Generation Of Skeletons Research Articles

Skeletal Editing: Ring Insertion for Direct Access to Heterocycles.

Skeleton editing has rapidly advanced as a synthetic methodology in recent years, significantly streamlining the synthesis process and gaining widespread acceptance in drug synthesis and development. This field encompasses diverse ring reactions, many of which exhibit immense potential in skeleton editing, facilitating the generation of novel ring skeletons. Notably, reactions that involve the cleavage of two distinct rings followed by the reformation of new rings through ring insertion play a pivotal role in the construction of novel ring skeletons. This article aims to compile and systematize this category of reactions, emphasizing the two primary reaction types and offering a thorough exploration of their associated complexities and challenges. Our endeavor is to furnish readers with comprehensive reaction strategies, igniting research interest and injecting fresh impetus into the advancement of this domain.

A Simple and Stable Centeredness Measure for 3D Curve Skeleton Extraction.

Existing methods for extracting 3D curve skeletons mostly suffer from the difficulty of finding the center points of 3D shapes and tedious manual adjustments of the thresholds for pruning spurious branches due to the influence of shape boundary perturbations. In this article, we present a method based on medial surfaces of 3D shapes for the convenient and fast extraction of high-quality curve skeletons. Our main contribution is a simple and stable centeredness measure. It is based on simulating fire propagation via the scheme of inside-out evolution from the interior to the boundary, differentiating it from existing methods that use the scheme of outside-in evolution from the boundary to the interior. Thus, our measure is much more localized, and it can be implemented with a high degree of parallelism. In addition, we propose measures to effectively suppress the influence of details to obtain a stable measurement, and employ minimum set covers to optimize the center points to generate compact skeletons, which enables spurious branches to be effectively excluded without the tedious work of manually adjusting thresholds. Our experiments show the superiority of our method over existing methods, including its convenient generation of clean, compact and centered curve skeletons while running much faster than state-of-the-art methods.

Eutypellazines N−S, new thiodiketopiperazines from a deep sea sediment derived fungus Eutypella sp. with anti-VRE activities

Chemical investigation of a deep sea sediment derived fungus Eutypella sp. MCCC 3A00281 resulted in the isolation of six new thiodiketopiperazine alkaloids, namely eutypellazines N-S (1−6). Their structures were elucidated on the basis of the extensive NMR and mass spectroscopic analysis, including the ECD data for the determination of absolute configuration. The structures of eutypellazines N-P (1−3) were characteristic of unique spirocyclic skeletons, while eutypellazines N-O bearing a spirocyclic tetrahydrobenzothiophene motif were found from wide type fungus for the first time. The biogenetic generation of the spirocyclic skeletons was postulated. Compounds 3–5 exhibited inhibitory effects against vancomycin-resistant enterococci (VRE), suggesting that they may be the potential inhibitors toward drug resistant pathogenic bacteria after the structural modification.

The Involvement of Nitric Oxide in Integration of Plant Physiological and Ultrastructural Adjustments in Response to Arsenic.

High arsenic (As) concentrations are toxic to all the living organisms and the cellular response to this metalloid requires the involvement of cell signaling agents, such as nitric oxide (NO). The As toxicity and NO signaling were analyzed in Pistia stratiotes leaves. Plants were exposed to four treatments, for 24 h: control; SNP [sodium nitroprusside (NO donor); 0.1 mg L-1]; As (1.5 mg L-1) and As + SNP (1.5 and 0.1 mg L-1, respectively). The absorption of As increased the concentration of reactive oxygen species and triggered changes in the primary metabolism of the plants. While photosynthesis and photorespiration showed sharp decrease, the respiration process increased, probably due to chemical similarity between arsenate and phosphate, which compromised the energy status of the cell. These harmful effects were reflected in the cellular structure of P. stratiotes, leading to the disruption of the cells and a possible programmed cell death. The damages were attenuated by NO, which was able to integrate central plant physiological processes, with increases in non-photochemical quenching and respiration rates, while the photorespiration level decreased. The increase in respiratory rates was essential to achieve cellular homeostasis by the generation of carbon skeletons and metabolic energy to support processes involved in responses to stress, as well to maintaining the structure of organelles and prevent cell death. Overall, our results provide an integrated view of plant metabolism in response to As, focusing on the central role of NO as a signaling agent able to change the whole plant physiology.

