Search results for: wolof word classification

Authors: Sanghamitra Roy

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In recent times, India has experienced the phenomenal rise in the number of registered vehicles and vehicular trips, particularly intra-city trips in most of its urban areas. The increase in vehicle ownership and use have increased parking demand immensely and accommodating the same is now a matter of big concern. Most cities do not have adequate off-street parking facilities thus forcing people to park on the streets. This has resulted in decreased carrying capacity, decreased traffic speed, increased congestion, and increased environmental problems. While integrated multi-modal transportation system is the answer to such problems, parking issues will continue to exist. In Kolkata, only 6.4% land is devoted for roads. The consequences of this huge crunch in road spaces coupled with increased parking demand are severe particularly in the CBD and major commercial areas, making the role of off-street parking facilities in Kolkata even more critical. To meaningfully address parking issues, it is important to identify the factors that influence parking demand so that it can be assessed and comprehensive parking policies and plans for the city can be formulated. This paper aims at identifying the factors that contribute towards parking demand for offices in Kolkata and their degree of correlation with parking demand. The study is limited to home-to-work trips located within Kolkata Municipal Corporation (KMC) where parking related issues are most pronounced. The data for the study is collected through personal interviews, questionnaires and direct observations from offices across the wards of KMC. SPSS is used for classification of the data and analyses of the same. The findings of this study will help in re-assessment of the parking requirements specified in The Kolkata Municipal Corporation Building Rules as a step towards alleviating parking related issues in the city.

Keywords: building rules, office spaces, parking demand, urbanization

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Authors: Thewodros K. Geberemariam

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The rapid physical expansion of urbanization coupled with aging infrastructure presents a unique decision and management challenges for many big city municipalities. Cities must therefore upgrade and maintain the existing aging urban drainage infrastructure systems to keep up with the demands. Given the overall contribution of assets to municipal revenue and the importance of infrastructure to the success of a livable city, many municipalities are currently looking for a robust and smart urban drainage infrastructure asset management solution that combines management, financial, engineering and technical practices. This robust decision-making shall rely on sound, complete, current and relevant data that enables asset valuation, impairment testing, lifecycle modeling, and forecasting across the multiple asset portfolios. On this paper, predictive computational intelligence (CI) and multi-class machine learning (ML) coupled with online, offline, and historical record data that are collected from an array of multi-parameter sensors are used for the extraction of different operational and non-conforming patterns hidden in structured and unstructured data to determine and produce actionable insight on the current and future states of the network. This paper aims to improve the strategic decision-making process by identifying all possible alternatives; evaluate the risk of each alternative, and choose the alternative most likely to attain the required goal in a cost-effective manner using historical and near real-time urban drainage infrastructure data for urban drainage infrastructures assets that have previously not benefited from computational intelligence and machine learning advancements.

Keywords: computational intelligence, machine learning, urban drainage infrastructure, machine learning, classification, prediction, asset management space

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Authors: Chi-Ching Lee, Po-Jung Huang, Kuo-Yang Huang, Petrus Tang

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Background: Recent advances in high-throughput research technologies such as new-generation sequencing and multi-dimensional liquid chromatography makes it possible to dissect the complete transcriptome and proteome in a single run for the first time. However, it is almost impossible for many laboratories to handle and analysis these “BIG” data without the support from a bioinformatics team. We aimed to provide a web-based analysis platform for users with only limited knowledge on bio-computing to study the functional genomics and proteomics. Method: We use NCI-60 as an example dataset to demonstrate the power of the web-based analysis platform and data delivering system: C-eXpress takes a simple text file that contain the standard NCBI gene or protein ID and expression levels (rpkm or fold) as input file to generate a distribution map of gene/protein expression levels in a heatmap diagram organized by color gradients. The diagram is hyper-linked to a dynamic html table that allows the users to filter the datasets based on various gene features. A dynamic summary chart is generated automatically after each filtering process. Results: We implemented an integrated database that contain pre-defined annotations such as gene/protein properties (ID, name, length, MW, pI); pathways based on KEGG and GO biological process; subcellular localization based on GO cellular component; functional classification based on GO molecular function, kinase, peptidase and transporter. Multiple ways of sorting of column and rows is also provided for comparative analysis and visualization of multiple samples.

Keywords: cancer, visualization, database, functional annotation

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Authors: C. M. Williams, R. English, P. King, I. M. Brown

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Introduction: Pseudoangiomatous Stromal Hyperplasia (PASH) is a benign fibrous proliferation of breast stroma affecting predominantly premenopausal women with no significant increased risk of breast cancer. Informal recommendations for management have continued to evolve over recent years from surgical excision to observation, although there are no specific national guidelines. This study assesses the safety of a non-surgical approach to PASH management by review of cases at a single centre. Methods: Retrospective case series review (January 2011 – August 2016) was conducted on consecutive PASH cases. Diagnostic classification (clinical, radiological and histological), management outcomes, and breast cancer incidence were recorded. Results: 43 patients were followed up for median of 25 months (3-64) with 75% symptomatic at presentation. 12% of cases (n=5) had a radiological score (BIRADS MMG or US) ≥ 4 of which 3 were confirmed malignant. One further malignancy was detected and proven radiologically occult and contralateral. No patients were diagnosed with a malignancy during follow-up. Treatment evolved from 67% surgical in 2011 to 33% in 2016. Conclusions: The management of PASH has transitioned in line with other published experience. The preliminary findings suggest this appears safe with no evidence of missed malignancies; however, longer follow up is required to confirm long-term safety. Recommendations: PASH with suspicious radiological findings ( ≥ U4/R4) warrants multidisciplinary discussion for excision. In the absence of histological or radiological suspicion of malignancy, PASH can be safely managed without surgery.

