Search results for: DNA sequences classification

Authors: Soha A. Bahanshal, Byung G. Kim

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Identification of patients at high risk for hospital readmission is of crucial importance for quality health care and cost reduction. Predicting hospital readmissions among diabetic patients has been of great interest to many researchers and health decision makers. We build a prediction model to predict hospital readmission for diabetic patients within 30 days of discharge. The core of the prediction model is a modified k Nearest Neighbor called Hybrid Fuzzy Weighted k Nearest Neighbor algorithm. The prediction is performed on a patient dataset which consists of more than 70,000 patients with 50 attributes. We applied data preprocessing using different techniques in order to handle data imbalance and to fuzzify the data to suit the prediction algorithm. The model so far achieved classification accuracy of 80% compared to other models that only use k Nearest Neighbor.

Keywords: machine learning, prediction, classification, hybrid fuzzy weighted k-nearest neighbor, diabetic hospital readmission

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Authors: Mohammadreza Hajialigol, Nargues Falahi Charkhabi, Fatemeh Shahryari, Saadat Sarikhani

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BACKGROUND AND OBJECTIVES Iran is the third producer of Persian walnut worldwide. However, its walnut trees have been under threat from decline during last decade. Walnut canker caused by B. nigrifluens and B. rubrifaciens was recorded in multiple regions of Iran. Furthermore, Brenneria rosae subsp. rosae and Gibbsiella quercinecans were recently recognized as responsible for walnut decline in northwestern Iran. This study aimed to identify the causal agent of walnut decline in Kermanshah and Isfahan. MATERIAL AND METHODS Symptomatic samples were collected from affected walnut trees of Kermanshah and Isfahan provinces. The pathogenicity of strains was proved on immature walnut fruits cv. ‘Hartley’ and young green twigs of two-year-old walnut seedling cv. ‘Chandler’. Pathogenic strains were subjected to conventional phenotypic tests. 16S rRNA, gyrB, and infB genes were partially amplified and sequenced. RESULTS Irregular longitudinal cankers and dark lesions were observed in the outer and inner bark, respectively. Twenty-four strains were isolated on EMB-agar media. Fourteen strains were able to cause necrosis and a dark-colored region in the mesocarp and on young green twigs around the inoculation site 14 and 30 days post-inoculation, respectively. Strains were able to hydrolyze Tween 20, Tween 80, gelatin and esculin, however, did not produce indole or urease. Pairwise comparison, the 16S rRNA gene nucleotide sequences of strain I2 were 100% identical with those of Rahnella victoriana FRB 225T. Moreover, a phylogenetic tree reconstructed based on the concatenated sequences of two housekeeping gene fragments, gyrB (601 bp) and infB (615 bp), revealed that the strains I2, I5, and KE6 were clustered with R. victoriana FRB 225T. CONCLUSION To the best of our knowledge, this is the first report of R. victoriana in association with walnut decline. This result is necessary to find resistant genotypes.

Keywords: emerging pathogens, Iran, juglans regia, MLSA

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Authors: Bhekisipho Twala, Mantepu Masetshaba, Ramapulana Nkoana

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Multiple classifier systems combine several individual classifiers to deliver a final classification decision. However, an increasingly controversial question is whether such systems can outperform the single best classifier, and if so, what form of multiple classifiers system yields the most significant benefit. Also, multi-target tracking detection using multiple sensors is an important research field in mobile techniques and military applications. In this paper, several multiple classifiers systems are evaluated in terms of their ability to predict a system’s failure or success for multi-sensor target tracking tasks. The Bristol Eden project dataset is utilised for this task. Experimental and simulation results show that the human activity identification system can fulfill requirements of target tracking due to improved sensors classification performances with multiple classifier systems constructed using boosting achieving higher accuracy rates.

Keywords: single classifier, ensemble learning, multi-target tracking, multiple classifiers

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Authors: Dwi Arisandi Wijaya, Ernawati Arifin Giri-Rachman, Neni Nurainy

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Typhoid fever disease can be prevented by using a polysaccharide-based vaccine Vi which is a virulence factor of S.typhi. To produce high yield Vi polysaccharide from bacteria, it is important to know the biosynthesis of Vi polysaccharide and the regulators involved. In the In vivo condition, S. typhi faces different osmolarity, and the bacterial two-component system OmpR-EnvZ, regulate by up and down Capsular Vi polysaccharide biosynthesis. A high yielded Vi Polysaccharide strain, S. typhi strain C6524 used to study the effect of media osmolarity on Vi polysaccharide biosynthesis and the osmoregulation pattern of S. typhi strain C6524. The methods were performed by grown S. typhi strain C6524 grown on medium with 50 mM, 100 mM, and 150 mM osmolarity with the batch system. Vi polysaccharide concentration was measured by ELISA method. For further investigation of the osmoregulation pattern of strain C6524, the osmoregulator gene, OmpR, has been isolated and sequenced using the specific primer of the OmpR gene. Nucleotide sequence analysis is done with BLAST and Lallign. Amino Acid sequence analysis is done with Prosite and Multiple Sequence Alignment. The results of cultivation showed the average content of polysaccharide Vi for 50 mM, 100 mM, and 150 mM osmolarities 11.49 μg/mL, 12.06 μg/mL, and 14.53 μg/mL respectively. Analysis using Anova stated that the osmolarity treatment of 150 mM significantly affects Vi content. Analysis of nucleotide sequences shows 100% identity between S. typhi strain C6524 and Ty2. Analysis of amino acid sequences shows that the OmpR response regulator protein of the C6524 strain also has a α4-β5-α5 motif which is important for the regulatory activation system when phosphorylation occurs by domain kinase. This indicates that the regulator osmolarity response of S. typhi strain C6524 has no difference with the response regulator owned by S. typhi strain Ty2. A high Vi response rate in the 150 mM osmolarity treatment requires further research for RcsB-RcsC, another two-component system involved in Vi Biosynthesis.

