Search results for: gene expression programming (GEP

Authors: Nazish Badar

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In early 2009, Pandemic type A (H1N1) Influenza virus emerged globally. Since then, it has continued circulation causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in Influenza A (H1N1) pdm09 viruses from 2009-15 and their relevance with the current vaccine viruses. Methods: Respiratory specimens were collected with influenza-like illness and Severe Acute Respiratory Illness. Samples were processed according to CDC protocol. Sequencing and phylogenetic analysis of Haemagglutinin (HA) and neuraminidase (NA) genes was carried out comparing representative isolates from Pakistan viruses. Results: Between Jan2009 - Feb 2016, 1870 (13.2%) samples were positive for influenza A out of 14086. During the pandemic period (2009–10), Influenza A/ H1N1pdm 09 was the dominant strain with 366 (45%) of total influenza positives. In the post-pandemic period (2011–2016), a total of 1066 (59.6%) cases were positive Influenza A/ H1N1pdm 09 with co-circulation of different Influenza A subtypes. Overall, the Pakistan A(H1N1) pdm09 viruses grouped in two genetic clades. Influenza A(H1N1)pdm09 viruses only ascribed to Clade 7 during the pandemic period whereas viruses belong to clade 7 (2011) and clade 6B (2015) during the post-pandemic years. Amino acid analysis of the HA gene revealed mutations at positions S220T, I338V and P100S specially associated with outbreaks in all the analyzed strains. Sequence analyses of post-pandemic A(H1N1)pdm09 viruses showed additional substitutions at antigenic sites; S179N,K180Q (SA), D185N, D239G (CA), S202A (SB) and at receptor binding sites; A13T, S200P when compared with pandemic period. Substitution at Genetic markers; A273T (69%), S200P/T (15%) and D239G (7.6%) associated with severity and E391K (69%) associated with virulence was identified in viruses isolated during 2015. Analysis of NA gene revealed outbreak markers; V106I (23%) among pandemic and N248D (100%) during post-pandemic Pakistan viruses. Additional N-Glycosylation site; HA S179N (23%), NA I23T(7.6%) and N44S (77%) in place of N386K(77%) were only found in post-pandemic viruses. All isolates showed histidine (H) at position 275 in NA indicating sensitivity to neuraminidase inhibitors. Conclusion: This study shows that the Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Certain key substitutions in the receptor binding site and few changes indicative of virulence were also detected in post-pandemic strains. Therefore, it is imperative to continue monitoring of the viruses for early identification of potential variants of high virulence or emergence of drug-resistant variants.

Keywords: Influenza A (H1N1) pdm09, evolutionary analysis, post pandemic period, Pakistan

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Authors: M. Mousavi-Daramoroudi, H. Yousefnia, F. Abbasi-Davani, S. Zolghadri

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In this study, ¹⁷⁷Lu-DOTATOC was prepared under optimized conditions (radiochemical purity: > 99%, radionuclidic purity: > 99%). The percentage of injected dose per gram (%ID/g) was calculated for organs up to 168 h post injection. Compartmental model was applied to mathematical description of the drug behaviour in tissue at different times. The biodistribution data showed the significant excretion of the radioactivity from the kidneys. The adrenal and pancreas, as major expression sites for somatostatin receptor (SSTR), had significant uptake. A pharmacokinetic model of ¹⁷⁷Lu-DOTATOC was presented by compartmental analysis which demonstrates the behavior of the complex.

Keywords: biodistribution, compartmental modeling, ¹⁷⁷Lu, Octreotide

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Authors: Kumari Rekha, Mathur K Dhananjay, Maheshwari Deepanshu, Nautiyal Nidhi, Shubham Smriti, Laal Deepika, Sinha Swati, Kumar Anupam, Biswas Subhrajit, Shiv Kumar Sarin

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Background: Mesenchymal stem cells are multipotent stem cells derived from mesoderm and are used for therapeutic purposes because of their self-renewal, homing capacity, Immunomodulatory capability, low immunogenicity and mitochondrial transfer signaling. MSCs have the ability to regulate the mechanism of both innate as well as adaptive immune responses through the modulation of cellular response and the secretion of inflammatory mediators. Different sources of MSC are UC MSC, BM MSC, Dental Pulp, and Adipose MSC. The most frequent source used is umbilical cord tissue due to its being easily available and free of limitations of collection procedures from respective hospitals. The immunosuppressive role of MSCs is particularly interesting for clinical use since it confers resistance to rejection by the host immune response. Methodology: In this study, T helper cells (TH4), Cytotoxic T cells (CD-8), immunoregulatory cells (CD25 +FOXP3+) are compared from isolated MSC from three different methods, UC Dissociation Kit (Miltenyi), Explant Culture and Collagenase Type-IV. To check the immunomodulatory property, these MSCs were seeded with PBMC(Coculture) in CD3 coated 24 well plates. Cd28 antibody was added in coculture for six days. The coculture was analyzed in FACS Verse flow cytometry. Results: From flow cytometry analysis of coculture, it found that All over T helper cells (CD4+) number p<0.0264 increases in (All Enzymes) MSC rather than explant MSC(p>0.0895) as compared to Collagenase(p>0.7889) in a coculture of Activated T cell and Mesenchymal Stem Cell. Similar T reg cells (CD25+, FOXP3+) expression p<0.0234increases in All Enzymes), decreases in Explant and Collagenase. Experiments have shown that MSCs can also directly prevent the cytotoxic activity of CD8 lymphocytes mainly by blocking their proliferation rather than by inhibiting the cytotoxic effect. And promoting the t-reg cells, which helps in the mediation of immune response in various diseases. Conclusion: MSC suppress Cytotoxic CD8 T cell and Enhance immunoregulatory T reg (CD4+, CD25+, FOXP3+) Cell expression. Thus, MSC maintains a proper balance(ratio) between CD4 T cells and Cytotoxic CD8 T cells.

