Search results for: biological ontology

Authors: Mahan Qwamizadeh, Kun Zhou, Zuoqi Zhang, Yong Wei Zhang

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Typical load-bearing biological materials like bone, mineralized tendon and shell, are biocomposites made from both organic (collagen) and inorganic (biomineral) materials. This amazing class of materials with intrinsic internally designed hierarchical structures show superior mechanical properties with regard to their weak components from which they are formed. Extensive investigations concentrating on static loading conditions have been done to study the biological materials failure. However, most of the damage and failure mechanisms in load-bearing biological materials will occur whenever their structures are exposed to dynamic loading conditions. The main question needed to be answered here is: What is the relation between the layout and architecture of the load-bearing biological materials and their dynamic behavior? In this work, a staggered model has been developed based on the structure of natural materials at nanoscale and Finite Element Analysis (FEA) has been used to study the dynamic behavior of the structure of load-bearing biological materials to answer why the staggered arrangement has been selected by nature to make the nanocomposite structure of most of the biological materials. The results showed that the staggered structures will efficiently attenuate the stress wave rather than the layered structure. Furthermore, such staggered architecture is effectively in charge of utilizing the capacity of the biostructure to resist both normal and shear loads. In this work, the geometrical parameters of the model like the thickness and aspect ratio of the mineral inclusions selected from the typical range of the experimentally observed feature sizes and layout dimensions of the biological materials such as bone and mineralized tendon. Furthermore, the numerical results validated with existing theoretical solutions. Findings of the present work emphasize on the significant effects of dynamic behavior on the natural evolution of load-bearing biological materials and can help scientists to design bioinspired materials in the laboratories.

Keywords: load-bearing biological materials, nanostructure, staggered structure, stress wave decay

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Authors: Arun Prabhakar

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Threat modeling is an important activity carried out in the initial stages of the development lifecycle that helps in building proactive security measures in the product. Though there are many techniques and tools available today, one of the common challenges with the traditional methods is the lack of a systematic approach in identifying security threats. The proposed solution describes an organized model by defining ontologies that help in building patterns to enumerate threats. The concepts of graph theory are applied to build the pattern for discovering threats for any given scenario. This graph-based solution also brings in other benefits, making it a customizable and scalable model.

Keywords: directed acyclic graph, ontology, patterns, threat identification, threat modeling

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Authors: Ivan Stanev, Maria Koleva

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A common platform for automated programming (CPAP) is defined in details. Two versions of CPAP are described: Cloud-based (including the set of components for classic programming, and the set of components for combined programming) and KBASE based (including the set of components for automated programming, and the set of components for ontology programming). Four KBASE products (module for automated programming of robots, intelligent product manual, intelligent document display, and intelligent form generator) are analyzed and CPAP contributions to automated programming are presented.

Keywords: automated programming, cloud computing, knowledge based software engineering, service oriented architecture

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Authors: Shen Jian, Hu Jie, Qi Jin, Liu Wei Jie, Chen Ji Yi, Peng Ying Hong

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In order to settle the problem of acquiring case in biological related to design problems, a biometrics instance acquisition method based on text mining is presented. Through the construction of corpus text vector space and knowledge mining, the feature selection, similarity measure and case retrieval method of text in the field of biology are studied. First, we establish a vector space model of the corpus in the biological field and complete the preprocessing steps. Then, the corpus is retrieved by using the vector space model combined with the functional keywords to obtain the biological domain examples related to the design problems. Finally, we verify the validity of this method by taking the example of text.

