Search results for: peptide designing

Authors: Muhammad Younis

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A ternary 4-point approximating non-stationary subdivision scheme has been introduced that generates the family of $C^2$ limiting curves. The theory of asymptotic equivalence is being used to analyze the convergence and smoothness of the scheme. The comparison of the proposed scheme has been demonstrated using different examples with the existing 4-point ternary approximating schemes, which shows that the limit curves of the proposed scheme behave more pleasantly and can generate conic sections as well.

Keywords: ternary, non-stationary, approximation subdivision scheme, convergence and smoothness

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Authors: Nora Geczy

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In today’s architectural practice, during the process of designing public, educational, healthcare and cultural space, human-centered architectural designs helping spatial orientation, safe space usage and the appropriate spatial sequence of actions are gaining increasing importance. Related to the methodology of designing public buildings, several scientific experiments in spatial recognition, spatial analysis and spatial psychology with regard to the components of space producing mental and physiological effects have been going on at the Department of Architectural Design and the Interdisciplinary Student Workshop (IDM) at the Széchenyi István University, Győr since 2013. Defining the creation of preventive, anticipated spatial design and the architectural tools of spatial comfort of public buildings and their practical usability are in the limelight of our research. In the experiments applying eye-tracking cameras, we studied the way public spaces are used, especially concentrating on the characteristics of spatial behaviour, orientation, recognition, the sequence of actions, and space usage. Along with the role of mental maps, human perception, and interaction problems in public spaces (at railway stations, galleries, and educational institutions), we analyzed the spatial situations influencing psychological and ergonomic factors. We also analyzed the eye movements of the experimental subjects in dynamic situations, in spatial procession, using stairs and corridors. We monitored both the consequences and the distorting effects of the ocular dominance of the right eye on spatial orientation; we analyzed the gender-based differences of women and men’s orientation, stress-inducing spaces, spaces affecting concentration and the spatial situation influencing territorial behaviour. Based on these observations, we collected the components of creating public interior spaces, which -according to our theory- contribute to the optimal usability of public spaces. We summed up our research in criteria for design, including 10 points. Our further goals are testing design principles needed for optimizing orientation and space usage, their discussion, refinement, and practical usage.

Keywords: architecture, eye-tracking, human-centered spatial design, public interior spaces, visual perception

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Authors: Tori Reddy Dodla, Laura Ann Jones

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The objective of this study was to propose strategies to improve the efficiency of Knowledge Management Systems (KMS). This study highlights best practices from various industries to create an overall summary of Knowledge Management (KM) and efficiency in organizational performance. Results indicated eleven best practices for maximizing the efficiency of organizational KMS that can be divided into four categories: Designing the KMS, Identifying Case Studies, Implementing the KMS, and Promoting adoption and usage. Our findings can be used as a foundation for scholars to conduct further research on KMS efficiency.

Keywords: artificial intelligence, knowledge management efficiency, knowledge management systems, organizational performance

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Authors: Abdollah Sobhani, Hossein Vaseghi-Dodaran

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Proteomics is defined as the study of the component of a cell, tissue and biological fluid. This technique has the potential to identify protein biomarkers of a disease states. In this study which was performed on bovine ovarian follicular cysts (BOFC), eight proteins are over expressed in BOFC that these proteins could be useful biomarkers for BOFC. The difference between serum proteome pattern cows affected by postpartum endometritis with healthy cows revealed that concentrations orosomucoid was decreased in endometritis. The comparison proteome of brucella abortus between laboratory adapted strains and clinical isolates could be useful to better understand this disease and vaccine development. Proteomics experiments identified new proteins and pathways that may be important in future hypothesis-driven studies of glucocorticoid-induced immunosuppression. Understanding the molecular mechanisms of effective parameters on male fertility is essential for obtaining high reproductive efficiency by decreasing cost and time. The investigations on proteome of high fertility spermatozoa indicated that expression of some proteins such as casein kinase 2 (CKII) prime poly peptide and tyrosine kinase in high fertility spermatozoa was higher compared to low fertility spermatozoa. Also, some evidence has indicated that variation in protein types and amounts in seminal fluid regulates fertility indexes in dairy bull. In conclusion, proteomics is a useful technique for discovering drugs, vaccine development, and diagnosis disease by biomarkers and improvement of reproduction efficiency.