Keywords: osmoregulator, OmpR, Salmonella, Vi polysaccharide

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Authors: Amanda T. Badaró, Douglas F. Barbin, Sofia T. Garcia, Maria Teresa P. S. Clerici, Amanda R. Ferreira

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Food fortification is the intentional addition of a nutrient in a food matrix and has been widely used to overcome the lack of nutrients in the diet or increasing the nutritional value of food. Fortified food must meet the demand of the population, taking into account their habits and risks that these foods may cause. Wheat and its by-products, such as semolina, has been strongly indicated to be used as a food vehicle since it is widely consumed and used in the production of other foods. These products have been strategically used to add some nutrients, such as fibers. Methods of analysis and quantification of these kinds of components are destructive and require lengthy sample preparation and analysis. Therefore, the industry has searched for faster and less invasive methods, such as Near-Infrared Spectroscopy (NIR). NIR is a rapid and cost-effective method, however, it is based on indirect measurements, yielding high amount of data. Therefore, NIR spectroscopy requires calibration with mathematical and statistical tools (Chemometrics) to extract analytical information from the corresponding spectra, as Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). PCA is well suited for NIR, once it can handle many spectra at a time and be used for non-supervised classification. Advantages of the PCA, which is also a data reduction technique, is that it reduces the data spectra to a smaller number of latent variables for further interpretation. On the other hand, LDA is a supervised method that searches the Canonical Variables (CV) with the maximum separation among different categories. In LDA, the first CV is the direction of maximum ratio between inter and intra-class variances. The present work used a portable infrared spectrometer (NIR) for identification and classification of pure and fiber-fortified semolina samples. The fiber was added to semolina in two different concentrations, and after the spectra acquisition, the data was used for PCA and LDA to identify and discriminate the samples. The results showed that NIR spectroscopy associate to PCA was very effective in identifying pure and fiber-fortified semolina. Additionally, the classification range of the samples using LDA was between 78.3% and 95% for calibration and 75% and 95% for cross-validation. Thus, after the multivariate analysis such as PCA and LDA, it was possible to verify that NIR associated to chemometric methods is able to identify and classify the different samples in a fast and non-destructive way.

Keywords: Chemometrics, fiber, linear discriminant analysis, near-infrared spectroscopy, principal component analysis, semolina

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Authors: Anum Ali, Kashaf ad Dooja, Asif Saleem

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The future smart cities trend will be towards Internet of Things (IoT); IoT creates dynamic connections in a ubiquitous manner. Smart cities offer ease and flexibility for daily life matters. By using small devices that are connected to cloud servers based on IoT, network traffic between these devices is growing exponentially, whose security is a concerned issue, since ratio of cyber attack may make the network traffic vulnerable. This paper discusses the latest machine learning approaches in related work further to tackle the increasing rate of cyber attacks, machine learning algorithm is applied to IoT-based network traffic data. The proposed algorithm train itself on data and identify different sections of devices interaction by using supervised learning which is considered as a classifier related to a specific IoT device class. The simulation results clearly identify the attacks and produce fewer false detections.

Keywords: IoT, traffic security, deep learning, classification

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Authors: Ali Ulvi Uzer

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Data reduction is an important topic in the field of pattern recognition applications. The basic concept is the reduction of multitudinous amounts of data down to the meaningful parts. The Principal Component Analysis (PCA) method is frequently used for data reduction. The Support Vector Machine (SVM) method is a discriminative classifier formally defined by a separating hyperplane. In other words, given labeled training data, the algorithm outputs an optimal hyperplane which categorizes new examples. This study offers a hybrid approach that uses the PCA for data reduction and Support Vector Machines (SVM) for classification. In order to detect the accuracy of the suggested system, two boreholes taken from the soil sample was used. The classification accuracies for this dataset were obtained through using ten-fold cross-validation method. As the results suggest, this system, which is performed through size reduction, is a feasible system for faster recognition of dataset so our study result appears to be very promising.

Keywords: feature selection, sequential forward selection, support vector machines, soil sample

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Authors: Tatiana Tunon, Gottfried Pestal

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Government agencies responsible for the management of fisheries resources publish many types of grey literature, and these materials are increasingly accessible to the public on agency websites. However, scope and quality vary considerably, and end-users need meta-data about the report series when deciding whether to use the information (e.g. apply the methods, include the results in a systematic review), or when prioritizing materials for archiving (e.g. library holdings, reference databases). A proposed taxonomy for these report series was developed based on a review of 41 report series from 6 government agencies in 4 countries (Canada, New Zealand, Scotland, and United States). Each report series was categorized according to multiple criteria describing peer-review process, content, and purpose. A robust classification tree was then fitted to these descriptions, and the resulting taxonomic groups were used to compare agency output from 4 countries using reports available in their online repositories.

