bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays
Authors: Furusawa Chikara , Ono Naoaki , Suzuki Shingo , Agata Tomoharu , Shimizu Hiroshi , Yomo Tetsuya 
Published: November 2008

Abstract
Motivation: High-density DNA microarrays provide us with useful tools for analyzing DNA and RNA comprehensively. However, the background signal caused by the non-specific binding (NSB) between probe and target makes it difficult to obtain accurate measurements. To remove the background signal, there is a set of background probes on Affymetrix Exon arrays to represent the amount of non-specific signals, and an accurate estimation of non-specific signals using these background probes is desirable for improvement of microarray analyses.
Results: We developed a thermodynamic model of NSB on short nucleotide microarrays in which the NSBs are modeled by duplex formation of probes and multiple hypothetical targets. We fitted the observed signal intensities of the background probes with those expected by the model to obtain the model parameters. As a result, we found that the presented model can improve the accuracy of prediction of non-specific signals in comparison with previously proposed methods. This result will provide a useful method to correct for the background signal in oligonucleotide microarray analysis.
Availability: The software is implemented in the R language and can be downloaded from our website (http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/MSNS/).
Contact: furusawa@ist.osaka-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Excess acoustic absorption attributable to the biological modification of seawater viscosity
Authors: Rhodes Christopher J. 
Published: November 2008

Abstract
Rhodes, C. J. 2008. Excess acoustic absorption attributable to the biological modification of seawater viscosity. – ICES Journal of Marine Science, 65: 1747–1750. There is increasing evidence that a ubiquitous species of oceanic phytoplankton (Phaeocystis globosa) can significantly modify the rheological properties of seawater. The effect is seasonal and, during spring when the species multiplies rapidly, one can observe large increases in the viscosity of the seawater they inhabit. One of the principal determinants of acoustic absorption in a fluid is viscosity, so in addition to the well-understood modulations attributable to temperature- and salinity-dependent molecular relaxation, there may be an additional absorption component resulting from the presence of phytoplankton. Using data from recent measurements of biologically induced excess viscosity during blooms of P. globosa, the additional acoustic absorption attributable to the presence of this organism is estimated. This suggests that a novel, biologically induced acoustic-absorption mechanism may be observable in seawater for frequencies >100 kHz. The implications for a variety of at-sea acoustic-measurement activities are noted.
Chlororespiration and Grana Hyperstacking: How an Arabidopsis Double Mutant Can Survive Despite Defects in Starch Biosynthesis and Daily Carbon Export from Chloroplasts
Authors: Häusler Rainer E. , Geimer Stefan , Kunz Hans Henning , Schmitz Jessica , Dörmann Peter , Bell Kirsten , Hetfeld Sonja , Guballa Andre , Flügge Ulf-Ingo 
Published: November 2008

Abstract
An Arabidopsis (Arabidopsis thaliana) double mutant impaired in starch biosynthesis and the triose phosphate/phosphate translocator (adg1-1/tpt-1) is characterized by a diminished utilization of photoassimilates and the concomitant consumption of reducing power and energy produced in the photosynthetic light reaction. In order to guarantee survival, the double mutant responds to this metabolic challenge with growth retardation, an 80% decline in photosynthetic electron transport, diminished chlorophyll contents, an enhanced reduction state of plastoquinone in the dark (up to 50%), a perturbation of the redox poise in leaves (increased NADPH/NADP ratios and decreased ascorbate/dehydroascorbate ratios), hyperstacking of grana thylakoids, and an increased number of plastoglobules. Enhanced oxygen consumption and applications of inhibitors of alternative mitochondrial and chloroplast oxidases (AOX and PTOX) suggest that chlororespiration as well as mitochondrial respiration are involved in the enhanced plastoquinone reduction state in the dark. Transcript amounts of PTOX and AOX were diminished and nucleus-encoded components related to plastidic NADH reductase (NDH1) were increased in adg1-1/tpt-1 compared with the wild type. Cytochrome b 559, proposed to be involved in the reoxidation of photosystem II, was not regulated at the transcriptional level. The hyperstacking of grana thylakoids mimics adaptation to low light, and increased plastoglobule numbers suggest a response to enhanced oxidative stress. Altered chloroplast organization combined with perturbations in the redox poise suggests that adg1-1/tpt-1 could be a tool for the in vivo study of retrograde signaling mechanisms controlling the coordinated expression of nucleus- and plastome-encoded photosynthetic genes.
Functional Characterization of a Higher Plant Sphingolipid Δ4-Desaturase: Defining the Role of Sphingosine and Sphingosine-1-Phosphate in Arabidopsis
Authors: Michaelson Louise V. , Zäuner Simone , Markham Jennifer E. , Haslam Richard P. , Desikan Radhika , Mugford Sarah , Albrecht Sandra , Warnecke Dirk , Sperling Petra , Heinz E. , Napier Johnathan A. 
Published: November 2008

