporters. Here we show that in Yersinia pestis, irp2, a gene encoding the synthetase (HMWP2) for the siderophore yersiniabactin (Ybt) is required for growth under Zn2+-deficient conditions in a strain lacking ZnuABC. Moreover, growth stimulation with exogenous, purified apo-Ybt provides evidence that Ybt may serve as a zincophore for Zn2+ acquisition. Studies with the Zn2+-dependent transcriptional reporter znuA∷lacZ indicate that the ability to synthesize Ybt affects the levels of intracellular Zn2+. However, the outer membrane receptor Psn and TonB as well as the inner membrane (IM) ABC transporter YbtPQ, that are required for Fe3+ acquisition by Ybt, are not needed for Ybt-dependent Zn2+ uptake. In contrast, the predicted IM protein YbtX, a member of the Major Facilitator Superfamily, was essential for Ybt-dependent Zn2+ uptake. Finally, we show that the ZnuABC system and the Ybt synthetase HMWP2, presumably by Ybt synthesis, both contribute to the development of a lethal infection in a septicemic plague mouse model. PMID:24979062

Unicameral (simple) and aneurysmal bone cysts: the effect of insufficient curettage on recurrence.

PubMed

Çelik, Suat; Uludağ, Abuzer; Tosun, Hacı Bayram; Serbest, Sancar; Gürger, Murat; Kılıç, Sabahattin

2016-01-01

Curettage of the cyst and bone grafting are the most common methods used in the treatment of unicameral bone cysts (UBC) and aneurysmal bone cysts (ABC). Recurrence of these cysts is often associated with insufficient curettage of the cyst during surgery. In this study, we aimed to evaluate the effect of insufficient curettage on recurrence in patients with UBC and ABC. The retrospective study included 18 patients with UBC and 14 patients with ABC that were surgically treated by curettage and bone grafting in our clinic between 2006-2013. Mean age was 19.80 (range, 4-50) years in the patients with UBC and 21.76 (range, 4-56) in the patients with ABC. The diagnosis of the cysts was established both clinically and radiologically. Mean follow-up period was 36 (range, 6-60) months both in the patients with UBC and ABC. The patients with recurrence underwent a second curettage and grafting procedure. Healing and recurrence were evaluated according to modified Neer's scale. Recurrence occurred in 8 patients. Of these, 5 patients underwent a second curettage and grafting procedure and 3 patients were lost to follow-up. Complete healing occurred in all the patients that underwent a second curettage and grafting procedure. The achievement of complete healing in the patients that underwent a second curettage and grafting procedure indicates that the recurrence of UBC and ABC is associated with insufficient curettage.

Knowing the ABCs: A Comparative Effectiveness Study of Two Methods of Diabetes Education

PubMed Central

Naik, Aanand D.; Teal, Cayla R.; Rodriguez, Elisa; Haidet, Paul

2011-01-01

Objective To test an active-learning, empowerment approach to teaching patients about the “diabetes ABCs” (hemoglobin A1C, systolic blood pressure, and low density lipoprotein cholesterol). Methods 84 (97%) diabetic patients who participated in a randomized effectiveness trial of two clinic-based group educational methods and completed a post-intervention assessment. The empowerment arm participated in a group session that incorporated two educational innovations (a conceptual metaphor to foster understanding, and team-based learning methods to foster active learning). The traditional diabetes education arm received a didactic group session focused on self-management and educational materials about the diabetes ABCs. Participants in both arms received individual review of their current ABC values. Results A questionnaire evaluated knowledge, understanding, and recall of the diabetes ABCs was administered three months after enrollment in the study. At three months, participants in the empowerment group demonstrated greater understanding of the diabetes ABCs (P<.0001), greater knowledge of their own values (P<.0001), and greater knowledge of guideline-derived target goals for the ABCs compared with participants in the traditional arm (P<.0001). Conclusion An active-learning, empowerment-based approach applied to diabetes education can lead to greater understanding and knowledge retention. Practice Implications An empowerment approach to education can facilitate informed, activated patients and increase performance of self-management behaviors. PMID:21300516

A Novel Artificial Bee Colony Algorithm Based on Internal-Feedback Strategy for Image Template Matching

PubMed Central

Gong, Li-Gang

2014-01-01

Image template matching refers to the technique of locating a given reference image over a source image such that they are the most similar. It is a fundamental mission in the field of visual target recognition. In general, there are two critical aspects of a template matching scheme. One is similarity measurement and the other is best-match location search. In this work, we choose the well-known normalized cross correlation model as a similarity criterion. The searching procedure for the best-match location is carried out through an internal-feedback artificial bee colony (IF-ABC) algorithm. IF-ABC algorithm is highlighted by its effort to fight against premature convergence. This purpose is achieved through discarding the conventional roulette selection procedure in the ABC algorithm so as to provide each employed bee an equal chance to be followed by the onlooker bees in the local search phase. Besides that, we also suggest efficiently utilizing the internal convergence states as feedback guidance for searching intensity in the subsequent cycles of iteration. We have investigated four ideal template matching cases as well as four actual cases using different searching algorithms. Our simulation results show that the IF-ABC algorithm is more effective and robust for this template matching mission than the conventional ABC and two state-of-the-art modified ABC algorithms do. PMID:24892107

Suppression of c-Myc is involved in multi-walled carbon nanotubes' down-regulation of ATP-binding cassette transporters in human colon adenocarcinoma cells

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

Wang, Zhaojing; Xu, Yonghong; Meng, Xiangning

Over-expression of ATP-binding cassette (ABC) transporters, a large family of integral membrane proteins that decrease cellular drug uptake and accumulation by active extrusion, is one of the major causes of cancer multi-drug resistance (MDR) that frequently leads to failure of chemotherapy. Carbon nanotubes (CNTs)-based drug delivery devices hold great promise in enhancing the efficacy of cancer chemotherapy. However, CNTs' effects on the ABC transporters remain under-investigated. In this study, we found that multiwalled carbon nanotubes (MWCNTs) reduced transport activity and expression of ABC transporters including ABCB1/Pgp and ABCC4/MRP4 in human colon adenocarcinoma Caco-2 cells. Proto-oncogene c-Myc, which directly regulates ABCmore » gene expression, was concurrently decreased in MWCNT-treated cells and forced over-expression of c-Myc reversed MWCNTs' inhibitory effects on ABCB1 and ABCC4 expression. MWCNT-cell membrane interaction and cell membrane oxidative damage were observed. However, antioxidants such as vitamin C, β-mecaptoethanol and dimethylthiourea failed to antagonize MWCNTs' down-regulation of ABC transporters. These data suggest that MWCNTs may act on c-Myc, but not through oxidative stress, to down-regulate ABC transporter expression. Our findings thus shed light on CNTs' novel cellular effects that may be utilized to develop CNTs-based drug delivery devices to overcome ABC transporter-mediated cancer chemoresistance.« less

Using single-case experimental design methodology to evaluate the effects of the ABC method for nursing staff on verbal aggressive behaviour after acquired brain injury.

PubMed

Winkens, Ieke; Ponds, Rudolf; Pouwels, Climmy; Eilander, Henk; van Heugten, Caroline

2014-01-01

The ABC method is a basic and simplified form of behavioural modification therapy for use by nurses. ABC refers to the identification of Antecedent events, target Behaviours, and Consequent events. A single-case experimental AB design was used to evaluate the effects of the ABC method on a woman diagnosed with olivo-ponto-cerebellar ataxia. Target behaviour was verbal aggressive behaviour during ADL care, assessed at 9 time points immediately before implementation of the ABC method and at 36 time points after implementation. A randomisation test showed a significant treatment effect between the baseline and intervention phases (t = .58, p = .03; ES [Nonoverlap All Pairs] = .62). Visual analysis, however, showed that the target behaviour was still present after implementation of the method and that on some days the nurses even judged the behaviour to be more severe than at baseline. Although the target behaviour was still present after treatment, the ABC method seems to be a promising tool for decreasing problem behaviour in patients with acquired brain injury. It is worth investigating the effects of this method in future studies. When interpreting single-subject data, both visual inspection and statistical analysis are needed to determine whether treatment is effective and whether the effects lead to clinically desirable results.

