Search results for: genome rearrangement distance

Authors: Patrick M. Stanton, William R. McCumber

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Using a large dataset of more than 2,400 individual microfinance institutions (MFIs) from 120 countries from 1999 to 2016, this study finds that nearly half of the international MFIs operate as for-profit institutions. Formal institutions (business regulatory environment, property rights, social protection, and a developed financial sector) impact the likelihood of MFIs being for-profit across countries. Cultural differences across countries (power distance, individualism, masculinity, and indulgence) seem to be a factor in the legal status of the MFI (non-profit or for-profit). MFIs in countries with stronger formal institutions, a greater degree of power distance, and a higher degree of collectivism experience better financial and social performance.

Keywords: Hofstede cultural dimensions, international finance, microfinance institutions, non-profite

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Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: E. Batista, R. Mendes, A. Furtado, M. C. Ferreira, I. Godinho, J. A. Sousa, M. Alvares, R. Martins

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Syringe pumps are commonly used for drug delivery in hospitals and clinical environments. These instruments are critical in neonatology and oncology, where any variation in the flow rate and drug dosing quantity can lead to severe incidents and even death of the patient. Therefore it is very important to determine the accuracy and precision of these devices using the suitable calibration methods. The Volume Laboratory of the Portuguese Institute for Quality (LVC/IPQ) uses two different methods to calibrate syringe pumps from 16 nL/min up to 20 mL/min. The Interferometric method uses an interferometer to monitor the distance travelled by a pusher block of the syringe pump in order to determine the flow rate. Therefore, knowing the internal diameter of the syringe with very high precision, the travelled distance, and the time needed for that travelled distance, it was possible to calculate the flow rate of the fluid inside the syringe and its uncertainty. As an alternative to the gravimetric and the interferometric method, a methodology based on the application of optical technology was also developed to measure flow rates. Mainly this method relies on measuring the increase of volume of a drop over time. The objective of this work is to compare the results of the calibration of two syringe pumps using the different methodologies described above. The obtained results were consistent for the three methods used. The uncertainties values were very similar for all the three methods, being higher for the optical drop method due to setup limitations.

Keywords: calibration, flow, interferometry, syringe pump, uncertainty

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Authors: Deepti Kumari, Upamanyu Hore

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Cities are an example of a human-modified environment with few fragments of urban green spaces, which are widely considered for urban biodiversity. The study aims to address the avifaunal diversity in urban parks based on the park size and their urbanization intensity. Also, understanding the key factors affecting species composition and structure as birds are a good indicator of a healthy ecosystem, and they are sensitive to changes in the environment. A 50 m-long line-transect method is used to survey birds in 39 urban parks in Delhi, India. Habitat variables, including vegetation (percentage of non-native trees, percentage of native trees, top canopy cover, sub-canopy cover, diameter at breast height, ground vegetation cover, shrub height) were measured using the quadrat method along the transect, and disturbance variables (distance from water, distance from road, distance from settlement, park area, visitor rate, and urbanization intensity) were measured using ArcGIS and google earth. We analyzed species data for diversity and richness. We explored the relation of species diversity and richness to habitat variables using the multi-model inference approach. Diversity and richness are found significant in different park sizes and their urbanization intensity. Medium size park supports more diversity, whereas large size park has more richness. However, diversity and richness both declined with increasing urbanization intensity. The result of CCA revealed that species composition in urban parks was positively associated with tree diameter at breast height and distance from the settlement. On the model selection approach, disturbance variables, especially distance from road, urbanization intensity, and visitors are the best predictors for the species richness of birds in urban parks. In comparison, multiple regression analysis between habitat variables and bird diversity suggested that native tree species in the park may explain the diversity pattern of birds in urban parks. Feeding guilds such as insectivores, omnivores, carnivores, granivores, and frugivores showed a significant relation with vegetation variables, while carnivores and scavenger bird species mainly responded with disturbance variables. The study highlights the importance of park size in urban areas and their urbanization intensity. It also indicates that distance from the settlement, distance from the road, urbanization intensity, visitors, diameter at breast height, and native tree species can be important determining factors for bird richness and diversity in urban parks. The study also concludes that the response of feeding guilds to vegetation and disturbance in urban parks varies. Therefore, we recommend that park size and surrounding urban matrix should be considered in order to increase bird diversity and richness in urban areas for designing and planning.

