Transformation Templates Research Articles

CRISPR/Cas9 improves targeted knock-in efficiency in Aspergillusoryzae

Aspergillus oryzae is an important fungus in food and industrial enzyme production. In A. oryzae, targeted knock-in transformation is primarily limited to homologous recombination (HR)-based systems, in which non-homologous end-joining (NHEJ)-disruptant hosts are required. However, preparation of hosts and transformation templates for such systems is laborious, in addition to other disadvantages. In the present study, we examined alternative targeted knock-in mediated by CRISPR/Cas9, in which a microhomology-mediated end-joining (MMEJ) and single-strand annealing (SSA) repair system was employed. This approach enabled the efficient development of targeted knock-in transformants without host preparation using only a short homology template. We conclude that this new method could be applied to facilitate the transformation of A. oryzae, and will make it easier to acquire targeted knock-in transformants, especially from industrially important non-model strains.

Experimental Comparison of PC-Trees and PQ-Trees

PQ-trees and PC-trees are data structures that represent sets of linear and circular orders, respectively, subject to constraints that specific subsets of elements have to be consecutive. While equivalent to each other, PC-trees are conceptually much simpler than PQ-trees; updating a PC-tree so that a set of elements becomes consecutive requires only a single operation, whereas PQ-trees use an update procedure that is described in terms of nine transformation templates that have to be recursively matched and applied. Despite these theoretical advantages, to date no practical PC-tree implementation is available. This might be due to the original description by Hsu and McConnell [ 14 ] in some places only sketching the details of the implementation. In this paper, we describe two alternative implementations of PC-trees. For the first one, we follow the approach by Hsu and McConnell, filling in the necessary details and also proposing improvements on the original algorithm. For the second one, we use a different technique for efficiently representing the tree using a Union-Find data structure. In an extensive experimental evaluation we compare our implementations to a variety of other implementations of PQ-trees that are available on the web as part of academic and other software libraries. Our results show that both PC-tree implementations beat their closest fully correct competitor, the PQ-tree implementation from the OGDF library [ 6 , 15 ], by a factor of 2 to 4, showing that PC-trees are not only conceptually simpler but also fast in practice. Moreover, we find the Union-Find-based implementation, while having a slightly worse asymptotic runtime, to be twice as fast as the one based on the description by Hsu and McConnell.

IBiR : Bug-report-driven Fault Injection

Much research on software engineering relies on experimental studies based on fault injection. Fault injection, however, is not often relevant to emulate real-world software faults since it “blindly” injects large numbers of faults. It remains indeed challenging to inject few but realistic faults that target a particular functionality in a program. In this work, we introduce iBiR , a fault injection tool that addresses this challenge by exploring change patterns associated to user-reported faults. To inject realistic faults, we create mutants by re-targeting a bug-report-driven automated program repair system, i.e., reversing its code transformation templates. iBiR is further appealing in practice since it requires deep knowledge of neither code nor tests, just of the program’s relevant bug reports. Thus, our approach focuses the fault injection on the feature targeted by the bug report. We assess iBiR by considering the Defects4J dataset. Experimental results show that our approach outperforms the fault injection performed by traditional mutation testing in terms of semantic similarity with the original bug, when applied at either system or class levels of granularity, and provides better, statistically significant estimations of test effectiveness (fault detection). Additionally, when injecting 100 faults, iBiR injects faults that couple with the real ones in around 36% of the cases, while mutation testing achieves less than 4%.

Enhanced Template Protection Algorithms Based on Fuzzy Vault and Cuckoo Hashing for Fingerprint Biometrics

Biometrics provides better authentication. Unprotected biometrics is open to attacks from intruders as stolen biometrics may not be revocable. Although there are several points where attacks can be launched on biometric systems, template databases are said to be the most frequently attacked. When a template database is attacked, attackers can add fresh templates, modify the existing ones, copy or steal templates and later construct a spoof from it or replay it back into the biometric system to impersonate a genuine user. Several template security systems have been presented in the literature to secure biometric templates. Fuzzy vault, as proposed by many researchers is, to some extent, one of the best algorithms to achieve template protection as it has good security. Fuzzy vault, however, lacks irreversibility, revocability, and diversity. To address these disadvantages and strengthen fuzzy vault, this study combines a noninvertible feature transformation template protection algorithm known as cuckoo hashing that possesses irreversibility, revocability, and diversity properties with a fuzzy vault for privacy. The study used fingerprint biometrics as it is widely used. The proposed algorithm was implemented in the MATLAB 2016a environment using FVC 2004 DB1 fingerprint public database. The proposed algorithm recorded a FAR of 0.01% and an FRR value of 0.09% with an EER of 0.05%.

