Search results for: data databases

Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: K. W. Nam, B. J. Kim, S. J. Lee

Abstract:

Along with the development of network infrastructures, such as high-speed Internet and mobile environment, the explosion of multimedia data is expanding the range of multimedia services beyond voice and data services. Amid this flow, research is actively being done on the creation, management, and transmission of metadata on digital content to provide different services to users. This paper proposes a system for the insertion, storage, and retrieval of metadata about digital content. The metadata server with Binary XML was implemented for efficient storage space and retrieval speeds, and the transport data size required for metadata retrieval was simplified. With the proposed system, the metadata could be inserted into the moving objects in the video, and the unnecessary overlap could be minimized by improving the storage structure of the metadata. The proposed system can assemble metadata into one relevant topic, even if it is expressed in different media or in different forms. It is expected that the proposed system will handle complex network types of data.

Keywords: video, multimedia, metadata, editing tool, XML

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Authors: Catarina Ramos Pereira, Jorge Rodrigues, Natália Oliveira, Jorge Machado, Maria Begoña Criado, Jorge Machado, Henri J. Greten

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Background: Parkinson's disease is a multi-system neurodegenerative disorder characterized by motor and non-motor symptoms. To slow disorder progression, different treatment options are now available, but in most cases, these therapeutic strategies also involve the presence of important side effects. This has led many patients to pursue complementary therapies, such as acupuncture, to alleviate PD symptoms. Therefore, an update on the efficacy of this treatment for patients of PD is of great value. This work presents a systematic review of the efficacy of acupuncture treatments in relieving PD symptoms. Methods: EMBASE, Medline, Pubmed, Science Direct, The Cochrane Library, Cochrane Central Register of Controlled Trials (Central), and Scielo databases were systematically searched from January 2011 through July 2021. Randomized controlled trials (RCTs) published in English with all types of acupuncture treatment were included. The selection and analysis of the articles were conducted by two blinding authors through the Rayyan application. Results: 720 potentially relevant articles were identified; 52 RCTs met our inclusion criteria. After the exclusion of 35, we found 17 eligible. The included RCTs reported positive effects for acupuncture plus conventional treatment compared with conventional treatment alone in the UPDRS score. Conclusions: Additional evidence should be supported by rigorous methodological strategies. Although firm conclusions cannot be drawn, acupuncture treatment, in the framework of an interdisciplinary care team, appears to have positive effects on PD symptoms.

Keywords: systematic review, Parkinson disease, acupuncture, traditional Chinese medicine

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Authors: Luís Pina

Abstract:

The conservation of marine biodiversity keeps ecosystems in balance and ensures the sustainable use of resources. In this context, technological resources have been used for monitoring marine species to allow biologists to obtain data in real-time. There are different mobile applications developed for data collection for monitoring purposes, but these systems are designed to be utilized only on third-generation (3G) phones or smartphones with Internet access and in rural parts of the developing countries, Internet services and smartphones are scarce. Thus, the objective of this work is to develop a system to monitor marine turtles using Unstructured Supplementary Service Data (USSD), which users can access through basic mobile phones. The system aims to improve the data collection mechanism and enhance the effectiveness of current systems in monitoring sea turtles using any type of mobile device without Internet access. The system will be able to report information related to the biological activities of marine turtles. Also, it will be used as a platform to assist marine conservation entities to receive reports of illegal sales of sea turtles. The system can also be utilized as an educational tool for communities, providing knowledge and allowing the inclusion of communities in the process of monitoring marine turtles. Therefore, this work may contribute with information to decision-making and implementation of contingency plans for marine conservation programs.

