Search results for: interval graph

Authors: Huei Lin Lee, Wee Sim Choo

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The effects of blanching, boiling and steaming on the ascorbic acid content, total phenolic content and colour in cauliflower (Brassica oleraceavar. Botrytis) was investigated. It was found that blanching was the best thermal processing to be applied on cauliflower compared to boiling and steaming processes. Blanching and steaming processes on cauliflower retained most of the ascorbic acid content (AAC) compared to those of boiling. As for the total phenolic content (TPC), blanching process retained a higher TPC in cauliflower compared to those of boiling and steaming processes. There were no significant differences between the TPC of boiled and steamed cauliflowers. As for the colour measurement, there were no significant differences in the colour of the cauliflower at different lead time (after processing to the point of consumption) of 30 minutes interval up to 3 hours but there were slight variations in L*, a*, and b* values among the thermal processed cauliflowers (blanched, boiled and steamed). The cauliflowers in this study were found to give a desirable white colour (L* value in the range of 77-83) in all the three thermal processes (blanching, boiling and steaming). There was no significant difference on the effect of lead time (30-minutes interval up to 3 hours) in raw and all the three thermal processed (blanched, boiled and steamed) cauliflowers.

Keywords: ascorbic acid, cauliflower, colour, phenolics

Procedia PDF Downloads 294

Authors: C. M. Nur Syazwani, M. K. Ahmad Imran, Rizal E. M. Nasir

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The study on BWB UV begins in UiTM since 2005 and three designs have been studied and published. The latest designs are Baseline-III and inspired by birds that have features and aerodynamics behaviour of cruising birds without flapping capability. The aircraft featuring planform and configuration are similar to the bird. Baseline-III has major flaws particularly in its low lift-to-drag ratio, stability and issues regarding limited controllability. New design known as Baseline-IV replaces straight, swept wing to delta wing and have a broader tail compares to the Baseline-III’s. The objective of the study is to investigate aerodynamics of Baseline-IV bird-inspired BWB aircraft. This will be achieved by theoretical calculation and wind tunnel experiments. The result shows that both theoretical and wind tunnel experiments of Baseline-IV graph of CL and CD versus alpha are quite similar to each other in term of pattern of graph slopes and values. Baseline-IV has higher lift coefficient values at wide range of angle of attack compares to Baseline-III. Baseline-IV also has higher maximum lift coefficient, higher maximum lift-to-drag and lower parasite drag. It has stable pitch moment versus lift slope but negative moment at zero lift for zero angle-of-attack tail setting. At high angle of attack, Baseline-IV does not have stability reversal as shown in Baseline-III. Baseline-IV is proven to have improvements over Baseline-III in terms of lift, lift-to-drag ratio and pitch moment stability at high angle-of-attack.

Keywords: blended wing-body, bird-inspired blended wing-body, aerodynamic, stability

Procedia PDF Downloads 481

Authors: Yogita Tulsian, R. S. Gupta, K. F. Laserson

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Background: Delays in the diagnosis and treatment of TB facilitates disease transmission in the community, so we conducted a study to evaluate the burden of and risk factors for delay in TB diagnosis and initiation of TB treatment among patients in the private and public sectors in Udaipur district, Rajasthan, India. Methods: A retrospective cohort study was conducted among 100 new sputum-positive TB. Patients were interviewed in the intensive phase of treatment September 2013-November 2013 Long total diagnosis delay (TDD) was defined as a time interval between first symptom to confirmed diagnosis > 30 days. Long health treatment delay (HTD) was defined as a time interval between confirmed diagnosis to treatment initiation > 7 days. Results: We observed a median TDD of 55 days (range: 7-136 days) in the public sector and of 92 days (11-380 days) in the private sector. Long TDD in the private sector was significantly associated with middle-higher socio-economic status (Risk Ratio (RR): 2;95% CI: 1.3-3). The reasons reported from the private sector for long TDD were suspect TB patients not advised for sputum examination (RR: 42; 95% CI:2.6-660), practise of self-medication (RR: 17.4; 95% CI: 1.1-267), or lack of awareness (RR: 9.7;95% CI: 0.6-145). The median HTD in the public sector was 3 days (range: 0-14 days), and in the private sector, 2 days (range: 0-11 days) (non-significant difference). Conclusions: Long TDD in private sector may be improved through sputum referral for all suspect TB cases and better education to all regarding TB.

Keywords: diagnosis delay, treatment delay, privatesector, public sector

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Authors: Ho-Won Jung, Donghun Lee, Hyung-Jin Kim

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Predictive analytics (data analysis) uses a subset of measurements (the features, predictor, or independent variable) to predict another measurement (the outcome, target, or dependent variable) on a single person or unit. It applies empirical methods in statistics, operations research, and machine learning to predict the future, or otherwise unknown events or outcome on a single or person or unit, based on patterns in data. Most analyses of metabolic syndrome are not predictive analytics but statistical explanatory studies that build a proposed model (theory building) and then validate metabolic syndrome predictors hypothesized (theory testing). A proposed theoretical model forms with causal hypotheses that specify how and why certain empirical phenomena occur. Predictive analytics and explanatory modeling have their own territories in analysis. However, predictive analytics can perform vital roles in explanatory studies, i.e., scientific activities such as theory building, theory testing, and relevance assessment. In the context, this study is to demonstrate how to use our predictive analytics to support theory building (i.e., hypothesis generation). For the purpose, this study utilized a big data predictive analytics platform TM based on a co-occurrence graph. The co-occurrence graph is depicted with nodes (e.g., items in a basket) and arcs (direct connections between two nodes), where items in a basket are fully connected. A cluster is a collection of fully connected items, where the specific group of items has co-occurred in several rows in a data set. Clusters can be ranked using importance metrics, such as node size (number of items), frequency, surprise (observed frequency vs. expected), among others. The size of a graph can be represented by the numbers of nodes and arcs. Since the size of a co-occurrence graph does not depend directly on the number of observations (transactions), huge amounts of transactions can be represented and processed efficiently. For a demonstration, a total of 13,254 metabolic syndrome training data is plugged into the analytics platform to generate rules (potential hypotheses). Each observation includes 31 predictors, for example, associated with sociodemographic, habits, and activities. Some are intentionally included to get predictive analytics insights on variable selection such as cancer examination, house type, and vaccination. The platform automatically generates plausible hypotheses (rules) without statistical modeling. Then the rules are validated with an external testing dataset including 4,090 observations. Results as a kind of inductive reasoning show potential hypotheses extracted as a set of association rules. Most statistical models generate just one estimated equation. On the other hand, a set of rules (many estimated equations from a statistical perspective) in this study may imply heterogeneity in a population (i.e., different subpopulations with unique features are aggregated). Next step of theory development, i.e., theory testing, statistically tests whether a proposed theoretical model is a plausible explanation of a phenomenon interested in. If hypotheses generated are tested statistically with several thousand observations, most of the variables will become significant as the p-values approach zero. Thus, theory validation needs statistical methods utilizing a part of observations such as bootstrap resampling with an appropriate sample size.