Keywords: MSC, disease, T cell, T regulatory

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Authors: S. Tandon, A. Oussoren

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Clothing is a need for all humans. Besides serving the commonly understood function of protection, it also is a means of self-expression and adornment. However, most clothing for people with disabilities is developed to respond to their functional needs merely. Such clothing aggravates feelings of inadequacy and lowers their self-esteem. Investigations into apparel-related barriers faced by women with disabilities and their expectations and desires about clothing pointed to a huge void in terms of well-designed inclusive clothing. The incredible stories and experiences shared by the participants in this research highlighted the fact that people with disabilities wanted to feel, dress, and look at how they wanted to look by wearing what they wanted to wear. Clothing should be about self-expression – reflecting their moods, taste, and style and not limited to fulfilling merely their functional needs. Inclusive Design for Regaining Lost Identity was undertaken to design and develop accessible clothing that is inclusive and fashionable to foster psycho-social well-being and to enhance the self-esteem of women with disabilities. The research explored inclusive design solutions for the saree – a traditional Indian garment for women. The saree is an elaborate garment that requires precise draping, which makes the saree complicated to wear and inconvenient to carry, particularly for women with physical disabilities. For many women in India, the saree remains the customary dress, especially for work and occasions, yet minimal advancement has been made to enhance its accessibility and ease of use. The project followed a qualitative research approach whilst incorporating a combination of methods, which consisted of a questionnaire, an interview, and co-creation workshops. The research adhered to the principles of applied research such that the designed products aim to solve a problem that is functional and purposeful. In order to reduce the complications and to simplify the wrapping of the garment fabric around the body, different combinations of pre-stitching of the layers of the saree were created to investigate the outcomes. The technology of 3D drawing and printing was employed to develop feasible fasteners keeping in mind the participants’ movement limitations and to enhance their agency with these newly designed fasteners. The underlying principle of the project is that every individual should be able to access life the way they wish to and should not have to compromise their desires due to their disability.

Keywords: accessibility, co-creation, design ethics, inclusive

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Authors: Quan Gu, Daniel Dimitrov

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BingleSeq was developed as a shiny-based, intuitive, and comprehensive application that enables the analysis of single-Cell RNA-Sequencing count data. This was achieved via incorporating three state-of-the-art software packages for each type of RNA sequencing analysis, alongside functional annotation analysis and a way to assess the overlap of differential expression method results. At its current state, the functionality implemented within BingleSeq is comparable to that of other applications, also developed with the purpose of lowering the entry requirements to RNA Sequencing analyses. BingleSeq is available on GitHub and will be submitted to R/Bioconductor.

Keywords: bioinformatics, functional annotation analysis, single-cell RNA-sequencing, transcriptomics

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Authors: Julio Vicente Cateia

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This paper aims to assess the role of informality and trade facilitation on the export probability of Guinea-Bissau. We include informality in the Féchet function, which gives the expression for the country's supply probability. We find that Guinea-Bissau is about 7.2% less likely to export due to the 1% increase in informality. The export's probability increases by about 1.7%, 4%, and 1.1% due to a 1% increase in trade facilitation, R&D stock, and year of education. These results are significant at the usual levels. We suggest a development agenda aimed at reducing the level of informality in this country.

Keywords: development, trade, informality, trade facilitation, economy of Guinea-Bissau

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Authors: Mohammadjavad Sotoudeheian

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Heart failure (HF) prevalence, as a global cardiovascular problem, is increasing gradually. A variety of molecular mechanisms contribute to HF. Proteins involved in cardiac contractility regulation, such as ion channels and calcium handling proteins, are altered. Additionally, epigenetic modifications and gene expression can lead to altered cardiac function. Moreover, inflammation and oxidative stress contribute to HF. The progression of HF can be attributed to mitochondrial dysfunction that impairs energy production and increases apoptosis. Molecular mechanisms such as these contribute to the development of cardiomyocyte defects and HF and can be therapeutically targeted. The heart's contractile function is controlled by cardiomyocytes. Calpain, and its related molecules, including Bax, VEGF, and AMPK, are among the proteins involved in regulating cardiomyocyte function. Apoptosis is facilitated by Bax. Cardiomyocyte apoptosis is regulated by this protein. Furthermore, cardiomyocyte survival, contractility, wound healing, and proliferation are all regulated by VEGF, which is produced by cardiomyocytes during inflammation and cytokine stress. Cardiomyocyte proliferation and survival are also influenced by AMPK, an enzyme that plays an active role in energy metabolism. They all play key roles in apoptosis, angiogenesis, hypertrophy, and metabolism during myocardial inflammation. The role of calpains has been linked to several molecular pathways. The calpain pathway plays an important role in signal transduction and apoptosis, as well as autophagy, endocytosis, and exocytosis. Cell death and survival are regulated by these calcium-dependent cysteine proteases that cleave proteins. As a result, protein fragments can be used for various cellular functions. By cleaving adhesion and motility proteins, calcium proteins also contribute to cell migration. HF may be brought about by calpain-mediated pathways. Many physiological processes are mediated by the calpain molecular pathways. Signal transduction, cell death, and cell migration are all regulated by these molecular pathways. Calpain is activated by calcium binding to calmodulin. In the presence of calcium, calmodulin activates calpain. Calpains are stimulated by calcium, which increases matrix metalloproteinases (MMPs). In order to develop novel treatments for these diseases, we must understand how this pathway works. A variety of myocardial remodeling processes involve calpains, including remodeling of the extracellular matrix and hypertrophy of cardiomyocytes. Calpains also play a role in maintaining cardiac homeostasis through apoptosis and autophagy. The development of HF may be in part due to calpain-mediated pathways promoting cardiomyocyte death. Numerous studies have suggested the importance of the Ca2+ -dependent protease calpain in cardiac physiology and pathology. Therefore, it is important to consider this pathway to develop and test therapeutic options in humans that targets calpain in HF. Apoptosis, autophagy, endocytosis, exocytosis, signal transduction, and disease progression all involve calpain molecular pathways. Therefore, it is conceivable that calpain inhibitors might have therapeutic potential as they have been investigated in preclinical models of several conditions in which the enzyme has been implicated that might be treated with them. Ca 2+ - dependent proteases and calpains contribute to adverse ventricular remodeling and HF in multiple experimental models. In this manuscript, we will discuss the calpain molecular pathway's important roles in HF development.