Keywords: proteomics, reproduction, biomarker, immunity

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Authors: I. Khabbazi, R. Ghasemi

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This paper presents a combination of both robust nonlinear controller and nonlinear controller for a class of nonlinear 4Y Octorotor UAV using Back-stepping and sliding mode controller. The robustness against internal and external disturbance and decoupling control are the merits of the proposed paper. The proposed controller decouples the Octorotor dynamical system. The controller is then applied to a 4Y Octorotor UAV and its feature will be shown.

Keywords: sliding mode, backstepping, decoupling, octorotor UAV

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Authors: L. Parisi

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A method which allows a diabetic quadriplegic patient that has had four limb amputations (above the knee and elbow) to self-administer injections of insulin has been designed. The aim of this research project is to improve a quadriplegic patient’s self-management, affected by diabetes, by designing a suitable device for self-administering insulin.The quadriplegic patient affected by diabetes has to be able to self-administer insulin safely and independently to guarantee stable healthy conditions. The device also should be designed to adapt to a number of different varying personal characteristics such as height and body weight.

Keywords: robotic arm, self-administration, insulin, diabetes, quadriplegia

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Authors: Ireneusz Majsterek, Dariusz Pytel, J. Alan Diehl

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PKR-like ER kinase (PERK) is serine/threonie endoplasmic reticulum (ER) transmembrane kinase activated during ER-stress. PERK can activate signaling pathways known as unfolded protein response (UPR). Attenuation of translation is mediated by PERK via phosphorylation of eukaryotic initiation factor 2α (eIF2α), which is necessary for translation initiation. PERK activation also directly contributes to activation of Nrf2 which regulates expression of anti-oxidant enzymes. An increased phosphorylation of eIF2α has been reported in Alzheimer disease (AD) patient hippocampus, indicating that PERK is activated in this disease. Recent data have revealed activation of PERK signaling in non-Hodgkins lymphomas. Results also revealed that loss of PERK limits mammary tumor cell growth in vitro and in vivo. Consistent with these observations, activation of UPR in vitro increases levels of the amyloid precursor protein (APP), the peptide from which beta-amyloid plaques (AB) fragments are derived. Finally, proteolytic processing of APP, including the cleavages that produce AB, largely occurs in the ER, and localization coincident with PERK activity. Thus, we expect that PERK-dependent signaling is critical for progression of many types of diseases (human cancer, neurodegenerative disease and other). Therefore, modulation of PERK activity may be a useful therapeutic target in the treatment of different diseases that fail to respond to traditional chemotherapeutic strategies, including Alzheimer’s disease. Our goal will be to developed therapeutic modalities targeting PERK activity.

Keywords: PERK kinase, small molecule inhibitor, neurodegenerative disease, Alzheimer’s disease

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Authors: Pajaree Naramitpanich, Natchanok Jansawang, Panwilai Chomchid

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The aims of this are compared between the students’ logical thinking abilities of their learning for designing the 5-lesson instructional plans of the 2-instructional methods, namely; the STEM Education and the Creative Learning Process (CLP) for developing students’ logical thinking abilities that a sample consisted of 90 students from two chemistry classes of different learning outcomes in Wapi Phathum School with the cluster random sampling technique was used at the 11th grade level. To administer of their learning environments with the 45-experimenl student group by the STEM Education method and the 45-controlling student group by the Creative Learning Process. These learning different groups were obtained using the 5 instruments; the 5-lesson instructional plans of the STEM Education and the Creative Learning Process to enhance the logical thinking tests on Mineral issue were used. The efficiency of the Creative Learning Processes (CLP) Model and the STEM Education’s innovations of these each five instructional lesson plans based on criteria are higher than of 80/80 standard level with the IOC index from the expert educators. The averages mean scores of students’ learning achievement motives were assessed with the Pre and Post Techniques and Logical Thinking Ability Test (LTAT) and dependent t-test analysis were differentiated between the CLP and the STEM, significantly. Students’ perceptions of their chemistry classroom environment inventories with the MCI with the CLP and the STEM methods also were found, differently. Associations between students’ perceptions of their chemistry classroom learning environment inventories on the CLP Model and the STEM Education learning designs toward their logical thinking abilities toward chemistry, the predictive efficiency of R2 values indicate that 68% and 76% of the variances in students’ logical thinking abilities toward chemistry to their controlling and experimental chemistry classroom learning environmental groups with the MCI were correlated at .05 levels, significantly. Implementations of this result are showed the students’ learning by the CLP of the potential thinking life-changing roles in most their logical thinking abilities that it is revealed that the students perceive their abilities to be highly learning achievement in chemistry group are differentiated with the STEM education of students’ outcomes.

