Modular Mechanism Research Articles

Screening of gene signatures for rheumatoid arthritis and osteoarthritis based on bioinformatics analysis.

The current study aimed to identify gene signatures during rheumatoid arthritis (RA) and osteoarthritis (OA), and used these to elucidate the underlying modular mechanisms. Using the Gene Expression Omnibus database, the present study obtained the GSE7669 mRNA expression microarray data from RA and OA synovial fibroblasts (n=6 each). The differentially expressed genes (DEGs) in RA synovial samples compared with OA samples were identified using the Linear Models for Microarray Analysis package. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation Visualization and Integrated Discovery. A protein-protein interaction network was constructed and the modules were further analyzed using the Molecular Complex Detection plugin of Cytoscape. A total of 181 DEGs were identified by comparing RA and OA synovial samples (96 up- and 85 downregulated genes). The significant DEGs in module 1, including collagen, type I, α 1 (COL1A1), COL3A1, COL4A1 and COL11A1, were predominantly enriched in the extracellular matrix (ECM)-receptor interaction and focal adhesion pathways. Additionally, significant DEGs in module 2, including radical S-adenosyl methionine domain containing 2 (RSAD2), 2′-5′-oligoadenylate synthetase 2 (OAS2), myxovirus (influenza virus) resistance 1 (MX1) and ISG15 ubiquitin-like modifier (ISG15), were predominantly associated with immune function pathways. In conclusion, the present study indicated that RSAD2, OAS2, MX1 and ISG15 may be notable gene signatures in RA development via regulation of the immune response. COL3A1, COL4A1, COL1A1 and COL11A1 may be important gene signatures in OA development via involvement in the pathways of ECM-receptor interactions and focal adhesions.

Evolution of symbiosis in hermatypic corals: A model of the past, present, and future

This work can be considered a prequel to our previous paper on coral bleaching induced by global warming. We once again investigate, using Finsler geometry, dynamical energy budget theory and nonlinear modular mechanics, the origin of endosymbiosis, between reef-building corals and the algae. We assume their relationship starts out as entosymbiosis, with the algal organism living on the external surfaces of host coral exoskeleton, but with both gradually adapting to each other over evolutionary time-scales. Our main conclusion is that such an evolutionary conversion is possible and indeed is quite likely.

Designing a new science-policy communication mechanism for the UN Convention to Combat Desertification

The United Nations Convention to Combat Desertification (UNCCD) has lacked an efficient mechanism to access scientific knowledge since entering into force in 1996. In 2011 it decided to convene an Ad Hoc Working Group on Scientific Advice (AGSA) and gave it a unique challenge: to design a new mechanism for science-policy communication based on the best available scientific evidence. This paper outlines the innovative ‘modular mechanism’ which the AGSA proposed to the UNCCD in September 2013, and how it was designed. Framed by the boundary organization model, and an understanding of the emergence of a new multi-scalar and polycentric style of governing, the modular mechanism consists of three modules: a Science-Policy Interface (SPI); an international self-governing and self-organizing Independent Non-Governmental Group of Scientists; and Regional Science and Technology Hubs in each UNCCD region. Now that the UNCCD has established the SPI, it is up to the worldwide scientific community to take the lead in establishing the other two modules. Science-policy communication in other UN environmental conventions could benefit from three generic principles corresponding to the innovations in the three modules—joint management of science-policy interfaces by policy makers and scientists; the production of synthetic assessments of scientific knowledge by autonomous and accountable groups of scientists; and multi-scalar and multi-directional synthesis and reporting of knowledge.

Editorial: Evolutionary Theory: Fringe or Central to Psychological Science.

Editorial: Evolutionary Theory: Fringe or Central to Psychological Science.

Design of Nonoverconstrained Energy-Efficient Multi-Axis Servo Presses for Deep-Drawing Applications1

Servo-actuated presses may provide maximum pressing force at any ram position in the same manner that hydraulic presses do, while offering several benefits in terms of precision, energy-conversion efficiency, and simplicity, due to their lack of hydraulic circuitry and oil. Several press builders have developed servo-actuated presses; however, issues relating to overconstrained multi-axis architecture have been disregarded. This study proposes an innovative method to avoid overconstrained architectures in multi-axis presses, by implementing a family of modular parallel mechanisms that connect multiple servo-axes to the press ram. Parallel mechanisms, which can be applied in several fields of robotics and industrial automation, exhibit important benefits for the application at hand, including high-load capacity, stiffness, and compactness. A biaxial industrial servo press prototype with a nonoverconstrained and modular architecture was built and presented as a proof of concept. Each axis comprises a servomotor, a gearbox reducer, and a ball-screw transmission. It is shown that such a press may be constructed from commercially available components, achieving high energy efficiency and high press force with relatively simple construction. A direct comparison with an equivalent hydraulic-press model is carried out, thus highlighting the servo press energy efficiency.