Keywords: calpain, heart failure, autophagy, apoptosis, cardiomyocyte

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Authors: Bernstein Ran, Shafir Tal, Tsachor Rachelle, Studd Karen, Schuster Assaf

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Laban Movement Analysis (LMA), developed in the dance community over the past seventy years, is an effective method for observing, describing, notating, and interpreting human movement to enhance communication and expression in everyday and professional life. Many applications that use motion capture data might be significantly leveraged if the Laban qualities will be recognized automatically. This paper presents an automated recognition method of Laban qualities from motion capture skeletal recordings and it is demonstrated on the output of Microsoft’s Kinect V2 sensor.

Keywords: Laban movement analysis, multitask learning, Kinect sensor, machine learning

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Authors: Azam Mohammadbagheri, Bahram Fathi

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DEA has become a very popular method of performance measure, but it still suffers from some shortcomings. One of these shortcomings is the issue of having multiple optimal solutions to weights for efficient DMUs. The cross efficiency evaluation as an extension of DEA is proposed to avoid this problem. Lam (2010) is also proposed a mixed-integer linear programming formulation based on linear discriminate analysis and super efficiency method (MILP model) to avoid having multiple optimal solutions to weights. In this study, we modified MILP model to determine more suitable weight sets and also evaluate the energy efficiency of MENA countries as an application of the proposed model.

Keywords: data envelopment analysis, discriminate analysis, cross efficiency, MILP model

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Authors: Patricia Portugal Marques de Carvalho Lourenço

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Pop Music embodies both the music that is popular with the audiences and the one that is widespread amongst the general public associated with a state of mind and rhythm. Tai Chi epitomises Yin and Yang, two interconnected opposite states of being. Undivided, they are one, a neutral state of consciousness that does not swing to either pole. It remains constant and even minded. Sound flows and vibrations cause movement, a physical response to the tempo. When an excessive movement is reached leads to stillness therefore, extreme Yang leads to Yin. Pop Music and Tai Chi are comparable to state of inner being versus a state of outer being, emotional control versus emotional expression, stillness, and movement; opposites that are independent of one another yet interdependent concepts in motion.

Keywords: Pop music, C-Pop, Tai Chi, Ba Gua, communication, entertainment education

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Authors: Emanuela Chiarella, Clelia Nisticò, Nicola Lombardo, Giovanna Lucia Piazzetta, Nadia Lobello, Maria Mesuraca

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Killian’s Antrochoanal Polyp is a benign lesion of the maxillary sinus characterized by unilateral nasal obstruction, pus discharge, and headache. It affects, more commonly children and young adults. Although its etiology still remains unclear, chronic inflammation, autoreactivity, allergies, and viral infections are strongly associated with its formation and development, resulting in nasal tissue remodeling. We aimed to investigate the stem cells components which reside in this pathological tissue. In particular, we adopted a protocol for the isolation and culturing of mesenchymal stem cells from surgical biopsies of three Killian nasal polyp patients (KNP-MSCs) as well as from their healthy nasal tissue (HNT-MSCs) that were used as controls. The immunophenotype profile of HNT-MSCs and KNP-MSCs was more similar, with a marked positivity for CD73, CD90, and CD105 expression, while being negative for CD34 and CD14 haematopoietic genes. Cell proliferation assay showed that KNP-MSCs had a replicative disadvantage compared to HNT-MSCs, as evidenced by the significantly lower number of cells in the S-phase of the cell cycle. KNP-MSCs also took longer to close a wound than HNT-MSCs, indicating a partial epithelial phenotype in which low levels of ICAM-1 mRNA and a significant increase in E-CAD transcript were detectable. Subsequently, the differentiation potential of both MSCs populations was analyzed by inducing osteoblastic or adipocyte differentiation for up to 20 days. KNP-MSCs showed the ability to differentiate into osteoblasts, although ALP activity as well as the number and size of calcium deposits were lower than osteogenic induced-HNT-MSCs. Also, mRNA levels of osteoblastic marker genes (OCN, OPN, OSX, RUNX2) resulted lower compared to control cell population. Instead, the analysis of the adipogenic differentiation potential showed a similar behavior between KNP-MSCs and HNT-MSCs considering that the amount of lipid droplets, the expression of adipocyte-specific genes (FABP4, AdipoQ, PPARγ2, LPL) and the content of triacylglycerols were almost overlapping. Taken together, these results first demonstrated that Killian's nasal polyp is a source of mesenchymal stem cells with self-renewal and multi-differentiative capabilities.

