Search results for: Marvin sketch

Authors: Virupakshaiah DBM, Madiha Ahmed, Smita T. Patil, Chandrakanth Kelmani

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Tuberculosis (TB) is a bacterial infectious disease caused by the obligate human pathogen, Mycobacterium tuberculosis. Multidrug-resistant tuberculosis (MDR-TB) is a global reality that threatens tuberculosis control. Resistance to antibiotic Rifampicin, occurs in 95% of cases through nucleotide substitutions in an 81-bp core region of the rpoB i.e; beta subunit of DNA dependant RNA polymerase. In this paper, we studied the Rifampicin-rpoB receptor interactions In silico. First, homology modeling was performed to obtain the three dimensional structure of Mycobacterium rpoB. Sixty analogs of Rifampicin were prepared using Marvin sketch software. Both original Rifampicin and the analogs were docked with rpoB and energy values were obtained. Out of sixty analogs, 43 analogs had lesser energy values than conventional Rifampicin and hence are predicted to have greater binding affinity to rpoB. Thus, this study offers a route for the development of Rifampicin analogs against multi drug resistant Mycobacterium rpoB.

Keywords: Marvin Sketch, Mycobacterium tuberculosis, Rifampicin, rpoB.

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Authors: Virupakshaiah DBM, Chandrakanth Kelmani, Rachanagouda Patil, Prasad Hegade

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Severe acute respiratory syndrome (SARS) is a respiratory disease in humans which is caused by the SARS coronavirus. The treatment of coronavirus-associated SARS has been evolving and so far there is no consensus on an optimal regimen. The mainstream therapeutic interventions for SARS involve broad-spectrum antibiotics and supportive care, as well as antiviral agents and immunomodulatory therapy. The Protein- Ligand interaction plays a significant role in structural based drug designing. In the present work we have taken the receptor Angiotensin converting enzyme 2 and identified the drugs that are commonly used against SARS. They are Lopinavir, Ritonavir, Ribavirin, and Oseltamivir. The receptor Angiotensin converting enzyme 2 (ACE-2) was docked with above said drugs and the energy value obtained are as follows, Lopinavir (-292.3), Ritonavir (-325.6), Oseltamivir (- 229.1), Ribavirin (-208.8). Depending on the least energy value we have chosen the best two drugs out of the four conventional drugs. We tried to improve the binding efficiency and steric compatibility of the two drugs namely Ritonavir and Lopinavir. Several modifications were made to the probable functional groups (phenylic, ketonic groups in case of Ritonavir and carboxylic groups in case of Lopinavir respectively) which were interacting with the receptor molecule. Analogs were prepared by Marvin Sketch software and were docked using HEX docking software. Lopinavir analog 8 and Ritonavir analog 11 were detected with significant energy values and are probable lead molecule. It infers that some of the modified drugs are better than the original drugs. Further work can be carried out to improve the steric compatibility of the drug based upon the work done above for a more energy efficient binding of the drugs to the receptor.

Keywords: Protein data bank, Rasmol, Marvin sketch, Hexdocking.

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Authors: Aditi Shukla, Ambarish S. Vidyarthi, Subir Samanta

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The worldwide prevalence of H3N2 influenza virus and its increasing resistance to the existing drugs necessitates for the development of an improved/better targeting anti-influenza drug. H3N2 influenza neuraminidase is one of the two membrane-bound proteins belonging to group-2 neuraminidases. It acts as key player involved in viral pathogenicity and hence, is an important target of anti-influenza drugs. Oseltamivir is one of the potent drugs targeting this neuraminidase. In the present work, we have taken subtype N2 neuraminidase as the receptor and probable analogs of oseltamivir as drug molecules to study the protein-drug interaction in anticipation of finding efficient modified candidate compound. Oseltamivir analogs were made by modifying the functional groups using Marvin Sketch software and were docked using Schrodinger-s Glide. Oseltamivir analog 10 was detected to have significant energy value (16% less compared to Oseltamivir) and could be the probable lead molecule. It infers that some of the modified compounds can interact in a novel manner with increased hydrogen bonding at the active site of neuraminidase and it might be better than the original drug. Further work can be carried out such as enzymatic inhibition studies; synthesis and crystallizing the drug-target complex to analyze the interactions biologically.