Keywords: benign breast disease, conservative management, malignancy, pseudoangiomatous stromal hyperplasia, surgical excision

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Authors: Wei Wen Yang, Emily Chia Yu Su

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Dengue fever is a mosquito-borne tropical infectious disease caused by the dengue virus. After infection, symptoms usually start from three to fourteen days. Dengue virus may cause a high fever and at least two of the following symptoms, severe headache, severe eye pain, joint pains, muscle or bone pain, vomiting, feature skin rash, and mild bleeding manifestation. In addition, recovery will take at least two to seven days. Dengue fever has rapidly spread in tropical and subtropical areas in recent years. Several phenomena around the world such as global warming, urbanization, and international travel are the main reasons in boosting the spread of dengue. In Taiwan, epidemics occur annually, especially during summer and fall seasons. On the other side, Singapore government also has announced the amounts number of dengue cases spreading in Singapore. As the serious epidemic of dengue fever outbreaks in Taiwan and Singapore, countries around the Asia-Pacific region are becoming high risks of susceptible to the outbreaks and local hub of spreading the virus. To improve public safety and public health issues, firstly, we are going to use Microsoft Excel and SAS EG to do data preprocessing. Secondly, using support vector machines and decision trees builds predict model, and analyzes the infectious cases between Taiwan and Singapore. By comparing different factors causing vector mosquito from model classification and regression, we can find similar spreading patterns where the disease occurred most frequently. The result can provide sufficient information to predict the future dengue infection outbreaks and control the diffusion of dengue fever among countries.

Keywords: dengue fever, Taiwan, Singapore, Aedes aegypti

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Authors: Shamsulhaq Amin

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Drought can arise from several hydrometeorological phenomena that result in insufficient precipitation, soil moisture, and surface and groundwater flow, leading to conditions that are considerably drier than the usual water content or availability. Drought is often assessed using indices that are associated with meteorological, agricultural, and hydrological phenomena. In order to effectively handle drought disasters, it is essential to accurately determine the kind, intensity, and extent of the drought using drought characterization. This information is critical for managing the drought before, during, and after the rehabilitation process. Over a hundred drought assessments have been created in literature to evaluate drought disasters, encompassing a range of factors and variables. Some models utilise solely hydrometeorological drivers, while others employ remote sensing technology, and some incorporate a combination of both. Comprehending the entire notion of drought and taking into account drought indices along with their calculation processes are crucial for researchers in this discipline. Examining several drought metrics in different studies requires additional time and concentration. Hence, it is crucial to conduct a thorough examination of approaches used in drought indices in order to identify the most straightforward approach to avoid any discrepancies in numerous scientific studies. In case of practical application in real-world, categorizing indices relative to their usage in meteorological, agricultural, and hydrological phenomena might help researchers maximize their efficiency. Users have the ability to explore different indexes at the same time, allowing them to compare the convenience of use and evaluate the benefits and drawbacks of each. Moreover, certain indices exhibit interdependence, which enhances comprehension of their connections and assists in making informed decisions about their suitability in various scenarios. This study provides a comprehensive assessment of various drought indices, analysing their types and computation methodologies in a detailed and systematic manner.

Keywords: drought classification, drought severity, drought indices, agricultur, hydrological

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Authors: Brindha Senthil Kumar, Payel Chakraborty, Senthil Kumar Nachimuthu, Arindam Maitra, Prem Nath

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Gastric cancer is predominantly caused by demographic and diet factors as compared to other cancer types. The aim of the study is to predict Early Gastric Cancer (ECG) from diet and lifestyle factors using supervised machine learning algorithms. For this study, 160 healthy individual and 80 cases were selected who had been followed for 3 years (2016-2019), at Civil Hospital, Aizawl, Mizoram. A dataset containing 11 features that are core risk factors for the gastric cancer were extracted. Supervised machine algorithms: Logistic Regression, Naive Bayes, Support Vector Machine (SVM), Multilayer perceptron, and Random Forest were used to analyze the dataset using Python Jupyter Notebook Version 3. The obtained classified results had been evaluated using metrics parameters: minimum_false_positives, brier_score, accuracy, precision, recall, F1_score, and Receiver Operating Characteristics (ROC) curve. Data analysis results showed Naive Bayes - 88, 0.11; Random Forest - 83, 0.16; SVM - 77, 0.22; Logistic Regression - 75, 0.25 and Multilayer perceptron - 72, 0.27 with respect to accuracy and brier_score in percent. Naive Bayes algorithm out performs with very low false positive rates as well as brier_score and good accuracy. Naive Bayes algorithm classification results in predicting ECG showed very satisfactory results using only diet cum lifestyle factors which will be very helpful for the physicians to educate the patients and public, thereby mortality of gastric cancer can be reduced/avoided with this knowledge mining work.

Keywords: Early Gastric cancer, Machine Learning, Diet, Lifestyle Characteristics

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Authors: Aldrin Avergas, Quennie Mariel Peñaranda, Niña Karen San Miguel, Alexis Katrina Agustin, Peralta Xusha Mae, Maria Luisa Sison

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The research is entitled “The Relationship of Socioeconomic Status and Levels of Delinquency among Senior High School Students with Secured Attachment to their Mothers”. The researchers had explored the relationship between socioeconomic status and delinquent tendencies among grade 11 students. The objective of the research is to discover if delinquent behavior will have a relationship with the current socio-economic status of an adolescent student having a warm relationship with their mothers. The researchers utilized three questionnaires that would measure the three variables of the study, namely: (1) 1SEC 2012: The New Philippines Socioeconomic Classification System was used to show the current socioeconomic status of the respondents, (2) Self-Reported Delinquency – Problem Behavior Frequency Scale was utilized to determine the individual's frequency in engaging to delinquent behavior, and (3) Inventory of Parent and Peer Attachment Revised (IPPA-R) was used to determine the attachment style of the respondents. The researchers utilized a quantitative research design, specifically correlation research. The study concluded that there is no significant relationship between socioeconomic status and academic delinquency despite the fact that these participants had secured attachment to their mother hence this research implies that delinquency is not just a problem for students belonging in the lower socio-economic status and that even having a warm and close relationship with their mothers is not sufficient enough for these students to completely be free from engaging in delinquent acts. There must be other factors (such as peer pressure, emotional quotient, self-esteem or etc.) that are might be contributing to delinquent behaviors.

