Search results for: biomarker discovery

Authors: Yaara Oppenheimer-Shaanan, Nimrod Nachmias, Marina Campos Rocha, Neta Schlezinger, Noam Dotan, Asaf Levy

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Fusarium oxysporum, a fungus that attacks a broad range of plants and can cause infections in humans, operates across different kingdoms. This pathogen encounters varied conditions, such as temperature, pH, and nutrient availability, in plant and human hosts. The Fusarium oxysporum species complex, pervasive in soils globally, can affect numerous plants, including key crops like tomatoes and bananas. Controlling Fusarium infections can involve biocontrol agents that hinder the growth of harmful strains. Our research developed a computational method to identify toxin domains within a vast number of microbial genomes, leading to the discovery of nine distinct toxins capable of killing bacteria and fungi, including Fusarium. These toxins appear to function as enzymes, causing significant damage to cellular structures, membranes and DNA. We explored biological control using bacteria that produce polymorphic toxins, finding that certain bacteria, non-pathogenic to plants, offer a safe biological alternative for Fusarium management, as they did not harm macrophage cells or C. elegans. Additionally, we elucidated the 3D structures of two toxins with their protective immunity proteins, revealing their function as unique DNases. These potent toxins are likely instrumental in microbial competition within plant ecosystems and could serve as biocontrol agents to mitigate Fusarium wilt and related diseases.

Keywords: microbial toxins, antifungal, Fusarium oxysporum, bacterial-fungal intreactions

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Authors: Benedicte Madon, Marion Pillet, Justine Castrec, Quentin Fonatine, Pierre Lejeune, Michel Marengo, Helene Thomas

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Biodiversity in port ecosystems faces many anthropic pressures from port activities. The maritime industry and port areas have been under scrutiny regarding their environmental impacts. In the port value chain, port managers need to implement actions to fulfil environmental certifications and European Directive requirements. This paper seeks to highlight the lessons learned and opportunities through the QUAMPO project to move towards port biodiversity restoration in Corsica using innovative biomonitoring in the goal of obtaining green certification.

Keywords: biomonitoring, port, water quality, invertebrate, corsica, biomarker, trace elements, HAP, PCB, certification

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Authors: Aidin Foroutan, David S. Wishart, Leluo L. Guan, Carolyn Fitzsimmons

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Maximizing efficiency and growth potential of beef cattle requires not only genetic selection (i.e. residual feed intake (RFI)) but also adequate nutrition throughout all stages of growth and development. Nutrient restriction during gestation has been shown to negatively affect post-natal growth and development as well as fertility of the offspring. This, when combined with RFI may affect progeny traits. This study aims to investigate the impact of selection for divergent genetic potential for RFI and maternal nutrition during early- to mid-gestation, on bull calf traits such as fertility and muscle development using multiple ‘omics’ approaches. Comparisons were made between High-diet vs. Low-diet and between High-RFI vs. Low-RFI animals. An epigenetics experiment on semen samples identified 891 biomarkers associated with growth and development. A gene expression study on Longissimus thoracis muscle, semimembranosus muscle, liver, and testis identified 4 genes associated with muscle development and immunity of which Myocyte enhancer factor 2A [MEF2A; induces myogenesis and control muscle differentiation] was the only differentially expressed gene identified in all four tissues. An initial metabolomics experiment on serum samples using nuclear magnetic resonance (NMR) identified 4 metabolite biomarkers related to energy and protein metabolism. Once all the biomarkers are identified, bioinformatics approaches will be used to create a database covering all the ‘omics’ data collected from this project. This database will be broadened by adding other information obtained from relevant literature reviews. Association analyses with these data sets will be performed to reveal key biological pathways affected by RFI and maternal nutrition. Through these association studies between the genome and metabolome, it is expected that candidate biomarker genes and metabolites for feed efficiency, fertility, and/or muscle development are identified. If these gene/metabolite biomarkers are validated in a larger animal population, they could potentially be used in breeding programs to select superior animals. It is also expected that this work will lead to the development of an online tool that could be used to predict future traits of interest in an animal given its measurable ‘omics’ traits.

Keywords: biomarker, maternal nutrition, omics, residual feed intake

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Authors: Meisam Omidi, M. Mirijalili, Mohammadmehdi Choolaei, Z. Sharifi, F. Haghiralsadat, F. Yazdian

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In this work, we have used arrays of micromechanical piezoresistive cantilever with different geometries to detect carcinoembryonic antigen (CEA), which is known as an important biomarker associated with various cancers such as the colorectal, lung, breast, pancreatic, and bladder cancer. The sensing principle is based on the surface stress changes induced by antigen–antibody interaction on the microcantilevers surfaces. Different concentrations of CEA in a human serum albumin (HSA) solution were detected as a function of the deflection of the beams. According to the experiments, it was revealed that microcantilevers have surface stress sensitivities in the order of 8 (mJ/m). This matter allows them to detect CEA concentrations as low as 3 ng/mL or 18 pM. This indicates the fact that the self-sensing microcantilever approach is beneficial for pathological tests.

Keywords: micromechanical biosensors, carcinoembryonic antigen (CEA), surface stress

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Authors: Matthias Stange

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In the early modern period, a different image of man began to prevail in Europe. The focus was on the self-determined human being and his abilities. At first, these developments could be seen in Italian painting and architecture, which again oriented itself to the concepts and forms of antiquity. For example, through the discovery of perspective representation by Brunelleschi or later the orthogonal projection by Alberti, after the ancient knowledge of optics had been forgotten in the Middle Ages. The understanding of reality in the Middle Ages was not focused on the sensually perceptible world but was determined by ecclesiastical dogmas. The empirical part of this study examines the rediscovery and development of perspective. With the paradigm of antiquity, the figure of the architect was also recognised again - the cultural man trained theoretically and practically in numerous subjects, as Vitruvius describes him. In this context, the role of the architect, the influence on the painting of the Quattrocento as well as the influence on architectural representation in the Baroque period are examined. Baroque is commonly associated with the idea of illusionistic appearance as opposed to the tangible reality presented in the Renaissance. The study has shown that the central perspective projection developed by Filippo Brunelleschi enabled another understanding of seeing and the dissemination of painted images. Brunelleschi's development made it possible to understand the sight of nature as a reflection of what is presented to the viewer's eye. Alberti later shortened Brunelleschi's central perspective representation for practical use in painting. In early modern Italian architecture and painting, these developments apparently supported each other. The pictorial representation of architecture initially served the development of an art form before it became established in building practice itself.