Keywords: GSM, marine biology, marine turtles, unstructured supplementary service data (USSD)

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Authors: Oussama Hafferssas, Hiba Benyahia, Amina Madani, Nassima Zeriri

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Although data nowadays has multiple forms; from text to images, and from audio to videos, yet text is still the most used one at a public level. At an academical and research level, and unlike other forms, text can be considered as the easiest form to process. Therefore, a brunch of Data Mining researches has been always under its shadow, called "Text Mining". Its concept is just like data mining’s, finding valuable patterns in data, from large collections and tremendous volumes of data, in this case: Text. Named entity recognition (NER) is one of Text Mining’s disciplines, it aims to extract and classify references such as proper names, locations, expressions of time and dates, organizations and more in a given text. Our approach "Octopub" does not aim to find new ways to improve named entity recognition process, rather than that it’s about finding a new, and yet smart way, to use NER in a way that we can extract sentiments of millions of people using Social Networks as a limitless information source, and Marketing for product promotion as the main domain of application.

Keywords: textmining, named entity recognition(NER), sentiment analysis, social media networks (SN, SMN), business intelligence(BI), marketing

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Authors: Mohammadreza Ashouri, Majid Bayatian

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Analysis of fire data is a way for the implementation of any plan to improve the level of safety in cities. Such an analysis is able to reveal signs of changes in a given period and can be used as a measure of safety. The information of about 66,341 fires (from 2002 to 2012) released by Tehran Safety Services and Fire-Fighting Organization and data on the population and the number of households provided by Tehran Municipality and the Statistical Yearbook of Iran were extracted. Using the data, the fire changes, the rate of injuries, and mortality rate were determined and analyzed. The rate of injuries and mortality rate of fires per one million population of Tehran were 59.58% and 86.12%, respectively. During the study period, the number of fires and fire stations increased by 104.38% and 102.63%, respectively. Most fires (9.21%) happened in the 4th District of Tehran. The results showed that the recorded fire data have not been systematically planned for fire prevention since one of the ways to reduce injuries caused by fires is to develop a systematic plan for necessary actions in emergency situations. To determine a reliable source for fire prevention, the stages, definitions of working processes and the cause and effect chains should be considered. Therefore, a comprehensive statistical system should be developed for reported and recorded fire data.

Keywords: fire statistics, fire analysis, accident prevention, Tehran

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Authors: Nam Don Kim, Jungho Moon, Tae Yun Chung

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This paper proposes an Internet of Things (IoT) based virtualization platform for providing smart tourism services. The virtualization platform provides a consistent access interface to various types of data by naming IoT devices and legacy information systems as pathnames in a virtual file system. In the other words, the IoT virtualization platform functions as a middleware which uses the metadata for underlying collected data. The proposed platform makes it easy to provide customized tourism information by using tourist locations collected by IoT devices and additionally enables to create new interactive smart tourism services focused on the tourist locations. The proposed platform is very efficient so that the provided tourism services are isolated from changes in raw data and the services can be modified or expanded without changing the underlying data structure.

Keywords: internet of things (IoT), IoT platform, serviceplatform, virtual file system (VSF)

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Authors: Slim Namouchi, Bruno Vallet, Imed Riadh Farah

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3D urban models provide powerful tools for decision making, urban planning, and smart city services. The accuracy of this 3D based systems is directly related to the quality of these models. Since manual large-scale modeling, such as cities or countries is highly time intensive and very expensive process, a fully automatic 3D building generation is needed. However, 3D modeling process result depends on the input data, the proprieties of the captured objects, and the required characteristics of the reconstructed 3D model. Nowadays, producing 3D real-world model is no longer a problem. Remotely sensed data had experienced a remarkable increase in the recent years, especially data acquired using unmanned aerial vehicles (UAV). While the scanning techniques are developing, the captured data amount and the resolution are getting bigger and more precise. This paper presents a literature review, which aims to identify different methods of automatic 3D buildings extractions either from LiDAR or the combination of LiDAR and satellite or aerial images. Then, we present open source technologies, and data models (e.g., CityGML, PostGIS, Cesiumjs) used to integrate these models in geospatial base layers for smart city services.