Keywords: classification tree, fisheries, government, grey literature

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Authors: Ping Tan, Xiaomeng Su, Yi Shen

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The motion intention in the motor imagery braincomputer interface is identified by classifying the event-related desynchronization (ERD) and event-related synchronization ERS characteristics of sensorimotor rhythm (SMR) in EEG signals. When the subject imagines different limbs or different parts moving, the rhythm components and bandwidth will change, which varies from person to person. How to find the effective sensorimotor frequency band of subjects is directly related to the classification accuracy of brain-computer interface. To solve this problem, this paper proposes a Minimum Distance to Riemannian Mean Classification method based on Non-Uniform Filter Banks. During the training phase, the EEG signals are decomposed into multiple different bandwidt signals by using multiple band-pass filters firstly; Then the spatial covariance characteristics of each frequency band signal are computered to be as the feature vectors. these feature vectors will be classified by the MDRM (Minimum Distance to Riemannian Mean) method, and cross validation is employed to obtain the effective sensorimotor frequency bands. During the test phase, the test signals are filtered by the bandpass filter of the effective sensorimotor frequency bands, and the extracted spatial covariance feature vectors will be classified by using the MDRM. Experiments on the BCI competition IV 2a dataset show that the proposed method is superior to other classification methods.

Keywords: non-uniform filter banks, motor imagery, brain-computer interface, minimum distance to Riemannian mean

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Authors: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

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Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

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Authors: Dercan Gencbas, Hatice Bebis, Sue Moorhead

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In the nursing process, many of the nursing classification systems were created to be used in international. From these, NANDA-I, Nursing Outcomes Classification (NOC) and Nursing Interventions Classification (NIC). In this direction, the main objective of this study is to establish a model for caregivers in hospitals and communities in Turkey and to ensure that nursing outputs are assessed by NOC-based measures. There are many scales to measure Urinary Incontinence (UI), which is very common in children, in old age, vaginal birth, NOC scales are ideal for use in the nursing process for comprehensive and holistic assessment, with surveys available. For this reason, the purpose of this study is to evaluate the validity of the NOC outputs and indicators used for UI NANDA-I. This research is a methodological study. In addition to the validity of scale indicators in the study, how much they will contribute to recovery after the nursing intervention was assessed by experts. Scope validations have been applied and calculated according to Fehring 1987 work model. According to this, nursing inclusion criteria and scores were determined. For example, if experts have at least four years of clinical experience, their score was 4 points or have at least one year of the nursing classification system, their score was 1 point. The experts were a publication experience about nursing classification, their score was 1 point, or have a doctoral degree in nursing, their score was 2 points. If the expert has a master degree, their score was 1 point. Total of 55 experts rated Fehring as a “senior degree” with a score of 90 according to the expert scoring. The nursing interventions to be applied were asked to what extent these indicators would contribute to recovery. For coverage validity tailored to Fehring's model, each NOC and NOC indicator from specialists was asked to score between 1-5. Score for the significance of indicators was from 1=no precaution to 5=very important. After the expert opinion, these weighted scores obtained for each NOC and NOC indicator were classified as 0.8 critical, 0.8 > 0.5 complements, > 0.5 are excluded. In the NANDA-I / NOC / NIC system (guideline), 5 NOCs proposed for nursing diagnoses for UI were proposed. These outputs are; Urinary Continence, Urinary Elimination, Tissue Integrity, Self CareToileting, Medication Response. After the scales are translated into Turkish, the weighted average of the scores obtained from specialists for the coverage of all 5 NOCs and the contribution of nursing initiatives exceeded 0.8. After the opinions of the experts, 79 of the 82 indicators were calculated as critical, 3 of the indicators were calculated as supplemental. Because of 0.5 > was not obtained, no substance was removed. All NOC outputs were identified as valid and usable scales in Turkey. In this study, five NOC outcomes were verified for the evaluation of the output of individuals who have received nursing knowledge of UI and variant types. Nurses in Turkey can benefit from the outputs of the NOC scale to perform the care of the elderly incontinence.

Keywords: nursing outcomes, content validity, nursing diagnosis, urinary incontinence

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Authors: Min L. Stewart, Patrick Johnston

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Predictive coding has been proposed as a general explanatory framework for understanding the neural mechanisms of perception. As such, an underweighting of perceptual priors has been hypothesised to underpin a range of differences in inferential and sensory processing in autism spectrum disorders. However, empirical evidence to support this has not been well established. The present study uses an electroencephalography paradigm involving changes of facial identity and person category (actors etc.) to explore how levels of autistic traits (AT) affect predictive coding at multiple stages in the visual processing hierarchy. The study uses a rapid serial presentation of faces, with hierarchically structured sequences involving both periodic and aperiodic repetitions of different stimulus attributes (i.e., person identity and person category) in order to induce contextual expectations relating to these attributes. It investigates two main predictions: (1) significantly larger and late neural responses to change of expected visual sequences in high-relative to low-AT, and (2) significantly reduced neural responses to violations of contextually induced expectation in high- relative to low-AT. Preliminary frequency analysis data comparing high and low-AT show greater and later event-related-potentials (ERPs) in occipitotemporal areas and prefrontal areas in high-AT than in low-AT for periodic changes of facial identity and person category but smaller ERPs over the same areas in response to aperiodic changes of identity and category. The research advances our understanding of how abnormalities in predictive coding might underpin aberrant perceptual experience in autism spectrum. This is the first stage of a research project that will inform clinical practitioners in developing better diagnostic tests and interventions for people with autism.

