482 research outputs found

    Applications of Artificial Intelligence in Battling Against Covid-19: A Literature Review

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    Š 2020 Elsevier Ltd. All rights reserved.Colloquially known as coronavirus, the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), that causes CoronaVirus Disease 2019 (COVID-19), has become a matter of grave concern for every country around the world. The rapid growth of the pandemic has wreaked havoc and prompted the need for immediate reactions to curb the effects. To manage the problems, many research in a variety of area of science have started studying the issue. Artificial Intelligence is among the area of science that has found great applications in tackling the problem in many aspects. Here, we perform an overview on the applications of AI in a variety of fields including diagnosis of the disease via different types of tests and symptoms, monitoring patients, identifying severity of a patient, processing covid-19 related imaging tests, epidemiology, pharmaceutical studies, etc. The aim of this paper is to perform a comprehensive survey on the applications of AI in battling against the difficulties the outbreak has caused. Thus we cover every way that AI approaches have been employed and to cover all the research until the writing of this paper. We try organize the works in a way that overall picture is comprehensible. Such a picture, although full of details, is very helpful in understand where AI sits in current pandemonium. We also tried to conclude the paper with ideas on how the problems can be tackled in a better way and provide some suggestions for future works.Peer reviewe

    Computational approaches to study drug resistance mechanisms

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    Drug resistance is a major obstacle faced by therapists in treating complex diseases like cancer, epilepsy, arthritis and HIV infected patients. The reason behind these phenomena is either protein mutation or the changes in gene expression level that induces resistance to drug treatments. These mutations affect the drug binding activity, hence resulting in failure of treatment. All this information has been stored in PubMed directories as text data. Extracting useful knowledge from an unstructured textual data is a challenging task for biologists, since biomedical literature is growing exponentially on a daily basis. Building an automated method for such tasks is gaining much attention among researchers. In this thesis we have developed a disease categorized database ZK DrugResist that automatically extracts mutations and expression changes associated with drug resistance from PubMed. This tool also includes semantic relations extracted from biomedical text covering drug resistance and established a server including both of these features. Our system was tested for three relations, Resistance (R), Intermediate (I) and Susceptible (S) by applying hybrid feature set. From the last few decades the focus has changed to hybrid approaches as it provides better results. In our case this approach combines rule-based methods with machine learning techniques. The results showed 97.7% accuracy with 96% precision, recall and F-measure. The results have outperformed the previously existing relation extraction systems thus facilitating computational analysis of drug resistance against complex diseases and further can be implemented on other areas of biomedicine. Literature is filled with HIV drug resistance providing the worth of training data as compared to other diseases, hence we developed a computational method to predict HIV resistance. For this we combined both sequence and structural features and applied SVM and Random Forests classifiers. The model was tested on the mutants of HIV-1 protease and reverse transcriptase.Taken together the features we have used in our method, total contact energies among multiple mutations have a strong impact in predicting resistance as they are crucial in understanding the interactions of HIV mutants. The combination of sequence-structure features o↵ers high accuracy with support vector machines as compared to Random Forests classifier. Both single and acquisition of multiple mutations are important in predicting HIV resistance to certain drug treatments. We have discovered the practicality of these features; hence these can be used in the future to predict resistance for other complex diseases. Another way to deal drug resistance is the application of drug repurposing. Drug often binds to more that one targets defined as polypharmacology which can be applied to drug repositioning also referred as therapeutic switching. The traditional drug discovery and development is a high-priced and tedious process, thus making drug repurposing a popular alternate strategy. We have proposed a method based on similarity scheme that predicts both approved and novel targets for drug and new disease associations. We combined PPI, biological pathways, binding site structural similarities and disease-disease similarity measures. We used sixty drugs for training the algorithm and tested it on eight separate drugs. The results showed 95% accuracy in predicting the approved and novel targets surpassing the existing methods. All these parameters help in elucidating the unknown associations between drug and diseases for finding the new uses for old drugs. Hence repurposing offers novel candidates from existing pool of drugs providing a ray of hope in combating drug resistance

    11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

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    Network-driven strategies to integrate and exploit biomedical data