Keywords: Mesenchymal stem cells, adipogenic differentiation, osteogenic differentiation, EMT

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Authors: Maddalena Arigoni, Maria Luisa Ratto, Raffaele A. Calogero, Luca Alessandri

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The presence of tumor heterogeneity, where distinct cancer cells exhibit diverse morphological and phenotypic profiles, including gene expression, metabolism, and proliferation, poses challenges for molecular prognostic markers and patient classification for targeted therapies. Understanding the causes and progression of cancer requires research efforts aimed at characterizing heterogeneity, which can be facilitated by evolving single-cell sequencing technologies. However, analyzing single-cell data necessitates computational methods that often lack objective validation. Therefore, the establishment of benchmarking datasets is necessary to provide a controlled environment for validating bioinformatics tools in the field of single-cell oncology. Benchmarking bioinformatics tools for single-cell experiments can be costly due to the high expense involved. Therefore, datasets used for benchmarking are typically sourced from publicly available experiments, which often lack a comprehensive cell annotation. This limitation can affect the accuracy and effectiveness of such experiments as benchmarking tools. To address this issue, we introduce omics benchmark experiments designed to evaluate bioinformatics tools to depict the heterogeneity in single-cell tumor experiments. We conducted single-cell RNA sequencing on six lung cancer tumor cell lines that display resistant clones upon treatment of EGFR mutated tumors and are characterized by driver genes, namely ROS1, ALK, HER2, MET, KRAS, and BRAF. These driver genes are associated with downstream networks controlled by EGFR mutations, such as JAK-STAT, PI3K-AKT-mTOR, and MEK-ERK. The experiment also featured an EGFR-mutated cell line. Using 10XGenomics platform with cellplex technology, we analyzed the seven cell lines together with a pseudo-immunological microenvironment consisting of PBMC cells labeled with the Biolegend TotalSeq™-B Human Universal Cocktail (CITEseq). This technology allowed for independent labeling of each cell line and single-cell analysis of the pooled seven cell lines and the pseudo-microenvironment. The data generated from the aforementioned experiments are available as part of an online tool, which allows users to define cell heterogeneity and generates count tables as an output. The tool provides the cell line derivation for each cell and cell annotations for the pseudo-microenvironment based on CITEseq data by an experienced immunologist. Additionally, we created a range of pseudo-tumor tissues using different ratios of the aforementioned cells embedded in matrigel. These tissues were analyzed using 10XGenomics (FFPE samples) and Curio Bioscience (fresh frozen samples) platforms for spatial transcriptomics, further expanding the scope of our benchmark experiments. The benchmark experiments we conducted provide a unique opportunity to evaluate the performance of bioinformatics tools for detecting and characterizing tumor heterogeneity at the single-cell level. Overall, our experiments provide a controlled and standardized environment for assessing the accuracy and robustness of bioinformatics tools for studying tumor heterogeneity at the single-cell level, which can ultimately lead to more precise and effective cancer diagnosis and treatment.

Keywords: single cell omics, benchmark, spatial transcriptomics, CITEseq

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Authors: Marwa Hussien Mohamed, Mohamed Helmy Khafagy

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Map-Reduce is a programming model which is widely used to extract valuable information from enormous volumes of data. Map-reduce designed to support heterogeneous datasets. Apache Hadoop map-reduce used extensively to uncover hidden pattern like data mining, SQL, etc. The most important operation for data analysis is joining operation. But, map-reduce framework does not directly support join algorithm. This paper explains and compares two-way and multi-way map-reduce join algorithms for map reduce also we implement MR join Algorithms and show the performance of each phase in MR join algorithms. Our experimental results show that map side join and map merge join in two-way join algorithms has the longest time according to preprocessing step sorting data and reduce side cascade join has the longest time at Multi-Way join algorithms.

Keywords: Hadoop, MapReduce, multi-way join, two-way join, Ubuntu

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Authors: Nico Fuchs, Fabian Wüllhorst, Laura Maier, Dirk Müller

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The decarbonization of building stocks necessitates the modernization of existing buildings. Key measures for this include reducing energy demands through insulation of the building envelope, replacing heat generators, and installing solar systems. Given limited financial resources, it is impractical to modernize all buildings in a portfolio simultaneously; instead, prioritization of buildings and modernization measures for a given planning horizon is essential. Optimization models for modernization pathways can assist portfolio managers in this prioritization. However, modeling and solving these large-scale optimization problems, often represented as mixed-integer problems (MIP), necessitates simplifying the operation of building energy systems particularly with respect to system dynamics and transient behavior. This raises the question of which level of simplification remains sufficient to accurately account for realistic costs and emissions of building energy systems, ensuring a fair comparison of different modernization measures. This study addresses this issue by comparing a two-stage simulation-based optimization approach with a single-stage mathematical optimization in a mixed-integer linear programming (MILP) formulation. The simulation-based approach serves as a benchmark for realistic energy system operation but requires a restriction of the solution space to discrete choices of modernization measures, such as the sizing of heating systems. After calculating the operation of different energy systems in terms of the resulting final energy demands in simulation models on a first stage, the results serve as input for a second stage MILP optimization, where the design of each building in the portfolio is optimized. In contrast to the simulation-based approach, the MILP-based approach can capture a broader variety of modernization measures due to the efficiency of MILP solvers but necessitates simplifying the building energy system operation. Both approaches are employed to determine the cost-optimal design and dimensioning of several buildings in a portfolio to meet climate targets within limited yearly budgets, resulting in a modernization pathway for the entire portfolio. The comparison reveals that the MILP formulation successfully captures design decisions of building energy systems, such as the selection of heating systems and the modernization of building envelopes. However, the results regarding the optimal dimensioning of heating technologies differ from the results of the two-stage simulation-based approach, as the MILP model tends to overestimate operational efficiency, highlighting the limitations of the MILP approach.

