Model System For Interactions Research Articles

Unfolding and partial refolding of a cellulase from the SDS-denatured state: From β-sheet to α-helix and back

Globular proteins are typically unfolded by SDS to form protein-decorated micelle-like structures. Several proteins have been shown subsequently to refold by addition of the nonionic surfactant octaethylene glycol monododecyl ether (C12E8). Thus SDS converts β-lactoglobulin, which has mainly β-sheet secondary structure, into a state rich in α-helicality, while addition of C12E8 leads to refolding and recovery of the original β-sheet structure. Here we extend these studies to the large β-sheet-rich cellulase Cel7b from Humicola insolens whose enzymatic activity provides a very sensitive refolding parameter. The enzymes widespread usage in the detergent industry makes it an obvious model system for protein-surfactant interactions. SDS-unfolding and subsequent refolding using C12E8 were investigated at pH 4.2 using near- and far-UV circular dichroism (CD), small-angle X-ray scattering (SAXS), isothermal titration calorimetry (ITC), size-exclusion chromatography (SEC) and activity measurements. The Cel7b:SDS complex can be described as a random configuration of 3–4 connected core-shell structures in which the protein is converted to a mainly α-helical secondary structure. Addition of C12E8 recovers almost all the secondary structure, part of the tertiary structure, about 50% of the activity and dissociates part of the protein population completely from detergent micelles. The lack of complete refolding may be due to charge neutralisation of Cel7b by SDS, kinetically trapping the enzyme into aggregated structures. In support of this, aggregates did not form when C12E8 was first mixed with Cel7b followed by addition of SDS. Formation of such aggregates may be a general phenomenon hampering quantitative refolding from the SDS-denatured state.

Linker Dependence of Avidity in Multivalent Interactions Between Disordered Proteins

Multidomain proteins often interact through several independent binding sites connected by disordered linkers. The architecture of such linkers affects avidity by modulating the effective concentration of intramolecular binding. The linker dependence of avidity has been estimated theoretically using simple physical models, but such models have not been tested experimentally because the effective concentrations could not be measured directly. We have developed a model system for bivalent protein interactions connected by disordered linkers, where the effective concentration can be measured using a competition experiment. We characterized the bivalent protein interactions kinetically and thermodynamically for a variety of linker lengths and interaction strengths. In total, this allowed us to critically assess the existing theoretical models of avidity in disordered, multivalent interactions. As expected, the onset of avidity occurs when the effective concentration reached the dissociation constant of the weakest interaction. Avidity decreased monotonously with linker length, but only by a third of what is predicted by theoretical models. We suggest that the length dependence of avidity is attenuated by compensating mechanisms such as linker interactions or entanglement. The direct role of linkers in avidity suggests they provide a generic mechanism for allosteric regulation of disordered, multivalent proteins.

Library Space of the CIS Countries as a Self-organizing System: Research Methodology

The article reveals the research methodology of the library space of the Commonwealth of Independent States (CIS) based on the theory of self-organization (synergetics). Synergetics as the direction of post-non-classical science was developed at the end of the last — the beginning of the new Millennium in the works of a number of researchers who proved the universality of this methodology and its applicability to the study of processes occurring in society. However, until the 2000s, this methodology did not get worthy application in the library science. The relevance of this study is that the modern library science requires a new worldview-methodological approach to the investigation of processes taking place in the cultural and library sphere, which will help to develop and enrich the successfully used method of system analysis. Based on this, the author sets the task to study the library space of the CIS as a self-organizing system that is in the process of evolution over a long historical period. The article considers the library space as a dynamically developing system of social nature. The author traces its cause-and-effect relations, conditions and factors in historical perspective and modern aspects. The concept of “library space of the CIS countries” arose after the disintegration of the Soviet Union in 1991 and as a result of formation of the CIS to refer to the form of interstate library interaction and cooperation. The article studies the library space of the CIS countries as a system of interaction of libraries formed in the post-Soviet period, the basis of which is their belonging to the Commonwealth of Independent States, within which the interstate relations of libraries are developing, basing on long historical and cultural ties between them; and the Russian language is the language of professional and interpersonal communication. The author presents the descriptive model of interaction system of libraries of the CIS countries with the main features and principles of construction. The article establishes that the CIS library space is characterized by features of a complex, open, dynamic self-organizing system. The methodological nature and theoretical philosophical significance of the article make it interesting for librarians, science theorists and cultural scientists.