Keywords: text mining, vector space model, feature selection, biologically inspired design

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Authors: Diego Alejandro Espíndola-Fernández, Ana María Posada-Cano, Dagnóvar Aristizábal-Ocampo, Jaime Alberto Gallo-Villegas

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Background: With the increase in life expectancy, aging has been subject of frequent research, and therefore multiple strategies have been proposed to quantify the advance of the years based on the known physiology of human senescence. For several decades, attempts have been made to characterize these changes through the concept of biological age, which aims to integrate, in a measure of time, structural or functional variation through biomarkers in comparison with simple chronological age. The objective of this scoping review is to deepen the updated concept of measuring biological age composed of biomarkers in the general population and to summarize recent evidence to identify gaps and priorities for future research. Methods: A scoping review was conducted according to the five-phase methodology developed by Arksey and O'Malley through a search of five bibliographic databases to February 2021. Original articles were included with no time or language limit that described the biological age composed of at least two biomarkers in those over 18 years of age. Results: 674 articles were identified, of which 105 were evaluated for eligibility and 65 were included with information on the measurement of biological age composed of biomarkers. Articles from 1974 of 15 nationalities were found, most observational studies, in which clinical or paraclinical biomarkers were used, and 11 different methods described for the calculation of the composite biological age were informed. The outcomes reported were the relationship with the same measured biomarkers, specified risk factors, comorbidities, physical or cognitive functionality, and mortality. Conclusions: The concept of biological age composed of biomarkers has evolved since the 1970s and multiple methods of its quantification have been described through the combination of different clinical and paraclinical variables from observational studies. Future research should consider the population characteristics, and the choice of biomarkers against the proposed outcomes to improve the understanding of aging variables to direct effective strategies for a proper approach.

Keywords: biological age, biological aging, aging, senescence, biomarker

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Authors: Oliver Arana

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Within the common vein of social understanding, surrealism is often understood to rely on disconcerting images and fragmented collage, both in its visual representation and literary manifestations. By tracing the history and literature of surrealism, the author makes the argument that there were certain factions within Latin America that employed characteristics of surrealism in order to reach some sense of understanding, and not to further complicate or disorient -an aim that most closely aligns to Freudian psychoanalysis. Psychoanalysis should, however, be a comparable practice only to understand how Latin American surrealism had more of a concrete goal than its European counterpart. The primary subject of the paper is the Mexican poet, Pita Amor, who has retroactively been associated with the movement; and therefore, it should be duly noted that the adjective, surrealism, only applies to her as something that describes traits within the literary lexicon.

Keywords: Latin America, Pita Amor, poetry, surrealism

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Authors: Hoda Dehghani, Zahra Dehghani

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Considering the obvious growth and variety of veterinary biological product and increase consumption and also the price, it is necessary to establish the rules and serious monitoring of this products which are less expensive than the original products. The scope of this research is the study of comparing the registration criteria and procedures of veterinary biological drugs in the world's leading agencies such as EMA, FDA, and WHO. For this, purpose the rules and regulations for registration of these drugs in prestigious organizations such as the FDA, EMA and WHO were examined and compared with the existing legislation in Iran. Studies show that EMA is the forefront of the compilation and registration of drugs in the world. China is a one of the greatest country in the development of drugs and establishes very closely guidelines with creditable global guidelines, and Now, is the first country to implement the rules codified in the Far East and followed by china, India and, South Korea and Taiwan have taken incorporate the industry's top ranking in Asia. At now, Asia by creating appropriate indicators not only as a powerful center in the field of drug delivery but also as a competitor to the United States is a major source of drug discovery and creation of innovation. the activities such as clinical trials and pharmaceutical investment is the speed of technology on the continent.

Keywords: veterinary biological product, regulation of registration, biological products, regularity authorities

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Authors: O. Balamane-Zizi, L. M. Rouidi, A. Boukhrissa, N. Daas, H. Ait-amar

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The objective of this study was to test the possibility of a mixed treatment (physical-chemical and biological) of Ouled Fayet leachates which date of 10 years and has a large fraction of hard COD that can be reduced by coagulation-flocculation. Previous batch tests showed the possibility of applying the physical-chemical and biological treatments separately; the removal efficiencies obtained in this case were not interesting. We propose, therefore, to test the possibility of a combined treatment, in order to improve the quality of the leachates. Estimation of the treatment’s effectiveness was done by analysis of some pollution parameters such as COD, suspended solids, and heavy metals (particularly iron and nickel). The main results obtained after the combination of treatments, show reduction rate of about 63% for COD, 73% for suspended solids and 80% for iron and nickel. We also noted an improvement in the turbidity of treated leachates.