Keywords: design, the lesson instructional plans, the stem education, the creative learning process, logical thinking ability, different, learning outcome, student, chemistry class

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Authors: Mannika Garg, N. Srinivas Murthy, Sunish Nair

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TeamIndus is only Indian team participated in the Google Lunar X Prize (GLXP). GLXP is an incentive prize space competition which is organized by the XPrize Foundation and sponsored by Google. The main objective of the mission is to soft land a rover on the moon surface, travel minimum displacement of 500 meters and transmit HD and NRT videos and images to the Earth. Team Indus is designing a Lunar Lander which carries Rover with it and deliver onto the surface of the moon with a soft landing. For lander to survive throughout the mission, energy is required to operate all attitude control sensors, actuators, heaters and other necessary components. Photovoltaic solar array systems are the most common and primary source of power generation for any spacecraft. The scope of this paper is to provide a system-level approach for designing the solar array systems of the lander to generate required power to accomplish the mission. For this mission, the direction of design effort is to higher efficiency, high reliability and high specific power. Towards this approach, highly efficient multi-junction cells have been considered. The design is influenced by other constraints also like; mission profile, chosen spacecraft attitude, overall lander configuration, cost effectiveness and sizing requirements. This paper also addresses the various solar array design challenges such as operating temperature, shadowing, radiation environment and mission life and strategy of supporting required power levels (peak and average). The challenge to generate sufficient power at the time of surface touchdown, due to low sun elevation (El) and azimuth (Az) angle which depends on Lunar landing site, has also been showcased in this paper. To achieve this goal, energy balance analysis has been carried out to study the impact of the above-mentioned factors and to meet the requirements and has been discussed in this paper.

Keywords: energy balance analysis, multi junction solar cells, photovoltaic, reliability, spacecraft attitude

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Authors: Muhammad Usman, Munir Ahmed

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The demand of high-rise buildings has grown fast during the past decades. The design of these buildings by using RC core wall have been widespread nowadays in many countries. The RC core wall (RCCW) buildings encompasses central core wall and boundary columns joined through post tension slab at different floor levels. The core wall often provides greater stiffness as compared to the collective stiffness of the boundary columns. Hence, the core wall dominantly resists lateral loading i.e. wind or earthquake load. Non-linear response history analysis (NLRHA) procedure is the finest seismic design procedure of the times for designing high-rise buildings. The modern design tools for nonlinear response history analysis and performance based design has provided more confidence to design these structures for high-rise buildings. NLRHA requires selection and scaling of ground motions to match design spectrum for site specific conditions. Designers use several techniques for scaling ground motion records (time series). Time domain and frequency domain scaling are most commonly used which comprises their own benefits and drawbacks. Due to lengthy process of NLRHA, application of only one technique is conceivable. To the best of author’s knowledge, no consensus on the best procedures for the selection and scaling of the ground motions is available in literature. This research aims to provide the finest ground motion scaling technique specifically for designing 40 story high-rise RCCW buildings. Seismic response of 40 story RCCW building is checked by applying both the frequency domain and time domain scaling. Variable sites are selected in three critical seismic zones of Pakistan. The results indicates that there is extensive variation in seismic response of building for these scaling. There is still a need to build a consensus on the subjected research by investigating variable sites and buildings heights.

Keywords: 40-storied RC core wall building, nonlinear response history analysis, ground motions, time domain scaling, frequency domain scaling

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Authors: Samira Kalantary, Zohre Saatzade

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Wireless Mesh Networks (WMNs) are low-cost access networks built on cooperative routing over a backbone composed of stationary wireless routers. WMNs must deal with the highly unstable wireless medium. Thus, routing metrics and protocols are evolving by designing algorithms that consider link quality to choose the best routes. In this work, we analyse the state of the art in WMN metrics and propose taxonomy for WMN routing protocols. Performance measurements of a wireless mesh network deployed using various routing metrics are presented and corroborate our analysis.

Keywords: wireless mesh networks, routing protocols, routing metrics, bioinformatics

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Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

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Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

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Authors: Alireza Alesaadi

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Reliability analysis is a powerful method for determining the weak points of the electrical networks. In designing of electrical network, it is tried to design the most reliable network with minimal system shutting down, but it is usually associated with increasing the cost. In this paper, using adaptive genetic algorithm, a method was presented that provides the most reliable system with a certain economical cost. Finally, the proposed method is applied to a sample network and results will be analyzed.

