Search results for: gene bank

Authors: Eric Bang

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Interactions between receptors and ligands are crucial for many essential biological processes, including neurotransmission and metabolism. Ligand-receptor analyses that examine cell behavior and interactions often utilize cell type-specific RNA expressions from single-cell RNA sequencing (scRNA-seq) data. Using CellPhoneDB, a public repository consisting of ligands, receptors, and ligand-receptor interactions, the cell-cell interactions were explored in a specific scRNA-seq dataset from kidney tissue and portrayed the results with dot plots and heat maps. Depending on the type of cell, each ligand-receptor pair was aligned with the interacting cell type and calculated the positori probabilities of these associations, with corresponding P values reflecting average expression values between the triads and their significance. Using single-cell data (sample kidney cell references), genes in the dataset were cross-referenced with ones in the existing CellPhoneDB dataset. For example, a gene such as Pleiotrophin (PTN) present in the single-cell data also needed to be present in the CellPhoneDB dataset. Using the single-cell transcriptomics data via slide-seq and reference data, the CellPhoneDB program defines cell types and plots them in different formats, with the two main ones being dot plots and heat map plots. The dot plot displays derived measures of the cell to cell interaction scores and p values. For the dot plot, each row shows a ligand-receptor pair, and each column shows the two interacting cell types. CellPhoneDB defines interactions and interaction levels from the gene expression level, so since the p-value is on a -log10 scale, the larger dots represent more significant interactions. By performing an interaction analysis, a significant interaction was discovered for myeloid and T-cell ligand-receptor pairs, including those between Secreted Phosphoprotein 1 (SPP1) and Fibronectin 1 (FN1), which is consistent with previous findings. It was proposed that an effective protocol would involve a filtration step where cell types would be filtered out, depending on which ligand-receptor pair is activated in that part of the tissue, as well as the incorporation of the CellPhoneDB data in a streamlined workflow pipeline. The filtration step would be in the form of a Python script that expedites the manual process necessary for dataset filtration. Being in Python allows it to be integrated with the CellPhoneDB dataset for future workflow analysis. The manual process involves filtering cell types based on what ligand/receptor pair is activated in kidney cells. One limitation of this would be the fact that some pairings are activated in multiple cells at a time, so the manual manipulation of the data is reflected prior to analysis. Using the filtration script, accurate sorting is incorporated into the CellPhoneDB database rather than waiting until the output is produced and then subsequently applying spatial data. It was envisioned that this would reveal wherein the cell various ligands and receptors are interacting with different cell types, allowing for easier identification of which cells are being impacted and why, for the purpose of disease treatment. The hope is this new computational method utilizing spatially explicit ligand-receptor association data can be used to uncover previously unknown specific interactions within kidney tissue.

Keywords: bioinformatics, Ligands, kidney tissue, receptors, spatial transcriptome

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Authors: Baljeet Singh Saharan

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Bioremediation is the demand of the day. Tannery and textile effluents/waste waters have lots of pollution due to presence of hexavalent Chromium. Methodologies used in the present investigations include isolation, cultivation and purification of bacterial strain. Further characterization techniques and 16S rRNA sequencing were performed. Efficient bacterial strain capable of reducing hexavalent chromium was obtained. The strain can be used for bioremediation of industrial effluents containing hexavalent Cr. A gram negative, rod shaped and yellowish pigment producing bacterial strain from tannery effluent was isolated using nutrient agar. The 16S rRNA gene sequence similarity indicated that isolate SA13A is associated with genus Luteimonas (99%). This isolate has been found to reduce 100% of hexavalent chromium Cr (VI) (100 mg L-1) 100% in 16 h. Growth conditions were optimized for Cr (VI) reduction. Maximum reduction was observed at a temperature of 37 °C and pH 8.0. Additionally, Luteimonas aestuarii SA13A showed resistance against various heavy metals like Cr+6, Cr+3, Cu+2, Zn+2, Co+2, Ni+2 and Cd+2 . Hence, Luteimonas aestuarii SA13A could be used as potent Cr (VI) reducing strain as well as significant bioremediator in heavy metal contaminated sites.

Keywords: bioremediation, chromium, eco-friendly, heavy metals

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin 1), whose disruption leads to increased drought stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1 is regulated in response to drought stress by alternative splicing.

Keywords: alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance

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Authors: Chung-Young Lee, Se-Hee Ahn, Ilhwan Kim, Du-Min Go, Dae-Yong Kim, Jun-Gu Choi, Youn-Jeong Lee, Jae-Hong Kim, Hyuk-Joon Kwon

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The polymerase of avian influenza A virus (AIV) is a heterotrimer composed of PB2, PB1 and PA. PB2 plays a role in overcoming the host barrier; however, the genetic prerequisites for avian PB2 to acquire mammalian pathogenic mutations have not been well elucidated. Here, we demonstrated that key amino acid mutations (I66M, I109V and I133V, collectively referred to as MVV) of prototypic avian PB2 increase the replication efficiency of recombinant PR8 virus carrying the mutated PB2 in both avian and mammalian hosts. The MVV mutations caused no weight loss in mice, but they did allow replication in infected lungs, and the viruses acquired fatal mammalian pathogenic mutations such as Q591R/K, E627K, or D701N in the infected lungs. The MVV mutations are located at the interfaces of the trimer and are predicted to increase the strength of this structure. Thus, gaining MVV mutations might be the first step for AIV to acquire mammalian pathogenicity. These results provide new insights into the evolution of AIV in birds and mammals.