Keywords: CityGML, LiDAR, remote sensing, SIG, Smart City, 3D urban modeling

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Authors: Ahmed Noor Al-qayyim, Barlas Özden Çağlayan

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Structural failure is caused mainly by damage that often occurs on structures. Many researchers focus on obtaining very efficient tools to detect the damage in structures in the early state. In the past decades, a subject that has received considerable attention in literature is the damage detection as determined by variations in the dynamic characteristics or response of structures. This study presents a new damage identification technique. The technique detects the damage location for the incomplete structure system using output data only. The method indicates the damage based on the free vibration test data by using “Two Points - Condensation (TPC) technique”. This method creates a set of matrices by reducing the structural system to two degrees of freedom systems. The current stiffness matrices are obtained from optimization of the equation of motion using the measured test data. The current stiffness matrices are compared with original (undamaged) stiffness matrices. High percentage changes in matrices’ coefficients lead to the location of the damage. TPC technique is applied to the experimental data of a simply supported steel beam model structure after inducing thickness change in one element. Where two cases are considered, the method detects the damage and determines its location accurately in both cases. In addition, the results illustrate that these changes in stiffness matrix can be a useful tool for continuous monitoring of structural safety using ambient vibration data. Furthermore, its efficiency proves that this technique can also be used for big structures.

Keywords: damage detection, optimization, signals processing, structural health monitoring, two points–condensation

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Authors: P. Senthil Kumari

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Main concerns in data mining investigation are social controls of data mining for handling ambiguity, noise, or incompleteness on text data. We describe an innovative approach for unplanned text data detection of community networks achieved by classification mechanism. In a tangible domain claim with humble secrecy backgrounds provided by community network for evading annoying content is presented on consumer message partition. To avoid this, mining methodology provides the capability to unswervingly switch the messages and similarly recover the superiority of ordering. Here we designated learning-centered mining approaches with pre-processing technique to complete this effort. Our involvement of work compact with rule-based personalization for automatic text categorization which was appropriate in many dissimilar frameworks and offers tolerance value for permits the background of comments conferring to a variety of conditions associated with the policy or rule arrangements processed by learning algorithm. Remarkably, we find that the choice of classifier has predicted the class labels for control of the inadequate documents on community network with great value of effect.

Keywords: text mining, data classification, community network, learning algorithm

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Authors: Haythem A. Nakkas, Philip J. Scott, Jim S. Briggs

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This paper reports a structured literature review of the application of Health Information Technology in developing countries, defined as the World Bank categories Low-income countries, Lower-middle-income, and Upper-middle-income countries. The aim was to identify and classify the various applications of health information technology to assess its current state in developing countries and explore potential areas of research. We offer specific analysis and application of HIT in Libya as one of the developing countries. Method: A structured literature review was conducted using the following online databases: IEEE, Science Direct, PubMed, and Google Scholar. Publication dates were set for 2000-2013. For the PubMed search, publications in English, French, and Arabic were specified. Using a content analysis approach, 159 papers were analyzed and a total number of 26 factors were identified that affect the adoption of health information technology. Results: Of the 2681 retrieved articles, 159 met the inclusion criteria which were carefully analyzed and classified. Conclusion: The implementation of health information technology across developing countries is varied. Whilst it was initially expected financial constraints would have severely limited health information technology implementation, some developing countries like India have nevertheless dominated the literature and taken the lead in conducting scientific research. Comparing the number of studies to the number of countries in each category, we found that Low-income countries and Lower-middle-income had more studies carried out than Upper-middle-income countries. However, whilst IT has been used in various sectors of the economy, the healthcare sector in developing countries is still failing to benefit fully from the potential advantages that IT can offer.

Keywords: developing countries, developed countries, factors, failure, health information technology, implementation, libya, success

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Authors: Ivan Balachin, Geanette Polanco, Jiang Xingliang, Hu Qin

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The problem of global warming raised up interest towards renewable energy sources. To reduce cost of wind energy is a challenge. Before building of wind park conditions such as: average wind speed, direction, time for each wind, probability of icing, must be considered in the design phase. Operation values used on the setting of control systems also will depend on mentioned variables. Here it is proposed a procedure to be include in the evaluation of the performance of a wind turbine, based on the amplitude of wind changes, the number of changes and their duration. A generic study case based on actual data is presented. Data analysing techniques were applied to model the power required for yaw system based on amplitude and data amount of wind changes. A theoretical model between time, amplitude of wind changes and angular speed of nacelle rotation was identified.