Keywords: reliability, adaptive genetic algorithm, electrical network, communication engineering

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Authors: Yessica Nataliani, Miin-Shen Yang

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Cell formation (CF) is an important step in group technology. It is used in designing cellular manufacturing systems using similarities between parts in relation to machines so that it can identify part families and machine groups. There are many CF methods in the literature, but there is less spectral clustering used in CF. In this paper, we propose a spectral clustering algorithm for machine-part CF. Some experimental examples are used to illustrate its efficiency. Overall, the spectral clustering algorithm can be used in CF with a wide variety of machine/part matrices.

Keywords: group technology, cell formation, spectral clustering, grouping efficiency

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Authors: Azhan Azhar, Mohammed Sakib, Zaurez Ahmad

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The energy we receive from the sun is known as solar energy, and it is a reliable, long-lasting, eco-friendly and the most widely used energy source in the 21st century. It is. There are several techniques for harnessing solar energy, and we are all seeing large utility-scale projects to collect maximum amperes from the sun using current technologies. Solar PV is now on the rise as a means of harvesting energy from the sun. Moving a step further, our project is focused on designing an All-in-one portable Solar Energy based solution. We considered the minimum load conditions and evaluated the requirements of various devices utilized in this study to resolve the power requirements of small stores, hawkers, or travelers.

Keywords: DOD-depth of discharge, pulse width modulation charge controller, renewable energy, solar PV- solar photovoltaic

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Authors: Pejman Hosseiniun, Rose Shayeghi, Alireza Farzaneh, Abolghasem Ghasempour

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Using LED lamps as lighting resources with new technology in designing lighting systems has been studied in this article. In this respect a history of LED emergence, its different manufacturing methods and technologies were revised, then their structure, light production line, its application and benefits in lighting industry has been evaluated. Finally, there is a comparison between these lamps and ordinary lamps to assess light parameters as well as energy consumption using DIALux software. Considering the results of analogies LED lamps have lower consumption and more lighting yield, therefore they are more economically feasible. Color variety, longer usage lap (circa 10 years) and compatibility with DC voltages are other LED lamps perquisites.

Keywords: LED, lighting efficiency, lighting intensity, luminance

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Authors: Satya Eswari Jujjavarapu, Swast Dhagat

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Contagious diseases enact severe public health problems and have upsetting consequences. The cyclic lipopeptides explained by bacteria Bacillus, Paenibacillus, Pseudomonas, Streptomyces, Serratia, Propionibacterium and fungus Fusarium are very critical in confining the pathogens. As the degree of drug resistance upsurges in unparalleled manner, the perseverance of searching novel cyclic lipopeptides is being professed. The intense study has shown the implication of these bioactive compounds extending beyond antibacterial and antifungal. Lipopeptides, composed of single units of peptide and fatty acyl moiety, show broad spectrum antimicrobial effects. Among the surplus of cyclic lipopeptides, only few have materialized as strong antibiotics. For their functional vigor, polymyxin, daptomycin, surfactin, iturin and bacillomycin have been integrated in mainstream healthcare. In our work daptomycin has been a major part of antimicrobial resource since the past decade. Daptomycin, a cyclic lipopeptide consists of 13-member amino acid with a decanoyl side-chain. This structure of daptomycin confers it the mechanism of action through which it forms pore in the bacterial cell membrane resulting in the death of cell. Daptomycin is produced by Streptococccus roseoporus and acts against Streptococcus pneumonia (PSRP), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). The PDB structure and ligands of daptomycin are available online. The molecular docking studies of these ligands with the lipopeptides were performed and their docking score and glide energy were recorded.

Keywords: daptomycin, molecular docking, structure-based drug design, lipopeptide

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Authors: Dusittorn Ngamying

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The research on Thatsana Nataya Chatri Dance: A Creative Conservation Process of Cultural Performing Arts for Competition was aimed at 1) studying the creative conservation process of cultural performing arts; 2) creating conservation process of cultural performing arts of Thatsana Nataya Chatri dance; and 3) utilizing the created performing arts for the competition. The study was conducted using the qualitative research method in the Central region provinces of Thailand through documentary study and data from field observations, interviews and focus group meetings. Data were collected from 50 informants consisting of 10 experts on the subject, 30 practitioners and 10 general information providers. The data collection instruments consisted of participatory and non-participatory forms, structured and non-structured interview schedules and focus group note forms. The data were verified by the triangulation technique and presented using the descriptive analysis. The results of the study reveal that the creative conservation process of cultural performing arts should be initiated by those who have experienced using a prior knowledge in the pursuit of new knowledge. The new knowledge is combined to generate creative work with the conservation process in 9 aspects: acquiring the related knowledge, creating theme and inspiration, designing the music and melody, designing costumes, inventing dance postures, selecting dancers, transferring the dance postures, preparing the stage and performance equipment, planning the performance event. Inventing the conservation process of cultural performing arts Thatsana Nataya Chatri dance consists of 33 dance postures and 14 transformed patterns. The performance requires 6 dancers, 3 males and 3 females. Costume features both male and female classical and modified dancer’s costumes. The duration of the show takes 5 minutes. As for the application for the competition, this creative work has been selected by Dramatic Works Association (Thailand) to represent Thailand at the Lombok International Dance Sports Festival 2015 held at Lombok, Indonesia. The team has been awarded the Second Place in the Traditional Dance category.