Keywords: avian influenza A virus, prototypic PB2, polymerase activity, mammalian pathogenicity, first-step mutations

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Authors: Muhammad Babar Shahzad

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The purpose of our study is to investigate the relationship between perceived job autonomy and turnover intention in sales & marketing staff. Perceived job autonomy is considered one of most studied dimension of Job Characteristic Model. But still there is a confusion in scholars about predictive role of perceived job autonomy in turnover intention. In line of more complex research on this relation, we investigated the relationship between perceived job autonomy and turnover intention. Did nature of job have any impact on this relationship. On the call of different authors we take interactive effect of perceived job autonomy and procedural justice on turnover intention. Predictive role of distributive justice to employee outcomes is not deniable. But predictive role of distributive justice will be prone in different contextual influences. Interactive role of distributive justice and perceived job autonomy is also not tested before. We collected date from 279 marketing and sales managers working in financial institution, FMCG industries, Pharamesutical Industry & Bank. Strong and direct negative relation was found in perceived job autonomy, distributive justice & procedural justice on turnover intention. Distributive and procedural justice is also amplifying the negative relationship of perceived job autonomy and turnover intention. Limitation and future direction for research is also discussed.

Keywords: perceived job autonomy, turnover intention, procedural justice, distributive job

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Authors: Luna Moni Das

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This paper is an attempt to study the channel dynamics in the area bounded by the foothills of the eastern Himalayas in the north, the Brahmaputra in the south and southeast and eastern side and the Subansiri River in the west. There are many streams in this region and only a few are perennial. There are two major anabranches of the Brahmaputra called Kharkutia Xuti and Charikoria. All of these makes it a very dynamic area. The analysis done in this paper is based on the remote sensing data and mapping of the channel planforms in GIS environment. The temporal trend of the change in channel planform has been produced. This study shows that, during the period from 1973 to 2013, the streams/rivers originating in the north have experienced a reduction in the total length. The other most important result is that even though the western edge of Majuli Island is eroding faster there is a formation of a larger island in between Charikoria and Brahmaputra, that comprises of Majuli island and parts of Dhakuakhana subdivision of Lakhimpur District along the south of Charikoria river. The field study shows that the Kharkutia Xuti, that divides Majuli from Dhakuakhana, do not experience any flow from the Brahmaputra for the major portion of the year and Charikoria has developed as a major anabranch of the Brahmaputra.

Keywords: channel dynamics, Brahmaputra river, Majuli Island, sinuosity

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Authors: Naveed Ghani, Samreen Javed

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In today’s heterogeneous network environment, there is a growing demand for distrust clients to jointly execute secure network to prevent from malicious attacks as the defining task of propagating malicious code is to locate new targets to attack. Residual risk is always there no matter what solutions are implemented or whet so ever security methodology or standards being adapted. Security is the first and crucial phase in the field of Computer Science. The main aim of the Computer Security is gathering of information with secure network. No one need wonder what all that malware is trying to do: It's trying to steal money through data theft, bank transfers, stolen passwords, or swiped identities. From there, with the help of our survey we learn about the importance of white listing, antimalware programs, security patches, log files, honey pots, and more used in banks for financial data protection but there’s also a need of implementing the IPV6 tunneling with Crypto data transformation according to the requirements of new technology to prevent the organization from new Malware attacks and crafting of its own messages and sending them to the target. In this paper the writer has given the idea of implementing IPV6 Tunneling Secessions on private data transmission from financial organizations whose secrecy needed to be safeguarded.

Keywords: network worms, malware infection propagating malicious code, virus, security, VPN

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Authors: Montoya C.A., Erina J., Erina I.

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The purpose of this research is to assess the performance and impact of CSR on business in the banking sector in Australia by applying the financial indicators of 20 ASX banks for the period from 2016-2017. The authors carried out CSR assessment in several stages of research: 1) gathering the nonfinancial and financial indicators of 20 ASX listed banks (available were only 16) from the annual reports of Australian banks for 2016 and 2017; 2) calculation of bank performance indicators using such financial indicators as return on assets (ROA), return on equity (ROE), efficiency ratio and net interest margin; 3) analysis of financial data using cross-sectional regression and answers to the research questions. Based on the obtained research results, the authors obtained answers to the initially raised research questions and came to a conclusion that Q1 - Insignificant positive coefficient result - slight positive relationship between CSR disclosure and business performance 2016; Q2 - Insignificant negative coefficient result - slight negative relationship between CSR disclosure and business performance 2017; Q3 - Insignificant positive coefficient result - slight positive relationship between CSR disclosure and business performance.