Keywords: field data processing, regression determination, wind turbine performance, wind turbine placing, yaw system losses

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Authors: Tadesse Melaku Abegaz, Akshaya Srikanth Bahagavathula, Abdulla Shehab Sheab, Asim Hassen

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Objectives: Non-adherence and discontinuation of anticoagulant therapy lead to increased ischemic stroke risk and contributes to suboptimal outcomes of the anticoagulant treatment. This systematic review and meta-analysis were aimed to investigate the adherence to NOACs and adverse events in patients with AF. Methods: Original research articles conducted on patients with AF and using any NOACs (dabigatran, rivoraxaban and apixaban) reporting adherence for at least 35 days were included. Scientific databases including PubMed, Web of Science, and Google Scholar were searched using MeSH keywords to obtaining literature researched between 2008 to till June, 2016. Study characteristics, patient’s sociodemographic and clinical characteristics, medication adherence levels and bleeding events reported were recorded. Results: The overall sample size of the six studies is 1,640,157, with CHADS2 scores < 2 in 551 patients, CHADS2-VASc ≥ 2 in 62,232 AF patients. Three-forth [75.6% (95%CI= 66.5-84.8), p < 0.001] are adherent to NOACs. However, a higher rate [72.7% (62.5-82.9), p < 0.001] of adherence was observed with Dabigatran than Apixaban [59.9% (3.2-123.1), p=0.063] and Rivaroxaban [59.3% (38.7-80.0), p<0.001]. Sub-group analysis revealed that nearly 57% of the AF patients on NOACs have CHADS2 scores < 2 and 20% of these patients were non-adherent to NOACs. Overall bleeding events rate associated with NOACs non-adherent AF patients was found to be 7.5% (0.2-14.8), p=0.045. However, nearly 11.2% of AF patients experienced bleeding events were non-adherent to NOAC medications. A higher proportion of bleeding events were noticed with Dabigatran (14.7%). Conclusions: Adherence rates, while uniformly suboptimal, nevertheless varied considerably, lowest at 59.3% for rivaroxaban and 59.9% for apixaban, followed by dabigatran (75.6%). Overall bleeding events associated with NOACs rates were 7.5%. However, lower adherence to NOACs was associated with worse outcomes among patients with greater stroke risk.

Keywords: atrial fibrillation, bleeding events, meta-analysis, novel oral anticoagulants

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Authors: Masoud Charkhabi

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We examine trade theory with this motivation. The full set of World Trade Organization data are organized into country-year pairs, each treated as a different entity. Topological Data Analysis reveals that among the 16 region and 240 region-year pairs there exists in fact a distinguishable group of region-period pairs. The generally accepted periods of shifts from dissimilar-dissimilar to similar-similar trade in goods among regions are examined from this new perspective. The period breaks are treated as cumulative and are flexible. This type of all-subsets analysis is motivated from computer science and is made possible with Lossy Compression and Graph Theory. The results question many patterns in similar-similar to dissimilar-dissimilar trade. They also show indications of economic shifts that only later become evident in other economic metrics.

Keywords: econometrics, globalization, network science, topological data, analysis, trade theory, visualization, world trade

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Authors: Muhammad Awais Shafique, Eiji Hato, Hideki Yaginuma

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Recently GPS data is used in a lot of studies to automatically reconstruct travel patterns for trip survey. The aim is to minimize the use of questionnaire surveys and travel diaries so as to reduce their negative effects. In this paper data acquired from GPS and accelerometer embedded in smart phones is utilized to predict the mode of transportation used by the phone carrier. For prediction, Support Vector Machine (SVM) and Adaptive boosting (AdaBoost) are employed. Moreover a unique method to improve the prediction results from these algorithms is also proposed. Results suggest that the prediction accuracy of AdaBoost after improvement is relatively better than the rest.