Keywords: building energy system optimization, model accuracy in optimization, modernization pathways, building stock decarbonization

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Authors: Roberto Coppo, Francesca Orso, Daniela Dettori, Elena Quaglino, Lei Nie, Mehran M. Sadeghi, Daniela Taverna

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Malignant melanoma is currently the fifth most common cancer in the white population and it is fatal in its metastatic stage. Several research studies in recent years have provided evidence that cancer initiation and progression are driven by genetic alterations of the tumor and paracrine interactions between tumor and microenvironment. Scattered data show that the Endothelial and Smooth muscle cell-Derived Neuropilin-like molecule (ESDN) controls cell proliferation and movement of stroma and tumor cells. To investigate the role of ESDN in the tumor microenvironment during melanoma progression, murine melanoma cells (B16 or B16-F10) were injected in ESDN knockout mice in order to evaluate how the absence of ESDN in stromal cells could influence melanoma progression. While no effect was found on primary tumor growth, increased cell extravasation and lung metastasis formation was observed in ESDN knockout mice compared to wild type controls. In order to understand how cancer cells cross the endothelial barrier during metastatic dissemination in an ESDN-null microenvironment, structure, and permeability of lung blood vessels were analyzed. Interestingly, ESDN knockout mice showed structurally altered and more permeable vessels compared to wild type animals. Since cell surface molecules mediate the process of tumor cell extravasation, the expression of a panel of extravasation-related ligands and receptors was analyzed. Importantly, modulations of N-cadherin, E-selectin, ICAM-1 and VAP-1 were observed in ESDN knockout endothelial cells, suggesting the presence of a favorable tumor microenvironment which facilitates melanoma cell extravasation and metastasis formation in the absence of ESDN. Furthermore, a potential contribution of immune cells in tumor dissemination was investigated. An increased recruitment of macrophages in the lungs of ESDN knockout mice carrying subcutaneous B16-F10 tumors was found. In conclusion, our data suggest a functional role of ESDN in the tumor microenvironment during melanoma progression and the identification of the mechanisms that regulate tumor cell extravasation could lead to the development of new therapies to reduce metastasis formation.

Keywords: melanoma, tumor microenvironment, extravasation, cell surface molecules

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Authors: Nilubon Kurubanjerdjit, Nattakarn Iam-On, Ka-Lok Ng

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MicroRNAs are small non-coding RNA found in many different species. They play crucial roles in cancer such as biological processes of apoptosis and proliferation. The identification of microRNA-target genes can be an essential first step towards to reveal the role of microRNA in various cancer types. In this paper, we predict miRNA-target genes for lung cancer by integrating prediction scores from miRanda and PITA algorithms used as a feature vector of miRNA-target interaction. Then, machine-learning algorithms were implemented for making a final prediction. The approach developed in this study should be of value for future studies into understanding the role of miRNAs in molecular mechanisms enabling lung cancer formation.

Keywords: microRNA, miRNAs, lung cancer, machine learning, Naïve Bayes, SVM

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Authors: Rabah Iratni, Husain El Hasasna, Khawlah Athamneh, Halima Al Sameri, Nehla Benhalilou, Asma Al Rashedi

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Background: Cancer therapies have witnessed great advances in the recent past, however, cancer continues to be a leading cause of death, with colorectal cancer being the fourth cause of cancer-related deaths. Colorectal cancer affects both sexes equally with poor survival rate once it metastasizes. Phytochemicals, which are plant derived compounds, have been on a steady rise as anti-cancer drugs due to the accumulation of evidences that support their potential. Here, we investigated the anticancer effect of Rhus coriaria on colon cancer cells. Material and Method: Human colon cancer HT-29 cell line was used. Protein expression and protein phosphorylation were examined using Western blotting. Transcription activity was measure using Quantitative RT-PCR. Human tumoral clonogenic assay was used to assess cell survival. Senescence was assessed by the senescence-associated beta-galactosidase assay. Results: Rhus coriaria extract (RCE) was found to significantly inhibit the viability and colony growth of human HT-29 colon cancer cells. RCE induced senescence and cell cycle arrest at G1 phase. These changes were concomitant with upregulation of p21, p16, downregulation of cyclin D1, p27, c-myc and expression of Senescence-associated-β-Galactosidase activity. Moreover, RCE induced non-canonical beclin-1independent autophagy and subsequent apoptotic cell death through activation of activation caspase 8 and caspase 7. The blocking of autophagy by 3-methyladenine (3-MA) or chloroquine (CQ) reduced RCE-induced cell death. Further, RCE induced DNA damage, reduced mutant p53 protein level and downregulated phospho-AKT and phospho-mTOR, events that preceded autophagy. Mechanistically, we found that RCE inhibited the AKT and mTOR pathway, a regulator of autophagy, by promoting the proteasome-dependent degradation of both AKT and mTOR proteins. Conclusion: Our findings provide strong evidence that Rhus coriaria possesses strong anti-colon cancer activity through induction of senescence and autophagic cell death, making it a promising alternative or adjunct therapeutic candidate against colon cancer.

