Search results for: computational diagnostics

Authors: Abdullah Saeidi, Aydin Gülses, Christan Flörke

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Skin cancer of the face region is the most common type of malignancy and surgical excision is the preferred approach. However, the clinical long term results reported in the literature are still controversial. Objectives: To describe; 1. Demographical characteristics 2. Affected site, distribution and TNM classification regarding tumor type 3. Surgical aspects • Surgical removal: excision principles, safety margins, the need for secondary resection, primary reconstruction/ defect closure, anesthesia protocol, duration of hospital stay (if any) • Secondary intervention for defect closure/reconstruction: Flap technique, anesthesia protocol, duration of hospital stay (if any), postoperative wound management etc. 4. Tumor recurrences 5. Clinical outcomes 6. Studying the possible therapy approach throw Biostatistical relation and correlation between multiple Histological, diagnostics and clinical Faktors. following surgical ablation of the skin cancer of the head and neck region. Methods: Selection and statistical analysis of medical records of patients who had admitted to the Department of Oral and Maxillofacial Surgery, Universitätsklinikum Schleswig Holstein, Campus Kiel during the period of 2015-2019 will be retrospectively evaluated. Data will be collected via ORBIS Information-Management-System (ORBIS AG, Saarbrücken, Germany).

Keywords: non melanoma skin cancer, face skin cancer, skin reconstruction, non melanoma skin cancer recurrence, non melanoma skin cancer metastases

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Authors: Salma El Hajjami, Jamal Malki, Alain Bouju, Mohammed Berrada

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With the expansion of machine learning and data mining in the context of Big Data analytics, the common problem that affects data is class imbalance. It refers to an imbalanced distribution of instances belonging to each class. This problem is present in many real world applications such as fraud detection, network intrusion detection, medical diagnostics, etc. In these cases, data instances labeled negatively are significantly more numerous than the instances labeled positively. When this difference is too large, the learning system may face difficulty when tackling this problem, since it is initially designed to work in relatively balanced class distribution scenarios. Another important problem, which usually accompanies these imbalanced data, is the overlapping instances between the two classes. It is commonly referred to as noise or overlapping data. In this article, we propose an approach called: One Side Behavioral Noise Reduction (OSBNR). This approach presents a way to deal with the problem of class imbalance in the presence of a high noise level. OSBNR is based on two steps. Firstly, a cluster analysis is applied to groups similar instances from the minority class into several behavior clusters. Secondly, we select and eliminate the instances of the majority class, considered as behavioral noise, which overlap with behavior clusters of the minority class. The results of experiments carried out on a representative public dataset confirm that the proposed approach is efficient for the treatment of class imbalances in the presence of noise.

Keywords: machine learning, imbalanced data, data mining, big data

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Authors: Ognen Kostovski, Svetozar Antovic, Rubens Jovanovic, Irena Kostovska, Nikola Jankulovski

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Introduction:Colorectal carcinoma (CRC) is one of the most common malignancies in the world. The cancer stem cell (CSC) markers are associated with aggressive cancer types and poor prognosis. The aim of study was to determine whether the expression of colorectal cancer stem cell markers CD133 and CD44 could be significant in prediction of clinically aggressive form of CRC. Materials and methods: Our study included ninety patients (n=90) with CRC. Patients were divided into two subgroups: with metatstatic CRC and non-metastatic CRC. Tumor samples were analyzed with standard histopathological methods, than was performed immunohistochemical analysis with monoclonal antibodies against CD133 and CD44 stem cell markers. Results: High coexpression of CD133 and CD44 was observed in 71.4% of patients with metastatic disease, compared to 37.9% in patients without metastases. Discordant expression of both markers was found in 8% of the subgroup with metastatic CRC, and in 13.4% of the subgroup without metastatic CRC. Statistical analyses showed a significant association of increased expression of CD133 and CD44 with the disease stage, T - category and N - nodal status. With multiple regression analysis the stage of disease was designate as a factor with the greatest statistically significant influence on expression of CD133 (p <0.0001) and CD44 (p <0.0001). Conclusion: Our results suggest that the coexpression of CD133 and CD44 have an important role in prediction of clinically aggressive form of CRC. Both stem cell markers can be routinely implemented in standard pathohistological diagnostics and can be useful markers for pre-therapeutic oncology screening.

