Search results for: endpoints identification

Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

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Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

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Authors: Kalpana Sharma, Jyoti Mann

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The study was designed towards institutional analysis for a clear understanding of the process involved in functioning and layout of determinants influencing physical education teacher’s education program in India. This further can be recommended for selection of parameters for creating sector benchmarking for physical education teachers training institutions across India. 165 stakeholders involving students, teachers, parents, administrators were surveyed from the identified seven institutions and universities from different states of India. They were surveyed on the basis of seven broad parameters which were associated with the post graduate physical education program in India. A physical education program assessment tool of 52 items was designed to administer it among the stakeholders selected for the survey. An item analysis of the contents was concluded through the review process from selected experts working in higher education with experience in teacher training program in physical education. The data was collected from the stakeholders of the selected institutions through Physical Education Program Assessment Tool (PEPAT). The hypothesis that PE teacher education program is independent of physical education institutions was significant. The study directed a need towards robust admission process emphasizing on identification, selection of potential candidates and quality control of intake with the scientific process developed according to the Indian education policies and academic structure. The results revealed that the universities do not have similar functional and delivery process related to the physical education teacher training program. The study reflects towards the need for physical education universities and institutions to identify the best practices to be followed regarding the functioning of delivery of physical education programs at various institutions through strategic management studies on the identified parameters before establishing strict standards and norms for achieving excellence in physical education in India.

Keywords: assessment, benchmarking, curriculum, physical education, teacher education

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Authors: Adegoriola Mayowa I., Lai Joseph H. K., Yung Esther H. K., Chan Edwin H. K.

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Heritage buildings (HBs) as structures with historical and architectural relevance that form an integral part of contemporary society. These buildings deserve to be protected for as long as possible to retain their significance. Therefore, the need to prioritize HB maintenance management is pertinent. However, the decision-making process of HBMM can be relatively daunting. The decision-making challenge may be attributed to the multiple 'stakeholders' expectation and requirement which needs to be met. To this end, professionals in the built environment have identified the need to apply the strategic concept of facilities management (FM) in decision making. Furthermore, the different maintenance dimensions have been applied to maintenance management of residential, commercial, and health facilities. Unfortunately, these different maintenance approaches, such as FM, sustainable FM, urban FM, green FM, and strategic FM, are yet to be fully explored in the decision-making process of HBMM. To bridge this gap, this study focuses on developing a framework for strategic decision-making HBMM, which helps achieve HBMM sustainability. At the study's inception, relevant works of literature in the domains of HBMM and FM were conducted. This review helped in the identification of contemporary maintenance practices and their applicability to HBMM. Afterward, a conceptual framework to aid decision-making in HBMM was developed. This framework integrated the concept of FM scope (people, place, process, and technology) while ensuring that decisions plans were made at strategic, tactical, and operational levels. Also, the different characteristics of HBs and stakeholders' requirements were considered in the framework. The conceptual framework presents a holistic guide for professionals in HBMM to ensure that decision processes and outcomes are practical and efficient. It also contributes to the existing body of knowledge on the integration of FM in HBMM. Furthermore, it will serve as a basis for future studies by applying the conceptualized framework in actual cases.

Keywords: decision-making, facility management, strategy, sustainability, heritage building, maintenance

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Authors: Marinko Maslaric, Maja Jokic

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When searching for fast and long term responses, sustainable logistics and supply chain applications have developed irrefutable theories and hypotheses towards market requirements. Nevertheless, there are certain misunderstandings on how the implementation of sustainability principles (social, economical, and environmental) and concepts should work in practice, more specifically, within a humanitarian supply chain management context. This paper will focus on the review and analysis of risk management concepts in humanitarian supply chain in order to identify their compliance with sustainable principles. In this direction, the study will look for strategies that suggest: minimization of environmental impacts throughout the reduction of resources consumption, depreciation of logistics costs, including supply chain ones, minimization of transportation and service costs, elaboration of quality performance of supply chain and logistics, and reduction of supply chain delivery time. On the side of meeting all defense, trades and humanitarian logistics needs, the research will be aligned to UN Sustainable Development Goals, standards, and performances. It will start with relevant strategies for identification of risk indicators and it will end with suggestion of valuable strategic approaches for their minimization or total prevention. Finally, a content analysis will propose a suitable methodological structure for the creation of most sustainable strategy in risk management of humanitarian supply chain. Content analysis will accompany thorough, consistent and methodical approach of literature review for potential disaster risk management plan. Thereupon, the propositions of this research will look for contemporary literature gaps, with respect to operate the literature analysis and to suggest the appropriate sustained risk low master plan. The indicated is here to secure the high quality of logistics practices in hazardous events.