AbstractThe role of Δ4-unsaturated sphingolipid long-chain bases such as sphingosine was investigated in Arabidopsis (Arabidopsis thaliana). Identification and functional characterization of the sole Arabidopsis ortholog of the sphingolipid Δ4-desaturase was achieved by heterologous expression in Pichia pastoris. A P. pastoris mutant disrupted in the endogenous sphingolipid Δ4-desaturase gene was unable to synthesize glucosylceramides. Synthesis of glucosylceramides was restored by the expression of Arabidopsis gene At4g04930, and these sphingolipids were shown to contain Δ4-unsaturated long-chain bases, confirming that this open reading frame encodes the sphingolipid Δ4-desaturase. At4g04930 has a very restricted expression pattern, transcripts only being detected in pollen and floral tissues. Arabidopsis insertion mutants disrupted in the sphingolipid Δ4-desaturase At4g04930 were isolated and found to be phenotypically normal. Sphingolipidomic profiling of a T-DNA insertion mutant indicated the absence of Δ4-unsaturated sphingolipids in floral tissue, also resulting in the reduced accumulation of glucosylceramides. No difference in the response to drought or water loss was observed between wild-type plants and insertion mutants disrupted in the sphingolipid Δ4-desaturase At4g04930, nor was any difference observed in stomatal closure after treatment with abscisic acid. No differences in pollen viability between wild-type plants and insertion mutants were detected. Based on these observations, it seems unlikely that Δ4-unsaturated sphingolipids and their metabolites such as sphingosine-1-phosphate play a significant role in Arabidopsis growth and development. However, Δ4-unsaturated ceramides may play a previously unrecognized role in the channeling of substrates for the synthesis of glucosylceramides.
Antiquity and Function ofCASTORandPOLLUX, the Twin Ion Channel-Encoding Genes Key to the Evolution of Root Symbioses in Plants
Authors: Chen Caiyan , Fan Cui , Gao Muqiang , Zhu Hongyan 
Published: November 2008

AbstractRoot symbioses with arbuscular mycorrhizal fungi and rhizobial bacteria share a common signaling pathway in legumes. Among the common symbiosis genes are CASTOR and POLLUX, the twin homologous genes in Lotus japonicus that encode putative ion channel proteins. Here, we show that the orthologs of CASTOR and POLLUX are ubiquitously present and highly conserved in both legumes and nonlegumes. Using rice (Oryza sativa) as a study system, we employ reverse genetic tools (knockout mutants and RNA interference) to demonstrate that Os-CASTOR and Os-POLLUX are indispensable for mycorrhizal symbiosis in rice. Furthermore, a cross-species complementation test indicates that Os-POLLUX can restore nodulation, but not rhizobial infection, to a Medicago truncatula dmi1 mutant.
TheArabidopsis onset of leaf death5Mutation of Quinolinate Synthase Affects Nicotinamide Adenine Dinucleotide Biosynthesis and Causes Early Ageing
Authors: Schippers Jos H.M. , Nunes-Nesi Adriano , Apetrei Roxana , Hille Jacques , Fernie Alisdair R. , Dijkwel Paul P. 
Published: November 2008

AbstractLeaf senescence in Arabidopsis thaliana is a strict, genetically controlled nutrient recovery program, which typically progresses in an age-dependent manner. Leaves of the Arabidopsis onset of leaf death5 (old5) mutant exhibit early developmental senescence. Here, we show that OLD5 encodes quinolinate synthase (QS), a key enzyme in the de novo synthesis of NAD. The Arabidopsis QS was previously shown to carry a Cys desulfurase domain that stimulates reconstitution of the oxygen-sensitive Fe-S cluster that is required for QS activity. The old5 lesion in this enzyme does not affect QS activity but it decreases its Cys desulfurase activity and thereby the long-term catalytic competence of the enzyme. The old5 mutation causes increased NAD steady state levels that coincide with increased activity of enzymes in the NAD salvage pathway. NAD plays a key role in cellular redox reactions, including those of the tricarboxylic acid cycle. Broad-range metabolite profiling of the old5 mutant revealed that it contains higher levels of tricarboxylic acid cycle intermediates and nitrogen-containing amino acids. The mutant displays a higher respiration rate concomitant with increased expression of oxidative stress markers. We postulate that the alteration in the oxidative state is integrated into the plant developmental program, causing early ageing of the mutant.
EFD Is an ERF Transcription Factor Involved in the Control of Nodule Number and Differentiation inMedicago truncatula
Authors: Vernié Tatiana , Moreau Sandra , de Billy Françoise , Plet Julie , Combier Jean-Philippe , Rogers Christian , Oldroyd Giles , Frugier Florian , Niebel Andreas , Gamas Pascal 
Published: November 2008