Keywords: colorectal carcinoma, stem cells, CD133+, CD44+

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Authors: Milena Nanova, Radul Shishkov, Damyan Damov, Martin Georgiev

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This research paper presents an in-depth exploration of the use of generative design in urban residential architecture, with a dual focus on aligning aesthetic values with legal and environmental constraints. The study aims to demonstrate how generative design methodologies can innovate residential building designs that are not only legally compliant and environmentally conscious but also aesthetically compelling. At the core of our research is a specially developed generative design framework tailored for urban residential settings. This framework employs computational algorithms to produce diverse design solutions, meticulously balancing aesthetic appeal with practical considerations. By integrating site-specific features, urban legal restrictions, and environmental factors, our approach generates designs that resonate with the unique character of urban landscapes while adhering to regulatory frameworks. The paper places emphasis on algorithmic implementation of the logical constraint and intricacies in residential architecture by exploring the potential of generative design to create visually engaging and contextually harmonious structures. This exploration also contains an analysis of how these designs align with legal building parameters, showcasing the potential for creative solutions within the confines of urban building regulations. Concurrently, our methodology integrates functional, economic, and environmental factors. We investigate how generative design can be utilized to optimize buildings' performance, considering them, aiming to achieve a symbiotic relationship between the built environment and its natural surroundings. Through a blend of theoretical research and practical case studies, this research highlights the multifaceted capabilities of generative design and demonstrates practical applications of our framework. Our findings illustrate the rich possibilities that arise from an algorithmic design approach in the context of a vibrant urban landscape. This study contributes an alternative perspective to residential architecture, suggesting that the future of urban development lies in embracing the complex interplay between computational design innovation, regulatory adherence, and environmental responsibility.

Keywords: generative design, computational design, parametric design, algorithmic modeling

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Authors: Joseph Amponsah

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This research proposes an equation to predict and determine the momentum source equation term after factoring in the radial friction between the fluid and the blades and the impeller's propulsive power. This research aims to look at how CFD software can be used to predict the effect of flows in nuclear reactor stirred tanks through a momentum source equation and the concentration distribution of tracers that have been introduced in reactor tanks. The estimated findings, including the dimensionless concentration curves, power, and pumping numbers, dimensionless velocity profiles, and mixing times 4, were contrasted with results from tests in stirred containers. The investigation was carried out in Part I for vessels that were agitated by one impeller on a central shaft. The two types of impellers employed were an ordinary Rushton turbine and a 6-bladed 45° pitched blade turbine. The simulations made use of numerous reference frame techniques and the common k-e turbulence model. The impact of the grid type was also examined; unstructured, structured, and unique user-defined grids were looked at. The CFD model was used to simulate the flow field within the Rushton turbine nuclear reactor stirred tank. This method was validated using experimental data that were available close to the impeller tip and in the bulk area. Additionally, analyses of the computational efficiency and time using MRF and SM were done.

Keywords: Ansys fluent, momentum equation, CFD, prediction

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Authors: J. L. Bhagoria, Ajeet Kumar Giri

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A computational investigation of various flow characteristics with artificial roughness in the form of V-types discrete ribs, heated wall of rectangular duct for turbulent flow with Reynolds number range (3800-15000) and p/e (5 to 12) has been carried out with k-e turbulence model is selected by comparing the predictions of different turbulence models with experimental results available in literature. The current study evaluates thermal performance behavior, heat transfer and fluid flow behavior in a v shaped duct with discrete roughened ribs mounted on one of the principal wall (solar plate) by computational fluid dynamics software (Fluent 6.3.26 Solver). In this study, CFD has been carried out through designing 3-demensional model of experimental solar air heater model analysis has been used to perform a numerical simulation to enhance turbulent heat transfer and Reynolds-Averaged Navier–Stokes analysis is used as a numerical technique and the k-epsilon model with near-wall treatment as a turbulent model. The thermal efficiency enhancement because of selected roughness is found to be 16-24%. The result predicts a significant enhancement of heat transfer as compared to that of for a smooth surface with different P’ and various range of Reynolds number.