Keywords: adolescents, delinquency, high school students, secured attachment style, socioeconomic status

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Authors: Atour Taghipour

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In the real world each manufacturing company is an independent business unit. These business units are linked to each other through upstream and downstream linkages. The management of these linkages is called coordination which, could be considered as a difficult engineering task. The degree of difficulty of coordination depends on the type and the nature of information exchanged between partners as well as the structure of relationship from mutual to the network structure. The literature of manufacturing systems comprises a wide range of varieties of methods and approaches of coordination. In fact, two main streams of research can be distinguished: central coordination versus decentralized coordination. In the centralized systems a high degree of information exchanges is required. The high degree of information exchanges sometimes leads to difficulties when independent members do not want to share information. In order to address these difficulties, decentralized approaches of coordination of operations planning decisions based on some minimal information sharing have been proposed in many academic disciplines. This paper first proposes a framework of analysis in order to analyze the proposed approaches in the literature, based on this framework which includes the similarities between approaches we categorize the existing approaches. This classification can be used as a research map for future researches. The result of our paper highlights several opportunities for future research. First, it is proposed to develop more dynamic and stochastic mechanisms of planning coordination of manufacturing units. Second, in order to exploit the complementarities of approaches proposed by diverse science discipline, we propose to integrate the techniques of coordination. Finally, based on our approach we proposed to develop coordination standards to guaranty both the complementarity of these approaches as well as the freedom of companies to adopt any planning tools.

Keywords: network coordination, manufacturing, operations planning, supply chain

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Authors: Gabriela Silva-Maceda, Silvia Romero-Contreras

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Spanish is a more transparent language than English given that it has more direct correspondences between sounds and letters. It has become important to understand how decoding and linguistic comprehension contribute to reading comprehension in the framework of the widely known Simple View Model. This study aimed to identify the level of prediction by these two components in a sample of 1st to 4th grade children attending two schools in central Mexico (one public and one private). Within each school, ten children were randomly selected in each grade level, and their parents were asked about reading habits and socioeconomic information. In total, 79 children completed three standardized tests measuring decoding (pseudo-word reading), linguistic comprehension (understanding of paragraphs) and reading comprehension using subtests from the Clinical Evaluation of Language Fundamentals-Spanish, Fourth Edition, and the Test de Lectura y Escritura en Español (LEE). The data were analyzed using hierarchical regression, with decoding as a first step and linguistic comprehension as a second step. Results showed that decoding accounted for 19.2% of the variance in reading comprehension, while linguistic comprehension accounted for an additional 10%, adding up to 29.2% of variance explained: F (2, 75)= 15.45, p <.001. Socioeconomic status derived from parental questionnaires showed a statistically significant association with the type of school attended, X2 (3, N= 79) = 14.33, p =.002. Nonetheless when analyzing the Simple View components, only decoding differences were statistically significant (t = -6.92, df = 76.81, p < .001, two-tailed); reading comprehension differences were also significant (t = -3.44, df = 76, p = .001, two-tailed). When socioeconomic status was included in the model, it predicted a 5.9% unique variance, even when already accounting for Simple View components, adding to a 35.1% total variance explained. This three-predictor model was also significant: F (3, 72)= 12.99, p <.001. In addition, socioeconomic status was significantly correlated with the amount of non-textbook books parents reported to have at home for both adults (rho = .61, p<.001) and children (rho= .47, p<.001). Results converge with a large body of literature finding socioeconomic differences in reading comprehension; in addition this study suggests that these differences were also present in decoding skills. Although linguistic comprehension differences between schools were expected, it is argued that the test used to collect this variable was not sensitive to linguistic differences, since it came from a test to diagnose clinical language disabilities. Even with this caveat, results show that the components of the Simple View Model can predict less than a third of the variance in reading comprehension in Spanish. However, the results also suggest that a fuller model of reading comprehension is obtained when considering the family’s socioeconomic status, given the potential differences shown by the socioeconomic status association with books at home, factors that are particularly important in countries where inequality gaps are relatively large.

Keywords: decoding, linguistic comprehension, reading comprehension, simple view model, socioeconomic status, Spanish

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Authors: Ethan James

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Over one billion people worldwide suffer from some level of vision loss or blindness as a result of progressive retinal diseases. Many patients, particularly in developing areas, are incorrectly diagnosed or undiagnosed whatsoever due to unconventional diagnostic tools and screening methods. Artificial intelligence (AI) based on deep learning (DL) convolutional neural networks (CNN) have recently gained a high interest in ophthalmology for its computer-imaging diagnosis, disease prognosis, and risk assessment. Optical coherence tomography (OCT) is a popular imaging technique used to capture high-resolution cross-sections of retinas. In ophthalmology, DL has been applied to fundus photographs, optical coherence tomography, and visual fields, achieving robust classification performance in the detection of various retinal diseases including macular degeneration, diabetic retinopathy, and retinitis pigmentosa. However, there is no complete diagnostic model to analyze these retinal images that provide a diagnostic accuracy above 90%. Thus, the purpose of this project was to develop an AI model that utilizes machine learning techniques to automatically diagnose specific retinal diseases from OCT scans. The algorithm consists of neural network architecture that was trained from a dataset of over 20,000 real-world OCT images to train the robust model to utilize residual neural networks with cyclic pooling. This DL model can ultimately aid ophthalmologists in diagnosing patients with these retinal diseases more quickly and more accurately, therefore facilitating earlier treatment, which results in improved post-treatment outcomes.

Keywords: artificial intelligence, deep learning, imaging, medical devices, ophthalmic devices, ophthalmology, retina

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Authors: Mohammad Saber Eslamlou

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Morphology of Islamic cities has been extensively studied by researchers of Islamic cities and different theories could be found about it. In this regard, there exist much difference in method of analysis, classification, recognition, confrontation and comparative method of urban morphology. The present paper aims to examine the previous methods, approaches and insights and that how Dr. Giulia Annalinda Neglia dealt with the analysis of morphology of Islamic cities. Neglia is assistant professor in University of Bari, Italy (UNIBA) who has published numerous papers and books on Islamic cities. I introduce her works in the field of morphology of Islamic cities. And then, her thoughts, insights and research methodologies are presented and analyzed in critical perspective. This is a qualitative research on her written works, which have been classified in three major categories. The first category consists mainly of her works on morphology and physical shape of Islamic cities. The results of her works’ review suggest that she has used Moratoria typology in investigating morphology of Islamic cities. Moreover, overall structure of the cities under investigation is often described linear; however, she’s against to define a single framework for the recognition of morphology in Islamic cities. She states that ‘to understand the physical complexity and irregularities in Islamic cities, it is necessary to study the urban fabric by typology method, focusing on transformation processes of the buildings’ form and their surrounding open spaces’ and she believes that fabric of each region in the city follows from the principles of an specific period or urban pattern, in particular, Hellenistic and Roman structures. Furthermore, she believes that it is impossible to understand the morphology of a city without taking into account the obvious and hidden developments associated with it, because form of building and their surrounding open spaces are written history of the city.