Embedding attribute grammars and their extensions using functional zippers

Attribute grammars are a suitable formalism to express complex software language analysis and manipulation algorithms, which rely on multiple traversals of the underlying syntax tree. Attribute grammars have been extended with mechanisms such as reference, higher-order and circular attributes. Such extensions provide a powerful modular mechanism and allow the specification of complex computations. This paper studies an elegant and simple, zipper-based embedding of attribute grammars and their extensions as first class citizens. In this setting, language specifications are defined as a set of independent, off-the-shelf components that can easily be composed into a powerful, executable language processor. Techniques to describe automatic bidirectional transformations between grammars in this setting are also described. Several real examples of language specification and processing programs have been implemented.

Functional Design in Rehabilitation: Modular Mechanisms for Ankle Complex

This paper is aimed at presenting an innovative ankle rehabilitation device based on a parallel mechanism. A functional analysis and design are described to obtain a device able to guarantee ankle movement while patient's body remains stationary. Human ankle is a challenging context where a series of joints are highly integrated. The proposed rehabilitation device permits a patient with walking defects to improve his or her gait. The research focuses on plantar-flexion-dorsiflexion movement. The robust design starts from an accurate modelling of ankle movements during walking, assessing motion data from healthy individuals and patients. The kinematics analysis and functional evaluations lead the study and development of the articulated system. In particular, results of simulations support the effectiveness of the current design. A 3D prototype is presented highlighting that the ankle motion is successfully demonstrated.

Complete genome sequences of T5-related Escherichia coli bacteriophages DT57C and DT571/2 isolated from horse feces.

We report the complete genome sequencing of two Escherichia coli T5-related bacteriophages, DT57C and DT571/2, isolated from the same specimen of horse feces. These two isolates share 96% nucleotide sequence identity and can thus be considered representatives of the same novel species within the genus T5likevirus. The observed variation in the ltfA gene of these phages, resulting from a recent recombination event, may explain the observed host-range differences, suggesting that a modular mechanism makes a significant contribution to the short-term evolution (or adaptation) of T5-like phage genomes in the intestinal ecosystem. Comparison of our isolates to their closest relative, coliphage T5, revealed high overall synteny of the genomes and high conservation of the sequences of almost all structural proteins as well as of the other proteins with identified functions. At the same time, numerous alterations and non-orthologous replacements of non-structural protein genes (mostly of those with unknown functions) as well as substantial differences in tail fiber locus organization support the conclusion that DT57C and DT571/2 form a species-level group clearly distinct from bacteriophage T5.

Experimental Research Regarding The Motion Capacity Of A Robotic Arm

Abstract This paper refers to the development of necessary experiments which obtained dynamic parameters (force, displacement) for a modular mechanism with multiple vertebrae. This mechanism performs functions of inspection and intervention in small spaces. Mechanical structure allows functional parameters to achieve precise movements to an imposed target. Will be analyzed the dynamic of the mechanisms using simulation instruments DimamicaRobot.tst under TestPoint programming environment and the elasticity of the tension cables. It will be changes on the mechanism so that spatial movement of the robotic arm is optimal.

Identification of therapeutic targets for breast cancer using biological informatics methods.

The present study aimed to investigate the modular mechanisms underlying breast cancer and identify potential targets for breast cancer treatment. The differentially expressed genes (DEGs) between breast cancer and normal cells were assessed using microarray data obtained from the Gene Expression Omnibus database. Gene ontology (GO) and pathway enrichment analyses were performed in order to investigate the functions of these DEGs. Subsequently, the protein-protein interaction (PPI) network was constructed using the Cytoscape software. The identified subnetworks were further analyzed using the Molecular Complex Detection plugin. In total, 571 genes (241 upregulated and 330 downregulated genes) were found to be differentially expressed between breast cancer and normal cells. The GO terms significantly enriched by DEGs included cell adhesion, immune response and extracellular region, while the most significant pathways included focal adhesion and complement and coagulation cascade pathways. The PPI network was established with 273 nodes and 718 edges, while fibronectin 1 (FN1, degrees score, 39), interleukin 6 (IL6; degree score, 96) and c-Fos protein (degree score, 32) were identified as the hub proteins in subnetwork 2. These dysregulated genes were found to be involved in the development of breast cancer. The FN1, IL6 and FOS genes may therefore be potential targets in the treatment of breast cancer.