Keywords: explanatory modeling, metabolic syndrome, predictive analytics, theory building

Procedia PDF Downloads 244

Authors: Wenjun Hou, Marek Perkowski

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The Traveling Salesman problem is famous in computing and graph theory. In short, it asks for the Hamiltonian cycle of the least total weight in a given graph with N nodes. All variations on this problem, such as those with K-bounded-degree nodes, are classified as NP-complete in classical computing. Although several papers propose theoretical high-level designs of quantum algorithms for the Traveling Salesman Problem, no quantum circuit implementation of these algorithms has been created up to our best knowledge. In contrast to previous papers, the goal of this paper is not to optimize some abstract complexity measures based on the number of oracle iterations, but to be able to evaluate the real circuit and time costs of the quantum computer. Using the emerging quantum programming language Q# developed by Microsoft, which runs quantum circuits in a quantum computer simulation, an implementation of the bounded-degree problem and its respective quantum circuit were created. To apply Grover’s algorithm to this problem, a quantum oracle was designed, evaluating the cost of a particular set of edges in the graph as well as its validity as a Hamiltonian cycle. Repeating the Grover algorithm with an oracle that finds successively lower cost each time allows to transform the decision problem to an optimization problem, finding the minimum cost of Hamiltonian cycles. N log₂ K qubits are put into an equiprobablistic superposition by applying the Hadamard gate on each qubit. Within these N log₂ K qubits, the method uses an encoding in which every node is mapped to a set of its encoded edges. The oracle consists of several blocks of circuits: a custom-written edge weight adder, node index calculator, uniqueness checker, and comparator, which were all created using only quantum Toffoli gates, including its special forms, which are Feynman and Pauli X. The oracle begins by using the edge encodings specified by the qubits to calculate each node that this path visits and adding up the edge weights along the way. Next, the oracle uses the calculated nodes from the previous step and check that all the nodes are unique. Finally, the oracle checks that the calculated cost is less than the previously-calculated cost. By performing the oracle an optimal number of times, a correct answer can be generated with very high probability. The oracle of the Grover Algorithm is modified using the recalculated minimum cost value, and this procedure is repeated until the cost cannot be further reduced. This algorithm and circuit design have been verified, using several datasets, to generate correct outputs.

Keywords: quantum computing, quantum circuit optimization, quantum algorithms, hybrid quantum algorithms, quantum programming, Grover’s algorithm, traveling salesman problem, bounded-degree TSP, minimal cost, Q# language

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Authors: Chinwe Pearl Poly-Mbah, Evelyn Obioma, Juliet Amajuoyi

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The investigation here reported examined growth and yield responses of Cucumber to manure rates in Owerri, Southeastern Nigeria. Fruit vegetables are widely cultivated and produced in Northern Nigeria but greatly consumed in Southern Nigeria where cucumbers command high demand and price but are minimally cultivated. Unfortunately, farmers in northern Nigeria incur lots of losses because cucumber is a perishable vegetable and is transported all the way from the northern Nigeria where cucumbers are produced to Southern Nigeria where cucumbers are consumed, hence the high cost of cucumber fruits in Southern Nigeria. There is a need, therefore, to evolve packages that will enhance cucumber production in Southern Nigeria. The main objective of this study was to examine the effects of poultry manure rates on the growth and yield of cucumber in Owerri, South Eastern Nigeria. Specifically, this study was designed to assess the effect of poultry manure rates on number of days to 50% seedling emergence, vine length/plant, leaf area per plant and the number of leaves produced per plant. The design used for the experiment was Randomized Complete Block Design (RCBD) with three blocks (replications). Treatment consisted of four rates of well-decomposed poultry manure at the rate of 0 tons/ha, 2 tons/ha, 4 tons/ha and 6 tons/ha. Data were collected on number of days to 50% seedling emergence, vine length per plant at two weeks interval, leaf number per plant at two weeks interval, leaf area per plant at two weeks interval, number of fruits produced per plant, and fresh weight of fruits per plant at harvest. Results from the analysis of variance (ANOVA) showed that there were highly significant effects (P=0.05) of poultry manure on growth and yield parameters studied which include number of days to 50% seedling emergence, vine length per plant, leaf number per plant, leaf area per plant, fruit number and fruit weight per plant such that increase in poultry manure rates lead to increase in growth and yield parameters studied. Therefore, the null hypothesis (Ho) was rejected, while the alternative hypothesis was accepted. Farmers should be made to know that growing cucumber with poultry manure in southeastern Nigeria agro ecology is a successful enterprise

Keywords: cucumber, effects, growth and yield, manure

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Authors: Ben Cheikh Asma, Bouafia Nabiha, Ammar Asma, Ezzi Olfa, Meddeb Khaoula, Chouchène Imed, Boussarsar Hamadi, Njah Mansour