Keywords: CFD, solar collector, airheater, thermal efficiency

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Authors: Ágota Ábrahám, Md Nurul Islam, Karimane Zeghbib, Gábor Kemenesi, Sazeda Akter

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Collecting palm sap as a food source is an everyday practice in some parts of the world. However, the consumption of palm juice has been associated with regular infections and epidemics in parts of Bangladesh. This is attributed to fruit-eating bats and other vertebrates or invertebrates native to the area, contaminating the food with their body secretions during the collection process. The frequent intake of palm juice, whether as a processed food product or in its unprocessed form, is a common phenomenon in large areas. The range of pathogens suitable for human infection resulting from this practice is not yet fully understood. Additionally, the high sugar content of the liquid makes it an ideal culture medium for certain bacteria, which can easily propagate and potentially harm consumers. Rapid diagnostics, especially in remote locations, could mitigate health risks associated with palm juice consumption. The primary objective of this research is the rapid genomic detection and risk assessment of bacteria that may cause infections in humans through the consumption of palm juice. Utilizing state-of-the-art third-generation Nanopore metagenomic sequencing technology based on 16S rRNA, and identified bacteria primarily involved in fermenting processes. The swift metagenomic analysis, coupled with the widespread availability and portability of Nanopore products (including real-time analysis options), proves advantageous for detecting harmful pathogens in food sources without relying on extensive industry resources and testing.

Keywords: raw date palm sap, NGS, metabarcoding, food safety

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Authors: Yue Shuai Zhao, Rong Ping Shao, Wei Sun, Guo Hua Ren, Yong Wang, Li Chen Sun

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A large-scale cryopump (DN1250) used in large vacuum leak detecting system was designed and its performance experimentally investigated by Beijing Institute of Spacecraft Environment Engineering. The cryopump was cooled by four closed cycle helium refrigerators (two dual stage refrigerators and two single stage refrigerators). Detailed numerical analysis of the heat transfer in the first stage array and the second stage array were performed by using computational fluid dynamic method (CFD). Several design parameters were considered to find the effect on the temperature distribution and the cooldown time. The variation of thermal conductivity and heat capacity with temperature was taken into account. The thermal analysis method based on numerical techniques was introduced in this study, the heat transfer in the first stage array and the second stage cryopanel was carefully analyzed to determine important considerations in the thermal design of the cryopump. A performance test system according to the RNEUROP standards was built to test main performance of the cryopump. The experimental results showed that the structure of first stage array which was optimized by the method could meet the requirement of the cryopump well. The temperature of the cryopanel was down to 10K within 300 min, and the result of the experiment was accordant with theoretical analysis' conclusion. The test also showed that the pumping speed for N2 of the pump was up to 57,000 L/s, and the crossover was over than 300,000 Pa•L.

Keywords: cryopump, temperature distribution, thermal analysis, CFD Simulation

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Authors: Heval Serhat Uluk, Sam M. Dakka, Kuldeep Singh, Richard Jefferson-Loveday

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This paper will focus on the suitability of a trapped vortex combustor as a candidate for gas turbine combustor objectives to minimize pressure drop across the combustor and investigate aerodynamic performance. Non-reacting simulation of axisymmetric cavity trapped vortex combustors were simulated to investigate the pressure drop for various cavity aspect ratios of 0.3, 0.6, and 1 and for air mass flow rates of 14 m/s, 28 m/s, and 42 m/s. A numerical study of an axisymmetric trapped vortex combustor was carried out by using two-dimensional and three-dimensional computational domains. A comparison study was conducted between Reynolds Averaged Navier Stokes (RANS) k-ε Realizable with enhanced wall treatment and RANS k-ω Shear Stress Transport (SST) models to find the most suitable turbulence model. It was found that the k-ω SST model gives relatively close results to experimental outcomes. The numerical results were validated and showed good agreement with the experimental data. Pressure drop rises with increasing air mass flow rate, and the lowest pressure drop was observed at 0.6 cavity aspect ratio for all air mass flow rates tested, which agrees with the experimental outcome. A mixing enhancement study showed that 30-degree angle air injectors provide improved fuel-air mixing.