Keywords: creative conservation process, cultural performing arts, Thatsana Nataya Chatri dance, competition

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Authors: Masami Usui

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After 9/11, the American literary scene was confronted with new perspectives that enabled both writers and readers to recognize the hidden aspects of their political, economic, legal, social, and cultural phenomena. There appeared an argument over new and challenging multicultural aspects after 9/11 and this argument is presented by a tension of space related to 9/11. In Amy Waldman’s the Submission (2011), designing both the memorial park and the family network has a significant meaning in establishing the progress of understanding from multiple perspectives. The most intriguing and controversial topic of racism is reflected in the Submission, where one young architect’s blind entry to the competition for the memorial of Ground Zero is nominated, yet he is confronted with strong objections and hostility as soon as he turns out to be a Muslim named Mohammad Khan. This ‘Khan’ issue, immediately enlarged into a social controversial issue on American soil, causes repeated acts of hostility to Muslim women by ignorant citizens all over America. His idea of the park is to design a new concept of tracing the cultural background of the open space. Against his will, his name is identified as the ‘ingredient’ of the networking of the resistant community with his supporters: on the other hand, the post 9/11 hysteria and victimization is presented in such family associations as the Angry Family Members and Grieving Family Members. These rapidly expanding networks, whether political or not, constructed by the internet, embody the contemporary societal connection and representation. The contemporary quest for the significance of human relationships is recognized as a quest for global peace. Designing both the memorial park and the communication networks strengthens a process of facing the shared conflicts and healing the survivors’ trauma. The tension between the idea and networking of the Garden for the memorial site and the collapse of Ground Zero signifies the double mission of the site: to establish the space to ease the wounded and to remember the catastrophe. Reading the design of these icons of 9/11 in the Submission means that decoding the myth of globalization and its representations in this century.

Keywords: American literature, cultural studies, globalization, literature of catastrophe

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Authors: Ved Vrat Verma, Rani Gupta, Manisha Goel

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γ-glutamyltranspeptidase (GGT: EC 2.3.2.2) is an N-terminal nucleophile hydrolase conserved in all three domains of life. GGT plays a key role in glutathione metabolism where it catalyzes the breakage of the γ-glutamyl bonds and transfer of γ-glutamyl group to water (hydrolytic activity) or amino acids or short peptides (transpeptidase activity). GGTs from bacteria, archaea, and eukaryotes (human, rat and mouse) are homologous proteins sharing >50% sequence similarity and conserved four layered αββα sandwich like three dimensional structural fold. These proteins though similar in their structure to each other, are quite diverse in their enzyme activity: some GGTs are better at hydrolysis reactions but poor in transpeptidase activity, whereas many others may show opposite behaviour. GGT is known to be involved in various diseases like asthma, parkinson, arthritis, and gastric cancer. Its inhibition prior to chemotherapy treatments has been shown to sensitize tumours to the treatment. Microbial GGT is known to be a virulence factor too, important for the colonization of bacteria in host. However, all known inhibitors (mimics of its native substrate, glutamate) are highly toxic because they interfere with other enzyme pathways. However, a few successful efforts have been reported previously in designing species specific inhibitors. We aim to leverage the diversity seen in GGT family (pathogen vs. eukaryotes) for designing specific inhibitors. Thus, in the present study, we have used DIVERGE software to identify sites in GGT proteins, which are crucial for the functional and structural divergence of these proteins. Since, type II divergence sites vary in clade specific manner, so type II divergent sites were our focus of interest throughout the study. Type II divergent sites were identified for pathogen vs. eukaryotes clusters and sites were marked on clade specific representative structures HpGGT (2QM6) and HmGGT (4ZCG) of pathogen and eukaryotes clade respectively. The crucial divergent sites within 15 A radii of the binding cavity were highlighted, and in-silico mutations were performed on these sites to delineate the role of these sites on the mechanism of catalysis and protein folding. Further, the amino acid network (AAN) analysis was also performed by Cytoscape to delineate assortative mixing for cavity divergent sites which could strengthen our hypothesis. Additionally, molecular dynamics simulations were performed for wild complexes and mutant complexes close to physiological conditions (pH 7.0, 0.1 M ionic strength and 1 atm pressure) and the role of putative divergence sites and structural integrities of the homologous proteins have been analysed. The dynamics data were scrutinized in terms of RMSD, RMSF, non-native H-bonds and salt bridges. The RMSD, RMSF fluctuations of proteins complexes are compared, and the changes at protein ligand binding sites were highlighted. The outcomes of our study highlighted some crucial divergent sites which could be used for novel inhibitors designing in a species-specific manner. Since, for drug development, it is challenging to design novel drug by targeting similar protein which exists in eukaryotes, so this study could set up an initial platform to overcome this challenge and help to deduce the more effective targets for novel drug discovery.