Keywords: humanitarian logistics, sustainability, supply chain risk, risk management plan

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Authors: Pia Moschall, Kathrin Sackmann

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Considering a purchasing volume of around two trillion Euros per year, which equals about 14% of the European Union’s gross domestic product, European public authorities have significant market power. Making use of this market power by prioritizing the procurement of green products and services offers a great potential to contribute to the Green New Deal. The market demand that is created by Green Public Procurement (GPP) sets incentives for European producers to design and develop Green Products and Eco-Innovations. However, most procurement still does not consider environmental criteria. The goal of the work is to encourage the adaptation of GPP in the European Union. To this end, the drivers for the adaptation were investigated over different case studies. The paper analyzes good-practice cases from European authorities from 2010 to 2020 that were provided by the European Commission. This analysis was guided by Philipp Mayring’s method of qualitative content analysis, whereby the inductively formed categories led to the identification of nine major drivers. The most important ones are ‘use of official guidelines and standards, ‘political support and requirements as well as ‘market research and involvement.’ Further, the paper discusses mutual dependencies between several drivers and how to exploit them. A supporting infrastructure was identified as a crucial factor for the successful adaption of green public procurement. In the next step, the work aims to examine on which administrative level the single drivers can be implemented most effectively. Practical implications of this research are recommendations on how to create a supporting structure on a municipal, federal and national level, including training for the responsible staff, support tools, as well as guidelines and standards for involved stakeholders.

Keywords: content analysis, green public procurement, public authorities, sustainable procurement

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Authors: Rajkumar Ghosh

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The Out-of-Sequence Thrust (OOST) is a common phenomenon in collisional tectonic settings like the Himalayas. These OOSTs are activated in different locations at different time frames. These OOST are linked with the multiple Himalayan Thrusts. Apart from minimal documentation in geological mapping for OOST, there exists a lack of field data to establish OOST in the field. This work has considered three thrusts from NW Himalaya in Himachal Pradesh with published data from other sources, allowing a re-examination for correlation of OOST. For the Sutlej section, the approach has been to do fieldwork and microstructural studies. The information related to the cross-cut signature of S/C- and relative time relation could help to predict the nature of OOST. The activation timing, along with the basis of identification of OOST in Higher Himalayan, was documented in various literature. Compilation of the Grain Boundary Migration (GBM) associated temperature range (400–750 °C) was documented from microstructural studies along the Jhakri-Chaura section. No such significant temperature variation across thrusts was observed. Strain variation paths using S Ʌ C angle measurement were carried out along the Jeori-Wangtu transect to distinguish overprinting structures for OOSTs. Near the Chaura Thrust (CT), angular variation of S Ʌ C was documented, and it varies within a range of 15° - 28 °. Along the NH22 (National Highway, 22), all tectonic units of the orogen are exposed in NW Himalaya, INDIA. But there are inherent difficulties in finding field evidence of OOST, largely due to the lack of adequate surface morphology, including topography and drainage pattern.

Keywords: out-of-sequence thrust (OOST), main central thrust (MCT), south tibetan detachment system (STDS), jhakri thrust (JT), sarahan thrust (ST), chaura thrust (CT), higher himalaya (HH), greater himalayan crystalline (GHC)

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Authors: Aisha Liaquat Ali, Ghulam Sarwar Gachal, Muhammad Yusuf Sheikh

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The Parrot rose ringed (Psittaculla krameri) commonly known as Tota, belongs to the order ‘Psittaciformes’ and family ‘Psittacidea’. Its sub-species inhabiting Pakistan are Psittaculla borealis. The parrot rose-ringed has been categorized the least concern species, the core aim of the present study is to investigate the ecology and taxonomy of parrot (rose-ringed). Sampling was obtained for the taxonomic identification from various adjoining areas in City Mirpurkhas by non-random method, which was conducted from Feb to June 2017. The different parameters measured with the help of a vernier caliper, foot scale, digital weighing machine. Body parameters were measured via; length of body, length of the wings, length of tail, mass in grams. During present study, a total number of 36 specimens were collected from different localities of City Mirpurkhas (38.2%) were male and (62.7%) were female. Maximum population density of Psittaculla Krameri borealis (52.9%) was collected from Sindh Horticulture Research Station (fruit farm) Mirpurkhas. Minimum no: of Psittaculla krameri borealis (5.5%) collected in urban parks. It was observed that Psittaculla krameri borealis were in dense population during the months of ‘May’ and ‘June’ when the temperature ranged between 20°C and 45°C. A Psittaculla krameri borealis female was found the heaviest in body weight. The species of parrot (rose ringed) captured during study having green plumage, coverts were gray, upper beak, red and lower beak black, shorter tail in female long tail in the male which was similar to the Psittaculla krameri borealis.