Keywords: aerodynamic, computational fluid dynamics, propulsion, trapped vortex combustor

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Authors: Yu-Chen Hsu, Kuang C. Lin

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The artificial lung called extracorporeal membrane oxygenation (ECMO) is an important medical machine that supports persons whose heart and lungs dysfunction. Previously, investigation of steady deoxygenated blood flows passing through hollow fibers for oxygen transport was carried out experimentally and computationally. The present study computationally analyzes the effect of biological pulsatile flow on the oxygen transport in blood. A 2-D model with a pulsatile flow condition is employed. The power law model is used to describe the non-Newtonian flow and the Hill equation is utilized to simulate the oxygen saturation of hemoglobin. The dimensionless parameters for the physical model include Reynolds numbers (Re), Womersley parameters (α), pulsation amplitudes (A), Sherwood number (Sh) and Schmidt number (Sc). The present model with steady-state flow conditions is well validated against previous experiment and simulations. It is observed that pulsating flow amplitudes significantly influence the velocity profile, pressure of oxygen (PO2), saturation of oxygen (SO2) and the oxygen mass transfer rates (m ̇_O2). In comparison between steady-state and pulsating flows, our findings suggest that the consideration of pulsating flow in the computational model is needed when Re is raised from 2 to 10 in a typical range for flow in artificial lung.

Keywords: artificial lung, oxygen transport, non-Newtonian flows, pulsating flows

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Authors: Karen C. Olufokunbi, Odetunji A. Odejobi

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The discourse of this paper is the examination of the generation, accumulation and growth of e-waste in a developing country. Images and other data about computer e-waste were collected using a digital camera, 290 copies of questionnaire and three structured interviews using Obafemi Awolowo University (OAU), Ile-Ife, Nigeria environment as a case study. The numerical data were analysed using R data analysis and process tool. Automata-based techniques and Petri net modeling tool were used to design and simulate a computational model for the recovery of saleable materials from e-waste. The R analysis showed that at a 95 percent confidence level, the computer equipment that will be disposed by 2020 will be 417 units. Compared to the 800 units in circulation in 2014, 50 percent of personal computer components will become e-waste. This indicates that personal computer components were in high demand due to their low costs and will be disposed more rapidly when replaced by new computer equipment Also, 57 percent of the respondents discarded their computer e-waste by throwing it into the garbage bin or by dumping it. The simulated model using Coloured Petri net modelling tool for the process showed that the e-waste dynamics is a forward sequential process in the form of a pipeline meaning that an e-waste recovery of saleable materials process occurs in identifiable discrete stages indicating that e-waste will continue to accumulate and grow in volume with time.

Keywords: Coloured Petri net, computational modelling, electronic waste, electronic waste process dynamics

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Authors: Yutaro Kyuma, Sung-Jun Yoo, Kazuhide Ito

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A commuter bus remains important as a means to network public transportation between railway stations and terminals within cities. In some cases, the boarding time becomes longer, and the boarding rate tends to be higher corresponding to the development of urban cities. The interior environmental quality, e.g. temperature and air quality, in a commuter bus is relatively heterogeneous and complex compared to that of an indoor environment in buildings due to several factors: solar radiative heat – which comes from large-area windows –, inadequate ventilation rate caused by high density of commuters, and metabolic heat generation from travelers themselves. In addition to this, under conditions where many passengers ride in the enclosed space, contact and airborne infectious risk have attracted considerable attention in terms of public health. From this point of view, it is essential to develop the prediction method for assessment of interior environmental quality and infection risk in commuter bus cabins. In this study, we developed a numerical commuter bus model integrated with computer simulated persons to reproduce realistic indoor environment conditions with high occupancy during commuting. Here, computer simulated persons were newly designed considering different types of geometries, e.g., standing position, seating position, and individual differences. Here we conducted coupled computational fluid dynamics (CFD) analysis with radiative heat transfer analysis under steady state condition. Distributions of heterogeneous air flow patterns, temperature, and moisture surrounding the human body under some different ventilation system were analyzed by using CFD technique, and skin surface temperature distributions were analyzed using thermoregulation model that integrated into computer simulated person. Through these analyses, we discussed the interior environmental quality in specific commuter bus cabins. Further, inhaled air quality of each passenger was also analyzed. This study may have possibility to design the ventilation system in bus for improving thermal comfort of occupants.