Keywords: Australia, banks, business performance, CSR

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Authors: Albert Maake, Ifunanya Isama

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International remittances to developing countries reached US$ 485 billion in 2018. By 2015, the East African region had surpassed US$3.5 mark. Considering this, there is no argument as to the contribution of Diaspora remittances as an alternative source of funds in the development process of the developing countries. Nevertheless, this paper seeks to argue that good governance in areas such as policy design, implementation and monitoring play a critical role in the sustainable development process of a nation as opposed to Diaspora remittances in general. Therefore this study intends at analyzing the contribution of Governance as opposed to that of Diaspora remittances for nation development. Employing documentary analysis technique, the secondary data with respect to the countries under study on Diaspora remittances will be collected. Selected indicators for Governance-HDI, Debt-to-GDP Ratio and Corruption Index, will be sourced from the World Bank Data for the purpose of consistency and where applicable the Central Statistical Agencies of the Nations under study. By means of descriptive statistics and content analysis the data will be comparatively analyzed to highlight the unique experiences in Rwanda and Kenya. The findings and interpretations from the study will affirm and promote capacity building for best practices in good governance for the countries under study.

Keywords: diaspora remittance, governance, Kenya, Rwanda, sustainable development

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Authors: Josephine Wanja Nyatia

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The relationship between vegetation and soil erosion deserves attention due to its scientific importance and practical applications. A great deal of information is available about the mechanisms and benefits of vegetation in the control of soil erosion, but the effects of soil erosion on vegetation development and succession is poorly documented. Research shows that soil erosion is the most important driving force for the degradation of upland and mountain ecosystems. Soil erosion interferes with the process of plant community development and vegetation succession, commencing with seed formation and impacting throughout the whole growth phase and affecting seed availability, dispersal, germination and establishment, plant community structure and spatial distribution. There have been almost no studies on the effects of soil erosion on seed development and availability, of surface flows on seed movement and redistribution, and their influences on soil seed bank and on vegetation establishment and distribution. However, these effects may be the main cause of low vegetation cover in regions of high soil erosion activity, and these issues need to be investigated. Moreover, soil erosion is not only a negative influence on vegetation succession and restoration but also a driving force of plant adaptation and evolution. Consequently, we need to study the effects of soil erosion on ecological processes and on development and regulation of vegetation succession from the points of view of pedology and vegetation, plant and seed ecology, and to establish an integrated theory and technology for deriving practical solutions to soil erosion problems

Keywords: soil erosion, vegetation, development, seed availability

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Authors: Sung-Hee Hwang, Michael Lee

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Upregulated Src activity has been implicated in a variety of cancers. Thus, Src family tyrosine kinase (SFK) inhibitors are often effective cancer treatments. Here, we investigate the role of autophagy in ATG5 knockout cell lines generated by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas mediated genome editing. The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA–DNA complementarity to identify target sites for sequence specific double-stranded DNA (dsDNA) cleavage. Interestingly, ATG5 KO cells clearly showed a greater proliferation rate than WT NIH 3T3 cells, implying that autophagy induction is cytotoxic. Also, the clonogenic survival of ATG5 KO cells was greater than WT cells. The MTT assay revealed that the cytotoxic effect of PP2 was weaker on ATG5 knockout cells than that WT cells. The conversion of non-autophagic LC3-I to autophagic LC3-II and RT-PCR confirmed the functional gene knockout. Furthermore, Cyto-ID autophagy assay also revealed that PP2 failed to induce autophagy in ATG5 knockout cells. Together, our findings suggest that the resistance to PP2 in ATG5 knockout cells is associated with defective autophagy.

Keywords: ATG5 knockout, Autophagy, CRISPR/Cas9, PP2

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Authors: Ibrahim Ilker Ozyigit, Ertugrul Filiz, Seda Birbilener, Semsettin Kulac, Zeki Severoglu

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In this study, we have performed genetic diversity analysis of Tilia tomentosa genotypes by using randomly amplified polymorphic DNA (RAPD) primers. A total of 28 genotypes, including 25 members from the urban ecosystem and 3 genotypes from forest ecosystem as outgroup were used. 8 RAPD primers produced a total of 53 bands, of which 48 (90.6 %) were polymorphic. Percentage of polymorphic loci (P), observed number of alleles (Na), effective number of alleles (Ne), Nei's (1973) gene diversity (h), and Shannon's information index (I) were found as 94.29 %, 1.94, 1.60, 0.34, and 0.50, respectively. The unweighted pair-group method with arithmetic average (UPGMA) cluster analysis revealed that two major groups were observed. The genotypes of urban and forest ecosystems showed a high genetic similarity between 28% and 92% and these genotypes did not separate from each other in UPGMA tree. Also, urban and forest genotypes clustered together in principal component analysis (PCA).

Keywords: Tilia tomentosa, genetic diversity, urban ecosystem, RAPD, UPGMA

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Authors: Karima Afif, Jacinthe Clouthier, Marie-Ève Gaboury-Bonhomme, Véronique Provencher, Morgane Leclercq

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This paper investigates how food banks have secured and improved their supply chain resilience to pursue their mission during COVID-19. More specifically, the implications of the COVID-19 outbreak on the food aid needs, donations, operations, and mission of food banks are explored. To develop an in-depth understanding of the reactions and actions that they have been taken, a qualitative approach has been adopted using a multiple case study design. Data from two focus groups, 12 semi-structured interviews with key informants covering all supply chain levels, and field notes from 7 workplace observations in donation points, food bank facilities, and community-based organizations in Québec (Canada) are triangulated. The results highlight that the pandemic has significantly and unpredictably increased the number of food aid demands, causing significant operational challenges for the food banks supply chain, as well as an unprecedented shortage of donations to food banks. Besides, the sanitary measures have required several adaptative strategies. These implications have caused food banks to enhance their operational flexibility, optimize their logistics operations, enhance their human resources management, and expand collaboration within their supply chain.