Formal system interactive failure analysis method based on systems theoretic process analysis model

Interactive failures are failures caused by two or more components that often occur in complex systems when the system is modified, upgraded, or simply designed inadequately. However, the official guideline provided, namely, common cause analysis, cannot discover these problems. It cannot establish a complex interactive system model, nor can it provide a unified analysis method for all parts of the system. Another method, systems theoretic process analysis, is limited to the control system.To solve this problem, a method called system theoretic formal analysis method (STFAM) is proposed in this paper. STFAM establishes a system-component-interactive model that provides an abundance of interactive information for failure analysis and presents a unified model to support the analysis of multiple components in the system. It is divided into three steps. First, a hierarchical system structure is built and then transformed into a formalized state machine. Next, the interactive failures are determined and converted into a linear temporal logic or computation tree logic model. Finally, NuSMV is used to verify the model and record the results. To evaluate the proposed method, a practical problem that occurred in full-authority digital engine control, in which in some cases, the valve closes for unknown reasons until the system is reset is presented. An analysis of the issue demonstrates the effectiveness of our method.

Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites.

Kinetoplastids are a group of parasites that includes several medically-important species. These human-infective species are transmitted by insect vectors in which the parasites undergo specific developmental transformations. For each species, this includes a stage in which parasites adhere to insect tissue via a hemidesmosome-like structure. Although this structure has been described morphologically, it has never been molecularly characterized. We are using Crithidia fasciculata, an insect parasite that produces large numbers of adherent parasites inside its mosquito host, as a model kinetoplastid to investigate both the mechanism of adherence and the signals required for differentiation to an adherent form. An advantage of C. fasciculata is that adherent parasites can be generated both in vitro, allowing a direct comparison to cultured swimming forms, as well as in vivo within the mosquito. Using RNAseq, we identify genes associated with adherence in C. fasciculata. As almost all of these genes have orthologs in other kinetoplastid species, our findings may reveal shared mechanisms of adherence, allowing investigation of a crucial step in parasite development and disease transmission. In addition, dual-RNAseq allowed us to explore the interaction between the parasites and the mosquito. Although the infection is well-tolerated, anti-microbial peptides and other components of the mosquito innate immune system are upregulated. Our findings indicate that C. fasciculata is a powerful model system for probing kinetoplastid-insect interactions.

The Parasitic Wasp, Cotesia congregata (Say), Consists of Two Incipient Species Isolated by Asymmetric Reproductive Incompatibility and Hybrid Inability to Overcome Host Defenses

Parasitic wasps are highly diverse and play a major role in suppression of herbivorous insect pest populations. Several previously identified species of parasitic wasps have been found to be complexes of cryptic species resulting from adaptations to specific hosts or host foodplants. Cotesia congregata (Say) (Hymenoptera: Braconidae), which has long served as a model system for host-parasitoid interactions, can be used for investigating the process of diversification among sympatric populations that differ in host and host foodplant usage. Two incipient species of C. congregata have been identified in the USA mid-Atlantic region, “MsT wasps” originate from Manduca sexta (L.) (Lepidoptera: Sphingidae) on tobacco and “CcC wasps” originate from Ceratomia catalpae (Boisduval) (Lepidoptera: Sphingidae) on catalpa. Both wasp sources can develop in either host species. Hybrids resulting from MsT♂xCcC♀ crosses are fertile, whereas hybrids from CcC♂xMsT♀ crosses are typically sterile. In this study, we compared relative expression in vivo of seven C. congregata bracovirus (CcBV) genes among MsT and CcC parental and hybrid crosses. Also, we established hybrid crosses between MsT and CcC wasps and four additional host foodplant sources of C. congregata. Patterns of relative expression in vivo of MsT and CcC CcBV genes differed; a few were not expressed in hosts parasitized by CcC wasps. Overall, relative expression of CcBV genes from MsT and CcC wasps did not differ with respect to the host species parasitized. Low or absent expression of CcBV genes was found in hosts parasitized by sterile hybrids. For the most part, the other four host-foodplant wasp sources were reproductively compatible with either MsT or CcC wasps and hybrid crosses with the alternative wasp source were asymmetrically sterile. Crosses involving CcC males or MsT females produced sterile hybrids that lacked mature ovaries. Cumulatively, results indicate that C. congregata is composed of two sympatric incipient species that can utilize multiple host species rather than several host-associated races or cryptic species.