Keywords: computational fluid dynamics, CFD, computer simulated person, CSP, contaminant, indoor environment, public health, ventilation

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Authors: Maria Zinnia Bardas Hoffmann

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Contrastive Analysis (CA) is the systematic comparison between two languages. It stems from the notion that errors are caused by interference of the L1 system in the acquisition process of an L2. CA represents a useful tool to understand the nature of learning and acquisition. Also, this particular method promises a path to un-derstand the nature of underlying cognitive processes, even when other factors such as intrinsic motivation and teaching strategies were found to best explain student’s problems in acquisition. CA study is justified not only from the need to get a deeper understanding of the nature of SLA, but as an invaluable source to provide clues, at a cognitive level, for those general processes involved in rule formation and abstract thought. It is relevant for cross disciplinary studies and the fields of Computational Thought, Natural Language processing, Applied Linguistics, Cognitive Linguistics and Math Theory. That being said, this paper intends to address here as well its own set of constraints and limitations. Finally, this paper: (a) aims at identifying some of the difficulties students may find in their learning process due to the nature of their specific variety of L1, Rio de la Plata Spanish (RPS), (b) represents an attempt to discuss the necessity for specific models to approach CA.

Keywords: second language acquisition, applied linguistics, contrastive analysis, applied contrastive analysis English language department, meta-linguistic rules, cross-linguistics studies, computational thought, natural language processing

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Authors: Jiao Sun, Li Pan, Shijun Liu

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Recommender systems have been widely used in contemporary industry, and plenty of work has been done in this field to help users to identify items of interest. Collaborative Filtering (CF, for short) algorithm is an important technology in recommender systems. However, less work has been done in automobile recommendation system with the sharp increase of the amount of automobiles. What’s more, the computational speed is a major weakness for collaborative filtering technology. Therefore, using MapReduce framework to optimize the CF algorithm is a vital solution to this performance problem. In this paper, we present a recommendation of the users’ comment on industrial automobiles with various properties based on real world industrial datasets of user-automobile comment data collection, and provide recommendation for automobile providers and help them predict users’ comment on automobiles with new-coming property. Firstly, we solve the sparseness of matrix using previous construction of score matrix. Secondly, we solve the data normalization problem by removing dimensional effects from the raw data of automobiles, where different dimensions of automobile properties bring great error to the calculation of CF. Finally, we use the MapReduce framework to optimize the CF algorithm, and the computational speed has been improved times. UV decomposition used in this paper is an often used matrix factorization technology in CF algorithm, without calculating the interpolation weight of neighbors, which will be more convenient in industry.

Keywords: collaborative filtering, recommendation, data normalization, mapreduce

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Authors: Alexander N. Pisarchik, Parth Chholak

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Intrinsic brain noise was estimated via magneto-encephalograms (MEG) recorded during perception of flickering visual stimuli with frequencies of 6.67 and 8.57 Hz. First, we measured the mean phase difference between the flicker signal and steady-state event-related field (SSERF) in the occipital area where the brain response at the flicker frequencies and their harmonics appeared in the power spectrum. Then, we calculated the probability distribution of the phase fluctuations in the regions of frequency locking and computed its kurtosis. Since kurtosis is a measure of the distribution’s sharpness, we suppose that inverse kurtosis is related to intrinsic brain noise. In our experiments, the kurtosis value varied among subjects from K = 3 to K = 5 for 6.67 Hz and from 2.6 to 4 for 8.57 Hz. The majority of subjects demonstrated leptokurtic kurtosis (K < 3), i.e., the distribution tails approached zero more slowly than Gaussian. In addition, we found a strong correlation between kurtosis and brain complexity measured as the correlation dimension, so that the MEGs of subjects with higher kurtosis exhibited lower complexity. The obtained results are discussed in the framework of nonlinear dynamics and complex network theories. Specifically, in a network of coupled oscillators, phase synchronization is mainly determined by two antagonistic factors, noise, and the coupling strength. While noise worsens phase synchronization, the coupling improves it. If we assume that each neuron and each synapse contribute to brain noise, the larger neuronal network should have stronger noise, and therefore phase synchronization should be worse, that results in smaller kurtosis. The described method for brain noise estimation can be useful for diagnostics of some brain pathologies associated with abnormal brain noise.