Keywords: city, Islamic city, Giulia Annalinda Neglia, morphology

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Authors: Qingsong Xiong, Cheng Yuan, Qingzhao Kong, Haibei Xiong

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Deep-learning-driven approaches based on vibration responses have attracted larger attention in rapid structural condition assessment while obtaining sufficient measured training data with corresponding labels is relevantly costly and even inaccessible in practical engineering. This study proposes an integrated label propagation network for structural condition assessment, which is able to diffuse the labels from continuously-generating measurements by intact structure to those of missing labels of damage scenarios. The integrated network is embedded with damage-sensitive features extraction by deep autoencoder and pseudo-labels propagation by optimized fuzzy clustering, the architecture and mechanism which are elaborated. With a sophisticated network design and specified strategies for improving performance, the present network achieves to extends the superiority of self-supervised representation learning, unsupervised fuzzy clustering and supervised classification algorithms into an integration aiming at assessing damage conditions. Both numerical simulations and full-scale laboratory shaking table tests of a two-story building structure were conducted to validate its capability of detecting post-earthquake damage. The identifying accuracy of a present network was 0.95 in numerical validations and an average 0.86 in laboratory case studies, respectively. It should be noted that the whole training procedure of all involved models in the network stringently doesn’t rely upon any labeled data of damage scenarios but only several samples of intact structure, which indicates a significant superiority in model adaptability and feasible applicability in practice.

Keywords: autoencoder, condition assessment, fuzzy clustering, label propagation

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Authors: Ayu Dwi Hardiyanti, Bernardus Anggit Winahyu, I. Gusti Agung Ayu Sugita Sari, Lestari Sutra Simamora, I. Wayan Warmada

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The Penosogan Formation sandstone, that has Middle Miosen age, has been deemed as a reservoir potential based on sample data from sandstone outcrop in Kebakalan and Kedawung villages, Karangsambung sub-district, Kebumen Regency, Central Java. This research employs the following analytical methods; petrography, X-ray diffraction (XRD), and porosity test. Based on the presence of micritic sandstone, muddy micrite, and muddy sandstone, the Penosogan Formation sandstone has a fine-coarse granular size and middle-to-fine sorting. The composition of the sandstone is mostly made up of plagioclase, skeletal grain, and traces of micrite. The percentage of clay minerals based on petrographic analysis is 10% and appears to envelop grain, resulting enveloping grain which reduces the porosity of rocks. The porosity types as follows: interparticle, vuggy, channel, and shelter, with an equant form of cement. Moreover, the diagenesis process involves compaction, cementation, authigenic mineral growth, and dissolving due to feldspar alteration. The maturity of the reservoir can be seen through the X-ray diffraction analysis results, using ethylene glycol solution for clay minerals fraction transformed from smectite–illite. Porosity test analysis showed that the Penosogan Formation sandstones has a porosity value of 22% based on the Koeseomadinata classification, 1980. That shows high maturity is very influential for the quality of reservoirs sandstone of the Penosogan Formation.

Keywords: sandstone reservoir, Penosogan Formation, smectite, XRD

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Authors: S. Abdi Goudazri, R. Ziaie Moayed, A. Nazeri

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Loose soils normally are of weak bearing capacity due to their structural nature. Being exposed to heavy traffic loads, they would fail in most cases. To tackle the aforementioned issue, geotechnical engineers have come up with different approaches; one of which is making use of geosynthetic-reinforced soil-aggregate systems. As these polymeric reinforcements have highlighted economic and environmentally-friendly features, they have become widespread in practice during the last decades. The present research investigates the efficiency of four different types of these reinforcements in increasing the bearing capacity of two-layered soil sections using a series California Bearing Ratio (CBR) test. The studied sections are comprised of a 10 cm-thick layer of no. 161 Firouzkooh sand (weak subgrade) and a 10 cm-thick layer of compacted aggregate materials (base course) classified as SP and GW according to the United Soil Classification System (USCS), respectively. The aggregate layer was compacted to the relative density (Dr) of 95% at the optimum water content (Wopt) of 6.5%. The applied reinforcements were including two kinds of geocomposites (type A and B), a geotextile, and a geogrid that were embedded at the interface of the lower and the upper layers of the soil-aggregate system. As the standard CBR mold was not appropriate in height for this study, the mold used for soaked CBR tests were utilized. To make a comparison between the results of stress-settlement behavior in the studied specimens, CBR values pertinent to the penetrations of 2.5 mm and 5 mm were considered. The obtained results demonstrated 21% and 24.5% increments in the amount of CBR value in the presence of geocomposite type A and geogrid, respectively. On the other hand, the effect of both geotextile and geocomposite type B on CBR values was generally insignificant in this research.

Keywords: geosynthetics, geogrid, geotextile, CBR test, increasing bearing capacity

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Authors: Parul Johri, Mala Trivedi

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Major Intrinsic proteins (MIPs), actively involved in the passive transport of small polar molecules across the membranes of almost all living organisms. MIPs that specifically transport water molecules are named aquaporins (AQPs). The permeability of membranes is actively controlled by the regulation of the amount of different MIPs present but also in some cases by phosphorylation and dephosphorylation of the channel. Based on sequence similarity, MIPs have been classified into many categories. All of the proteins are made up of the 20 amino acids, the only difference is there in their orientations. Again all the 20 amino acids are made up of the basic five elements namely: carbon, hydrogen, oxygen, sulphur and nitrogen. These elements are responsible for giving the amino acids the properties of hydrophilicity/hydrophobicity which play an important role in protein interactions. The hydrophobic amino acids characteristically have greater number of carbon atoms as carbon is the main element which contributes to hydrophobic interactions in proteins. It is observed that the carbon level of proteins in different species is different. In the present work, we have taken a sample set of 150 aquaporins proteins from Uniprot database and a dynamic programming code was written to calculate the carbon percentage for each sequence. This carbon percentage was further used to barcode the aqauporins of animals and plants. The protein taken from Oryza sativa, Zea mays and Arabidopsis thaliana preferred to have carbon percentage of 31.8 to 35, whereas on the other hand sequences taken from Mus musculus, Saccharomyces cerevisiae, Homo sapiens, Bos Taurus, and Rattus norvegicus preferred to have carbon percentage of 31 to 33.7. This clearly demarks the carbon range in the aquaporin proteins from plant and animal origin. Hence the atom level analysis of protein sequences can provide us with better results as compared to the residue level comparison.