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Background: Hospital Acquired Infection (HAI) constitutes an important worldwide health problem. It was associated with high mortality rate in intensive care units (ICU). This study aimed to determine HAI mortality rate in Tunisian intensive care units and identify its risk factors. Methods: We conducted a prospective observational cohort study over a 12 months period (September 15th 2015 to September 15 th 2016) in the adult medical ICU of University Hospital-Farhat Hached (Sousse-Tunisia). All patients admitted in the ICU for more than 48 hours were included in the study. We used an anonymous standardized survey record form to collect data by a medical hygienist assisted by an intensivist. We adopted definitions of Center for Diseases Control and prevention of Atlanta to detect HAI, Kaplan Meier survival analysis and Cox proportional hazard regression to identify independent risk factor of HAI mortality. Results: Of 171 patients, 67 developed ICU-acquired infection (global incidence rate=39.2%). The mean age of patients was 59 ± 21.2 years and 60.8% were male. The most frequently identified infections were pulmonary acquired infection (ventilator associated pneumonia (VAP) and infected atelectasis with density rates 21.4 VAP/1000 days of mechanical ventilation and 9.4 infected atelectasis /1000 days of mechanical ventilation; respectively) and central venous catheter associated infection (CVC - AI) with density rate 28.4 CVC-AI / 1000 CVC-days). HAI mortality rate was 66.7% (n=44). The median survival was 20 days 3.36, 95% Confidential Interval [13.39 – 26.60]. Specific mortality rates according to infectious site were 65.5%, 36.4% and 4.5% respectively for VAP, CVC associated infection and infected atelectasis. In univariate analysis, a significant associations between mortality and cardiovascular history (p=0.04) tracheotomy (p=0.00), peripheral venous catheterization (p=0.04), VAP (p=0.04) and infected atelectasis (p=0.04) were detected. Independent risk factors for HAI mortality were VAP with Hazard Ratio = 3.14, 95% Confidential Interval [1.63 – 6.05] (p=0.001) and tracheotomy (Hazard Ratio=0.22, 95% Confidential Interval [0.10 – 0.44], p=0.000). Conclusions: In the present study, hospital acquired infection mortality rate was relatively high. We need to intensify the fight against these infections especially ventilator-associated pneumonia that is associated with higher risk of mortality in many studies. Thus, more effective infection control interventions were necessary in our hospital.

Keywords: hospital acquired infection, intensive care unit, mortality, risk factors

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Authors: Meriem Taleb, Ghania Tail, Fatma Zohra Kara, Brahim Djedouani, T. Moussa

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Forensic entomology has grown immensely as a discipline in the past thirty years. The main purpose of forensic entomology is to establish the post mortem interval or PMI. Three days after the death, insect evidence is often the most accurate and sometimes the only method of determining elapsed time since death. This work presents the estimation of the PMI in an experiment to test the reliability of the accumulated degree days (ADD) method and the application of this method in a real case. The study was conducted at the Laboratory of Entomology at the National Institute for Criminalistics and Criminology of the National Gendarmerie, Algeria. The domestic rabbit Oryctolagus cuniculus L. was selected as the animal model. On 08th July 2012, the animal was killed. Larvae were collected and raised to adulthood. Estimation of oviposition time was calculated by summing up average daily temperatures minus minimum development temperature (also specific to each species). When the sum is reached, it corresponds to the oviposition day. Weather data were obtained from the nearest meteorological station. After rearing was accomplished, three species emerged: Lucilia sericata, Chrysomya albiceps, and Sarcophaga africa. For Chrysomya albiceps species, a cumulation of 186°C is necessary. The emergence of adults occured on 22nd July 2012. A value of 193.4°C is reached on 9th August 2012. Lucilia sericata species require a cumulation of 207°C. The emergence of adults occurred on 23rd, July 2012. A value of 211.35°C is reached on 9th August 2012. We should also consider that oviposition may occur more than 12 hours after death. Thus, the obtained PMI is in agreement with the actual time of death. We illustrate the use of this method during the investigation of a case of a decaying human body found on 03rd March 2015 in Bechar, South West of Algerian desert. Maggots were collected and sent to the Laboratory of Entomology. Lucilia sericata adults were identified on 24th March 2015 after emergence. A sum of 211.6°C was reached on 1st March 2015 which corresponds to the estimated day of oviposition. Therefore, the estimated date of death is 1st March 2015 ± 24 hours. The estimated PMI by accumulated degree days (ADD) method seems to be very precise. Entomological evidence should always be used in homicide investigations when the time of death cannot be determined by other methods.

Keywords: forensic entomology, accumulated degree days, postmortem interval, diptera, Algeria

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Authors: Preeti Sharma

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This paper deals with the Stancu type generalization of Lupaş-Durrmeyer operators. We establish some direct results in the polynomial weighted space of continuous functions defined on the interval [0, 1]. Also, Voronovskaja type theorem is studied.

Keywords: Lupas-Durrmeyer operators, polya distribution, weighted approximation, rate of convergence, modulus of continuity

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Authors: Yen-Luan Chen

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Maintenance has a great impact on the capacity of production and on the quality of the products, and therefore, it deserves continuous improvement. Maintenance procedure done before a failure is called preventive maintenance (PM). Sequential PM, which specifies that a system should be maintained at a sequence of intervals with unequal lengths, is one of the commonly used PM policies. This article proposes a generalized sequential PM policy for a system subject to shocks with imperfect maintenance and random working time. The shocks arrive according to a non-homogeneous Poisson process (NHPP) with varied intensity function in each maintenance interval. As a shock occurs, the system suffers two types of failures with number-dependent probabilities: type-I (minor) failure, which is rectified by a minimal repair, and type-II (catastrophic) failure, which is removed by a corrective maintenance (CM). The imperfect maintenance is carried out to improve the system failure characteristic due to the altered shock process. The sequential preventive maintenance-last (PML) policy is defined as that the system is maintained before any CM occurs at a planned time Ti or at the completion of a working time in the i-th maintenance interval, whichever occurs last. At the N-th maintenance, the system is replaced rather than maintained. This article first takes up the sequential PML policy with random working time and imperfect maintenance in reliability engineering. The optimal preventive maintenance schedule that minimizes the mean cost rate of a replacement cycle is derived analytically and determined in terms of its existence and uniqueness. The proposed models provide a general framework for analyzing the maintenance policies in reliability theory.