Keywords: Alberti, Brunelleschi, central perspective projection, orthogonal projection, quattrocento, baroque

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Authors: Parthiban Srinivasan

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With recent advances in computational power and access to enough data in biosciences, artificial intelligence methods are increasingly being used in drug discovery research. These methods are essentially a series of advanced statistics based exercises that review the past to indicate the likely future. Our goal is to develop a model that accurately predicts biological activity and toxicity parameters for novel compounds. We have compiled a robust library of over 150,000 chemical compounds with different pharmacological properties from literature and public domain databases. The compounds are stored in simplified molecular-input line-entry system (SMILES), a commonly used text encoding for organic molecules. We utilize an automated process to generate an array of numerical descriptors (features) for each molecule. Redundant and irrelevant descriptors are eliminated iteratively. Our prediction engine is based on a portfolio of machine learning algorithms. We found Random Forest algorithm to be a better choice for this analysis. We captured non-linear relationship in the data and formed a prediction model with reasonable accuracy by averaging across a large number of randomized decision trees. Our next step is to apply deep neural network (DNN) algorithm to predict the biological activity and toxicity properties. We expect the DNN algorithm to give better results and improve the accuracy of the prediction. This presentation will review all these prominent machine learning and deep learning methods, our implementation protocols and discuss these techniques for their usefulness in biomedical and health informatics.

Keywords: deep learning, drug discovery, health informatics, machine learning, toxicity prediction

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Authors: Mustafa Alshawaqfeh, Bilal Wajidy, Echin Serpedin, Jan Suchodolski

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Inflammatory Bowel disease (IBD) is a disease of the colon with characteristic inflammation. Clinically IBD is detected using laboratory tests (blood and stool), radiology tests (imaging using CT, MRI), capsule endoscopy and endoscopy. There are two variants of IBD referred to as Ulcerative Colitis (UC) and Crohn’s disease. This study employs a hybrid feature selection method that combines a correlation-based variable ranking approach with exhaustive search wrapper methods in order to find potential biomarkers for UC. The proposed biomarkers presented accurate discriminatory power thereby identifying themselves to be possible ingredients to UC therapeutics.

Keywords: ulcerative colitis, biomarker detection, feature selection, inflammatory bowel disease (IBD)

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Authors: Yumeng Ma, Fang Wang, Jinxia Huang

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Researchers put forward higher requirements for efficient acquisition and utilization of domain knowledge in the big data era. As literature is an effective way for researchers to quickly and accurately understand the research situation in their field, the knowledge discovery based on literature has become a new research method. As a tool to organize and manage knowledge in a specific domain, the subject knowledge base can be used to mine and present the knowledge behind the literature to meet the users' personalized needs. This study designs the construction route of the subject knowledge base for specific research problems. Information extraction method based on knowledge engineering is adopted. Firstly, the subject knowledge model is built through the abstraction of the research elements. Then under the guidance of the knowledge model, extraction rules of knowledge points are compiled to analyze, extract and correlate entities, relations, and attributes in literature. Finally, a database platform based on this structured knowledge is developed that can provide a variety of services such as knowledge retrieval, knowledge browsing, knowledge q&a, and visualization correlation. Taking the construction practices in the field of activating blood circulation and removing stasis as an example, this study analyzes how to construct subject knowledge base based on literature knowledge extraction. As the system functional test shows, this subject knowledge base can realize the expected service scenarios such as a quick query of knowledge, related discovery of knowledge and literature, knowledge organization. As this study enables subject knowledge base to help researchers locate and acquire deep domain knowledge quickly and accurately, it provides a transformation mode of knowledge resource construction and personalized precision knowledge services in the data-intensive research environment.

Keywords: knowledge model, literature knowledge extraction, precision knowledge services, subject knowledge base

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Authors: Andreea Campu, Ilinica Muresan, Simona Cainap, Simion Astilean, Monica Focsan