Early Recurrence of a Solid Variant of Aneurysmal Bone Cyst in a Young Child After Resection: Technique and Literature Review and Two-year Follow-up After Corpectomy.

PubMed

Samir Barakat, Ahmed; Alsingaby, Hisham; Shousha, Mootaz; El Saghir, Hesham; Boehm, Heinrich

2018-05-15

Aneurysmal bone cysts (ABCs) are considered to be rare benign tumors that may affect long bones or the vertebral column. Their incidence varies and is reported to be 1.4% of all benign skeletal tumors. The solid-variant aneurysmal bone cyst (S-ABC) is even rarer and constitutes 3.5% to 7% of all vertebral ABCs. We report the case of an Enneking stage 3 S-ABC in a 5-year-old boy at C7 that showed rapid local recurrence after primary excision from posterior and dorsal stabilization requiring ventral corpectomy and posterior excision of the right lateral mass and right posterolateral fusion. Histologic examination disclosed an S-ABC. To our knowledge, this is the first case of S-ABC described in the literature that used both anterior and posterior approaches and complete corpectomy. Over a 2-year period, the patient showed no radiologic or clinical signs of local recurrence with excellent neurologic function. Solid-variant aneurysmal bone cysts are difficult to diagnose and treat, and careful clinical and radiologic assessment should be done to tailor an appropriate surgical plan to prevent recurrence and neurologic sequelae. To the best of our knowledge, there are to date no publications that studied the behavior of this subtype.

Introduction of argon beam coagulation functionality to robotic procedures using the ABC D-Flex probe: equivalency to an existing laparoscopic instrument

NASA Astrophysics Data System (ADS)

Merchel, Renée. A.; Barnes, Kelli S.; Taylor, Kenneth D.

2015-03-01

INTRODUCTION: The ABC® D-Flex Probe utilizes argon beam coagulation (ABC) technology to achieve hemostasis during minimally invasive surgery. A handle on the probe allows for integration with robotic surgical systems and introduces ABC to the robotic toolbox. To better understand the utility of D-Flex, this study compares the performance of the D-Flex probe to an existing ABC laparoscopic probe through ex vivo tissue analysis. METHODS: Comparisons were performed to determine the effect of four parameters: ABC device, tissue type, activation duration, and distance from tissue. Ten ABC D-Flex probes were used to create 30 burn samples for each comparison. Ex vivo bovine liver and porcine muscle were used as tissue models. The area and depth of each burn was measured using a light microscope. The resulting dimensional data was used to correlate tissue effect with each variable. RESULTS: D-Flex created burns which were smaller in surface area than the laparoscopic probe at all power levels. Additionally, D-Flex achieved thermal penetration levels equivalent to the laparoscopic probe. CONCLUSION: D-Flex implements a small 7F geometry which creates a more focused beam. When used with robotic precision, quick localized superficial hemostasis can be achieved with minimal collateral damage. Additionally, D-Flex achieved equivalent thermal penetration levels at lower power and argon flow-rate settings than the laparoscopic probe.

Low levels of graphene and graphene oxide inhibit cellular xenobiotic defense system mediated by efflux transporters.

PubMed

Liu, Su; Jiang, Wei; Wu, Bing; Yu, Jing; Yu, Haiyan; Zhang, Xu-Xiang; Torres-Duarte, Cristina; Cherr, Gary N

2016-01-01

Low levels of graphene and graphene oxide (GO) are considered to be environmentally safe. In this study, we analyzed the potential effects of graphene and GO at relatively low concentrations on cellular xenobiotic defense system mediated by efflux transporters. The results showed that graphene (<0.5 μg/mL) and GO (<20 μg/mL) did not decrease cell viability, generate reactive oxygen species, or disrupt mitochondrial function. However, graphene and GO at the nontoxic concentrations could increase calcein-AM (CAM, an indicator of membrane ATP-binding cassette (ABC) transporter) activity) accumulation, indicating inhibition of ABC transporters' efflux capabilities. This inhibition was observed even at 0.005 μg/mL graphene and 0.05 μg/mL GO, which are 100 times and 400 times lower than their lowest toxic concentration from cytotoxicity experiments, respectively. The inhibition of ABC transporters significantly increased the toxicity of paraquat and arsenic, known substrates of ABC transporters. The inhibition of ABC transporters was found to be based on graphene and GO damaging the plasma membrane structure and fluidity, thus altering functions of transmembrane ABC transporters. This study demonstrates that low levels of graphene and GO are not environmentally safe since they can significantly make cell more susceptible to other xenobiotics, and this chemosensitizing activity should be considered in the risk assessment of graphene and GO.

Sustainable urban stormwater management in the tropics: An evaluation of Singapore's ABC Waters Program

NASA Astrophysics Data System (ADS)

Lim, H. S.; Lu, X. X.

2016-07-01

The Active Beautiful Clean (ABC) Waters Program was implemented in 2006 as part of Singapore's stormwater management strategy and reflects the country's move towards Water Sensitive Urbanism through the adoption of Low-Impact Development (LID) ideology and practices. It is the first holistic and comprehensive LID program in the tropics and holds promise for extension to other tropical cities. This paper presents a comprehensive summary of the goals, LID practices (ABC design features) and design considerations as well as results of several monitored sites, including a constructed wetland, two rain gardens, green roofs and three canal restoration projects. We evaluate the ABC Waters Program based on these initial results and consider the challenges, issues and the research needs for it to meet its hydrological and water quality remediation goals. So far, the ABC design features evaluated perform well in removing particulates. Performance in nutrient removal is poor. With over 60 projects completed within 10 years, post-project monitoring and evaluation is necessary and complements on-going laboratory and modelling research projects conducted by local academic institutions.

Simulated sugar factory wastewater remediation kinetics using algal-bacterial raceway reactor promoted by polyacrylate polyalcohol.

PubMed

Memon, Abdul Rehman; Andresen, John; Habib, Muddasar; Jaffar, Muhammad

2014-04-01

The remediation kinetics of simulated sugar factory wastewater (SFW) using an algal-bacterial culture (ABC) of Chlorella vulgaris in association with Pseudomonas putida in a raceway reactor was found to be enhanced by 89% with the addition of 80ppm of copolymer Polyacrylate polyalcohol (PAPA). This was achieved by efficient suspension of the ABC throughout the water body maintaining optimum pH and dissolved oxygen that led to rapid COD removal and improved algal biomass production. The suspension of the ABC using the co-polymer PAPA maintained a DO of 8-10mgl(-1) compared to 2-3mgl(-1) when not suspended. As a result, the non-suspended ABC only achieved a 50% reduction in COD after 96h compared to a 89% COD removal using 80ppm PAPA suspension. In addition, the algae biomass increased from 0.4gl(-1)d(-1) for the non-suspended ABC to 1.1gl(-1)d(-1) when suspended using 80ppm PAPA. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular Characterization of Feline Infectious Peritonitis Virus Strain DF-2 and Studies of the Role of ORF3abc in Viral Cell Tropism

PubMed Central

Farsang, Attila; Zádori, Zoltán; Hornyák, Ákos; Dencső, László; Almazán, Fernando; Enjuanes, Luis; Belák, Sándor

2012-01-01

The full-length genome of the highly lethal feline infectious peritonitis virus (FIPV) strain DF-2 was sequenced and cloned into a bacterial artificial chromosome (BAC) to study the role of ORF3abc in the FIPV-feline enteric coronavirus (FECV) transition. The reverse genetic system allowed the replacement of the truncated ORF3abc of the original FIPV DF-2 genome with the intact ORF3abc of the canine coronavirus (CCoV) reference strain Elmo/02. The in vitro replication kinetics of these two viruses was studied in CrFK and FCWF-4 cell lines, as well as in feline peripheral blood monocytes. Both viruses showed similar replication kinetics in established cell lines. However, the strain with a full-length ORF3 showed markedly lower replication of more than 2 log10 titers in feline peripheral blood monocytes. Our results suggest that the truncated ORF3abc plays an important role in the efficient macrophage/monocyte tropism of type II FIPV. PMID:22438554

Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective.

PubMed

Greene, Nicholas P; Kaplan, Elise; Crow, Allister; Koronakis, Vassilis

2018-01-01

The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking.

ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes.