Keywords: accelerometer, AdaBoost, GPS, mode prediction, support vector machine

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Authors: Eric Kumar, Erica Cochran, Zhiang Zhang, Wei Liang, Ronak Mody

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The objective of this article was to create a modelling framework that exposes the marginal costs of shifting workloads across geographically distributed data-centers. Geographical distribution of internet services helps to optimize their performance for localized end users with lowered communications times and increased availability. However, due to the geographical and temporal effects, the physical embodiments of a service's data center infrastructure can vary greatly. In this work, we first identify that the sources of variances in the physical infrastructure primarily stem from local weather conditions, specific user traffic profiles, energy sources, and the types of IT hardware available at the time of deployment. Second, we create a traffic simulator that indicates the IT load at each data-center in the set as an approximator for user traffic profiles. Third, we implement a framework that quantifies the global level energy demands using building energy models and the traffic profiles. The results of the model provide a time series of energy demands that can be used for further life cycle analysis of internet services.

Keywords: data-centers, energy, life cycle, network simulation

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Authors: Marcho Setiawan Handok, Samuel S. Lemma, Abdoulaye Fofana, Naseef Mansoor

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This paper is proposing a method to predict the outcome of the National Football League match with data from 2019 to 2022 and compare it with other popular models. The model uses open-source statistical data of each team, such as passing yards, rushing yards, fumbles lost, and scoring. Each statistical data has offensive and defensive. For instance, a data set of anticipated values for a specific matchup is created by comparing the offensive passing yards obtained by one team to the defensive passing yards given by the opposition. We evaluated the model’s performance by contrasting its result with those of established prediction algorithms. This research is using a neural network to predict the score of a National Football League match and then predict the winner of the game.

Keywords: game prediction, NFL, football, artificial neural network

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Authors: Mehdi Khaki, Ehsan Forootan, Joseph Awange, Michael Kuhn

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Terrestrial water storage, as a source of freshwater, plays an important role in human lives. Hydrological models offer important tools for simulating and predicting water storages at global and regional scales. However, their comparisons with 'reality' are imperfect mainly due to a high level of uncertainty in input data and limitations in accounting for all complex water cycle processes, uncertainties of (unknown) empirical model parameters, as well as the absence of high resolution (both spatially and temporally) data. Data assimilation can mitigate this drawback by incorporating new sets of observations into models. In this effort, we use multi-mission satellite-derived remotely sensed observations to improve the performance of World-Wide Water Resources Assessment system (W3RA) hydrological model for estimating terrestrial water storages. For this purpose, we assimilate total water storage (TWS) data from the Gravity Recovery And Climate Experiment (GRACE) and surface soil moisture data from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) into W3RA. This is done to (i) improve model estimations of water stored in ground and soil moisture, and (ii) assess the impacts of each satellite of data (from GRACE and AMSR-E) and their combination on the final terrestrial water storage estimations. These data are assimilated into W3RA using the Ensemble Square-Root Filter (EnSRF) filtering technique over Mississippi Basin (the United States) and Murray-Darling Basin (Australia) between 2002 and 2013. In order to evaluate the results, independent ground-based groundwater and soil moisture measurements within each basin are used.

Keywords: data assimilation, GRACE, AMSR-E, hydrological model, EnSRF

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Authors: Parker Townes, Aisouda Savadlou, Shoshana Weiss, Marina Jarenova, Suzzane Ferris, Dan Devoe, Russel Schachar, Scott Patten, Tomas Lange, Marlena Colasanto, Holly McGinn, Paul Arnold

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Some research suggests obsessive-compulsive disorder (OCD) is associated with impaired executive functioning: higher-level mental processes involved in carrying out tasks and solving problems. Relevant literature was identified systematically through online databases. Meta-analyses were conducted for task performance metrics reported by at least two articles. Results were synthesized by the executive functioning domain measured through each performance metric. Heterogeneous literature was identified, typically involving few studies using consistent measures. From 29 included studies, analyses were conducted on 33 performance metrics from 12 tasks. Results suggest moderate associations of working memory (two out of five tasks presented significant findings), planning (one out of two tasks presented significant findings), and visuospatial abilities (one out of two tasks presented significant findings) with OCD in youth. There was inadequate literature or contradictory findings for other executive functioning domains. These findings suggest working memory, planning, and visuospatial abilities are impaired in pediatric OCD, with mixed results. More work is needed to identify the effect of age and sex on these results. Acknowledgment: This work was supported by the Alberta Innovates Translational Health Chair in Child and Youth Mental Health. The funders had no role in the design, conducting, writing, or decision to submit this article for publication.