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Acute myocardial infarction (AMI) is the most severe cardiovascular disease, which has threatened human lives for decades, thus a continuous interest is directed towards the detection of cardiac biomarkers such as cardiac troponin I (cTnI) in order to predict risk and, implicitly, fulfill the early diagnosis requirements in AMI settings. Microfluidics is a major technology involved in the development of efficient sensing devices with real-time fast responses and on-site applicability. Microfluidic devices have gathered a lot of attention recently due to their advantageous features such as high sensitivity and specificity, miniaturization and portability, ease-of-use, low-cost, facile fabrication, and reduced sample manipulation. The integration of gold nanoparticles into the structure of microfluidic sensors has led to the development of highly effective detection systems, considering the unique properties of the metallic nanostructures, specifically the Localized Surface Plasmon Resonance (LSPR), which makes them highly sensitive to their microenvironment. In this scientific context, herein, we propose the implementation of a novel detection device, which successfully combines the efficiency of gold bipyramids (AuBPs) as signal transducers and thermal generators with the sample-driven advantages of the microfluidic channels into a miniaturized, portable, low-cost, specific, and sensitive test for the dual LSPR-thermographic cTnI detection. Specifically, AuBPs with longitudinal LSPR response at 830 nm were chemically synthesized using the seed-mediated growth approach and characterized in terms of optical and morphological properties. Further, the colloidal AuBPs were deposited onto pre-treated silanized glass substrates thus, a uniform nanoparticle coverage of the substrate was obtained and confirmed by extinction measurements showing a 43 nm blue-shift of the LSPR response as a consequence of the refractive index change. The as-obtained plasmonic substrate was then integrated into a microfluidic “Y”-shaped polydimethylsiloxane (PDMS) channel, fabricated using a Laser Cutter system. Both plasmonic and microfluidic elements were plasma treated in order to achieve a permanent bond. The as-developed microfluidic plasmonic chip was further coupled to an automated syringe pump system. The proposed biosensing protocol implicates the successive injection inside the microfluidic channel as follows: p-aminothiophenol and glutaraldehyde, to achieve a covalent bond between the metallic surface and cTnI antibody, anti-cTnI, as a recognition element, and target cTnI biomarker. The successful functionalization and capture of cTnI was monitored by LSPR detection thus, after each step, a red-shift of the optical response was recorded. Furthermore, as an innovative detection technique, thermal determinations were made after each injection by exposing the microfluidic plasmonic chip to 785 nm laser excitation, considering that the AuBPs exhibit high light-to-heat conversion performances. By the analysis of the thermographic images, thermal curves were obtained, showing a decrease in the thermal efficiency after the anti-cTnI-cTnI reaction was realized. Thus, we developed a microfluidic plasmonic chip able to operate as both LSPR and thermal sensor for the detection of the cardiac troponin I biomarker, leading thus to the progress of diagnostic devices.

Keywords: gold nanobipyramids, microfluidic device, localized surface plasmon resonance detection, thermographic detection

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Authors: Fahad Hanash Alzahrani

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This paper describes some recent advances in a quickly developing area of data storing and processing based on Data Warehouses and Data Mining techniques, which are associated with software, hardware, data mining algorithms and visualisation techniques having common features for any specific problems and tasks of their implementation.

Keywords: data warehouse, data mining, knowledge discovery in databases, on-line analytical processing

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Authors: Muhammad Ishaqa, Quanchao Zhanga, Qian Wangb

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The Indus Valley Civilization is predominantly found in the northeast of Afghanistan, Pakistan, and the northwest of India and is considered one of the four ancient civilizations of the Old World, as well as the first urban civilization in South Asia. In 1920, John Marshall and other archaeologists established the existence of this civilization. Over the course of a century, India and Pakistan have made significant advancements in their joint archaeological investigation and excavation, contributing to the study of the Indus Valley Civilization. Given the importance of early discovery and confirmation of this civilization, our research focuses on the academic history of its archaeology by gathering published research material. Our research begins by collecting research data associated with the Indus Valley Civilization and documenting the process of archaeological investigations and excavations from the 19th century until the present day. We also summarize the archaeological works conducted during different periods. Furthermore, we present the primary academic views on the Indus Civilization from the 19th century until the present, explaining their developmental process and highlighting recent research. This forms a foundation for further study. We discovered that the archaeological research of the Indus Civilization is significantly influenced by Western archaeology and has yet to establish an independent, local research system. We delve into the three primary sites of the Indus Valley Civilization - Harappa, Mohenjo-Daro, and Chanhudaro - discussing their history and archaeological excavation records. Our findings indicate that the Indus Civilization is solely dependent on archaeology, distinguishing it from the Sumerian Civilization and verifying that it originates from the Bronze Age of the Indus Valley. Lastly, we examine the primary academic issues associated with the Indus Civilization in greater depth. These issues include climate environment, political system, primitive religion, and academic contribution.

Keywords: Indus Valley civilization, archaeology, Harappa, Mohenjo-Daro

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Authors: Chih-Ping Chang

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Different from traditional objective evidence, social media evidence has its own characteristics with easily tampering, recoverability, and cannot be read without using other devices (such as a computer). Simply taking a screenshot from social network sites must be questioned its original identity. When the police search and seizure digital information, a common way they use is to directly print out digital data obtained and ask the signature of the parties at the presence, without taking original digital data back. In addition to the issue on its original identity, this conduct to obtain evidence may have another two results. First, it will easily allege that is tampering evidence because the police wanted to frame the suspect and falsified evidence. Second, it is not easy to discovery hidden information. The core evidence associated with crime may not appear in the contents of files. Through discovery the original file, data related to the file, such as the original producer, creation time, modification date, and even GPS location display can be revealed from hidden information. Therefore, how to show this kind of evidence in the courtroom will be arguably the most important task for ruling social media evidence. This article, first, will introduce forensic software, like EnCase, TCT, FTK, and analyze their function to prove the identity with another digital data. Then turning back to the court, the second part of this article will discuss legal standard for authentication of social media evidence and application of that forensic software in the courtroom. As the conclusion, this article will provide a rethinking, that is, what kind of authenticity is this rule of evidence chase for. Does legal system automatically operate the transcription of scientific knowledge? Or furthermore, it wants to better render justice, not only under scientific fact, but through multivariate debating.

Keywords: federal rule of evidence, internet forensic, printouts as evidence, social media evidence, United States v. Vayner

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Authors: Adegoke Yinka Adebayo

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An understanding of the critical product attributes that impact on in vivo performance is key to the production of safe and effective medicines. Thus, a key driver for our research is the development of new basic science and technology underpinning the development of new pharmaceutical products. Research includes the structure and properties of drugs and excipients, biopharmaceutical characterisation, pharmaceutical processing and technology and formulation and analysis.