Keywords: Mirpurkhas Sindh Pakistan, environmental ecology, parrot, rose-ringed, taxonomy

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Authors: Md. Ehsan, Cyrus Ashok Arupratan Atis

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Significantly lower cost, bulk availability, absence of identification color additives and relative ease of mixing with fuels have made gas-field condensates a lucrative option as adulterant for gasoline in Bangladesh. Widespread adulteration of fuels with gas-field condensates being a problem existing mainly in developing countries like Bangladesh, Nigeria etc., research works regarding the effect of such fuel adulteration are very limited. Since the properties of the gas-field condensate vary widely depending on geographical location, studies need to be based on local condensate feeds. This study quantitatively evaluates the effects of blending of gas-field condensates with gasoline(octane) in terms of - fuel properties, engine performance and exhaust emission. Condensate samples collected from Kailashtila gas field were blended with octane, ranging from 30% to 75% by volume. However for blends with above 60% condensate, cold starting of engine became difficult. Investigation revealed that the condensate samples had significantly higher distillation temperatures compared to octane, but were not far different in terms of heating value and carbon residues. Engine tests showed Kailashtila blends performing quite similar to octane in terms of power and thermal efficiency. No noticeable knocking was observed from in-cylinder pressure traces. For all the gasoline-condensate blends the test engine ran with relatively leaner air-fuel mixture delivering slightly lower CO emissions but HC and NOx emissions were similar to octane. Road trials of a test vehicle in real traffic condition and on a standard gradient using 50%(v/v) gasoline-condensate blend were also carried out. The test vehicle did not exhibit any noticeable difference in drivability compared to octane.

Keywords: condensates, engine performance, fuel adulteration, gasoline-condensate blends

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Authors: Jose D. Zapata-Torres, Esteban Naranjo-Gutiérrez, Angela M. Martínez-Valencia, Jenny J. Chaparro-Gutiérrez, David Villar-Argaiz

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Reports of drug resistance have been made in every livestock host and to every anthelmintic class. In some regions of world, the extremely high prevalence of multi-drug resistance in nematodes of sheep and goats threatens the viability of small-ruminant industries. In the region of Antioquia, Colombia, no reports of nematode resistance have been documented due to a lack of veterinary diagnostic laboratories. The objective of this study was to evaluate the efficacy of albendazole, fenbendazole, and levamisole to control gastrointestinal nematodes in goat farms of Antioquia by doing fecal egg count reduction tests. A total of 139 crossbreed goats from four separate farms were sampled for feces prior to, and 14 days following anthelmintc treatments. Individual fecal egg counts were performed using the modified three chamber McMaster technique. The anthelmintics administered at day 0 were albendazole (farm 1, n=63), fenbendazole (farm 2, n=20), and levamisole (farm 3 and 4, n= 37, and 19). Larval cultures were used to identify the genus of nematodes using Baermann`s technique and the morphological keys for identification of L3 in small ruminants. There was no difference in fecal egg counts between 0 and 14, with means (±SD) of 1681,5 ± 2121,5 and 1715,12 ± 1895,4 epg (eggs per gram), respectively. The egg count reductions for each anthelmintic and farm were 25,86% for albendazole (farm 1), 0% for fenbendazole (farm 2), 0% (farm 3), and 5,5% (farm 4) for levamisole. The genus of nematodes identified was predominantly Haemonchus spp., with 70,27% and 82,81% for samples from day 0 and 14, respectively. These results provide evidence of a total state of resistance to 3 common anthelmintics. Further research is needed to design integrate management programs to control nematodes in small ruminants in Colombia.

Keywords: anthelmintics, goat, haemonchus, resistance

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Authors: Dong Tran, Thanh Dac Van, Ly Le

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Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

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Authors: Guoqiang Yu, Mehrana Mohtasebi, Jinghong Sun, Thomas Pittman

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Malignant glioma (MG) is the most common type of primary malignant brain tumor. Surgical resection of MG remains the cornerstone of therapy, and the extent of resection correlates with patient survival. A limiting factor for resection, however, is the difficulty in differentiating the tumor from normal tissue during surgery. Fluorescence imaging is an emerging technique for real-time intraoperative visualization of MGs and their boundaries. However, most clinical-grade neurosurgical operative microscopes with fluorescence imaging ability are hampered by low adoption rates due to high cost, limited portability, limited operation flexibility, and lack of skilled professionals with technical knowledge. To overcome the limitations, we innovatively integrated miniaturized light sources, flippable filters, and a recording camera to the surgical eye loupes to generate a wearable fluorescence eye loupe (FLoupe) device for intraoperative imaging of fluorescent MGs. Two FLoupe prototypes were constructed for imaging of Fluorescein and 5-aminolevulinic acid (5-ALA), respectively. The wearable FLoupe devices were tested on tumor-simulating phantoms and patients with MGs. Comparable results were observed against the standard neurosurgical operative microscope (PENTERO® 900) with fluorescence kits. The affordable and wearable FLoupe devices enable visualization of both color and fluorescence images with the same quality as the large and expensive stationary operative microscopes. The wearable FLoupe device allows for a greater range of movement, less obstruction, and faster/easier operation. Thus, it reduces surgery time and is more easily adapted to the surgical environment than unwieldy neurosurgical operative microscopes.