Keywords: obsessive-compulsive disorder, neurocognition, executive functioning, adolescents, children

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

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Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: Jacob Wahl, Jane Zhang

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This paper describes the development and characterization of a prototype IoT network for use with agricultural imaging and monitoring applications. The sensor and gateway nodes are designed using the ESP32 SoC with integrated Bluetooth Low Energy 4.2 and Wi-Fi. A development board, the Arducam IoTai ESP32, is used for prototyping, testing, and power measurements. Google’s Firebase is used as the cloud storage site for image data collected by the sensor. The sensor node captures images using the OV2640 2MP camera module and transmits the image data to the gateway via Bluetooth Low Energy. The gateway then uploads the collected images to Firebase via a known nearby Wi-Fi network connection. This image data can then be processed and analyzed by computer vision and machine learning pipelines to assess crop growth or other needs. The sensor node achieves a wireless transmission data throughput of 220kbps while consuming 150mA of current; the sensor sleeps at 162µA. The sensor node device lifetime is estimated to be 682 days on a 6600mAh LiPo battery while acquiring five images per day based on the development board power measurements. This network can be utilized by any application that requires high data rates, low power consumption, short-range communication, and large amounts of data to be transmitted at low-frequency intervals.

Keywords: Bluetooth low energy, ESP32, firebase cloud, IoT, smart farming

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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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Authors: Aanh Eduardo Dimate-Garcia, Diana Carolina Rodriguez-Romero, Edna Yuliana Gonzalez Rincon, Diana Marcela Pardo Lopez, Yessica Garibello Cubillos

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Musculoskeletal disorders (MD) are the new epidemic of chronic diseases, are multifactorial and affect the different productive sectors. Although there are multiple instruments to evaluate the static and dynamic load, the method of repetitive occupational action (OCRA) seems to be an attractive option. Objective: It is aimed to analyze the use of the OCRA method and the prevalence of MD in workers of various productive sectors according to the literature (2007-2018). Materials and Methods: A literature review (following the PRISMA statement) of studies aimed at assessing the level of biomechanical risk (OCRA) and the prevalence of MD in the databases Scielo, Science Direct, Scopus, ProQuest, Gale, PubMed, Lilacs and Ebsco was realized; 7 studies met the selection criteria; the majority are quantitative (cross section). Results: it was evidenced (gardening and flower-growers) in this review that 79% of the conditions related to the task require physical requirements and involve repetitive movements. In addition, of the high appearance of DM in the high-low back, upper and lower extremities that are produced by the frequency of the activities carried out (footwear production). Likewise, there was evidence of 'very high risks' of developing MD (salmon industry) and a medium index (OCRA) for repetitive movements that require special care (U-Assembly line). Conclusions: the review showed the limited use of the OCRA method for the detection of MD in workers from different sectors, and this method can be used for the detection of biomechanical risk and the appearance of MD.

Keywords: checklist, cumulative trauma disorders, musculoskeletal diseases, repetitive movements

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Authors: Lauren C. Porter, Andrew Curtis, Eric Jefferis, Susanne Mitchell