Keywords: supply chain resilience, food banks, food donations, food aid, COVID-19

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Authors: A. T. Adetunji, F. B. Lewu, R. Mundembe

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Plants require nitrogen (N) to support desired production levels. Nitrogen is available to plants in the form of nitrate or ammonium, which are transported into the cell with the aid of various transport proteins. Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which nitrogen is preferentially absorbed by plants. Solanum tuberosum AMT1 (StAMT1) was characterized using molecular biology and bioinformatics methods. Nucleotide database sequences were used to design AMT1-specific primers which were used to amplify the AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned StAMT1 to the AMT1 family. The deduced amino acid sequences showed that StAMT1 is 92%, 83% and 76% similar to Solanum lycopersicum LeAMT1.1, Lotus japonicus LjAMT1.1 and Solanum lycopersicum LeAMT1.2 respectively. StAMT1 fragments were shown to correspond to the 5th - 10th trans-membrane domains. Residue StAMT1 D15 is predicted to be essential for ammonium transport, while mutations of StAMT1 S76A may further enhance ammonium transport.

Keywords: ammonium transporter, bioinformatics, nitrogen, primers, Solanum tuberosum

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Authors: Hamid Hossein Khezri, Afsaneh Javdani-Mallak

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Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Cannabidiol (CBD) is one of the members of cannabinoid compounds found in cannabis. CBD and Cannabinol (CBN), as the other extract of plant Cannabis were able to reduce myofascial pain in rats with immunosuppressive and anti-inflammatory activities. In this study, we accomplished protein-protein BLAST, and the sequence was found to be for Gamma-aminobutyric acid receptor subunit alpha-1 (GBRA1) chain A and its 3D structure was subsequently downloaded from Protein Data Bank. The structures of the ligands, cannabinol, and cannabidiol, were obtained from PubChem. After the necessary process of the obtained files, AutoDock Vina was used to perform molecular docking. Docking between the ligands and GBRA1 chain A revealed that cannabinol has a higher affinity to GBRA1 (binding energy = -7.5 kcal/mol) compared to cannabidiol (binding energy = -6.5 kcal/mol). Furthermore, cannabinol seems to be able to interact with 10 residues of the protein, out of which 3 are in the neurotransmitter-gated ion-channel transmembrane domain of GBRA1, whereas cannabidiol interacts with two other residues. Although the results of this project do not indicate the activating /or inhibitory capability of the studied compounds, it suggests that cannabinol can act as a relatively strong ligand for GBRA1.

Keywords: protein-ligand docking, cannabinol, cannabidiol, GBRA1

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Authors: Abdelazeem Algammal, Reham Abouelmaatti, Xiaokun Li, Jisheng Ma, Eman Abdelnaby, Wael Elfeil

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Toll-like receptors (TLRs) are the best understood of the innate immune receptors that detect infections in vertebrates. However, the fish TLRs also exhibit very distinct features and a large diversity, which is likely derived from their diverse evolutionary history and the distinct environments that they occupy. Little is known about the fish immune system structure. Our work was aimed to identify and clone the Nile tilapiaTLR-3 as a model of freshwater fish species; we cloned the full-length cDNA sequence of Nile tilapia (Oreochromis niloticus) TLR-3 and according to our knowledge, it is the first report illustrating tilapia TLR-3. The complete cDNA sequence of Nile tilapia TLR-3 was 2736 pair base and it encodes a polypeptide of 912 amino acids. Analysis of the deduced amino acid sequence indicated that Nile tilapia TLR-3 has typical structural features and main components of proteins belonging to the TLR family. Our results illustrate a complete and functional Nile tilapia TLR-3 and it is considered an ortholog of the other vertebrate’s receptor.

Keywords: Nile tilapia, TLR-3, cloning, gene expression

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Authors: Reza Eka Putra

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Pamsimas is a community based drinking water supply and sanitation program which is contributed by local community, local government, central government, and World Bank with the aim of achieving Water Supply and Sanitation - the Millennium Development Goals (WSS-MDGs) target. This program is supported by the Ministry of Public Works as the executing agency with the cooperation of Ministry of Interior and the Ministry of Health. Field observations were conducted in two rural samples of 2009 beneficiaries Pamsimas West Java, which is in Ponggang Village, Subang District. The study was evaluated through several parameters, including technical, health, and empowerment aspect. Evaluation was done by comparing the parameters of success that has been set by Pamsimas through Pamsimas book manuals with the parameters from Sanitation & Infrastructure course regarding the appropriate application of technology in society. The result of the study is that the potency of the community before the program is implemented in the village is the determining factor. Stronger cooperation pattern in Ponggang Vilage results in a successful program. Both villages showed a pattern of behavior changes from indiscriminate defecation to sanitary latrine use. Besides, there is a decline in the number of cases of diarrheal disease since the year of Pamsimas implementation.