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    [eng] In the quest for understanding complex biological systems, the scientific community has been delving into protein, chemical and disease biology, populating biomedical databases with a wealth of data and knowledge. Currently, the field of biomedicine has entered a Big Data era, in which computational-driven research can largely benefit from existing knowledge to better understand and characterize biological and chemical entities. And yet, the heterogeneity and complexity of biomedical data trigger the need for a proper integration and representation of this knowledge, so that it can be effectively and efficiently exploited. In this thesis, we aim at developing new strategies to leverage the current biomedical knowledge, so that meaningful information can be extracted and fused into downstream applications. To this goal, we have capitalized on network analysis algorithms to integrate and exploit biomedical data in a wide variety of scenarios, providing a better understanding of pharmacoomics experiments while helping accelerate the drug discovery process. More specifically, we have (i) devised an approach to identify functional gene sets associated with drug response mechanisms of action, (ii) created a resource of biomedical descriptors able to anticipate cellular drug response and identify new drug repurposing opportunities, (iii) designed a tool to annotate biomedical support for a given set of experimental observations, and (iv) reviewed different chemical and biological descriptors relevant for drug discovery, illustrating how they can be used to provide solutions to current challenges in biomedicine.[cat] En la cerca d’una millor comprensió dels sistemes biològics complexos, la comunitat científica ha estat aprofundint en la biologia de les proteïnes, fàrmacs i malalties, poblant les bases de dades biomèdiques amb un gran volum de dades i coneixement. En l’actualitat, el camp de la biomedicina es troba en una era de “dades massives” (Big Data), on la investigació duta a terme per ordinadors se’n pot beneficiar per entendre i caracteritzar millor les entitats químiques i biològiques. No obstant, la heterogeneïtat i complexitat de les dades biomèdiques requereix que aquestes s’integrin i es representin d’una manera idònia, permetent així explotar aquesta informació d’una manera efectiva i eficient. L’objectiu d’aquesta tesis doctoral és desenvolupar noves estratègies que permetin explotar el coneixement biomèdic actual i així extreure informació rellevant per aplicacions biomèdiques futures. Per aquesta finalitat, em fet servir algoritmes de xarxes per tal d’integrar i explotar el coneixement biomèdic en diferents tasques, proporcionant un millor enteniment dels experiments farmacoòmics per tal d’ajudar accelerar el procés de descobriment de nous fàrmacs. Com a resultat, en aquesta tesi hem (i) dissenyat una estratègia per identificar grups funcionals de gens associats a la resposta de línies cel·lulars als fàrmacs, (ii) creat una col·lecció de descriptors biomèdics capaços, entre altres coses, d’anticipar com les cèl·lules responen als fàrmacs o trobar nous usos per fàrmacs existents, (iii) desenvolupat una eina per descobrir quins contextos biològics corresponen a una associació biològica observada experimentalment i, finalment, (iv) hem explorat diferents descriptors químics i biològics rellevants pel procés de descobriment de nous fàrmacs, mostrant com aquests poden ser utilitzats per trobar solucions a reptes actuals dins el camp de la biomedicina

    Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes

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    Ribonucleic acids are gradually becoming relevant players among putative drug targets, thanks to the increasing amount of structural data exploitable for the rational design of selective and potent binders that can modulate their activity. Mainly, this information allows employing different computational techniques for predicting how well would a ribonucleic-targeting agent fit within the active site of its target macromolecule. Due to some intrinsic peculiarities of complexes involving nucleic acids, such as structural plasticity, surface charge distribution, and solvent-mediated interactions, the application of routinely adopted methodologies like molecular docking is challenged by scoring inaccuracies, while more physically rigorous methods such as molecular dynamics require long simulation times which hamper their conformational sampling capabilities. In the present work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of unbinding kinetics, to characterize RNA-ligand complexes. In this article, we explored its applicability as a post-docking refinement tool on RNA in complex with small molecules, highlighting the capability of this method to identify the native binding mode among a set of decoys across various pharmaceutically relevant test cases

    In Silico Strategies for Prospective Drug Repositionings

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    The discovery of new drugs is one of pharmaceutical research's most exciting and challenging tasks. Unfortunately, the conventional drug discovery procedure is chronophagous and seldom successful; furthermore, new drugs are needed to address our clinical challenges (e.g., new antibiotics, new anticancer drugs, new antivirals).Within this framework, drug repositioning—finding new pharmacodynamic properties for already approved drugs—becomes a worthy drug discovery strategy.Recent drug discovery techniques combine traditional tools with in silico strategies to identify previously unaccounted properties for drugs already in use. Indeed, big data exploration techniques capitalize on the ever-growing knowledge of drugs' structural and physicochemical properties, drug–target and drug–drug interactions, advances in human biochemistry, and the latest molecular and cellular biology discoveries.Following this new and exciting trend, this book is a collection of papers introducing innovative computational methods to identify potential candidates for drug repositioning. Thus, the papers in the Special Issue In Silico Strategies for Prospective Drug Repositionings introduce a wide array of in silico strategies such as complex network analysis, big data, machine learning, molecular docking, molecular dynamics simulation, and QSAR; these strategies target diverse diseases and medical conditions: COVID-19 and post-COVID-19 pulmonary fibrosis, non-small lung cancer, multiple sclerosis, toxoplasmosis, psychiatric disorders, or skin conditions

    Corpses, Guns, Penises and Private Military and Security Corporations

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    The purpose of this dissertation is to reconceptualise how the work of private military and security companies (PMSCs) comes to matter. The overarching argument is: PMSC work is made to matter through an entanglement of ‘things’, agencies and processes that are not exclusively bound to the needs or desires of clients, regulators or PMSCs themselves. The word matter is used in a dual-sense of becoming meaningful and becoming materialized. I advance the possibility that PMSC work comes to matter through multifaceted enactments of human, formerly human (e.g. the dead), not exclusively human (e.g. penises), and non-human (e.g. guns) agencies. Simultaneously I perform a thorough accounting of the four processes – privatizing, militarizing, securing and commercializing– that overdetermine what this works means to global relations of security. Constituting the (meta-)theoretical apparatus of this dissertation is an entanglement of post-human, queer and feminist considerations of materiality, agency and agents, normativity and accountability. By privileging a post-human, queer and feminist analysis I produce an uncommon understanding of PMSC work that reconfigures the boundaries of what actually matters amongst global relations of security. I also offer an incisive critique of the political-economic processes that overdetermine the meaning of the work that PMSCs perform
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