Keywords: optimization, preventive maintenance, random working time, minimal repair, replacement, reliability

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Authors: Xiang Jia, Zhijun Cheng

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The residual lifetime of a product is the operation time between the current time and the time point when the failure happens. The residual lifetime estimation is rather important in reliability analysis. To predict the residual lifetime, it is necessary to assume or verify a particular distribution that the lifetime of the product follows. And the two-parameter Weibull distribution is frequently adopted to describe the lifetime in reliability engineering. Due to the time constraint and cost reduction, a life testing experiment is usually terminated before all the units have failed. Then the censored data is usually collected. In addition, other information could also be obtained for reliability analysis. The expert judgements are considered as it is common that the experts could present some useful information concerning the reliability. Therefore, the residual lifetime is estimated for Weibull distribution by fusing the censored data and expert judgements in this paper. First, the closed-forms concerning the point estimate and confidence interval for the residual lifetime under the Weibull distribution are both presented. Next, the expert judgements are regarded as the prior information and how to determine the prior distribution of Weibull parameters is developed. For completeness, the cases that there is only one, and there are more than two expert judgements are both focused on. Further, the posterior distribution of Weibull parameters is derived. Considering that it is difficult to derive the posterior distribution of residual lifetime, a sample-based method is proposed to generate the posterior samples of Weibull parameters based on the Monte Carlo Markov Chain (MCMC) method. And these samples are used to obtain the Bayes estimation and credible interval for the residual lifetime. Finally, an illustrative example is discussed to show the application. It demonstrates that the proposed method is rather simple, satisfactory, and robust.

Keywords: expert judgements, information fusion, residual lifetime, Weibull distribution

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Authors: Suzan Arslanturk, Mohammad-Reza Siadat, Theophilus Ogunyemi, Ananias Diokno

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Missing data is a common challenge in statistical analyses of most clinical survey datasets. A variety of methods have been developed to enable analysis of survey data to deal with missing values. Imputation is the most commonly used among the above methods. However, in order to minimize the bias introduced due to imputation, one must choose the right imputation technique and apply it to the correct type of missing data. In this paper, we have identified different types of missing values: missing data due to skip pattern (SPMD), undetermined missing data (UMD), and genuine missing data (GMD) and applied rough set imputation on only the GMD portion of the missing data. We have used rough set imputation to evaluate the effect of such imputation on prediction by generating several simulation datasets based on an existing epidemiological dataset (MESA). To measure how well each dataset lends itself to the prediction model (logistic regression), we have used p-values from the Wald test. To evaluate the accuracy of the prediction, we have considered the width of 95% confidence interval for the probability of incontinence. Both imputed and non-imputed simulation datasets were fit to the prediction model, and they both turned out to be significant (p-value < 0.05). However, the Wald score shows a better fit for the imputed compared to non-imputed datasets (28.7 vs. 23.4). The average confidence interval width was decreased by 10.4% when the imputed dataset was used, meaning higher precision. The results show that using the rough set method for missing data imputation on GMD data improve the predictive capability of the logistic regression. Further studies are required to generalize this conclusion to other clinical survey datasets.

Keywords: rough set, imputation, clinical survey data simulation, genuine missing data, predictive index

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Authors: Wirat Sonchan, Pratoom Moungmee, Anek Sootmongkol

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This study aimed to examine the effects of a circuit training program on muscle strength, agility, anaerobic performance and cardiovascular endurance. The study involved 24 freshmen (age 18.87+0.68 yr.) male students of the Faculty of Sport Science, Burapha University. They sample study were randomly divided into two groups: Circuit Training group (CT; n=12) and a Control group (C; n=12). Baseline data on height, weight, muscle strength (hand grip dynamometer and leg strength dynamometer), agility (agility T-Test), and anaerobic performance (Running-based Anaerobic Sprint Test) and cardiovascular endurance (20 m Endurance Shuttle Run Test) were collected. The circuit training program included one circuit of eight stations of 30/60 seconds of work/rest interval with two cycles in Week 1-4, and 60/90 seconds of work/rest interval with three cycles in Week 5-8, performed three times per week. Data were analyzed using paired t-tests and independent sample t-test. Statistically significance level was set at 0.05. The results show that after 8 weeks of a training program, muscle strength, agility, anaerobic capacity and cardiovascular endurance increased significantly in the CT Group (p < 0.05), while significant increase was not observed in the C Group (p < 0.05). The results of this study suggest that the circuit training program improved muscle strength, agility, anaerobic capacity and cardiovascular endurance of the study subjects. This program may be used as a guideline for selecting a set of exercise to improve physical fitness.

Keywords: circuit training, physical fitness, cardiovascular endurance, anaerobic performance

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Authors: Falana Yetunde Olaitan, Ijah U. J. J, Solebo Shakirat O.

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Genetically modified crops are already phenomenally successful and are grown worldwide in more than eighteen countries on more than 67 million hectares. Nigeria, in October 2018, approved Bacillus thuringiensis (Bt) cotton and maize; therefore, the need to carry out environmental risk assessment studies. A total of 15 4L octagonal ceramic pots were filled with 4kg of soil and placed on the bench in 2 rows of 10 pots each and the 3rd row of 5 pots, 1st-row pots were used to plant GM cotton seeds, while the 2nd-row pots were used for non-GM cotton seeds and the 3rd row of 5 pots served as control, all in the screen house. Soil samples for metagenomic DNA extraction were collected at random and at the monthly interval after planting at a distance of 2mm from the plant’s root and at a depth of 10cm using a sterile spatula. Soil samples for physicochemical analysis were collected before planting and after harvesting the GM and non-GM crops as well as from the control soil. The DNA was extracted, quantified and sequenced; Sample 1A (DNA from GM cotton Soil at 1st interval) gave the lowest sequence read with 0.853M while sample 2B (DNA from GM cotton Soil at 2nd interval) gave the highest with 5.785M, others gave between 1.8M and 4.7M. The samples treatment were grouped into four, Group 1 (GM cotton soil from 1 to 3 intervals) had between 800,000 and 5,700,000 strains of microbes (SOM), Group 2 (non GM cotton soil from 1 to 3 intervals) had between 1,400,600 and 4,200,000 SOM, Group 3 (control soil) had between 900,000 and 3,600,000 SOM and Group 4 (initial soil) had between 3,700,000 and 4,000,000 SOM. The microbes observed were predominantly bacteria (including archaea), fungi, dark matter alongside protists and phages. The predominant bacterial groups were the Terrabacteria (Bacillus funiculus, Bacillus sp.), the Proteobacteria (Microvirga massiliensis, sphingomonas sp.) and the Archaea (Nitrososphaera sp.), while the fungi were Aspergillus fischeri and Fusarium falciforme. The comparative analysis between groups was done using JACCARD PERMANOVA beta diversity analysis at P-value not more than 0.76 and there was no significant pair found. The pH for initial, GM cotton, non-GM cotton and control soil were 6.28, 6.26, 7.25, 8.26 and the percentage moisture was 0.63, 0.78, 0.89 and 0.82, respectively, while the percentage Nitrogen was observed to be 17.79, 1.14, 1.10 and 0.56 respectively. Other parameters include, varying concentrations of Potassium (0.46, 1,284.47, 1,785.48, 1,252.83 mg/kg) and Phosphorus (18.76, 17.76, 16.87, 15.23 mg/kg) were recorded for the four treatments respectively. The soil consisted mainly of silt (32.09 to 34.66%) and clay (58.89 to 60.23%), reflecting the soil texture as silty – clay. The results were then tested with ANOVA at less than 0.05 P-value and no pair was found to be significant as well. The results suggest that the GM crops have no significant effect on microbial ecology and physicochemical properties of the soil and, in turn, no direct or indirect effects on human health.

