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Search results for: DNA ONTOLOGIES (INFORMATION RETRIEVAL)
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Virtual engineering process (VEP): a knowledge representation approach for building bio-inspired distributed manufacturing DNA
PublicationThe objective of this research is to provide a user-friendly and effective way of representing engineering processes for distributed manufacturing systems so that they can develop, accumulate and share knowledge. The basic defini-tion and principle of the approach is introduced first and then the prototype version of the system is developed and demonstrated with case studies, which verify the feasibility of the proposed approach....
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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Automatic detection and correction of detuned singing system for use with query-by-humming applications
PublicationThe aim of the paper is to present an idea of using the automatic detection and correction of detuned singing as a subsystem in query-by-humming (QBH) applications. The common approach to searching for a requested song basing on the melody retrieved from hummed pattern usually employs the so-called Parsons code or melody contour. In such a case information about sound pitch is discarded. It was thought out that an additional module...
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublicationFor many decades it was an accepted dogma of molecular genetics that the expression of genes is a “one-way-road” leading only in one direction from DNA to RNA to proteins. Recent discoveries in modern molecular genetics have challenged this dogma showing that specific RNA molecules play a central role in controlling the activity of genes by changing the structure of DNA sequences, targeting other RNAs for degradation or blocking...
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Stream Reasoning to Improve Decision-Making in Cognitive Systems
PublicationABSTRACT Cognitive Vision Systems have gained a lot of interest from industry and academia recently, due to their potential to revolutionize human life as they are designed to work under complex scenes, adapting to a range of unforeseen situations, changing accordingly to new scenarios and exhibiting prospective behavior. The combination of these properties aims to mimic the human capabilities and create more intelligent and efficient...
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Implementing Virtual Engineering Objects (VEO) with the Set of Experience Knowledge Structure (SOEKS)
PublicationThis paper illustrates the idea of Virtual Engineering Object (VEO) powered by Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA). A VEO is the knowledge representation of an engineering object, having embodiment of all its associated knowledge and experience within it. Moreover, VEO is a specialization of Cyber-Physical System (CPS) in terms of that its extension in knowledge gathering and reuse, whereas CPS...
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Diagnostic Accuracy of Liquid Biopsy in Endometrial Cancer
PublicationBackground: Liquid biopsy is a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, the potential of this method in endometrial cancer (EC) remains poorly explored. We studied the utility of tumor educated platelets (TEPs) and circulating tumor DNA (ctDNA) for preoperative EC diagnosis, including histology determination. Methods:...
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Decisional-DNA Based Smart Production Performance Analysis Model
Publicationn order to allocate resources effectively according to the production plan and to reduce disturbances, a framework for smart production performance analysis is proposed in this article. Decisional DNA based knowledge models of engineering objects, processes and factory are developed within the proposed framework. These models are the virtual representation of manufacturing resources, and with help of Internet of Things, are capable...
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Contextual Knowledge to Enhance Workplace Hazard Recognition and Interpretation in a Cognitive Vision Platform
PublicationThe combination of vision and sensor data together with the resulting necessity for formal representations builds a central component of an autonomous Cyber Physical System for detection and tracking of laborers in workplaces environments. This system must be adaptable and perceive the environment as automatically as possible, performing in a variety of plants and scenes without the necessity of recoding the application for each...
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The influence of global climate change on the environmental fate of anthropogenic pollution released from the permafrost
PublicationThis article presents a review of information related to the influence of potential permafrost degradation on the environmental fate of chemical species which are relased and stored, classified as potential influence in future Antarctic environment. Considering all data regarding climate change prediction, this topic may prove important issue for the future state of the Antarctic environment. A detailed survey on soil and permafrost...
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A universal method for the identification of genes encoding amatoxins and phallotoxins in poisonous mushrooms
PublicationABSTRACT Background. As the currently known diagnostic DNA targets amplified in the PCR assays for detection of poisonous mushrooms have their counterparts in edible species, there is a need to design PCR primers specific to the genes encoding amanitins and phallotoxins, which occur only in poisonous mushrooms. Objective. The aim of the study was testing of PCR-based method for detection of all genes encoding hepatotoxic cyclic...