Keywords: landfill leachates, COD, physical-chemical treatment, biological treatment

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Authors: Micheal Olaolu Arowolo, Muhammad Azam, Fei He, Mihail Popescu, Dong Xu

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As the quantity of biological articles rises, so does the number of biological route figures. Each route figure shows gene names and relationships. Annotating pathway diagrams manually is time-consuming. Advanced image understanding models could speed up curation, but they must be more precise. There is rich information in biological pathway figures. The first step to performing image understanding of these figures is to recognize gene names automatically. Classical optical character recognition methods have been employed for gene name recognition, but they are not optimized for literature mining data. This study devised a method to recognize an image bounding box of gene name as a photo using deep Siamese neural network models to outperform the existing methods using ResNet, DenseNet and Inception architectures, the results obtained about 84% accuracy.

Keywords: biological pathway, gene identification, object detection, Siamese network

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Authors: Abul B. M. M. K. Islam, Mandar Dave, Roderick V. Jensen, Ashok R. Amin

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A systems approach was applied to characterize differentially expressed transcripts, bioinformatics pathways, and proteins and prostaglandins (PGs) from lung fibroblasts procured from wild-type (WT), COX-1-/- and COX-2-/- mice to understand system level control mechanism. Bioinformatics analysis of COX-2 and COX-1 ablated cells induced COX-1 and COX-2 specific signature respectively, which significantly overlapped with an 'IL-1β induced inflammatory signature'. This defined novel cross-talk signals that orchestrated coordinated activation of pathways of sterile inflammation sensed by cellular stress. The overlapping signals showed significant over-representation of shared pathways for interferon y and immune responses, T cell functions, NOD, and toll-like receptor signaling. Gene Ontology Biological Process (GOBP) and pathway enrichment analysis specifically showed an increase in mRNA expression associated with: (a) organ development and homeostasis in COX-1-/- cells and (b) oxidative stress and response, spliceosomes and proteasomes activity, mTOR and p53 signaling in COX-2-/- cells. COX-1 and COX-2 showed signs of functional pathways committed to cell cycle and DNA replication at the genomics level. As compared to WT, metabolomics analysis revealed a significant increase in COX-1 mRNA and synthesis of basal levels of eicosanoids (PGE2, PGD2, TXB2, LTB4, PGF1α, and PGF2α) in COX-2 ablated cells and increase in synthesis of PGE2, and PGF1α in COX-1 null cells. There was a compensation of PGE2 and PGF1α in COX-1-/- and COX-2-/- cells. Collectively, these results support a broader, differential and collaborative regulation of both COX-1 and COX-2 pathways at the metabolic, signaling, and genomics levels in cellular homeostasis and sterile inflammation induced by cellular stress.

Keywords: cyclooxygenases, inflammation, lung fibroblasts, systemic

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Authors: Lucia Carrion Gordon, Maria Gabriela Lopez Yanez

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This project focuses on heritage concepts and their importance in every evolving and changing Digital Era where system solutions have to be sustainable, efficient and suitable to the basic needs. The prototype has to cover the principal requirements for the case studies. How to preserve the sociological ideas of dances in Ecuador like ‘La Bomba’ is the best example and challenge to preserve the intangible data. The same idea is applicable with books and music. The History and how to keep it, is the principal mission of Heritage Preservation. The dance of La Bomba is rooted on a specific movement system whose main part is the sideward hip movement. La Bomba´s movement system is the surface manifestation of a whole system of knowledge whose principal characteristics are the historical relation of Chote˜nos with their land and their families.

Keywords: digital preservation, heritage, IT management, data, metadata, ontology, serendipity

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Authors: Ricardo Avila, Gabriel Lopes, Vania Vidal, Jose Macedo

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This proposal aims for semantic enrichment between glossaries using the Simple Knowledge Organization System (SKOS) vocabulary to discover synonyms, hyponyms and hyperonyms semiautomatically, in Brazilian Portuguese, generating new semantic relationships based on WordNet. To evaluate the quality of this proposed model, experiments were performed by the use of two sets containing new relations, being one generated automatically and the other manually mapped by the domain expert. The applied evaluation metrics were precision, recall, f-score, and confidence interval. The results obtained demonstrate that the applied method in the field of Oil Production and Extraction (E&P) is effective, which suggests that it can be used to improve the quality of terminological mappings. The procedure, although adding complexity in its elaboration, can be reproduced in others domains.