Keywords: genetically modified crop, microbial ecology, physicochemical properties, metagenomics, DNA, soil

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Authors: Thanusha D. Abeywickrama, Inoka C. Perera, Genji Kurisu

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Tuberculosis, considered being as the ninth leading cause of death worldwide, cause from a single infectious agent M. tuberculosis and the drug resistance nature of this bacterium is a continuing threat to the world. Therefore TB preventing treatment is expanding, where this study designed to analyze the regulatory mechanism of GntR transcriptional regulator gene Rv0792c, which lie between several genes codes for some hypothetical proteins, a monooxygenase and an oxidoreductase. The gene encoding Rv0792c was cloned into pET28a and expressed protein was purified to near homogeneity by Nickel affinity chromatography. It was previously reported that the protein binds within the intergenic region (BS region) between Rv0792c gene and monooxygenase (Rv0793). This resulted in binding of three protein molecules with the BS region suggesting tight control of monooxygenase as well as its own gene. Since monooxygenase plays a key role in metabolism, this gene may have a global regulatory role. The natural ligand for this regulator is still under investigation. In relation to the Rv0792 protein structure, a Circular Dichroism (CD) spectrum was carried out to determine its secondary structure elements. Percentage-wise, 17.4% Helix, 21.8% Antiparallel, 5.1% Parallel, 12.3% turn and 43.5% other were revealed from CD spectrum data under room temperature. Differential Scanning Calorimetry (DSC) was conducted to assess the thermal stability of Rv0792, which the melting temperature of protein is 57.2 ± 0.6 °C. The graph of heat capacity (Cp) versus temperature for the best fit was obtained for non-two-state model, which concludes the folding of Rv0792 protein occurs through stable intermediates. Peak area (∆HCal ) and Peak shape (∆HVant ) was calculated from the graph and ∆HCal / ∆HVant was close to 0.5, suggesting dimeric nature of the protein.

Keywords: CD spectrum, DSC analysis, GntR transcriptional regulator, protein structure

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Authors: Xin Yuan, Yuji Ryu

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The indoor environment has a significant impact on occupants and a suitable indoor thermal environment can improve the children’s physical health and study efficiency during school hours. In this study, we explored the thermal environment in infant facilities classrooms for infants and children aged 1-5 and evaluated their thermal comfort. An infant facility in Fukuoka, Japan was selected for a case study to capture the infant and children’s thermal comfort characteristics in summer and winter from August 2019 to February 2020. Previous studies have pointed out using PMV indices to evaluate the thermal comfort for children could create errors that may lead to misleading results. Thus, to grasp the actual thermal environment and thermal comfort characteristics of infants and children, we retrieved the operative temperature of each child through the thermal model, based on the sensible heat transfer from the skin to the environment, and the measured classroom indoor temperature, relative humidity, and pocket temperature of children’s shorts. The statistical and comparative analysis of the results shows that (1) the operative temperature showed a large individual difference among children, with the maximum reached 6.25 °C. (2) The children might feel slightly cold in the classrooms in summer, with the frequencies of operative temperature within the interval of 26-28 ºC were only 5.33% and 16.6% for children respectively. (3) The thermal environment around children is more complicated in winter the operative temperature could exceed or fail to reach the thermal comfort temperature zone (20-23 ºC interval). (4) The environmental conditions surrounding the children may account for the reduction of their thermal comfort. The findings contribute to improving the understanding of the infant and children’s thermal comfort and provide valuable information for designers and governments to develop effective strategies for the indoor thermal environment considering the perspective of children.

Keywords: infant and children, thermal environment, thermal model, operative temperature.

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Authors: M. Nekri, A. Khelladi

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The world wide web network is a network with a complex topology, the main properties of which are the distribution of degrees in power law, A low clustering coefficient and a weak average distance. Modeling the web as a graph allows locating the information in little time and consequently offering a help in the construction of the research engine. Here, we present a model based on the already existing probabilistic graphs with all the aforesaid characteristics. This work will consist in studying the web in order to know its structuring thus it will enable us to modelize it more easily and propose a possible algorithm for its exploration.

Keywords: clustering coefficient, preferential attachment, small world, web community

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Authors: Ke Zhang, Yongli Zhu

