Exploring the Cold-Adaptation Mechanism of Serine Hydroxymethyltransferase by Comparative Molecular Dynamics Simulations

Cold-adapted enzymes feature a lower thermostability and higher catalytic activity compared to their warm-active homologues, which are considered as a consequence of increased flexibility of their molecular structures. The complexity of the (thermo)stability-flexibility-activity relationship makes it difficult to define the strategies and formulate a general theory for enzyme cold adaptation. Here, the psychrophilic serine hydroxymethyltransferase (pSHMT) from Psychromonas ingrahamii and its mesophilic counterpart, mSHMT from Escherichia coli, were subjected to μs-scale multiple-replica molecular dynamics (MD) simulations to explore the cold-adaptation mechanism of the dimeric SHMT. The comparative analyses of MD trajectories reveal that pSHMT exhibits larger structural fluctuations and inter-monomer positional movements, a higher global flexibility, and considerably enhanced local flexibility involving the surface loops and active sites. The largest-amplitude motion mode of pSHMT describes the trends of inter-monomer dissociation and enlargement of the active-site cavity, whereas that of mSHMT characterizes the opposite trends. Based on the comparison of the calculated structural parameters and constructed free energy landscapes (FELs) between the two enzymes, we discuss in-depth the physicochemical principles underlying the stability-flexibility-activity relationships and conclude that (i) pSHMT adopts the global-flexibility mechanism to adapt to the cold environment and, (ii) optimizing the protein-solvent interactions and loosening the inter-monomer association are the main strategies for pSHMT to enhance its flexibility.     

Some concerns regarding the CAT16 chromatic adaptation transform

In recent literature, a new chromatic adaptation transform, CAT16, has been published to improve upon the widely used CAT02 model. The CAT16 model is based on the form of the CAT02 transform adopted in CIECAM02, but uses a slightly different sensor space to fix some gamut problems plaguing CIECAM02 and adopts a two-step CAT to ensure symmetry and transitivity. CAT16 is included in CAM16 but is also being promoted as a stand-alone CAT, one that can be used outside of the CAM16 model. However, the use of CAT16 as a stand-alone model can cause inconsistencies in the calculated corresponding colors due to the presence of the relative luminance of the adapting white (Y_w) in the von Kries-Ives gain control factors. Such inconsistencies are not present for the stand-alone version of the CAT02 model, which, unlike the version adopted in CIECAM02, does not include the Y_w factors. CAT16 should therefore be modified by omitting the Y_w factors. In this article, we will briefly discuss these issues in more detail and provide a consistent two-step CAT adopting the CAT16 sensor space.     

Investigation on effects of adapting chromaticities and luminance on color appearance on computer displays using memory colors

CAT02, the most widely used chromatic adaptation transform to characterize the chromatic adaptation mechanism in the human visual system, includes a factor D to characterize the degree of chromatic adaptation. This factor, however, is only determined by the luminance level of the adapting field and surround. This study was designed to investigate how the change of adapting chromaticities and the simultaneous changes of adapting chromaticities and luminance affect the degree of chromatic adaptation and color appearance on computer displays. The human observers adjusted the color appearance of various familiar objects and cubes on different display backgrounds. A higher degree of chromatic adaptation was found when using familiar objects, which was likely due to the cognitive mechanism. Both the adapting chromaticities and luminance significantly affected the degree of chromatic adaptation, with a lower degree under an adapting condition with a lower adapting correlated color temperature and a lower adapting luminance. In addition, the effect of adapting luminance on colorfulness (known as the Hunt Effect) was likely to be overpredicted in CAM02-UCS, which merits further investigations.     

Covariance matrix adaptation evolution strategy based design of fixed structure robust H∞ loop shaping controller

This paper proposes the application of Covariance Matrix Adaptation Evolution Strategy (CMA-ES) in fixed structure H_∞ loop shaping controller design. Integral Time Absolute Error (ITAE) performance requirement is incorporated as a constraint with an objective of maximization of stability margin in the fixed structure H_∞ loop shaping controller design problem. Pneumatic servo system, separating tower process and F18 fighter aircraft system are considered as test systems. The CMA-ES designed fixed structure H_∞ loop-shaping controller is compared with the traditional H_∞ loop shaping controller, non-smooth optimization and Heuristic Kalman Algorithm (HKA) based fixed structure H_∞ loop shaping controllers in terms of stability margin. 20% perturbation in the nominal plant is used to validate the robustness of the CMA-ES designed H_∞ loop shaping controller. The effect of Finite Word Length (FWL) is considered to show the implementation difficulties of controller in digital processors. Simulation results demonstrated that CMA-ES based fixed structure H_∞ loop shaping controller is suitable for real time implementation with good robust stability and performance.     