PubMed

Fichant, Gwennaele; Basse, Marie-Jeanne; Quentin, Yves

2006-03-01

The ATP-binding cassette (ABC) transporters are one of the major classes of active transporters. They are widespread in archaea, bacteria, and eukaryota, indicating that they have arisen early in evolution. They are involved in many essential physiological processes, but the majority import or export a wide variety of compounds across cellular membranes. These systems share a common architecture composed of four (exporters) or five (importers) domains. To identify and reconstruct functional ABC transporters encoded by archaeal and bacterial genomes, we have developed a bioinformatic strategy. Cross-reference to the transport classification system is used to predict the type of compound transported. A high quality of annotation is achieved by manual verification of the predictions. However, in order to face the rapid increase in the number of published genomes, we also include analyses of genomes issuing directly from the automated strategy. Querying the database (http://www-abcdb.biotoul.fr) allows to easily retrieve ABC transporter repertories and related data. Additional query tools have been developed for the analysis of the ABC family from both functional and evolutionary perspectives.

In vitro methanol production from methyl coenzyme M using the Methanosarcina barkeri MtaABC protein complex.

PubMed

Dong, Ming; Gonzalez, Tara D; Klems, Meghan M; Steinberg, Lisa M; Chen, Wilfred; Papoutsakis, Eleftherios T; Bahnson, Brian J

2017-09-01

Methanol:coenzyme M methyltransferase is an enzyme complex composed of three subunits, MtaA, MtaB, and MtaC, found in methanogenic archaea and is needed for their growth on methanol ultimately producing methane. MtaABC catalyzes the energetically favorable methyl transfer from methanol to coenzyme M to form methyl coenzyme M. Here we demonstrate that this important reaction for possible production of methanol from the anaerobic oxidation of methane can be reversed in vitro. To this effect, we have expressed and purified the Methanosarcina barkeri MtaABC enzyme, and developed an in vitro functional assay that demonstrates MtaABC can catalyze the energetically unfavorable (ΔG° = 27 kJ/mol) reverse reaction starting from methyl coenzyme M and generating methanol as a product. Demonstration of an in vitro ability of MtaABC to produce methanol may ultimately enable the anaerobic oxidation of methane to produce methanol and from methanol alternative fuel or fuel-precursor molecules. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1243-1249, 2017. © 2017 American Institute of Chemical Engineers.

Iowa ABC connections.

DOT National Transportation Integrated Search

2015-06-01

For several years the Iowa Department of Transportation (DOT), Iowa State University, the Federal Highway Administration, : and several Iowa counties have been working to develop accelerated bridge construction (ABC) concepts, details, and processes....

How can activity-based costing methodology be performed as a powerful tool to calculate costs and secure appropriate patient care?

PubMed

Lin, Blossom Yen-Ju; Chao, Te-Hsin; Yao, Yuh; Tu, Shu-Min; Wu, Chun-Ching; Chern, Jin-Yuan; Chao, Shiu-Hsiung; Shaw, Keh-Yuong

2007-04-01

Previous studies have shown the advantages of using activity-based costing (ABC) methodology in the health care industry. The potential values of ABC methodology in health care are derived from the more accurate cost calculation compared to the traditional step-down costing, and the potentials to evaluate quality or effectiveness of health care based on health care activities. This project used ABC methodology to profile the cost structure of inpatients with surgical procedures at the Department of Colorectal Surgery in a public teaching hospital, and to identify the missing or inappropriate clinical procedures. We found that ABC methodology was able to accurately calculate costs and to identify several missing pre- and post-surgical nursing education activities in the course of treatment.

50 CFR 622.389 - Adjustment of management measures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... biological catch (ABC) and ABC control rules, rebuilding plans, sale and purchase restrictions, transfer at sea provisions, and restrictions relative to conditions of harvested fish (maintaining fish in whole...

Overexpression of Both ERG11 and ABC2 Genes Might Be Responsible for Itraconazole Resistance in Clinical Isolates of Candida krusei

PubMed Central

He, Xiaoyuan; Zhao, Mingfeng; Chen, Jinyan; Wu, Rimao; Zhang, Jianlei; Cui, Rui; Jiang, Yanyu; Chen, Jie; Cao, Xiaoli; Xing, Yi; Zhang, Yuchen; Meng, Juanxia; Deng, Qi; Sui, Tao

2015-01-01

Objective To study the main molecular mechanisms responsible for itraconazole resistance in clinical isolates of Candida krusei. Methods The 14α-demethylases encoded by ERG11 gene in the 16 C.krusei clinical isolates were amplified by polymerase chain reaction (PCR), and their nucleotide sequences were determined to detect point mutations. Meanwhile, ERG11 and efflux transporters (ABC1 and ABC2) genes were determined by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) for their expression in itraconazole-resistant (R), itraconazole-susceptible dose dependent (SDD) and itraconazole-susceptible (S) C.krusei at the mRNA level. Results We found 7-point mutations in ERG11 gene of all the C.krusei clinical isolates, including 6 synonymous mutations and 1 missense mutation (C44T). However, the missense mutation was found in the three groups. The mRNA levels of ERG11 gene in itraconazole-resistant isolates showed higher expression compared with itraconazole-susceptible dose dependent and itraconazole-susceptible ones (P = 0.015 and P = 0.002 respectively). ABC2 gene mRNA levels in itraconazole-resistant group was significantly higher than the other two groups, and the levels of their expression in the isolates appeared to increase with the decrease of susceptibility to itraconazole (P = 0.007 in SDD compared with S, P = 0.016 in SDD with R, and P<0.001 in S with R respectively). While ABC1 gene presented lower expression in itraconazole resistant strains. However, the mRNA levels of ERG11, ABC1 and ABC2 in a C.krusei (CK10) resistant to both itraconazole and voriconazole were expressed highest in all the itraconazole-resistant isolates. Conclusions There are ERG11 gene polymorphisms in clinical isolates of C.krusei. ERG11 gene mutations may not be involved in the development of itraconazole resistance in C.krusei. ERG11 and ABC2 overexpression might be responsible for the acquired itraconazole resistance of these clinical isolates. PMID:26308936

Tolerance to quaternary ammonium compound disinfectants may enhance growth of Listeria monocytogenes in the food industry.

PubMed

Møretrø, Trond; Schirmer, Bjørn C T; Heir, Even; Fagerlund, Annette; Hjemli, Pernille; Langsrud, Solveig

2017-01-16

The antibacterial effect of disinfectants is crucial for the control of Listeria monocytogenes in food processing environments. Tolerance of L. monocytogenes to sublethal levels of disinfectants based on quaternary ammonium compounds (QAC) is conferred by the resistance determinants qacH and bcrABC. The presence and distribution of these genes have been anticipated to have a role in the survival and growth of L. monocytogenes in food processing environments where QAC based disinfectants are in common use. In this study, a panel of 680 L. monocytogenes from nine Norwegian meat- and salmon processing plants were grouped into 36 MLVA profiles. The presence of qacH and bcrABC was determined in 101 isolates from the 26 most common MLVA profiles. Five MLVA profiles contained qacH and two contained bcrABC. Isolates with qacH and bcrABC showed increased tolerance to the QAC Benzalkonium chloride (BC), with minimal inhibitory concentrations (MICs) of 5-12, 10-13 and <5ppm for strains with qacH (two allele variants observed), bcrABC, and neither gene, respectively. Isolates with qacH or bcrABC were not more tolerant to BC in bactericidal tests in suspension or in biofilms compared with isolates lacking the genes. Water residue samples collected from surfaces in meat processing plants after QAC disinfection had bactericidal effect against L. monocytogenes when the sample BC levels were high (>100ppm). A sample with lower BC concentrations (14ppm of chain length C-12 and 2.7ppm of chain length C-14) inhibited growth of L. monocytogenes not containing bcrABC or qacH, compared to strains with these genes. The study has shown that L. monocytogenes harbouring the QAC resistance genes qacH and bcrABC are prevalent in the food industry and that residuals of QAC may be present in concentrations after sanitation in the industry that result in a growth advantage for bacteria with such resistance genes. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

HLA-B*57:01 allele prevalence in HIV-infected North American subjects and the impact of allele testing on the incidence of abacavir-associated hypersensitivity reaction in HLA-B*57:01-negative subjects.