Keywords: H3N2 Influenza, Neuraminidase, Oseltamiviranalogs, structure based drug designing

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Authors: Dagmar Monett, Sven-Erik Kujat, Marvin Hartmann

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This paper discusses the use of a template-based approach for documenting high-quality requirements as part of course projects in an undergraduate Software Engineering course. In order to ease some of the Requirements Engineering activities that are performed when defining requirements by using the template, a new CASE tool, RED:WIRE, was first developed and later tested by students attending the course. Two questionnaires were conceived around a study that aims to analyze the new tool’s learnability as well as other obtained results concerning its usability in particular and the Requirements Engineering skills developed by the students in general.

Keywords: CASE tool, collaborative learning, requirements engineering, undergraduate teaching.

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Authors: Seyed Habib A. Rahmati, Mohsen Sadegh Amalnick

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Different terms of the Statistical Process Control (SPC) has sketch in the fuzzy environment. However, Measurement System Analysis (MSA), as a main branch of the SPC, is rarely investigated in fuzzy area. This procedure assesses the suitability of the data to be used in later stages or decisions of the SPC. Therefore, this research focuses on some important measures of MSA and through a new method introduces the measures in fuzzy environment. In this method, which works based on Buckley approach, imprecision and vagueness nature of the real world measurement are considered simultaneously. To do so, fuzzy version of the gauge capability (Cg and Cgk) are introduced. The method is also explained through example clearly.

Keywords: SPC, MSA, gauge capability, Cg, Cgk.

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Authors: L. Ludovic, R. Daniel, S-E Tbahriti

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Database management systems that integrate user preferences promise better solution for personalization, greater flexibility and higher quality of query responses. This paper presents a tentative work that studies and investigates approaches to express user preferences in queries. We sketch an extend capabilities of SQLf language that uses the fuzzy set theory in order to define the user preferences. For that, two essential points are considered: the first concerns the expression of user preferences in SQLf by so-called fuzzy commensurable predicates set. The second concerns the bipolar way in which these user preferences are expressed on mandatory and/or optional preferences.

Keywords: Flexible query language, relational database, userpreference.

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Authors: Shuen-Tai Wang, Hsi-Ya Chang

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Cloud virtualization technologies are becoming more and more prevalent, cloud users usually encounter the problem of how to access to the virtualized remote desktops easily over the web without requiring the installation of special clients. To resolve this issue, we took advantage of the HTML5 technology and developed web-based remote desktop. It permits users to access the terminal which running in our cloud platform from anywhere. We implemented a sketch of web interface following the cloud computing concept that seeks to enable collaboration and communication among users for high performance computing. Given the development of remote desktop virtualization, it allows to shift the user’s desktop from the traditional PC environment to the cloud platform, which is stored on a remote virtual machine rather than locally. This proposed effort has the potential to positively provide an efficient, resilience and elastic environment for online cloud service. This is also made possible by the low administrative costs as well as relatively inexpensive end-user terminals and reduced energy expenses.

Keywords: Virtualization, Remote Desktop, HTML5, Cloud Computing.

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Authors: Joseph Maloba Makokha

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Idea generation is an important part of the design process, and many strategies to support this stage have been developed. As artificial intelligence (AI) gains adoption in many domains, we need to understand its role, if any, in the design process. This paper introduces the concept of a “Disruptive Interjector”, an AI system that frequently interjects with suggestions based on observing what a user does. The concept emanates from a study that was conducted with pairs of humans on one hand, and human-AI pairs on the other collaborating on idea generation by sketching. Results from a study show that participants who collaborated with, and took cues from the AI sketch suggestions generated more ideas; and also had more ideas ranked by experts as “creative” compared to two humans working together on the same tasks. It is notable that while researchers from diverse fields of engineering, psychology, art and others have explored conditions and environments that enhance people's creativity - and have provided insights on creativity in general - there still exists a gap on the role that AI can play on creativity. We attempt to narrow this gap.

Keywords: Artificial intelligence, design collaboration, creativity, human-machine collaboration, machine learning.