Keywords: ontology matching, mapping enrichment, semantic web, linked data, SKOS

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Authors: S. N. Derrar, M. Sekkal-Rahal

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The Nonlinear optics (NLO) technique is widely used in the field of biological imaging. In fact, grafting biological entities with a high NLO response on tissues and cells enhances the NLO responses of these latter, and ameliorates, consequently, their biological imaging quality. In this optics, we carried out a theoretical study, in the aim of analyzing the peptide bonds created between alanine amino acid and both unnatural amino acids: L-Dopa and Azatryptophan, respectively. Ramachandran plots have been performed for these systems, and their structural parameters have been analyzed. The NLO responses of these peptides have been reported by calculating the first hyperpolarizability values of all the minima found on the plots. The use of such unnatural amino acids as endogenous probing molecules has been investigated through this study. The Density Functional Theory (DFT) has been used for structural properties, while the Second-order Møller-Plesset Perturbation Theory (MP2) has been employed for the NLO calculations.

Keywords: biological imaging, hyperpolarizability, nonlinear optics, probing molecule

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Authors: Deepa Vijay, Chellammal Surianarayanan, Gopinath Ganapathy

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Requirements of a software project serve as a guideline for the entire project team which enable the team towards producing the right outcome. As requirements are the key in deciding the success of the project, it should be specified in an unambiguous manner. Also, the requirements should be complete and consistent. It should be interpreted in the same way by the entire software project team as the customer interprets. Specifying requirements in textual manner is common in software development. This leads to poor understanding of the requirements which results in more errors and degraded quality. There are some literatures which focus on semantic way of specifying functional requirement which ensure the consistency and completeness of requirements. Alternately in the work, a method is proposed to map the syntactic requirements with corresponding semantics in the form of ontologies. This improves the understanding of requirements, prevents errors and improves quality.

Keywords: functional requirement, ontology, requirements management, semantics

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Authors: Nassima Khanfri, Ali Boucenna

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As metallic nanoparticles are increasingly used in many economic sectors, there is interest in the biological and environmental safety of their production. The main methods of synthesizing nanoparticales are chemical and physical approaches that are often expensive and potentially harmful to the environment. The present study is devoted to the possibility of the synthesis of silver nanoparticales and zinc oxide from silver nitrate and zinc acetate using basilica plant extracts. The products obtained are characterized by various analysis techniques, such as UV/V, XRD, MEB-EDX, FTIR, and RAMAN. These analyzes confirm the crystalline nature of AgNps and ZnONps. These crystalline powders having effective biological activities regarding the antioxidant and antibacterial, which could be used in several biological applications.

Keywords: green synthesis, bio-reduction, metals nan Oparticales, Plants extracts

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Authors: Parvaneh Mahmoudi, Ahmad Moeni, Seyed Mojtaba Khayam Nekoei, Mohsen Mardi, Mehrshad Zeinolabedini, Ghasem Hosseini Salekdeh