Three-dimensionally ordered macroporous Pr6O11 and Tb4O7 with mesoporous walls: Preparation, characterization, and catalytic activity for CO oxidation

Three-dimensionally ordered macroporous (3DOM) praseodymium oxide and terbium oxide with mesoporous walls and cubic crystal structures have been successfully fabricated with polymethyl methacrylate (PMMA) as hard template and F127, sucrose, and l-lysine as surfactant. Physicochemical properties of the materials were characterized by means of numerous techniques. It is shown that the Pr6O11 and Tb4O7 samples displayed a 3DOM architecture with polycrystalline wormhole-like mesoporous walls. The nature of surfactant and solvent and calcination condition had important effects on the pore structure and surface area of the final product. The introduction of surfactant and the partial carbonization of sucrose or l-lysine favored the enhancement in surface area of the 3DOM-structured materials, with the 3DOM Pr6O11 and Tb4O7 samples derived with F127 showing the highest surface areas of 32.0 and 25.2m2/g, respectively. The low-temperature reducibility of the Pr6O11 and Tb4O7 samples decreased according to the sequences of Pr6O11-F127>Pr6O11-Sucrose>Pr6O11-Lysine and Tb4O7-F127>Tb4O7-Sucrose>Tb4O7-Lysine, coinciding with the order in surface oxygen vacancy density. The improved physicochemical properties associated with the generation of 3DOM skeletons and wormhole-like mesoporous walls rendered the Pr6O11-F127 and Tb4O7-F127 samples to perform the best in the oxidation of CO.

Dynamic and Speculative Polyhedral Parallelization Using Compiler-Generated Skeletons

We propose a framework based on an original generation and use of algorithmic skeletons, and dedicated to speculative parallelization of scientific nested loop kernels, able to apply at run-time polyhedral transformations to the target code in order to exhibit parallelism and data locality. Parallel code generation is achieved almost at no cost by using binary algorithmic skeletons that are generated at compile-time, and that embed the original code and operations devoted to instantiate a polyhedral parallelizing transformation and to verify the speculations on dependences. The skeletons are patched at run-time to generate the executable code. The run-time process includes a transformation selection guided by online profiling phases on short samples, using an instrumented version of the code. During this phase, the accessed memory addresses are used to compute on-the-fly dependence distance vectors, and are also interpolated to build a predictor of the forthcoming accesses. Interpolating functions and distance vectors are then employed for dependence analysis to select a parallelizing transformation that, if the prediction is correct, does not induce any rollback during execution. In order to ensure that the rollback time overhead stays low, the code is executed in successive slices of the outermost original loop of the nest. Each slice can be either a parallel version which instantiates a skeleton, a sequential original version, or an instrumented version. Moreover, such slicing of the execution provides the opportunity of transforming differently the code to adapt to the observed execution phases, by patching differently one of the pre-built skeletons. The framework has been implemented with extensions of the LLVM compiler and an x86-64 runtime system. Significant speed-ups are shown on a set of benchmarks that could not have been handled efficiently by a compiler.

ChemInform Abstract: A Diastereocontrolled Route to 10‐Arylpyrrolo[1,2‐b]isoquinolines.

The diastereocontrolled preparation of a series of 10-aryl-substituted pyrroloisoquinolines is achieved through a synthetic design that involves two key cyclization steps. First, the iodine(III)-mediated reaction of a series of N-benzylpentynamides leads to the generation of the 5-aroylpyrrolidinone skeletons. Finally, after reduction of the generated ketone group into the corresponding carbinol, the effect of a number of different acidic conditions was studied to assist the second cyclization step that occurs through an aromatic electrophilic substitution process. The study of the stereochemical course of this step led us to conclude that it takes place through a SN1 mechanism with very high (>95% anti) diastereocontrol.

A Diastereocontrolled Route to 10-Arylpyrrolo[1,2-b]isoquinolines

The diastereocontrolled preparation of a series of 10-aryl-substituted pyrroloisoquinolines is achieved through a synthetic design that involves two key cyclization steps. First, the iodine(III)-mediated reaction of a series of N-benzylpentynamides leads to the generation of the 5-aroylpyrrolidinone skeletons. Finally, after reduction of the generated ketone group into the corresponding carbinol, the effect of a number of different acidic conditions was studied to assist the second cyclization step that occurs through an aromatic electrophilic substitution process. The study of the stereochemical course of this step led us to conclude that it takes place through a S(N)1 mechanism with very high (>95% anti) diastereocontrol.

