Search results for: supervised multi-class classification

Authors: Hong Geng, Zaiyu Fan

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With the acceleration of urbanization and motorization in China, the scale of cities and the travel distance of residents are constantly expanding, and the number of cars is continuously increasing, so the urban traffic problem is more and more serious. Traffic congestion, environmental pollution, energy consumption, travel safety and direct interference between traffic and other urban activities are increasingly prominent problems brought about by motorized development. This not only has a serious impact on the lives of the residents but also has a major impact on the healthy development of the city. The paper found that, in order to solve the development of motorization, a number of problems will arise; urban planning and traffic planning and design in residential planning often take into account the development of motorized traffic but neglects the demand for street life. This kind of planning has resulted in the destruction of the traditional communication space of the residential area, the pollution of noise and exhaust gas, and the potential safety risks of the residential area, which has disturbed the previously quiet and comfortable life of the residential area, resulting in the inconvenience of residents' life and the loss of street vitality. Based on these facts, this paper takes a residential area in Wuhan as the research object, through the actual investigation and research, from the perspective of micro-transformation analysis, combined with the concept of traffic micro-reconstruction governance. And research puts forward the residential traffic optimization strategies such as strengthening the interaction and connection between the residential area and the urban street system, street traffic classification and organization.

Keywords: micro-transformation, residential traffic, residents demand, traffic microcirculation

Procedia PDF Downloads 101

Authors: Ammar Said Ahmed, M. Reissmann, R. Bortfeldt, G. A. Brockmann

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Milk protein genetic variants are of interest for characterizing domesticated mammalian species and breeds, and for studying associations with economic traits. The aim of this work was to analyze milk protein genetic variation in the Sudanese native cattle breeds, which have been gradually declining in numbers over the last years due to the breed substitution, and indiscriminate crossbreeding. The genetic variation at three milk protein genes αS1-casein (CSN1S1), αS2-casein (CSN1S2) and ƙ-casein (CSN3) was investigated in 250 animals belonging to five Bos indicus cattle breeds of Sudan (Butana, Kenana, White-nile, Erashy and Elgash). Allele specific primers were designed for five SNPs determine the CSN1S1 variants B and C, the CSN1S2 variants A and B, the CSN3 variants A, B and H. Allele, haplotype frequencies and genetic distances (D) were calculated and the phylogenetic tree was constructed. All breeds were found to be polymorphic for the studied genes. The CSN1S1*C variant was found very frequently (>0.63) in all analyzed breeds with highest frequency (0.82) in White-nile cattle. The CSN1S2*A variant (0.77) and CSN3*A variant (0.79) had highest frequency in Kenana cattle. Eleven haplotypes in casein gene cluster were inferred. Six of all haplotypes occurred in all breeds with remarkably deferent frequencies. The estimated D ranged from 0.004 to 0.049. The most distant breeds were White-nile and Kenana (D 0.0479). The results presented contribute to the genetic knowledge of indigenous cattle and can be used for proper definition and classification of the Sudanese cattle breeds as well as breeding, utilization, and potential development of conservation strategies for local breeds.

Keywords: milk protein, genetic variation, casein haplotype, Bos indicus

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Authors: Xiaohua Zhu, Lingling Ma, Yongguang Zhao

