Recent Submissions

  • Quantitative Phosphoproteomic Using Titanium Dioxide Micro-Columns and Label-Free Quantitation

    Barrios-Llerena, Martin E.; Le Bihan, Thierry (Mass Spectrometry of Proteins, Springer New York, 2019-04-12) [Book Chapter]
    Phosphorylation events are important during cellular function. Analysis of phosphorylation in complex samples has been extensively studied using large-scale phosphopeptide enrichment methods. Quantitative analysis of the enriched phosphopeptides is subsequently performed using label-based methodologies (e.g., SILAC, iTRAQ, and others). Here we describe the protocol for the quantitative analysis of phosphopeptides, enriched with titanium dioxide micro-column, using an intensity-based label-free quantitation.
  • Strigolactone Biosynthesis and Signal Transduction

    Jia, Kunpeng; Li, Changsheng; Bouwmeester, Harro J.; Al-Babili, Salim (Strigolactones - Biology and Applications, Springer International Publishing, 2019-04-02) [Book Chapter]
    Strigolactones (SLs) are a group of carotenoid derivatives that act as a hormone regulating plant development and response to environmental stimuli. SLs are also released into soil as a signal indicating the presence of a host for symbiotic arbuscular mycorrhizal fungi and root parasitic weeds. In this chapter, we provide an overview on the enormous progress that has been recently made in elucidating SL biosynthesis and signal transduction. We describe the tailoring pathway from the carotenoid precursor to the central intermediate carlactone, highlighting the stereospecificity of the involved enzymes, the all-trans/9-cis-β-carotene isomerase (D27), the 9-cis-specific CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), as well as CCD8 and its unusual catalytic activity. We then outline the oxidation of carlactone by cytochrome P450 enzymes, such as the Arabidopsis MORE AXILLARY GROWTH 1 (MAX1), into different SLs and the role of other enzymes in generating this diversity, and discuss why plants produce many different SLs. This is followed by depicting hormonal and nutritional factors that regulate SL biosynthesis and release, and by a description of transport mechanisms. In the second part of our chapter, we focus on SL perception and signal transduction, describing the SL receptor DECREASED APICAL DOMINANCE 2 (DAD2)/DWARF14 (D14) and its unique features, the central function of protein degradation mediated by the F-box protein MAX2 and its homologs. We also discuss the latest advances in understanding how SLs regulate the transcription of target genes and the role of SMXL/D53 transcription inhibitors.
  • Genetic Engineering for the Improvement of Oil Content and Associated Traits in Jatropha curcas L.

    Mastan, Shaik G.; Rathore, Mangal Singh; Kumari, Swati; Muppala, Reddy P.; Kumar, Nitish (Jatropha, Challenges for a New Energy Crop, Springer Singapore, 2019-03-29) [Book Chapter]
    Interminably increasing petroleum rates and exhaustion of fossil reserves have ignited a global search for substitutes to renewable fuel sources. Many oil-generating plants, crops and trees have been considered for biofuel; among these Jatropha curcas is regarded as one of the most promising oilseed plants as its seeds contain oil content up to 35%. Because fossil oil consumption is increasing day-by-day, there is an urgent need to enhance the oil content. Transgenic technology is one of the advanced techniques that have been applied to enhance oil content and modify the composition of fatty acids in seed oils. Increasing seed oil content can be done by modifying the enzyme’s level expression in the triacylglycerol biosynthetic pathway. In this chapter, an effort is made to highlight the potential of transgenic technology towards the enhancement of the oil content and in altering the candidate gene expression for biosynthesis of triacylglycerol.
  • Concentrated Photovoltaic (CPV): From Deserts to Rooftops

    Burhan, Muhammad; Shahzad, Muhammad Wakil; Ng, Kim Choon (Lecture Notes in Computer Science, Springer International Publishing, 2019-03-29) [Book Chapter]
    The current photovoltaic market is completely dominated by the conventional single junction PV panels, despite the fact that the highest energy efficiency of multi-junction solar cells is in the form of concentrated photovoltaic (CPV) system. CPV technology has faced many challenges of reliability and performance since its conception. However, despite much improvement in design and reliability, CPV technology is still unable to gain the attention of customers and energy planners with its high-performance potential. Due to its response to only solar beam radiations, CPV systems are believed to be only suitable to operate in clear sky weather conditions. That’s why the current gigantic CPV systems are only designed to be installed in open desert regions. It is still lacking the same application scope which the conventional PV is experiencing. With the aim to boost its market potential, in this chapter, a compact CPV design is discussed with low cost but highly accurate performance, to be targeted to install at the rooftop of commercial and residential building in the urban region. In addition, the performance of CPV system is also evaluated and compared with the different conventional PV system in the tropical weather condition with low beam radiation availability.
  • Methods for the recombinant expression of active tyrosine kinase domains: Guidelines and pitfalls