Cancer Immune Control Dynamics (CICD): A clinical data driven model of systemic immunity.

e21058 Background: Recent clinical advances in cancer immuno-therapeutics underscore the need for improved understanding of the complex relationship between cancer and the multiple, multi-functional, inter-dependent, cellular and humoral mediators/regulators of the human immune system. This will lead to improvements in the efficacy of existing immune therapies (patient selection; drug combinations) and insight into new therapeutic targets that may significantly reduce the time to new therapeutics discoveries capable of meaningful clinical impacts. Methods: A systems analysis approach (Cancer Immune Control Dynamics, CICD) attempts to identify the differences between systemic immune homeostasis of healthy volunteers versus patients with metastatic malignant melanoma based on serial measurements of a set of conventional peripheral blood biomarkers of immune function (15 cell subsets and 35 cytokines) assessed daily over 7-10 days. The modeling strategy takes aerospace engineering control theory and system identification algorithms to analyze the state of an individual’s immune system based on the biomarkers’ dynamic non-linear oscillatory behaviors. The analysis framework builds on the classical predator-prey equations commonly used to model biological system dynamics. Tens of thousands of biologically possible biomarker interactions are modeled by a set of matrix equations that creates a system interaction model. CICD quantifies the system equations with biomarker values and solves it to measure the interactions. Results: Quantification of thousands of unique biomarker relationships per participant enables classification based on their immune profile rather than their clinical diagnosis and a basis for a visualization of a person’s immunity state. Conclusions: Results provide initial evidence that a model-based analysis of serially collected biomarker data can lead to biological insights into human immunity, of potential benefit in clinical decisions. It is anticipated that CICD-based capabilities will provide tools to specifically address cancer and treatment modulated (immune checkpoint inhibitors) parameters of human immunity, revealing clinically relevant biological interactions.

Decentralised resilient autonomous control architecture for dynamic microgrids

Microgrids serve as an integral part of future power distribution systems. Typically, microgrids are managed by centralised controllers. There are two major concerns about using a single centralised controller. The controller can become a performance and reliability bottleneck for the entire system, where its failure can bring the entire system down. Excessive communication delays can also degrade the system performance. As a solution, a true decentralised control architecture for microgrids is proposed, designed, developed, and tested here. Distributing the controls to local agents decreases the possibility of network congestion to occur. Decentralisation will also enhance the reliability of the system since the single point of failure is replaced by a distributed architecture. The proof-of-concept of true decentralisation of microgrid control architecture is implemented using Hardware-in-the-Loop Platform. Device level and system level controller and interaction models are defined for a self-coordination. Also, microgrid energy management system (EMS) and control case scenarios are demonstrated. The experimental results show the robustness of the proposed architecture.

Modeling Interactive Systems at the Business Level: Inter-Action Diagram

This paper presents the Inter-Action diagram as an element to capture useful information in the design of interactive systems. The Inter-Action diagram allows designers to enrich the modeling of interactive systems at the business abstraction level. This paper shows how Inter-Action Modeling has been enriched since it emerged as a proposal to provide a high-level model, which can be subdivided and, which represents the evolution, according to time, of the processes of the system. The components that support this Inter-Action Modeling and its importance for the development of interactive systems are also exposed.

Indirect bridge modal parameters identification with one stationary and one moving sensors and stochastic subspace identification

A new indirect strategy is proposed to estimate the bridge modal parameters from the dynamic responses of two vehicles using stochastic subspace identification technique. The effect of ambient excitation, such as ongoing traffic, is simulated as white-noise excitation at the bridge supports. The state-space model of the vehicle-bridge interaction system is derived for a single-degree-of-freedom quarter-car model and the bridge deck modeled as a simply-supported Euler-Bernoulli beam. Bridge modal frequencies can be estimated accurately from the vehicle responses. Two instrumented vehicles are required to estimate the bridge mode shapes, with one serving as a fixed reference sensor and the other as a moving sensor. The measured accelerations from the vehicles are divided into segments and each pair of signal segments forms a state-space identification problem. Local mode shape value from each signal segment can be estimated using the reference-based SSI method. A rescaling on the local mode shape values is applied to construct the global mode shapes. Effects of the bridge surface roughness, measurement noise and vehicle properties on the mode shape identification are also numerically studied. A vehicle-bridge interaction model in the laboratory serves for the experimental validation of the proposed strategy. Both numerical and experimental results show that the proposed method can estimate the bridge modal parameters with acceptable accuracy.

