scholarly journals Applications of molecular networks in biomedicine

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Monica Chagoyen ◽  
Juan A G Ranea ◽  
Florencio Pazos
Keyword(s):  
Single Gene ◽  
Point Of View ◽  
Molecular Networks ◽  
Large Sets ◽  
Software Packages ◽  
Number Of Genes ◽  
Complex Phenomena ◽  
Network Approaches ◽  
Molecular Components ◽  
Standard Software

Abstract Due to the large interdependence between the molecular components of living systems, many phenomena, including those related to pathologies, cannot be explained in terms of a single gene or a small number of genes. Molecular networks, representing different types of relationships between molecular entities, embody these large sets of interdependences in a framework that allow their mining from a systemic point of view to obtain information. These networks, often generated from high-throughput omics datasets, are used to study the complex phenomena of human pathologies from a systemic point of view. Complementing the reductionist approach of molecular biology, based on the detailed study of a small number of genes, systemic approaches to human diseases consider that these are better reflected in large and intricate networks of relationships between genes. These networks, and not the single genes, provide both better markers for diagnosing diseases and targets for treating them. Network approaches are being used to gain insight into the molecular basis of complex diseases and interpret the large datasets associated with them, such as genomic variants. Network formalism is also suitable for integrating large, heterogeneous and multilevel datasets associated with diseases from the molecular level to organismal and epidemiological scales. Many of these approaches are available to nonexpert users through standard software packages.

scholarly journals Jasmonates and Plant Salt Stress: Molecular Players, Physiological Effects, and Improving Tolerance by Using Genome-Associated Tools

2021 ◽  
Vol 22 (6) ◽  
pp. 3082
Author(s):  
Celia Delgado ◽  
Freddy Mora-Poblete ◽  
Sunny Ahmar ◽  
Jen-Tsung Chen ◽  
Carlos R. Figueroa
Keyword(s):  
Salt Stress ◽  
Abiotic Stresses ◽  
Synergistic Effects ◽  
Antioxidant Response ◽  
Crop Productivity ◽  
Point Of View ◽  
Physiological Effects ◽  
Crop Tolerance ◽  
Molecular Components ◽  
Ja Signaling

Soil salinity is one of the most limiting stresses for crop productivity and quality worldwide. In this sense, jasmonates (JAs) have emerged as phytohormones that play essential roles in mediating plant response to abiotic stresses, including salt stress. Here, we reviewed the mechanisms underlying the activation and response of the JA-biosynthesis and JA-signaling pathways under saline conditions in Arabidopsis and several crops. In this sense, molecular components of JA-signaling such as MYC2 transcription factor and JASMONATE ZIM-DOMAIN (JAZ) repressors are key players for the JA-associated response. Moreover, we review the antagonist and synergistic effects between JA and other hormones such as abscisic acid (ABA). From an applied point of view, several reports have shown that exogenous JA applications increase the antioxidant response in plants to alleviate salt stress. Finally, we discuss the latest advances in genomic techniques for the improvement of crop tolerance to salt stress with a focus on jasmonates.

scholarly journals When good ligands go bad

2014 ◽  
Vol 70 (a1) ◽  
pp. C1269-C1269
Author(s):  
Ethan Merritt
Keyword(s):  
Task Force ◽  
Structure Refinement ◽  
Binding Pocket ◽  
Software Packages ◽  
Protein Model ◽  
Protein Components ◽  
First Time ◽  
Standard Software ◽  
New Protein