A multi-criteria decision-making approach to help resource-exhausted areas choose suitable transformation templates—The example of Wansheng in Chongqing, China

• Differences in conditions lead choose suitable transformation templates difficult. • Interaction between problems are critical in select suitable transformation templates. • ANP and DEMATEL can complement each other to make evaluation more accurate. • Administrative-led models are suitable for solving current problems. • Market-led models are suitable for further transformation development. China and other major economies of the world have invested considerable resources to assist resource-exhausted areas in their development. But few regions have improved the stagnant state of development. The literature suggests that the lack of assistance provided to decision-makers when choosing suitable transformation templates often results in the selection of poor templates that are not suitable for a given region. This is an important factor that contributes to the difficulties among resource-exhausted areas to achieve transformation. This paper describes an application of hybrid Multi Criteria Decision Making (MCDM) technique for the selection of optimum template for the resource-exhausted region. The proposed model, Fuzzy Analytical Network Process (Fuzzy-ANP) is integrated with Fuzzy Decision-Making Trial and Evaluation Laboratory (Fuzzy-DEMATEL) to evaluate the research object and candidate templates. Evaluation is based on problems (criteria) including the developing new industries, improving governance capabilities, enhancing the ability to attract production, reducing unemployment, restoring an ecological environment and transformation the original resource-mining industry. Fuzzy-ANP and Fuzzy-DEMATEL are used to determine the priority of these criteria for the research region and for candidate template regions from two viewpoints: the importance of each issue, and the ability of each issue to influence other issues. This paper selects Wangsheng as research region and Ruhr, Chikuho, Lorraine and Houston as templates. The obtain preference order of the templates for Fuzzy-ANP and Fuzzy-DEMATEL are Houston > Lorraine > Chikuho > Ruhr and Ruhr > Chikuho > Houston > Lorraine respectively. Combining two results, the order of the templates is Chkuho > Lorranie > Houston > Ruhr. Chikuho is selected as template for Wansheng transformation.

Reconstructing 3D Model from Single‐View Sketch with Deep Neural Network

In this paper, we introduce a novel 3D shape reconstruction method from a single‐view sketch image based on a deep neural network. The proposed pipeline is mainly composed of three modules. The first module is sketch component segmentation based on multimodal DNN fusion and is used to segment a given sketch into a series of basic units and build a transformation template by the knots between them. The second module is a nonlinear transformation network for multifarious sketch generation with the obtained transformation template. It creates the transformation representation of a sketch by extracting the shape features of an input sketch and transformation template samples. The third module is deep 3D shape reconstruction using multifarious sketches, which takes the obtained sketches as input to reconstruct 3D shapes with a generative model. It fuses and optimizes features of multiple views and thus is more likely to generate high‐quality 3D shapes. To evaluate the effectiveness of the proposed method, we conduct extensive experiments on a public 3D reconstruction dataset. The results demonstrate that our model can achieve better reconstruction performance than peer methods. Specifically, compared to the state‐of‐the‐art method, the proposed model achieves a performance gain in terms of the five evaluation metrics by an average of 25.5% on the man‐made model dataset and 23.4% on the character object dataset using synthetic sketches and by an average of 31.8% and 29.5% on the two datasets, respectively, using human drawing sketches.

Fabrication of Nonmetal-Modulated Dual Metal-Organic Platform for Overall Water Splitting and Rechargeable Zinc-Air Batteries.