Keywords: millenium development goals, community develpoment, water supply, sanitation

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Authors: S. O. Ekpo

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Environmental science deals with everyday challenges such as a cell for call for good and safe quality air, water, food and healthy leaving condition which include destruction of biodiversity and how to conserve these natural resources for sustainable development. Biodiversity or species richness is the sum of all the different species of animals, plants, fungi and microorganisms leaving on earth and variety of habitats in which they leave. Human beings leave on plants and animals on daily basis for food, clothing, medicine, housing, research and trade or commerce; besides this, biodiversity serves to purify the air, water and land of contaminant, and recycle useful materials for continual use of man. However, man continual incessant exploitation and exploration has affected biodiversity negatively in many ways such habitant fragmentation and destruction, introduction of invasive species, pollution, overharvesting, prediction and pest control amongst others. Measures such as recycling material, establishing natural parks, sperm bank, limiting the exploitation of renewable resources to sustainable yield and urban and industrial development as well as prohibiting hunting endangered species and release of non native live forms into an area will go a long way towards conserving biodiversity for continues profitable yield.

Keywords: biodiversity, conservation, exploitation and exploration sustainable yield, recycling of materials

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Authors: Farrah Putri Salmanida, Mei-Li Wu, Rika Wahyuningtyas, Wen-Bin Chung, Hso-Chi Chaung, Ko-Tung Chang

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Within the field of immunotherapy, oncolytic virotherapy (OVT) employs dual approaches that directly eliminate tumor cells while preserving healthy ones and indirectly reprogram the tumor microenvironment (TME) to elicit antitumor responses. Within the TME, tumor associated macrophages (TAMs) manifest characteristics akin to those of anti-inflammatory M2 macrophages, thus earning the designation of M2-like TAMs. In prior research, two antigens denoted as A1 (g6Ld10T) and A3 (ORF6L5), derived from a complete sequence of ORF5 with partial sequence of ORF6 in Porcine Reproductive and Respiratory Syndrome Virus Genotype 2 (PRRSV-2), demonstrated the capacity to repolarize M2-type porcine alveolar macrophages (PAMs) into M1 phenotypes. In this study, we sought for utilizing OVT strategies by introducing A1 or A3 on TAMs to endow them with the anti-tumor traits of M1 macrophages while retaining their capacity to target cancer cells. Upon exposing human THP-1-derived M2 macrophages to a cross-species test with 2 µg/ml of either A1 or A3 for 24 hours, real time PCR revealed that A3, but not A1, treated cells exhibited upregulated gene expressions of M1 markers (CCR7, IL-1ß, CCL2, Cox2, CD80). These cells reacted to virus-derived antigen, as evidenced by increased expression of pattern-recognition receptors TLR3, TLR7, and TLR9, subsequently providing feedback in the form of type I interferon responses like IFNAR1, IFN-ß, IRF3, IRF7, OAS1, Mx1, and ISG15. Through an MTT assay, only after 15 µg/ml of A3 treatment could the cell viability decrease, with a predicted IC50 of 16.96 µg/ml. Interestingly, A3 caused dose-dependent toxicity to a rat C6 glial cancer cell line even at doses as low as 2.5 µg/ml and reached its IC50 at 9.419 µg/ml. Using Annexin V/7AAD staining and PCR test, we deduced that a significant proportion of C6 cells were undergoing the early apoptosis phase predominantly through the intrinsic apoptosis cascade involving Bcl-2 family proteins. Following this stage, we conducted a test on A3’s repolarization ability, which revealed a significant rise in M1 gene expression markers, such as TNF, CD80, and IL-1ß, in M2-like TAMs generated in vitro from murine RAW264.7 macrophages grown with conditioned medium of 4T1 breast cancer cells. This was corroborated by the results of transcriptome analysis, which revealed that the primary subset among the top 10 to top 30 significantly upregulated differentially expressed genes (DEGs) dominantly consisted of M1 macrophages profiles, including Ccl3, Ccl4, Csf3, TNF, Bcl6b, Stc1, and Dusp2. Our findings unveiled the remarkable potential of the PRRSV-derived antigen A3 to repolarize macrophages while also being capable of selectively inducing apoptosis in cancerous cells. While further in vivo study is needed for A3, it holds promise as an adjuvant by its dual effects in cancer therapy modalities.

Keywords: cancer cell apoptosis, interferon responses, macrophage repolarization, recombinant protein

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Authors: Mariam Khaled, Noha Farag, Ghada Mohamed Abdel Salam, Khaled Abu-Aisha, Mohamed El-Azizi