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Authors: Shuen-Tai Wang, Yu-Ching Lin, Hsi-Ya Chang

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With the development of virtualization technologies, a new type of service named cloud computing service is produced. Cloud users usually encounter the problem of how to use the virtualized platform easily over the web without requiring the plug-in or installation of special software. The object of this paper is to develop a system and a method enabling process interfacing within an automation scenario for accessing remote application by using the web browser. To meet this challenge, we have devised a web-based interface that system has allowed to shift the GUI application from the traditional local environment to the cloud platform, which is stored on the remote virtual machine. We designed the sketch of web interface following the cloud virtualization concept that sought to enable communication and collaboration among users. We describe the design requirements of remote application technology and present implementation details of the web application and its associated components. We conclude that this effort has the potential to provide an elastic and resilience environment for several application services. Users no longer have to burden the system maintenances and reduce the overall cost of software licenses and hardware. Moreover, this remote application service represents the next step to the mobile workplace, and it lets user to use the remote application virtually from anywhere.

Keywords: Virtualization technology, virtualized platform, web interface, remote application.

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Authors: Andrew Hwang

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The average American worker sits for thirteen hours a day, often with poor posture and infrequent breaks, which can lead to health issues and back problems. The Smart Cushion was created to alert individuals of their poor postures, and may potentially alleviate back problems and correct poor posture. The Smart Cushion is a portable, rectangular, foam cushion, with five strategically placed pressure sensors, that utilizes an Arduino Uno circuit board and specifically designed software, allowing it to collect data from the five pressure sensors and store the data on an SD card. The data is then compiled into graphs and compared to controlled postures. Before volunteers sat on the cushion, their levels of back pain were recorded on a scale from 1-10. Data was recorded for an hour during sitting, and then a new, corrected posture was suggested. After using the suggested posture for an hour, the volunteers described their level of discomfort on a scale from 1-10. Different patterns of sitting postures were generated that were able to serve as early warnings of potential back problems. By using the Smart Cushion, the areas where different volunteers were applying the most pressure while sitting could be identified, and the sitting postures could be corrected. Further studies regarding the relationships between posture and specific regions of the body are necessary to better understand the origins of back pain; however, the Smart Cushion is sufficient for correcting sitting posture and preventing the development of additional back pain.

Keywords: Arduino Sketch Algorithm, biomedical technology, pressure sensors, Smart Cushion.

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Authors: Feyzan Tuzkaya, Nihan S. Soylu, Çağlar Solak, Hilal Peker, Mehmet Peker, Kemal Özeralp, Ceren Mete, Ezgi Mehmetoğlu, Mehmet Karasu, Cihan Elçi, Ece Akca, Melek Göregenli

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Perception, evaluation and representation of the environment have been the subject of many disciplines including psychology, geography and architecture. In environmental and social psychology literature there are several evidences which suggest that cognitive representations about a place consisted of not only geographic items but also social and cultural. Mental representations of residence area or a country are influenced and determined by social-demographics, the physical and social context. Thus, all mental representations of a given place are also social representations. Cognitive maps are the main and common instruments that are used to identify spatial images and the difference between physical and subjective environments. The aim of the current study is investigating the mental and social representations of Turkey in university students’ minds. Data was collected from 249 university students from different departments (i.e. psychology, geography, history, tourism departments) of Ege University. Participants were requested to reflect Turkey in their mind onto the paper drawing sketch maps. According to the results, cognitive maps showed geographic aspects of Turkey as well as the context of symbolic, cultural and political reality of Turkey. That is to say, these maps had many symbolic and verbal items related to critics on social and cultural problems, ongoing ethnic and political conflicts, and actual political agenda of Turkey. Additionally, one of main differentiations in these representations appeared in terms of the East and West side of the Turkey, and the representations of the East and West was varied correspondingly participants’ cultural background, their ethnic values, and where they have born. The results of the study were discussed in environmental and social psychological perspective considering cultural and social values of Turkey and current political circumstances of the country.

Keywords: Cognitive maps, East and West, politics, social representations, Turkey.