"Tools for validating structural models of proteins are relatively mature and widely implemented. New protein crystallographers are introduced early on to the importance of monitoring conformance with expected φ/ψ values, favored rotamers, and local stereochemistry. The protein model is validated by the PDB at the time of deposition using criteria that are also available in the standard software packages used to refine the model being deposited. By contrast, crystallographers are typically much less familiar with procedures to validate key non-protein components of the model – cofactors, substrates, inhibitors, etc. It has been estimated that as many as a third of all ligands in the PDB exhibit preventable errors of some sort, ranging from minor deviations in expected bond angles to wholly implausible placement in the binding pocket. Following recommendations from the wwPDB Validation Task Force, the PDB recently began validating ligand geometry as an integral part of deposition processing. This means that many crystallographers will soon receive for the first time a ""grade"" on the quality of ligands in the structure they have just deposited. Some will be surprised, as I was following my first PDB deposition of 2014, at how easily bad ligand geometry can slip through the cracks in supposedly robust structure refinement protocols that their lab has used for many years. I will illustrate use of current tools for generating ligand restraints to guide model refinement. One is the jligand+coot+cprodrg pipeline integrated into the CCP4 suite. Another is the Grade web server provided as a community resource by Global Phasing Ltd. Furthermore I will show examples from recent in-house refinements of how things can still go wrong even if you do use these tools, and how we recovered. The new PDB deposition checks may expose errors in your ligand descriptions after the fact. This presentation may help you avoid introducing those errors in the first place."

scholarly journals Calculation of fire resistance of building structures in software packages

2019 ◽  
Vol 91 ◽  
pp. 02007 ◽  
Author(s):  
Ivan Dmitriev ◽  
Vladimir Lyulikov ◽  
Olga Bazhenova ◽  
Dmitry Bayanov
Keyword(s):  
Fire Resistance ◽  
Fire Regimes ◽  
Point Of View ◽  
Temperature Fields ◽  
Software Systems ◽  
Building Structures ◽  
The Finite Element Method ◽  
Fire Load ◽  
Software Packages ◽  
Intuitive User Interface

In the article a review of modern software systems allowing calculating the distribution of temperature fields in a structure in time, without loading and with it (the fire resistance limit of structures) under conditions of a special fire load has been given. The algorithm of the finite element method is used for the calculations, on which each of the considered complexes is based. Specifically: Sofistik, Abaqus, Normcad, Ansys, Robot structure. Comparative analysis has been made from the point of view of intuitive user interface, the possibilities of modeling various conditions and fire regimes, tools for communication with other software complexes and the format of output of results. The results demonstrating the capabilities of the post-processor Sofistik have been presented.

scholarly journals The role of agent-based modeling and multi-agent systems in flood-based hydrological problems: a brief review

2019 ◽  
Vol 11 (4) ◽  
pp. 1580-1602 ◽  
Author(s):  
Jose Simmonds ◽  
Juan A. Gómez ◽  
Agapito Ledezma
Keyword(s):  
Information And Communication Technologies ◽  
Hydrological Cycle ◽  
Point Of View ◽  
Multi Agent Systems ◽  
Agent Based ◽  
Spatial And Temporal Scales ◽  
Agent Systems ◽  
Multi Agent ◽  
Complex Phenomena ◽  
Data Driven Modeling

Abstract Flood problems are complex phenomena with a direct relationship with the hydrological cycle; these are natural processes occurring in water systems, that interact at different spatial and temporal scales. In modeling the hydrological phenomena, traditional approaches, like physics-based mathematical equations and data-driven modeling (DDM) are used. Advances in hydroinformatics are helping to understand these physical processes, with improvements in the collection and analysis of hydrological data, information and communication technologies (ICT), and geographic information systems (GIS), offering opportunities for innovations in model implementation, to improve decision support for the response to societally important floods impacting our societies. This paper offers a brief review of agent-based models (ABMs) and multi-agent systems (MASs) methodologies' applications for solutions to flood problems, their management, assessment, and efforts for forecasting stream flow and flood events. Significant observations from this review include: (i) contributions of agent technologies, as a growing methodology in hydrology; (ii) limitations; (iii) capabilities of dealing with distributed and complex domains; and (iv), the capabilities of MAS as an increasingly accepted point of view applied to flood modeling, with examples presented to show the variety of system combinations that are practical on a specialized architectural level for developing and deploying sophisticated flood forecasting systems.

scholarly journals Clinical and Genetic Overview of Paroxysmal Movement Disorders and Episodic Ataxias