PubMed

Small, Catherine Butkus; Margolis, David A; Shaefer, Mark S; Ross, Lisa L

2017-04-11

The presence of the HLA-B*57:01 allele in HIV-infected subjects is associated with a higher risk of abacavir-associated hypersensitivity reaction (ABC HSR). HLA-B*57:01 allele prevalence varies in different populations, but HLA-B*57:01 testing with immunological confirmation has had a negative predictive value for ABC HSR between 97 and 100%. In the ASSURE study (EPZ113734), the HLA-B*57:01 prevalence in virologically suppressed, antiretroviral treatment-experienced, HIV-infected subjects from the United States, including Puerto Rico, was assessed. Three hundred eighty-five subjects were screened; 13 were HLA-B*57:01 positive and 372 were negative. Only HLA-B*57:01-negative, abacavir-naive subjects were eligible to enroll into the ASSURE trial. Eleven of the 13 subjects who possessed the HLA-B*57:01 allele were white, the other 2 were African-American. There was no geographic clustering of HLA-B*57:01-positive subjects, and the incidence correlated roughly with those states with the greatest numbers of subjects screened. Similarly, there was no statistically significant correlation between subjects who possessed or lacked the allele and age, gender, ethnicity or CD4+ T-cell numbers. The incidence of ABC HSR following abacavir initiation was also evaluated. Only 1 of 199 HLA-B*57:01-negative subjects (an African-American male) randomized to receive abacavir-containing treatment developed symptoms consistent with suspected ABC HSR; ABC HSR was not immunologically confirmed. These findings confirm the utility of HLA-B*57:01 allele testing to reduce the frequency of ABC HSR. The prevalence of HLA-B*57:01 positivity was higher in white than in African-American subjects. In HLA-B*57:01-negative subjects, suspected ABC HSR is very rare, but should lead to discontinuation of abacavir when ABC HSR cannot be definitively excluded from the differential diagnosis. The ASSURE (EPZ113734) study was registered on ClinicalTrials.gov registration on April 8th 2010 and the registration number is NCT01102972.

Characterization and expression profiling of ATP-binding cassette transporter genes in the diamondback moth, Plutella xylostella (L.).

PubMed

Qi, Weiping; Ma, Xiaoli; He, Weiyi; Chen, Wei; Zou, Mingmin; Gurr, Geoff M; Vasseur, Liette; You, Minsheng

2016-09-27

ATP-binding cassette (ABC) transporters are one of the major transmembrane protein families found in all organisms and play important roles in transporting a variety of compounds across intra and extra cellular membranes. In some species, ABC transporters may be involved in the detoxification of substances such as insecticides. The diamondback moth, Plutella xylostella (L.), a destructive pest of cruciferous crops worldwide, is an important species to study as it is resistant to many types of insecticides as well as biological control Bacillus thuringiensis toxins. A total of 82 ABC genes were identified from our published P. xylostella genome, and grouped into eight subfamilies (ABCA-H) based on phylogenetic analysis. Genes of subfamilies ABCA, ABCC and ABCH were found to be expanded in P. xylostella compared with those in Bombyx mori, Manduca sexta, Heliconius melpomene, Danaus plexippus, Drosophila melanogaster, Tetranychus urticae and Homo sapiens. Phylogenetic analysis indicated that many of the ABC transporters in P. xylostella are orthologous to the well-studied ABC transporter genes in the seven other species. Transcriptome- and qRT-PCR-based analysis elucidated physiological effects of ABC gene expressions of P. xylostella which were developmental stage- and tissue-specific as well as being affected by whether or not the insects were from an insecticide-resistant strain. Two ABCC and one ABCA genes were preferentially expressed in midgut of the 4th-instar larvae of a susceptible strain (Fuzhou-S) suggesting their potential roles in metabolizing plant defensive chemicals. Most of the highly expressed genes in insecticide-resistant strains were also predominantly expressed in the tissues of Malpighian tubules and midgut. This is the most comprehensive study on identification, characterization and expression profiling of ABC transporter genes in P. xylostella to date. The diversified features and expression patterns of this gene family may be associated with the evolutionary capacity of this species to develop resistance to a wide range of insecticides and biological toxins. Our findings provide a solid foundation for future functional studies on specific ABC transporter genes in P. xylostella, and for further understanding of their physiological roles and regulatory pathways in insecticide resistance.

Investigation of the quaternary structure of an ABC transporter in living cells using spectrally resolved resonance energy transfer

NASA Astrophysics Data System (ADS)

Singh, Deo Raj

Forster resonance energy transfer (FRET) has become an important tool to study proteins inside living cells. It has been used to explore membrane protein folding and dynamics, determine stoichiometry and geometry of protein complexes, and measure the distance between two molecules. In this dissertation, we use a method based on FRET and optical micro-spectroscopy (OptiMiS) technology, developed in our lab, to probe the structure of dynamic (as opposed to static) protein complexes in living cells. We use this method to determine the association stoichiometry and quaternary structure of an ABC transporter in living cells. Specifically, the transporter we investigate originates from the pathogen Pseudomonas aeruginosa, which is a Gram-negative bacterium with several virulence factors, lipopolysaccharides being one of them. This pathogen coexpresses two unique forms of lipopolysaccharides on its surface, the A- and B-bands. The A-band polysaccharides, synthesized in the cytoplasm, are translocated into the periplasm through an ATP-binding-cassette (ABC) transporter consisting of a transmembranar protein, Wzm, and a nucleotide-binding protein, Wzt. In P. aeruginosa, all of the biochemical studies of A-band LPS are concentrated on the stages of the synthesis and ligation of polysaccharides (PSs), leaving the export stage involving ABC transporter unexplored. The mode of PS export through ABC transporters is still unknown. This difficulty is due to the lack of information about sub-unit composition and structure of this bi-component ABC transporter. Using the FRET-OptiMiS combination method developed by our lab, we found that Wzt forms a rhombus-shaped homo-tetramer which becomes a square upon co-expression with Wzm, and that Wzm forms a square-shaped homo-tetramer both in the presence and absence of Wzt. Based on these results, we propose a structural model for the double-tetramer complex formed by the bi-component ABC transporter in living cells. An understanding of the structure and behavior of this ABC transporter will help develop antibiotics targeting the biosynthesis of the A-band LPS endotoxin.

Bone-bonding behavior of alumina bead composite.

PubMed

Shinzato, S; Kobayashi, M; Choju, K; Kokubo, T; Nakamura, T

1999-08-01

Previously we developed an alumina bead composite (ABC) consisting of alumina bead powder (AL-P) and bisphenol-alpha-glycidyl methacrylate (Bis-GMA)-based resin and reported its excellent osteoconductivity in rat tibiae. In the present study, are evaluated histologically and mechanically the effect of alumina crystallinity on the osteoconductivity and bone-bonding strength of the composite. AL-P was manufactured by fusing crushed alpha-alumina powder and quenching it. The AL-P was composed mainly of amorphous and delta-crystal phases of alumina. Its average particle size was 3.5 microm, and it took a spherical form. Another composite (alpha ALC), filled with pure alpha-alumina powder (alpha AL-P), was used as a referential material. The proportion of powder added to each composite was 70% w/w. Mechanical testing of ABC and alpha ALC indicated that they would be strong enough for use under weight-bearing conditions. The affinity indices for ABC, determined using male Wistar rat tibiae, were significantly higher than those for alpha ALC (p < 0.0001) up to 8 weeks. Composite plates (15 x 10 x 2 mm) that had an uncured surface layer on one side were made in situ in a rectangular mold. One of the plates was implanted into the proximal metaphysis of the tibia of a male Japanese white rabbit, and the failure load was measured by a detaching test 10 weeks after implantation. The failure loads for ABC on its uncured surface [1.91+/-1.23 kgf (n = 8)] were significantly higher than those for alpha ALC on its uncured surface [0.35+/-0.33 kgf (n = 8); (p < 0.0001)], and they also were significantly higher than those for ABC on the other (cured surface) side (p < 0.0001). Histological examinations using rabbit tibiae revealed bone ingrowth into the composite only on the uncured surface of ABC. This study revealed that the amorphous phase of alumina and formation of an uncured surface layer are needed for the osteoconductive and bone-bonding ability of ABC. ABC shows promise as a basis for the development of a highly osteoconductive and mechanically strong biomaterial.