Keywords: drug discovery, drug development, drug delivery

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Authors: K. S. Suganya, R. Nedunchezhian

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In recent years, blockchain technology has been found to be the most significant discovery in this digital era, after the discovery of the Internet and Cloud Computing. Blockchain is a simple, distributed public ledger that contains all the user’s transaction details in a block. The global copy of the block is then shared among all its peer-peer network users after validation by the Blockchain miners. Once a block is validated and accepted, it cannot be altered by any users making it a trust-free transaction. It also resolves the problem of double-spending by using traditional cryptographic methods. Since the advent of bitcoin, blockchain has been the backbone for all its transactions. But in recent years, it has found its roots and uses in many fields like Smart Contracts, Smart City management, healthcare, etc. Identity management against digital identity theft has become a major concern among financial and other organizations. To solve this digital identity theft, blockchain technology can be employed with existing identity management systems, which maintain a distributed public ledger containing details of an individual’s identity containing information such as Digital birth certificates, Citizenship number, Bank details, voter details, driving license in the form of blocks verified on the blockchain becomes time-stamped, unforgeable and publicly visible for any legitimate users. The main challenge in using blockchain technology to prevent digital identity theft is ensuring the pseudo-anonymity and privacy of the users. This survey paper will exert to study the blockchain concepts, consensus protocols, and various blockchain-based Digital Identity Management systems with their research scope. This paper also discusses the role of Blockchain in COVID-19 pandemic management by self-sovereign identity and supply chain management.

Keywords: blockchain, consensus protocols, bitcoin, identity theft, digital identity management, pandemic, COVID-19, self-sovereign identity

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Authors: Peng Hou

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Natural products produced from marine bacteria serve as an immense reservoir for anti-infective drugs and therapeutic agents. Nowadays, heterologous expression of gene clusters of interests has been widely adopted as an effective strategy for natural product discovery. Briefly, the heterologous expression flowchart would be: biosynthetic gene cluster identification, pathway construction and expression, and product detection. However, gene cluster capture using traditional Transformation-associated recombination (TAR) protocol is low-efficient (0.5% positive colony rate). To make things worse, most of these putative new natural products are only predicted by bioinformatics analysis such as antiSMASH, and their corresponding natural products biosynthetic pathways are either not expressed or expressed at very low levels under laboratory conditions. Those setbacks have inspired us to focus on seeking new technologies to efficiently edit and refractor of biosynthetic gene clusters. Recently, two cutting-edge techniques have attracted our attention - the CRISPR-Cas9 and Gibson Assembly. By now, we have tried to pretreat Brevibacillus laterosporus strain genomic DNA with CRISPR-Cas9 nucleases that specifically generated breaks near the gene cluster of interest. This trial resulted in an increase in the efficiency of gene cluster capture (9%). Moreover, using Gibson Assembly by adding/deleting certain operon and tailoring enzymes regardless of end compatibility, the silent construct (~80kb) has been successfully refactored into an active one, yielded a series of analogs expected. With the appearances of the novel molecular tools, we are confident to believe that development of a high throughput mature pipeline for DNA assembly, transformation, product isolation and identification would no longer be a daydream for marine natural product discovery.

Keywords: biosynthesis, CRISPR-Cas9, DNA assembly, refactor, TAR cloning

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Authors: Ji Su Kim, Bo Ram Choi, Ju Yeon Cho, Hyukjin Lee

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Epidermal growth factor receptor (EGFR) 19 deletion mutation gene is over-expressed in carcinoma patient. EGFR 19 deletion mutation is known as typical biomarker of non-small cell lung cancer (NSCLC), which one section in the coding exon 19 of EGFR is deleted. Therefore, there have been many attempts over the years to detect EGFR 19 deletion mutation for replacing conventional diagnostic method such as PCR and tissue biopsy. We developed a simple and facile detection platform based on Rolling Circle Amplification (RCA), which provides highly amplified products in isothermal amplification of the ligated DNA template. Limit of detection (~50 nM) and a faster detection time (~30 min) could be achieved by introducing RCA.

Keywords: EGFR19, cancer, diagnosis, rolling circle amplification (RCA), hydrogel

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Authors: B. Gonzalez-Yebra, H. Barajas, P. Palomares, M. Hernandez, O. Torres, M. Ayala, A. L. González, G. Vazquez-Ortiz, M. L. Guzman

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Leukemia arises by molecular alterations of the normal hematopoietic stem cell (HSC) transforming it into a leukemic stem cell (LSC) with high cell proliferation, self-renewal, and cell differentiation. Chronic myeloid leukemia (CML) originates from an LSC-leading to elevated proliferation of myeloid cells and acute lymphoblastic leukemia (ALL) originates from an LSC development leading to elevated proliferation of lymphoid cells. In both cases, LSC can be identified by multicolor flow cytometry using several antibodies. However, to date, LSC levels in peripheral blood (PB) are not established well enough in ALL and CML patients. On the other hand, the detection of the minimal residue disease (MRD) in leukemia is mainly based on the identification of the mRNA bcr-abl gene in CML patients and some other genes in ALL patients. There is no a properly biomarker to detect MDR in both types of leukemia. The objective of this study was to determine mRNA bcr-abl and the percentage of LSC in peripheral blood of patients with CML and ALL and identify a possible association between the amount of LSC in PB and clinical data. We included in this study 19 patients with Leukemia. A PB sample was collected per patient and leukocytes were obtained by Ficoll gradient. The immunophenotype for LSC CD34+ was done by flow cytometry analysis with CD33, CD2, CD14, CD16, CD64, HLA-DR, CD13, CD15, CD19, CD10, CD20, CD34, CD38, CD71, CD90, CD117, CD123 monoclonal antibodies. In addition, to identify the presence of the mRNA bcr-abl by RT-PCR, the RNA was isolated using TRIZOL reagent. Molecular (presence of mRNA bcr-abl and LSC CD34+) and clinical results were analyzed with descriptive statistics and a multiple regression analysis was performed to determine statistically significant association. In total, 19 patients (8 patients with ALL and 11 patients with CML) were analyzed, 9 patients with de novo leukemia (ALL = 6 and CML = 3) and 10 under treatment (ALL = 5 and CML = 5). The overall frequency of mRNA bcr-abl was 31% (6/19), and it was negative in ALL patients and positive in 80% in CML patients. On the other hand, LSC was determined in 16/19 leukemia patients (%LSC= 0.02-17.3). The Novo patients had higher percentage of LSC (0.26 to 17.3%) than patients under treatment (0 to 5.93%). The amount of LSC was significantly associated with the amount of LSC were: absence of treatment, the absence of splenomegaly, and a lower number of leukocytes, negative association for the clinical variables age, sex, blasts, and mRNA bcr-abl. In conclusion, patients with de novo leukemia had a higher percentage of circulating LSC than patients under treatment, and it was associated with clinical parameters as lack of treatment, absence of splenomegaly and a lower number of leukocytes. The mRNA bcr-abl detection was only possible in the series of patients with CML, and molecular detection of LSC could be identified in the peripheral blood of all leukemia patients, we believe the identification of circulating LSC may be used as biomarker for the detection of the MRD in leukemia patients.