Surfactant-mediated PMMA-templating fabrication and characterization of three-dimensionally ordered macroporous Eu 2O 3 and Sm 2O 3 with mesoporous walls

Three-dimensionally ordered macroporous (3DOM) europium oxide and samarium oxide with mesoporous walls and cubic crystal structures have been successfully fabricated with polymethyl methacrylate (PMMA) as hard template and F127, sucrose, and l-lysine as surfactant. The as-fabricated rare earth oxides were characterized by means of X-ray diffraction, thermogravimetric analysis, differential scanning calorimetric analysis, Fourier-transform infrared spectroscopy, scanning electron microscope, transmission electron microscopy, selected-area electron diffraction, nitrogen adsorption–desorption, ultraviolet–visible diffuse reflectance spectroscopy, and photoluminescence spectroscopy. It is shown that the as-fabricated Eu 2O 3 and Sm 2O 3 samples displayed 3DOM architectures with polycrystalline wormhole-like mesoporous walls. The nature of surfactant and solvent and calcination parameter had important effects on the pore structure and surface area of the final product. The introduction of surfactant and the carbonization of sucrose or l-lysine favored the enhancement in surface area of the 3DOM-structured materials, with the 3DOM Eu 2O 3 and Sm 2O 3 samples derived in the presence of sucrose possessing the highest surface area of 36.8 and 32.6 m 2 g −1, respectively. The 3DOM Eu 2O 3 and Sm 2O 3 samples showed much better UV-light absorption capacity than their bulk counterparts. The PL study revealed that the luminescent properties could be modified by tailoring the pore structure of Eu 2O 3 and Sm 2O 3. The unique physical properties associated with the generation of 3DOM skeletons and wormhole-like mesoporous walls make such materials useful for the applications in optics and heterogeneous catalysis.

Unifying Architectural and Behavioural Specifications of Distributed Components

We present a novel specification language called JDC to be used at design phase of distributed components. The extensive seek for asynchrony in distributed components demands new techniques for its specification that have not been addressed before. We propose to focus the specification on its data-flow; this allows to reason about inter-component synchronisations produced by a data-driven synchronisation model. The language is endowed with enough formality so it allows a constructive approach; it allows the generation of behaviour models which can be model-checked, and the generation of code skeletons with the control flow of components. Globally, this approach aims at generating components with strong guarantees w.r.t. their behaviour.

Characterization of a dammarenediol synthase in Centella asiatica (L.) Urban

To elucidate the exact function of CabAS in Centella asiatica, which was previously reported as a putative beta-amyrin synthase [Plant Cell Rep, 24:304-311, 2005], this gene was functionally expressed in the lanosterol synthase-deficient yeast mutant (erg7). After inducing the CabAS gene with galactose, a peak consistent with the dammarenediol standard was detected in LC/APCIMS analyses and the accumulated product was confirmed as dammarenediol. CabAS should therefore be renamed to C. asiatica dammarenediol synthase (CaDDS). The confirmation of this gene function may allow us to better understand the generation of numerous triterpene carbon skeletons.

THE SI* MODELING FRAMEWORK: METAMODEL AND APPLICATIONS

Security Requirements Engineering is emerging spurred by the realization that security must be dealt from the early phases of the system development process. Modeling languages in this field are challenging as they must provide concepts appropriate in order to talk about security within an organization. In previous work we introduced the SI* modeling language tailored to capture security aspects of socio-technical systems. SI* is founded on four main notions, namely supervision, permission, delegation, and trust. In this paper, we present the SI* metamodel. We also present some frameworks and methodologies founded on this modeling language for the analysis of security and dependability requirements as well as the exploration of design alternatives and the generation of skeletons of secure business processes. The paper also presents a development environment that uses the SI* metamodel as its basis core.

MizarMode—an integrated proof assistance tool for the Mizar way of formalizing mathematics

The Emacs authoring environment for Mizar (MizarMode) is today the authoring tool of choice for many (probably the majority of) Mizar authors. This article describes the MizarMode and focuses on the proof assistance functions and tools available in it. We start with the explanation of the design principles behind the Mizar system, and show how these design principles—mainly the concentration on simple and intuitive human-oriented proofs—have helped Mizar in developing and maintaining a very large body of formalized mathematics. Mizar is a non-programmable and non-tactical verifier: the proofs are developed in the traditional “write—compile—correct” software programming loop. While this method is in the beginning more laborious than the methods employed in tactical and programmable proof assistants, it makes the “proof code” in the long-run more readable, maintainable and reusable. This seems to be a crucial factor for a long-term and large-scale formalization effort. MizarMode has been designed with the aim to facilitate this kind of proof development by a number of “code-generating”, “code-browsing” and “code-searching” methods, and tools programmed or integrated within it. These methods and tools now include, e.g., the automated generation of proof skeletons, semantic browsing of the articles and abstracts, structured viewing, proof advice using trained machine learning tools like the Mizar Proof Advisor, deductive tools like MoMM, etc. We give an overview of these proof-assistance tools and their integration in the MizarMode, and also discuss some emerging and future extensions such as integration of external theorem proving assistance.