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Video Classification Technology in a Knowledge-Vision-Integration Platform for Personal Protective Equipment Detection: An Evaluation
PublicationThis work is part of an effort for the development of a Knowledge-Vision Integration Platform for Hazard Control (KVIP-HC) in industrial workplaces, adaptable to a wide range of industrial environments. This paper focuses on hazards resulted from the non-use of personal protective equipment (PPE), and examines a few supervised learning techniques to compose the proposed system for the purpose of recognition of three protective...
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Experience-Oriented Intelligence for Internet of Things
PublicationThe Internet of Things (IoT) has gained significant attention from industry as well as academia during the past decade. The main reason behind this interest is the capabilities of the IoT for seamlessly integrating classical networks and networked objects, and hence allows people to create an intelligent environment based on this powerful integration. However, how to extract useful information from data produced by IoT and facilitate...
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Hazard Control in Industrial Environments: A Knowledge-Vision-Based Approach
PublicationThis paper proposes the integration of image processing techniques (such as image segmentation, feature extraction and selection) and a knowledge representation approach in a framework for the development of an automatic system able to identify, in real time, unsafe activities in industrial environments. In this framework, the visual information (feature extraction) acquired from video-camera images and other context based gathered...
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Influence of Thermal Imagery Resolution on Accuracy of Deep Learning based Face Recognition
PublicationHuman-system interactions frequently require a retrieval of the key context information about the user and the environment. Image processing techniques have been widely applied in this area, providing details about recognized objects, people and actions. Considering remote diagnostics solutions, e.g. non-contact vital signs estimation and smart home monitoring systems that utilize person’s identity, security is a very important factor....
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Image Representation for Cognitive Systems Using SOEKS and DDNA: A Case Study for PPE Compliance
PublicationCognitive Vision Systems have gained significant interest from academia and industry during the past few decade, and one of the main reasons behind this is the potential of such technologies to revolutionize human life as they intend to work under complex visual scenes, adapting to a comprehensive range of unforeseen changes, and exhibiting prospective behavior. The combination of these properties aims to mimic the human capabilities...
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Bioaccumulation of Metals in Tissues of Marine Animals, Part I: the Role and Impact of Heavy Metals on Organisms
PublicationHeavy metals contribute to the anthropogenic contamination of marine ecosystems. Some of them are essential to the life processes of organisms; others are toxic, even at low concentrations. They penetrate organisms via food, respiratory pathways or the skin. The extent to which metals penetrate organisms is measured by the bioconcentration and bioaccumulation factors and also by their transport between organisms at different trophic...
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Towards an experience based collective computational intelligence for manufacturing
PublicationKnowledge based support can play a vital role not only in the new fast emerging information and communication technology based industry, but also in traditional manufacturing. In this regard, several domain specific research endeavors have taken place in the past with limited success. Thus, there is a need to develop a flexible domain independent mechanism to capture, store, reuse, and share manufacturing knowledge. Consequently,...
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SYNAT_MUSIC_GENRE_FV_173
Open Research DataThis is the original dataset containing 51582 music tracks (22 music genres) and 173 element-feature vector [1-6,9]. A collection of more than 50000 music excerpts described with a set of descriptors obtained through the analysis of 30-second mp3 recordings was gathered in a database called SYNAT. The SYNAT database was realized by the Gdansk University...
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SYNAT Music Genre Parameters PCA 19
Open Research DataThe dataset contains feature vector after Principal Component Analysis (PCA) performing, so there are 11 music genres and 19-element vector derived from music excerpts. Originally, a feature vector containing 173 elements was conceived in earlier research studies carried out by the team of authors [1-6]. A collection of 52532 music excerpts described...
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SYNAT_PCA_48
Open Research DataThere is a series of datasets containing feature vectors derived from music tracks. The dataset contains 51582 music tracks (22 music genres) and feature vector after Principal Component Analysis (PCA) performing, so there are 48-element vectors derived from music excerpts. Originally, a feature vector containing 173 elements was conceived in earlier...
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SYNAT_PCA_11
Open Research DataThe dataset contains 51582 music tracks (22 music genres) and feature vector after Principal Component Analysis (PCA) performing, so there are 11-element vectors derived from music excerpts. Originally, a feature vector containing 173 elements was conceived in earlier research studies carried out by the team of authors [1-6]. A collection of more than...