Keywords: stem cells, leukemia, biomarkers, flow cytometry

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Authors: Kanduru Lokesh, Venkitasamy Kesavan

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The unique structural features of spiro-oxindoles with diverse biological activities have made them privileged structures in new drug discovery. The key structural characteristic of these compounds is the spiro ring fused at the C-3 position of the oxindole core with varied heterocyclic motifs. Structural diversification of heterocyclic scaffolds to synthesize new chemical entities as pharmaceuticals and agrochemicals is one of the important goals of synthetic organic chemists. Nitrogen and oxygen containing heterocycles are by far the most widely occurring privileged structures in medicinal chemistry. The structural complexity and distinct three-dimensional arrangement of functional groups of these privileged structures are generally responsible for their specificity against biological targets. Structurally diverse compound libraries have proved to be valuable assets for drug discovery against challenging biological targets. Thus, identifying a new combination of substituents at C-3 position on oxindole moiety is of great importance in drug discovery to improve the efficiency and efficacy of the drugs. The development of suitable methodology for the synthesis of spiro-oxindole compounds has attracted much interest often in response to the significant biological activity displayed by the both natural and synthetic compounds. So creating structural diversity of oxindole scaffolds is need of the decade and formidable challenge. A general way to improve synthetic efficiency and also to access diversified molecules is through the annulation reactions. Annulation reactions allow the formation of complex compounds starting from simple substrates in a single transformation consisting of several steps in an ecologically and economically favorable way. These observations motivated us to develop the annulation reaction protocol to enable the synthesis of a new class of spiro-oxindole motifs which in turn would enable the enhancement of molecular diversity. As part of our enduring interest in the development of novel, efficient synthetic strategies to enable the synthesis of biologically important oxindole fused spirocarbocyclic systems, We have developed an efficient methodology for the construction of highly functionalized spirocarbocyclic oxindoles through [4+2] annulation of phthalides via Hauser annulation. functionalized spirocarbocyclic oxindoles was accomplished for the first time in the literature using Hauser annulation strategy. The reaction between methyleneindolinones and arylsulfonylphthalides catalyzed by cesium carbonate led to the access of new class of biologically important spiro[indoline-3,2'-naphthalene] derivatives in very good yields. The synthetic utility of the annulated product was further demonstrated by fluorination Using NFSI as a fluorinating agent to furnish corresponding fluorinated product.

Keywords: Hauser-Kraus annulation, spiro carbocyclic oxindoles, oxindole-ester, fluoridation

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Authors: Eyup Ozkan, Ozkan U. Nalbantoglu, Aycan Gundogdu, Mehmet Hora, A. Emre Onuk

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The human microbiome has been associated with cardiological conditions and this relationship is becoming to be defined beyond the gastrointestinal track. In this study, we investigate the alteration in circulatory microbiota in the context of Coronary Artery Disease (CAD). We received circulatory blood samples from suspected CAD patients and maintain 16S ribosomal RNA sequencing to identify each patient’s microbiome. It was found that Corynebacterium and Methanobacteria genera show statistically significant differences between healthy and CAD patients. The overall biodiversities between the groups were observed to be different revealed by machine learning classification models. We also achieve and demonstrate the performance of a diagnostic method using circulatory blood microbiome-based estimation.

Keywords: coronary artery disease, blood microbiome, machine learning, angiography, next-generation sequencing

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Authors: Yulan Wu

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With the rapid development of social media, the issue of fake news has gained considerable prominence, drawing the attention of both the public and governments. The widespread dissemination of false information poses a tangible threat across multiple domains of society, including politics, economy, and health. However, much research has concentrated on supervised training models within specific domains, their effectiveness diminishes when applied to identify fake news across multiple domains. To solve this problem, some approaches based on domain labels have been proposed. By segmenting news to their specific area in advance, judges in the corresponding field may be more accurate on fake news. However, these approaches disregard the fact that news records can pertain to multiple domains, resulting in a significant loss of valuable information. In addition, the datasets used for training must all be domain-labeled, which creates unnecessary complexity. To solve these problems, an unsupervised domain knowledge discovery framework for fake news detection is proposed. Firstly, to effectively retain the multidomain knowledge of the text, a low-dimensional vector for each news text to capture domain embeddings is generated. Subsequently, a feature extraction module utilizing the unsupervisedly discovered domain embeddings is used to extract the comprehensive features of news. Finally, a classifier is employed to determine the authenticity of the news. To verify the proposed framework, a test is conducted on the existing widely used datasets, and the experimental results demonstrate that this method is able to improve the detection performance for fake news across multiple domains. Moreover, even in datasets that lack domain labels, this method can still effectively transfer domain knowledge, which can educe the time consumed by tagging without sacrificing the detection accuracy.

