Search results for "COMPUTATION"
showing 10 items of 7362 documents
Exploring the Human-Nipah Virus Protein-Protein Interactome
2017
ABSTRACT Nipah virus is an emerging, highly pathogenic, zoonotic virus of the Paramyxoviridae family. Human transmission occurs by close contact with infected animals, the consumption of contaminated food, or, occasionally, via other infected individuals. Currently, we lack therapeutic or prophylactic treatments for Nipah virus. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. This aim led us to perform the present work, in which we identified 101 human-Nipah virus protein-protein interactions (PPIs), most of which (88) are novel. This data set provides a comprehensive view of the host complexes that are manip…
Repurposing old drugs to fight multidrug resistant cancers.
2020
Overcoming multidrug resistance represents a major challenge for cancer treatment. In the search for new chemotherapeutics to treat malignant diseases, drug repurposing gained a tremendous interest during the past years. Repositioning candidates have often emerged through several stages of clinical drug development, and may even be marketed, thus attracting the attention and interest of pharmaceutical companies as well as regulatory agencies. Typically, drug repositioning has been serendipitous, using undesired side effects of small molecule drugs to exploit new disease indications. As bioinformatics gain increasing popularity as an integral component of drug discovery, more rational approa…
Computational Fluid Dynamics Suggests Ecological Diversification among Stem-Gnathostomes.
2020
Summary The evolutionary assembly of the vertebrate bodyplan has been characterized as a long-term ecological trend toward increasingly active and predatory lifestyles, culminating in jawed vertebrates that dominate modern vertebrate biodiversity [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 ]. This contrast is no more stark than between the earliest jawed vertebrates and their immediate relatives, the extinct jawless, dermal armor-encased osteostracans, which have conventionally been interpreted as benthic mud-grubbers with poor swimming capabilities and low maneuverability [ 9 , 10 , 11 , 12 ]. Using computational fluid dynamics, we show that osteostracan headshield morphology is compatible with a dive…
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy
2017
The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use. Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org . Because it uses novel mapping algorithms VISMapper is remarkably faster t…
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
2018
Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.
Functional Genomics in Wine Yeast: DNA Arrays and Next Generation Sequencing
2017
Since their very beginning, DNA array and next-generation sequencing technologies have been used with Saccharomyces cerevisiae cells. In the last 7 years, an increasing number of studies have focused on the study of wine strains and winemaking. The uncovering of the genomic features of these strains and expression profiles under the different stressful conditions that they have to deal with have contributed significantly to the knowledge of how this amazing microorganism can convert grape must into a drink that has enormously influenced mankind for 7000 years.This review presents a synopsis of DNA array and next-generation sequencing (NGS) technologies and focus mainly in their use in study…
Strategic Syntheses of Vine and Wine Resveratrol Derivatives to Explore their Effects on Cell Functions and Dysfunctions
2018
Trans-resveratrol, the most well-known polyphenolic stilbenoid, is found in grapes and accordingly in wine and it is considered to be beneficial for human health, especially towards the aging-linked cell alterations by providing numerous biological activities, such as anti-oxidant, antitumoral, antiviral, anti-inflammatory, neuroprotective, and platelet anti-aggregation properties. Although trans-resveratrol is a promising molecule, it cannot be considered as a drug, due to its weak bio-availability and fast metabolism. To overcome these weaknesses, several research teams have undertaken the synthesis of innovative trans-resveratrol derivatives, with the aim to increase its solubility in wa…
Stability of stationary solutions in models of the Calvin cycle
2017
Abstract In this paper results are obtained concerning the number of positive stationary solutions in simple models of the Calvin cycle of photosynthesis and the stability of these solutions. It is proved that there are open sets of parameters in the model of Zhu et al. (2009) for which there exist two positive stationary solutions. There are never more than two isolated positive stationary solutions but under certain explicit special conditions on the parameters there is a whole continuum of positive stationary solutions. It is also shown that in the set of parameter values for which two isolated positive stationary solutions exist there is an open subset where one of the solutions is asym…
Prospects and challenges for computer simulations of monolayer-protected metal clusters
2021
Precise knowledge of chemical composition and atomic structure of functional nanosized systems, such as metal clusters stabilized by an organic molecular layer, allows for detailed computational work to investigate structure-property relations. Here, we discuss selected recent examples of computational work that has advanced understanding of how these clusters work in catalysis, how they interact with biological systems, and how they can make self-assembled, macroscopic materials. A growing challenge is to develop effective new simulation methods that take into account the cluster-environment interactions. These new hybrid methods are likely to contain components from electronic structure t…
A study on time discretization and adaptive mesh refinement methods for the simulation of cancer invasion: The urokinase model
2016
In the present work we investigate a model that describes the chemotactically and proteolytically driven tissue invasion by cancer cells. The model is a system of advection-reaction-diffusion equations that takes into account the role of the serine protease urokinase-type plasminogen activator. The analytical and numerical study of such a system constitutes a challenge due to the merging, emerging, and traveling concentrations that the solutions exhibit. Classical numerical methods applied to this system necessitate very fine discretization grids to resolve these dynamics in an accurate way. To reduce the computational cost without sacrificing the accuracy of the solution, we apply adaptive…