The fast development of portable water-splitting devices has led to a great deal of work on rechargeable metal-air batteries or solar cells; however, the lack of affordable multifunctional electrocatalysts still hampers their widespread applications. Herein, a well-aligned ternary metal (oxy)hydroxide nanostructure is a sacrificial pseudomorphic transformation template of an integrated metal-organic network on the carbon cloth (CC) surface, that is, the Fe-doped metal-organic framework (MOF) ZnNiCoSe@CC nanosheet network, exhibiting powerful and efficient multifunctional electrocatalysts such as the oxygen reduction reaction, oxygen evolution reaction, and hydrogen evolution reaction in alkaline media combined with desirable electrode kinetics. As a proof-of-concept observational study, the nanostructured Fe-doped MOF ZnNiCoSe@CC could be used as air-cathode materials in the rechargeable metal-air battery. The fabricated device delivered higher open-circuit voltage, higher capacity, and peak power density, excellent discharge-charge performance, and long cycle life. Thus, our research creates a unique perspective on the development of highly portable air electrodes with a favorable electrocatalytic application of overall water-splitting reaction.

Template-based AADL automatic code generation

Embedded real-time systems employ a variety of operating system platforms. Consequently, for automatic code generation, considerable redevelopment is needed when the platform changes. This results in major challenges with respect to the automatic code generation process of the architecture analysis and design language (AADL). In this paper, we propose a method of template-based automatic code generation to address this issue. Templates are used as carriers of automatic code generation rules from AADL to the object platform. These templates can be easily modified for different platforms. Automatic code generation for different platforms can be accomplished by formulating the corresponding generation rules and transformation templates. We design a set of code generation templates from AADL to the object platform and develop an automatic code generation tool. Finally, we take a typical Data Processing Unit (DPU) system as a case study to test the tool. It is demonstrated that the auto-generated codes can be compiled and executed successfully on the object platform.

Partially safe evolution of software product lines

Software Product Lines allow the automatic generation of related products built with reusable artefacts. In this context, developers may need to perform changes and check whether products are affected. A strategy to perform such analysis is verifying behaviour preservation through the use of formal theories. The product line refinement notion requires behaviour preservation for all existing products. Nevertheless, in evolution scenarios like bug fixes, some products intentionally have their behaviour changed. To support developers in these and other unsafe scenarios, we define a theory of partial product line refinement that helps to precisely understand which products are affected by a change. This provides a kind of impact analysis that could, for example, reduce test effort, since only affected products need to be tested. We provide properties such as compositionality, which deals with changes to a specific product line element, and general properties to support developers when safe and partially safe scenarios are combined. We also define a set of transformation templates, which are classified according to their compatibility to specific types of product lines. To evaluate our work, we analyse two product lines: Linux and Soletta, to discover if our templates could be helpful in evolving these systems.

Transformation optics based on unitary vectors and Fermat's principle for arbitrary spatial transformation design.

A methodology of designing an arbitrary transformation using transformation optics (TO) based on unitary vectors and Fermat's principle is presented. The TO equation is derived in terms of grid coordinates. The geometry of the transformed space is stored in the grid coordinates rather than the transformation functions. This allows the crafting of an arbitrary transformation by combining several transformation templates together. The touch interface is employed to intuitively apply the transformations. The resulting material parameters are calculated from the proposed method and verified using the anisotropic finite-difference frequency-domain method. Five examples are presented to demonstrate the capability of this method.

Development of technology for consolidation and synchronization of data of industrial-purpose integrated automated systems

The technology for synchronization and consolidation of production data of industrial-purpose integrated automated systems was developed. The technology is the architectural concepts of constructing and using a single consolidated information environment of the industrial enterprise. The functioning of a single consolidated environment occurs via the central link - a single integrated automated system that performs the functions of management of integration and exchange of data between various production systems. For correct presentation of data in various integrated automated systems, the mathematical model of production data transformation in a single intermediate format, which uses data transformation templates and establishes links between objects in these industrial-purpose systems was developed. Using a single consolidated environment provides information support of administrative decision-making on the major life cycle stages of the product. This support is based on presenting credible and operational design, production, planning and reference data used by various integrated automated systems in various departments and services of industrial enterprises. The research results as the basis for the integration methodology of automation processes of technical training, planning and operations management.