Keywords: fake news, deep learning, natural language processing, multiple domains

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Authors: Amna J. Ghith, Khaled Abu Zid, Khairia Youssef, Nasser Saad

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Backgrounds: The multikinase and vascular endothelial growth factor (VEGF) receptor inhibitors interrupt the pathway by which angiogenesis becomes established and promulgated, resulting in the inadequate nourishment of metastatic disease. VEGFR-2 has been the principal target of anti-angiogenic therapies. We disclose the new thieno pyrimidines as inhibitors of VEGFR-2 designed by a molecular modeling approach with increased synergistic activity and decreased side effects. Purpose: 2-substituted thieno pyrimidines are designed and synthesized with anticipated anticancer activity based on its in silico molecular docking study that supports the initial pharmacophoric hypothesis with a same binding mode of interaction at the ATP-binding site of VEGFR-2 (PDB 2QU5) with high docking score. Methods: A series of compounds were designed using discovery studio 4.1/CDOCKER with a rational that mimic the pharmacophoric features present in the reported active compounds that targeted VEGFR-2. An in silico ADMET study was also performed to validate the bioavailability of the newly designed compounds. Results: The Compounds to be synthesized showed interaction energy comparable to or within the range of the benzimidazole inhibitor ligand when docked with VEGFR-2. ADMET study showed comparable results most of the compounds showed absorption within (95-99) zone varying according to different substitutions attached to thieno pyrimidine ring system. Conclusions: A series of 2-subsituted thienopyrimidines are to be synthesized with anticipated anticancer activity and according to docking study structure requirement for the design of VEGFR-2 inhibitors which can act as powerful anticancer agents.

Keywords: docking, discovery studio 4.1/CDOCKER, heterocycles based anticancer agents, 2-subsituted thienopyrimidines

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Authors: Dorota Witkowska, Paweł Gosek, Lukasz Swiecicki, Wojciech Jernajczyk, Bruce J. West, Miroslaw Latka

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In clinical practice, the selection of an antidepressant often degrades to lengthy trial-and-error. In this work we employ a normalized wavelet power of alpha waves as a biomarker of antidepressant treatment response. This novel EEG metric takes into account both non-stationarity and intersubject variability of alpha waves. We recorded resting, 19-channel EEG (closed eyes) in 22 inpatients suffering from unipolar (UD, n=10) or bipolar (BD, n=12) depression. The EEG measurement was done at the end of the short washout period which followed previously unsuccessful pharmacotherapy. The normalized alpha wavelet power of 11 responders was markedly different than that of 11 nonresponders at several, mostly temporoparietal sites. Using the prediction of treatment response based on the normalized alpha wavelet power, we achieved 81.8% sensitivity and 81.8% specificity for channel T4.

Keywords: alpha waves, antidepressant, treatment outcome, wavelet

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Authors: Taha SamadSoltani, Peyman Rezaei Hachesu, Marjan GhaziSaeedi, Maryam Zolnoori

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Introduction: Data mining defined as a process to find patterns and relationships along data in the database to build predictive models. Application of data mining extended in vast sectors such as the healthcare services. Medical data mining aims to solve real-world problems in the diagnosis and treatment of diseases. This method applies various techniques and algorithms which have different accuracy and precision. The purpose of this study was to apply knowledge discovery and data mining techniques for the diagnosis of asthma based on patient symptoms and history. Method: Data mining includes several steps and decisions should be made by the user which starts by creation of an understanding of the scope and application of previous knowledge in this area and identifying KD process from the point of view of the stakeholders and finished by acting on discovered knowledge using knowledge conducting, integrating knowledge with other systems and knowledge documenting and reporting.in this study a stepwise methodology followed to achieve a logical outcome. Results: Sensitivity, Specifity and Accuracy of KNN, SVM, Naïve bayes, NN, Classification tree and CN2 algorithms and related similar studies was evaluated and ROC curves were plotted to show the performance of the system. Conclusion: The results show that we can accurately diagnose asthma, approximately ninety percent, based on the demographical and clinical data. The study also showed that the methods based on pattern discovery and data mining have a higher sensitivity compared to expert and knowledge-based systems. On the other hand, medical guidelines and evidence-based medicine should be base of diagnostics methods, therefore recommended to machine learning algorithms used in combination with knowledge-based algorithms.

Keywords: asthma, datamining, classification, machine learning

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Authors: Tomas Makaras, Gintaras Svecevičius

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Landfill waste is a common problem as it has an economic and environmental impact even if it is closed. Landfill waste contains a high density of various persistent compounds such as heavy metals, organic and inorganic materials. As persistent compounds are slowly-degradable or even non-degradable in the environment, they often produce sublethal or even lethal effects on aquatic organisms. The aims of the present study were to estimate sublethal effects of the Kairiai landfill (WGS: 55°55‘46.74“, 23°23‘28.4“) leachate on the locomotor activity of rainbow trout Oncorhynchus mykiss juveniles using the original system package developed in our laboratory for automated monitoring, recording and analysis of aquatic organisms’ activity, and to determine patterns of fish behavioral response to sublethal effects of leachate. Four different concentrations of leachate were chosen: 0.125; 0.25; 0.5 and 1.0 mL/L (0.0025; 0.005; 0.01 and 0.002 as part of 96-hour LC50, respectively). Locomotor activity was measured after 5, 10 and 30 minutes of exposure during 1-minute test-periods of each fish (7 fish per treatment). The threshold-effect-concentration amounted to 0.18 mL/L (0.0036 parts of 96-hour LC50). This concentration was found to be even 2.8-fold lower than the concentration generally assumed to be “safe” for fish. At higher concentrations, the landfill leachate solution elicited behavioral response of test fish to sublethal levels of pollutants. The ability of the rainbow trout to detect and avoid contaminants occurred after 5 minutes of exposure. The intensity of locomotor activity reached a peak within 10 minutes, evidently decreasing after 30 minutes. This could be explained by the physiological and biochemical adaptation of fish to altered environmental conditions. It has been established that the locomotor activity of juvenile trout depends on leachate concentration and exposure duration. Modeling of these parameters showed that the activity of juveniles increased at higher leachate concentrations, but slightly decreased with the increasing exposure duration. Experiment results confirm that the behavior of rainbow trout juveniles is a sensitive and rapid biomarker that can be used in combination with the system for fish behavior monitoring, registration and analysis to determine sublethal concentrations of pollutants in ambient water. Further research should be focused on software improvement aimed to include more parameters of aquatic organisms’ behavior and to investigate the most rapid and appropriate behavioral responses in different species. In practice, this study could be the basis for the development and creation of biological early-warning systems (BEWS).