Keywords: hierarchical visual processing, face processing, perceptual hierarchy, prediction error, predictive coding

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Authors: Gizem Eser Erdek

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This study is research on predicting the remaining life of industrial cutting tools used in the industrial production process with deep learning methods. When the life of cutting tools decreases, they cause destruction to the raw material they are processing. This study it is aimed to predict the remaining life of the cutting tool based on the damage caused by the cutting tools to the raw material. For this, hole photos were collected from the hole-drilling machine for 8 months. Photos were labeled in 5 classes according to hole quality. In this way, the problem was transformed into a classification problem. Using the prepared data set, a model was created with convolutional neural networks, which is a deep learning method. In addition, VGGNet and ResNet architectures, which have been successful in the literature, have been tested on the data set. A hybrid model using convolutional neural networks and support vector machines is also used for comparison. When all models are compared, it has been determined that the model in which convolutional neural networks are used gives successful results of a %74 accuracy rate. In the preliminary studies, the data set was arranged to include only the best and worst classes, and the study gave ~93% accuracy when the binary classification model was applied. The results of this study showed that the remaining life of the cutting tools could be predicted by deep learning methods based on the damage to the raw material. Experiments have proven that deep learning methods can be used as an alternative for cutting tool life estimation.

Keywords: classification, convolutional neural network, deep learning, remaining life of industrial cutting tools, ResNet, support vector machine, VggNet

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Authors: Igor Perechuda, Wojciech Cieśliński

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The paper identifies the features of Polish sports clubs in the particular organizational forms: profit and nonprofit. Identification and description of these features is carried out in terms of financial efficiency of the given organizational form. Under the terms of the efficiency the research allows you to specify the advantages of particular organizational sports club form and the following limitations. Paper considers features of sports clubs in range of Polish conditions as legal regulations. The sources of the functioning efficiency of sports clubs may lie in the organizational forms in which they operate. Each of the available forms can be considered either a for-profit or nonprofit enterprise. Depending on this classification there are different capabilities of increasing organizational and financial efficiency of a given sports club. Authors start with general classification and difference between for-profit and non-profit sport clubs. Next identifies specific financial and organizational conditions of both organizational form and then show examples of mixed activity forms and their efficiency effect.

Keywords: financial efficiency, for-profit, non-profit, sports club

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Authors: Sibel Kurt

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In this study, with the use of Goffee and Jones’s corporate culture classification and the scale of this classification, there aimed to analyze a company’s corporate culture which does not have a public relations or communication department. First of all, the type of corporate culture in the company had been determined. Then it questioned if there are subcultures which formed according to demographics or the department of work. In the survey questionnaire, there are 53 questions total. 6 of these questions are about demographics, and 47 of them are about corporate culture. 152 personnel of the company had answered the survey, and the data have been evaluated according to frequency, descriptive, and compare means tests. The type of corporate culture of the company was determined as the 'communal' from the typology of Goffee and Jones in the positive form. There are no subcultures in the company which bases on the demographics, but only one subculture has determined according to the department of work. As a result, the absence of public relations department, personnel’s low level of awareness about corporate culture, and the lack of information between management and employees has been revealed.

Keywords: corporate culture, subculture, public relations, organizational communication

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Authors: T. Garlan, I. Gabelotaud, S. Lucas, E. Marchès

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Production of a global sedimentological seabed map has been initiated in 1995 to provide the necessary tool for searches of aircraft and boats lost at sea, to give sedimentary information for nautical charts, and to provide input data for acoustic propagation modelling. This original approach had already been initiated one century ago when the French hydrographic service and the University of Nancy had produced maps of the distribution of marine sediments of the French coasts and then sediment maps of the continental shelves of Europe and North America. The current map of the sediment of oceans presented was initiated with a UNESCO's general map of the deep ocean floor. This map was adapted using a unique sediment classification to present all types of sediments: from beaches to the deep seabed and from glacial deposits to tropical sediments. In order to allow good visualization and to be adapted to the different applications, only the granularity of sediments is represented. The published seabed maps are studied, if they present an interest, the nature of the seabed is extracted from them, the sediment classification is transcribed and the resulted map is integrated in the world map. Data come also from interpretations of Multibeam Echo Sounder (MES) imagery of large hydrographic surveys of deep-ocean. These allow a very high-quality mapping of areas that until then were represented as homogeneous. The third and principal source of data comes from the integration of regional maps produced specifically for this project. These regional maps are carried out using all the bathymetric and sedimentary data of a region. This step makes it possible to produce a regional synthesis map, with the realization of generalizations in the case of over-precise data. 86 regional maps of the Atlantic Ocean, the Mediterranean Sea, and the Indian Ocean have been produced and integrated into the world sedimentary map. This work is permanent and permits a digital version every two years, with the integration of some new maps. This article describes the choices made in terms of sediment classification, the scale of source data and the zonation of the variability of the quality. This map is the final step in a system comprising the Shom Sedimentary Database, enriched by more than one million punctual and surface items of data, and four series of coastal seabed maps at 1:10,000, 1:50,000, 1:200,000 and 1:1,000,000. This step by step approach makes it possible to take into account the progresses in knowledge made in the field of seabed characterization during the last decades. Thus, the arrival of new classification systems for seafloor has improved the recent seabed maps, and the compilation of these new maps with those previously published allows a gradual enrichment of the world sedimentary map. But there is still a lot of work to enhance some regions, which are still based on data acquired more than half a century ago.