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Leaf Area Index (LAI) is a key structural characteristic of crops and plays a significant role in precision agricultural management and farmland ecosystem modeling. However, LAI retrieved from different resolution data contain a scaling bias due to the spatial heterogeneity and model non-linearity, that is, there is scale effect during multi-scale LAI estimate. In this article, a typical farmland in semi-arid regions of Chinese Inner Mongolia is taken as the study area, based on the combination of PROSPECT model and SAIL model, a multiple dimensional Look-Up-Table (LUT) is generated for multiple crops LAI estimation from unmanned aerial vehicle (UAV) hyperspectral data. Based on Taylor expansion method and computational geometry model, a scale transfer model considering both difference between inter- and intra-class is constructed for scale effect analysis of LAI inversion over inhomogeneous surface. The results indicate that, (1) the LUT method based on classification and parameter sensitive analysis is useful for LAI retrieval of corn, potato, sunflower and melon on the typical farmland, with correlation coefficient R2 of 0.82 and root mean square error RMSE of 0.43m2/m-2. (2) The scale effect of LAI is becoming obvious with the decrease of image resolution, and maximum scale bias is more than 45%. (3) The scale effect of inter-classes is higher than that of intra-class, which can be corrected efficiently by the scale transfer model established based Taylor expansion and Computational geometry. After corrected, the maximum scale bias can be reduced to 1.2%.

Keywords: leaf area index (LAI), scale effect, UAV-based hyperspectral data, look-up-table (LUT), remote sensing

Procedia PDF Downloads 424

Authors: Tahani Aljohani, Jialin Yu, Alexandra. I. Cristea

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The more an educational system knows about a learner, the more personalised interaction it can provide, which leads to better learning. However, asking a learner directly is potentially disruptive, and often ignored by learners. Especially in the booming realm of MOOC Massive Online Learning platforms, only a very low percentage of users disclose demographic information about themselves. Thus, in this paper, we aim to predict learners’ demographic characteristics, by proposing an approach using linguistically motivated Deep Learning Architectures for Learner Profiling, particularly targeting gender prediction on a FutureLearn MOOC platform. Additionally, we tackle here the difficult problem of predicting the gender of learners based on their comments only – which are often available across MOOCs. The most common current approaches to text classification use the Long Short-Term Memory (LSTM) model, considering sentences as sequences. However, human language also has structures. In this research, rather than considering sentences as plain sequences, we hypothesise that higher semantic - and syntactic level sentence processing based on linguistics will render a richer representation. We thus evaluate, the traditional LSTM versus other bleeding edge models, which take into account syntactic structure, such as tree-structured LSTM, Stack-augmented Parser-Interpreter Neural Network (SPINN) and the Structure-Aware Tag Augmented model (SATA). Additionally, we explore using different word-level encoding functions. We have implemented these methods on Our MOOC dataset, which is the most performant one comparing with a public dataset on sentiment analysis that is further used as a cross-examining for the models' results.

Keywords: deep learning, data mining, gender predication, MOOCs

Procedia PDF Downloads 118

Authors: Leila M. Carvalho, Maria Erica S. Oliveira, Arnoud C. Neto, Elza I. Ida, Massami Shimokomaki, Marta S. Madruga

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The quality of broiler breast meat is changing as a result of the continuing emphasis on genetic selection for a more efficient meat production. Breast meat has been classified as PSE (pale, soft, exudative), DFD (dark, firm, dry) and normal color meat, and recently a third group has emerged: the so-called PFN (pale, firm, non-exudative) meat. This classification was based on pH, color and functional properties. The aim of this work was to confirm the existence of PFN and PSE meat by biochemical characterization and functional properties. Twenty four hours of refrigerated fillet, Pectoralis major, m. samples (n= 838) were taken from Cobb flocks 42-48 days old, obtained in Northeastern Brazil tropical region, the Northeastern, considered to have only dry and wet seasons. Color (L*), pH, water holding capacity (WHC), values were evaluated and compared with PSE group samples. These samples were classified as Normal (465.8), PSE meat (L*≥53; pH<5.8) and PFN (L*≥53; pH>5.8). The occurrence of control meat, PSE and PFN was 69.09%, 11.10% and 19.81%, respectively. Samples from PFN presented 4.0-5.0% higher WHC in relation to PSE meat and similar to control group. These results are explained by the fact that PSE meat syndrome occurs because of higher protein denaturation as the consequence of a simultaneous lower pH values under warm carcass sooner after slaughtering impairing the myofibril proteins functional properties. Conversely, PFN samples follow normal glycolysis rate maintaining the normal proteins activities. In conclusion, the results reported herein confirm the existence of this emerging broiler meat group with similar properties as control group and it should be considered as normal breast meat group.