Keywords: fish behavior biomarker, landfill leachate, locomotor activity, rainbow trout juveniles, sublethal effects

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Authors: S. Ahmed John

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Marine forms-bacteria, actinobacteria, cynobacteria, fungi, microalgae, seaweeds mangroves and other halophytes an extremely important oceanic resources and constituting over 90% of the oceanic biomass. The marine natural products have lead to the discovery of many compounds considered worthy for clinical applications. The marine sources have the highest probability of yielding natural products. Natural derivatives play an important role to prevent the cancer incidences as synthetic drug transformation in mangrove. 28.12% of anticancer compound extracted from the mangroves. Exchocaria agollocha has the anti cancer compounds. The present investigation reveals the potential of the Exchocaria agollocha with biotechnological applications for anti cancer, antimicrobial drug discovery, environmental remediation, and developing new resources for the industrial process. The anti-cancer activity of Exchocaria agollocha was screened from 3.906 to 1000 µg/ml of concentration with the dilution leads to 1:1 to 1:128 following methanol and chloroform extracts. The cell viability in the Exchocaria agollocha was maximum at the lower concentration where as low at the higher concentration of methanol and chloroform extracts when compare to control. At 3.906 concentration, 85.32 and 81.96 of cell viability was found at 1:128 dilution of methanol and chloroform extracts respectively. At the concentration of 31.25 following 1:16 dilution, the cell viability was 65.55 in methanol and 45.55 in chloroform extracts. However, at the higher concentration, the cell viability 22.35 and 8.12 was recorded in the extracts of methanol and chloroform. The cell viability was more in methanol when compare to chloroform extracts at lower concentration. The present findings gives current trends in screening and the activity analysis of metabolites from mangrove resources and to expose the models to bring a new sustain for tackling cancer. Bioactive compounds of Exchocaria agollocha have extensive use in treatment of many diseases and serve as a compound and templates for synthetic modification.

Keywords: bio-active product, compounds, natural products and microalgae

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Authors: Dmitry K. Shaytan, Georgy D. Laptev

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In our research we aimed to test a managerial approach for the fuzzy front end (FFE) of innovation by creating controlled experiment/ business case in a breakthrough innovation development. The experiment was in the sport industry and covered all aspects of the customer discovery stage from ideation to prototyping followed by patent application. In the paper we describe and analyze mile stones, tasks, management challenges, decisions made to create the break through innovation, evaluate overall managerial efficiency that was at the considered FFE stage. We set managerial outcome of the FFE stage as a valid product concept in hand. In our paper we introduce hypothetical construct “Q-factor” that helps us in the experiment to distinguish quality of FFE outcomes. The experiment simulated for entrepreneur the FFE of innovation and put on his shoulders responsibility for the outcome of valid product concept. While developing managerial approach to reach the outcome there was a decision to look on product concept from the cognitive psychology and cognitive science point of view. This view helped us to develop the profile of a person whose projection (mental representation) of a new product could optimize for a manager or entrepreneur FFE activities. In the experiment this profile was tested to develop breakthrough innovation for swimmers. Following the managerial approach the product concept was created to help swimmers to feel/sense water. The working prototype was developed to estimate the product concept validity and value added effect for customers. Based on feedback from coachers and swimmers there were strong positive effect that gave high value for customers, and for the experiment – the valid product concept being developed by proposed managerial approach for the FFE. In conclusions there is a suggestion of managerial approach that was derived from experiment.

Keywords: concept development, concept testing, customer discovery, entrepreneurship, entrepreneurial management, idea generation, idea screening, startup management

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Authors: Aliasghar Mehdizadeh Dastjerdi, Francisco Camara Pereira

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The increasing complexity and demand of transport services strains transportation systems especially in urban areas with limited possibilities for building new infrastructure. The solution to this challenge requires changes of travel behavior. One of the proposed means to induce such change is multimodal travel apps. This paper describes a study of the intention to use a real-time multi-modal travel app aimed at motivating travel behavior change in the Greater Copenhagen Region (Denmark) toward promoting sustainable transport options. The proposed app is a multi-faceted smartphone app including both travel information and persuasive strategies such as health and environmental feedback, tailoring travel options, self-monitoring, tunneling users toward green behavior, social networking, nudging and gamification elements. The prospective for mobility management travel apps to stimulate sustainable mobility rests not only on the original and proper employment of the behavior change strategies, but also on explicitly anchoring it on established theoretical constructs from behavioral theories. The theoretical foundation is important because it positively and significantly influences the effectiveness of the system. However, there is a gap in current knowledge regarding the study of mobility-management travel app with support in behavioral theories, which should be explored further. This study addresses this gap by a social cognitive theory‐based examination. However, compare to conventional method in technology adoption research, this study adopts a reverse approach in which the associations between theoretical constructs are explored by Max-Min Hill-Climbing (MMHC) algorithm as a hybrid causal discovery method. A technology-use preference survey was designed to collect data. The survey elicited different groups of variables including (1) three groups of user’s motives for using the app including gain motives (e.g., saving travel time and cost), hedonic motives (e.g., enjoyment) and normative motives (e.g., less travel-related CO2 production), (2) technology-related self-concepts (i.e. technophile attitude) and (3) use Intention of the travel app. The questionnaire items led to the formulation of causal relationships discovery to learn the causal structure of the data. Causal relationships discovery from observational data is a critical challenge and it has applications in different research fields. The estimated causal structure shows that the two constructs of gain motives and technophilia have a causal effect on adoption intention. Likewise, there is a causal relationship from technophilia to both gain and hedonic motives. In line with the findings of the prior studies, it highlights the importance of functional value of the travel app as well as technology self-concept as two important variables for adoption intention. Furthermore, the results indicate the effect of technophile attitude on developing gain and hedonic motives. The causal structure shows hierarchical associations between the three groups of user’s motive. They can be explained by “frustration-regression” principle according to Alderfer's ERG (Existence, Relatedness and Growth) theory of needs meaning that a higher level need remains unfulfilled, a person may regress to lower level needs that appear easier to satisfy. To conclude, this study shows the capability of causal discovery methods to learn the causal structure of theoretical model, and accordingly interpret established associations.