Keywords: fluorescence guided surgery, malignant glioma, neurosurgical operative microscope, wearable fluorescence imaging device

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Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

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Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

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Authors: Rachel Wachtendonk, John Calambokidis, Kiirsten Flynn

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Large marine mammals can serve as an indicator of the overall state of the environment due to their long lifespan and apex position in marine food webs. Reductions in prey, driven by changes in environmental conditions can have resounding impacts on the trophic system as a whole; this can manifest in reduced fat stores that are visible on large whales. Poor health can lead to reduced survivorship and fitness, both of which can be detrimental to a recovering population. A non-invasive technique was used for monitoring blue whale health and for seeing if it changes with ocean conditions. Digital photographs of blue whales taken in the NE Pacific by Cascadia Research and collaborators from 2005-2018 (n=3,545) were scored for overall body condition based on visible vertebrae and body shape on a scale of 0-3 where a score of 0 indicated best body condition and a score of 3 indicated poorest. The data was analyzed to determine if there were patterns in the health of whales across years and whether overall poor health was related to oceanographic conditions and predictors of prey abundance on the California coast. The year was a highly significant factor in body condition (Chi-Square, p<0.001). The proportion of whales showing poor body condition (scores 2 & 3) overall was 33% but by year varied widely from a low of 18% (2008) to a high of 55% (2015). The only two years where >50% of animals had poor body condition were 2015 and 2017 (no other year was above 45%). The 2015 maximum proportion of whales in poor body condition coincide with the marine heat wave that affected the NE Pacific 2014-16 and impacted other whale populations. This indicates that the scoring method was an effective way to evaluate blue whale health and how they respond to a changing ocean.

Keywords: blue whale, body condition, environmental variability, photo-identification

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Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: Burcu Babadağ Savaş, Nihal Orlu, Güler Balcı Alparslan, Ertuğrul Çolak, Cengiz Korkmaz

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Introduction/objectives: We aimed to investigate the effect of humor on pain and state anxiety in patients with rheumatoid arthritis (RA) receiving biologic intravenous (IV) infusion therapy. Method: The study sample consisted of 36 patients who met the classification criteria for RA and inclusion criteria in a rheumatology outpatient clinic at a university hospital between September 2020 and November 2021. Two sample groups were formed: the intervention group (watching a comedy movie) (n=18) and the control group (n=18). The intervention group consisted of the patient watching a comedy movie of his/her choice from an archive created by the researchers during the biological IV infusion therapy (approximately 90-120 minutes). The data collection instruments used before and after the test were the descriptive identification form, the visual analog scale (VAS), and the state anxiety scale. Results: The mean VAS scores of patients in the intervention group were 5.05 ± 2.01 in the pre-test and 2.61 ± 1.91 in the post-test. The mean state anxiety scores of patients in the intervention group were 45.94 ± 9.97 in the pre-test and 34.22 ± 6.57 in the post-test. Thus, patients who watched comedy movies during biologic IV infusion therapy in the infusion center had a greater reduction in pain scores than the control group and the effect size was small. Although there was a decrease in state anxiety scores in both groups, there was no significant difference between groups and the effect size was not relevant. Conclusions: During IV infusion therapy, watching comedy movies is recommended as a nursing care intervention for reducing pain in patients with RA in cooperation with other health professionals.

Keywords: watching comedy movie, humor, pain, anxiety, nursing, care

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Authors: Muhammad Ghaffar Doggar, Farah

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The primary objective of this feasibility study is to conduct a techno-financial assessment for installation of biomass based power plant in Faisalabad division. The study involves identification of best site for power plant followed by an assessment of biomass resource potential in the area and propose power plant of suitable size. The study also entailed comprehensive supply chain analysis to determine biomass fuel pricing, transportation and storage. Further technical and financial analyses have been done for selection of appropriate technology for the power plant and its financial viability, respectively. The assessment of biomass resources and the subsequent technical analysis revealed that 20 MW biomass power plant could be implemented at one of the locations near Faisalabad city i.e. AARI Site, Near Chak Jhumra district Faisalabad, Punjab province. Three options for steam pressure; namely, 70 bar, 90 bar and 100 bar boilers have been considered. Using international experience and prices on power plant technology and local prices on locally available equipment, the study concludes biomass fuel price of around 50 US dollars (USD) per ton when delivered to power plant site. The electricity prices used for feasibility calculations were 0.13 USD per KWh for electricity from a locally financed project and 0.11 USD per KWh for internationally financed power plant. For local financing the most viable choice is the 70 bar solution and with international financing, the most feasible solution is using a 90 bar boiler. Between the two options, the internationally financed 90 bar boiler setup gives better financial results than the locally financed 70 bar boiler project. It has been concluded that 20 MW with 90 bar power plant and internationally financed would have an equity IRR of 23% and a payback period of 7 years. This will be a cheap option for installation of power plants.