2020 ◽  
Vol 21 (10) ◽  
pp. 3603 ◽  
Author(s):  
Giacomo Garone ◽  
Alessandro Capuano ◽  
Lorena Travaglini ◽  
Federica Graziola ◽  
Fabrizia Stregapede ◽  
...  
Keyword(s):  
Movement Disorders ◽  
Molecular Mechanisms ◽  
Neurological Diseases ◽  
Single Gene ◽  
Point Of View ◽  
Whole Exome ◽  
Genetic Features ◽  
Neurogenetic Disorders ◽  
Next Generation Sequencing Ngs ◽  
Molecular Bases

Paroxysmal movement disorders (PMDs) are rare neurological diseases typically manifesting with intermittent attacks of abnormal involuntary movements. Two main categories of PMDs are recognized based on the phenomenology: Paroxysmal dyskinesias (PxDs) are characterized by transient episodes hyperkinetic movement disorders, while attacks of cerebellar dysfunction are the hallmark of episodic ataxias (EAs). From an etiological point of view, both primary (genetic) and secondary (acquired) causes of PMDs are known. Recognition and diagnosis of PMDs is based on personal and familial medical history, physical examination, detailed reconstruction of ictal phenomenology, neuroimaging, and genetic analysis. Neurophysiological or laboratory tests are reserved for selected cases. Genetic knowledge of PMDs has been largely incremented by the advent of next generation sequencing (NGS) methodologies. The wide number of genes involved in the pathogenesis of PMDs reflects a high complexity of molecular bases of neurotransmission in cerebellar and basal ganglia circuits. In consideration of the broad genetic and phenotypic heterogeneity, a NGS approach by targeted panel for movement disorders, clinical or whole exome sequencing should be preferred, whenever possible, to a single gene approach, in order to increase diagnostic rate. This review is focused on clinical and genetic features of PMDs with the aim to (1) help clinicians to recognize, diagnose and treat patients with PMDs as well as to (2) provide an overview of genes and molecular mechanisms underlying these intriguing neurogenetic disorders.

scholarly journals Copy number networks to guide combinatorial therapy for cancer and other disorders

2014 ◽  
Author(s):  
Andy Lin ◽  
Desmond James Smith
Keyword(s):  
Drug Treatment ◽  
Protein Interactions ◽  
Copy Number ◽  
Genetic Interaction ◽  
Single Gene ◽  
Growth Factor Receptor ◽  
Molecular Networks ◽  
Protein Protein Interactions ◽  
Gene Pairs ◽  
Cancer Networks

The dwindling drug pipeline is driving increased interest in the use of genome datasets to inform drug treatment. In particular, networks based on transcript data and protein-protein interactions have been used to design therapies that employ drug combinations. But there has been less focus on employing human genetic interaction networks constructed from copy number alterations (CNAs). These networks can be charted with sensitivity and precision by seeking gene pairs that tend to be amplified and/or deleted in tandem, even when they are located at a distance on the genome. Our experience with radiation hybrid (RH) panels, a library of cell clones that have been used for genetic mapping, have shown this tool can pinpoint statistically significant patterns of co-inherited gene pairs. In fact, we were able to identify gene pairs specifically associated with the mechanism of cell survival at single gene resolution. The strategy of seeking correlated CNAs can also be used to map survival networks for cancer. Although the cancer networks have lower resolution, the RH network can be leveraged to provide single gene specificity in the tumor networks. In a survival network for glioblastoma possessing single gene resolution, we found that the epidermal growth factor receptor (EGFR) oncogene interacted with 46 genes. Of these genes, ten (22%) happened to be targets for existing drugs. Here, we briefly review the previous use of molecular networks to design novel therapies. We then highlight the potential of using correlated CNAs to guide combinatorial drug treatment in common medical conditions. We focus on therapeutic opportunities in cancer, but also offer examples from autoimmune disorders and atherosclerosis.

scholarly journals Foreign policy expertise: Polyvariety of research approaches in political science

2021 ◽  
Vol 21 (2) ◽  
pp. 196-202
Author(s):  
Oleg V. Onopko ◽  
Keyword(s):  
Foreign Policy ◽  
Political Science ◽  
Current Practice ◽  
Point Of View ◽  
Holistic View ◽  
Special Knowledge ◽  
Multi Level ◽  
Methodological Approaches ◽  
Network Approaches ◽  
Expert Community