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Gastric and colorectal cancers are among the most frequent causes of cancer-associated mortalities in Africa. They have been considered as a global public health concern, as nearly one million new cases are reported per year. IL-1β is a pro-inflammatory cytokine-produced by activated macrophages and monocytes- and a member of the IL-1 family. The inactive IL-1β precursor is cleaved and activated by caspase-1 enzyme, which itself is activated by the assembly of intracellular structures defined as NLRP3 (Nod Like receptor P3) inflammasomes. Activated IL-1β stimulates the Interleukin-1 receptor type-1 (IL-1R1), which is responsible for the initiation of a signal transduction pathway leading to cell proliferation. It has been proven that the IL-1β gene is a highly polymorphic gene in which single nucleotide polymorphisms (SNPs) may affect its expression. It has been previously reported that SNPs including base transitions between C and T at positions, -511 (C-T; dbSNP: rs16944) and -31 (C-T; dbSNP: rs1143627), from the transcriptional start site, contribute to the pathogenesis of gastric and colorectal cancers by affecting IL-1β levels. Altered production of IL-1β due to such polymorphisms is suspected to stimulate an amplified inflammatory response and promote Epithelial Mesenchymal Transition leading to malignancy. Allele frequency distribution of the IL-1β-31 and -511 SNPs, in different populations, and their correlation to the incidence of gastric and colorectal cancers, has been intriguing to researchers worldwide. The current study aims to investigate allele distributions of the IL-1β SNPs among gastric and colorectal cancers Egyptian patients. In order to achieve to that, 89 Biopsy and surgical specimens from the antrum and corpus mucosa of chronic gastritis subjects and gastric and colorectal carcinoma patients was collected for DNA extraction followed by restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR). The amplified PCR products of IL-1β-31C > T and IL-1β-511T > C were digested by incubation with the restriction endonuclease enzymes ALu1 and Ava1. Statistical analysis was carried out to determine the allele frequency distribution in the three studied groups. Also, the effect of the IL-1β -31 and -511 SNPs on nuclear factor binding was analyzed using Fluorescence Electrophoretic Mobility Shift Assay (EMSA), preceded by nuclear factor extraction from gastric and colorectal tissue samples and LPS stimulated monocytes. The results of this study showed that a significantly higher percentage of Egyptian gastric cancer patients have a homozygous CC genotype at the IL-1β-31 position and a heterozygous TC genotype at the IL-1β-511 position. Moreover, a significantly higher percentage of the colorectal cancer patients have a homozygous CC genotype at the IL-1β-31 and -511 positions as compared to the control group. In addition, the EMSA results showed that IL-1β-31C/T and IL-1β-511T/C SNPs do not affect nuclear factor binding. Results of this study suggest that the IL-1β-31 C/T and IL-1β-511 T/C may be correlated to the incidence of gastric cancer in Egyptian patients; however, similar findings couldn’t be proven in the colorectal cancer patients group for the IL-1β-511 T/C SNP. This is the first study to investigate IL-1β -31 and -511 SNPs in the Egyptian population.

Keywords: colorectal cancer, Egyptian patients, gastric cancer, interleukin-1β, single nucleotide polymorphisms

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Authors: Deepak Loura

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Production and productivity of several crops in the country continue to be adversely affected by biotic (e.g., Insect-pests and diseases) and abiotic (e.g., water temperature and salinity) stresses. Over-dependence on pesticides and other chemicals is economically non-viable for the resource-poor farmers of our country. Further, pesticides can potentially affect human and environmental safety. While traditional breeding techniques and proper- management strategies continue to play a vital role in crop improvement, we need to judiciously use biotechnology approaches for the development of genetically modified crops addressing critical problems in the improvement of crop plants for sustainable agriculture. Modern biotechnology can help to increase crop production, reduce farming costs, and improve food quality and the safety of the environment. Genetic engineering is a new technology which allows plant breeders to produce plants with new gene combinations by genetic transformation of crop plants for improvement of agronomic traits. Advances in recombinant DNA technology have made it possible to have genes between widely divergent species to develop genetically modified or genetically engineered plants. Plant genetic engineering provides the strength to harness useful genes and alleles from indigenous microorganisms to enrich the gene pool for developing genetically modified (GM) crops that will have inbuilt (inherent) resistance to insect pests, diseases, and abiotic stresses. Plant biotechnology has made significant contributions in the past 20 years in the development of genetically engineered or genetically modified crops with multiple benefits. A variety of traits have been introduced in genetically engineered crops which include (i) herbicide resistance. (ii) pest resistance, (iii) viral resistance, (iv) slow ripening of fruits and vegetables, (v) fungal and bacterial resistance, (vi) abiotic stress tolerance (drought, salinity, temperature, flooding, etc.). (vii) quality improvement (starch, protein, and oil), (viii) value addition (vitamins, micro, and macro elements), (ix) pharmaceutical and therapeutic proteins, and (x) edible vaccines, etc. Multiple genes in transgenic crops can be useful in developing durable disease resistance and a broad insect-control spectrum and could lead to potential cost-saving advantages for farmers. The development of transgenic to produce high-value pharmaceuticals and the edible vaccine is also under progress, which requires much more research and development work before commercially viable products will be available. In addition, molecular-aided selection (MAS) is now routinely used to enhance the speed and precision of plant breeding. Newer technologies need to be developed and deployed for enhancing and sustaining agricultural productivity. There is a need to optimize the use of biotechnology in conjunction with conventional technologies to achieve higher productivity with fewer resources. Therefore, genetic modification/ engineering of crop plants assumes greater importance, which demands the development and adoption of newer technology for the genetic improvement of crops for increasing crop productivity.