Utilizing Expert Knowledge in Estimating Future STS Costs

NASA Technical Reports Server (NTRS)

Fortner, David B.; Ruiz-Torres, Alex J.

2004-01-01

A method of estimating the costs of future space transportation systems (STSs) involves classical activity-based cost (ABC) modeling combined with systematic utilization of the knowledge and opinions of experts to extend the process-flow knowledge of existing systems to systems that involve new materials and/or new architectures. The expert knowledge is particularly helpful in filling gaps that arise in computational models of processes because of inconsistencies in historical cost data. Heretofore, the costs of planned STSs have been estimated following a "top-down" approach that tends to force the architectures of new systems to incorporate process flows like those of the space shuttles. In this ABC-based method, one makes assumptions about the processes, but otherwise follows a "bottoms up" approach that does not force the new system architecture to incorporate a space-shuttle-like process flow. Prototype software has been developed to implement this method. Through further development of software, it should be possible to extend the method beyond the space program to almost any setting in which there is a need to estimate the costs of a new system and to extend the applicable knowledge base in order to make the estimate.

ATP-Binding Cassette Proteins: Towards a Computational View of Mechanism

NASA Astrophysics Data System (ADS)

Liao, Jielou

2004-03-01

Many large machine proteins can generate mechanical force and undergo large-scale conformational changes (LSCC) to perform varying biological tasks in living cells by utilizing ATP. Important examples include ATP-binding cassette (ABC) transporters. They are membrane proteins that couple ATP binding and hydrolysis to the translocation of substrates across membranes [1]. To interpret how the mechanical force generated by ATP binding and hydrolysis is propagated, a coarse-grained ATP-dependent harmonic network model (HNM) [2,3] is applied to the ABC protein, BtuCD. This protein machine transports vitamin B12 across membranes. The analysis shows that subunits of the protein move against each other in a concerted manner. The lowest-frequency modes of the BtuCD protein are found to link the functionally critical domains, and are suggested to be responsible for large-scale ATP-coupled conformational changes. [1] K. P. Locher, A. T. Lee and D. C. Rees. Science 296, 1091-1098 (2002). [2] Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. Biophys. J. 80, 505-515(2002); M. M Tirion, Phys. Rev. Lett. 77, 1905-1908 (1996). [3] J. -L. Liao and D. N. Beratan, 2003, to be published.

A comparative study of an ABC and an artificial absorber for truncating finite element meshes

NASA Technical Reports Server (NTRS)

Oezdemir, T.; Volakis, John L.

1993-01-01

The type of mesh termination used in the context of finite element formulations plays a major role on the efficiency and accuracy of the field solution. The performance of an absorbing boundary condition (ABC) and an artificial absorber (a new concept) for terminating the finite element mesh was evaluated. This analysis is done in connection with the problem of scattering by a finite slot array in a thick ground plane. The two approximate mesh truncation schemes are compared with the exact finite element-boundary integral (FEM-BI) method in terms of accuracy and efficiency. It is demonstrated that both approximate truncation schemes yield reasonably accurate results even when the mesh is extended only 0.3 wavelengths away from the array aperture. However, the artificial absorber termination method leads to a substantially more efficient solution. Moreover, it is shown that the FEM-BI method remains quite competitive with the FEM-artificial absorber method when the FFT is used for computing the matrix-vector products in the iterative solution algorithm. These conclusions are indeed surprising and of major importance in electromagnetic simulations based on the finite element method.

The ABCs of Sex Ed.

ERIC Educational Resources Information Center

Sroka, Stephen R.

2002-01-01

Cites statistics on extent of sexually transmitted diseases and pregnancies among adolescents; describes ideological dispute over how to teach sex education; advocates teaching the ABCs of sex education: Abstinence, Be Monogamous, and Condoms. (PKP)

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

Mittauer, Kathryn E.; Deraniyagala, Rohan; Li, Jonathan G.

Purpose: Recent knowledge on the effects of cardiac toxicity warrants greater precision for left-sided breast radiotherapy. Different breath-hold (BH) maneuvers (abdominal vs thoracic breathing) can lead to chest wall positional variations, even though the patient’s tidal volume remains consistent. This study aims to investigate the feasibility of using optical tracking for real-time quality control of active breathing coordinator (ABC)-assisted deep inspiration BH (DIBH). Methods: An in-house optical tracking system (OTS) was used to monitor ABC-assisted DIBH. The stability and localization accuracy of the OTS were assessed with a ball-bearing phantom. Seven patients with left-sided breast cancer were included. A free-breathingmore » (FB) computed tomography (CT) scan and an ABC-assisted BH CT scan were acquired for each patient. The OTS tracked an infrared (IR) marker affixed over the patient’s xiphoid process to measure the positional variation of each individual BH. Using the BH within which the CT scan was performed as the reference, the authors quantified intra- and interfraction BH variations for each patient. To estimate the dosimetric impact of BH variations, the authors studied the positional correlation between the marker and the left breast using the FB CT and BH CT scans. The positional variations of 860 BHs as measured by the OTS were retrospectively incorporated into the original treatment plans to evaluate their dosimetric impact on breast and cardiac organs [heart and left anterior descending (LAD) artery]. Results: The stability and localization accuracy of the OTS was within 0.2 mm along each direction. The mean intrafraction variation among treatment BHs was less than 2.8 mm in all directions. Up to 12.6 mm anteroposterior undershoot, where the patient’s chest wall displacement of a BH is less than that of a reference BH, was observed with averages of 4.4, 3.6, and 0.1 mm in the anteroposterior, craniocaudal, and mediolateral directions, respectively. A high positional correlation between the marker and the breast was found in the anteroposterior and craniocaudal directions with respective Pearson correlation values of 0.95 and 0.93, but no mediolateral correlation was found. Dosimetric impact of BH variations on breast coverage was negligible. However, the mean heart dose, mean LAD dose, and max LAD dose were estimated to increase from 1.4/7.4/18.6 Gy (planned) to 2.1/15.7/31.0 Gy (delivered), respectively. Conclusions: In ABC-assisted DIBH, large positional variation can occur in some patients, due to their different BH maneuvers. The authors’ study has shown that OTS can be a valuable tool for real-time quality control of ABC-assisted DIBH.« less

Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris).

PubMed

Cornille, A; Salcedo, A; Kryvokhyzha, D; Glémin, S; Holm, K; Wright, S I; Lascoux, M

2016-01-01

Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids. © 2015 John Wiley & Sons Ltd.

Sam Donaldson: Tips From a Cancer Survivor

MedlinePlus

... Home Current Issue Past Issues Special Section Sam Donaldson: Tips From a Cancer Survivor Past Issues / Spring ... courtesy of ABC News For 40 years, Sam Donaldson has worked for ABC News, reporting from virtually ...

Step 2: Know Your Diabetes ABCs

MedlinePlus

... please turn JavaScript on. Feature: Type 2 Diabetes Step 2: Know Your Diabetes ABCs Past Issues / Fall ... 2 Diabetes" Articles Diabetes Is Serious But Manageable / Step 1: Learn About Diabetes / Step 2: Know Your ...

An improved artificial bee colony algorithm based on balance-evolution strategy for unmanned combat aerial vehicle path planning.

PubMed

Li, Bai; Gong, Li-gang; Yang, Wen-lun

2014-01-01

Unmanned combat aerial vehicles (UCAVs) have been of great interest to military organizations throughout the world due to their outstanding capabilities to operate in dangerous or hazardous environments. UCAV path planning aims to obtain an optimal flight route with the threats and constraints in the combat field well considered. In this work, a novel artificial bee colony (ABC) algorithm improved by a balance-evolution strategy (BES) is applied in this optimization scheme. In this new algorithm, convergence information during the iteration is fully utilized to manipulate the exploration/exploitation accuracy and to pursue a balance between local exploitation and global exploration capabilities. Simulation results confirm that BE-ABC algorithm is more competent for the UCAV path planning scheme than the conventional ABC algorithm and two other state-of-the-art modified ABC algorithms.

A test of the ABC model underlying rational emotive behavior therapy.