Keywords: diversity, feeding guild, urban park, urbanization intensity

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Authors: Tzu-Jung Tseng, Pei-Hsuen Han, Tsung-Hsueh Lu

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Background: Ensuring patients with ST-elevation myocardial infarction (STEMI) access to hospitals that could perform percutaneous coronary intervention (PCI) in time is an important concern of healthcare managers. One commonly used the method to assess the coverage of population access to PCI hospital is the use GIS-estimated linear distance (crow's fly distance) between the district centroid and the nearest PCI hospital. If the distance is within a given distance (such as 20 km), the entire population of that district is considered to have appropriate access to PCI. The premise of using district centroid to estimate the coverage of population resident in that district is that the people live in the district are evenly distributed. In reality, the population density is not evenly distributed within the administrative district, especially in rural districts. Fortunately, the Taiwan government released basic statistical area (on average 450 population within the area) recently, which provide us an opportunity to estimate the coverage of population access to PCI services more accurate. Objectives: We aimed in this study to compare the population covered by a give PCI hospital according to traditional administrative district versus basic statistical area. We further examined if the differences between two geographic units used would be larger in a rural area than in urban area. Method: We selected two hospitals in Tainan City for this analysis. Hospital A is in urban area, hospital B is in rural area. The population in each traditional administrative district and basic statistical area are obtained from Taiwan National Geographic Information System, Ministry of Internal Affairs. Results: Estimated population live within 20 km of hospital A and B was 1,515,846 and 323,472 according to traditional administrative district and was 1,506,325 and 428,556 according to basic statistical area. Conclusion: In urban area, the estimated access population to PCI services was similar between two geographic units. However, in rural areas, the access population would be overestimated.

Keywords: accessibility, basic statistical area, modifiable areal unit problem (MAUP), percutaneous coronary intervention (PCI)

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Authors: E. J. Spamer, J. M. Van Zyl, MHA Combrinck

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The Unit for Open Distance Learning (UODL) at the North-West University (NWU), South Africa was established in 2013 with its main function to deliver open distance learning (ODL) programmes to approximately 30 000 students from the Faculties of Education Sciences, Health Sciences, Theology and Arts and Culture. Quality operational and administrative processes are key components in the delivery of these programmes and they need to function optimally for students to be successful in their studies. Operational and administrative processes include aspects such as applications, registration, dissemination of study material, availability of electronic platforms, the management of assessment, and the dissemination of important information. To be able to ensure and enhance quality during these processes, it is vital to determine students’ perceptions with regards to these mentioned processes. A questionnaire was available online and also distributed to the 63 tuition centres. The purpose of this research was to determine the perceptions of ODL students from NWU regarding operational and administrative processes. 1903 students completed and submitted the questionnaire. The data was quantitatively analysed and discussed. Results indicated that the majority of students are satisfied with the operational and administrative processes; however, the results also indicated some areas that need improvement. The data gathered is important to identify strengths and areas for improvement and form part of a bigger strategy of qualitative assurance at the UODL.

Keywords: administrative support, ODL programmes, quantitative study, students' perceptions

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Authors: Yan Rongxin, Sun Wei, Li Weidan

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Based on the acoustics cascade sound theory, the mechanism of air leak sound producing, transmitting and signal detecting has been analyzed. A formula of the sound power, leak size and air pressure in the spacecraft has been built, and the relationship between leak sound pressure and receiving direction and distance has been studied. The center frequency in millimeter diameter leak is more than 20 kHz. The situation of air leaking from spacecraft to space has been simulated and an experiment of different leak size and testing distance and direction has been done. The sound pressure is in direct proportion to the cosine of the angle of leak to sensor. The portable ultrasonic leak detector has been developed, whose minimal leak rate is 10^-1 Pa·m³/s, the testing radius is longer than 20 mm, the mass is less than 1.0 kg, and the electric power is less than 2.2 W.

Keywords: leak testing, manned spacecraft, sound transmitting, ultrasonic

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Authors: Kaowen Grace Chang

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Urban green spaces play an important role in promoting wellbeing through the sense of relaxation for urban residents. Among many designing factors, what the principal ones that could effectively influence people’s sense of relaxation? And, what are the relationship between the sense of relaxation and those factors? Regarding those questions, there is still little evidence for sufficient support. Therefore, the purpose of this study, based on individual responses to environmental information, is to investigate the landscape factors that relate to well-being through the sense of relaxation in mixed-use urban environments. We conducted the experimental design and model construction utilizing choice-based conjoint analysis to test the factors of plant arrangement pattern, plant trimming condition, the distance to visible automobile, the number of landmark objects, and the depth of view. Through the operation of balanced fractional orthogonal design, the goal is to know the relationship between the sense of relaxation and different designs. In a result, the three factors of plant trimming condition, the distance to visible automobile, and the depth of view shed are significantly effective to the sense of relaxation. The stronger magnitude of maintenance and trimming, the further distance to visible automobiles, and deeper view shed that allow the users to see further scenes could significantly promote green space users’ sense of relaxation in urban green spaces.