Keywords: γ-glutamyltranspeptidase, divergence, species-specific, drug design

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Authors: Tivani Phosa Mashamba-Thompson, Mahmoud E. S. Soliman

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To date, the cause of neurodegeneration is not well understood and diseases that stem from neurodegeneration currently have no known cures. Cathepsin B (CB) enzyme is known to be involved in the production of peptide neurotransmitters and toxic peptides in neurodegenerative diseases (NDs). CA-074Me is a membrane-permeable irreversible selective cathepsin B (CB) inhibitor as confirmed by in vivo studies. Due to the lack of the crystal structure, the binding mode of CA-074Me with the human CB at molecular level has not been previously reported. The main aim of this study is to gain an insight into the binding mode of CB CA-074Me to human CB using various computational tools. Herein, molecular dynamics simulations, binding free energy calculations and per-residue energy decomposition analysis were employed to accomplish the aim of the study. Another objective was to identify novel CB inhibitors based on the structure of CA-074Me using fragment based drug design using scaffold hoping drug design approach. Results showed that two of the designed ligands (hit 1 and hit 2) were found to have better binding affinities than the prototype inhibitor, CA-074Me, by ~2-3 kcal/mol. Per-residue energy decomposition showed that amino acid residues Cys29, Gly196, His197 and Val174 contributed the most towards the binding. The Van der Waals binding forces were found to be the major component of the binding interactions. The findings of this study should assist medicinal chemist towards the design of potential irreversible CB inhibitors.

Keywords: cathepsin B, scaffold hopping, docking, molecular dynamics, binding-free energy, neurodegerative diseases

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Authors: Cristian Baldini

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‘Diabesity’ is a term for diabetes occurring in the context of obesity. The positive effect of LCHF diets (low-carb, high-fat diets) is well documented: LCHF diets are at least as effective as other dietary strategies for reducing body weight, improving glycaemic control, and reducing both hyperinsulinaemia and blood glucose (reduction of HbA1c) in type 2 diabetes and have unique positive effects on blood lipid concentrations and cardiovascular risk factors. Also, in obese insulin-resistant women, food fried in extra-virgin olive oil significantly reduced both insulin and C-peptide responses after a meal. This case study shows that if combined, both dietary strategies produce a strong effect on blood glucose, resulting in a “forced” reduction of exogenous insulin injection to avoid the problem of hypoglycaemia. Blood tests after three months of this dietary treatment show how HbA1c, triglycerides, and blood lipid profile (LDL, HDL, Total Cholesterol) are improved despite the reduction of exogenous insulin injection of 80% with a parallel body weight decrease of 15%. For continuous glucose monitoring (CGM), the patient used FreeStyle Libre before and after the dietary treatment. In order to check general body functions and glycosuria, the patient used the urine test Multistix 10 SG Siemens.

Keywords: diabetes, obesity, diabesity, fat, fried foods

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Authors: Muhammad Yasir, Debarun Dutta, Mark Willcox