Keywords: broiler breast meat, funcional properties, PFN, PSE

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Authors: Rita Bagheri, Javed Ahmed, Humayra Bashir, M. Irfan Qureshi

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Agriculture lands suffer from a combination of stresses such as salinity and metal contamination including cadmium at the same time. Under such condition of multiple stresses, plant may exhibit unique responses different from the stress occurring individually. Thus, it would be interesting to investigate that how plant respond to combined stress at level of antioxidants and proteome expression, and identifying the proteins which are involved in imparting stress tolerance. With an approach of comparative proteomics and antioxidant analysis, present study investigates the response of Spinacia oleracea to salt (NaCl), cadmium (Cd), and their combination (NaCl+Cd) stress. Two-dimensional gel electrophoresis was used for resolving leaf proteome, and proteins of interest were identified using PDQuest software. A number of proteins expressed differentially, those indicated towards their roles in imparting stress tolerance, were digested by trypsin and analyzed on mass spectrometer for peptide mass fingerprinting (PMF). Data signals were then matched with protein databases using MASCOT. Results show that NaCl, Cd and both together (NaCl+Cd) induce oxidative stress which was highest in combined stress of Cd+NaCl. Correspondingly, the activities of enzymatic antioxidants viz., SOD, APX, GR and CAT, and non-enzymatic antioxidants had highest changes under combined stress compares to single stress over their respective controls. Among the identified proteins, several interesting proteins were identified that may be have role in Spinacia oleracia tolerance in individual and combinatorial stress of salt and cadmium. The functional classification of identified proteins indicates the importance and necessity of keeping higher ratio of defence and disease responsive proteins.

Keywords: Spinacia oleracea, Cd, salinity, proteomics, antioxidants, combinatorial stress

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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

Procedia PDF Downloads 137

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

Procedia PDF Downloads 596

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

Procedia PDF Downloads 115

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

Procedia PDF Downloads 215

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: 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

Procedia PDF Downloads 167

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: 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: 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: Ana Violante, Jodie Maccarrone, Maria Fimiani

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In the United States, over 30 million people are hospitalized annually for conditions that require acute, 24-hour, supervised care. The experience of hospitalization can be traumatic, exposing the patient to loss of control, autonomy, and productivity. Furthermore, 40% of patients admitted to hospitals for general medical illness have a comorbid psychiatric diagnosis. Research suggests individuals admitted with psychiatric comorbidities experience poorer health outcomes, higher utilization rates and increased overall cost of care. Empirical work suggests hospital settings that include a consultation liaison (CL) service report reduced length of stay, lower costs per patient, improved medical staff and patient satisfaction and reduced readmission after 180 days. Despite the overall positive impact CL services can have on patient care, it is estimated that only 1% - 2.8% of hospital admits receive these services, and most research has been conducted by the field of psychiatry. Health psychologists could play an important role in increasing access to this valuable service, though the extent to which health psychologists participate in CL settings is not well known. Objective: Outline the preliminary findings from an empirical study to understand how many APPIC internship training programs offer adult consultation liaison rotations within inpatient hospital settings nationally, as well as describe the specific nature of these training experiences. Research Method/Design: Data was exported into Excel from the 2022-2023 APPIC Directory categorized as “health psychology” sites. It initially returned a total of 537 health training programs out 1518 total programs (35% of all APPIC programs). A full review included a quantitative and qualitative comprehensive review of the APPIC program summary, the site website, and program brochures. The quantitative review extracted the number of training positions; amount of stipend; location or state of program, patient, population, and rotation. The qualitative review examined the nature of the training experience. Results: 29 (5%) of all APPIC health psychology internship training programs (2%) respectively of all APPIC training internship programs offering internship CL training were identified. Of the 29 internship training programs, 16 were exclusively within a pediatric setting (55%), 11 were exclusively within an adult setting (38%), and two were a mix of pediatric and adult settings (7%). CL training sites were located to 19 states, offering a total of 153 positions nationally, with Florida containing the largest number of programs (4). Only six programs offered 12-month training opportunities while the rest offered CL as a major (6 month) to minor (3-4 month) rotation. The program’s stipend for CL training positions ranged from $25,000 to $62,400, with an average of $32,056. Conclusions: These preliminary findings suggest CL training and services are currently limited. Training opportunities that do exist are mostly limited to minor, short rotations and governed by psychiatry. Health psychologists are well-positioned to better define the role of psychology in consultation liaison services and enhance and formalize existing training protocols. Future research should explore in more detail empirical outcomes of CL services that employ psychology and delineate the contributions of psychology from psychiatry and other disciplines within an inpatient hospital setting.