Keywords: marine sedimentology, seabed map, sediment classification, world ocean

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Authors: M. G. Dirodi, G. Gugliotta, C. Leonardi

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The member states shall establish zones and agglomerations throughout their territory to assess and manage air quality in order to comply with European directives. In Italy decree 155/2010, transposing Directive 2008/50/EC on ambient air quality and cleaner air for Europe, merged into a single act the previous provisions on ambient air quality assessment and management, including those resulting from the implementation of Directive 2004/107/EC relating to arsenic, cadmium, nickel, mercury, and polycyclic aromatic hydrocarbons in ambient air. Decree 155/2010 introduced stricter rules for identifying zones on the basis of the characteristics of the territory in spite of considering pollution levels, as it was in the past. The implementation of such new criteria has reduced the great variability of the previous zoning, leading to a significant reduction of the total number of zones and to a complete and uniform ambient air quality assessment and management throughout the Country. The present document is related to the new zones definition in Italy according to Decree 155/2010. In particular, the paper contains the description and the analysis of the outcome of zoning and classification.

Keywords: zones, agglomerations, air quality assessment, classification

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Authors: Othman E. Othman, Agnés Germot, Daniel Petit, Abderrahman Maftah

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Threats to the biodiversity are increasing due to the loss of genetic diversity within the species utilized in agriculture. Due to the progressive substitution of the less productive, locally adapted and native breeds by highly productive breeds, the number of threatened breeds is increased. In these conditions, it is more strategically important than ever to preserve as much the farm animal diversity as possible, to ensure a prompt and proper response to the needs of future generations. Mitochondrial (mtDNA) sequencing has been used to explain the origins of many modern domestic livestock species. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. Because of the eastern location of Egypt in the Mediterranean basin and the presence of fat-tailed sheep breeds- character quite common in Turkey and Syria- where genotypes that seem quite primitive, the phylogenetic studies of Egyptian sheep breeds become particularly attractive. We aimed in this work to clarify the genetic affinities, biodiversity and phylogeny of five Egyptian sheep breeds using cytochrome B sequencing. Blood samples were collected from 63 animals belonging to the five tested breeds; Barki, Rahmani, Ossimi, Saidi and Sohagi. The total DNA was extracted and the specific primer allowed the conventional PCR amplification of the cytochrome B region of mtDNA (approximately 1272 bp). PCR amplified products were purified and sequenced. The alignment of Sixty-three samples was done using BioEdit software. DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 34 polymorphic sites leading to the formation of 18 haplotypes. The haplotype diversity in five tested breeds ranged from 0.676 in Rahmani breed to 0.894 in Sohagi breed. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Rahmani and Saidi (D: 1.674 and Dxy: 0.00150) while the highest distance was observed between Ossimi and Sohagi (D: 5.233 and Dxy: 0.00475). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of the 63 analyzed samples were aligned with references sequences of different haplogroups. The phylogeny result showed the presence of three haplogroups (HapA, HapB and HapC) in the 63 examined samples. The other two haplogroups described in literature (HapD and HapE) were not found. The result showed that 50 out of 63 tested animals cluster with haplogroup B (79.37%) whereas 7 tested animals cluster with haplogroup A (11.11%) and 6 animals cluster with haplogroup C (9.52%). In conclusion, the phylogenetic reconstructions showed that the majority of Egyptian sheep breeds belonging to haplogroup B which is the dominant haplogroup in Eastern Mediterranean countries like Syria and Turkey. Some individuals are belonging to haplogroups A and C, suggesting that the crosses were done with other breeds for characteristic selection for growth and wool quality.

Keywords: cytochrome B, diversity, phylogheny, Egyptian sheep breeds

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Authors: Almahd Alshereef, Ahmed Alkilany, Hammad Said, Azuraliza Abu Bakar

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From time to time, electrical power grid is directed by the National Electricity Operator to conduct load shedding, which involves hours' power outages on the area of this study, Southern Electrical Grid of Libya (SEGL). Load shedding is conducted in order to alleviate pressure on the National Electricity Grid at times of peak demand. This approach has chosen a set of categories to study load-shedding problem considering the effect of the demand priorities on the operation of the power system during emergencies. Classification of category region for load shedding problem is solved by a new algorithm (the harmony algorithm) based on the "random generation list of category region", which is a possible solution with a proximity degree to the optimum. The obtained results prove additional enhancements compared to other heuristic approaches. The case studies are carried out on SEGL.