Keywords: aquaporins, carbon, dynamic prgramming, MIPs

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Authors: Zafar Iqbal Bhatti

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The present research aims to examine and evaluate the frequencies and practices of verb complementation patterns in English newspaper social columns published in Pakistan and Britain. The research will demonstrate that Pakistani English is a non-native variety of English having its own unique usual and logical characteristics, affected by way of the native languages and the culture, upon syntactic levels, making the variety users aware that any differences from British or American English that are systematic and regular, or another English language, are not even if they are unique, erroneous forms and typical characteristics of several kinds. The objectives are to examine the verb complementation patterns that British and Pakistani social columnists use in relation to their syntactic categories. Secondly, to compare the verb complementation patterns used in Pakistani and British English newspapers social columns. This study will figure out various verb complementation patterns in Pakistani and British English newspaper social columns and their occurrence and distribution. The word classes express different functions of words, such as action, event, or state of being. This research aims to evaluate whether there are any appreciable differences in the verb complementation patterns used in Pakistani and British English newspaper social columns. The results will show the number of varieties of verb complementation patterns in selected English newspapers social columns. This study will fill the gap of previous studies conducted in this field as they only explore a little about the differences between Pakistani and British English newspapers. It will also figure out a variety of languages used in Pakistani and British English journals, as well as regional and cultural values and variations. The researcher will use AntConc software in this study to extract the data for analysis. The researcher will use a concordance tool to identify verb complementation patterns in selected data. Then the researcher will manually categorize them because the same type of adverb can sometimes be used for various purposes. From 1st June 2022 to 30th Sep. 2022, a four-month written corpus of the social columns of PE and BE newspapers will be collected and analyzed. For the analysis of the research questions, 50 social columns will be selected from Pakistani newspapers and 50 from British newspapers. The researcher will collect a representative sample of data from Pakistani and British English newspaper social columns. The researcher will manually analyze the complementation patterns of each verb in each sentence, and then the researcher will determine how frequently each pattern occurs. The researcher will use syntactic characteristics of the verb complementation elements according to the description by Downing and Locke (2006). The researcher will examine all of the verb complementation patterns in the data, and the frequency and distribution of each verb complementation pattern will be evaluated using the software. The researcher will explore every possible verb complementation pattern in Pakistani and British English before calculating the occurrence and abundance of each verb pattern. The researcher will explore every possible verb complementation pattern in Pakistani English before calculating the frequency and distribution of each pattern.

Keywords: verb complementation, syntactic categories, newspaper social columns, corpus

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Authors: Silvija Šiljeg, Ivan Marić, Ante Šiljeg

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The accessibility of urban green spaces (UGS) is an integral element in the quality of life. Due to rapid urbanization, UGS studies have become a key element in urban planning. The potential benefits of space for its inhabitants are frequently analysed. A functional transport network system and the optimal spatial distribution of urban green surfaces are the prerequisites for maintaining the environmental equilibrium of the urban landscape. An accessibility analysis was conducted as part of the Urban Green Belts Project (UGB). The development of a GIS database for Zadar was the first step in generating the UGS accessibility indicator. Data were collected using the supervised classification method of multispectral LANDSAT images and manual vectorization of digital orthophoto images (DOF). An analysis of UGS accessibility according to the ANGst standard was conducted in the first phase of research. The accessibility indicator was generated on the basis of seven objective measurements, which included average UGS surface per capita and accessibility according to six functional levels of green surfaces. The generated indicator was compared with subjective measurements obtained by conducting a survey (718 respondents) within statistical units. The collected data reflected individual assessments and subjective evaluations of UGS accessibility. This study highlighted the importance of using objective and subjective measures in the process of understanding the accessibility of urban green surfaces. It may be concluded that when evaluating UGS accessibility, residents emphasize the immediate residential environment, ignoring higher UGS functional levels. It was also concluded that large areas of UGS within a city do not necessarily generate similar satisfaction with accessibility. The heterogeneity of output results may serve as guidelines for the further development of a functional UGS city network.

Keywords: urban green spaces (UGS), accessibility indicator, subjective and objective measurements, Zadar

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Authors: Netasha Shaikh, Bryony Wood, Demitra Tsivos, Michael Knight, Risto Kauppinen, Elizabeth Coulthard

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Background: Effective treatment of dementia will require early diagnosis, before significant brain damage has accumulated. Memory loss is an early symptom of Alzheimer’s disease (AD). The hippocampus, a brain area critical for memory, degenerates early in the course of AD. The hippocampus comprises several subfields. In contrast to healthy aging where CA3 and dentate gyrus are the hippocampal subfields with most prominent atrophy, in AD the CA1 and subiculum are thought to be affected early. Conventional clinical structural neuroimaging is not sufficiently sensitive to identify preferential atrophy in individual subfields. Here, we will explore the sensitivity of new magnetic resonance imaging (MRI) sequences designed to interrogate medial temporal regions as an early marker of Alzheimer’s. As it is likely a combination of tests may predict early Alzheimer’s disease (AD) better than any single test, we look at the potential efficacy of such imaging alone and in combination with standard and novel cognitive tasks of hippocampal dependent memory. Methods: 20 patients with mild cognitive impairment (MCI), 20 with mild-moderate AD and 20 age-matched healthy elderly controls (HC) are being recruited to undergo 3T MRI (with sequences designed to allow volumetric analysis of hippocampal subfields) and a battery of cognitive tasks (including Paired Associative Learning from CANTAB, Hopkins Verbal Learning Test and a novel hippocampal-dependent abstract word memory task). AD participants and healthy controls are being tested just once whereas patients with MCI will be tested twice a year apart. We will compare subfield size between groups and correlate subfield size with cognitive performance on our tasks. In the MCI group, we will explore the relationship between subfield volume, cognitive test performance and deterioration in clinical condition over a year. Results: Preliminary data (currently on 16 participants: 2 AD; 4 MCI; 9 HC) have revealed subfield size differences between subject groups. Patients with AD perform with less accuracy on tasks of hippocampal-dependent memory, and MCI patient performance and reaction times also differ from healthy controls. With further testing, we hope to delineate how subfield-specific atrophy corresponds with changes in cognitive function, and characterise how this progresses over the time course of the disease. Conclusion: Novel sequences on a MRI scanner such as those in route in clinical use can be used to delineate hippocampal subfields in patients with and without dementia. Preliminary data suggest that such subfield analysis, perhaps in combination with cognitive tasks, may be an early marker of AD.