Keywords: brain, flickering, magnetoencephalography, MEG, visual perception, perception time

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Authors: Ellen Van Den Oord, Julien Marie Jan Ferdinand Van Campen

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This article introduces a computationally efficient method for stacking sequence blending of composite structures. The computational efficiency makes the presented method especially interesting for composite structures with a large number of design regions. Optimization of composite structures with an unequal load distribution may lead to locally optimized thicknesses and ply orientations that are incompatible with one another. Blending constraints can be enforced to achieve structural continuity. In literature, many methods can be found to implement structural continuity by means of stacking sequence blending in one way or another. The complexity of the problem makes the blending of a structure with a large number of adjacent design regions, and thus stacking sequences, prohibitive. In this work the local stacking sequence optimization is preconditioned using a method found in the literature that couples the mechanical behavior of the laminate, in the form of lamination parameters, to blending constraints, yielding near-optimal easy-to-blend designs. The preconditioned design is then fed to the scheme using cellular automata that have been developed by the authors. The method is applied to the benchmark 18-panel horseshoe blending problem to demonstrate its performance. The computational efficiency of the proposed method makes it especially suited for composite structures with a large number of design regions.

Keywords: composite, blending, optimization, lamination parameters

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Authors: Joel Ballesteros, Harriet Jane Caleja, Florian Del Mundo, Cherrie Pascual

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Diffraction-based sensing was utilized in the quantification of human ferritin in blood serum to provide an alternative to label-based immunoassays currently used in clinical diagnostics and researches. The diffraction intensity was measured by the diffractive optics technology or dotLab™ system. Two methods were evaluated in this study: direct immunoassay and direct sandwich immunoassay. In the direct immunoassay, human ferritin was captured by human ferritin antibodies immobilized on an avidin-coated sensor while the direct sandwich immunoassay had an additional step for the binding of a detector human ferritin antibody on the analyte complex. Both methods were repeatable with coefficient of variation values below 15%. The direct sandwich immunoassay had a linear response from 10 to 500 ng/mL which is wider than the 100-500 ng/mL of the direct immunoassay. The direct sandwich immunoassay also has a higher calibration sensitivity with value 0.002 Diffractive Intensity (ng mL-1)-1) compared to the 0.004 Diffractive Intensity (ng mL-1)-1 of the direct immunoassay. The limit of detection and limit of quantification values of the direct immunoassay were found to be 29 ng/mL and 98 ng/mL, respectively, while the direct sandwich immunoassay has a limit of detection (LOD) of 2.5 ng/mL and a limit of quantification (LOQ) of 8.2 ng/mL. In terms of accuracy, the direct immunoassay had a percent recovery of 88.8-93.0% in PBS while the direct sandwich immunoassay had 94.1 to 97.2%. Based on the results, the direct sandwich immunoassay is a better diffraction-based immunoassay in terms of accuracy, LOD, LOQ, linear range, and sensitivity. The direct sandwich immunoassay was utilized in the determination of human ferritin in blood serum and the results are validated by Chemiluminescent Magnetic Immunoassay (CMIA). The calculated Pearson correlation coefficient was 0.995 and the p-values of the paired-sample t-test were less than 0.5 which show that the results of the direct sandwich immunoassay was comparable to that of CMIA and could be utilized as an alternative analytical method.

Keywords: biosensor, diffraction, ferritin, immunoassay

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Authors: Stewart A. Keir, Faik A. Hamad

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This study aims to use both analytical and experimental methods of analysis to examine the accuracy of Computational Fluid Dynamics (CFD) models that can then be used for more complex analyses, accurately representing more elaborate flow phenomena such as internal shockwaves and boundary layers. The geometry used in the analytical study and CFD model is taken from the experimental rig. The analytical study is undertaken using isentropic and adiabatic relationships and the output of the analytical study, the 'shockwave location tool', is created. The results from the analytical study are then used to optimize the redesign an experimental rig for more favorable placement of pressure taps and gain a much better representation of the shockwaves occurring in the divergent section of the nozzle. The CFD model is then optimized through the selection of different parameters, e.g. turbulence models (Spalart-Almaras, Realizable k-epsilon & Standard k-omega) in order to develop an accurate, robust model. The results from the CFD model can then be directly compared to experimental and analytical results in order to gauge the accuracy of each method of analysis. The CFD model will be used to visualize the variation of various parameters such as velocity/Mach number, pressure and turbulence across the shock. The CFD results will be used to investigate the interaction between the shock wave and the boundary layer. The validated model can then be used to modify the nozzle designs which may offer better performance and ease of manufacture and may present feasible improvements to existing high-speed flow applications.