Keywords: optimization, harmony algorithm, load shedding, classification

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Authors: Hamzeh Awad

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Disability is considered to be a worldwide complex phenomenon which rising at a phenomenal rate and caused by many different factors. Chronic diseases such as cardiovascular disease and diabetes can lead to mobility disability in particular and disability in general. The ICF is an integrative bio-psycho-social model of functioning and disability and considered by the World Health Organization (WHO) to be a reference for disability classification using its categories and core set to classify disorder’s functional limitations. Specialist programs at Sultan Bin Abdul Aziz Humanitarian City (SBAHC) are providing both inpatient and outpatient services have started to implement the ICF and use it as a problem solving tool in Rehab. Diabetes is leading contributing factor for disability and considered epidemic in several Gulf countries including the Kingdom of Saudi Arabia (KSA), where its prevalence continues to increase dramatically. Metabolic disorders, mainly diabetes are not well covered in Rehab field. The purpose of this study is present to research and clinical rehabilitation field of DREAM and ICF as a framework in clinical and research setting in Rehab service. Also, shed the light on using the ICF as problem solving tool at SBAHC. There are synergies between disability causes and wider public health priorities in relation to both chronic disease and disability prevention. Therefore, there is a need for strong advocacy and understanding of the role of ICF as a reference in Rehab settings in Middle East if we wish to seize the opportunity to reverse current trends of acquired disability in the region.

Keywords: international classification of functioning, disability and health (ICF), prototype, rehabilitation and diabetes

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

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Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase– pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed- specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization

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Authors: Tsega Asresa Mengistu, Getahun Tigistu

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Computer vision is an artificial intelligence subfield that allows computers and systems to retrieve meaning from digital images. It is applied in various fields of study self-driving cars, video surveillance, agriculture, Quality control, Health care, construction, military, and everyday life. Aromatic and medicinal plants are botanical raw materials used in cosmetics, medicines, health foods, and other natural health products for therapeutic and Aromatic culinary purposes. Herbal industries depend on these special plants. These plants and their products not only serve as a valuable source of income for farmers and entrepreneurs, and going to export not only industrial raw materials but also valuable foreign exchange. There is a lack of technologies for the classification and identification of Aromatic and medicinal plants in Ethiopia. The manual identification system of plants is a tedious, time-consuming, labor, and lengthy process. For farmers, industry personnel, academics, and pharmacists, it is still difficult to identify parts and usage of plants before ingredient extraction. In order to solve this problem, the researcher uses a deep learning approach for the efficient identification of aromatic and medicinal plants by using a convolutional neural network. The objective of the proposed study is to identify the aromatic and medicinal plant Parts and usages using computer vision technology. Therefore, this research initiated a model for the automatic classification of aromatic and medicinal plants by exploring computer vision technology. Morphological characteristics are still the most important tools for the identification of plants. Leaves are the most widely used parts of plants besides the root, flower and fruit, latex, and barks. The study was conducted on aromatic and medicinal plants available in the Ethiopian Institute of Agricultural Research center. An experimental research design is proposed for this study. This is conducted in Convolutional neural networks and Transfer learning. The Researcher employs sigmoid Activation as the last layer and Rectifier liner unit in the hidden layers. Finally, the researcher got a classification accuracy of 66.4 in convolutional neural networks and 67.3 in mobile networks, and 64 in the Visual Geometry Group.

Keywords: aromatic and medicinal plants, computer vision, deep convolutional neural network

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Authors: Mohammad W. Dewan, Jahangir Alam, Khurshida Sharmin

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Synthetic fibers (carbon, glass, aramid, etc.) are generally utilized to make composite materials for better mechanical and thermal properties. However, they are expensive and non-biodegradable. In the perspective of Bangladesh, jute fibers are available, inexpensive, and comprising good mechanical properties. The improved properties (i.e., low cost, low density, eco-friendly) of natural fibers have made them a promising reinforcement in hybrid composites without sacrificing mechanical properties. In this study, jute and e-glass fiber reinforced hybrid composite materials are fabricated utilizing hand lay-up followed by a compression molding technique. Room temperature cured two-part epoxy resin is used as a matrix. Approximate 6-7 mm thick composite panels are fabricated utilizing 17 layers of woven glass and jute fibers with different fiber layering sequences- only jute, only glass, glass, and jute alternatively (g/j/g/j---) and 4 glass - 9 jute – 4 glass (4g-9j-4g). The fabricated composite panels are analyzed through fiber volume calculation, tensile test, bending test, and water absorption test. The hybridization of jute and glass fiber results in better tensile, bending, and water absorption properties than only jute fiber-reinforced composites, but inferior properties as compared to only glass fiber reinforced composites. Among different fiber layering sequences, 4g-9j-4g fibers layering sequence resulted in better tensile, bending, and water absorption properties. The effect of chemical treatment on the woven jute fiber and chopped glass microfiber infusion are also investigated in this study. Chemically treated jute fiber and 2 wt. % chopped glass microfiber infused hybrid composite shows about 12% improvements in flexural strength as compared to untreated and no micro-fiber infused hybrid composite panel. However, fiber chemical treatment and micro-filler do not have a significant effect on tensile strength.