Keywords: urban green space, landscape planning and design, sense of relaxation, choice model

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Authors: Guorong Sui, Xingwei Jia, Fei Tong, Xiumin Gao

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Camera calibration is a fundamental issue of high precision noncontact measurement. And it is necessary to analyze and study the reliability and application range of its linear model which is often used in the camera calibration. According to the imaging features of monocular cameras, a camera model which is based on the image pixel coordinates and three dimensional space coordinates is built. Using our own customized template, the image pixel coordinate is obtained by the subpixel corner detection method. Without considering the aberration of the optical system, the feature extraction and linearity analysis of the line segment in the template are performed. Moreover, the experiment is repeated 11 times by constantly varying the measuring distance. At last, the linearity of the camera is achieved by fitting 11 groups of data. The camera model measurement results show that the relative error does not exceed 1%, and the repeated measurement error is not more than 0.1 mm magnitude. Meanwhile, it is found that the model has some measurement differences in the different region and object distance. The experiment results show this linear model is simple and practical, and have good linearity within a certain object distance. These experiment results provide a powerful basis for establishment of the linear model of camera. These works will have potential value to the actual engineering measurement.

Keywords: camera linear model, geometric imaging relationship, image pixel coordinates, three dimensional space coordinates, sub-pixel corner detection

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Authors: Nemat Sokhandan Bashir

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Threats from viruses to agricultural crops could be even larger than the losses caused by the other pathogens because, in many cases, the viral infection is latent but crucial from an epidemic point of view. Wild vegetation can be a source of many viruses that eventually find their destiny in crop plants. Although often asymptomatic in wild plants due to adaptation, they can potentially cause serious losses in crops. Therefore, exploring viruses in wild vegetation is very important. Recently, omics have been quite useful for exploring plant viruses from various plant sources, especially wild vegetation. For instance, we have discovered viruses such as Ambrossia asymptomatic virus I (AAV-1) through the application of metagenomics from Oklahoma Prairie Reserve. Accordingly, extracts from randomly-sampled plants are subjected to high speed and ultracentrifugation to separated virus-like particles (VLP), then nucleic acids in the form of DNA or RNA are extracted from such VLPs by treatment with phenol—chloroform and subsequent precipitation by ethanol. The nucleic acid preparations are separately treated with RNAse or DNAse in order to determine the genome component of VLPs. In the case of RNAs, the complementary cDNAs are synthesized before submitting to DNA sequencing. However, for VLPs with DNA contents, the procedure would be relatively straightforward without making cDNA. Because the length of the nucleic acid content of VPLs can be different, various strategies are employed to achieve sequencing. Techniques similar to so-called "chromosome walking" may be used to achieve sequences of long segments. When the nucleotide sequence data were obtained, they were subjected to BLAST analysis to determine the most related previously reported virus sequences. In one case, we determined that the novel virus was AAV-l because the sequence comparison and analysis revealed that the reads were the closest to the Indian citrus ringspot virus (ICRSV). AAV—l had an RNA genome with 7408 nucleotides in length and contained six open reading frames (ORFs). Based on phylogenies inferred from the replicase and coat protein ORFs of the virus, it was placed in the genus Mandarivirus.

Keywords: wild, plant, novel, metagenomics

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Authors: Jagdeep Nayak, Biswajit Paul, Anup Gupta

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Characterization of coal refuses to fly ash, and steel slag from steel industries have been performed to develop a mixture of both these materials to enhance strength properties of their utilization in other sectors like mine fill, construction work, etc. A large amount of Linz-Donawitz (LD) slag and fly ash waste are generated from steel and thermal power industries respectively. Management of these wastes is problematic, and their reutilization may provide a sustainable waste management option. LD slag and fly ash mixed in different proportions were tested to analyse the micro structural improvement and hardening rate of the matrix. Mixing of activators such as sodium hydroxide and potassium silicate with silica-alumina of LD slag-fly ash mixture, geopolymeric structure were found to be developed. The effect of geo-polymerization behaviour and subsequent structural rearrangement has been studied using compressibility; shear strength and permeability tests followed by micro-graphical analysis. Densification in the mixture was observed along with an improvement of geotechnical properties due to the addition of LD slag. Due to suitable strength characteristics of these two waste materials as mixture, it can be used in the various construction field or may be used as a filling material in mine voids.

Keywords: LD slag, fly-ash, geopolymer, strength property, compressibility

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Authors: Bola M. Tunde-Awe

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The study investigated the influence of teacher’s non-verbal communication on secondary school students’ learning outcomes in English language. The study was a survey research. Participants were three hundred Senior Secondary School II students randomly selected from ten schools in Akoko South West Local Government Area of Ondo State, Nigeria. The instrument used for data collection was a questionnaire containing twenty items on a four-point Likert scale which measured teacher’s use of three types of non-verbal communication modes: body movement, eye contact and spatial distance. The data collected was analysed using simple percentage. Findings revealed that teacher’s use of these non-verbal communication modes enhanced learners’ learning outcomes in English language: a total of 271 (90.33%) participants affirmed that teacher’s body language influenced their learning of English; 224 (74.66%) maintained the same stand for eye contact; while 202 (67.33%) affirmed that teacher’s spatial distance had positive influence. Consequent upon these findings, it was recommended that teachers of English language should constantly utilize non-verbal communication in their instructional delivery. Also, non-verbal communication modes should be included in teacher education programme to equip prospective pre-service teachers with the art of non-verbal communication.