Keywords: Alzheimer's disease, dementia, memory, cognition, hippocampus

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Authors: Varsha Tol, Laila Garda, Neelam Bhardwaj, Malata Usar

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In India, differently- abled girls suffer from a “dual stigma” of being female and physically challenged. The general consensus is that they are incapable of standing on their own two feet. It was observed that these girls do not have access to educational programs as most hostels do not keep them after the tenth grade. They are forced to return to a life of poverty and are often considered a liability by their families. Higher education is completely ignored. Parents focus on finding a husband and passing on their ‘burden’ to someone else. An innovative, intervention for differently-abled adolescent girls with the express purpose of mainstreaming them into society was started by Helplife. The objective was to enrich the lives of these differently abled adolescent girls through precise research, focused intervention and professionalism. This programme addresses physical, mental and social rehabilitation of the girls who come from impoverished backgrounds. These adolescents are reached by word of mouth, snowball technique and through the network of the NGO. Applications are invited from potential candidates which are scrutinized by a panel of experts. Selection criteria include her disability, socio-economic status, and desire and drive to make a difference in her own life. The six main areas of intervention are accommodation, education, health, professional courses, counseling and recreational activities. Each girl on an average resides in Helplife for a period of 2-3 years. Analysis of qualitative data collected at various time points indicates holistic development of character. A quality of life questionnaire showed a significant improvement in scores at three different time points in 75% of the current population under intervention i.e. 19 girls. Till date, 25 girls have successfully passed out from the intervention program completing their graduation/post-graduation. Currently, we have 19 differently abled girls housed in three flats in Pune district of Maharashtra. Out of which 14 girls are pursuing their graduation or post-graduation. Six of the girls are working in jobs in various sectors. In conclusion it may be noted with adequate support and guidance the sky is the limit. This journey of 12 years has been a learning for us with ups and downs modifying the intervention at every step. Helplife has a belief of impacting positively, individual lives of differently abled girls in order to empower them in a holistic manner. The intervention has a positive impact on differently abled girls. They serve as role models to other differently abled girls indicating that this is a road map to success by getting empowered to live with full potential and get integrated in the society in a dignified way.

Keywords: differently-abled, dual-stigma, empowerment, youth

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Authors: Yanyan Wang

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This paper on second language teaching and learning uses conversation analysis (CA) approach and focuses on how second language learners of Chinese do repair when making clarification requests. In order to demonstrate their behavior in interaction, a comparison was made to study the differences between native speakers of Chinese with non-native speakers of Chinese. The significance of the research is to make second language teachers and learners aware of repair and how to seek clarification. Utilizing the methodology of CA, the research involved two sets of naturally occurring recordings, one of native speaker students and the other of non-native speaker students. Both sets of recording were telephone talks between students and teachers. There were 50 native speaker students and 50 non-native speaker students. From multiple listening to the recordings, the parts with repairs for clarification were selected for analysis which included the moments in the talk when students had problems in understanding or hearing the speaker and had to seek clarification. For example, ‘Sorry, I do not understand ‘and ‘Can you repeat the question? ‘were the parts as repair to make clarification requests. In the data, there were 43 such cases from native speaker students and 88 cases from non-native speaker students. The non-native speaker students were more likely to use repair to seek clarification. Analysis on how the students make clarification requests during their conversation was carried out by investigating how the students initiated problems and how the teachers repaired the problems. In CA term, it is called other-initiated self-repair (OISR), which refers to student-initiated teacher-repair in this research. The findings show that, in initiating repair, native speaker students pay more attention to mutual understanding (inter-subjectivity) while non-native speaker students, due to their lack of language proficiency, pay more attention to their status of knowledge (epistemic) switch. There are three major differences: 1, native Chinese students more often initiate closed-class OISR (seeking specific information in the request) such as repeating a word or phrases from the previous turn while non-native students more frequently initiate open-class OISR (not specifying clarification) such as ‘sorry, I don’t understand ‘. 2, native speakers’ clarification requests are treated by the teacher as understanding of the content while non-native learners’ clarification requests are treated by teacher as language proficiency problem. 3, native speakers don’t see repair as knowledge issue and there is no third position in the repair sequences to close repair while non-native learners take repair sequence as a time to adjust their knowledge. There is clear closing third position token such as ‘oh ‘ to close repair sequence so that the topic can go back. In conclusion, this paper uses conversation analysis approach to compare differences between native Chinese speakers and non-native Chinese learners in their ways of conducting repair when making clarification requests. The findings are useful in future Chinese language teaching and learning, especially in teaching pragmatics such as requests.

Keywords: conversation analysis (CA), clarification request, second language (L2), teaching implication

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Authors: Vinay Kumar, M. Kishor, Sathyanarayana Rao Ts

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Background: Growth of elderly people in the general population in recent years is termed as ‘greying of the world’ where there is a shift from high mortality & fertility to low mortality and fertility, resulting in an increased proportion of older people as seen in India. Improved health care promises longevity but socio-economic factors like poverty, joint families and poor services pose a psychological threat. Epidemiological data regarding the prevalence of mental disorders in geriatric population with physical illness is required for proper health planning. Methods: Sixty consecutive elderly patients aged 60 years or above of both sexes, reporting with physical illness to general outpatient registration counter of JSS Medical College and Hospital, Mysore, India, were considered for the Study. With informed consent, they were screened with General Health Questionnaire (GHQ-12) and were further evaluated for diagnosing mental disorders according to WHO International Classification of Diseases (ICD-10) criteria. Results: Mental disorders were detected in 48.3%, predominantly depressive disorders, nicotine dependence, generalized anxiety disorder, alcohol dependence and least was dementia. Most common physical illness was cardiovascular disease followed by metabolic, respiratory and other diseases. Depressive disorders, substance dependence and dementia were more associated with cardiovascular disease compared to metabolic disease and respiratory diseases were more associated with nicotine dependence. Conclusions: Depression and Substance use disorders among elderly population is of concern, which needs to be further studied with larger population. Psychiatric morbidity will adversely have an impact on physical illness which needs proper assessment and management. This will enhance our understanding and prioritize our planning for future.