Automatic quadrilateral mesh generation and quality improvement techniques for an improved combination method

This paper developed an automatic quadrilateral meshing system to resolve the numerical simulation problems in the fields of geological mechanics, hydraulics, hydrology, and water resources. An improved combination method was proposed to automatically convert Delaunay triangular meshes into quadrilateral meshes by combining adjacent pairs of triangles through searching advancing-front edges. In order to implement the full conversion, seven combination patterns were established to select appropriate pairs of adjacent triangles. To handle the residual triangles, each nearest pair of residual triangles were moved to each other along a proper path and recombined into a quadrilateral. The movement of residual triangles was implemented through the destruction and reconstruction of neighboring quadrilaterals. A transformation template was established to convert the only residual triangle in each domain into quadrilaterals. To ensure the geometric topology of the resulting mesh, nine topological optimization modes were proposed to improve the topological connections of the degenerated quadrilaterals especially those on the boundaries of the mesh. An area-weighted Laplacian method was used to smooth the interior nodes, and an objective function method was employed to adjust the positions of special nodes. Finally, practical examples of two treatment strategies for river and overland flows were provided to demonstrate the accuracy and reliability of the meshing and optimization algorithms proposed in this paper.

Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes

The semantic interoperability of electronic healthcare records (EHRs) systems is a major challenge in the medical informatics area. International initiatives pursue the use of semantically interoperable clinical models, and ontologies have frequently been used in semantic interoperability efforts. The objective of this paper is to propose a generic, ontology-based, flexible approach for supporting the automatic transformation of clinical models, which is illustrated for the transformation of Clinical Element Models (CEMs) into openEHR archetypes. Our transformation method exploits the fact that the information models of the most relevant EHR specifications are available in the Web Ontology Language (OWL). The transformation approach is based on defining mappings between those ontological structures. We propose a way in which CEM entities can be transformed into openEHR by using transformation templates and OWL as common representation formalism. The transformation architecture exploits the reasoning and inferencing capabilities of OWL technologies. We have devised a generic, flexible approach for the transformation of clinical models, implemented for the unidirectional transformation from CEM to openEHR, a series of reusable transformation templates, a proof-of-concept implementation, and a set of openEHR archetypes that validate the methodological approach. We have been able to transform CEM into archetypes in an automatic, flexible, reusable transformation approach that could be extended to other clinical model specifications. We exploit the potential of OWL technologies for supporting the transformation process. We believe that our approach could be useful for international efforts in the area of semantic interoperability of EHR systems.

A Robust Template Matching Algorithm Based on Reducing Dimensions

Template matching is a fundamental problem in pattern recognition, which has wide applications, especially in industrial inspection. In this paper, we propose a 1-D template matching algorithm which is an alternative for 2-D full search block matching algorithms. Our approach consists of three steps. In the first step the images are converted from 2-D into 1-D by summing up the intensity values of the image in two directions horizontal and vertical. In the second step, the template matching is performed among 1-D vectors using the similarity function sum of square difference. Finally, the decision will be taken based on the value of similarity function. Transformation template image and sub-images in the source image from 2-D grey level information into 1-D information vector reduce the dimensionality of the data and accelerate the computations. Experimental results show that the computational time of the proposed approach is faster and performance is better than three basic template matching methods. Moreover, our approach is robust to detect the target object with changes of illumination in the template also when the Gaussian noise added to the source image.

A Component Model for Model Transformations

Model-driven engineering promotes an active use of models to conduct the software development process. In this way, models are used to specify, simulate, verify, test and generate code for the final systems. Model transformations are key enablers for this approach, being used to manipulate instance models of a certain modelling language. However, while other development paradigms make available techniques to increase productivity through reutilization, there are few proposals for the reuse of model transformations across different modelling languages. As a result, transformations have to be developed from scratch even if other similar ones exist. In this paper, we propose a technique for the flexible reutilization of model transformations. Our proposal is based on generic programming for the definition and instantiation of transformation templates, and on component-based development for the encapsulation and composition of transformations. We have designed a component model for model transformations, supported by an implementation currently targeting the Atlas Transformation Language (ATL). To evaluate its reusability potential, we report on a generic transformation component to analyse workflow models through their transformation into Petri nets, which we have reused for eight workflow languages, including UML Activity Diagrams, YAWL and two versions of BPMN.