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Due to rapid load growths in today’s highly electrified societies and the requirement for green energy sources, large-scale wind farm power transmission system is constantly developing. This system is a typical multi-terminal power supply system, whose structure of the network topology of transmission lines is complex. What’s more, it locates in the complex terrain of mountains and grasslands, thus increasing the possibility of transmission line faults and finding the fault location with difficulty after the faults and resulting in an extremely serious phenomenon of abandoning the wind. In order to solve these problems, a fault location method for multi-terminal transmission line based on wind farm characteristics and improved single-ended traveling wave positioning method is proposed. Through studying the zero sequence current characteristics by using the characteristics of the grounding transformer(GT) in the existing large-scale wind farms, it is obtained that the criterion for judging the fault interval of the multi-terminal transmission line. When a ground short-circuit fault occurs, there is only zero sequence current on the path between GT and the fault point. Therefore, the interval where the fault point exists is obtained by determining the path of the zero sequence current. After determining the fault interval, The location of the short-circuit fault point is calculated by the traveling wave method. However, this article uses an improved traveling wave method. It makes the positioning accuracy more accurate by combining the single-ended traveling wave method with double-ended electrical data. What’s more, a method of calculating the traveling wave velocity is deduced according to the above improvements (it is the actual wave velocity in theory). The improvement of the traveling wave velocity calculation method further improves the positioning accuracy. Compared with the traditional positioning method, the average positioning error of this method is reduced by 30%.This method overcomes the shortcomings of the traditional method in poor fault location of wind farm transmission lines. In addition, it is more accurate than the traditional fixed wave velocity method in the calculation of the traveling wave velocity. It can calculate the wave velocity in real time according to the scene and solve the traveling wave velocity can’t be updated with the environment and real-time update. The method is verified in PSCAD/EMTDC.

Keywords: grounding transformer, multi-terminal transmission line, short circuit fault location, traveling wave velocity, wind farm

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Authors: Alexander N. Savostyanov, Tatiana A. Dolgorukova, Elena A. Esipenko, Mikhail S. Zaleshin, Margherita Malanchini, Anna V. Budakova, Alexander E. Saprygin, Tatiana A. Golovko, Yulia V. Kovas

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EEG correlates of mathematical and trait anxiety level were studied in 52 healthy Russian-speakers during execution of error-recognition tasks with lexical, arithmetic and algebraic conditions. Event-related spectral perturbations were used as a measure of brain activity. The ERSP plots revealed alpha/beta desynchronizations within a 500-3000 ms interval after task onset and slow-wave synchronization within an interval of 150-350 ms. Amplitudes of these intervals reflected the accuracy of error recognition, and were differently associated with the three conditions. The correlates of anxiety were found in theta (4-8 Hz) and beta2 (16-20 Hz) frequency bands. In theta band the effects of mathematical anxiety were stronger expressed in lexical, than in arithmetic and algebraic condition. The mathematical anxiety effects in theta band were associated with differences between anterior and posterior cortical areas, whereas the effects of trait anxiety were associated with inter-hemispherical differences. In beta1 and beta2 bands effects of trait and mathematical anxiety were directed oppositely. The trait anxiety was associated with increase of amplitude of desynchronization, whereas the mathematical anxiety was associated with decrease of this amplitude. The effect of mathematical anxiety in beta2 band was insignificant for lexical condition but was the strongest in algebraic condition. EEG correlates of anxiety in theta band could be interpreted as indexes of task emotionality, whereas the reaction in beta2 band is related to tension of intellectual resources.

Keywords: EEG, brain activity, lexical and numerical error-recognition tasks, mathematical and trait anxiety

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Authors: Jeff Chak-Fu Wong, Tony Chun Yin Yip

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The transition from secondary school to university seems exciting for many first-year students but can be more challenging than expected. Enabling instructors to know students’ learning habits and styles enhances their understanding of the students’ learning backgrounds, allows teachers to provide better support for their students, and has therefore high potential to improve teaching quality and learning, especially in any mathematics-related courses. The aim of this research is to collect students’ data using online surveys, to analyze students’ factors using learning analytics and educational data mining and to discover the characteristics of the students at risk of falling behind in their studies based on students’ previous academic backgrounds and collected data. In this paper, we use correlation-based distance methods and mutual information for measuring student factor relationships. We then develop a factor network using the Minimum Spanning Tree method and consider further study for analyzing the topological properties of these networks using social network analysis tools. Under the framework of mutual information, two graph-based feature filtering methods, i.e., unsupervised and supervised infinite feature selection algorithms, are used to analyze the results for students’ data to rank and select the appropriate subsets of features and yield effective results in identifying the factors affecting students at risk of failing. This discovered knowledge may help students as well as instructors enhance educational quality by finding out possible under-performers at the beginning of the first semester and applying more special attention to them in order to help in their learning process and improve their learning outcomes.

Keywords: students' academic performance, correlation-based distance method, social network analysis, feature selection, graph-based feature filtering method

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Authors: Babak Bahri, Fatemeh Yassaee Meybodi, Changiz Eslahchi

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In the pursuit of effective cancer therapies, the exploration of combinatorial drug regimens is crucial to leverage synergistic interactions between drugs, thereby improving treatment efficacy and overcoming drug resistance. However, identifying synergistic drug pairs poses challenges due to the vast combinatorial space and limitations of experimental approaches. This study introduces ClusterSyn, a machine learning (ML)-powered framework for classifying anti-cancer drug synergy scores. ClusterSyn employs a two-step approach involving drug clustering and synergy score prediction using a fully connected deep neural network. For each cell line in the training dataset, a drug graph is constructed, with nodes representing drugs and edge weights denoting synergy scores between drug pairs. Drugs are clustered using the Markov clustering (MCL) algorithm, and vectors representing the similarity of drug pairs to each cluster are input into the deep neural network for synergy score prediction (synergy or antagonism). Clustering results demonstrate effective grouping of drugs based on synergy scores, aligning similar synergy profiles. Subsequently, neural network predictions and synergy scores of the two drugs on others within their clusters are used to predict the synergy score of the considered drug pair. This approach facilitates comparative analysis with clustering and regression-based methods, revealing the superior performance of ClusterSyn over state-of-the-art methods like DeepSynergy and DeepDDS on diverse datasets such as Oniel and Almanac. The results highlight the remarkable potential of ClusterSyn as a versatile tool for predicting anti-cancer drug synergy scores.

