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Search results for: DNA ONTOLOGIES (INFORMATION RETRIEVAL)
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Smart innovation process enhancement using SOEKS and decisional DNA
PublicationProduct innovation always requires a foundation based on both knowledge and experience. The production and innovation process of products is very similar to the evolution process of humans. The genetic information of humans is stored in genes, chromosomes and DNA. Similarly, the information about the products can be stored in a system having virtual genes, chromosomes and decisional DNA (DDNA). The present paper proposes...
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Comparison of Lithuanian and Polish Consonant Phonemes Based on Acoustic Analysis – Preliminary Results
PublicationThe goal of this research is to find a set of acoustic parameters that are related to differences between Polish and Lithuanian language consonants. In order to identify these differences, an acoustic analysis is performed, and the phoneme sounds are described as the vectors of acoustic parameters. Parameters known from the speech domain as well as those from the music information retrieval area are employed. These parameters are...
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Music Mood Visualization Using Self-Organizing Maps
PublicationDue to an increasing amount of music being made available in digital form in the Internet, an automatic organization of music is sought. The paper presents an approach to graphical representation of mood of songs based on Self-Organizing Maps. Parameters describing mood of music are proposed and calculated and then analyzed employing correlation with mood dimensions based on the Multidimensional Scaling. A map is created in which...
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Modeling the Customer’s Contextual Expectations Based on Latent Semantic Analysis Algorithms
PublicationNowadays, in the age of Internet, access to open data detects the huge possibilities for information retrieval. More and more often we hear about the concept of open data which is unrestricted access, in addition to reuse and analysis by external institutions, organizations and people. It’s such information that can be freely processed, add another data (so-called remix) and then published. More and more data are available in text...
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Methods for Elucidation of DNA-Anticancer Drug Interactions and Their Applications in the Development of New Drugs
PublicationDNA damaging agents including anthracyclines, camptothecins and platinum drugs are among most frequently used drugs in the chemotherapeutic routine. Due to their relatively low selectivity for cancer cells, administration is associated with adverse side effects, whereas the inherent genotoxicity of these drugs is associated with risk of developing secondary cancers. Development of new drugs, which could be spared of these drawbacks...
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Set of Experience and Decisional DNA: Experience-Based Knowledge Structures
PublicationThis chapter presents a description of Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA), argumentation for a knowledge representation, composition, configuration and metrics. SOEKS is a combination of filtered and amalgamated information obtained from formal decision events. It facilitates effective explicit representation of decisional experience taken from different technologies. SOEKS comprises variables,...
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Examining Feature Vector for Phoneme Recognition
PublicationThe aim of this paper is to analyze usability of descriptors coming from music information retrieval to the phoneme analysis. The case study presented consists in several steps. First, a short overview of parameters utilized in speech analysis is given. Then, a set of time and frequency domain-based parameters is selected and discussed in the context of stop consonant acoustical characteristics. A toolbox created for this purpose...
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A CONTEXT IN RECOMMENDER SYSTEMS
PublicationRecommender systems aim to propose potentially interesting items to a user based on his preferences or previous interaction with the system. In the last decade, researcher found out that known recommendation techniques are not sufficient to predict user decisions. It has been noticed that user preferences strongly depend on the context in which he currently is. This raises new challenges for the researchers such as how to obtain...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Low-Level Music Feature Vectors Embedded as Watermarks
PublicationIn this paper a method consisting in embedding low-level music feature vectors as watermarks into a musical signal is proposed. First, a review of some recent watermarking techniques and the main goals of development of digital watermarking research are provided. Then, a short overview of parameterization employed in the area of Music Information Retrieval is given. A methodology of non-blind watermarking applied to music-content...
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Comparative Study of Self-Organizing Maps vs. Subjective Evaluation of Quality of Allophone Pronunciation for Nonnative English Speakers
PublicationThe purpose of this study was to apply Self-Organizing Maps to differentiate between the correct and the incorrect allophone pronunciations and to compare the results with subjective evaluation. Recordings of a list of target words, containing selected allophones of English plosive consonants, the velar nasal and the lateral consonant, were made twice. First, the target words were read from the list by 9 non-native speakers and...