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Saffron (Crocus sativus L.) is one of the most important spice and medicinal plants. The three-branch style of C. sativus flowers are the most important economic part of the plant and known as saffron, which has several medicinal properties. Despite the economic and biological significance of this plant, knowledge about its molecular characteristics is very limited. In the present study, we, for the first time, constructed a comprehensive dataset for C. sativus stigma through de novo transcriptome sequencing. We performed de novo transcriptome sequencing of C. sativus stigma using the Illumina paired-end sequencing technology. A total of 52075128 reads were generated and assembled into 118075 unigenes, with an average length of 629 bp and an N50 of 951 bp. A total of 66171unigenes were identified, among them, 66171 (56%) were annotated in the non-redundant National Center for Biotechnology Information (NCBI) database, 30938 (26%) were annotated in the Swiss-Prot database, 10273 (8.7%) unigenes were mapped to 141 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, while 52560 (44%) and 40756 (34%) unigenes were assigned to Gen Ontology (GO) categories and Eukaryotic Orthologous Groups of proteins (KOG), respectively. In addition, 65 candidate genes involved in three stages of crocin biosynthesis were identified. Finally, transcriptome sequencing of saffron stigma was used to identify 6779 potential microsatellites (SSRs) molecular markers. High-throughput de novo transcriptome sequencing provided a valuable resource of transcript sequences of C. sativus in public databases. In addition, most of candidate genes potentially involved in crocin biosynthesis were identified which could be further utilized in functional genomics studies. Furthermore, numerous obtained SSRs might contribute to address open questions about the origin of this amphiploid spices with probable little genetic diversity.

Keywords: saffron, transcriptome, NGS, bioinformatic

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Authors: Manolo Dulva Hina, Clement Thierry, Assia Soukane, Amar Ramdane-Cherif

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In this paper, we presented our innovative way of determining the driving context for a driving assistance system. We invoke the fusion of all parameters that describe the context of the environment, the vehicle and the driver to obtain the driving context. We created a training set that stores driving situation patterns and from which the system consults to determine the driving situation. A machine-learning algorithm predicts the driving situation. The driving situation is an input to the fission process that yields the action that must be implemented when the driver needs to be informed or assisted from the given the driving situation. The action may be directed towards the driver, the vehicle or both. This is an ongoing work whose goal is to offer an alternative driving assistance system for safe driving, green driving and comfortable driving. Here, ontologies are used for knowledge representation.

Keywords: cognitive driving, intelligent transportation system, multimodal system, ontology, machine learning

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Authors: Charalabos Antonatos, Mariza Panoutsopoulou, Georgios K. Georgakilas, Evangelos Evangelou, Yiannis Vasilopoulos

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The extended tissue damage and severe clinical outcomes of autoimmune diseases, accompanied by the high annual costs to the overall health care system, highlight the need for an efficient therapy. Increasing knowledge over the pathophysiology of specific chronic inflammatory diseases, namely Psoriasis (PsO), Inflammatory Bowel Diseases (IBD) consisting of Crohn’s disease (CD) and Ulcerative colitis (UC), and Rheumatoid Arthritis (RA), has provided insights into the underlying mechanisms that lead to the maintenance of the inflammation, such as Tumor Necrosis Factor alpha (TNF-α). Hence, the anti-TNFα biological agents pose as an ideal therapeutic approach. Despite the efficacy of anti-TNFα agents, several clinical trials have shown that 20-40% of patients do not respond to treatment. Nowadays, high-throughput technologies have been recruited in order to elucidate the complex interactions in multifactorial phenotypes, with the most ubiquitous ones referring to transcriptome quantification analyses. In this context, a random effects meta-analysis of available gene expression cDNA microarray datasets was performed between responders and non-responders to anti-TNFα therapy in patients with IBD, PsO, and RA. Publicly available datasets were systematically searched from inception to 10th of November 2020 and selected for further analysis if they assessed the response to anti-TNFα therapy with clinical score indexes from inflamed biopsies. Specifically, 4 IBD (79 responders/72 non-responders), 3 PsO (40 responders/11 non-responders) and 2 RA (16 responders/6 non-responders) datasetswere selected. After the separate pre-processing of each dataset, 4 separate meta-analyses were conducted; three disease-specific and a single combined meta-analysis on the disease-specific results. The MetaVolcano R package (v.1.8.0) was utilized for a random-effects meta-analysis through theRestricted Maximum Likelihood (RELM) method. The top 1% of the most consistently perturbed genes in the included datasets was highlighted through the TopConfects approach while maintaining a 5% False Discovery Rate (FDR). Genes were considered as Differentialy Expressed (DEGs) as those with P ≤ 0.05, |log2(FC)| ≥ log2(1.25) and perturbed in at least 75% of the included datasets. Over-representation analysis was performed using Gene Ontology and Reactome Pathways for both up- and down-regulated genes in all 4 performed meta-analyses. Protein-Protein interaction networks were also incorporated in the subsequentanalyses with STRING v11.5 and Cytoscape v3.9. Disease-specific meta-analyses detected multiple distinct pro-inflammatory and immune-related down-regulated genes for each disease, such asNFKBIA, IL36, and IRAK1, respectively. Pathway analyses revealed unique and shared pathways between each disease, such as Neutrophil Degranulation and Signaling by Interleukins. The combined meta-analysis unveiled 436 DEGs, 86 out of which were up- and 350 down-regulated, confirming the aforementioned shared pathways and genes, as well as uncovering genes that participate in anti-inflammatory pathways, namely IL-10 signaling. The identification of key biological pathways and regulatory elements is imperative for the accurate prediction of the patient’s response to biological drugs. Meta-analysis of such gene expression data could aid the challenging approach to unravel the complex interactions implicated in the response to anti-TNFα therapy in patients with PsO, IBD, and RA, as well as distinguish gene clusters and pathways that are altered through this heterogeneous phenotype.