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A wealth of research has been generated examining the variation in crime across neighborhoods. However, there is also a striking degree of crime concentration within neighborhoods. A number of studies show that a small percentage of street segments, intersections, or addresses account for a large portion of crime. Not surprisingly, a focus on these crime hot spots can be an effective strategy for reducing community level crime and related ills, such as health problems. However, research is also limited in an important respect. Studies tend to use official data to identify hot spots, such as 911 calls or calls for service. While the use of call data may be more representative of the actual level and distribution of crime than some other official measures (e.g. arrest data), call data still suffer from the 'dark figure of crime.' That is, there is most certainly a degree of error between crimes that occur versus crimes that are reported to the police. In this study, we present an alternative method of identifying crime hot spots, that does not rely on official data. In doing so, we highlight the potential utility of neighborhood-insiders to identify and understand crime dynamics within geographic spaces. Specifically, we use spatial video and geo-narratives to record the crime insights of 36 police, ex-offenders, and residents of a high crime neighborhood in northeast Ohio. Spatial mentions of crime are mapped to identify participant-identified hot spots, and these are juxtaposed with calls for service (CFS) data. While there are bound to be differences between these two sources of data, we find that one location, in particular, a corner store, emerges as a hot spot for all three groups of participants. Yet it does not emerge when we examine CFS data. A closer examination of the space around this corner store and a qualitative analysis of narrative data reveal important clues as to why this store may indeed be a hot spot, but not generate disproportionate calls to the police. In short, our results suggest that researchers who rely solely on official data to study crime hot spots may risk missing some of the most dangerous places.

Keywords: crime, narrative, video, neighborhood

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Authors: Nasim Eslamirad, Mahdi Rasoulinezhad, Francesco De Luca, Sadok Ben Yahia, Kimmo Sakari Lylykangas, Francesco Pilla

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With the ongoing urbanization, cities face increasing environmental challenges impacting human well-being. To tackle these issues, data-driven approaches in urban analysis have gained prominence, leveraging urban data to promote sustainability. Integrating Machine Learning techniques enables researchers to analyze and predict complex environmental phenomena like Urban Heat Island occurrences in urban areas. This paper demonstrates the implementation of data-driven approach and interpretable Machine Learning algorithms with interpretability techniques to conduct comprehensive data analyses for sustainable urban design. The developed framework and algorithms are demonstrated for Tallinn, Estonia to develop sustainable urban strategies to mitigate urban heat waves. Geospatial data, preprocessed and labeled with UHI levels, are used to train various ML models, with Logistic Regression emerging as the best-performing model based on evaluation metrics to derive a mathematical equation representing the area with UHI or without UHI effects, providing insights into UHI occurrences based on buildings and urban features. The derived formula highlights the importance of building volume, height, area, and shape length to create an urban environment with UHI impact. The data-driven approach and derived equation inform mitigation strategies and sustainable urban development in Tallinn and offer valuable guidance for other locations with varying climates.

Keywords: data-driven approach, machine learning transparent models, interpretable machine learning models, urban heat island effect

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Authors: Ibrahim A. Adeniran, Rui F. Zhu, Man S. Wong

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Owing to the insufficiency in the spatial representativeness and continuity of in situ temperature measurements from weather stations (WS), the use of temperature measurement from WS for large-range diurnal analysis in heterogenous landscapes has been limited. This has made the accurate estimation of land surface temperature (LST) from remotely sensed data more crucial. Moreover, the study of dynamic interaction between the atmosphere and the physical surface of the Earth could be enhanced at both annual and diurnal scales by using optimal LST data derived from satellite sensors. The tradeoff between the spatial and temporal resolution of LSTs from satellite’s thermal infrared sensors (TIRS) has, however, been a major challenge, especially when high spatiotemporal LST data are recommended. It is well-known from existing literature that polar satellites have the advantage of high spatial resolution, while geostationary satellites have a high temporal resolution. Hence, this study is aimed at designing a framework for the cross-comparison of LST data from polar and geostationary satellites in a heterogeneous landscape. This could help to understand the relationship between the LST estimates from the two satellites and, consequently, their integration in diurnal LST analysis. Landsat-8 satellite data will be used as the representative of the polar satellite due to the availability of its long-term series, while the Himawari-8 satellite will be used as the data source for the geostationary satellite because of its improved TIRS. For the study area, Hong Kong Special Administrative Region (HK SAR) will be selected; this is due to the heterogeneity in the landscape of the region. LST data will be retrieved from both satellites using the Split window algorithm (SWA), and the resulting data will be validated by comparing satellite-derived LST data with temperature data from automatic WS in HK SAR. The LST data from the satellite data will then be separated based on the land use classification in HK SAR using the Global Land Cover by National Mapping Organization version3 (GLCNMO 2013) data. The relationship between LST data from Landsat-8 and Himawari-8 will then be investigated based on the land-use class and over different seasons of the year in order to account for seasonal variation in their relationship. The resulting relationship will be spatially and statistically analyzed and graphically visualized for detailed interpretation. Findings from this study will reveal the relationship between the two satellite data based on the land use classification within the study area and the seasons of the year. While the information provided by this study will help in the optimal combination of LST data from Polar (Landsat-8) and geostationary (Himawari-8) satellites, it will also serve as a roadmap in the annual and diurnal urban heat (UHI) analysis in Hong Kong SAR.