Keywords: compression molding, chemical treatment, hybrid composites, mechanical properties

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Authors: Heichia Wang, Yalan Chao

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Social inequality is a persistent problem. One of the ways to solve this problem is through education. At present, vulnerable groups are often less geographically accessible to educational resources. However, compared with educational resources, communication equipment is easier for vulnerable groups. Now that information and communication technology (ICT) has entered the field of education, today we can accept the convenience that ICT provides in education, and the mobility that it brings makes learning independent of time and place. With mobile learning, teachers and students can start discussions in an online chat room without the limitations of time or place. However, because liquidity learning is quite convenient, people tend to solve problems in short online texts with lack of detailed information in a lack of convenient online environment to express ideas. Therefore, the ICT education environment may cause misunderstanding between teachers and students. Therefore, in order to better understand each other's views between teachers and students, this study aims to clarify the essays of the analysts and classify the students into several types of learning questions to clarify the views of teachers and students. In addition, this study attempts to extend the description of possible omissions in short texts by using external resources prior to classification. In short, by applying a short text classification, this study can point out each student's learning problems and inform the instructor where the main focus of the future course is, thus improving the ICT education environment. In order to achieve the goals, this research uses convolutional neural network (CNN) method to analyze short discussion content between teachers and students in an ICT education environment. Divide students into several main types of learning problem groups to facilitate answering student problems. In addition, this study will further cluster sub-categories of each major learning type to indicate specific problems for each student. Unlike most neural network programs, this study attempts to extend short texts with external resources before classifying them to improve classification performance. In short, by applying the classification of short texts, we can point out the learning problems of each student and inform the instructors where the main focus of future courses will improve the ICT education environment. The data of the empirical process will be used to pre-process the chat records between teachers and students and the course materials. An action system will be set up to compare the most similar parts of the teaching material with each student's chat history to improve future classification performance. Later, the function of short text classification uses CNN to classify rich chat records into several major learning problems based on theory-driven titles. By applying these modules, this research hopes to clarify the main learning problems of students and inform teachers that they should focus on future teaching.

Keywords: ICT education improvement, social equality, short text analysis, convolutional neural network

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Authors: Lavanya Annadi, Fahimeh Jafari

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Transportation brings immense benefits to society, but it also has its costs. Costs include such as the cost of infrastructure, personnel and equipment, but also the loss of life and property in traffic accidents on the road, delays in travel due to traffic congestion and various indirect costs in terms of air transport. More research has been done to identify the various factors that affect road accidents, such as road infrastructure, traffic, sociodemographic characteristics, land use, and the environment. The aim of this research is to predict the probabilistic crash prediction of vehicles using machine learning due to natural and structural reasons by excluding spontaneous reasons like overspeeding etc., in the United States. These factors range from weather factors, like weather conditions, precipitation, visibility, wind speed, wind direction, temperature, pressure, and humidity to human made structures like road structure factors like bump, roundabout, no exit, turning loop, give away, etc. Probabilities are dissected into ten different classes. All the predictions are based on multiclass classification techniques, which are supervised learning. This study considers all crashes that happened in all states collected by the US government. To calculate the probability, multinomial expected value was used and assigned a classification label as the crash probability. We applied three different classification models, including multiclass Logistic Regression, Random Forest and XGBoost. The numerical results show that XGBoost achieved a 75.2% accuracy rate which indicates the part that is being played by natural and structural reasons for the crash. The paper has provided in-deep insights through exploratory data analysis.

Keywords: road safety, crash prediction, exploratory analysis, machine learning

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Authors: Judith Mogouong, Philippe Constant, Robert Lavallee, Claude Guertin

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The emerald ash borer (EAB) is an exotic wood borer insect native from China, which is associated with important environmental and economic damages in North America. Beetles are known to be vectors of microbial communities related to their adaptive capacities. It is now established that environmental stress factors may induce physiological events on the host trees, such as phytochemical changes. Consequently, that may affect the establishment comportment of herbivorous insect. Considering the number of insects collected on ash trees (insects’ density) as an abiotic factor related to stress damage, the aim of our study was to explore the dynamic of EAB gut microbial community genome (microbiome) when facing that factor and to monitor its diversity. Insects were trapped using specific green Lindgren© traps. A gradient of the captured insect population along the St. Lawrence River was used to create three levels of insects’ density (low, intermediate, and high). After dissection, total DNA extracted from insect guts of each level has been sent for amplicon sequencing of bacterial 16S rRNA gene and fungal ITS2 region. The composition of microbial communities among sample appeared largely diversified with the Simpson index significantly different across the three levels of density for bacteria. Add to that; bacteria were represented by seven phyla and twelve classes, whereas fungi were represented by two phyla and seven known classes. Using principal coordinate analysis (PCoA) based on Bray Curtis distances of 16S rRNA sequences, we observed a significant variation between the structure of the bacterial communities depending on insects’ density. Moreover, the analysis showed significant correlations between some bacterial taxa and the three classes of insects’ density. This study is the first to present a complete overview of the bacterial and fungal communities associated with the gut of EAB base on culture-independent methods, and to correlate those communities with a potential stress factor of the host trees.