Keywords: biotechnology, plant genetic engineering, genetically modified, biotic, abiotic, disease resistance

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Authors: Ajibola O. Akinrinde, Andrew Swanson, Remy Tiako

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There exist significant losses on transmission lines due to distance, as power generating stations could be located far from some isolated settlements. Standalone wind farms could be a good choice of alternative power generation for such settlements that are far from the grid due to factors of long distance or socio-economic problems. However, uncompensated wind farms consume reactive power since wind turbines are induction generators. Therefore, capacitor banks are used to compensate reactive power, which in turn improves the voltage profile of the network. Although capacitor banks help improving voltage profile, they also undergo switching actions due to its compensating response to the variation of various types of load at the consumer’s end. These switching activities could cause transient overvoltage on the network, jeopardizing the end-life of other equipment on the system. In this paper, the overvoltage caused by these switching activities is investigated using the IEEE bus 14-network to represent a standalone wind farm, and the simulation is done using ATP/EMTP software. Scenarios involving the use of pre-insertion resistor and pre-insertion inductor, as well as controlled switching was also carried out in order to decide the best mitigation option to reduce the overvoltage.

Keywords: capacitor banks, IEEE bus 14-network, pre-insertion resistor, standalone wind farm

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Authors: Chokri Slim

Abstract:

The objective of this research is attempting to respond to this question: Is there a significant difference between the regression model and statistical learning models in predicting credit risk management? A Multiple Linear Regression (MLR) model was compared with neural networks including Multi-Layer Perceptron (MLP), and a Support vector regression (SVR). The population of this study includes 50 listed Banks in Tunis Stock Exchange (TSE) market from 2000 to 2016. Firstly, we show the factors that have significant effect on the quality of loan portfolios of banks in Tunisia. Secondly, it attempts to establish that the systematic use of objective techniques and methods designed to apprehend and assess risk when considering applications for granting credit, has a positive effect on the quality of loan portfolios of banks and their future collectability. Finally, we will try to show that the bank governance has an impact on the choice of methods and techniques for analyzing and measuring the risks inherent in the banking business, including the risk of non-repayment. The results of empirical tests confirm our claims.

Keywords: credit risk management, multiple linear regression, principal components analysis, artificial neural networks, support vector machines

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Authors: Ali Bayram, Burak Uz, Remzi Yiğiter

Abstract:

The impairment of lipid metabolism in the central nervous system has been suggested as a critical factor of Alzheimer’s disease (AD) pathogenesis. Homo sapiens acyl-coenyme A synthetase short-chain family member 2 (ACSS2) gene encodes the enzyme acetyl-Coenzyme A synthetase (AMP forming; AceCS) providing acetyl-coenzyme A (Ac-CoA) for various physiological processes, such as cholesterol and fatty acid synthesis, as well as the citric acid cycle. We investigated ACSS2, transcript variant 1 (ACSS2*1), mRNA levels in the peripheral blood mononuclear cells (PBMC) of patients with AD and compared them with the controls. The study group comprised 50 patients with the diagnosis of AD who have applied to Gaziantep University Faculty of Medicine, and Department of Neurology. 49 healthy individuals without any neurodegenerative disease are included as controls. ACSS2 mRNA expression in PBMC of AD/control patients was 0.495 (95% confidence interval: 0.410-0.598), p= .000000001902). Further studies are needed to better clarify this association.

Keywords: Alzheimer’s disease, ACSS2 Genes, mRNA expression, RT-PCR

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Authors: Sezin Ekşioğlu

Abstract:

Multilabel classification has a huge importance for several applications, it is also a challenging research topic. It is a kind of supervised learning that contains binary targets. The distance between multilabel and binary classification is having more than one class in multilabel classification problems. Features can belong to one class or many classes. There exists a wide range of applications for multi label prediction such as image labeling, text categorization, gene functionality. Even though features are classified in many classes, they may not always be properly classified. There are many ensemble methods for the classification. However, most of the researchers have been concerned about better multilabel methods. Especially little ones focus on both efficiency of classifiers and pairwise relationships at the same time in order to implement better multilabel classification. In this paper, we worked on modified ensemble methods by getting benefit from k-Nearest Neighbors and neural network structure to address issues within a beneficial way and to get better impacts from the multilabel classification. Publicly available datasets (yeast, emotion, scene and birds) are performed to demonstrate the developed algorithm efficiency and the technique is measured by accuracy, F1 score and hamming loss metrics. Our algorithm boosts benchmarks for each datasets with different metrics.

Keywords: multilabel, classification, neural network, KNN

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Authors: Okolo Chimaobi Valentine, Obidigbo Chizoba

Abstract:

As a basic physiology need, the threat to sufficient food production is the threat to human survival. Food security has been an issue that has gained global concern. This paper looks at the food security in Nigeria by assessing the availability of food and accessibility of the available food. The paper employed multiple linear regression technique and graphic trends of growth rates of relevant variables to show the situation of food security in Nigeria. Results of the tests revealed that population growth rate was higher than the growth rate of food availability in Nigeria for the earlier period of the study. Commercial bank credit to the agricultural sector, foreign exchange utilization for food and the Agricultural Credit Guarantee Scheme Fund (ACGSF) contributed significantly to food availability in Nigeria. Food prices grew at a faster rate than the average income level, making it difficult to access sufficient food. It implies that prior to the year 2012; there was insufficient food to feed the Nigerian populace. However, continued credit to the food and agricultural sector will ensure sustained and sufficient production of food in Nigeria. Microfinance banks should make sufficient credit available to the smallholder farmer. The government should further control and subsidize the rising price of food to make it more accessible by the people.