A Systems Model of Dyadic Nonverbal Interaction

This article discusses a new systems model of dyadic nonverbal interaction. The model builds on earlier theories by integrating partners’ parallel sending and receiving nonverbal processes into a broader, dynamic ecological system. It does so in two ways. First, it moves the level of description beyond the individual level to the coordination of both partners’ contributions to the interaction. Second, it recognizes that the relationships between (a) individuals’ characteristics and processes and (b) the social ecology of the interaction setting are reciprocal and best analyzed at the systems level. Thus, the systems model attempts to describe and explain the dynamic interplay among individual, dyadic, and environmental processes in nonverbal interactions. The potential utility and the limitations of the systems model are discussed and the implications for future research considered. Although the systems model is focused explicitly on face-to-face nonverbal communication, it has considerable relevance for digital communication. Specifically, this model provides a useful framework for examining the social effects of mobile device use and as a template for studying human–robot interactions.

Mesenchymal Stem Cell Isolation from Pulp Tissue and Co-Culture with Cancer Cells to Study Their Interactions.

Cancer as a multistep process and complicated disease is not only regulated by individual cell proliferation and growth but also controlled by tumor environment and cell-cell interactions. Identification of cancer and stem cell interactions, including changes in extracellular environment, physical interactions, and secreted factors, might enable the discovery of new therapy options. We combine known co-culture techniques to create a model system for mesenchymal stem cells (MSCs) and cancer cell interactions. In the current study, dental pulp stem cells (DPSCs) and PC-3 prostate cancer cell interactions were examined by direct and indirect co-culture techniques. Condition medium (CM) obtained from DPSCs and 0.4 µm pore sized trans-well membranes were used to study paracrine activity. Co-culture of different cell types together was performed to study direct cell-cell interaction. The results revealed that CM increased cell proliferation and decreased apoptosis in prostate cancer cell cultures. Both CM and trans-well system increased cell migration capacity of PC-3 cells. Cells stained with different membrane dyes were seeded into the same culture vessels, and DPSCs participated in a self-organized structure with PC-3 cells under this direct co-culture condition. Overall, the results indicated that co-culture techniques could be useful for cancer and MSC interactions as a model system.

Incremental 3D Cuboid Modeling with Drift Compensation.

This paper presents a framework of incremental 3D cuboid modeling by using the mapping results of an RGB-D camera based simultaneous localization and mapping (SLAM) system. This framework is useful in accurately creating cuboid CAD models from a point cloud in an online manner. While performing the RGB-D SLAM, planes are incrementally reconstructed from a point cloud in each frame to create a plane map. Then, cuboids are detected in the plane map by analyzing the positional relationships between the planes, such as orthogonality, convexity, and proximity. Finally, the position, pose, and size of a cuboid are determined by computing the intersection of three perpendicular planes. To suppress the false detection of the cuboids, the cuboid shapes are incrementally updated with sequential measurements to check the uncertainty of the cuboids. In addition, the drift error of the SLAM is compensated by the registration of the cuboids. As an application of our framework, an augmented reality-based interactive cuboid modeling system was developed. In the evaluation at cluttered environments, the precision and recall of the cuboid detection were investigated, compared with a batch-based cuboid detection method, so that the advantages of our proposed method were clarified.

A Concept of the Interactive Information and Modeling System for Gas Dynamics and Multidisciplinary Research

A Concept of the Interactive Information and Modeling System for Gas Dynamics and Multidisciplinary Research

Integrating User Design and Formal Models within PVSio-Web

Creating formal models of interactive systems has wide reaching benefits, not only for verifying low-level correctness, but also as a tool for ensuring user interfaces behave logically and consistently. Despite this, tools for designing user experiences and tools for creating and working with formal models are typically distinctly separate systems. This work aims to bridge this divide by allowing the generation of state machine diagrams and formal models via a simple, interactive prototyping tool that mirrors the basic functionality of many modern digital prototyping applications.

Plasmon excitation and subsequent isomerization dynamics in naphthalene and azulene under fast proton interaction.