Keywords: autophagy, proteasome degradation, senescence, mTOR, apoptosis, Beclin-1

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Authors: Sophio Kobauri, Temur Kantaria, Nina Kulikova, David Tugushi, Ramaz Katsarava

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The elaboration of effective drug delivery vehicles is still topical nowadays since targeted drug delivery is one of the most important challenges of the modern nanomedicine. The last decade has witnessed enormous research focused on synthetic cationic polymers (CPs) due to their flexible properties, in particular as non-viral gene delivery systems, facile synthesis, robustness, not oncogenic and proven gene delivery efficiency. However, the toxicity is still an obstacle to the application in pharmacotherapy. For overcoming the problem, creation of new cationic compounds including the polymeric nano-size particles – nano-containers (NCs) loading with different pharmaceuticals and biologicals is still relevant. In this regard, a variety of NCs-based drug delivery systems have been developed. We have found that amino acid-based biodegradable polymers called as pseudo-proteins (PPs), which can be cleared from the body after the fulfillment of their function are highly suitable for designing pharmaceutical NCs. Among them, one of the most promising are NCs made of biodegradable Cationic PPs (CPPs). For preparing new cationic NCs (CNCs), we used CPPs composed of positively charged amino acid L-arginine (R). The CNCs were fabricated by two approaches using: (1) R-based homo-CPPs; (2) Blends of R-based CPPs with regular (neutral) PPs. According to the first approach NCs we prepared from CPPs 8R3 (composed of R, sebacic acid and 1,3-propanediol) and 8R6 (composed of R, sebacic acid and 1,6-hexanediol). The NCs prepared from these CPPs were 72-101 nm in size with zeta potential within +30 ÷ +35 mV at a concentration 6 mg/mL. According to the second approach, CPPs 8R6 was blended in organic phase with neutral PPs 8L6 (composed of leucine, sebacic acid and 1,6-hexanediol). The NCs prepared from the blends were 130-140 nm in size with zeta potential within +20 ÷ +28 mV depending on 8R6/8L6 ratio. The stability studies of fabricated NCs showed that no substantial change of the particle size and distribution and no big particles’ formation is observed after three months storage. In vitro biocompatibility study of the obtained NPs with four different stable cell lines: A549 (human), U-937 (human), RAW264.7 (murine), Hepa 1-6 (murine) showed both type cathionic NCs are biocompatible. The obtained data allow concluding that the obtained CNCs are promising for the application as biodegradable drug delivery vehicles. This work was supported by the joint grant from the Science and Technology Center in Ukraine and Shota Rustaveli National Science Foundation of Georgia #6298 'New biodegradable cationic polymers composed of arginine and spermine-versatile biomaterials for various biomedical applications'.

Keywords: biodegradable polymers, cationic pseudo-proteins, nano-containers, drug delivery vehicles

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Authors: Manal M. Kame, Zeinab A. Demerdash, Hanan G. El-Baz, Salwa M. Hassan, Faten M. Salah, Wafaa Mansour, Olfat Hammam

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Cord blood (CB) derived Unrestricted Somatic Stem Cells (USSCs) with their multipotentiality hold great promise in liver regeneration. This work aims at evaluation of the therapeutic potentiality of USSCs in two experimental models of chronic liver injury induced either by S. mansoni infection in balb/c mice or CCL4 injection in hamsters. Isolation, propagation, and characterization of USSCs from CB samples were performed. USSCs were induced to differentiate into osteoblasts, adipocytes and hepatocyte-like cells. Cells of the third passage were transplanted in two models of liver fibrosis: (1) Twenty hamsters were induced to liver fibrosis by repeated i. p. injection of 100 μl CCl4 /hamster for 8 weeks. This model was designed as; 10 hamsters with liver fibrosis and treated with i.h. injection of 3x106 USSCs (USSCs transplanted group), 10 hamsters with liver fibrosis (pathological control group), and 10 hamsters with healthy livers (normal control group). (2) Murine chronics S.mansoni model: twenty mice were induced to liver fibrosis with S. mansoni ceracariae (60 cercariae/ mouse) using the tail immersion method and left for 12 weeks. This model was designed as; 10 mice with liver fibrosis were transplanted with i. v. injection of 1×106 USCCs (USSCs transplanted group). Other 2 groups were designed as in hamsters model. Animals were sacrificed 12 weeks after USSCs transplantation, and their liver sections were examined for detection of human hepatocyte-like cells by immunohistochemistry staining. Moreover, liver sections were examined for fibrosis level, and fibrotic indices were calculated. Sera of sacrificed animals were tested for liver functions. CB USSCs, with fibroblast-like morphology, expressed high levels of CD44, CD90, CD73 and CD105 and were negative for CD34, CD45, and HLA-DR. USSCs showed high expression of transcripts for Oct4 and Sox2 and were in vitro differentiated into osteoblasts, adipocytes. In both animal models, in vitro induced hepatocyte-like cells were confirmed by cytoplasmic expression of glycogen, alpha-fetoprotein, and cytokeratin18. Livers of USSCs transplanted group showed engraftment with human hepatocyte-like cells as proved by cytoplasmic expression of human alpha-fetoprotein, cytokeratin18, and OV6. In addition, livers of this group showed less fibrosis than the pathological control group. Liver functions in the form of serum AST & ALT level and serum total bilirubin level were significantly lowered in USSCs transplanted group than pathological control group (p < 0.001). Moreover, the fibrotic index was significantly lower (p< 0.001) in USSCs transplanted group than pathological control group. In addition liver sections, of i. v. injection of 1×106 USCCs of mice, stained with either H&E or sirius red showed diminished granuloma size and a relative decrease in hepatic fibrosis. Our experimental liver fibrosis models transplanted with CB-USSCs showed liver engraftment with human hepatocyte-like cells as well as signs of liver regeneration in the form of improvement in liver function assays and fibrosis level. These data provide hope that human CB- derived USSCs are introduced as multipotent stem cells with great potentiality in regenerative medicine & strengthens the concept of cellular therapy for the treatment of liver fibrosis.