The main theoretical and methodological approaches that are used in Russian and world political science to study foreign policy expertise and related problems are analyzed in the article. The author concludes that there are so called “procedural”, institutional, system, and network approaches. From the point of view of the first one, foreign policy expertise is a special activity or procedure that is carried out by subjects with special knowledge and status. The institutional approach focuses on particular expert organizations (mostly think tanks) that work in the field of foreign policy and international relations. It is effective in exploring the features of their organizational structure and functioning, history, and current practice. The system approach is inherent primarily in Russian scholarly works on foreign policy expertise. Historians were the first to use it for this purpose. The network methodology is mostly used to study the expert community as a complex of multi-level subjects participating in the assessment and making of foreign policy decisions. Despite the fact that these approaches give a relatively holistic view on foreign policy expertise, there still are problem areas associated with it, which have not yet become the object of theorizing within political science.

Եղիա Տեմիրճիպաշյան. Բազմավաստակ գրողն ու մտավորականը

2021 ◽  
pp. 31-45
Author(s):  
Պետրոս Դեմիրճյան
Keyword(s):  
Public Life ◽  
Philosophy Of History ◽  
Cultural Development ◽  
Point Of View ◽  
Historical Time ◽  
Creative Thought ◽  
History Of ◽  
Armenian Literature ◽  
Complex Phenomena ◽  
The 19Th Century

Writer, publicist, philosopher, pedagogue, editor Yeghia Temirchipashyan (1851–1908) occupies a special place in the history of Armenian literature and, in particular, in the national-social, educational and cultural development of the last quarter of the 19th century. He was destined to live and create for our people, truly, in a crucial historical time, when not only national and public life, but also scientific and meaningful creative thought was undergoing rapid reforms. In the oppressive atmosphere of the Sultan’s Turkey, even the creative spirit of Armenians tried to find a way out of the developments taking place in the world, the sources of progress and the latest ways. In the system of communication and internal transfers, Y. Temirchipashyan gave priority to the present time. Soberly assessing the current requirements of life, he felt and realized that time has changed, the human being has changed. That is why, considering the Mashtots Grabar adored, he advocated the use of a manifests when assessing the complex phenomena of the transition time experienced by him from the point of view of the life and progress of the nation and society as a whole. In his famous articles entitled “The Evolution of the Beauty” “The Element of the Philosophy of History”, “A Hassle over Bringing up Girls or a Speech of Broom”, encouraging the influx of European literary, scientific and philosophical thought into the Armenian reality, he was against the intention to accept with open arms all the shepherds and currents coming from the West. At the same time, having mastered new aesthetic and philosophical trends, he also encouraged reading “nutritious, strengthening, awaking books”, and did not stop believing in the optimistic prospects of the nation and the Motherland.

scholarly journals Cavitating Flow Calculations in Industry

2003 ◽  
Vol 9 (3) ◽  
pp. 163-170 ◽  
Author(s):  
Philippe Dupont ◽  
Tomoyoshi Okamura
Keyword(s):  
Centrifugal Pump ◽  
Design Process ◽  
Computational Fluid Dynamic ◽  
Fluid Dynamic ◽  
Point Of View ◽  
Prediction Methods ◽  
Software Packages ◽  
Commercial Code ◽  
Dynamic Software ◽  
Computational Fluid Dynamic Software

This paper presents the experiences of two pump manufacturers with numerical cavitation prediction methods available in commercial computational fluid dynamic software or in codes developed in-house. The intention of the authors is to evaluate these methods and their capabilities in predicting the cavitating performance of pumps from an industrial point of view.In the first part of the article, benchmarks were set for three different commercial software packages on the basis of a comparison of measurements obtained for a centrifugal pump. In the second part, the results of a commercial code are compared, for different impellers, to those obtained with a simplified cavitation prediction code.The abilities and the benefits of the various approaches to cavitation prediction in the design process of a pump are discussed.

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