Keywords: CFD, nozzle, fluent, gas dynamics, shock-wave

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Authors: Coppa Federica, Iannello Giulia, Pennisi Stefania, Giuffrida Graziella, Lo Faro Riccardo, Cartelli Simone, Ferruggia Greta, Brundo Maria Violetta

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In recent years, a new field of basic research has emerged: the biology and physiology of extracellular vesicles and their application in diagnostics and therapy. In particular, exosomes attract the scientific community as nanovesicles of endosomal origin, which can be secreted by a variety of cells and are found in all biological fluids. Exosomes have recently gained attention also in the cosmetic field: in fact, they are used in creams, serums and masks for topical use, proving to have a series of therapeutic and anti-aging benefits. To date, the oral administration of exosomes is the subject of attention because it represents a non-invasive and efficient method for delivering bioactive molecules into the intestine. We decided to focus our research on the creation of a food supplement that contains various bioactive factors, vitamins, and a new technology called AMPLEX PLUS, containing a mixture of 20 different biologically active factors (GF20) and exosomes isolated and purified from bovine colostrum. We have demonstrated in vitro that this new supplement acts on telomerase, slowing down cell aging. Amplex plus increased the proliferation rate of cells and the addition of it reduced the rate of telomere shortening. Under oxidative stress conditions (H2O2 – induced), the TSR increased; however, treatment with colostrum appeared to attenuate this increase. In particular, after 2 weeks of treatment, AMPLEX plus increased the proliferation rate of cells and exerted a protective effect on telomere length erosion, reducing the rate of its shortening.

Keywords: AMPLEX PLUS, colostrum, exosomes, telomerase

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Authors: Pranav Gunhal., Krish Jhurani

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This study tackles the significant computational challenge of predicting excited state dynamics in organic photovoltaic (OPV) materials—a pivotal factor in the performance of solar energy solutions. Time-dependent density functional theory (TDDFT), though effective, is computationally prohibitive for larger and more complex molecules. As a solution, the research explores the application of transformer neural networks, a type of artificial intelligence (AI) model known for its superior performance in natural language processing, to predict excited state dynamics in OPV materials. The methodology involves a two-fold process. First, the transformer model is trained on an extensive dataset comprising over 10,000 TDDFT calculations of excited state dynamics from a diverse set of OPV materials. Each training example includes a molecular structure and the corresponding TDDFT-calculated excited state lifetimes and key electronic transitions. Second, the trained model is tested on a separate set of molecules, and its predictions are rigorously compared to independent TDDFT calculations. The results indicate a remarkable degree of predictive accuracy. Specifically, for a test set of 1,000 OPV materials, the transformer model predicted excited state lifetimes with a mean absolute error of 0.15 picoseconds, a negligible deviation from TDDFT-calculated values. The model also correctly identified key electronic transitions contributing to the excited state dynamics in 92% of the test cases, signifying a substantial concordance with the results obtained via conventional quantum chemistry calculations. The practical integration of the transformer model with existing quantum chemistry software was also realized, demonstrating its potential as a powerful tool in the arsenal of materials scientists and chemists. The implementation of this AI model is estimated to reduce the computational cost of predicting excited state dynamics by two orders of magnitude compared to conventional TDDFT calculations. The successful utilization of transformer neural networks to accurately predict excited state dynamics provides an efficient computational pathway for the accelerated discovery and design of new OPV materials, potentially catalyzing advancements in the realm of sustainable energy solutions.