Keywords: automatic weather station, Himawari-8, Landsat-8, land surface temperature, land use classification, split window algorithm, urban heat island

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Authors: Sandra H. Fukurozaki, Andre L. N. Silva, Joao B. F. Neto, Fernando J. G. Landgraf

Abstract:

Nowadays, the rare earth (RE) metals play an important role in emerging technologies that are crucial for the decarbonisation of the energy sector. Their unique properties have led to increasing clean energy applications, such as wind turbine generators, and hybrid and electric vehicles. Despite the substantial media coverage that has recently surrounded the mining and processing of rare earth metals, very little quantitative information is available concerning their subsequent life stages, especially related to the metallic production of didymium (Nd-Pr) in fluoride molten salt system. Here we investigate a gate to gate scale life cycle assessment (LCA) of the didymium electrolysis based on three different scenarios of operational conditions. The product system is modeled with SimaPro Analyst 8.0.2 software, and IMPACT 2002+ was applied as an impact assessment tool. In order to develop a life cycle inventories built in software databases, patents, and other published sources together with energy/mass balance were utilized. Analysis indicates that from the 14 midpoint impact categories evaluated, the global warming potential (GWP) is the main contributors to the total environmental burden, ranging from 2.7E2 to 3.2E2 kg CO2eq/kg Nd-Pr. At the damage step assessment, the results suggest that slight changes in materials flows associated with enhancement of current efficiency (between 2.5% and 5%), could lead a reduction up to 12% and 15% of human health and climate change damage, respectively. Additionally, this paper highlights the knowledge gaps and future research efforts needing to understand the environmental impacts of Nd-Pr electrolysis process from the life cycle perspective.

Keywords: didymium electrolysis, environmental impacts, life cycle assessment, rare earth metals

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Najrullah Khan, Athar Ali Khan

Abstract:

The Topp-Leone distribution was introduced by Topp- Leone in 1955. In this paper, an attempt has been made to fit Topp-Leone Generalized exponential (TPGE) distribution. A real survival data set is used for illustrations. Implementation is done using R and JAGS and appropriate illustrations are made. R and JAGS codes have been provided to implement censoring mechanism using both optimization and simulation tools. The main aim of this paper is to describe and illustrate the Bayesian modelling approach to the analysis of survival data. Emphasis is placed on the modeling of data and the interpretation of the results. Crucial to this is an understanding of the nature of the incomplete or 'censored' data encountered. Analytic approximation and simulation tools are covered here, but most of the emphasis is on Markov chain based Monte Carlo method including independent Metropolis algorithm, which is currently the most popular technique. For analytic approximation, among various optimization algorithms and trust region method is found to be the best. In this paper, TPGE model is also used to analyze the lifetime data in Bayesian paradigm. Results are evaluated from the above mentioned real survival data set. The analytic approximation and simulation methods are implemented using some software packages. It is clear from our findings that simulation tools provide better results as compared to those obtained by asymptotic approximation.

Keywords: Bayesian Inference, JAGS, Laplace Approximation, LaplacesDemon, posterior, R Software, simulation

Procedia PDF Downloads 535