Keywords: drug synergy, clustering, prediction, machine learning., deep learning

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Authors: Nada R. Abuknesha, John P. Morgan, Andrew J. Searle

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Information regarding post-mortem interval (PMI) in criminal investigations is vital to establish a time frame when reconstructing events. PMI is defined as the time period that has elapsed between the occurrence of death and the discovery of the corpse. Adipocere, commonly referred to as ‘grave-wax’, is formed when post-mortem adipose tissue is converted into a solid material that is heavily comprised of fatty acids. Adipocere is of interest to forensic anthropologists, as its formation is able to slow down the decomposition process. Therefore, analysing the changes in the patterns of fatty acids during the early decomposition process may be able to estimate the period of burial, and hence the PMI. The current study concerned the investigation of the fatty acid composition and patterns in buried pig fat tissue. This was in an attempt to determine whether particular patterns of fatty acid composition can be shown to be associated with the duration of the burial, and hence may be used to estimate PMI. The use of adipose tissue from the abdominal region of domestic pigs (Sus-scrofa), was used to model the human decomposition process. 17 x 20cm piece of pork belly was buried in a shallow artificial grave, and weekly samples (n=3) from the buried pig fat tissue were collected over an 11-week period. Marker fatty acids: palmitic (C16:0), oleic (C18:1n-9) and linoleic (C18:2n-6) acid were extracted from the buried pig fat tissue and analysed as fatty acid methyl esters using the gas chromatography system. Levels of the marker fatty acids were quantified from their respective standards. The concentrations of C16:0 (69.2 mg/mL) and C18:1n-9 (44.3 mg/mL) from time zero exhibited significant fluctuations during the burial period. Levels rose (116 and 60.2 mg/mL, respectively) and fell starting from the second week to reach 19.3 and 18.3 mg/mL, respectively at week 6. Levels showed another increase at week 9 (66.3 and 44.1 mg/mL, respectively) followed by gradual decrease at week 10 (20.4 and 18.5 mg/mL, respectively). A sharp increase was observed in the final week (131.2 and 61.1 mg/mL, respectively). Conversely, the levels of C18:2n-6 remained more or less constant throughout the study. In addition to fluctuations in the concentrations, several new fatty acids appeared in the latter weeks. Other fatty acids which were detectable in the time zero sample, were lost in the latter weeks. There are several probable opportunities to utilise fatty acid analysis as a basic technique for approximating PMI: the quantification of marker fatty acids and the detection of selected fatty acids that either disappear or appear during the burial period. This pilot study indicates that this may be a potential semi-quantitative methodology for determining the PMI. Ideally, the analysis of particular fatty acid patterns in the early stages of decomposition could be an additional tool to the already available techniques or methods in improving the overall processes in estimating PMI of a corpse.

Keywords: adipocere, fatty acids, gas chromatography, post-mortem interval

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

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

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

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Authors: Che Hsiu Chen, Su Yun Chen, Hon Wen Cheng

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Greater core stability may benefit sports performance by providing a foundation for greater force production in the upper and lower extremities. Core stability exercises on instability device (such as the TRX suspension systems) were found to be able to induce higher core muscle activity than performing on a stable surface. However, high intensity interval TRX suspension exercises training on sport performances remain unclear. The purpose of this study was to examine whether high intensity TRX suspension training could improve sport performance. Twenty-four healthy university female students (age 19.0 years, height 157.9 cm, body mass 51.3 kg, fat mass 25.2 %) were voluntarily participated in this study. After a familiarization session, each participant underwent five suspension exercises (e.g., hip abduction in plank alternative, hamstring curl, 45-degree row, lunge and oblique crunch). Each type of exercise was performed for 30 seconds, followed by 30 seconds break, two times per week for eight weeks while each exercise session was increased by 10 seconds every week. The results showed that the fat mass (about 12.92%) decreased significantly, sit and reach test (9%), 1 minute sit-up test (17.5%), standing broad jump (4.8%), physical fitness index (10.3%) increased significantly after 8-week high intensity TRX suspension training. Hence, eight weeks of high intensity interval TRX suspension exercises training can improve hamstring flexibility, trunk endurance, jump ability, aerobic fitness and fat mass percentage decreased substantially.

Keywords: core endurance, jump, flexibility, cardiovascular fitness

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Authors: Souad Slimani, Sylvain Gravier, Simon Schmidt

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Recently, several vertex identifying notions were introduced (identifying coloring, lid-coloring,...); these notions were inspired by identifying codes. All of them, as well as original identifying code, is based on separating two vertices according to some conditions on their closed neighborhood. Therefore, twins can not be identified. So most of known results focus on twin-free graph. Here, we show how twins can modify optimal value of vertex-identifying parameters for identifying coloring and locally identifying coloring.

Keywords: identifying coloring, locally identifying coloring, twins, separating

Procedia PDF Downloads 113

Authors: Yuxi Liu, Boris Belousov, Mehrzad Esmaeili Charkhab, Oliver Tessmann

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This paper presents a computational solution for designing reconfigurable interlocking structures that are fully assembled with SL Blocks. Formed by S-shaped and L-shaped tetracubes, SL Block is a specific type of interlocking puzzle. Analogous to molecular self-assembly, the aggregation of SL blocks will build a reversible hierarchical and discrete system where a single module can be numerously replicated to compose semi-interlocking components that further align, wrap, and braid around each other to form complex high-order aggregations. These aggregations can be disassembled and reassembled, responding dynamically to design inputs and changes with a unique capacity for reconfiguration. To use these aggregations as architectural structures, we developed computational tools that automate the configuration of SL blocks based on architectural design objectives. There are three critical phases in our work. First, we revisit the hierarchy of the SL block system and devise a top-down-type design strategy. From this, we propose two key questions: 1) How to translate 3D polyominoes into SL block assembly? 2) How to decompose the desired voxelized shapes into a set of 3D polyominoes with interlocking joints? These two questions can be considered the Hamiltonian path problem and the 3D polyomino tiling problem. Then, we derive our solution to each of them based on two methods. The first method is to construct the optimal closed path from an undirected graph built from the voxelized shape and translate the node sequence of the resulting path into the assembly sequence of SL blocks. The second approach describes interlocking relationships of 3D polyominoes as a joint connection graph. Lastly, we formulate the desired shapes and leverage our methods to achieve their reconfiguration within different levels. We show that our computational strategy will facilitate the efficient design of hierarchical interlocking structures with a self-replicating geometric module.