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Authors: Khaled Igbaria

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While Ba‘albakī ceased writing or publishing since 1964, it is considerable and significant to investigate Ba‘albakī’s influence on others. This paper examines her influence on three Lebanese women writers: Emily Nasrallah, Muná Jabbūr, and Hanan al-Shaykh. However, the aim is not simply to examine the influence of the writer on these three authors, but rather to note similarities and differences in the challenges they faced and the agendas they followed in their fiction writing. For each of these writers, this article will describe elements of their literature, and then sketch out the influence which Ba‘albakī has had on them. This paper relies on material from Sidawi because it includes interviews with the female writers discussed that are relevant to the current discussion. Sidawi asked them about Ba‘albakī and her influence on them, the challenges they faced, and how they coped with them. This paper points out their comments using their own words. To be clear, examining these writers' notes and works is beyond the scope of this paper. To sum up, there are significant parallels between the life and work of Ba‘albakī, and other Lebanese women writers such as Nasrallah, Jabbūr and al-Shaykh. Like Ba‘albakī, Nasrallah and al-Shaykh also suffered in their struggle against their families. Nasrallah and al-Shaykh, like Ba‘albakī, suffered because their society did not trust in their abilities and creativity. Ba‘albakī opted for isolation because of her conflict with patriarchal society including the Lebanese women’s groups, while Nasrallah’s isolation was because she preferred individualism and autonomy, and Jabbūr, as could be speculated, was not able to cope with the suffering caused by her role as a woman writer within Lebanese society. Whereas Ba‘albakī isolated herself from the Lebanese women’s groups, focusing instead on her feminist writing and joining the Shi'r group, Al-Shaykh and the Lebanese women’s groups are able to cooperate in harmony. Furthermore, while Nasrallah and Al-Shaykh continued to publish fiction, Ba‘albakī stopped publishing fiction in 1964. All of the above confirms not only that it is worthy to investigate deeply and academically both the biography and the works of Ba‘albakī, but also that she deserves to include her throughout the top great Arab female writers, at the time, like Al-Shaykh and Nawal El Saadawi.

Keywords: Feminist writing, Hanan Al-Shaykh, Laylá Ba‘albakī, Lebanese women writers, Muná Jabbūr.

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Authors: Walter Sebron, Hans Tschürtz, Peter Krebs

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The choice of applicable analysis methods in safety or systems engineering depends on the depth of knowledge about a system, and on the respective lifecycle phase. However, the analysis method chain still shows gaps as it should support system analysis during the lifecycle of a system from a rough concept in pre-project phase until end-of-life. This paper’s goal is to discuss an analysis method, the VISSE Shell Model Analysis (VISMA) method, which aims at closing the gap in the early system lifecycle phases, like the conceptual or pre-project phase, or the project start phase. It was originally developed to aid in the definition of the system boundary of electronic system parts, like e.g. a control unit for a pump motor. Furthermore, it can be also applied to non-electronic system parts. The VISMA method is a graphical sketch-like method that stratifies a system and its parts in inner and outer shells, like the layers of an onion. It analyses a system in a two-step approach, from the innermost to the outermost components followed by the reverse direction. To ensure a complete view of a system and its environment, the VISMA should be performed by (multifunctional) development teams. To introduce the method, a set of rules and guidelines has been defined in order to enable a proper shell build-up. In the first step, the innermost system, named system under consideration (SUC), is selected, which is the focus of the subsequent analysis. Then, its directly adjacent components, responsible for providing input to and receiving output from the SUC, are identified. These components are the content of the first shell around the SUC. Next, the input and output components to the components in the first shell are identified and form the second shell around the first one. Continuing this way, shell by shell is added with its respective parts until the border of the complete system (external border) is reached. Last, two external shells are added to complete the system view, the environment and the use case shell. This system view is also stored for future use. In the second step, the shells are examined in the reverse direction (outside to inside) in order to remove superfluous components or subsystems. Input chains to the SUC, as well as output chains from the SUC are described graphically via arrows, to highlight functional chains through the system. As a result, this method offers a clear and graphical description and overview of a system, its main parts and environment; however, the focus still remains on a specific SUC. It helps to identify the interfaces and interfacing components of the SUC, as well as important external interfaces of the overall system. It supports the identification of the first internal and external hazard causes and causal chains. Additionally, the method promotes a holistic picture and cross-functional understanding of a system, its contributing parts, internal relationships and possible dangers within a multidisciplinary development team.

Keywords: Analysis methods, functional safety, hazard identification, system and safety engineering, system boundary definition, system safety.

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