AbstractMechanisms regulating legume root nodule development are still poorly understood, and very few regulatory genes have been cloned and characterized. Here, we describe EFD (for ethylene response factor required for nodule differentiation), a gene that is upregulated during nodulation in Medicago truncatula. The EFD transcription factor belongs to the ethylene response factor (ERF) group V, which contains ERN1, 2, and 3, three ERFs involved in Nod factor signaling. The role of EFD in the regulation of nodulation was examined through the characterization of a null deletion mutant (efd-1), RNA interference, and overexpression studies. These studies revealed that EFD is a negative regulator of root nodulation and infection by Rhizobium and that EFD is required for the formation of functional nitrogen-fixing nodules. EFD appears to be involved in the plant and bacteroid differentiation processes taking place beneath the nodule meristem. We also showed that EFD activated Mt RR4, a cytokinin primary response gene that encodes a type-A response regulator. We propose that EFD induction of Mt RR4 leads to the inhibition of cytokinin signaling, with two consequences: the suppression of new nodule initiation and the activation of differentiation as cells leave the nodule meristem. Our work thus reveals a key regulator linking early and late stages of nodulation and suggests that the regulation of the cytokinin pathway is important both for nodule initiation and development.
Safety risk assessment on communication system based on satellite constellations with the analytic hierarchy process
Authors: Yulong Li , Xiande Wu , Zhongfu Li 
Published: November 2008

PurposeThe purpose of this paper is to develop an analytic hierarchy process (AHP) method in safety risk assessment on communication system based on satellite constellations through constructing safety risk index system.Design/methodology/approachAn empirical study using the AHP was carried out to find the relative weights of those assessment criterion and sub‐objectives of subsystem. Then the risk scores of 15 sub‐objectives and four subsystems were calculated applying the AHP method according to the assessment result of experts.FindingsAccording to the overall results from the estimation of experts the safety risk priority of net application is the highest and the safety risk priority of attack on physical equipment is the lowest. This explained that the possibility of a war in today's era, in which peace and development is the theme is very small, and risk prevention should focus more on the defense of network attacks from enemies.Practical implicationsThis paper provides a positive analysis of safety risk for a communication system based on satellite constellations and gives an opinion in accordance with the assessment result.Originality/valueAn AHP method was applied in the security risk assessment of communications systems on satellite constellation and the estimation of facing risk situation of the satellite communication system was presented according to the opinion of experts.
Model predictive control approach to global air collision avoidance
Authors: Bousson K. 
Published: November 2008

PurposeMost of the existing approaches for flight collision avoidance are concerned with local traffic alone for which the separation is based on the pairwise analysis of aircraft trajectory trends, which is not efficient with regard to some flight path requirements along waypoints. The purpose of this paper is to deal with the global collision avoidance problem which aims at separating aircraft taking into consideration the global traffic in a given area instead of considering them pairwise. It aims to model the concept of global collision avoidance and propose a validated algorithm for the purpose in the framework of free‐flight.Design/methodology/approachThe collision avoidance procedure computes online the appropriate speed and heading for each aircraft, at each sampling time‐instant, to generate a collision‐free flight trajectory along scheduled waypoints. The method accounts for automatic assignment of priority indexes that are updated from one control time horizon to the next. The paper considers here the case of aircraft flying at the same altitude, but the proposed method is easily extendable to the general 3D situation. Owing to the predictive features that are inherent to collision avoidance, the collision‐free trajectories are generated using model predictive control approach. A simulation example is presented in the end and its results show the suitability of the proposed approach.FindingsSince the model predictive control approach is used, the collision avoidance procedure is anticipative; therefore, the avoidance capability depends only on the prediction horizon rather than on the control horizon.Practical implicationsThe computation of the trajectory guidance information (speed and heading) at each time‐step is fast, therefore the proposed method is well suited for online processing requirements in real world applications.Originality/valueThe paper provides a flexible modelling framework and a computationally effective algorithm, both based on model predictive control concepts, to cope with global collision avoidance for flight safety enhancement in the framework of free‐flight.
A simulation environment for design and testing of aircraft adaptive fault‐tolerant control systems
Authors: Perhinschi M.G. , Napolitano M.R. , Campa G. 
Published: November 2008