Keywords: cord blood, liver fibrosis, stem cells, transplantation

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Authors: Elena M. Capitanul, Carlos A. Nunes Cosenza, Walid El Moudani, Felix Mora Camino

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The construction of a new airport or the extension of an existing one requires massive investments and many times public private partnerships were considered in order to make feasible such projects. One characteristic of these projects is uncertainty with respect to financial and environmental impacts on the medium to long term. Another one is the multistage nature of these types of projects. While many airport development projects have been a success, some others have turned into a nightmare for their promoters. This communication puts forward a new approach for airport investment risk assessment. The approach takes explicitly into account the degree of uncertainty in activity levels prediction and proposes milestones for the different stages of the project for minimizing risk. Uncertainty is represented through fuzzy dual theory and risk management is performed using dynamic programming. An illustration of the proposed approach is provided.

Keywords: airports, fuzzy logic, risk, uncertainty

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Authors: Elaheh Talebi, Fariba Yavari, Lucy Philip, Lesley Town

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The mining industry generates vast amounts of data, necessitating robust data management systems and advanced analytics tools to achieve better decision-making processes in the development of mining production and maintaining safety. This paper highlights the advantages of Power BI, a powerful intelligence tool, over traditional Excel-based approaches for effectively managing and harnessing mining data. Power BI enables professionals to connect and integrate multiple data sources, ensuring real-time access to up-to-date information. Its interactive visualizations and dashboards offer an intuitive interface for exploring and analyzing geotechnical data. Advanced analytics is a collection of data analysis techniques to improve decision-making. Leveraging some of the most complex techniques in data science, advanced analytics is used to do everything from detecting data errors and ensuring data accuracy to directing the development of future project phases. However, while Power BI is a robust tool, specific visualizations required by geotechnical engineers may have limitations. This paper studies the capability to use Python or R programming within the Power BI dashboard to enable advanced analytics, additional functionalities, and customized visualizations. This dashboard provides comprehensive tools for analyzing and visualizing key geotechnical data metrics, including spatial representation on maps, field and lab test results, and subsurface rock and soil characteristics. Advanced visualizations like borehole logs and Stereonet were implemented using Python programming within the Power BI dashboard, enhancing the understanding and communication of geotechnical information. Moreover, the dashboard's flexibility allows for the incorporation of additional data and visualizations based on the project scope and available data, such as pit design, rock fall analyses, rock mass characterization, and drone data. This further enhances the dashboard's usefulness in future projects, including operation, development, closure, and rehabilitation phases. Additionally, this helps in minimizing the necessity of utilizing multiple software programs in projects. This geotechnical dashboard in Power BI serves as a user-friendly solution for analyzing, visualizing, and communicating both new and historical geotechnical data, aiding in informed decision-making and efficient project management throughout various project stages. Its ability to generate dynamic reports and share them with clients in a collaborative manner further enhances decision-making processes and facilitates effective communication within geotechnical projects in the mining industry.

Keywords: geotechnical data analysis, power BI, visualization, decision-making, mining industry

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Authors: K. A. Gladkova, N. P. Babushkina, E. Y. Bragina

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Purpose: Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the major public health problems worldwide. It is clear that the immune response to M. tuberculosis infection is a relationship between inflammatory and anti-inflammatory responses in which Tumour Necrosis Factor-α (TNF-α) plays key roles as a pro-inflammatory cytokine. TNF-α involved in various cell immune responses via binding to its two types of membrane-bound receptors, TNFRSF1A and TNFRSF1B. Importantly, some variants of the TNFRSF1B gene have been considered as possible markers of host susceptibility to TB. However, the possible impact of such TNF-α and its receptor genes polymorphism on TB cases in Tomsk is missing. Thus, the purpose of our study was to investigate polymorphism of TNF-α (rs1800629) and its receptor TNFRSF1B (rs652625 and rs525891) genes in population of Tomsk and to evaluate their possible association with the development of pulmonary TB. Materials and Methods: The population distribution features of genes polymorphisms were investigated and made case-control study based on group of people from Tomsk. Human blood was collected during routine patients examination at Tomsk Regional TB Dispensary. Altogether, 234 TB-positive patients (80 women, 154 men, average age is 28 years old) and 205 health-controls (153 women, 52 men, average age is 47 years old) were investigated. DNA was extracted from blood plasma by phenol-chloroform method. Genotyping was carried out by a single-nucleotide-specific real-time PCR assay. Results: First, interpopulational comparison was carried out between healthy individuals from Tomsk and available data from the 1000 Genomes project. It was found that polymorphism rs1800629 region demonstrated that Tomsk population was significantly different from Japanese (P = 0.0007), but it was similar with the following Europeans subpopulations: Italians (P = 0.052), Finns (P = 0.124) and British (P = 0.910). Polymorphism rs525891 clear demonstrated that group from Tomsk was significantly different from population of South Africa (P = 0.019). However, rs652625 demonstrated significant differences from Asian population: Chinese (P = 0.03) and Japanese (P = 0.004). Next, we have compared healthy individuals versus patients with TB. It was detected that no association between rs1800629, rs652625 polymorphisms, and positive TB cases. Importantly, AT genotype of polymorphism rs525891 was significantly associated with resistance to TB (odds ratio (OR) = 0.61; 95% confidence interval (CI): 0.41-0.9; P < 0.05). Conclusion: To the best of our knowledge, the polymorphism of TNFRSF1B (rs525891) was associated with TB, while genotype AT is protective [OR = 0.61] in Tomsk population. In contrast, no significant correlation was detected between polymorphism TNF-α (rs1800629) and TNFRSF1B (rs652625) genes and alveolar TB cases among population of Tomsk. In conclusion, our data expands the molecular particularities associated with TB. The study was supported by the grant of the Russia for Basic Research #15-04-05852.