Keywords: non-verbal communication, body language, eye contact, spatial distance, learning outcomes

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Authors: M. Al Azri, M. Elzain, K. Bouziane, S. M. Chérif

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The electronic and magnetic properties of 6H-SiC with Mn impurities have been calculated using ab-initio calculations. Various configurations of Mn sites and Si and C vacancies were considered. The magnetic coupling between the two Mn atoms at substitutional and interstitials sites with and without vacancies is studied as a function of Mn atoms interatomic distance. It was found that the magnetic interaction energy decreases with increasing distance between the magnetic atoms. The energy levels appearing in the band gap due to vacancies and due to Mn impurities are determined. The calculated DOS’s are used to analyze the nature of the exchange interaction between the impurities. The band coupling model based on the p-d and d-d level repulsions between Mn and SiC has been used to describe the magnetism observed in each configuration. Furthermore, the impacts of applying U to Mn-d orbital on the magnetic moment have also been investigated. The results are used to understand the experimental data obtained on Mn- 6H-SiC (as-implanted and as –annealed) for various Mn concentration (CMn = 0.7%, 1.6%, 7%).

Keywords: ab-initio calculations, diluted magnetic semiconductors, magnetic properties, silicon carbide

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Authors: N. Thawornwisit, P. Pradoo, S. Nuypree, L. Jarukasetrporn, S. Jitpukdeebodintra

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Objective: The aim of this study was to evaluate the duration of the Enterococcus faecalis (E. faecalis) penetration into the gap between root canal wall and filling material at a 3 to 6 mm distance from the cementoenamel junction (CEJ) in the dislodged temporary filling, in vitro. Material and methods: Thirty-four single root canal mandibular premolars were divided into two experimental groups (N = 15) and one negative control (N = 4). Root canals were prepared and obturated with gutta-percha using lateral condensation technique, X-ray checked, and sterilized. Leakages were set up using the modified bacterial leakage model, and E. faecalis was used as a microbial marker. Leakages were evaluated at 3 and 7 days by culturing gutta-percha and dentine drilled from a 3-6 mm distance from CEJ. Broth turbidity was recorded and compared. Result: All four negative control and the 3-day experimental group showed no broth turbidity. For the 7-day experimental group, there was 33.3% leakage. Conclusion: Penetration of E. faecalis into the gap between root canal wall and filling material at a 3 to 6 mm distance from CEJ in the dislodged temporary filling were not found at three days. However, at seven days of exposure, bacteria could penetrate into the interface of the root canal and filling materials.

Keywords: coronal leakage, bacterial leakage model, enterococcus faecalis

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Authors: Sancho-Esper Franco, Rodríguez Sánchez Carla, Sánchez Carolina, Orús-Sanclemente Carlos

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Water scarcity is a reality that affects many regions of the world and is aggravated by climate change and population growth. Saving water has become an urgent need to ensure the sustainability of the planet and the survival of many communities, where youth and social networks play a key role in promoting responsible practices and adopting habits that contribute to environmental preservation. This study analyzes the persuasion capacity of messages designed to promote pro-environmental behaviors among youth. Specifically, it studies how the efficacy (effectiveness) of the response (personal response efficacy/effectiveness) and the perception of distance from the source of the message influence the water-saving behavior of the audience. To do so, two communication frameworks are combined. First, the Construal Level Theory, which is based on the concept of "psychological distance", that is, people, objects or events can be perceived as psychologically near or far, and this subjective distance (i.e., social, temporal, or spatial) determines their attitudes, emotions, and actions. This perceived distance can be social, temporal, or spatial. This research focuses on studying the spatial distance and social distance generated by cultural differences between influencers and their audience to understand how cultural distance can influence the persuasiveness of a message. Research on the effects of psychological distance between influencers-followers in the pro-environmental field is very limited, being relevant because people could learn specific behaviors suggested by opinion leaders such as influencers in social networks. Second, different approaches to behavioral change suggest that the perceived efficacy of a behavior can explain individual pro-environmental actions. People will be more likely to adopt a new behavior if they perceive that they are capable of performing it (efficacy belief) and that their behavior will effectively contribute to solving that problem (personal response efficacy). It is also important to study the different actors (social and individual) that are perceived as responsible for addressing environmental problems. Specifically, we analyze to what extent the belief individual’s water-saving actions are effective in solving the problem can influence water-saving behavior since this individual effectiveness increases people's sense of obligation and responsibility with the problem. However, in this regard, empirical evidence presents mixed results. Our study addresses the call for experimental studies manipulating different subtypes of response effectiveness to generate robust causal evidence. Based on all the above, this research analyzes whether cultural distance (local vs. international influencer) and the perception of effectiveness of behavior (personal response efficacy) (personal/individual vs. collective) affect the actual behavior and the intention to conserve water of social network users. An experiment of 2 (local influencer vs. international influencer) x 2 (effectiveness of individual vs. collective response) is designed and estimated. The results show that a message from a local influencer appealing to individual responsibility exerts greater influence on intention and actual water-saving behavior, given the cultural closeness between influencer-follower, and the appeal to individual responsibility increases the feeling of obligation to participate in pro-environmental actions. These results offer important implications for social marketing campaigns that seek to promote water conservation.