Toward the adaptation of component‐based architectures by model transformation: behind smart user interfaces

Graphical user interfaces are not always developed for remaining static. There are GUIs with the need of implementing some variability mechanisms. Component‐based GUIs are an ideal target for incorporating this kind of operations, because they can adapt their functionality at run‐time when their structure is updated by adding or removing components or by modifying the relationships between them. Mashup user interfaces are a good example of this type of GUI, and they allow to combine services through the assembly of graphical components. We intend to adapt component‐based user interfaces for obtaining smart user interfaces. With this goal, our proposal attempts to adapt abstract component‐based architectures by using model transformation. Our aim is to generate at run‐time a dynamic model transformation, because the rules describing their behavior are not pre‐set but are selected from a repository depending on the context. The proposal describes an adaptation schema based on model transformation providing a solution to this dynamic transformation. Context information is processed to select at run‐time a rule subset from a repository. Selected rules are used to generate, through a higher‐order transformation, the dynamic model transformation. This approach has been tested through a case study which applies different repositories to the same architecture and context. Moreover, a web tool has been developed for validation and demonstration of its applicability. The novelty of our proposal arises from the adaptation schema that creates a non pre‐set transformation, which enables the dynamic adaptation of component‐based architectures. Copyright © 2014 Copyright © 2014 John Wiley & Sons, Ltd.     

Deep multi-scale adversarial network with attention: A novel domain adaptation method for intelligent fault diagnosis

Data driven-based intelligent fault diagnosis methods, as a promising approach, have been widely employed in the health management and maintenance decision of rotating machinery. However, the domain shift phenomenon caused by internal and external interference inevitably exists in practical application scenarios, which significantly deteriorates the performances of the intelligent diagnosis model. And the preparation of label information in real complex scenes is usually time-consuming and expensive. To overcome these challenges, a novel unsupervised domain adaptation framework named deep multi-scale adversarial network with attention (MSANA) is introduced for machinery fault diagnosis. It is established based on two main components, one is the shared feature generator, which is constructed by two novel multi-scale modules with attention mechanism, and the other part is a fault pattern recognition module composed of two differentiated discriminators. While the multi-scale module is used to obtain rich features through different internal perceptual scales, the attention mechanism determines the weights of different scales, which promotes the dynamic adjustment performance and adaptive ability of the model. Then, decision boundary assisted adversarial learning strategy is employed to eliminate domain distribution differences and obtain domain-invariant features. A total of ten rolling bearing-based transfer scenarios and six gearbox-based transfer scenarios are adopted to evaluate the transferability of the proposed MSANA model, and the cross-domain transfer results show that it has superior transferability and stability.     

Bond strength and adaptation of pulp capping materials to dentin

This study evaluated the shear bond strength (SBS) and internal marginal adaptation of pulp‐capping materials to dentin. Flat occlusal deep dentin surfaces were produced and randomly assigned to two groups (sound or artificial caries‐affected dentin). The specimens in each group were assigned to one of seven subgroups according to the materials used: Biodentine, Theracal LC, Ultra‐Blend plus, Calcimol LC, ApaCal ART, EQUIA Forte, and Ionoseal. Buildups (3‐mm inner diameter and 2‐mm deep) were made over the dentin surfaces. The bonded specimens were tested under shear forces at a crosshead speed of 0.8 mm/min and fracture modes were determined using a stereomicroscope at 25× magnification. The materials were applied to the pulp floor of prepared Class I cavities and then the cavities were restored with composite resin. Restored molar teeth were subjected to 5,000 thermocycles and sectioned in a bucco–lingual direction. Resin replicas were made to determine the adaptation at the pulp floor with scanning electron microscopy. Significant differences were determined among both bond strengths and gap formations of the materials. EQUIA Forte applied to both dentin substrates had a significantly higher SBS than the other materials. The bond strength of each material was not influenced by the dentin condition. Biodentine (3.03%), EQUIA Forte (7.83%), and Theracal LC (13.37%) had lower gap formations compared to other materials but were not significantly different from each other.