Keywords: Geriatric, mental disorders, physical illness, psychiatry

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Authors: Isaac K. E. Ampomah, Seong-Bae Park, Sang-Jo Lee

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Over the past decade, there have been promising developments in Natural Language Processing (NLP) with several investigations of approaches focusing on Recognizing Textual Entailment (RTE). These models include models based on lexical similarities, models based on formal reasoning, and most recently deep neural models. In this paper, we present a sentence encoding model that exploits the sentence-to-sentence relation information for RTE. In terms of sentence modeling, Convolutional neural network (CNN) and recurrent neural networks (RNNs) adopt different approaches. RNNs are known to be well suited for sequence modeling, whilst CNN is suited for the extraction of n-gram features through the filters and can learn ranges of relations via the pooling mechanism. We combine the strength of RNN and CNN as stated above to present a unified model for the RTE task. Our model basically combines relation vectors computed from the phrasal representation of each sentence and final encoded sentence representations. Firstly, we pass each sentence through a convolutional layer to extract a sequence of higher-level phrase representation for each sentence from which the first relation vector is computed. Secondly, the phrasal representation of each sentence from the convolutional layer is fed into a Bidirectional Long Short Term Memory (Bi-LSTM) to obtain the final sentence representations from which a second relation vector is computed. The relations vectors are combined and then used in then used in the same fashion as attention mechanism over the Bi-LSTM outputs to yield the final sentence representations for the classification. Experiment on the Stanford Natural Language Inference (SNLI) corpus suggests that this is a promising technique for RTE.

Keywords: deep neural models, natural language inference, recognizing textual entailment (RTE), sentence-to-sentence relation

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Authors: Wendu Pang, Yaxin Luo, Junhong Li, Yu Zhao, Danni Cheng, Yufang Rao, Minzi Mao, Ke Qiu, Yijun Dong, Fei Chen, Jun Liu, Jian Zou, Haiyang Wang, Wei Xu, Jianjun Ren

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We aimed to compare the prognostic prediction value of positive lymph node number (PLNN) to the American Joint Committee on Cancer (AJCC) tumor, lymph node, and metastasis (TNM) staging system for patients with hypopharyngeal squamous cell carcinoma (HPSCC). A total of 826 patients with HPSCC from the Surveillance, Epidemiology, and End Results database (2004–2015) were identified and split into two independent cohorts: training (n=461) and validation (n=365). Univariate and multivariate Cox regression analyses were used to evaluate the prognostic effects of PLNN in patients with HPSCC. We further applied six Cox regression models to compare the survival predictive values of the PLNN and AJCC TNM staging system. PLNN showed a significant association with overall survival (OS) and cancer-specific survival (CSS) (P < 0.001) in both univariate and multivariable analyses, and was divided into three groups (PLNN 0, PLNN 1-5, and PLNN>5). In the training cohort, multivariate analysis revealed that the increased PLNN of HPSCC gave rise to significantly poor OS and CSS after adjusting for age, sex, tumor size, and cancer stage; this trend was also verified by the validation cohort. Additionally, the survival model incorporating a composite of PLNN and TNM classification (C-index, 0.705, 0.734) performed better than the PLNN and AJCC TNM models. PLNN can serve as a powerful survival predictor for patients with HPSCC and is a surrogate supplement for cancer staging systems.

Keywords: hypopharyngeal squamous cell carcinoma, positive lymph nodes number, prognosis, prediction models, survival predictive values

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Authors: Lamphong Volady

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The primary purpose of this study was to explore the traditional cuisine (local food) of Luangprabang Province in line with the Lao PDR’s One District One Product Policy. Another purpose of the study was to examine channels used to present local food, reasons to preserve and promote local food, as well as local food preservation and promotion strategies. It also aimed at testing correlation hypotheses whether there is a statistically significant relationship between enjoyment of having local food and willingness to promote local cuisines becoming international cuisines, attractiveness to consume local food, preservation and promotion of local food problems, and local people’s occupations. The Convergent Parallel Mixed Methods were employed in this study. The results of the study showed that several local cuisines were found to be local food of Luangprabang Province, namely Jeow Bon (Chilli dipping suace), Or Lam or aw lahm (stew buffalo skin, herbs, Mai sakaan), Kai Pan (River Weed Dry), Tam Mak Houng Luangprabang (Papaya Salad), Nang (Yam Buffalo Skin Dry), Sai Oor (Sausage), Laap Sin Koay Sai Mar-Keua Pao (Beef Salad with Roasted Eggplants), Orm Born (Taro leaves Stew), Oor Nor Mai (Bamboo Shoot Sausage), Jeow Nam Poo (Pickled Crab Chillies), Mok Dok Kae (steaming or roasting a Dok Kae Wrapp), Nor Sa Wan, Kao Noom Kee Noo, Kao Noom Ba Bin. It also depicted that YouTube, Facebook, and TikTok were multiple social channels or platforms which were found to be used to introduce traditional food as well as television, smartphone, word of mouth, Lao food fairs and other provincial events. The study also found that local food should be preserved and promoted since traditional food is not only ancestral, ancient, traditional, and local cuisines, but it is also wisdom, unique, and national cuisine. The study also found that people feel attracted to consuming local food because local food is delicious, unique, clean, nutritious, non-contaminated and natural. The study showed that lack of funds to produce local food, inadequate draw materials, lack material to store products, insufficient place to produce and lack of related organizations engagement were found to be problems for preserving and promoting traditional food. Finally, the result of the study revealed that there is a statistically significant weak relationship between enjoyment of having local food and willingness to promote local cuisines becoming international cuisines (R²= 4.5%), (p-value <0.001). There is a statistically significant moderate relationship between enjoyment of having local food and attractiveness to consume local food (R²= 7.8%), (p-value <0.001). However, there is a statistically insignificant relationship between enjoyment of having local food and preservation and promotion of local food problems (R²= 1.8%), (p-value = 0.086). It was found that there is a statistically insignificant relationship between enjoyment of having local food and local people’s occupations (R²= 0.0%), (p-value = 0.929).