Keywords: AARI, Ayub agriculture research institute, biomass - crops residue, KWh - electricity Units, MG - Muhammad Ghaffar

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Authors: A. Ghanbari Mardasi, N. Wu, C. Wu

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In this study, a spatial wavelet-based crack localization technique for a thick beam is presented. Wavelet scale in spatial wavelet transformation is optimized to enhance crack detection sensitivity. A windowing function is also employed to erase the edge effect of the wavelet transformation, which enables the method to detect and localize cracks near the beam/measurement boundaries. Theoretical model and vibration analysis considering the crack effect are first proposed and performed in MATLAB based on the Timoshenko beam model. Gabor wavelet family is applied to the beam vibration mode shapes derived from the theoretical beam model to magnify the crack effect so as to locate the crack. Relative wavelet coefficient is obtained for sensitivity analysis by comparing the coefficient values at different positions of the beam with the lowest value in the intact area of the beam. Afterward, the optimal wavelet scale corresponding to the highest relative wavelet coefficient at the crack position is obtained for each vibration mode, through numerical simulations. The same procedure is performed for cracks with different sizes and positions in order to find the optimal scale range for the Gabor wavelet family. Finally, Hanning window is applied to different vibration mode shapes in order to overcome the edge effect problem of wavelet transformation and its effect on the localization of crack close to the measurement boundaries. Comparison of the wavelet coefficients distribution of windowed and initial mode shapes demonstrates that window function eases the identification of the cracks close to the boundaries.

Keywords: edge effect, scale optimization, small crack locating, spatial wavelet

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Authors: Sayed Ahmed

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Religious activities that have evolved the sacred into a dynamic cultural phenomenon in the public realm of Sylhet, Bangladesh, and the spatiality of sacred sites and everyday practices in certain built forms have framed these phenomena. Religious rituals in Sylhet gave birth to unique practices of their own and have a vast impact even on contemporary spatial practices, while most Western researchers are not hopeful about the future of religion. However, despite extensive research on urban morphology and religion separately, there is limited literature on the relationship between these two topics to capture religious perceptions and experiences in urban spaces. This research will try to fill the existing gap and explain sacred within the range of Western sociological and philosophical tools implemented in third-world contexts, which was never highlighted before. This perspective of research puts forth the argument that urban morphology influences sacred experiences and how consecrated entities and religious activities shape the city's structure in return. The methodology of the research will map key morphological and religious variables. This mapping might include festival trajectories, street life observations, pedestrian densities, religious activities, public and private interface types with religious commodification, and the identification of blurred boundaries between sacred and profane on smaller to broader urban scales. To relate the derived cartography, illustrative (not representative) interviews about religious signs and symbols will be conducted and compared accordingly. The possible findings might reintroduce the diversity of religious practices in urban places and develop a decent concept of how sacred and urban morphology are mutually reinforcing the city, which has remained a vital nutrient for the survival of its inhabitants. Such infrequent conceptualizations of urban morphology and its relationship to symbolic sacralization are truly ‘outside’ to those that exist in the West.

Keywords: sylhet, religion, urban morphology, symbolic exchange, Baudrillard

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Authors: Juan Carlos Rubio Romero, Francico Salguero Caparros, Virginia Herrera-Pérez

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No one is in the slightest doubt about the high levels of risk involved in work in the construction industry. They are even higher in structural construction work. The Critical Decision Method (CDM) is a semi-structured interview technique that uses cognitive tests to identify the different disturbances that workers have to deal with in their work activity. At present, the vision of safety focused on daily performance and things that go well for safety and health management is facing the new paradigm known as Resilience Engineering. The aim of this study has been to describe the variability in formwork labour on concrete structures in the construction industry and, from there, to find out the resilient attitude of workers to unexpected events that they have experienced during their working lives. For this purpose, a series of semi-structured interviews were carried out with construction employees with extensive experience in formwork labour in Spain by applying the Critical Decision Method. This work has been the first application of the Critical Decision Method in the field of construction and, more specifically, in the execution of structures. The results obtained show that situations categorised as unthought-of are identified to a greater extent than potentially unexpected situations. The identification during these interviews of both expected and unexpected events provides insight into the critical decisions made and actions taken to improve resilience in daily practice in this construction work. From this study, it is clear that it is essential to gain more knowledge about the nature of the human cognitive process in work situations within complex socio-technical systems such as construction sites. This could lead to a more effective design of workplaces in the search for improved human performance.

Keywords: resilience engineering, construction industry, unthought-of situations, critical decision method

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Authors: Kumar Dron Shrivastav, Ankan Mukherjee Das, Arti Taneja, Harpreet Singh, Priya Ranjan, Rajiv Janardhanan

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Cervical cancer is one of the most common cancer among women worldwide which can be cured if detected early. Manual pathology which is typically utilized at present has many limitations. The current gold standard for cervical cancer diagnosis is exhaustive and time-consuming because it relies heavily on the subjective knowledge of the oncopathologists which leads to mis-diagnosis and missed diagnosis resulting false negative and false positive. To reduce time and complexities associated with early diagnosis, we require an interactive diagnostic tool for early detection particularly in developing countries where cervical cancer incidence and related mortality is high. Incorporation of digital pathology in place of manual pathology for cervical cancer screening and diagnosis can increase the precision and strongly reduce the chances of error in a time-specific manner. Thus, we propose a robust and interactive cervical cancer image analysis and diagnostic tool, which can categorically process both histopatholgical and cytopathological images to identify abnormal cells in the least amount of time and settings with minimum resources. Furthermore, incorporation of a set of specific parameters that are typically referred to for identification of abnormal cells with the help of open source software -’R’ is one of the major highlights of the tool. The software has the ability to automatically identify and quantify the morphological features, color intensity, sensitivity and other parameters digitally to differentiate abnormal from normal cells, which may improve and accelerate screening and early diagnosis, ultimately leading to timely treatment of cervical cancer.