PubMed

Ziegler, Daniel J; Leslie, Yvonne M

2003-02-01

The ABC model underlying Ellis's Rational Emotive Behavior Therapy predicts that people who think more irrationally should respond to daily stressors or hassles differently than do people who think less irrationally. This study tested this aspect of the ABC model. 192 college students were administered the Survey of Personal Beliefs and the Hassles Scale to measure irrational thinking and daily hassles, respectively. Students who scored higher on overall irrational thinking reported a significantly higher frequency of hassles than did those who scored lower on overall irrational thinking, while students who scored higher on awfulizing and low frustration tolerance reported a significantly greater intensity of hassles than did those who scored lower on awfulizing and low frustration tolerance. This indicates support for the ABC model, especially Ellis's construct of irrational beliefs central to this model.

eUnaG: a new ligand-inducible fluorescent reporter to detect drug transporter activity in live cells

PubMed Central

Yeh, Johannes T.-H.; Nam, Kwangho; Yeh, Joshua T.-H.; Perrimon, Norbert

2017-01-01

The absorption, distribution, metabolism and excretion (ADME) of metabolites and toxic organic solutes are orchestrated by the ATP-binding cassette (ABC) transporters and the organic solute carrier family (SLC) proteins. A large number of ABC and SLC transpoters exist; however, only a small number have been well characterized. To facilitate the analysis of these transporters, which is important for drug safety and physiological studies, we developed a sensitive genetically encoded bilirubin (BR)-inducible fluorescence sensor (eUnaG) to detect transporter-coupled influx/efflux of organic compounds. This sensor can be used in live cells to measure transporter activity, as excretion of BR depends on ABC and SLC transporters. Applying eUnaG in functional RNAi screens, we characterize l(2)03659 as a Drosophila multidrug resistant-associated ABC transporter. PMID:28176814

The Yersinia pestis siderophore, yersiniabactin, and the ZnuABC system both contribute to zinc acquisition and the development of lethal septicaemic plague in mice.

PubMed

Bobrov, Alexander G; Kirillina, Olga; Fetherston, Jacqueline D; Miller, M Clarke; Burlison, Joseph A; Perry, Robert D

2014-08-01

Bacterial pathogens must overcome host sequestration of zinc (Zn(2+) ), an essential micronutrient, during the infectious disease process. While the mechanisms to acquire chelated Zn(2+) by bacteria are largely undefined, many pathogens rely upon the ZnuABC family of ABC transporters. Here we show that in Yersinia pestis, irp2, a gene encoding the synthetase (HMWP2) for the siderophore yersiniabactin (Ybt) is required for growth under Zn(2+) -deficient conditions in a strain lacking ZnuABC. Moreover, growth stimulation with exogenous, purified apo-Ybt provides evidence that Ybt may serve as a zincophore for Zn(2+) acquisition. Studies with the Zn(2+) -dependent transcriptional reporter znuA::lacZ indicate that the ability to synthesize Ybt affects the levels of intracellular Zn(2+) . However, the outer membrane receptor Psn and TonB as well as the inner membrane (IM) ABC transporter YbtPQ, which are required for Fe(3+) acquisition by Ybt, are not needed for Ybt-dependent Zn(2+) uptake. In contrast, the predicted IM protein YbtX, a member of the Major Facilitator Superfamily, was essential for Ybt-dependent Zn(2+) uptake. Finally, we show that the ZnuABC system and the Ybt synthetase HMWP2, presumably by Ybt synthesis, both contribute to the development of a lethal infection in a septicaemic plague mouse model. © 2014 John Wiley & Sons Ltd.

The promise--and peril--of integrated cost systems.

PubMed

Cooper, R; Kaplan, R S

1998-01-01

Recent advances in managerial accounting have helped executives get the information they need to make good strategic decisions. But today's enterprise resource planning systems promise even greater benefits--the chance to integrate activity-based costing, operational-control, and financial reporting systems. But managers need to approach integration very thoughtfully, or they could end up with a system that drives decision making in the wrong direction. Operational-control and ABC systems have fundamentally different purposes. Their requirements for accuracy, timeliness, and aggregation are so different that no single, fully integrated approach can be adequate for both purposes. If an integrated system used real-time cost data instead of standard rates in its ABC subsystem, for example, the result would be dangerously distorted messages about individual product profitability--and that's precisely the problem ABC systems were originally designed to address. Proper linkage and feedback between the two systems is possible, however. Through activity-based budgeting, the ABC system is linked directly to operations control: managers can determine the supply and practical capacity of resources in forthcoming periods. Linking operational control to ABC is also possible. The activity-based portion of an operational control system collects information that, while it mustn't be fed directly into the activity-based strategic cost system, can be extremely useful once it's been properly analyzed. Finally, ABC and operational control can be linked to financial reporting to generate cost of goods sold and inventory valuations--but again, with precautions.

Unicameral (simple) and aneurysmal bone cysts: the effect of insufficient curettage on recurrence

PubMed Central

Çelik, Suat; Uludağ, Abuzer; Tosun, Hacı Bayram; Serbest, Sancar; Gürger, Murat; Kılıç, Sabahattin

2016-01-01

Introduction Curettage of the cyst and bone grafting are the most common methods used in the treatment of unicameral bone cysts (UBC) and aneurysmal bone cysts (ABC). Recurrence of these cysts is often associated with insufficient curettage of the cyst during surgery. In this study, we aimed to evaluate the effect of insufficient curettage on recurrence in patients with UBC and ABC. Methods The retrospective study included 18 patients with UBC and 14 patients with ABC that were surgically treated by curettage and bone grafting in our clinic between 2006-2013. Mean age was 19.80 (range, 4-50) years in the patients with UBC and 21.76 (range, 4-56) in the patients with ABC. The diagnosis of the cysts was established both clinically and radiologically. Mean follow-up period was 36 (range, 6-60) months both in the patients with UBC and ABC. The patients with recurrence underwent a second curettage and grafting procedure. Healing and recurrence were evaluated according to modified Neer's scale. Results Recurrence occurred in 8 patients. Of these, 5 patients underwent a second curettage and grafting procedure and 3 patients were lost to follow-up. Complete healing occurred in all the patients that underwent a second curettage and grafting procedure. Conclusion The achievement of complete healing in the patients that underwent a second curettage and grafting procedure indicates that the recurrence of UBC and ABC is associated with insufficient curettage. PMID:28154666

In Vitro Reassembly of the Ribose ATP-binding Cassette Transporter Reveals a Distinct Set of Transport Complexes*

PubMed Central

Clifton, Matthew C.; Simon, Michael J.; Erramilli, Satchal K.; Zhang, Huide; Zaitseva, Jelena; Hermodson, Mark A.; Stauffacher, Cynthia V.

2015-01-01

Bacterial ATP-binding cassette (ABC) importers are primary active transporters that are critical for nutrient uptake. Based on structural and functional studies, ABC importers can be divided into two distinct classes, type I and type II. Type I importers follow a strict alternating access mechanism that is driven by the presence of the substrate. Type II importers accept substrates in a nucleotide-free state, with hydrolysis driving an inward facing conformation. The ribose transporter in Escherichia coli is a tripartite complex consisting of a cytoplasmic ATP-binding cassette protein, RbsA, with fused nucleotide binding domains; a transmembrane domain homodimer, RbsC2; and a periplasmic substrate binding protein, RbsB. To investigate the transport mechanism of the complex RbsABC2, we probed intersubunit interactions by varying the presence of the substrate ribose and the hydrolysis cofactors, ATP/ADP and Mg2+. We were able to purify a full complex, RbsABC2, in the presence of stable, transition state mimics (ATP, Mg2+, and VO4); a RbsAC complex in the presence of ADP and Mg2+; and a heretofore unobserved RbsBC complex in the absence of cofactors. The presence of excess ribose also destabilized complex formation between RbsB and RbsC. These observations suggest that RbsABC2 shares functional traits with both type I and type II importers, as well as possessing unique features, and employs a distinct mechanism relative to other ABC transporters. PMID:25533465

The Transcriptional Regulators NorG and MgrA Modulate Resistance to both Quinolones and β-Lactams in Staphylococcus aureus▿

PubMed Central

Truong-Bolduc, Que Chi; Hooper, David C.