Keywords: social marketing, influencer, message framing, experiment, personal response efficacy, water saving

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Authors: Tomokazu Shirai, Akihiko Kondo

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Technologies of metabolic engineering or synthetic biology are essential for effective microbial bioproduction. It is especially important to develop an in silico tool for designing a metabolic pathway producing an unnatural and valuable chemical such as fossil materials of fuel or plastics. We here demonstrated two in silico tools for designing novel metabolic pathways: BioProV and HyMeP. Furthermore, we succeeded in creating an artificial metabolic pathway by enzyme engineering.

Keywords: bioinformatics, metabolic engineering, synthetic biology, genome scale model

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Authors: Bamidele Samson Alobalorun, Ifedotun Roseline Idowu

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Biometrics technologies apply the human body parts for their unique and reliable identification based on physiological traits. The iris recognition system is a biometric–based method for identification. The human iris has some discriminating characteristics which provide efficiency to the method. In order to achieve this efficiency, there is a need for feature extraction of the distinct features from the human iris in order to generate accurate authentication of persons. In this study, an approach for an iris recognition system using 2D Gabor for feature extraction is applied to iris templates. The 2D Gabor filter formulated the patterns that were used for training and equally sent to the hamming distance matching technique for recognition. A comparison of results is presented using two iris image subjects of different matching indices of 1,2,3,4,5 filter based on the CASIA iris image database. By comparing the two subject results, the actual computational time of the developed models, which is measured in terms of training and average testing time in processing the hamming distance classifier, is found with best recognition accuracy of 96.11% after capturing the iris localization or segmentation using the Daughman’s Integro-differential, the normalization is confined to the Daugman’s rubber sheet model.

Keywords: Daugman rubber sheet, feature extraction, Hamming distance, iris recognition system, 2D Gabor wavelet transform

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Authors: Shagufta Jabeen, Faez Jesse Firdaus Abdullah, Zunita Zakaria, Nurulfiza Mat Isa, Yung Chie Tan, Wai Yan Yee, Abdul Rahman Omar

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Pasteurella multocida is associated with acute, as well as, chronic infections in avian and bovine such as pasteurellosis and hemorrhagic septicemia (HS) in cattle and buffaloes. Iron is one of the most important nutrients for pathogenic bacteria including Pasteurella and acts as a cofactor or prosthetic group in several essential enzymes and is needed for amino acid, pyrimidine, and DNA biosynthesis. In our recent study, we showed that 2% of Pasteurella multocida serotype A strain PMTB2.1 encode for iron regulating genes (Accession number CP007205.1). Genome sequencing of other Pasteurella multocida serotypes namely PM70 and HB01 also indicated up to 2.5% of the respective genome encode for iron regulating genes, suggesting that Pasteurella multocida genome comprises of multiple systems for iron uptake. Since P. multocida PMTB2.1 has more than 40 CDs out of 2097 CDs (approximately 2%), encode for iron-regulated. The gene expression profiling of four iron-regulating genes namely fbpb, yfea, fece and fur were characterized under iron-restricted environment. The P. multocida strain PMTB2.1 was grown in broth with and without iron chelating agent and samples were collected at different time points. Relative mRNA expression profile of these genes was determined using Taqman probe based real-time PCR assay. The data analysis, normalization with two house-keeping genes and the quantification of fold changes were carried out using Bio-Rad CFX manager software version 3.1. Results of this study reflect that iron reduced environment has significant effect on expression profile of iron regulating genes (p < 0.05) when compared to control (normal broth) and all evaluated genes act differently with response to iron reduction in media. The highest relative fold change of fece gene was observed at early stage of treatment indicating that PMTB2.1 may utilize its periplasmic protein at early stage to acquire iron. Furthermore, down-regulation expression of fece with the elevated expression of other genes at later time points suggests that PMTB2.1 control their iron requirements in response to iron availability by down-regulating the expression of iron proteins. Moreover, significantly high relative fold change (p ≤ 0.05) of fbpb gene is probably associated with the ability of P. multocida to directly use host iron complex such as hem, hemoglobin. In addition, the significant increase (p ≤ 0.05) in fbpb and yfea expressions also reflects the utilization of multiple iron systems in P. multocida strain PMTB2.1. The findings of this study are very much important as relative scarcity of free iron within hosts creates a major barrier to microbial growth inside host and utilization of outer-membrane proteins system in iron acquisition probably occurred at early stage of infection with P. multocida. In conclusion, the presence and utilization of multiple iron system in P. multocida strain PMTB2.1 revealed the importance of iron in the survival of P. multocida.

