Topic Review Peer Reviewed
Information Security Risk Assessment
Information security risk assessment is an important part of enterprises’ management practices that helps to identify, quantify, and prioritize risks against criteria for risk acceptance and objectives relevant to the organization. Risk management refers to a process that consists of identification, management, and elimination or reduction of the likelihood of events that can negatively affect the resources of the information system to reduce security risks that potentially have the ability to affect the information system, subject to an acceptable cost of protection means that contain a risk analysis, analysis of the “cost-effectiveness” parameter, and selection, construction, and testing of the security subsystem, as well as the study of all aspects of security. 
  • 427
  • 13 Apr 2022
Topic Review
Smoothed-Particle Hydrodynamics
Smoothed-particle hydrodynamics is a computational mesh-free Lagrangian method developed by Gingold, Monaghan, and Lucy in 1977, initially intended for use in astrophysics.
  • 303
  • 08 Apr 2021
Topic Review
LncRNA-Protein Interactions
LncRNA can act as gene regulators, and like other epigenetic mechanisms are involved in numerous biological processes. They achieve their regulatory function with their ability to interact with a wide range of biological molecules, such as other nucleic acids and proteins. These lncRNA-protein interactions (LPI) are involved in many biological pathways including development and disease. A variety of computational LPI predictors exist, each applying different strategies to achieve their goals, and are dependent on a few biological databases containing subsets of experimentally validated LPI. Most modern lncRNA-protein interaction (LPI) prediction algorithms use machine learning approaches, where algorithms are trained on large datasets with attributes of interest.
  • 298
  • 05 Jul 2021
Topic Review
Alignment-Free Study of Viral Diversity
Viral sequence variation can expand the host repertoire, enhance the infection ability, and/or prevent the build-up of a long-term specific immunity by the host. The study of viral diversity is, thus, critical to understand sequence change and its implications for intervention strategies.
  • 266
  • 22 Sep 2021
Topic Review
Commercial Targeted Libraries in Drug Design
After the identification of a biological target (enzyme, receptor, protein and so on), the focus of the early phase of drug discovery rests on the identification of leads or compounds that exhibit pharmacological activity against this specific target. Compounds of interest are most often discovered in pre-existing libraries of compounds that can be either virtual or physical. Computer-aided methods which have become increasingly important over the years in drug development utilize virtual compound libraries. While physical compound libraries reach the number of millions of molecules, virtual compound libraries created by large pharmaceutical companies can range from 107 to 1018 molecules. Investigations of these libraries identifies specific molecules, synthetic pathways and focus on a specific chemical space. Targeted libraries are often smaller and are focused towards a specific chemical space. They are created by using relevant biological information with the aim to decrease the processing time associated with larger libraries while maintaining the most relevant chemical space where lead compounds can be found. Due to the fact that they required less computational or wet-lab labor to process they have become very popular with smaller laboratories which try to compete in the drug-development sector. Many modern vendors of compounds today offer such libraries, but the quality of the procedure used to define desired chemical space and select compounds is questionable.
  • 228
  • 25 May 2022
Topic Review
β-Adrenergic Stimulation
β-adrenergic receptor stimulation (β-ARS) is a physiological mechanism that regulates cardiovascular function under stress conditions or physical exercise, producing a positive inotropic (enhanced contraction), lusitropic (faster relaxation), and chronotropic (increased heart rate) effect. 
  • 202
  • 04 Aug 2021
Topic Review
Swarm Robotics
Swarm robotics is a dynamic research field that integrates two important concepts: Swarm Intelligence (SI) and Multi-Robotics System (MRS).
  • 184
  • 02 Jun 2022
Topic Review
Lattice Boltzmann Method
Biofilm growth and evolution are very complex interactions among physicochemical and biological processes. Mathematical models are critical to modern biotechnology—both in research and in the engineering practice. Thus, many models of biofilms have been developed to include various biofilm reactor modules. However, considerable challenges exist in modelling microbial processes where mesoscopic dynamics of nutrient transport must be coupled with microscopic bacteria growth and their elementary biochemical reactions at reactive or enzymatic interfaces, in addition to the microbiological and/or ecological aspects of the “micro” organisms involved in biofilms. Lattice Boltzmann Method (LBM) treats flows in terms of fictive parcels of particles which reside on a mesh and conduct translation according to collision steps entailing overall fluid-like behavior. The goal of this review is to discuss and identify the opportunities of applying different LBM-based models to specific areas of biofilm research as well as unique challenges that LBM-based models must overcome.
  • 178
  • 19 Jul 2021
Topic Review
Predicting the Evolution of Syntenies
Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders, while more relaxed definitions just require a certain similarity in gene content, and not necessarily in the same order. Regardless of the way they are identified, the goal is to characterize homologous genomic regions, i.e., regions deriving from a common ancestral region, reflecting a certain gene co-evolution that can enlighten important functional properties.
  • 165
  • 02 Jun 2021
Topic Review
Genome by Multidimensional Scaling
The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the physical interactions of genomes. In previous studies, DNA extrusion loops  were directly derived from Hi-C heat maps. By using Multidimensional Scaling (MDS), we can easily locate enhancers and promoters more precisely.
  • 165
  • 31 Oct 2021
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