Towards the flexible reuse of model transformations: A formal approach based on graph transformation

Model transformations are the heart and soul of Model-Driven Engineering (MDE). However, in order to increase the adoption of MDE by industry, techniques for developing model transformations in the large and raising the quality and productivity in their construction, like reusability, are still needed.In previous works, we developed a reutilization approach for graph transformations based on the definition of concepts, which gather the structural requirements needed by meta-models to qualify for the transformations. Reusable transformations are typed by concepts, becoming transformation templates. Transformation templates are instantiated by binding the concept to a concrete meta-model, inducing a retyping of the transformation for the given meta-model.This paper extends the approach allowing heterogeneities between the concept and the meta-model, thus increasing the reuse opportunities of transformation templates. Heterogeneities are resolved by using algebraic adapters which induce both a retyping and an adaptation of the transformation. As an alternative, the adapters can also be employed to induce an adaptation of the meta-model, and in this work we show the conditions for equivalence of both approaches to transformation reuse.

Tetranuclear Iron Complexes Bearing Benzenetetrathiolate Bridges as Four-Electron Transformation Templates and Their Electrocatalytic Properties for Proton Reduction

Two tetranuclear iron-sulfur complexes, (μ,μ-pbtt)[Fe(2)(CO)(6)](2) (pbtt = benzene-1,2,4,5-tetrathiolato, 3) and (μ,μ-obtt)[Fe(2)(CO)(6)](2) (obtt = benzene-1,2,3,4-tetrathiolato, 4), were prepared from reaction of Fe(3)(CO)(12) and the corresponding tetramercaptobenzene in THF, respectively. Complexes 5 and 6, (μ,μ-pbtt)[Fe(2)(CO)(5)L(1)][Fe(2)(CO)(5)L(2)] (L(1) = CO, L(2) = PPyr(3) (Pyr = N-pyrrolyl), 5; L(1) = L(2) = PPyr(3), 6) were obtained by controlling CO displacement of 3 with PPyr(3). Molecular structures of 3-6 were determined by spectroscopic and single-crystal X-ray analyses. All-CO Fe(4)S(4) complexes 3 and 4 each display four-electron reduction processes in consecutive chemically reversible two-electron reduction events with relatively narrow potential spans in the cyclic voltammograms. Phosphine-substituted Fe(4)S(4) complexes 5 and 6 exhibit two consecutive two-electron reduction events, which are not fully reversible. The electrocatalytic properties of 3 and 4 for proton reduction were studied using a series of carboxylic acids of increasing strength (CH(3)COOH, CH(2)ClCOOH, CHCl(2)COOH, CCl(3)COOH, and CF(3)COOH). The mechanisms for electrochemical proton reduction to hydrogen catalyzed by complex 3 as a function of acid strength are discussed.

A theory of software product line refinement

To safely evolve a software product line, it is important to have a notion of product line refinement that assures behavior preservation of the original product line products. So in this article we present a language independent theory of product line refinement, establishing refinement properties that justify stepwise and compositional product line evolution. Moreover, we instantiate our theory with the formalization of specific languages for typical product lines artifacts, and then introduce and prove soundness of a number of associated product line refinement transformation templates. These templates can be used to reason about specific product lines and as a basis to derive comprehensive product line refinement catalogues.

Flexible Model-to-Model Transformation Templates: An Application to ATL.

Model transformation is one of the core techniques in Model- Driven Engineering. Many transformation languages exist nowadays, but few oer mechanisms directed to the reuse of whole transformations or transformation fragments in dierent contexts. Taking inspiration from generic programming, in this paper we define model transformation templates. These templates are not defined over concrete meta-models, but on so-called meta-model concepts which later can be bound to specific meta-models. The binding mechanism is flexible as it permits mapping concepts and meta-models with certain kinds of structural heterogeneities. The approach is general and can be applied to any model transformation language. In this paper we report on its application to ATL.

Segmentation algorithm of complex ore images based on templates transformation and reconstruction

Lots of noises and heterogeneous objects with various sizes coexist in a complex image, such as an ore image; the classical image thresholding method cannot effectively distinguish between ores. To segment ore objects with various sizes simultaneously, two adaptive windows in the image were chosen for each pixel; the gray value of windows was calculated by Otsu’s threshold method. To extract the object skeleton, the definition principle of distance transformation templates was proposed. The ores linked together in a binary image were separated by distance transformation and gray reconstruction. The seed region of each object was picked up from the local maximum gray region of the reconstruction image. Starting from these seed regions, the watershed method was used to segment ore object effectively. The proposed algorithm marks and segments most objects from complex images precisely.