Keywords: gut microbiome, DNA, 16S rRNA sequences, emerald ash borer

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Authors: Yasmine Abu Adla, Racha Soubra, Milana Kasab, Mohamad O. Diab, Aly Chkeir

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Over the past several years, researchers have shown a great interest in assessing the mobility of elderly people to measure their functional status. Usually, such an assessment is done by conducting tests that require the subject to walk a certain distance, turn around, and finally sit back down. Consequently, this study aims to provide an at home monitoring system to assess the patient’s status continuously. Thus, we proposed a technique to automatically detect when a subject sits down while walking at home. In this study, we utilized a Doppler radar system to capture the motion of the subjects. More than 20 features were extracted from the radar signals, out of which 11 were chosen based on their intraclass correlation coefficient (ICC > 0.75). Accordingly, the sequential floating forward selection wrapper was applied to further narrow down the final feature vector. Finally, 5 features were introduced to the linear discriminant analysis classifier, and an accuracy of 93.75% was achieved as well as a precision and recall of 95% and 90%, respectively.

Keywords: Doppler radar system, stand-to-sit phase, TUG test, machine learning, classification

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Authors: Aadityaa Singla

Abstract:

The big five personality traits are as follows: openness, conscientiousness, extraversion, agreeableness, and neuroticism. In order to get an insight into their personality, many flocks to these categories, which each have different meanings/characteristics. This information is important not only to individuals but also to career professionals and psychologists who can use this information for candidate assessment or job recruitment. The links between AI and psychology have been well studied in cognitive science, but it is still a rather novel development. It is possible for various AI classification models to accurately predict a personality question via ten input questions. This would contrast with the hundred questions that normal humans have to answer to gain a complete picture of their five personality traits. In order to approach this problem, various AI classification models were used on a dataset to predict what a user may answer. From there, the model's prediction was compared to its actual response. Normally, there are five answer choices (a 20% chance of correct guess), and the models exceed that value to different degrees, proving their significance. By utilizing an MLP classifier, decision tree, linear model, and K-nearest neighbors, they were able to obtain a test accuracy of 86.643, 54.625, 47.875, and 52.125, respectively. These approaches display that there is potential in the future for more nuanced predictions to be made regarding personality.

Keywords: machine learning, personally, big five personality traits, cognitive science

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Authors: Ali̇ Si̇nan Soğanci

Abstract:

The cement stabilization is one of the ground improvement method applied worldwide to increase the strength of clayey soils. The using of cement has got lots of advantages compared to other stabilization methods. Cement stabilization can be done quickly, the cost is low and creates a more durable structure with the soil. Cement can be used in the treatment of a wide variety of soils. The best results of the cement stabilization were seen on silts as well as coarse-grained soils. In this study, blocks of clay were taken from the Apa-Hotamış conveyance channel route which is 125km long will be built in Konya that take the water with 70m3/sec from Mavi tunnel to Hotamış storage. Firstly, the index properties of clay samples were determined according to the Unified Soil Classification System. The experimental program was carried out on compacted soil specimens with 0%, 7 %, 15% and 30 % cement additives and the results of unconfined compression strength were discussed. The results of unconfined compression tests indicated an increase in strength with increasing cement content.

Keywords: cement stabilization, unconfined compression test, clayey soils, unified soil classification system.

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Authors: Aijing Luo, Zirui Xin, Yifeng Yuan

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Background: With the rapid development of the online health community, more and more patients or families are seeking health information on the Internet. Objective: This study aimed to discuss how to fully reveal the health information needs expressed by hypertensive patients in their questions in the online environment. Methods: This study randomly selected 1,000 text records from the question data of hypertensive patients from 2008 to 2018 collected from the website www.haodf.com and constructed a classification system through literature research and content analysis. This paper identified the background characteristics and questioning the intention of each hypertensive patient based on the patient’s question and used co-occurrence network analysis to explore the features of the health information needs of hypertensive patients. Results: The classification system for health information needs of patients with hypertension is composed of 9 parts: 355 kinds of drugs, 395 kinds of symptoms and signs, 545 kinds of tests and examinations , 526 kinds of demographic data, 80 kinds of diseases, 37 kinds of risk factors, 43 kinds of emotions, 6 kinds of lifestyles, 49 kinds of questions. The characteristics of the explored online health information needs of the hypertensive patients include: i)more than 49% of patients describe the features such as drugs, symptoms and signs, tests and examinations, demographic data, diseases, etc. ii) these groups are most concerned about treatment (77.8%), followed by diagnosis (32.3%); iii) 65.8% of hypertensive patients will ask doctors online several questions at the same time. 28.3% of the patients are very concerned about how to adjust the medication, and they will ask other treatment-related questions at the same time, including drug side effects, whether to take drugs, how to treat a disease, etc.; secondly, 17.6% of the patients will consult the doctors online about the causes of the clinical findings, including the relationship between the clinical findings and a disease, the treatment of a disease, medication, and examinations. Conclusion: In the online environment, the health information needs expressed by Chinese hypertensive patients to doctors are personalized; that is, patients with different background features express their questioning intentions to doctors. The classification system constructed in this study can guide health information service providers in the construction of online health resources, to help solve the problem of information asymmetry in communication between doctors and patients.

Keywords: online health community, health information needs, hypertensive patients, doctor-patient communication

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