Keywords: iron-related genes, real-time PCR, gene expression profiling, fold changes

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Authors: Faheem Shahzad Baloch, Muhammad Azhar Nadeem, Muhammad Amjad Nawaz, Ephrem Habyarimana, Gonul Comertpay, Tolga Karakoy, Rustu Hatipoglu, Mehmet Zahit Yeken, Vahdettin Ciftci

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Turkey is considered a bridge between Europe, Asia, and Africa and possibly played an important role in the distribution of many crops including common bean. Hundreds of common bean landraces can be found in Turkey, particularly in farmers’ fields, and they consistently contribute to the overall production. To investigate the existing genetic diversity and hybridization events between the Andean and Mesoamerican gene pools in the Turkish common bean, 188 common bean accessions (182 landraces and 6 modern cultivars as controls) were collected from 19 different Turkish geographic regions. These accessions were characterized using phenotypic data (growth habit and seed weight), geographic provenance, 12557 high-quality whole-genome DArTseq markers, and 3767 novel DArTseq loci were also identified. The clustering algorithms resolved the Turkish common bean landrace germplasm into the two recognized gene pools, the Mesoamerican and Andean gene pools. Hybridization events were observed in both gene pools (14.36% of the accessions) but mostly in the Mesoamerican (7.97% of the accessions), and was low relative to previous European studies. The lower level of hybridization witnessed the existence of Turkish common bean germplasm in its original form as compared to Europe. Mesoamerican gene pool reflected a higher level of diversity, while the Andean gene pool was predominant (56.91% of the accessions), but genetically less diverse and phenotypically more pure, reflecting farmers greater preference for the Andean gene pool. We also found some genetically distinct landraces and overall, a meaningful level of genetic variability which can be used by the scientific community in breeding efforts to develop superior common bean strains.

Keywords: bean germplasm, DArTseq markers, genotyping by sequencing, Turkey, whole genome diversity

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Authors: Bikis Muhammed, Sehra Sedigh Sarvestani, Ali R. Hurson, Lasanthi Gamage

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Vehicular traffic events have overly complex spatial correlations and temporal interdependencies and are also influenced by environmental events such as weather conditions. To capture these spatial and temporal interdependencies and make more realistic vehicular traffic predictions, graph neural networks (GNN) based traffic prediction models have been extensively utilized due to their capability of capturing non-Euclidean spatial correlation very effectively. However, most of the already existing GNN-based traffic prediction models have some limitations during learning complex and dynamic spatial and temporal patterns due to the following missing factors. First, most GNN-based traffic prediction models have used static distance or sometimes haversine distance mechanisms between spatially separated traffic observations to estimate spatial correlation. Secondly, most GNN-based traffic prediction models have not incorporated environmental events that have a major impact on the normal traffic states. Finally, most of the GNN-based models did not use an attention mechanism to focus on only important traffic observations. The objective of this paper is to study and make real-time vehicular traffic predictions while incorporating the effect of weather conditions. To fill the previously mentioned gaps, our prediction model uses a real-time driving distance between sensors to build a distance matrix or spatial adjacency matrix and capture spatial correlation. In addition, our prediction model considers the effect of six types of weather conditions and has an attention mechanism in both spatial and temporal data aggregation. Our prediction model efficiently captures the spatial and temporal correlation between traffic events, and it relies on the graph attention network (GAT) and Bidirectional bidirectional long short-term memory (Bi-LSTM) plus attention layers and is called GAT-BILSTMA.

Keywords: deep learning, real time prediction, GAT, Bi-LSTM, attention

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Authors: Adel Alblihy, Reem Ali, Mashael Algethami, Ahmed Shoqafi, Michael S. Toss, Juliette Brownlie, Natalie J. Tatum, Ian Hickson, Paloma Ordonez Moran, Anna Grabowska, Jennie N. Jeyapalan, Nigel P. Mongan, Emad A. Rakha, Srinivasan Madhusudan

Abstract:

Platinum resistance is a clinical challenge in ovarian cancer. Platinating agents induce DNA damage which activate Mre11 nuclease directed DNA damage signalling and response (DDR). Upregulation of DDR may promote chemotherapy resistance. Here we have comprehensively evaluated Mre11 in epithelial ovarian cancers. In clinical cohort that received platinum- based chemotherapy (n=331), Mre11 protein overexpression was associated with aggressive phenotype and poor progression free survival (PFS) (p=0.002). In the ovarian cancer genome atlas (TCGA) cohort (n=498), Mre11 gene amplification was observed in a subset of serous tumours (5%) which correlated highly with Mre11 mRNA levels (p<0.0001). Altered Mre11 levels was linked with genome wide alterations that can influence platinum sensitivity. At the transcriptomic level (n=1259), Mre11 overexpression was associated with poor PFS (p=0.003). ROC analysis showed an area under the curve (AUC) of 0.642 for response to platinum-based chemotherapy. Pre-clinically, Mre11 depletion by gene knock down or blockade by small molecule inhibitor (Mirin) reversed platinum resistance in ovarian cancer cells and in 3D spheroid models. Importantly, Mre11 inhibition was synthetically lethal in platinum sensitive XRCC1 deficient ovarian cancer cells and 3D-spheroids. Selective cytotoxicity was associated with DNA double strand break (DSB) accumulation, S-phase cell cycle arrest and increased apoptosis. We conclude that pharmaceutical development of Mre11 inhibitors is a viable clinical strategy for platinum sensitization and synthetic lethality in ovarian cancer.