Keywords: cervical cancer, early detection, digital Pathology, screening

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Authors: Sarono, Hamim Zaky Hadibasyir, dan Ridho Kurniawan

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Estimation of paddy production is one of the areas that can be examined using the techniques of remote sensing and geographic information systems (GIS) in the field of agriculture. The purpose of this research is to know the amount of the paddy production estimation and how remote sensing and geographic information systems (GIS) are able to perform analysis of paddy production estimation in Tegalallang and Payangan Sub district, Bali Province, Indonesia. The method used is the method of land suitability. This method associates a physical parameters which are to be embodied in the smallest unit of a mapping that represents a mapping unit in a particular field and connecting with its field productivity. Analysis of estimated production using standard land suitability from FAO using matching technique. The parameters used to create the land unit is slope (FAO), climate classification (Oldeman), landform (Prapto Suharsono), and soil type. Land use map consist of paddy and non paddy field information obtained from Geo-eye 1 imagery using visual interpretation technique. Landsat image of the Data used for the interpretation of the landform, the classification of the slopes obtained from high point identification with method of interpolation spline, whereas climate data, soil, use secondary data originating from institutions-related institutions. The results of this research indicate Tegallalang and Payangan Districts in known wetland suitability consists of S1 (very suitable) covering an area of 2884,7 ha with the productivity of 5 tons/ha and S2 (suitable) covering an area of 482,9 ha with the productivity of 3 tons/ha. The sum of paddy production estimation as a results in both districts are 31.744, 3 tons in one year.

Keywords: production estimation, paddy, remote sensing, geography information system, land suitability

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Authors: Arzyana Sunkar, Yanto Santosa

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The expansions of independent smallholdings in Indonesia are feared to increase the negative ecological impacts of oil palm plantation on biodiversity. Hence, research is required to identify the conservation importance of independent smallholder oil palm plantations on biodiversity. This paper discussed the role of independent smallholdings in the conservation of biodiversity in oil palm plantations and to compare it with High Conservation Value Forest as a conservation standard of RSPO. The research was conducted from March to April 2016. Data on biodiversity were collected on 16 plantations and 8 private oil palm plantations in the Districts of Kampar, Pelalawan, Kuantan, Singingi and Siak of Riau Province, Indonesia. In addition, data on community environmental perceptions of both smallholder plantation and High Conservation Value (HCV) Forest were also collected. Species that were observed were birds and earthworms. Data on birds were collected using transect method, while identification of earthworm was determine by taking some soil samples and counting the number of individual earthworm found for each worm species. The research used direct interview with oil palm owners and community members, as well as direct observation to examine the environmental conditions of each plantation. In general, field observation and measurement have found that birds species richness was higher in the forested HCV Forest. Nevertheless, if compared to non-forested HCV, bird’s species richness was higher in the independent smallholdings. On the other hand, different results were observed for earthworm, where the density was higher in the independent smallholdings than in the HCV. It can be concluded from this research that managing independent smallholder oil palm plantations and forested HCV forest could enhance biodiversity conservation. The results of this study justified the importance of retaining forested area to safeguard biodiversity in oil palm plantation.

Keywords: biodiversity conservation, high conservation value forest, independent smallholdings, oil palm plantations

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Authors: Thedy Yogasara, Fredy Agus

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In designing a product, it is currently crucial to focus not only on the product’s usability based on performance measures, but also on user experience (UX) that includes pragmatic and hedonic aspects of product use. These aspects play a significant role in fulfillment of user needs, both functionally and psychologically. Pragmatic quality refers to as product’s perceived ability to support the fulfillment of behavioral goals. It is closely linked to functionality and usability of the product. In contrast, hedonic quality is product’s perceived ability to support the fulfillment of psychological needs. Hedonic quality relates to the pleasure of ownership and use of the product, including stimulation for personal development and communication of user’s identity to others through the product. This study evaluates the pragmatic and hedonic aspects of gaming mice G600 and Razer Krait using AttrakDiff tool to create an improved design that is able to generate positive UX. AttrakDiff is a method that measures pragmatic and hedonic scores of a product with a scale between -3 to +3 through four attributes (i.e. Pragmatic Quality, Hedonic Quality-Identification, Hedonic Quality-Stimulation, and Attractiveness), represented by 28 pairs of opposite words. Based on data gathered from 15 participants, it is identified that gaming mouse G600 needs to be redesigned because of its low grades (pragmatic score: -0.838, hedonic score: 1, attractiveness score: 0.771). The redesign process focuses on the attributes with poor scores and takes into account improvement suggestions collected from interview with the participants. The redesigned mouse G600 is evaluated using the previous method. The result shows higher scores in pragmatic quality (1.929), hedonic quality (1.703), and attractiveness (1.667), indicating that the redesigned mouse is more capable of creating pleasurable experience of product use.