Keywords: anti-TNFα, autoimmune, meta-analysis, microarrays

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Authors: H. Shiu, M.S. Lu, Y.P. Tsai

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This study explored the impacts of CuO, TiO2, SiO2 nanoparticles on biological phosphorus removal. Experimental results showed that the phosphorus removal ability of phosphorus accumulating organism (PAO) was initially inhibited when CuO nanoparticle concentration was 5 mgl-1. The inhibition of phosphorus removal for 1000 mgl-1 of TiO2 with sunlight was higher than without sunlight case. The inhibition of phosphorus removal began at 500 mgl-1 SiO2 nanoparticle concentration. Inhibition became apparent when SiO2 nanoparticle concentration was up to 1000 mgl-1.

Keywords: nano copper oxide, nano titanium dioxide, nano silica, enhanced biological phosphate removal

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Authors: Mohammadsadegh Zanganehfar

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Since the modernism, movement, and appearance of modern architecture, an aggressive desire for a general design theory in the theoretical works of architects in the form of books and essays emerges. Since Robert Venturi and Denise Scott Brown’s published complexity and contradiction in architecture in 1966, the discourse of complexity and volumetric composition has been an important and controversial issue in the discipline. Ever since various theories and essays were involved in this discourse, this paper attempt to identify chaos theory as a scientific model of complexity and its relation to architecture design theory by conducting a qualitative analysis and multidisciplinary critical approach through architecture and basic sciences resources. As a result, we identify chaotic architecture as the correlation of chaos theory and architecture as an independent nonlinear design theory with specific characteristics and properties.

Keywords: architecture complexity, chaos theory, fractals, nonlinear dynamic systems, nonlinear ontology

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Authors: Er-Yuan Chuang

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Bio-mimetic matters have biological functionalities. This might be valuable in the development of versatile biomaterials. At biological fields, protein-based materials might be components to form a 3D network of extracellular biomolecules, containing growth factors. Also, the protein-based biomaterial provides biochemical and structural assistance of adjacent cells. In this study, we try to prepare protein based biomaterial, which was harvested from living animal. We analyzed it’s chemical, physical and biological property in vitro. Besides, in vivo bio-interaction of the prepared biomimetic matrix was tested in an animal model. The protein-based biomaterial has degradability and biocompatibility. This development could be used for tissue regenerations and be served as platform technologies.

Keywords: protein based, in vitro study, in vivo study, biomaterials

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Authors: Sahar Shahsavaripour Ghazanfarpour

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As our daily life depends on quality of built services by systems and using devices in our environment; so education and model of software′s quality will be so important. By daily growth in software′s systems and using them so much, progressing process and requirements′ evaluation in primary level of progress especially architecture level in software get more important. Modern driver architecture changes an in dependent model of a level into some specific models that their purpose is reducing number of software changes into an executive model. Process of designing software engineering is mid-automated. The needed quality attribute in designing architecture and quality attribute in representation are in architecture models. The main problem is the relationship between needs, and elements in some aspect with implicit models and input sources in process. It’s because there is no detection ability. The MART profile is use to describe real-time properties and perform plat form modeling.