Keywords: MRE11; XRCC1, ovarian cancer, platinum sensitization, synthetic lethality

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Authors: Hiba Akrout, Khaoula Hidouri, Béchir Chaouachi, Romdhane Ben Slama

Abstract:

A simple solar distiller has been constructed in order to desalt water via the solar distillation process. An experimental study has been conducted in June. The aim of this work is to study the effect of the distance between the cold condensing surface and the hot steam generation surface in order to optimize the geometric characteristics of a simple solar still. To do this, we have developed a mathematical model based on thermal and mass equations system. Subsequently, the equations system resolution has been made through a program developed on MATLAB software, which allowed us to evaluate the production of this system as a function of the distance separating the two surfaces. In addition, this model allowed us to determine the evolution of the humid air temperature inside the solar still as well as the humidity ratio profile all over the day. Simulations results show that the solar distiller production, as well as the humid air temperature, are proportional to the global solar radiation. It was also found that the air humidity ratio inside the solar still has a similar evolution of that of solar radiation. Moreover, the solar distiller average height augmentation, for constant water depth, induces the diminution of the production. However, increasing the water depth for a fixed average height of solar distiller reduces the production.

Keywords: distillation, solar energy, heat transfer, mass transfer, average height

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Authors: Amit Gupta, Deepak Juneja, Sorabh Gupta

Abstract:

This paper presents a model based on distance based approach (DBA) method employed for evaluation, selection, and ranking of replenishment policies for a single location inventory, which hitherto not developed in the literature. This work recognizes the significance of the selection problem, identifies the selection criteria, the relative importance of selection criteria for this research problem. The developed model is capable of comparing any number of alternate inventory policies for various selection criteria where cardinal values are assigned as a rating to alternate inventory polices for selection criteria and weights of selection criteria. The illustrated example demonstrates the model and presents the result in terms of ranking of replenishment policies.

Keywords: DBA, ranking, replenishment policies, selection criteria

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Authors: Rajan Ghimire

Abstract:

One of the diseases caused by the coronavirus shook the whole world. This situation challenged the education system across the world and compelled educators to shift to an online mode of teaching. Many academic institutions that were persistent to keep their traditional pedagogical approach were also forced to change their teaching methods. This study aims to assess science education students' experiences and perceptions of this global issue, especially on the science teaching and learning process. The study is based on qualitative research and through in-depth interviews with respondents and data is analyzed. Online distance teaching and learning processes meet the requirements of students who cannot or prefer not to participate in conventional classroom settings. But there are some challenges for the students and teachers in the science teaching learning process. This study recommends some points to all stakeholders.

Keywords: electronic devices, internet, online and distance learning, science education, educational policy

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Authors: Eid Badshah, Amjad Naseer, Muhammad Ashraf

Abstract:

In this paper full-scale brick masonry room along with the veranda of a typical school building was subjected to eight successive blast tests with increasing charge weights ranging from 0.5kg to 16.02kg at 3.66m fixed stand-off distance. Pressure-time histories were obtained by data acquisition system from pressure sensors, installed on different points of room as well as veranda columns. The resulting damage pattern of different locations was observed during each test. Weak zones of masonry room were identified. Scaled distances for different damage levels in masonry room were experimentally obtained. The results provided a basis for determining the response of masonry room building against blast loading in a specific threat scenario.

Keywords: peak pressure, composition-B, TNT, pressure sensor, scaled distance, masonry

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Authors: Semeh Ben Salem, Sami Naouali, Moetez Sallami

Abstract:

The increasing amount of collected data has limited the performance of the current analyzing algorithms. Thus, developing new cost-effective algorithms in terms of complexity, scalability, and accuracy raised significant interests. In this paper, a modified effective k-means based algorithm is developed and experimented. The new algorithm aims to reduce the computational load without significantly affecting the quality of the clusterings. The algorithm uses the City Block distance and a new stop criterion to guarantee the convergence. Conducted experiments on a real data set show its high performance when compared with the original k-means version.