Keywords: AttrakDiff, hedonic aspect, pragmatic aspect, product design, user experience

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Authors: Annet Namusoke, Annet Namayanja, Peter Wasswa, Shakirah Nampijja

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Common bean cultivar G2333 which offers broad resistance for anthracnose has been widely used as a source of resistance in breeding for anthracnose resistance. The cultivar is pyramided with three genes namely CO-4, CO-5 and CO-7 and of these three genes, the CO-4 gene has been found to offer the broadest resistance. The main aim of this work was to identify and validate easily assayable PCR based co-dominant molecular markers for selection of the CO-4 gene in segregating populations derived from crosses of G2333 with RWR 1946 and RWR 2075, two commercial Andean cultivars highly susceptible to anthracnose. Marker sequences for the study were obtained by blasting the sequence of the COK-4 gene in the Phaseolus gene database. Primer sequence pairs that were not provided from the Phaseolus gene database were designed by the use of Primer3 software. PCR conditions were optimized and the PCR products were run on 6% HPAGE gel. Results of the polymorphism test indicated that out of 18 identified markers, only two markers namely BM588 and BM211 behaved co-dominantly. Phenotypic evaluation for reaction to anthracnose disease was done by inoculating 21days old seedlings of three parents, F1 and F2 populations with race 7 of Colletotrichum lindemuthianum in the humid chamber. DNA testing of the BM588 marker onto the F2 segregating population of the crosses RWR 1946 x G 2333 and RWR 2075 x G2333 further revealed that the marker BM588 co-segregated with disease resistance with co-dominance of two alleles of 200bp and 400bp, fitting the expected segregation ratio of 1:2:1. The BM588 marker was significantly associated with disease resistance and gave promising results for marker assisted selection of the CO-4 gene in the breeding lines. Activities to validate the BM211 marker are also underway.

Keywords: codominant, Colletotrichum lindemuthianum, MAS, Phaseolus vulgaris

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Authors: Michael Lousis

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The systematic identification of the most conspicuous and significant errors made by learners during three-years of testing of their progress in learning Arithmetic throughout the development of the Kassel Project in England and Greece was accomplished. How much retentive these errors were over three-years in the officially provided school instruction of Arithmetic in these countries has also been shown. The learners’ errors in Arithmetic stemmed from a sample, which was comprised of two hundred (200) English students and one hundred and fifty (150) Greek students. The sample was purposefully selected according to the students’ participation in each testing session in the development of the three-year project, in both domains simultaneously in Arithmetic and Algebra. Specific teaching practices have been invented and are presented in this study for subverting these learners’ errors, which were found out to be retentive to the level of the nationally provided mathematical education of each country. The invention and the development of these proposed teaching practices were founded on the rationality of the theoretical accounts concerning the explanation, prediction and control of the errors, on the conceptual metaphor and on an analysis, which tried to identify the required cognitive components and skills of the specific tasks, in terms of Psychology and Cognitive Science as applied to information-processing. The aim of the implementation of these instructional practices is not only the subversion of these errors but the achievement of the mathematical competence, as this was defined to be constituted of three elements: appropriate representations - appropriate meaning - appropriately developed schemata. However, praxis is of paramount importance, because there is no independent of science ‘real-truth’ and because praxis serves as quality control when it takes the form of a cognitive method.

Keywords: arithmetic, cognitive science, cognitive psychology, information-processing paradigm, Kassel project, level of the nationally provided mathematical education, praxis, remedial mathematical teaching practices, retentiveness of errors

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Authors: Fatemeh Babaeian, Nemai Chandra Karmakar

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Chipless RFID system is a wireless system for tracking and identification which use passive tags for encoding data. The advantage of using chipless RFID tag is having a planar tag which is printable on different low-cost materials like paper and plastic. The printed tag can be attached to different items in the labelling level. Since the price of chipless RFID tag can be as low as a fraction of a cent, this technology has the potential to compete with the conventional optical barcode labels. However, due to the passive structure of the tag, data processing of the reflection signal is a crucial challenge. The captured reflected signal from a tag attached to an item consists of different components which are the reflection from the reader antenna, the reflection from the item, the tag structural mode RCS component and the antenna mode RCS of the tag. All these components are summed up in both time and frequency domains. The effect of reflection from the item and the structural mode RCS component can distort/saturate the frequency domain signal and cause difficulties in extracting the desired component which is the antenna mode RCS. Therefore, it is required to study the reflection of the tag in both time and frequency domains to have a better understanding of the nature of the captured chipless RFID signal. The other benefits of this study can be to find an optimised encoding technique in tag design level and to find the best processing algorithm the chipless RFID signal in decoding level. In this paper, the reflection from a typical backscattered chipless RFID tag with six resonances is analysed, and different components of the signal are separated in both time and frequency domains. Moreover, the time domain signal corresponding to each resonator of the tag is studied. The data for this processing was captured from simulation in CST Microwave Studio 2017. The outcome of this study is understanding different components of a measured signal in a chipless RFID system and a discovering a research gap which is a need to find an optimum detection algorithm for tag ID extraction.