Keywords: computational design, SL-blocks, 3D polyomino puzzle, combinatorial problem

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Authors: Amirhossein Dodankeh, Hadi Dabiryan, Saeed Hamze

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Using fabrics to reinforce composites considerably leads to improved mechanical properties, including resistance to the impact load and the energy absorption of composites. Warp-knitted spacer fabrics (WKSF) are fabrics consisting of two layers of warp-knitted fabric connected by pile yarns. These connections create a space between the layers filled by pile yarns and give the fabric a three-dimensional shape. Today because of the unique properties of spacer fabrics, they are widely used in the transportation, construction, and sports industries. Polyurethane (PU) foams are commonly used as energy absorbers, but WKSF has much better properties in moisture transfer, compressive properties, and lower heat resistance than PU foam. It seems that the use of warp-knitted spacer fabric reinforced PU foam (WKSFRF) can lead to the production and use of composite, which has better properties in terms of energy absorption from the foam, its mold formation is enhanced, and its mechanical properties have been improved. In this paper, the energy absorption efficiency (EAE) of WKSFRF under low-velocity impact is investigated experimentally. The contribution of the effect of each of the structural parameters of the WKSF on the absorption of impact energy has also been investigated. For this purpose, WKSF with different structures such as two different thicknesses, small and large mesh sizes, and position of the meshes facing each other and not facing each other were produced. Then 6 types of composite samples with different structural parameters were fabricated. The physical properties of samples like weight per unit area and fiber volume fraction of composite were measured for 3 samples of any type of composites. Low-velocity impact with an initial energy of 5 J was carried out on 3 samples of any type of composite. The output of the low-velocity impact test is acceleration-time (A-T) graph with a lot deviation point, in order to achieve the appropriate results, these points were removed using the FILTFILT function of MATLAB R2018a. Using Newtonian laws of physics force-displacement (F-D) graph was drawn from an A-T graph. We know that the amount of energy absorbed is equal to the area under the F-D curve. Determination shows the maximum energy absorption is 2.858 J which is related to the samples reinforced with fabric with large mesh, high thickness, and not facing of the meshes relative to each other. An index called energy absorption efficiency was defined, which means absorption energy of any kind of our composite divided by its fiber volume fraction. With using this index, the best EAE between the samples is 21.6 that occurs in the sample with large mesh, high thickness, and meshes facing each other. Also, the EAE of this sample is 15.6% better than the average EAE of other composite samples. Generally, the energy absorption on average has been increased 21.2% by increasing the thickness, 9.5% by increasing the size of the meshes from small to big, and 47.3% by changing the position of the meshes from facing to non-facing.

Keywords: composites, energy absorption efficiency, foam, geometrical parameters, low-velocity impact, warp-knitted spacer fabric

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Authors: B. Samuel Raj, Solomon R. D. Jebakumar

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Microbial fuel cells (MFCs) are an emerging and promising method for achieving sustainable energy since they can remove contaminated organic matter and simultaneously generate electricity. Our approach was driven in three different ways like Bacterial fuel cell, Soil Microbial fuel cell (Soil MFC) and Plant Microbial fuel cell (Plant MFC). Bacterial MFC: Sulphate reducing bacteria (SRB) were isolated and identified as the efficient electricigens which is able to produce ±2.5V (689mW/m2) and it has sustainable activity for 120 days. Experimental data with different MFC revealed that high electricity production harvested continuously for 90 days 1.45V (381mW/m2), 1.98V (456mW/m2) respectively. Biofilm formation was confirmed on the surface of the anode by high content screening (HCS) and scanning electron Microscopic analysis (SEM). Soil MFC: Soil MFC was constructed with low cost and standard Mudwatt soil MFC was purchased from keegotech (USA). Vermicompost soil (V1) produce high energy (± 3.5V for ± 400 days) compared to Agricultural soil (A1) (± 2V for ± 150 days). Biofilm formation was confirmed by HCS and SEM analysis. This finding provides a method for extracting energy from organic matter, but also suggests a strategy for promoting the bioremediation of organic contaminants in subsurface environments. Our Soil MFC were able to run successfully a 3.5V fan and three LED continuously for 150 days. Plant MFC: Amaranthus candatus (P1) and Triticum aestivium (P2) were used in Plant MFC to confirm the electricity production from plant associated microbes, four uniform size of Plant MFC were constructed and checked for energy production. P2 produce high energy (± 3.2V for 40 days) with harvesting interval of two times and P1 produces moderate energy without harvesting interval (±1.5V for 24 days). P2 is able run 3.5V fan continuously for 10days whereas P1 needs optimization of growth conditions to produce high energy.

Keywords: microbial fuel cell, biofilm, soil microbial fuel cell, plant microbial fuel cell

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Authors: Fergus Wade, Jasmine Makker, Matthew Jankinson, Aminah Qamar, Gemma Morrelli, Shayan Shah

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Background: Ambulance offload delays (AODs) affect patient outcomes. At baseline, the average AOD at Princess Royal University Hospital (PRUH) was 41 minutes, in breach of the 15-minute target. Aims: By February 2023, we aimed to reduce: the average AOD to 30 minutes percentage of AOD >30 minutes (PA30) to 25% and >60 minutes (PA60) to 10% Methods: Following a root-cause analysis, we implemented 2 Plan, Do, Study, Act (PDSA) cycles. PDSA-1 ‘Drop-and-run’: ambulances waiting >15 minutes for a handover left the patients in the Emergency Department (ED) and returned to the community. PDSA-2: Booking in the patients before the handover, allowing direct updates to online records, eliminating the need for handwritten notes. Outcome measures: AOD, PA30, and PA60, and process measures: total ambulances and patients in the ED were recorded for 16 weeks. Results: In PDSA-1, all parameters increased slightly despite unvarying ED crowding. In PDSA-2, two shifts in data were seen: initially, a sharp increase in the outcome measures consistent with increased ED crowding, followed by a downward shift when crowding returned to baseline (p<0.01). Within this interval, the AOD reduced to 29.9 minutes, and PA30 and PA60 were 31.2% and 9.2% respectively. Discussion/conclusion: PDSA-1 didn’t result in any significant changes; lack of compliance was a key cause. The initial upward shift in PDSA-2 is likely associated with NHS staff strikes. However, during the second interval, the AOD and the PA60 met our targets of 30 minutes and 10%, respectively, improving patient flow in the ED. This was sustained without further input and if maintained, saves 2 paramedic shifts every 3 days.

Keywords: ambulance offload, district general hospital, handover, quality improvement

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

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

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

Procedia PDF Downloads 110