Miniature Tripod with Parallel Kinematics for Use in Clean Room Medical Laboratory Applications

The paper presents the structure of a precise parallel tri-axle manipulator with the functionality of progressing-tilting table. The end effector of the device is a platform, for which three coordinates of position are defined. The manipulator has three degrees of freedom: movement perpendicular to the base and rotation in two mutually perpendicular axes contained in the surface parallel to the base.The concept of the positioning mechanism is based on parallel tripod kinematics where the end effector – the platform – is seated on three active limbs – actuators. The use of parallel kinematics allowed modular construction of the positioning mechanism. The developed modular functional mechanism with minimal number of elements in kinematic chain ensures high positioning resolution. The concept of application of eccentric mechanism for platform positioning is an original idea in this solution. The compact construction allows applying the manipulator in medical devices that require meeting of the hygienic conditions in the medical test and research laboratories. The possibility of the utilisation of the precise manipulator covers wide areas of science and technology where precise positioning of the object is required, e.g. sample positioning for microscopes, scanning systems.

Surface Roughness Identification of Cutting Product on Design Aspect Variation of Modular Axis Mechanism

The use of modular component in machine tool structure is an attempt to reduce the production cost. This paper presents the development of machine tool structure for low cutting force using the modular axis mechanism. Single axis mechanism was designed and varied the mover bearing, the length of slideway and the diameter of lead-screw. Cutting test was then performed using the variation. The experimental result shows that the dimension tolerance of linear bearing is the dominant aspect which affect on the product surface roughness. While the use of ball bearing in mover system, the motion looseness can be minimized affects on improving product surface finish.

Nonhomologous recombination between defective poliovirus and coxsackievirus genomes suggests a new model of genetic plasticity for picornaviruses.

ABSTRACTMost of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3′ end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses.

Reassembly of JIP1 scaffold complex in JNK MAP kinase pathway using heterologous protein interactions.

Formation of signaling protein complexes is crucial for proper signal transduction. Scaffold proteins in MAP kinase pathways are thought to facilitate complex assembly, thereby promoting efficient and specific signaling. To elucidate the assembly mechanism of scaffold complexes in mammals, we attempted to rationally rewire JIP1-dependent JNK MAP kinase pathway via alternative assembly of JIP1 complex. When JIP1-JNK docking interaction in the complex was replaced with heterologous protein interaction domains, such as PDZ domains and JNK-binding domains, a functional scaffold complex was reconstituted, and JNK signaling was rescued. Reassembly of JIP1 complex using heterologous protein interactions was sufficient for restoring of JNK MAP kinase pathway to induce signaling responses, including JNK activation and cell death. These results suggest a simple yet modular mechanism for JIP1 scaffold assembly in mammals.

A task-oriented modular and agent-based collaborative design mechanism for distributed product development

The rapid expansion of enterprises makes product collaborative design (PCD) a critical issue under the distributed heterogeneous environment, but as the collaborative task of large-scale network becomes more complicated, neither unified task decomposition and allocation methodology nor Agent-based network management platform can satisfy the increasing demands. In this paper, to meet requirements of PCD for distributed product development, a collaborative design mechanism based on the thought of modularity and the Agent technology is presented. First, the top-down 4-tier process model based on task-oriented modular and Agent is constructed for PCD after analyzing the mapping relationships between requirements and functions in the collaborative design. Second, on basis of sub-task decomposition for PCD based on a mixed method, the mathematic model of task-oriented modular based on multi-objective optimization is established to maximize the module cohesion degree and minimize the module coupling degree, while considering the module executable degree as a restriction. The mathematic model is optimized and simulated by the modified PSO, and the decomposed modules are obtained. Finally, the Agent structure model for collaborative design is put forward, and the optimism matching Agents are selected by using similarity algorithm to implement different task-modules by the integrated reasoning and decision-making mechanism with the behavioral model of collaborative design Agents. With the results of experimental studies for automobile collaborative design, the feasibility and efficiency of this methodology of task-oriented modular and Agent-based collaborative design in the distributed heterogeneous environment are verified. On this basis, an integrative automobile collaborative R&D platform is developed. This research provides an effective platform for automobile manufacturing enterprises to achieve PCD, and helps to promote product numeralization collaborative R&D and management development.

Contrasts between whole-plant and local nutrient levels determine root growth and death in Ailanthus altissima (Simaroubaceae).