    Díaz Galicia, M. Escarlet; Aldehaiman, Abdullah; Hong, Seungbeom; Arold, Stefan T.; Grunberg, Raik (Methods in Enzymology, Elsevier, 2019-03-26) [Book Chapter]
    Protein tyrosine kinases (PTKs) are key signaling molecules and important drug targets. Although the efficient recombinant production of active PTKs is important for both pharmaceutical industry and academic research, most PTKs are still obtained from conventional, expensive and time-consuming insect-cell based expression. Host toxicity, kinase inactivity, insolubility and heterogeneity are among the reasons thought to preclude PTK expression in Escherichia coli. Herein we review these presumed roadblocks and their possible solutions for bacterial expression of PTKs, and give an overview on kinase activity assays. Finally, we report our experiences and observations with the kinases Src, Lyn and FAK as examples to illustrate implementation, effects and pitfalls of E. coli expression and in vitro assaying of PTKs.
  • Particle Migration and Clogging in Radial Flow: A Microfluidics Study

    Zhao, Budi; Liu, Q.; Santamarina, Carlos (Water Resources Development and Management, Springer Singapore, 2019-03-25) [Book Chapter]
    Migratory particles in porous media experience mechanical and chemo-physical interactions with fluids, pore walls and other particles. The resulting forces (buoyant weight, drag, inertia, and electrical particle-particle and particle-wall) determine particle migration, adhesion and pore clogging. We investigate underlying pore-scale phenomena in convergent radial flow using microfluidic chips. Images reveal distinct clogging mechanics as a function of the particle mass density. The heavy glass particles collide with pore walls and the transient increase in the local volume fraction of particles enhances the probability of bridge formation and clogging at pore throats. On the other hand, quasi-buoyant latex particles follow streamlines closely, but can stick to nearby pore walls at pore constrictions as electrical attraction towards the wall overcomes the repulsive forces. A clogged pore increases the tortuosity of streamlines and promotes further clogging at nearby pores. Statistical data gathered through image analyses identify causal interactions between sequential clogging events.
  • Decision Tables and Tools for Study of Pareto-Optimal Points

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we consider some notions related to decision tables with many-valued decisions (the notions of table, directed acyclic graph for this table, uncertainty and completeness measures, and restricted information system) and discuss tools (statements and algorithms) for the work with Pareto optimal points.
  • Local and Global Approaches to Study of Decision and Inhibitory Trees and Rule Systems

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    This chapter is devoted to the study of time complexity of decision and inhibitory trees and rule systems over arbitrary sets of attributes represented by information systems.
  • Multi-pruning and Restricted Multi-pruning of Decision Trees

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we consider two questions related to decision trees: (i) how to construct decision trees with reasonable number of nodes and reasonable number of misclassifications when they are used for knowledge representation, and (ii) how to improve the prediction accuracy of decision trees when they are used as classifiers. We created so-called multi-pruning approach based on dynamic programming algorithms for bi-criteria optimization of CART-like decision trees relative to the number of nodes and the number of misclassifications. This approach allows us to construct the set of all Pareto optimal points and to derive, for each such point, decision trees with parameters corresponding to that point. Experiments with decision tables from the UCI ML Repository show that, very often, we can find a suitable Pareto optimal point and derive a decision tree with small number of nodes at the expense of small increment in the number of misclassifications. Multi-pruning approach includes a procedure which constructs decision trees that, as classifiers, often outperform decision trees constructed by CART. We considered a modification of multi-pruning approach (restricted multi-pruning) that requires less memory and time but usually keeps the quality of constructed trees as classifiers or as a way for knowledge representation. Based on the uncertainty measure abs which is applicable both to decision tables with single- and many-valued decisions, we extended the considered approaches to the case of decision tables with many-valued decisions.
  • Preliminary Results for Decision and Inhibitory Trees, Tests, Rules, and Rule Systems

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    Earlier, some relatively simple results were considered for binary decision tables with many-valued decisions: relationships among decision trees, rules and tests, bounds on their complexity, greedy algorithms for construction of decision trees, rules and tests, and dynamic programming algorithms for minimization of tree depth and rule length. In this chapter, we mention these results without proofs and extend them to inhibitory trees, tests, rules and rule systems over binary decision tables with many-valued decisions.
  • Three Approaches to Handle Inconsistency in Decision Tables

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we discuss main notions related to inconsistent decision tables, and three approaches to handle inconsistency in decision tables: decision tables with many-valued decisions (MVD approach), decision tables with generalized decisions (GD approach), and decision tables with most common decisions (MCD approach). After that, we compare complexity and classification accuracy of decision trees constructed by greedy heuristics in the frameworks of these approaches.
  • Bi-criteria Optimization Problem for Decision and Inhibitory Trees: Cost Versus Cost