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Separability Assessment of Selected Types of Vehicle-Associated Noise
PublicationMusic Information Retrieval (MIR) area as well as development of speech and environmental information recognition techniques brought various tools in-tended for recognizing low-level features of acoustic signals based on a set of calculated parameters. In this study, the MIRtoolbox MATLAB tool, designed for music parameter extraction, is used to obtain a vector of parameters to check whether they are suitable for separation of...
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Ontology-based text convolution neural network (TextCNN) for prediction of construction accidents
PublicationThe construction industry suffers from workplace accidents, including injuries and fatalities, which represent a significant economic and social burden for employers, workers, and society as a whole.The existing research on construction accidents heavily relies on expert evaluations,which often suffer from issues such as low efficiency, insufficient intelligence, and subjectivity.However, expert opinions provided in construction...
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From Individual to Collective: Intelligence Amplification with Bio-Inspired Decisional DNA and its Extensions
PublicationIn nature, deoxyribonucleic acid (DNA) contains the genetic instructions used in the development and functioning of all known living organisms. The idea behind our vision is to develop an artificial system, an architecture that would support discovering, adding, storing, improving and sharing information and knowledge among agents and organizations through experience. We propose a novel Knowledge Representation (KR) approach in...
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How Machine Learning Contributes to Solve Acoustical Problems
PublicationMachine learning is the process of learning functional relationships between measured signals (called percepts in the artificial intelligence literature) and some output of interest. In some cases, we wish to learn very specific relationships from signals such as identifying the language of a speaker (e.g. Zissman, 1996) which has direct applications such as in call center routing or performing a music information retrieval task...
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NLP Questions Answering Using DBpedia and YAGO
PublicationIn this paper, we present results of employing DBpedia and YAGO as lexical databases for answering questions formulated in the natural language. The proposed solution has been evaluated for answering class 1 and class 2 questions (out of 5 classes defined by Moldovan for TREC conference). Our method uses dependency trees generated from the user query. The trees are browsed for paths leading from the root of the tree to the question...
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Listening to Live Music: Life beyond Music Recommendation Systems
PublicationThis paper presents first a short review on music recommendation systems based on social collaborative filtering. A dictionary of terms related to music recommendation systems, such as music information retrieval (MIR), Query-by-Example (QBE), Query-by-Category (QBC), music content, music annotating, music tagging, bridging the semantic gap in music domain, etc. is introduced. Bases of music recommender systems are shortly presented,...
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DBpedia and YAGO Based System for Answering Questions in Natural Language
PublicationIn this paper we propose a method for answering class 1 and class 2 questions (out of 5 classes defined by Moldovan for TREC conference) based on DBpedia and YAGO. Our method is based on generating dependency trees for the query. In the dependency tree we look for paths leading from the root to the named entity of interest. These paths (referenced further as fibers) are candidates for representation of actual user intention. The...
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How do personality traits influence Open Government Data (OGD) adoption and usage? Investigating the indirect and moderating effects
PublicationOpen Government Data (OGD) research has focused for a long on the adoption and usage from the perspectives of users across different contexts. The underlying rationale for this specific focus is that OGD initiatives are undertaken to further citizen engagement with OGD for value generation and innovation purposes. Conceding that usage propensity is different across individuals, it is important to understand the influence of personality...
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Discovering Rule-Based Learning Systems for the Purpose of Music Analysis
PublicationMusic analysis and processing aims at understanding information retrieved from music (Music Information Retrieval). For the purpose of music data mining, machine learning (ML) methods or statistical approach are employed. Their primary task is recognition of musical instrument sounds, music genre or emotion contained in music, identification of audio, assessment of audio content, etc. In terms of computational approach, music databases...
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Towards Healthcare Cloud Computing
PublicationIn this paper we present construction of a software platform for supporting medical research teams, in the area of impedance cardiography, called IPMed. Using the platform, research tasks will be performed by the teams through computer-supported cooperative work. The platform enables secure medical data storing, access to the data for research group members, cooperative analysis of medical data and provide analysis supporting tools...