Algon: From Interchangeable Distributed Algorithms to Interchangeable Middleware

We present the design and implementation of a framework for interchangeable distributed algorithms. The algorithms are drawn from the set which includes mutual exclusion, deadlock detection and agreement protocols, and we have implemented several examples of the first tonsiswo of these. Algon cts of a library of algorithms, a framework for incorporating them into a new or existing system, and a tool for evaluating comparative performance. In this way, much of the complexity related to distributed systems can be isolated in its own component level and the programmer can choose from among different algorithms in the same class based on performance in a given application. Incorporating many algorithms in a single framework was made possible by the observation that algorithms in a given class, e.g. mutual exclusion, almost always expose the same methods. These methods interface with an Algon scheduler which maintains state and provides convenient hooks for the application to invoke the services of the algorithm.In this paper we describe the structure of Algon in detail, with a distributed deadlock detection algorithm as the case study. We then extend the notion of separation of concerns by creating an addition layer in Algon, underneath which the middleware that runs on each node can be interchanged, for example from Java-RMI to CORBA. Challenges in the re-tooling of the system, related to multiple inheritance, exceptions and the automatic generation of stubs and skeletons in our implementation language, Java, were overcome in novel ways. Algon has the potential to be a framework with a long life, as it can adapt to new middleware, such as .NET.

ABSTRACTING AND ENFORCING WEB SERVICE PROTOCOLS

Web services are emerging as a promising technology for the automation of inter-organizational interactions. As technology matures and the foundations of Web services become more solid, users will start to demand tools that facilitate the service development lifecycle. It is only when such tools become available that novel technologies become applied and enter the mainstream, since the complexity, cost and time necessary to deploy and manage solutions is dramatically reduced. In this paper, we present a framework and a tool that support the model-driven development of Web services. The idea consists in identifying key Web services abstractions, in addition to those of basic Web services standards, that enable the description of service policies and properties that are useful in practice. In this paper, we focus on service protocols, and specifically on conversation and trust negotiation protocols. These protocols are modeled by means of graphical tools and high-level languages so that they are easy to specify, understand, and evolve. The tools also support the automatic generation of service implementation skeletons based on these abstractions, manage the entire service lifecycle, and provide run-time support to verify that the interaction among clients and services occur in compliance with the specified policies.

Reinduction of Albatross Decision Rules with Pooled Activity-Travel Diary Data and an Extended Set of Land Use and Cost-Related Condition States

Operationalization of the Albatross model—a rule-based model of activity-travel scheduling—is described for applications on a national scale. For this purpose, the original model was extended to include the generation of schedule skeletons and travel cost variables. Furthermore, to account for the increase of scale of the study area, the location decision component of the model was completely restructured. The complete set of 27 decision trees involved in the decision process model were newly induced from several pooled existing activity diary data sets in the Netherlands. The results indicate that the goodness of fit of the model is satisfactory at the level of individual decisions as well as aggregate distributions.

Automated generation of control skeletons for use in animation

The animation of an articulated figure is typically accomplished through the use of a corresponding control skeleton. Although the control skeleton is an effective tool, the manual construction of the skeleton can be a laborious process often requiring several hours of work and a fair degree of proficiency with the animation software used. The focus of the research described here is the automatic generation of such control skeletons. To this end, two solutions to the problem are presented, one general and one specific. In both cases, the input is required to be a set of polygonal data that defines the figure, and the output is a description of a control skeleton to be used in animating that figure. The general solution is widely applicable; it makes very few assumptions about the figure given as input or about the type of control skeleton that should be generated. A system is described that divides the problem into a series of steps, each of which is performed automatically. The basic process involves discretizing the figure, approximating its medial surface, and using that surface to construct a control skeleton. The system can produce a reasonably good control skeleton for any of a variety of figures in as little as one or two minutes on a low-end PC. The specific solution builds upon the general one but is geared toward producing more desirable skeletons for the very common case involving human-like and animal-like figures. Certain assumptions are made about the figure and about the type of control skeleton desired. In addition, heuristics based upon human and animal anatomy are invoked to adjust the control skeleton so that it is more anatomically appropriate. The motivation for this solution is the belief that a more anatomically appropriate control skeleton allows for more natural looking movement of a human or animal-like figure. Partly to support that claim, the system can produce geometry for individual bones that might function as the anatomical skeleton of the figure. This skeletal geometry can form the foundation for additional anatomical modeling that might add more realism to the animation of the figure.