Keywords: MDA, DW, OMG, UML, AKB, software architecture, ontology, evaluation

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Authors: Noura Kichou, Manel Tafergguenit, Nabila Ghechtouli, Zakia Hank

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The aim of this work is to synthesize, characterize and evaluate the biological activity of two Ligands : glyoxime and dimethylglyoxime, and their metal Ni(II) chelates. The newly chelates were characterized by elemental analysis, IR, EPR, nuclear magnetic resonances (1H and 13C), and biological activity. The antibacterial and antifungal activities of the ligands and its metal complexes were screened against bacterial species (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli) and fungi (Candida albicans). Ampicillin and amphotericin were used as references for antibacterial and antifungal studies. The activity data show that the metal complexes have a promising biological activity comparable with parent free ligand against bacterial and fungal species. A structural, energetic, and electronic theoretical study was carried out using the DFT method, with the functional B3LYP and the gaussian program 09. A complete optimization of geometries was made, followed by a calculation of the frequencies of the normal modes of vibration. The UV spectrum was also interpreted. The theoretical results were compared with the experimental data.

Keywords: glyoxime, dimetylglyoxime, nickel, antibacterial activity

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Authors: Noura Kichou, Manel Tafergguenit, Nabila Ghechtouli, Zakia Hank

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The aim of this work is to synthesize, characterize and evaluate the biological activity of two Ligands: glyoxime and dimethylglyoxime, and their metal Ni(II) chelates. The newly chelates were characterized by elemental analysis, IR, EPR, nuclear magnetic resonances (1H and 13C), and biological activity. The antibacterial and antifungal activities of the ligands and its metal complexes were screened against bacterial species (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli) and fungi (Candida albicans). Ampicillin and amphotericin were used as references for antibacterial and antifungal studies. The activity data show that the metal complexes have a promising biological activity comparable with parent free ligand against bacterial and fungal species. A structural, energetic, and electronic theoretical study was carried out using the DFT method, with the functional B3LYP and the gaussian program 09. A complete optimization of geometries was made, followed by a calculation of the frequencies of the normal modes of vibration. The UV spectrum was also interpreted. The theoretical results were compared with the experimental data.

Keywords: glyoxime, dimetylglyoxime, nickel, antibacterial activity

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Authors: Fadoua Ouamani, Narjès Bellamine Ben Saoud, Henda Hajjami Ben Ghézala

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In the last few years and over the last decades, there was a growing interest in the development of Computer Supported Collaborative Learning (CSCL) environments. However, the existing systems ignore the variety of learners and their socio-cultural differences, especially in the case of distant and networked learning. In fact, within such collaborative learning environments, learners from different socio-cultural backgrounds may interact together. These learners evolve within various cultures and social contexts and acquire different socio-cultural values and behaviors. Thus, they should be assisted while communicating and collaborating especially in an intercultural group. Besides, the communication and collaboration tools provided to each learner must depend on and be adapted to her/his socio-cultural profile. The main goal of this paper is to present the proposed socio-cultural adaptation approach based on and guided by ontologies to adapt CSCL environments to the socio-cultural profiles of its users (learners or others).

Keywords: CSCL, socio-cultural profile, adaptation, ontology

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Authors: Carlos Escobar-del Pozo, César Ahumada-Monroy, Azael García-Rebolledo, Alberto Brambila-Solórzano, Gregorio Martínez-Sánchez, Luis Ortiz-Rincón

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Numerical simulations of flow in complex biological structures have gained considerable attention in the last years. However, the major issue is the validation of the results. The present work shows a Particle Image Velocimetry PIV flow visualization technique in complex biological structures, particularly in intracranial aneurysms. A methodology to reconstruct and generate a transparent model has been developed, as well as visualization and particle tracking techniques. The generated transparent models allow visualizing the flow patterns with a regular camera using the visualization techniques. The final goal is to use visualization as a tool to provide more information on the treatment and surgery decisions in aneurysms.