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Sound engineering as our commitment to its creators in Poland
PublicationSound engineering is an interdisciplinary and rapidly expanding domain. It covers many aspects, such as sound perception, studio and sound mastering technology, music information retrieval including content-based search systems and automatic music transcription frameworks, sound synthesis, sound restoration, electroacoustics, and other ones constituting multimedia technology. Moreover, machine learning methods applied to the topics...
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Question Answering System to Answer Questions About Technical Documentation
PublicationThis article ventures into the realm of specialized AI systems for question answering, with a specific focus on programming languages, using Rust as the case study. Our research harnesses the capabilities of BERT, a leading model in natural language processing, to explore its effectiveness in interpreting and responding to complex, domain-specific queries. We have developed a novel dataset, derived from Rust's detailed documentation,...
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Smart Decisional DNA Technology to Enhance Industry 4.0 Environment in Conjunction with Conventional Manufacturing
PublicationKnowledge-based support has become an indispensable part not only to the traditional manufacturing set-ups but also to the new fast-emerging Industry 4.0 scenario. In this regard, successful research has been performed and extensively reported to develop Decisional DNA based knowledge representation models of engineering object and engineering process called Virtual engineering object (VEO), Virtual engineering process (VEP) and...
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A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies
PublicationTriazoloacridinone C-1305, a potent antitumor agent recommended for Phase I clinical trials, exhibits high activity towards a wide range of experimental colon carcinomas, in many cases associated with complete tumor regression. C-1305 is a well-established dsDNA intercalator, yet no information on its mode of binding into DNA is available to date. Herein, we present the NMR-driven and MD-refined reconstruction of the 3D structures...
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Spectral Clustering Wikipedia Keyword-Based search Results
PublicationThe paper summarizes our research in the area of unsupervised categorization of Wikipedia articles. As a practical result of our research, we present an application of spectral clustering algorithm used for grouping Wikipedia search results. The main contribution of the paper is a representation method for Wikipedia articles that has been based on combination of words and links and used for categoriation of search results in this...
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Sound quality metrics applied to road noise evaluation
PublicationRoad noise monitoring systems typically measure sound levels in specific time periods. The more insightful approach suggests to measure also the nature of noise. Sound quality of sounds such as car noise can be objectively evaluated by several parameters. One of them is psychoacoustic annoyance, described by loudness, tone color, and the temporal structure of sound. In this paper the assessment of several sound quality parameters, such...
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Decisional DNA and Optimization Problem
PublicationMany researchers have proved that Decisional DNA (DDNA) and Set of Experience Knowledge Structure (SOEKS or SOE) is a technology capable of gathering information and converting it into knowledge to help decision-makers to make precise decisions in many ways. These techniques have a feature to combine with different tools, such as data mining techniques and web crawlers, helping organization collect information from different sources...
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Speech Analytics Based on Machine Learning
PublicationIn this chapter, the process of speech data preparation for machine learning is discussed in detail. Examples of speech analytics methods applied to phonemes and allophones are shown. Further, an approach to automatic phoneme recognition involving optimized parametrization and a classifier belonging to machine learning algorithms is discussed. Feature vectors are built on the basis of descriptors coming from the music information...
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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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"Spuścizna Rzeczpospolitej Obojga Narodów" : polskie, litewskie i białoruskie dziedzictwo pozostałe po rodzinie Pusłowskich
PublicationCelem pracy jest przedstawienie i porównanie wybranych dokumentów oraz archiwów rękopiśmiennych tworzących spuściznę pozostawioną przez szlachecką rodzinę Pusłowskich, zamieszkałą na terenach Wielkiego Księstwa Litewskiego, w czasach unii połączonego z Królestwem Polskim w Rzeczpospolitą Obojga Narodów. Rodzina ta posiadała majątki na terenie dzisiejszej Litwy i Białorusi od XVI w., a od XVIII w. na terenach polskich będących pod...
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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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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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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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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,...