• There is an ongoing debate about the importance of whole-plant control vs. local modular mechanisms for root growth. We conducted a split-root experiment with different patch/background levels of nitrogen to examine whether local root growth and death are controlled by local resource levels or at the whole-plant level.• Three microrhizotrons with 0, 10, and 100 µg N/g growth medium levels (74 g growth medium each) were attached to pots of high or low soil N in which one Ailanthus altissima individual was growing. One fine root was guided into each of the microrhizotrons and photographed every 4 d. Plants were harvested after 28 d; root growth and mortality in the microrhizotrons were recorded. Changes in root length, number of laterals, and interlateral length were determined from the photos and analyzed.• While overall plant growth was influenced by background N level, both patch and background N levels influenced root growth and mortality in patches. Local roots proliferated most when the patch N level was high and background level low, and they proliferated least and showed highest mortality when patch N was low and the background level high.• The fate of roots growing in a patch is influenced by the resource environment of the plant's other roots as well as the resource levels in the patch itself. Thus, the growth and death of roots in patches is determined by both modular and whole-plant mechanisms.

A Middleware-Based Simulation and Control Framework for Mobile Service Robots

A mobile service robot is a complex distributed system integrating various technologies and having large heterogeneity. In order to facilitate component development and system integration of the mobile service robots, a middleware-based simulation and control framework for system integration and application development, as well as the robotic functional component (RFC) framework with a simplified structure and an efficient transmission scheme, is proposed for mobile service robot systems. Designed to implement a distributed modular mechanism for a mobile service robot, the middleware-based framework for simulation and control is comprised of four layers: low-level abstraction layer, communication layer, high-level abstraction layer, and application layer. Common Object Request Broker Architecture (CORBA) and Robot Technology Middleware (RTM) are employed as middleware for the development of RFCs and for system integration. Communication between the components and the graphical programming tool is done by the communication layer (CORBA ORB). The conducted experiments validated the proposed framework in terms of ideal performance of reusability, interoperability, and extensibility, as well as indicated that the proposed RFC framework is simplified and easy enough to perform well in data transmission, which will reduce the costs and the threshold of robot development.

The Modular Parallel Mechanism of Single-Driven Multi-Legged Robots

This paper designs a modular parallel mechanism for single-driven multi-legged robots. The mechanism achieves the goal to coordinate the lifting and swinging of all the legs with only one actuator and has good motion characteristics. The mechanism is not only easy to control, but also capable to optimize the trajectory of the robot legs by changing the structure size of the mechanism. This paper implements the trajectory simulation and dynamic simulation of the key points of the mechanism on the basis of the kinematics model, and the results show that the mechanism has a good trajectory and motion characteristics. The modular parallel mechanism is also applicable to those multi-legged robots such as quadruped robots and eight-legged robots, indicating that it has a good scalability.

Improving workflow modularity using a concern-specific layer on top of Unify

Workflows are a popular means of automating processes in many domains, ranging from high-level business process modeling to lower-level web service orchestration. However, state-of-the-art workflow languages offer a limited set of modularization mechanisms. This results in monolithic workflow specifications, in which different concerns are scattered across the workflow and tangled with one another. This hinders the design, evolution, and reusability of workflows expressed in these languages. We address this problem through the Unify framework. This framework enables uniform modularization of workflows by supporting the specification of all workflow concerns – including crosscutting ones – in isolation of each other. These independently specified workflow concerns are connected to each other using workflow-specific connectors. In order to further facilitate the development of workflows, we enable the definition of concern-specific languages (CSLs) on top of the Unify framework. A CSL facilitates the expression of a family of workflow concerns by offering abstractions that map well to the concerns' domain. Thus, domain experts can add concerns to a workflow using concern-specific language constructs. We exemplify the specification of a workflow in Unify, and show the definition and application of two concern-specific languages built on top of Unify.

Substrate‐dependent dynamics of UDP‐galactopyranose mutase: Implications for drug design

Trypanosoma cruzi is the causative agent of Chagas disease, a neglected tropical disease that represents one of the major health challenges of the Latin American countries. Successful efforts were made during the last few decades to control the transmission of this disease, but there is still no treatment for the 10 million adults in the chronic phase of the disease. In T. cruzi, as well as in other pathogens, the flavoenzyme UDP-galactopyranose mutase (UGM) catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, a precursor of the cell surface β-galactofuranose that is involved in the virulence of the pathogen. The fact that UGM is not present in humans makes inhibition of this enzyme a good approach in the design of new Chagas therapeutics. By performing a series of computer simulations of T. cruzi UGM in the presence or absence of an active site ligand, we address the molecular details of the mechanism that controls the uptake and retention of the substrate. The simulations suggest a modular mechanism in which each moiety of the substrate controls the flexibility of a different protein loop. Furthermore, the calculations indicate that interactions with the substrate diphosphate moiety are especially important for stabilizing the closed active site. This hypothesis is supported with kinetics measurements of site-directed mutants of T. cruzi UGM. Our results extend our knowledge of UGM dynamics and offer new alternatives for the prospective design of drugs.