2007-01-01

MgrA is a known regulator of the expression of several multidrug transporters in Staphylococcus aureus. We identified another regulator of multiple efflux pumps, NorG, by its ability, like that of MgrA, to bind specifically to the promoter of the gene encoding the NorA efflux pump. NorG is a member of the family of the GntR-like transcriptional regulators, and it binds specifically to the putative promoters of the genes encoding multidrug efflux pumps NorA, NorB, NorC, and AbcA. Overexpression of norG produces a threefold increase in norB transcripts associated with a fourfold increase in the level of resistance to quinolones. In contrast, disruption of norG produces no change in the level of transcripts of norA, norB, and norC but causes an increase of at least threefold in the transcript level of abcA, associated with a fourfold increase in resistance to methicillin, cefotaxime, penicillin G, and nafcillin. Overexpression of cloned abcA caused an 8- to 128-fold increase in the level of resistance to all four β-lactam antibiotics. Furthermore, MgrA and NorG have opposite effects on norB and abcA expression. MgrA acts as an indirect repressor for norB and a direct activator for abcA, whereas NorG acts as a direct activator for norB and a direct repressor for abcA. PMID:17277059

Strategies for neurotrophin-3 and chondroitinase ABC release from freeze-cast chitosan-alginate nerve-guidance scaffolds.

PubMed

Francis, Nicola L; Hunger, Philipp M; Donius, Amalie E; Wegst, Ulrike G K; Wheatley, Margaret A

2017-01-01

Freeze casting, or controlled unidirectional solidification, can be used to fabricate chitosan-alginate (C-A) scaffolds with highly aligned porosity that are suitable for use as nerve-guidance channels. To augment the guidance of growth across a spinal cord injury lesion, these scaffolds are now evaluated in vitro to assess their ability to release neurotrophin-3 (NT-3) and chondroitinase ABC (chABC) in a controlled manner. Protein-loaded microcapsules were incorporated into C-A scaffolds prior to freeze casting without affecting the original scaffold architecture. In vitro protein release was not significantly different when comparing protein loaded directly into the scaffolds with release from scaffolds containing incorporated microcapsules. NT-3 was released from the C-A scaffolds for 8 weeks in vitro, while chABC was released for up to 7 weeks. Low total percentages of protein released from the scaffolds over this time period were attributed to limitation of diffusion by the interpenetrating polymer network matrix of the scaffold walls. NT-3 and chABC released from the scaffolds retained bioactivity, as determined by a neurite outgrowth assay, and the promotion of neurite growth across an inhibitory barrier of chondroitin sulphate proteoglycans. This demonstrates the potential of these multifunctional scaffolds for enhancing axonal regeneration through growth-inhibiting glial scars via the sustained release of chABC and NT-3. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

The Reverse Transcription Inhibitor Abacavir Shows Anticancer Activity in Prostate Cancer Cell Lines

PubMed Central

Molinari, Agnese; Parisi, Chiara; Bozzuto, Giuseppina; Toccacieli, Laura; Formisano, Giuseppe; De Orsi, Daniela; Paradisi, Silvia; Grober, OlÌ Maria Victoria; Ravo, Maria; Weisz, Alessandro; Arcieri, Romano; Vella, Stefano; Gaudi, Simona

2010-01-01

Background Transposable Elements (TEs) comprise nearly 45% of the entire genome and are part of sophisticated regulatory network systems that control developmental processes in normal and pathological conditions. The retroviral/retrotransposon gene machinery consists mainly of Long Interspersed Nuclear Elements (LINEs-1) and Human Endogenous Retroviruses (HERVs) that code for their own endogenous reverse transcriptase (RT). Interestingly, RT is typically expressed at high levels in cancer cells. Recent studies report that RT inhibition by non-nucleoside reverse transcriptase inhibitors (NNRTIs) induces growth arrest and cell differentiation in vitro and antagonizes growth of human tumors in animal model. In the present study we analyze the anticancer activity of Abacavir (ABC), a nucleoside reverse transcription inhibitor (NRTI), on PC3 and LNCaP prostate cancer cell lines. Principal Findings ABC significantly reduces cell growth, migration and invasion processes, considerably slows S phase progression, induces senescence and cell death in prostate cancer cells. Consistent with these observations, microarray analysis on PC3 cells shows that ABC induces specific and dose-dependent changes in gene expression, involving multiple cellular pathways. Notably, by quantitative Real-Time PCR we found that LINE-1 ORF1 and ORF2 mRNA levels were significantly up-regulated by ABC treatment. Conclusions Our results demonstrate the potential of ABC as anticancer agent able to induce antiproliferative activity and trigger senescence in prostate cancer cells. Noteworthy, we show that ABC elicits up-regulation of LINE-1 expression, suggesting the involvement of these elements in the observed cellular modifications. PMID:21151977

Balance Confidence and Falls in Non-Demented Essential Tremor Patients: The Role of Cognition

PubMed Central

Rao, Ashwini K.; Gilman, Arthur; Louis, Elan D.

2014-01-01

Objective To examine 1) the effect of cognitive ability on balance confidence and falls, 2) the relationship of balance confidence and falls with quantitative measures of gait, and 3) measures that predict falls, in people with Essential Tremor (ET). Design Cross-sectional study. Setting: General community. Participants One-hundred-eighty participants (132 people with ET and 48 controls). People with ET were divided into two groups based on the median score on the modified Mini Mental State Exam: ET-LCS vs. ET-HCS. Interventions Not applicable. Main Outcome Measures Activities of Balance Confidence-6 (ABC) scale and falls in the previous year. Results ET-LCS had lower ABC-6 scores and a greater number of falls than ET-HCS (p<0.05 for all measures) or controls (p<0.01 for all measures). Quantitative gait measures were significantly correlated with ABC-6 score and falls. Gait speed (p<0.007) and ABC-6 score (p<0.02) were significant predictors of falls. Receiver Operating Characteristic curve analysis revealed that gait speed < 0.9 m/s and ABC-6 score < 51% were associated with moderate sensitivity and specificity in identifying fallers. Conclusions People with ET with low cognitive scores have impaired gait, and report lower balance confidence, and higher number of falls than their counterparts with higher cognitive scores, and controls. We have identified assessments that are easily administered (gait speed and ABC-6 scale), and are associated with falls in ET. PMID:24769121

A Software Rejuvenation Framework for Distributed Computing

NASA Technical Reports Server (NTRS)

Chau, Savio

2009-01-01

A performability-oriented conceptual framework for software rejuvenation has been constructed as a means of increasing levels of reliability and performance in distributed stateful computing. As used here, performability-oriented signifies that the construction of the framework is guided by the concept of analyzing the ability of a given computing system to deliver services with gracefully degradable performance. The framework is especially intended to support applications that involve stateful replicas of server computers.

Modeling and control of operator functional state in a unified framework of fuzzy inference petri nets.

PubMed

Zhang, Jian-Hua; Xia, Jia-Jun; Garibaldi, Jonathan M; Groumpos, Petros P; Wang, Ru-Bin

2017-06-01

In human-machine (HM) hybrid control systems, human operator and machine cooperate to achieve the control objectives. To enhance the overall HM system performance, the discrete manual control task-load by the operator must be dynamically allocated in accordance with continuous-time fluctuation of psychophysiological functional status of the operator, so-called operator functional state (OFS). The behavior of the HM system is hybrid in nature due to the co-existence of discrete task-load (control) variable and continuous operator performance (system output) variable. Petri net is an effective tool for modeling discrete event systems, but for hybrid system involving discrete dynamics, generally Petri net model has to be extended. Instead of using different tools to represent continuous and discrete components of a hybrid system, this paper proposed a method of fuzzy inference Petri nets (FIPN) to represent the HM hybrid system comprising a Mamdani-type fuzzy model of OFS and a logical switching controller in a unified framework, in which the task-load level is dynamically reallocated between the operator and machine based on the model-predicted OFS. Furthermore, this paper used a multi-model approach to predict the operator performance based on three electroencephalographic (EEG) input variables (features) via the Wang-Mendel (WM) fuzzy modeling method. The membership function parameters of fuzzy OFS model for each experimental participant were optimized using artificial bee colony (ABC) evolutionary algorithm. Three performance indices, RMSE, MRE, and EPR, were computed to evaluate the overall modeling accuracy. Experiment data from six participants are analyzed. The results show that the proposed method (FIPN with adaptive task allocation) yields lower breakdown rate (from 14.8% to 3.27%) and higher human performance (from 90.30% to 91.99%). The simulation results of the FIPN-based adaptive HM (AHM) system on six experimental participants demonstrate that the FIPN framework provides an effective way to model and regulate/optimize the OFS in HM hybrid systems composed of continuous-time OFS model and discrete-event switching controller. Copyright © 2017 Elsevier B.V. All rights reserved.

Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective

PubMed Central

Greene, Nicholas P.; Kaplan, Elise; Crow, Allister; Koronakis, Vassilis

2018-01-01

The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking. PMID:29892271

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.

PubMed

Wagner, Tristan; Koch, Jürgen; Ermler, Ulrich; Shima, Seigo

2017-08-18

In methanogenic archaea, the carbon dioxide (CO 2 ) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferredoxin and the heterodisulfide of coenzymes M and B. Here, we present the structure of the native heterododecameric HdrABC-MvhAGD complex at 2.15-angstrom resolution. HdrB contains two noncubane [4Fe-4S] clusters composed of fused [3Fe-4S]-[2Fe-2S] units sharing 1 iron (Fe) and 1 sulfur (S), which were coordinated at the CCG motifs. Soaking experiments showed that the heterodisulfide is clamped between the two noncubane [4Fe-4S] clusters and homolytically cleaved, forming coenzyme M and B bound to each iron. Coenzymes are consecutively released upon one-by-one electron transfer. The HdrABC-MvhAGD atomic model serves as a structural template for numerous HdrABC homologs involved in diverse microbial metabolic pathways. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

ABC transporters and immunity: mechanism of self-defense.

PubMed

Hinz, Andreas; Tampé, Robert

2012-06-26

The transporter associated with antigen processing (TAP) is a prototype of an asymmetric ATP-binding cassette (ABC) transporter, which uses ATP binding and hydrolysis to translocate peptides from the cytosol to the lumen of the endoplasmic reticulum (ER). Here, we review molecular details of peptide binding and ATP binding and hydrolysis as well as the resulting allosteric cross-talk between the nucleotide-binding domains and the transmembrane domains that drive translocation of the solute across the ER membrane. We also discuss the general molecular architecture of ABC transporters and demonstrate the importance of structural and functional studies for a better understanding of the role of the noncanonical site of asymmetric ABC transporters. Several aspects of peptide binding and specificity illustrate details of peptide translocation by TAP. Furthermore, this ABC transporter forms the central part of the major histocompatibility complex class I (MHC I) peptide-loading machinery. Hence, TAP is confronted with a number of viral factors, which prevent antigen translocation and MHC I loading in virally infected cells. We review how these viral factors have been used as molecular tools to decipher mechanistic aspects of solute translocation and discuss how they can help in the structural analysis of TAP.

Phosphorylation of plastoglobular proteins in Arabidopsis thaliana

PubMed Central

Lohscheider, Jens N.; Friso, Giulia; van Wijk, Klaas J.

2016-01-01

Plastoglobules (PGs) are plastid lipid–protein particles with a small specialized proteome and metabolome. Among the 30 core PG proteins are six proteins of the ancient ABC1 atypical kinase (ABC1K) family and their locations in an Arabidopsis mRNA-based co-expression network suggested central regulatory roles. To identify candidate ABC1K targets and a possible ABC1K hierarchical phosphorylation network within the chloroplast PG proteome, we searched Arabidopsis phosphoproteomics data from publicly available sources. Evaluation of underlying spectra and/or associated information was challenging for a variety of reasons, but supported pSer sites and a few pThr sites in nine PG proteins, including five FIBRILLINS. PG phosphorylation motifs are discussed in the context of possible responsible kinases. The challenges of collection and evaluation of published Arabidopsis phosphorylation data are discussed, illustrating the importance of deposition of all mass spectrometry data in well-organized repositories such as PRIDE and ProteomeXchange. This study provides a starting point for experimental testing of phosho-sites in PG proteins and also suggests that phosphoproteomics studies specifically designed toward the PG proteome and its ABC1K are needed to understand phosphorylation networks in these specialized particles. PMID:26962209

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

DOE PAGES

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken; ...

2016-11-29

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less

Rerouting Cellular Electron Flux To Increase the Rate of Biological Methane Production

PubMed Central

Catlett, Jennie L.; Ortiz, Alicia M.

2015-01-01

Methanogens are anaerobic archaea that grow by producing methane, a gas that is both an efficient renewable fuel and a potent greenhouse gas. We observed that overexpression of the cytoplasmic heterodisulfide reductase enzyme HdrABC increased the rate of methane production from methanol by 30% without affecting the growth rate relative to the parent strain. Hdr enzymes are essential in all known methane-producing archaea. They function as the terminal oxidases in the methanogen electron transport system by reducing the coenzyme M (2-mercaptoethane sulfonate) and coenzyme B (7-mercaptoheptanoylthreonine sulfonate) heterodisulfide, CoM-S-S-CoB, to regenerate the thiol-coenzymes for reuse. In Methanosarcina acetivorans, HdrABC expression caused an increased rate of methanogenesis and a decrease in metabolic efficiency on methylotrophic substrates. When acetate was the sole carbon and energy source, neither deletion nor overexpression of HdrABC had an effect on growth or methane production rates. These results suggest that in cells grown on methylated substrates, the cell compensates for energy losses due to expression of HdrABC with an increased rate of substrate turnover and that HdrABC lacks the appropriate electron donor in acetate-grown cells. PMID:26162885

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

Niu, Mingshan; Jiangsu Key Laboratory of Bone Marrow Stem Cell, Xuzhou Medical College, Xuzhou, Jiangsu; Department of Hematology, Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu

Constitutive NF-κB activation is required for survival of activated B cell-like subtype of diffuse large B cell lymphoma (ABC-DLBCL). However, current NF-κB targeting strategies lack cancer cell specificity. Here, we identified a novel inhibitor, piperlongumine, features direct binding to NF-κB p65 subunit and suppression of p65 nuclear import. This was accompanied by NF-κB reporter activity suppression and NF-κB target gene downregulation. Moreover, mutation of Cys{sup 38} to Ser in p65 abolished this effect of piperlongumine on inhibition of p65 nuclear import. Furthermore, we show that piperlongumine selectively inhibited proliferation and induced apoptosis of ABC-DLBCL cells. Most notably, it has beenmore » reported that piperlongumine did not affect normal cells even at high doses and was nontoxic to animals. Hence, our current study provides new insight into piperlongumine's mechanism of action and novel approach to ABC-DLBCL target therapy. - Highlights: • Current NF-κB targeting strategies lack cancer cell specificity. • Piperlongumine inhibits NF-κB p65 subunit nuclear import via directly binding to p65. • Piperlongumine selectively inhibits proliferation of ABC-DLBCL cells. • This study provides a novel approach to ABC-DLBCL target therapy.« less

Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry

PubMed Central

Kiosze-Becker, Kristin; Ori, Alessandro; Gerovac, Milan; Heuer, André; Nürenberg-Goloub, Elina; Rashid, Umar Jan; Becker, Thomas; Beckmann, Roland; Beck, Martin; Tampé, Robert

2016-01-01

Ribosome recycling orchestrated by the ATP binding cassette (ABC) protein ABCE1 can be considered as the final—or the first—step within the cyclic process of protein synthesis, connecting translation termination and mRNA surveillance with re-initiation. An ATP-dependent tweezer-like motion of the nucleotide-binding domains in ABCE1 transfers mechanical energy to the ribosome and tears the ribosome subunits apart. The post-recycling complex (PRC) then re-initiates mRNA translation. Here, we probed the so far unknown architecture of the 1-MDa PRC (40S/30S·ABCE1) by chemical cross-linking and mass spectrometry (XL-MS). Our study reveals ABCE1 bound to the translational factor-binding (GTPase) site with multiple cross-link contacts of the helix–loop–helix motif to the S24e ribosomal protein. Cross-linking of the FeS cluster domain to the ribosomal protein S12 substantiates an extreme lever-arm movement of the FeS cluster domain during ribosome recycling. We were thus able to reconstitute and structurally analyse a key complex in the translational cycle, resembling the link between translation initiation and ribosome recycling. PMID:27824037

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

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

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less