Keywords: travel app, behavior change, persuasive technology, travel information, causality

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Authors: Quyen Vu Dang Ha, Oanh Truong Thi, Thuoc Tran Linh, Kent Carpenter, Thinh Doan Vu, Binh Dang Thuy

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Enzyme restriction site associated DNA (EzRAD) has recently emerged as a promising genomic approach for exploring fish genetic diversity on a genome-wide scale. This is a simplified method for genomic genotyping in non-model organisms and applied for SNPs discovery in the population genetics of freshwater and marine fish in the South of Vietnam. The observations of regional-scale differentiation of commercial freshwater fish (smallscale croakers Boesemania microlepis) and marine fish (emperor Lethrinus lentjan) are clarified. Samples were collected along Hau River and coastal area in the south and center Vietnam. 52 DNA samples from Tra Vinh, An Giang Province for Boesemania microlepis and 34 DNA samples of Lethrinus lentjan from Phu Quoc, Nha Trang, Da Nang Province were used to prepare EzRAD libraries from genomic DNA digested with MboI and Sau3AI. A pooled sample of regional EzRAD libraries was sequenced using the HiSeq 2500 Illumina platform. For Boesemania microlepis, the small scale population different from upstream to downstream of Hau river were detected, An Giang population exhibited less genetic diversity (SNPs per individual from 14 to 926), in comparison to Tra Vinh population (from 11 to 2172). For Lethrinus lentjan, the result showed the minor difference between populations in the Northern and the Southern Mekong River. The numbers of contigs and SNPs vary from 1315 to 2455 and from 7122 to 8594, respectively (P ≤ 0.01). The current preliminary study reveals regional scale population disconnection probably reflecting environmental changing. Additional sampling and EzRad libraries need to be implemented for resource management in the Mekong Delta.

Keywords: Boesemania microlepis, EzRAD, Lethrinus lentjan, SNPs

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Authors: Okpor Victor, Selegha Abrakasa

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Oil (Petroleum) spill occur frequently and in this era of a higher degree of awareness, it is pertinent that the trajectory of the spill is properly defined, to make certain of the area of impact by the spill. In this study, biomarkers that are known as the custodians of paleo information in oils are suggested to be used as reliable tools for defining the pathway of a spill. Samples were collected as tills alongside the GPS coordinates of the sample points suspected to have been impacted by a spill. Oils in the samples were extracted and analyzed as whole oil using GC–MS. Some biomarker parametric ratios were derived, and the ratio showed consistency of values along the sample trail from sample 1 to sample 20. The consistency of the values indicates that the oils at each sample point are the same hence the same value. This method can be used to validate the trajectory/pathway of a spill and also to define or establish a suspected pathway for a spill. The Oleanane/C30Hopane ratio showed good consistency and was suggested as a reliable parameter for establishing the trajectory of an oil spill.

Keywords: spill, biomarkers, trajectory, pathway

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Authors: Basiru Amuneni

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Astronomy is one domain with a rise in data. Traditional tools for data management have been employed in the quest for knowledge discovery. However, these traditional tools become limited in the face of big. One means of maximizing knowledge discovery for big data is the use of scientific visualisation. The aim of the work is to explore the possibilities offered by emerging creative technologies of Virtual Reality (VR) systems and game engines to visualize multiwavelength datasets. Game Engines are primarily used for developing video games, however their advanced graphics could be exploited for scientific visualization which provides a means to graphically illustrate scientific data to ease human comprehension. Modern astronomy is now in the era of multiwavelength data where a single galaxy for example, is captured by the telescope several times and at different electromagnetic wavelength to have a more comprehensive picture of the physical characteristics of the galaxy. Visualising this in an immersive environment would be more intuitive and natural for an observer. This work presents a standalone VR application that accesses galaxy FITS files. The application was built using the Unity Game Engine for the graphics underpinning and the OpenXR API for the VR infrastructure. The work used a methodology known as Design Science Research (DSR) which entails the act of ‘using design as a research method or technique’. The key stages of the galaxy modelling pipeline are FITS data preparation, Galaxy Modelling, Unity 3D Visualisation and VR Display. The FITS data format cannot be read by the Unity Game Engine directly. A DLL (CSHARPFITS) which provides a native support for reading and writing FITS files was used. The Galaxy modeller uses an approach that integrates cleaned FITS image pixels into the graphics pipeline of the Unity3d game Engine. The cleaned FITS images are then input to the galaxy modeller pipeline phase, which has a pre-processing script that extracts, pixel, galaxy world position, and colour maps the FITS image pixels. The user can visualise image galaxies in different light bands, control the blend of the image with similar images from different sources or fuse images for a holistic view. The framework will allow users to build tools to realise complex workflows for public outreach and possibly scientific work with increased scalability, near real time interactivity with ease of access. The application is presented in an immersive environment and can use all commercially available headset built on the OpenXR API. The user can select galaxies in the scene, teleport to the galaxy, pan, zoom in/out, and change colour gradients of the galaxy. The findings and design lessons learnt in the implementation of different use cases will contribute to the development and design of game-based visualisation tools in immersive environment by enabling informed decisions to be made.

Keywords: astronomy, visualisation, multiwavelenght dataset, virtual reality

Procedia PDF Downloads 61