Keywords: local food, preservation, promotion, traditional food, cuisines

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Authors: P. Massanyi, L. Kichi, T. Slanina, E. Kolesar, J. Danko, N. Lukac, E. Tvrda, R. Stawarz, A. Kolesarova

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Target of this study was the analysis of the impact of crude glycerol on canine spermatozoa motility, morphology, viability, and membrane integrity. Experiments were realized in vitro. In the study, semen from 5 large dog breeds was used. They were typical representatives of large breeds, coming from healthy rearing, regularly vaccinated and integrated to the further breeding. Semen collections were realized at the owners of animals and in the veterinary clinic. Subsequently the experiments were realized at the Department of Animal Physiology of the SUA in Nitra. The spermatozoa motility was evaluated using CASA analyzer (SpermVisionTM, Minitub, Germany) at the temperature 5 and 37°C for 5 hours. In the study, 13 motility parameters were evaluated. Generally, crude glycerol has generally negative effect on spermatozoa motility. Morphological analysis was realized using Hancock staining and the preparations were evaluated at magnification 1000x using classification tables of morphologically changed spermatozoa. Data clearly detected the highest number of morphologically changed spermatozoa in the experimental groups (know twisted tails, tail torso and tail coiling). For acrosome alterations swelled acrosomes, removed acrosomes and acrosomes with undulated membrane were detected. In this study also the effect of crude glycerol on spermatozoa membrane integrity were analyzed. The highest crude glycerol concentration significantly affects spermatozoa integrity. Results of this study show that crude glycerol has effect of spermatozoa motility, viability, and membrane integrity. Detected changes are related to crude glycerol concentration, temperature, as well as time of incubation.

Keywords: dog, semen, spermatozoa, acrosome, glycerol, CASA, viability

Procedia PDF Downloads 302

Authors: K. P. Fasalu Rahman

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The financial services industry of Islam include large number of institutions, such as investment banks and commercial banks, investment companies and mutual insurance companies. All types of these financial institutions should have to deal with many issues and risks in their field of work. Islamic banks should expect to face two types of risks: risks that are similar to those faced by conventional financial intermediaries and risks that are unique to the Islamic Banks due to their compliance with the Shariah. The use of financial services and products that comply with the Shariah principles cause special issues for supervision and risk management. Risks are uncertain future events that could influence the achievement of the bank’s objectives, including strategic, operational, financial and compliance objectives. In Islamic banks, effective risk management deserves special attention. As an operational problem, risk management is the classification and identification of methods, processes, and risks in banks to supervise, monitor and measure them. In comparison to conventional banks, Islamic banks face big difficulties in identifying and managing risks due to bigger complexities emerging from the profit loss sharing (PLS) concept and nature of particular risks of Islamic financing. As the developing of managing risks tool becomes very essential, especially in Islamic banking as most of the products are depending on PLS principle, identifying and measuring each type of risk is highly important and critical in any Islamic finance based systems. This paper highlights the special and general risks surrounding Islamic banking. And it investigates in detail the need for risk management in Islamic banks. In addition to analyzing the effectiveness of risk management strategies adopted by Islamic financial institutions at present, this research is also suggesting strategies for improving risk management process of Islamic banks in future.

Keywords: Islamic banking, management, risk, risk management

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Authors: Rian O. Miranda, Lidia V. de Sa, Julio C. Suita

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The Brazilian Nuclear Energy Commission (CNEN) is the main manufacturer of radiopharmaceuticals in Brazil. The Nuclear Engineering Institute (IEN), located at Rio de Janeiro, is one of its main centers of research and production, attending public and private hospitals in the state. This radiopharmaceutical production is used in diagnostic and therapy procedures and allows one and a half million nuclear medicine procedures annually. Despite this, the country is not self-sufficient to meet national demand, creating the need for importation and consequent dependence on other countries. However, IEN facilities were designed in the 60's, and today its structure is inadequate in relation to the good manufacturing practices established by sanitary regulator (ANVISA) and radiological protection leading to the need for a new project. In order to adapt and increase production in the country, a new plant will be built and integrated to the existing facilities with a new 30 MeV Cyclotron that is actually in project detailing process. Thus, it is proposed to survey current CNEN and ANVISA standards for radiopharmaceutical production facilities, as well as the radiological protection analysis of each area of the plant, following good manufacturing practices recommendations adopted nationally besides licensing exigencies for radioactive facilities. In this way, the main requirements for proper operation, equipment location, building materials, area classification, and maintenance program have been implemented. The access controls, interlocks, segregation zones and pass-through boxes integrated into the project were also analyzed. As a result, IEN will in future have the flexibility to produce all necessary radioisotopes for nuclear medicine application, more efficiently by simultaneously bombarding two targets, allowing the simultaneous production of two different radioisotopes, minimizing radiation exposure and saving operating costs.

Keywords: cyclotron, legislation, norms, production, radiopharmaceuticals

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Authors: Sophie Mills, Leila L. Touil, Richard Sisson

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Introduction: The TNM classification is the global standard for the staging of head and neck cancers. Accurate clinical-radiological staging of tumours (cTNM) is essential to predict prognosis, facilitate surgical planning and determine the need for other therapeutic modalities. This study aims to determine the accuracy of pre-operative cTNM staging using pathological TNM (pTNM) and consider possible causes of TNM stage migration, noting any variation throughout the COVID-19 pandemic. Materials and Methods: A retrospective cohort study examined records of patients with surgical management of head and neck cancer at a tertiary head and neck centre from November 2019 to November 2020. Data was extracted from Somerset Cancer Registry and histopathology reports. cTNM and pTNM were compared before and during the first wave of COVID-19, as well as with other potential prognostic factors such as tumour site and tumour stage. Results: 119 cases were identified, of which 52.1% (n=62) were male, and 47.9% (n=57) were female with a mean age of 67 years. Clinical and pathological staging differed in 54.6% (n=65) of cases. Of the patients with stage migration, 40.4% (n=23) were up-staged and 59.6% (n=34) were down-staged compared with pTNM. There was no significant difference in the accuracy of cTNM staging compared with age, sex, or tumour site. There was a statistically highly significant (p < 0.001) correlation between cTNM accuracy and tumour stage, with the accuracy of cTNM staging decreasing with the advancement of pTNM staging. No statistically significant variation was noted between patients staged prior to and during COVID-19. Conclusions: Discrepancies in staging can impact management and outcomes for patients. This study found that the higher the pTNM, the more likely stage migration will occur. These findings are concordant with the oncology literature, which highlights the need to improve the accuracy of cTNM staging for more advanced tumours.

Keywords: COVID-19, head and neck cancer, stage migration, TNM staging

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Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

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

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

Procedia PDF Downloads 116