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we study bi-criteria optimization problem cost versus cost for decision and inhibitory trees. We design an algorithm which constructs the set of Pareto optimal points for bi-criteria optimization problem for decision trees, and show how the constructed set can be transformed into the graphs of functions that describe the relationships between the studied cost functions. We extend the obtained results to the case of inhibitory trees. We consider two applications: study of 12 greedy heuristics as algorithms for single- and bi-criteria optimization of decision and inhibitory trees, and study of two relationships for decision trees related to knowledge representation—number of nodes versus depth and number of nodes versus average depth.
  • Bi-criteria Optimization Problem for Rules and Systems of Rules: Cost Versus Cost

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we consider algorithms which construct the sets of Pareto optimal points for bi-criteria optimization problems for decision rules and rule systems relative to two cost functions. We show how the constructed set of Pareto optimal points can be transformed into the graphs of functions which describe the relationships between the considered cost functions. We compare 13 greedy heuristics for construction of decision rules from the point of view of single-criterion optimization (relative to length or coverage) and bi-criteria optimization (relative to length and coverage). At the end of the chapter, we generalize the obtained results to the case of inhibitory rules and systems of inhibitory rules.
  • Bi-criteria Optimization Problem for Rules and Systems of Rules: Cost Versus Uncertainty (Completeness)

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we consider algorithms which construct the sets of Pareto optimal points for bi-criteria optimization problems for decision (inhibitory) rules and rule systems relative to a cost function and an uncertainty (completeness) measure. We show how the constructed set of Pareto optimal points can be transformed into the graphs of functions which describe the relationships between the considered cost function and uncertainty (completeness) measure. Computer experiments provide us with examples of trade-off between complexity and accuracy for decision and inhibitory rule systems.
  • Multi-stage Optimization of Decision and Inhibitory Rules

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we consider optimization of decision and inhibitory rules including multi-stage optimization relative to a sequence of cost functions. We discuss an algorithm for counting the number of optimal rules, and consider simulation of a greedy algorithm for construction of decision rule sets. We also discuss results of computer experiments with decision an inhibitory rules: existence of small systems of enough accurate decision rules that cover almost all rows, and existence of totally optimal decision and inhibitory rules that have minimum length and maximum coverage simultaneously.
  • Explaining Examples

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we discuss briefly main notions: problems with many-valued decisions, decision tables corresponding to these problems, decision and inhibitory trees, rules, and systems of rules. We consider only depth of trees, and length of rules and systems of rules. After that, we concentrate on consideration of simple examples of problems with many-valued decisions from different areas of applications: fault diagnosis, computational geometry, combinatorial optimization, and analysis of data. At the end, we discuss two examples which explain why we study not only decision but also inhibitory rules and trees.
  • Bi-criteria Optimization Problem for Decision (Inhibitory) Trees: Cost Versus Uncertainty (Completeness)

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we study bi-criteria optimization problems cost versus uncertainty for decision trees and cost versus completeness for inhibitory trees, and consider illustrative examples. The created tools allow us to understand complexity versus accuracy trade-off for decision and inhibitory trees and to choose appropriate trees.
  • Decision and Inhibitory Rules and Systems of Rules

    Alsolami, Fawaz; Azad, Mohammad; Chikalov, Igor; Moshkov, Mikhail (Management-Reihe Corporate Social Responsibility, Springer Berlin Heidelberg, 2019-03-13) [Book Chapter]
    In this chapter, we consider various types of decision and inhibitory rules and systems of rules. We discuss the notion of cost function for rules, the notion of decision rule uncertainty, and the notion of inhibitory rule completeness. Similar notions are introduced for systems of decision and inhibitory rules.
  • Graphite-Polyimide Sensor

    Nag, Anindya; Mukhopadhyay, Subhas Chandra; Kosel, Jürgen (Springer Series on Fluorescence, Springer Berlin Heidelberg, 2019-03-11) [Book Chapter]
    This chapter explains the fabrication and implementation of sensor patches developed from laser-induced polymer films. Photo-thermal induction of commercial films was done to form graphene that was subsequently used as electrodes in sensor patches via transferring them on sticky tapes. The sensor patches were used for different environmental and industrial applications like salinity sensing, taste sensing, and nitrate sensing.
  • Literature Review

    Nag, Anindya; Mukhopadhyay, Subhas Chandra; Kosel, Jürgen (Springer Series on Fluorescence, Springer Berlin Heidelberg, 2019-03-11) [Book Chapter]
    This chapter elucidates on some of the work done by different researchers on sensors developed from Carbon Nanotubes (CNTs) and graphene. Work done on the preparation and properties of CNTs and graphene are explained in addition to their employment as electrochemical, strain and electrical sensors. It also explains the work done on a range of wearable, flexible sensors, some of the network protocols used to operate them, the current challenges availing in the present scenario and some of the future opportunities in terms of market survey and betterment of the existing sensors.

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