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Biomaterial-associated infections are a multi-billion dollar burden globally. Antimicrobial peptide-based coatings may be able to prevent such infections. The aim of this study was to investigate the mechanism of action surface bound peptides (AMPs) against Pseudomonas aeruginosa 6294. Melimine and Mel4 were covalently attached to glass coverslips using azido-benzoic acid. Attachment was confirmed using X-ray photoelectron spectroscopy. P. aeruginosa was allowed to attach to AMP-coated glass for up to 6 hours. The effect of the surface-bound AMPs on bacterial cell membranes was evaluated using the dyes DiSC3-(5), Sytox green, SYTO 9 and propidium iodide with fluorescence microscopy. Release of cytoplasmic materials ATP and DNA/RNA were determined in the surrounding fluid. The amount of cell death was estimated by agar plate counts. The AMPs were successfully covalently bound to the glass as demonstrated by increases in %nitrogen of 3.6% (melimine) and 2.3% (Mel4) compared to controls. Immobilized peptides disrupted the cytoplasmic membrane potential of P. aeruginosa within 10 min. This was followed by the release of ATP after 2 h. Membrane permeabilization started at 3 h of contact with glass coated AMPs. There was a significant number of bacteria (59% for melimine; 36% for Mel-4) with damaged membranes after 4 h of contact. At the 6 h time point, release of DNA occurred with melimine releasing 2 times the amount of DNA/RNA than Mel4 surfaces (p < 0.05). Surface bound AMPs were able to disrupt cell membranes with subsequent release of cytoplasmic materials, and ultimately resulting in bacterial death.

Keywords: biomaterials, immobilized antimicrobial peptides, P. aeruginosa, mode of action

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Authors: Abdul Halim Abdul Razik, Ali Elkamel, Leonardo Simon

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Wheat straw is one of the alternative feedstocks that may be utilized for bioethanol production especially when sustainability criteria are the major concerns. To increase market competitiveness, optimal supply chain plays an important role since wheat straw is a seasonal agricultural residue. In designing the supply chain optimization model, economic profitability of the thermochemical and biochemical conversion routes options were considered. It was found that torrefied pelletization with gasification route to be the most profitable option to produce bioethanol from the lignocellulosic source of wheat straw.

Keywords: bio-ethanol, optimization, supply chain, wheat straw

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Authors: Saeid Jalilzadeh

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Designing of PSS and SVC controller based on Bacterial Foraging Algorithm (BFA) to improve the stability of power system is proposed in this paper. Same controllers for PSS and SVC has been considered and Single machine infinite bus (SMIB) system with SVC located at the terminal of generator is used to evaluate the proposed controllers. BFA is used to optimize the coefficients of the controllers. Finally simulation for a special disturbance as an input power of generator with the proposed controllers in order to investigate the dynamic behavior of generator is done. The simulation results demonstrate that the system composed with optimized controllers has an outstanding operation in fast damping of oscillations of power system.

Keywords: PSS, SVC, SMIB, optimize controller

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Authors: Rituraj Deka, Nomi Baruah

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The development of information technology during the past few years resulted in designing of more and more complex software. The outsourcing of software development makes a higher requirement for the management of software development project. Various software enterprises follow various paths in their pursuit of excellence, applying various principles, methods and techniques along the way. The new research is proving that CMMI and Agile methodologies can benefit from using both methods within organizations with the potential to dramatically improve business performance. The paper describes a mapping between CMMI key process areas (KPAs) and Feature-Driven Development (FDD) communication perspective, so as to increase the understanding of how improvements can be made in the software development process.

Keywords: Agile, CMMI, FDD, KPAs

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Authors: Spase Janevski

Abstract:

We, as designers, should be aware of the consequences of our material selection, at the early stages of the design process. Some of the designer’s decisions can have a very significant impact on design for sustainability. The influence of this concept has led to years of research studies into eco-friendly materials and their potentials for creating new sustainable products. In order to answer the question, 'how cork has become a design trend', this paper will present an overview of the implications of the concept of design for sustainability on the potential uses of cork material. A decade ago, cork as a material had an association with wine stoppers, but with the evolution of sustainable product design as part of the concept of design for sustainability, cork now offers product designers a wide range of new materials and applications. The purpose of this paper is to show how the phenomenon of sustainability has had an impact on the progress of the material which is currently not being an integral component of the design material palette. At the beginning, the nature of the relationship between cork and sustainability will be explained through the following stages: 1) fundamental understanding of the concept of Design for Sustainability and the importance of material selection for sustainable product design, and 2) the importance of cork oak trees for the environment and the environmental impacts of cork products. In order to examine and present the influence of the sustainability on the innovation in cork applications, the paper will provide a historical overview of designing with cork. The overview will consist of four stages: 1) pre-industrial period - the period when ancient nations used cork and amphoras to store their wine; 2) industrial period - emergence and industrialization of well-known wine stoppers; 3) post-industrial period - commercializing cork products in the area of floors and coverings and first developments in industrial research; and 4) the period when large cork realized the importance of sustainability and started to focus more markedly on research and development. The existence of new cork materials, the investigation in new applications and the investment in new innovations have proved that the sustainability approach has had a great influence on the revival of this material. In addition, the paper will present some of the new cork innovative materials and applications and their potentials for designing promising and sustainable solutions with additive manufacturing technologies, such as 3D printing. Lastly, the paper will introduce some questions for further study, such as the environmental impacts of the new hybrid materials and the gap between cork industry and cork research and development teams. The paper concludes by stating that cork is not only a material for wine stoppers anymore, thanks to the awareness of the concept of design for sustainability.