Keywords: pattern recognition, global terrorism database, Manhattan distance, k-means clustering, terrorism data analysis

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Authors: Dalibor Štys, Kryštof M. Stys, Maryia Chkalova, Petr Kouba, Aliaxandr Pautsina, Dalibor Štys Jr., Jana Pečenková, Denis Durniev, Tomáš Náhlík, Petr Císař

Abstract:

In this article, a construction and some properties of the 5iD viewer, the system recording simultaneously five views of a given experimental object is reported. Properties of the system are demonstrated on the analysis of fish schooling behavior. It is demonstrated the method of instrument calibration which allows inclusion of image distortion and it is proposed and partly tested also the method of distance assessment in the case that only two opposite cameras are available. Finally, we demonstrate how the state trajectory of the behavior of the fish school may be constructed from the entropy of the system.

Keywords: 3D positioning, school behavior, distance calibration, space vision, space distortion

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Authors: Juan Facetti, Rocky McBride, Karina Loup

Abstract:

The Chaco Region of Paraguay is a key biodiverse area for the conservation of jaguars (Panthera onca), the largest feline of the Americas. It comprises five eco-regions, which holds important but decreasing populations of this species. The last decades, the expansion of soybean over the Atlantic Forest, forced the translocation of cattle-ranches towards the Chaco. Few studies of Jaguar's population densities in the American hemisphere were done until now. In the region, the specie is listed as vulnerable or threatened and more information is needed to implement any conservation policy. Among the factors that threaten the populations are land-use change, habitat fragmentation, prey depletion and illegal hunting. Two largest eco-regions were studied: the Wet Chaco and the Dry Chaco. From 2002 more than 20 jaguars were captured and fitted with GPS-collar. Data collected from 11 GPS-collars were processed, transformed numerically and finally converted into maps for analyzing. 8.092 locations were determined for four adult females (AF) and one adult male (AM) in the Wet Chaco, and one AF, one juvenile male (JM) and four AM in the Dry Chaco, during 1,867 days. GIS and kernel methodology were used to calculate daily distance of movement, home range-HR (95% isopleth), and core area (considered as 50% isopleth). In the Wet Chaco HR were 56 Km2 and 238 km2 for females and males respectively; while in the Dry Chaco HR were 685 Km2 and 844.5 km2 for females and males respectively, and 172 Km2 for a juvenile. Core areas of individual activity for each jaguar, were on average 11.5 Km2 and 33.55 km2 for AF and AM respectively in the Wet Chaco, while in the Dry Chaco were larger: 115 km2 for five AM and 225 Km2 for an AF and 32.4 Km2 for a JM. In both ecoregions, only one relevant overlap of HR of adults was reported. During the reproduction season, the HR (95% K) of one AM overlapped 49.83% with that of one AF. At the Wet Chaco, the maximum daily distance moved by an AF was 14.5 Km and 11.6 Km for the AM, while the Maximum Mean Daily Moved (MMDM) distance was 5.6 km for an AF and 3.1 km for an AM. At the Dry Chaco, the maximum daily distance for an AF was 61.7Km., 50.9Km for the AM and 6.6 Km for the JM, while the MMDM distance was 13.2 km for an AM and 8.4 km for an AF. This study confirmed that, as the invasion to jaguar habitat increased, it resulted in fragmented landscapes that influence spacing patterns of jaguars. Males used largest HR that of the smaller females and males covers largest distances that of the females. There appeared to be important spatial segregation between not only females but also males. It is likely that the larger areas used by males are partly caused by the sexual dimorphism in body size that entails differences in prey requirements. These could explain the larger distances travelled daily by males.

Keywords: Chaco ecoregions, Jaguar, home range, Panthera onca, Paraguay

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Authors: Muhammad Hanif, Muhammad Salik

Abstract:

In the present research work we present the optical emission studies of the Indium (In)-Tin (Sn) plasma produced by the first (1064 nm) harmonic of an Nd: YAG nanosecond pulsed laser. The experimentally observed line profiles of neutral Indium (InI) and Tin (SnI) are used to extract the electron temperature (Te) using the Boltzmann plot method. Whereas, the electron number density (Ne) has been determined from the Stark broadening line profile method. The Te is calculated by varying the distance from the target surface along the line of propagation of plasma plume and also by varying the laser irradiance. Beside we have studied the variation of Ne as a function of laser irradiance as well as its variation with distance from the target surface.

Keywords: indium-tin plasma, laser ablation, optical emission spectroscopy, electron temperature, electron number density

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Authors: G. S. Thakur

Abstract:

This paper presents a Fuzzy Soft Recruitment Model (FSRM) for faculty selection of MHRD technical institutions. The selection criteria are based on 4-tier flexible structure in the institutions. The Advisory Committee on Faculty Recruitment (ACoFAR) suggested nine criteria for faculty in the proposed FSRM. The model Fuzzy Soft is proposed with consultation of ACoFAR based on selection criteria. The Fuzzy Soft distance similarity measures are applied for finding best faculty from the applicant pool.

Keywords: fuzzy soft set, fuzzy sets, fuzzy soft distance, fuzzy soft similarity measures, ACoFAR

Procedia PDF Downloads 333