Keywords: consultation liaison, health psychology, hospital setting, training

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Authors: Sofia Quaglia, Carmine Di Martino, Brendan Tierney

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Artificial Intelligence (A.I.) constitutes various aspects of modern life, from the Machine Learning algorithms predicting the stocks on Wall streets to the killing of belligerents and innocents alike on the battlefield. Moreover, the end goal is to create autonomous A.I.; this means that the presence of humans in the decision-making process will be absent. The question comes naturally: when an A.I. does something wrong when its behavior is harmful to the community and its actions go against the law, which is to be held responsible? This research’s subject matter in A.I. and Robot Ethics focuses mainly on Robot Rights and its ultimate objective is to answer the questions: (i) What is the function of rights? (ii) Who is a right holder, what is personhood and the requirements needed to be a moral agent (therefore, accountable for responsibility)? (iii) Can an A.I. be a moral agent? (ontological requirements) and finally (iv) if it ought to be one (ethical implications). With the direction to answer this question, this research project was done via a collaboration between the School of Computer Science in the Technical University of Dublin that oversaw the technical aspects of this work, as well as the Department of Philosophy in the University of Milan, who supervised the philosophical framework and argumentation of the project. Firstly, it was found that all rights are positive and based on consensus; they change with time based on circumstances. Their function is to protect the social fabric and avoid dangerous situations. The same goes for the requirements considered necessary to be a moral agent: those are not absolute; in fact, they are constantly redesigned. Hence, the next logical step was to identify what requirements are regarded as fundamental in real-world judicial systems, comparing them to that of ones used in philosophy. Autonomy, free will, intentionality, consciousness and responsibility were identified as the requirements to be considered a moral agent. The work went on to build a symmetrical system between personhood and A.I. to enable the emergence of the ontological differences between the two. Each requirement is introduced, explained in the most relevant theories of contemporary philosophy, and observed in its manifestation in A.I. Finally, after completing the philosophical and technical analysis, conclusions were drawn. As underlined in the research questions, there are two issues regarding the assignment of moral agency to artificial agent: the first being that all the ontological requirements must be present and secondly being present or not, whether an A.I. ought to be considered as an artificial moral agent. From an ontological point of view, it is very hard to prove that an A.I. could be autonomous, free, intentional, conscious, and responsible. The philosophical accounts are often very theoretical and inconclusive, making it difficult to fully detect these requirements on an experimental level of demonstration. However, from an ethical point of view it makes sense to consider some A.I. as artificial moral agents, hence responsible for their own actions. When considering artificial agents as responsible, there can be applied already existing norms in our judicial system such as removing them from society, and re-educating them, in order to re-introduced them to society. This is in line with how the highest profile correctional facilities ought to work. Noticeably, this is a provisional conclusion and research must continue further. Nevertheless, the strength of the presented argument lies in its immediate applicability to real world scenarios. To refer to the aforementioned incidents, involving the murderer of innocents, when this thesis is applied it is possible to hold an A.I. accountable and responsible for its actions. This infers removing it from society by virtue of its un-usability, re-programming it and, only when properly functioning, re-introducing it successfully