Keywords: cork, design for sustainability, innovation, sustainable materials

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Authors: Sanne Dollerup

Abstract:

This paper is an analysis of the store Tarina Tarantino through an exploration of different perspectives of play. It is based on Yelp reviews where customers disclose a very positive emotional reaction toward the store. The paper proposes some general principles for designing immersive stores based on ‘possible world’ theory. The aim is to disclose essential condition for customer engagement is an overall cohesiveness in all elements in a store. The most significant contribution in this paper is that products become props for role-playing in a store, hence making them central for maintaining that role outside the store.

Keywords: experience design, emotional brand attachment, retail design, case study

Procedia PDF Downloads 136

Authors: Sharon N. Nuñal, May Flor S. Muegue, Nizzy Hope N. Cartago, Raymund B. Parcon, Sheina B. Logronio

Abstract:

The antioxidant and anti-inflammatory potentials of Perna Viridis, Modiolus philippinarum, and Mytella charruana found in the Philippines were assessed. Mussel protein samples were hydrolyzed using trypsin, maturase, alcalase and pepsin at 1% and 2% concentrations and then fractionated through membrane filtration (<10 kDa and <30 kDa). Antioxidant assays showed that pepsin hydrolysate at 2% enzyme concentration exhibited the maximum activities for both 2,2-Diphenyl-1-picrylhydrazyl (DPPH) Radical Scavenging Activity (155-176 µM TE/mg protein) and 2,2-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging (67-68 µM TE/mg protein) assays while trypsin hydrolysate dominated the Ferric Reducing Antioxidant Power (FRAP) for the three mussel species. Lower molecular weight peptide fractions at <10 kDa exhibited better antioxidant activities than the higher molecular weight fractions. The anti-inflammatory activities of M. philippinarum and M. charruana showed comparable protein denaturation inhibition potentials with the highest in P. Viridis samples (98.93%). The 5-Lipoxygenase (5-LOX) inhibitory activities of mussel samples showed no significant difference with inhibition exceeding 70%. P. Viridis demonstrated the highest inhibition against Cyclooxygenase-2 (COX-2) at 56.19%, while the rest showed comparable activities. This study showed that the three mussel species are potential sources of bioactive peptides and lipids with antioxidant and anti-inflammatory properties.

Keywords: anti-inflammatory, antioxidant, bioactive properties, mussel

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Authors: Sina Mahdavi

Abstract:

Background and Objective: Multiple sclerosis (MS) is the most common inflammatory autoimmune disease of the central nervous system (CNS) that affects the myelination process in the CNS. Complex interactions of various "environmental or infectious" factors may act as triggers in autoimmunity and disease progression. The association between viral infections, especially Epstein-Barr virus (EBV) and MS, is one potential cause that is not well understood. In this study, we aim to summarize the available data on EBV infection in MS disease progression. Materials and Methods: For this study, the keywords "Multiple sclerosis," "Epstein-Barr virus," and "central nervous system" in the databases PubMed, Google Scholar, Sid, and MagIran between 2016 and 2022 were searched, and 14 articles were chosen, studied, and analyzed. Results: Demyelinated lesions isolated from MS patients contain EBNAs from EBV proteins. The EBNA1 domain contains a pentapeptide fragment identical to B-crystallin, a heat shock peptide, that is increased in peripheral B cells in response to B-crystallin infection, resulting in myelin-directed autoimmunity mediated by proinflammatory T cells. EBNA2, which is involved in the regulation of viral transcription, may enhance transcription from MS risk loci. A 7-fold increase in the risk of MS has been observed in EBV infection with HLA-DR15 synergy. Conclusion: EBV infection along with a variety of specific genetic risk alleles, cause inflammatory cascades in the CNS by infected B cells. There is a high expression of EBV during the course of MS, which indicates the relationship between EBV and MS, that this virus can play a role in the development of MS by creating an inflammatory state. Therefore, measures to modulate the expression of EBV may be effective in reducing inflammatory processes in demyelinated areas of MS patients.

Keywords: multiple sclerosis, Epstein-Barr virus, central nervous system, EBNAs

Procedia PDF Downloads 72