Keywords: aneurysms, PIV, flow visualization, particle tracking

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Authors: Sarra K. Ikhlef, Onita Basu

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Natural organic matter (NOM) removal efficiency using drinking water treatment biological filters can be highly influenced by backwashing conditions. Backwashing has the ability to remove the accumulated biomass and particles in order to regenerate the biological filters' removal capacity and prevent excessive headloss buildup. A lab scale system consisting of 3 biological filters was used in this study to examine the implications of different backwash strategies on biological filtration performance. The backwash procedures were evaluated based on their impacts on dissolved organic carbon (DOC) removals, biological filters’ biomass, backwash water volume usage, and particle removal. Results showed that under nutrient limited conditions, the simultaneous use of air and water under collapse pulsing conditions lead to a DOC removal of 22% which was significantly higher (p>0.05) than the 12% removal observed under water only backwash conditions. Employing a bed expansion of 20% under nutrient supplemented conditions compared to a 30% reference bed expansion while using the same amount of water volume lead to similar DOC removals. On the other hand, utilizing a higher bed expansion (40%) lead to significantly lower DOC removals (23%). Also, a backwash strategy that reduced the backwash water volume usage by about 20% resulted in similar DOC removals observed with the reference backwash. The backwash procedures investigated in this study showed no consistent impact on biological filters' biomass concentrations as measured by the phospholipids and the adenosine tri-phosphate (ATP) methods. Moreover, none of these two analyses showed a direct correlation with DOC removal. On the other hand, dissolved oxygen (DO) uptake showed a direct correlation with DOC removals. The addition of the extended terminal subfluidization wash (ETSW) demonstrated no apparent impact on DOC removals. ETSW also successfully eliminated the filter ripening sequence (FRS). As a result, the additional water usage resulting from implementing ETSW was compensated by water savings after restart. Results from this study provide insight to researchers and water treatment utilities on how to better optimize the backwashing procedure for the goal of optimizing the overall biological filtration process.

Keywords: biological filtration, backwashing, collapse pulsing, ETSW

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Authors: Keerthi S. Shetty, Annappa Basava

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In recent years, modelling of biological systems represented by biochemical reactions has become increasingly important in Systems Biology. Biological systems represented by biochemical reactions are highly stochastic in nature. Probabilistic model is often used to describe such systems. One of the main challenges in Systems biology is to combine absolute experimental data into probabilistic model. This challenge arises because (1) some molecules may be present in relatively small quantities, (2) there is a switching between individual elements present in the system, and (3) the process is inherently stochastic on the level at which observations are made. In this paper, we describe a novel idea of combining absolute experimental data into probabilistic model using tool R2. Through a case study of the Transcription Process in Prokaryotes we explain how biological systems can be written as probabilistic program to combine experimental data into the model. The model developed is then analysed in terms of intrinsic noise and exact sampling of switching times between individual elements in the system. We have mainly concentrated on inferring number of genes in ON and OFF states from experimental data.

Keywords: systems biology, probabilistic model, inference, biology, model

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Authors: Muhammad Azam, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu

Abstract:

The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than OCR results.

Keywords: biological pathway, image understanding, gene name recognition, object detection, Siamese network, VGG

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Authors: Yifan Fan, Xudong Luo, Pingping Lin

Abstract:

An essential task in the field of artificial intelligence is to allow computers to interact with people through natural language. Therefore, researches such as virtual assistants and dialogue systems have received widespread attention from industry and academia. The response generation plays a crucial role in dialogue systems, so to push forward the research on this topic, this paper surveys various methods for response generation. We sort out these methods into three categories. First one includes finite state machine methods, framework methods, and instance methods. The second contains full-text indexing methods, ontology methods, vast knowledge base method, and some other methods. The third covers retrieval methods and generative methods. We also discuss some hybrid methods based knowledge and deep learning. We compare their disadvantages and advantages and point out in which ways these studies can be improved further. Our discussion covers some studies published in leading conferences such as IJCAI and AAAI in recent years.

Keywords: deep learning, generative, knowledge, response generation, retrieval

Procedia PDF Downloads 113