The interaction of fast protons (velocity between 1.41 and 2.4 a.u.) with naphthalene and azulene is investigated as a model of an ion-polycyclic aromatic hydrocarbon interaction system. Production of various intact and fragment ions in coincidence with electron emission, electron transfer to projectile, or both is analyzed. The two targets being isomers, the rather obvious similarity in the fundamental ion-molecule collision energetics is quantitatively verified. The fast isomerization processes of cationic azulene are observed to be influencing its further dissociation channels such as C2H2 and H eliminations. A first ever attempt is presented here wherein single plasmon excitation in conjunction with isomerization dynamics is reported. Evidence from dication evaporation energetics is used to invoke the double plasmon excitation model. A model based on the multiplasmon resonance explains the observed proton velocity dependence of double to single ionization cross sections. Moreover an attempt is made to reinforce the proposition of double plasmon excitation by explaining the observed suppression of neutral H loss from dications as opposed to monocations.

Sit & Relax: Interactive Design of Body‐Supporting Surfaces

AbstractWe propose a novel method for interactive design of well‐fitting body‐supporting surfaces that is driven by the pressure distribution on the body's surface. Our main contribution is an interactive modeling system that utilizes captured body poses and computes an importance field that is proportional to the pressure distribution on the body for a given pose. This distribution indicates where the body should be supported in order to easily hold a particular pose, which is one of the measures of comfortable sitting. Using our approximation, we propose the entire workflow for interactive design of C2 smooth surfaces which serve as seats, or generally, as body supporting furniture for comfortable sitting. Finally, we also provide a design tool for Rhinoceros/Grasshopper that allows for interactive creation of single designs or entire multi‐person sitting scenarios. We also test the tool with design students and present several results. Our method aims at interactive design in order to help designers to create appropriate surfaces digitally without additional empirical design passes.

Multi‐objective optimisation for composite generation and transmission expansion planning considering offshore wind power and feed‐in tariffs

This study proposes a multi-objective mathematical optimisation model which includes minimisation of the investment costs of new offshore wind farm units, investment costs of new transmission lines, fuel costs, emissions of the fossil fuel generators as well as the maximisation of incentives for new generating units. The mathematical model can be used to determine the optimal expansion planning for generation and transmission facilities with consideration of the impact of location and feed-in tariffs for offshore wind power on the overall system capacity and efficiency. The proposed model is solved using CPLEX 12.6.3 solver in advanced interactive multidimensional modelling system and tested on the modified Garver 6-bus test system and the IEEE 24-bus reliability test system. Simulation results indicate that improving the incentive support scheme and minimisation of the total cost will improve the effective utilisation of offshore power.

Harmonic and power loss minimization in power systems incorporating renewable energy sources and locational marginal pricing

In composite expansion planning, improving the efficiency and power quality of power supplied from Renewable Energy Sources (RES) is highly essential. Therefore, this paper focuses on developing an optimal power flow optimization model for minimizing power loss and harmonics emanating from RES with emphasis on reducing their impact on the Locational Marginal Prices. In order to assess the magnitude of harmonics, grid modelling and simulation with RES such as wind and solar energy were carried out using the Electrical Transient Analyzer Program 12.6.0 software. The proposed mixed integer nonlinear programming mathematical model was solved using the Outer Approximation Algorithm solver in the advanced interactive multidimensional modelling system, and the efficiency of the model was tested on the modified IEEE 6 bus and 24 bus system. The results obtained from simulations reveal the efficiency of the proposed model in terms of effective cost reduction, nodal marginal price reduction, minimization of harmonic losses, and additional lines in the power system network.

3D Sketching using Multi-View Deep Volumetric Prediction

Sketch-based modeling strives to bring the ease and immediacy of drawing to the 3D world. However, while drawings are easy for humans to create, they are very challenging for computers to interpret due to their sparsity and ambiguity. We propose a data-driven approach that tackles this challenge by learning to reconstruct 3D shapes from one or more drawings. At the core of our approach is a deep convolutional neural network (CNN) that predicts occupancy of a voxel grid from a line drawing. This CNN provides an initial 3D reconstruction as soon as the user completes a single drawing of the desired shape. We complement this single-view network with an updater CNN that refines an existing prediction given a new drawing of the shape created from a novel viewpoint. A key advantage of our approach is that we can apply the updater iteratively to fuse information from an arbitrary number of viewpoints, without requiring explicit stroke correspondences between the drawings. We train both CNNs by rendering synthetic contour drawings from hand-modeled shape collections as well as from procedurally-generated abstract shapes. Finally, we integrate our CNNs in an interactive modeling system that allows users to seamlessly draw an object, rotate it to see its 3D reconstruction, and refine it by re-drawing from another vantage point using the 3D reconstruction as guidance.