Keywords: polymorphism, tuberculosis, TNF-α, TNFRSF1B gene

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Authors: Bader Alkandari, Jamal Y. Madouh, Ahmad M. Alkandari, Anwar A. Alnaqi

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A new formulation of fuzzy linear estimation problem is presented. It is formulated as a linear programming problem. The objective is to minimize the spread of the data points, taking into consideration the type of the membership function of the fuzzy parameters to satisfy the constraints on each measurement point and to insure that the original membership is included in the estimated membership. Different models are developed for a fuzzy triangular membership. The proposed models are applied to different examples from the area of fuzzy linear regression and finally to different examples for estimating the electrical load on a busbar. It had been found that the proposed technique is more suited for electrical load estimation, since the nature of the load is characterized by the uncertainty and vagueness.

Keywords: fuzzy regression, load estimation, fuzzy linear parameters, electrical load estimation

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Authors: Luke Galvani

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The cultural representations of people with disabilities are frequently biased which can lead to a general misunderstanding of disability. Representations of disabled deviance are especially problematic given that they typify or generally abstract disability as being abnormal, which then begin to take root in the cultural mind. This study utilizes critical discourse analysis to investigate how discourses of disabled sexual deviance are promoted within two major films that portray disabled sexual subjects. The findings indicate that perceptions of disabled sexual deviance are heightened by cinematic representations of sex and disability, which characterize disabled sexual expression as being undesirable due to the ephemeral and abnormal qualities ascribed to it.

Keywords: deviance, disability, discourse analysis, sexuality

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Authors: Chandan Hegde, K. Ashwini

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Commonsense reasoning is the simulation of human ability to make decisions during the situations that we encounter every day. It has been several decades since the introduction of this subfield of artificial intelligence, but it has barely made some significant progress. The modern computing aids also have remained impotent in this regard due to the absence of a strong methodology towards commonsense reasoning development. Among several accountable reasons for the lack of progress, drawing inference out of commonsense knowledge-base stands out. This review paper emphasizes on a detailed analysis of representation of reasoning uncertainties and feasible prospects of programming aids for drawing inferences. Also, the difficulties in deducing and systematizing commonsense reasoning and the substantial progress made in reasoning that influences the study have been discussed. Additionally, the paper discusses the possible impacts of an effective inference technique in commonsense reasoning.

Keywords: artificial intelligence, commonsense reasoning, knowledge base, uncertainty in reasoning

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Authors: A. Brahma

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The drying of hydraulics materials is unavoidable and conducted to important spontaneous deformations. In this study, we show that it is possible to describe the drying shrinkage of the high-performance concrete by a simple expression. A multiple regression model was developed for the prediction of the drying shrinkage of the high-performance concrete. The assessment of the proposed model has been done by a set of statistical tests. The model developed takes in consideration the main parameters of confection and conservation. There was a very good agreement between drying shrinkage predicted by the multiple regression model and experimental results. The developed model adjusts easily to all hydraulic concrete types.

Keywords: hydraulic concretes, drying, shrinkage, prediction, modeling

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Authors: Yvonne Christelle M. de Guzman, Charity Faye T. Cabie

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This study analyzed the contents of ten issues of Cosmopolitan Magazine from 2011 to 2015. The researcher found out the hegemony among Filipino women as dictated by Cosmopolitan magazine through the use of Semiotic Analysis, Laura Mulvey’s Male Gaze and Gramsci’s concept of hegemony. The researcher also looked at the themes of cover stories, words used to describe women, meanings behind the color of magazine’s front cover, clothing, physique and pose such as gesture and facial expression used by the cover girl. However, the entire content of the magazine was not taken into account.

Keywords: dominant ideology, male gaze, semiotics, women

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Authors: Anil Kumar Tripathi, Ratneshwer Gupta

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All the software engineering researches and best industry practices aim at providing software products with high degree of quality and functionality at low cost and less time. These requirements are addressed by the Component Based Software Engineering (CBSE) as well. CBSE, which deals with the software construction by components’ assembly, is a revolutionary extension of Software Engineering. CBSE must define and describe processes to assure timely completion of high quality software systems that are composed of a variety of pre built software components. Though these features provide distinct and visible benefits in software design and programming, they also raise some challenging problems. The aim of this work is to summarize the pertinent issues and considerations in CBSE to make an understanding in forms of concepts and observations that may lead to development of newer ways of dealing with the problems and challenges in CBSE.

Keywords: software component, component based software engineering, software process, testing, maintenance

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Authors: Sagar Hedaoo, Fazle Baki, Ahmed Azab

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In supply chain management, network design for scalable manufacturing facilities is an emerging field of research. Facility location allocation assigns facilities to customers to optimize the overall cost of the supply chain. To further optimize the costs, capacities of these facilities can be changed in accordance with customer demands. A mathematical model is formulated to fully express the problem at hand and to solve small-to-mid range instances. A dedicated constraint has been developed to restrict emissions in line with the Kyoto protocol. This problem is NP-Hard; hence, a simulated annealing metaheuristic has been developed to solve larger instances. A case study on the USA-Canada cross border crossing is used.

Keywords: emission, mixed integer linear programming, metaheuristic, simulated annealing

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Authors: Sri Poedjiastoeti

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One of the traits of living beings is eating. As the living beings, people must provide their life by taking material. They must assimilate for themselves with substances. They grow and develop themselves by changing what they eat and digest into their own substance. This happened in the so-called eating. This article aims to analyze distinction between human beings and other infrahumans when facing and eating food. It uses the analytical description with metaphysical anthropology approach. As a result, to give the expression that eating is not simply to put food in mouth, chew and swallow it. Eating constitutes a sacred ceremonial if it is done in accordance with human dignity. They face food with distance and moderation as well as civilize or make their behaviour better for it. Accordingly, they are being to be human.

Keywords: human beings, behaviour, eating, dignity

Procedia PDF Downloads 267