PurposeThe purpose of this paper is to present the development of a Matlab/Simulink‐based simulation environment for the design and testing of indirect and direct adaptive flight control laws with fault tolerant capabilities to deal with the occurrence of actuator and sensor failures.Design/methodology/approachThe simulation environment features a modular architecture and a detailed graphical user interface for simulation scenario set‐up. Indirect adaptive flight control laws are implemented based on an optimal control design and frequency domain‐based online parameter estimation. Direct adaptive flight control laws consist of non‐linear dynamic inversion performed at a reference nominal flight condition augmented with artificial neural networks (NNs) to compensate for inversion errors and abnormal flight conditions following the occurrence of actuator or sensor failures. Failure detection, identification, and accommodation schemes relying on neural estimators are developed and implemented.FindingsThe simulation environment provides a valuable platform for the evaluation and validation of fault‐tolerant flight control laws.Research limitations/implicationsThe modularity of the simulation package allows rapid reconfiguration of control laws, aircraft model, and detection schemes. This flexibility allows the investigation of various design issues such as: the selection of control laws architecture (including the type of the neural augmentation), the tuning of NN parameters, the selection of parameter identification techniques, the effects of anti‐control saturation techniques, the selection and the tuning of the control allocation scheme, as well as the selection and tuning of the failure detection and identification schemes.Originality/valueThe novelty of this research efforts resides in the development and the integration of a comprehensive simulation environment allowing a very detailed validation of a number of control laws for the purpose of verifying the performance of actuator and sensor failure detection, identification, and accommodation schemes.
A conception of voice guided general aviation aircraft
Authors: Rogalski Tomasz 
Published: November 2008

PurposeThe purpose of this paper is to present the generic conception of the aircraft control system with the voice command interpretation interface. The paper's intention is also to present the first steps of work under control system for general aviation aircraft, which assists pilots using speech interpretation module.Design/methodology/approachThe paper defines the main rules governing projecting and operating such systems, and defines and discusses the main functionality levels. The use of voice commands for the direct controlling of the flight of the plane is also presented and analyzed in detail.FindingsThe paper presents general rules, which could be applied for work under control systems with speech interpretation modules intended for general aviation aircraft.Practical implicationsThe analyses and opinions included in this paper can be generic basis for future projects, which will try to use pilot's voice command to control the general aviation airplane.Originality/valueThis paper presets some conception of the control system with the speech recognition interface. There are main rules generally defining both the structure and the functionality the of such aircraft control system, included in this paper.
Linear and nonlinear simulations of aircraft dynamics using body axis system
Authors: Ozdemir Ugur , Kavsaoglu Mehmet S. 
Published: November 2008

PurposeThe purpose of this paper is to present a comparison of nonlinear and linear simulations of aircraft dynamics to determine the divergence of the linear solution from the nonlinear solution.Design/methodology/approachThe general equations of motion of a transport aircraft are presented both in nonlinear and linear form. The nonlinear equations are solved by using the Runge Kutta method. Linear equations are solved numerically by using the Runge Kutta method and they are also solved exactly by using the Laplace transformation method. All of these solutions are obtained by using the body axis system. The results of the simulations are plotted for different control deflections.FindingsSolution of linear equations by both methods gave the same results as expected. There are important differences in amplitude and frequency of oscillations which are obtained by using nonlinear and linear equations. These differences increase with growing input control deflection. Therefore, it is appropriate to prefer nonlinear approach to obtain more satisfactory results.Research limitations/implicationsAccurate determination of the aerodynamic derivatives is important for the accuracy of the nonlinear solutions.Originality/valueMany classical approaches use stability axis system for the solution of linear equations. However, in this paper transfer functions of the aircraft are redefined in the body axis system, because stability axes change with angle of attack and some of the stability derivatives need to be re‐evaluated for each angle of attack. Moreover, in addition to classical text book, linear equations are also solved by using the 4th order Runge Kutta medhod.
A knowledge‐based conflict resolution tool for en‐route air traffic controllers
Authors: Özgür Metin , Cavcar Aydan 
Published: November 2008

PurposeThe purpose of this paper is to develop a knowledge‐based decision support tool used for assisting en‐route air traffic controllers by generating resolutions for dual aircraft conflicts after being integrated into a model‐based conflict detection and conflict resolution system.Design/methodology/approachAir traffic controller knowledge, which was obtained from the literature research, about solving aircraft conflicts is represented in a decision tree. Then it is written in Visual Basic programming language. With reference to several rules form the expert air traffic controller knowledge and some factors which affect controller conflict resolution process, the tool generates advisories consisting of eight kinds of separation strategies.FindingsThe paper finds that it is expected to increase the safety of air traffic system by supporting air traffic controller in conflict resolution process. Controller workload can be reduced by fast, reliable and acceptable resolution advisories of the tool.Research limitations/implicationsThe accuracy of decision tree is limited with the adequacy and quality of knowledge obtained from references, several assumptions and interpretation. Because of the unavailability of a model‐based conflict detection and resolution tool, the tool could not be evaluated in simulations.Originality/valueAfter being integrated into a model‐based decision support tool, it can reduce the deficiencies of the model‐based tool such as low degree of resolution acceptance by controllers and low‐resolution speed by providing expert air traffic controller knowledge to the tool.