Keywords: antenna mode RCS, chipless RFID tag, resonance, structural mode RCS

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Authors: Diane Ghanem, Whitney Kagabo, Rebecca Engels, Uma Srikumaran, Babar Shafiq

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Hospitalist co-management of orthopaedic surgery patients is a growing trend across the country. It was created as a collaborative effort to provide overarching care to patients with the goal of improving their postoperative care and decreasing in-hospital medical complications. The aim of this project is to provide a guide for implementing and optimizing a hospitalist co-management service in orthopaedic surgery. Key leaders from the hospitalist team, orthopaedic team and quality, safety and service team were identified. Multiple meetings were convened to discuss the comanagement service and determine the necessary building blocks behind an efficient and well-designed co-management framework. After meticulous deliberation, a consensus was reached on the final service agreement and a written guide was drafted. Fundamental features of the service include the identification of service stakeholders and leaders, frequent consensus meetings, a well-defined framework, with goals, program metrics and unified commands, and a regular satisfaction assessment to update and improve the program. Identified pearls for co-managing orthopaedic surgery patients are standardization, timing, adequate patient selection, and two-way feedback between hospitalists and orthopaedic surgeons to optimize the protocols. Developing a service agreement is a constant work in progress, with meetings, discussions, revisions, and multiple piloting attempts before implementation. It is a partnership created to provide hospitals with a streamlined admission process where at-risk patients are identified early, and patient care is optimized regardless of the number or nature of medical comorbidities. A wellestablished hospitalist co-management service can increase patient care quality and safety, as well as health care value.

Keywords: co-management, hospitalist co-management, implementation, orthopaedic surgery, quality improvement

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Authors: Hritik Bhattarai, Vivek Dumre, Ananya Neupane, Poonam Koirala, Anjali Singh

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The availability of clean and reliable groundwater is essential for the sustainment of human and environmental health. Groundwater is a crucial resource that contributes significantly to the total annual supply. However, over-exploitation has depleted groundwater availability considerably and led to some land subsidence. Determining the potential zone of groundwater is vital for protecting water quality and managing groundwater systems. Groundwater potential zones are marked with the assistance of Geographic Information System techniques. During the study, a standard methodology was proposed to determine groundwater potential using an integration of GIS and AHP techniques. When choosing the prospective groundwater zone, accurate information was generated to get parameters such as geology, slope, soil, temperature, rainfall, drainage density, and lineament density. However, identifying and mapping potential groundwater zones remains challenging due to aquifer systems' complex and dynamic nature. Then, ArcGIS was incorporated with a weighted overlay, and appropriate ranks were assigned to each parameter group. Through data analysis, MCDA was applied to weigh and prioritize the different parameters based on their relative impact on groundwater potential. There were three probable groundwater zones: low potential, moderate potential, and high potential. Our analysis showed that the central and lower parts of the Bagmati River Basin have the highest potential, i.e., 7.20% of the total area. In contrast, the northern and eastern parts have lower potential. The identified potential zones can be used to guide future groundwater exploration and management strategies in the region.

Keywords: groundwater, geographic information system, analytic hierarchy processes, multi-criteria decision analysis, Bagmati

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Authors: Sigal Barkai

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'Ironic Historiography' is a hybrid notion combining criticism of historical narratives concerning the Israeli state with ironic artistic expression. The paper will deal with questions of identities of native Israeli visual artists who chose to live out of the country, or to move back and forth to and from it. It will examine the ways these wanderings are reflected in their work. The paper discusses the work of 4 contemporary artists who produce artworks in diverse techniques and media, such as video, performance and installation art. Yael Bartana, Erez Israeli and Tamir Zadok are artists who constantly deal with Israeli nationality and history in their artwork, using ironic components. In comparison, the paper will review the works of Mika Rottenberg, who is now a New York based artist. She is concerned with global social issues and neglected specific national identity altogether. All of them use visual irony as a means of reflecting and criticizing society. The analysis was done in awareness of the life stories of the artists, in an attempt to trace the ways they establish their identities through their art. It was pre-supposed that these identities will be shaped in the in-between space of being an Israeli citizen and a citizen of the world. The study asks how ironic expression appears in their work, what kind of irony do they use and in what ways does it serves them. The methodology combined visual analysis, interviews with the artists, and analyzation of secondary discourses in the media. As theoretical background various fields of knowledge were used, such as literature and language studies, Sociology, and Visual Culture studies. The findings point out that visual and artistic irony has many different goals in the use of historiographic fiction. It can bind an artist to his homeland and native society, or it can help her to detach. It helps healing breaches in the in-between space, or it can be used as a means to completely detach from any identification with a native origin.

Keywords: visual art, irony, identities, Israel

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Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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