Keywords: artificial agency, correctional system, ethics, natural agency, responsibility

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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: 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

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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: Abiodun Afolabi, Rufus Adesoji Adedoyin

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This study investigated and compared the effects of gym-based exercise programme (GEBP) and audio-visual guided home-based exercise programme (AVGHBEP) on selected Anthropometric variables (Weight (W), Body Mass Index (BMI), Waist Circumference (WC), Hip Circumference (HC), Thigh Circumference (TC), Waist-Hip-Ratio (WHR), Waist-Height-Ratio (WHtR), Waist-Thigh-Ratio (WTR), Biceps Skinfold Thickness (BSFT), Triceps Skinfold Thickness (TSFT), Suprailliac Skinfold Thickness (SISFT), Subscapular Skinfold Thickness (SSSFT) and Percent Body Fat (PBF)); and Cardiovasular variables (Systolic Blood Pressure (SBP), Diastolic Blood Pressure (DBP) and Heart Rate (HR)) of overweight and obese students of Federal College of Education (Special), Oyo, Oyo State, Nigeria, with a view to providing information and evidence for GBEP and AVGHBEP in reducing overweight and obesity for promoting cardiovascular fitness. Eighty overweight and obese students (BMI ≥ 25 Kg/m²) were involved in this pretest-posttest quasi experimental study. Participants were randomly assigned into GBEP (n = 40) and AVGBBEP (n = 40) groups. Anthropometric and cardiovascular variables were measured using a weighing scale, height meter, tape measure, skinfold caliper and electronic sphygmomanometer following standard protocols. GBEP and AVGHBEP were implemented following a circuit training (aerobic and resistance training) pattern with a duration of 40-60 minutes, thrice weekly for twelve weeks. GBEP consisted of gymnasium supervised exercise programme while AVGHBEP is a Visual Display guided exercise programme conducted at the home setting. Data were analyzed by Descriptive and Inferential Statistics. The mean ages of the participants were 22.55 ± 2.55 and 23.65 ± 2.89 years for the GBEP group and AVGHBEP group, respectively. Findings showed that in the GBEP group, there were significant reductions in anthropometric variables and adiposity measures of Weight, BMI, BSFT, TSFT, SISFT, SSSFT, WC, HC, TC, WHtR, and PBF at week 12 of the study. Similarly, in the AVGHBEP group, there were significant reductions in Weight, BMI, BSFT, TSFT, SISFT, SSSFT, WC, HC, TC, WHtR and PBF at the 12th week of intervention. Comparison of the effects of GEBP and AVGHBEP on anthropometric variables and measures of adiposity showed that there was no significant difference between the two groups in weight, BMI, BSFT, TSFT, SISFT, SSSFT, WC, HC, TC, WHR, WHtR, WTR and PBF between the two groups at week 12 of the study. Furthermore, findings on the effects of exercise on programmes on cardiovascular variables revealed that significant reductions occurred in SBP in GBEP group and AVGHBEP group respectively. Comparison of the effects of GBEP and AVGHBEP on cardiovascular variables showed that there was no significant difference in SBP, DBP and HR between the two groups at week 12 of the study. It was concluded that the Audio-Visual Guided Home-based Exercise Programme was as effective as the Gym-Based Exercise Programme in causing a significant reduction in anthropometric variables and body fat among college students who are overweight and obese over a period of twelve weeks. Both Gymnasium-Based Exercise Programme and Audio-Visual Guided Home-Based Exercise Programme led to significant reduction in Systolic Blood Pressure over a period of weeks. Audio-Visual Guided Home-Based Exercise Programme can, therefore, be used as an alternative therapy in the non-pharmacological management of people who are overweight and obese.

Keywords: gym-based exercises, audio-visual guided home-based exercises, anthropometric parameters, cardiovascular parameters, overweight students, obese students

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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

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