Purification and characterization of phosphoenolpyruvate carboxylase from Brassica napus (rapeseed) suspension cell cultures: implications for phosphoenolpyruvate carboxylase regulation during phosphate starvation, and the integration of glycolysis with nitrogen assimilation.

Phosphoenolpyruvate carboxylase (PEPC) specific activity increased by 250% following 8 to 10 days of Pi starvation of Brassica napus suspension cells. Densitometric scanning of PEPC immunoblots revealed a close correlation between PEPC activity and the amount of the antigenic 104-kDa PEPC subunit. To further assess the influence of Pi deprivation on PEPC, the enzyme was purified from Pi-sufficient (+Pi) and Pi-starved (-Pi) cells to electrophoretic homogeneity and final specific activities of 37-40 micromol phosphoenolpyruvate utilized per min per mg protein. Gel filtration, SDS/PAGE, and CNBr peptide mapping indicated that the +Pi and -Pi PEPCs are both homotetramers composed of an identical 104-kDa subunit. Respective pH-activity profiles, phosphoenolpyruvate saturation kinetics, and sensitivity to L-malate inhibition were also indistinguishable. Kinetic studies and phosphatase treatments revealed that PEPC of the +Pi and -Pi cells exists mainly in its dephosphorylated (L-malate sensitive) form. Thus, up-regulation of PEPC activity in -Pi cells appears to be solely due to the accumulation of the same PEPC isoform being expressed in +Pi cells. PEPC activity was modulated by several metabolites involved in carbon and nitrogen metabolism. At pH 7.3, marked activation by glucose 6-phosphate and inhibition by L-malate, L-aspartate, L-glutamate, DL-isocitrate, rutin and quercetin was observed. The following paper provides a model for the coordinate regulation of B. napus PEPC and cytosolic pyruvate kinase by allosteric effectors. L-Aspartate and L-glutamate appear to play a crucial role in the control of the phosphoenolpyruvate branchpoint in B. napus, particularly with respect to the integration of carbohydrate partitioning with the generation of carbon skeletons required during nitrogen assimilation.

Efficient Morphological Set Transformations on Line Drawings

Image compression techniques have been recently used not only for reducing storage requirements, but also computational costs when processing images on low cost computers. This approach might be also of interest for processing large engineering drawings, where feature extraction techniques must be intensively applied for their segmentation into regions of interest for subsequent analysis. This paper explores this alternative using a simple run-length compression, leading to excellent results. Although this approach is not new and can be classified within the decomposition paradigm used since the early stages of line drawing image processing, the developed formalism allows directional morphological set transformations to be performed, on a low cost personal computer, faster than on costly parallel computers for the same, but uncompressed, images. This good performance is proved in two different applications: the generation of homotopic skeletons through thinning processes, and the extraction of linear features through serializing multiangle parallelism operations.

An accelerated triangulation method for computing the skeletons of free-form solid models

Shape skeletons are powerful geometric abstractions that provide useful intermediate representations for a number of geometric operations on solid models including feature recognition, shape decomposition, finite element mesh generation, and shape design. As a result there has been significant interest in the development of effective methods for skeleton generation of general free-form solids. In this paper we describe a method that combines Delaunay triangulation with local numerical optimization schemes for the generation of accurate skeletons of 3D implicit solid models. The proposed method accelerates the slow convergence of Voronoi diagrams to the skeleton, which, without optimization, would require impraelically large sample point sets and resulting meshes to attain acceptable accuracy. The Delaunay triangulation forms the basis for generating the topological structure of the skeleton. The optimization step of the process generates the geometry of the skeleton patches by moving the vertices of Delaunay tetrahedra and relocating their centres to form maximally inscribed spheres. The computational advantage of the optimization scheme is that it involves the solution of one small optimization problem per tetrahedron and its complexity is therefore only linear ( O( n)) in the number of points used for the skeleton approximation. We demonstrate the effectiveness of the method on a number of representative solid models.