Keywords: food, accessibility, availability, security

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Authors: Farida, M. Shehu, Shehu U. R. Aliyu

Abstract:

Access to finance has been recognized in the literature as one of the major impediments confronting small scale businesses (SSBs). This largely arises due to high lending rate, religious inclinations, collateral, etc. Islamic mode finance operates under Profit and Loss Sharing (PLS) arrangement between a borrower (business owner) and a lender (Islamic bank). This paper empirically assesses the determinants of predisposition of small scale business operators in Fagge local government area, Kano State, Nigeria, towards the PLS. Cross-sectional data from a sample of 291 small scale business operators was analyzed using logit and probit regression models. Empirical results reveal that while awareness and religion inclination positively drive interest towards the PLS, lending rate and collateral work against it. The paper, therefore, strongly recommends more advocacy campaigns and setting up of more Islamic banks in the country to cater for the financing and religious needs of SSBs in the study area.

Keywords: Islamic finance, logit and probit models, profit and loss sharing small scale businesses, finance, commerce

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Authors: Ilian Badjakov, Ivayla Dincheva, Violeta Kondakova, Rossitza Batchvarova

Abstract:

In this study, we present our initial results on the assessment of genetic diversity among wild Bulgarian berry accessions (Rubus idaeus L. Fragaria Vesca L., Vaccinium vitis-idaea L., Vaccinium myrtillus L.) using Random Amplified Polymorphic DNA (RAPDs) markers. Leaves and fruits were collected from two natural habitats - the Balkan Mountain and the Mountain of Orpheus - Rhodope Mountain. All accessions were screened for their polymorphism using five RAPD primers. The phylogenetic distances calculated from RAPD data ranged from 0.29 to 0.82 thus indicating that a high level of gene diversity is present in the selected genotypes. In order to characterize further the structure and grouping of berry accessions, a dendrogram deriving from UPGMA cluster analysis based on the genetic similarity (GS) coefficient matrix was designed. RAPD analysis provided to be efficient for discrimination of accessions within the same species with similar morphological characters

Keywords: Bulgarian wild berries, genetic diversity, RAPD, UPGMA

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Authors: Jan Cernohorsky

Abstract:

This article aims to assess the evolution of imperfect competition in selected banking markets, in particular in the banking markets of Slovakia, Poland, Hungary, Slovenia and Croatia. Another objective is to assess the evolution of the relationship of imperfect competition and profit development in the banking markets. The article first provides an overview of literature on the topic. It then measures the degree of imperfect competition in individual markets using the Herfindahl-Hirschman Index. The commonly used indicator of total assets was chosen as an indicator. Based on this measurement, the individual banking sectors are categorized into theoretical definitions of the various types of imperfect competition - namely all surveyed banking sectors falling within the theoretical definition of monopolistic competition. Subsequently, using correlation analysis, i.e., the Pearson correlation coefficient, or the Spearman correlation coefficient, the connection between the evolution of imperfect competition and the development of the gross profit on selected banking markets was surveyed. It was found that with the exception of the banking market in Slovenia, where there is a positive correlation; there is no correlation between the evolution of imperfect competition and profit development in the selected markets. This means a recommendation for the regulators that it is not appropriate to rationalize a higher degree of regulation in granting banking licenses on the size of the profits attained in the banking market, as the relationship between the degree of concentration in the banking market and the amount of profit according to our measurements does not exist.

Keywords: bank, banking system, imperfect competition, profitability

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Authors: Punya Tepsing

Abstract:

This research aimed to study the beliefs in auspicious materials of entrepreneurs in Muang Hat Yai. The data were collected via documentary research and field work including interviews, observations shops in Hat Yai which used auspicious materials to bring lucks to the shops. The results were as follows. The beliefs in auspicious materials that the entrepreneurs had were of three areas: 1) The auspicious materials could correct the improperness of the shop location, for example, the shop situated opposite a branch road, a shrine, or a bank. The owner usually corrected it by putting Chinese auspicious materials in front of or in the shop, for example, a lion holding a sword in his mouth, or a mirror, etc. 2) The auspicious materials could bring in more income. The owner of the shop usually put the auspicious materials such as a cat beckoning and a bamboo fish trap believed to trap money in front of or inside the shop. 3) The auspicious materials like turtles, paired fish and a monster holding the moon in his mouth could solve life problems including health, family, and safety problems. The use of these auspicious materials showed the blending of the beliefs of the Chinese shop entrepreneurs with the Thai folk beliefs. What is interesting is that Hat Yai is located near the three southern border provinces which are the unrest area and this may cause the number of tourists to decline. This prompted them to build a mechanism in adjusting themselves both to save their lives and to increase the number of customers. Auspicious materials can make them feel more confident.

Keywords: belief, auspicious materials, shop, entrepreneur, Maung Hat Yai

Procedia PDF Downloads 240