Keywords: transformer neural networks, organic photovoltaic materials, excited state dynamics, time-dependent density functional theory, predictive modeling

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Authors: Bo Jin

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A variety of process equipment having flow in and out is widely used in industrial land-based cryogenic facilities. In some of this equipment, such as vapor-liquid separator, a liquid level is established during the steady operation. As the implementation of such industrial processes extends to off-shore floating facilities, it is important to investigate the effect of sea motion on the process equipment partially filled with liquid. One important aspect to consider is the occurrence of sloshing therein. The flow characteristics are different from the classical study of sloshing, where the fluid is enclosed inside a vessel (e.g., storage tank) with no flow in or out. Liquid inside process equipment continuously flows in and out of the system. To understand this key difference, a Computational Fluid Dynamics (CFD) model is developed to simulate the liquid motion inside a partially filled cylinder with and without continuous flow in and out. For a partially filled vertical cylinder without any continuous flow in and out, the CFD model is found to be able to capture the well-known sloshing behavior documented in the literature. For the cylinder with a continuous steady flow in and out, the CFD simulation results demonstrate that the continuous flow suppresses sloshing. Given typical cryogenic fluid has very low viscosity, an analysis based on potential flow theory is developed to explain why flow into and out of the cylinder changes the natural frequency of the system and thereby suppresses sloshing. This analysis further validates the CFD results.

Keywords: computational fluid dynamics, CFD, cryogenic process equipment, off-shore floating processes, sloshing

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Authors: Ranjith Maniyeri, Ahamed C. Saleel

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Two-dimensional fluid flow over a stationary circular cylinder is one of the bench mark problem in the field of fluid-structure interaction in computational fluid dynamics (CFD). Motivated by this, in the present work, a two-dimensional computational model is developed using an improved version of immersed boundary method which combines the feedback forcing scheme of the virtual boundary method with Peskin’s regularized delta function approach. Lagrangian coordinates are used to represent the cylinder and Eulerian coordinates are used to describe the fluid flow. A two-dimensional Dirac delta function is used to transfer the quantities between the sold to fluid domain. Further, continuity and momentum equations governing the fluid flow are solved using fractional step based finite volume method on a staggered Cartesian grid system. The developed code is validated by comparing the values of drag coefficient obtained for different Reynolds numbers with that of other researcher’s results. Also, through numerical simulations for different Reynolds numbers flow behavior is well captured. The stability analysis of the improved version of immersed boundary method is tested for different values of feedback forcing coefficients.

Keywords: Feedback Forcing Scheme, Finite Volume Method, Immersed Boundary Method, Navier-Stokes Equations

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Authors: Di Wei, Xing Hu, Yangjun Chen, Baofeng Li, Hong Chen

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To achieve the research purpose of guiding the spatial morphology design of blocks through the indicators to obtain a good wind environment, it is necessary to find the most suitable type and value range of each urban spatial morphology indicator. At present, most of the relevant researches is based on the numerical simulation of the ideal block shape and rarely proposes the results based on the complex actual block types. Therefore, this paper firstly attempted to make theoretical speculation on the main factors influencing indicators' effectiveness by analyzing the physical significance and formulating the principle of each indicator. Then it was verified by the field wind environment measurement and statistical analysis, indicating that Porosity(P₀) can be used as an important indicator to guide the design of block wind environment in the case of deep street canyons, while Frontal Area Density (λF) can be used as a supplement in the case of shallow street canyons with no height difference. Finally, computational fluid dynamics (CFD) was used to quantify the impact of block height difference and street canyons depth on λF and P₀, finding the suitable type and value range of λF and P₀. This paper would provide a feasible wind environment index system for urban designers.

Keywords: urban spatial morphology indicator, urban microclimate, computational fluid dynamics, block ventilation, correlation analysis

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Authors: M. Cardenas-Garcia, P. P. Gonzalez-Perez

Abstract:

Intercellular communication is a necessary condition for cellular functions and it allows a group of cells to survive as a population. Throughout this interaction, the cells work in a coordinated and collaborative way which facilitates their survival. In the case of cancerous cells, these take advantage of intercellular communication to preserve their malignancy, since through these physical unions they can send signs of malignancy. The Wnt/β-catenin signaling pathway plays an important role in the formation of intercellular communications, being also involved in a large number of cellular processes such as proliferation, differentiation, adhesion, cell survival, and cell death. The modeling and simulation of cellular signaling systems have found valuable support in a wide range of modeling approaches, which cover a wide spectrum ranging from mathematical models; e.g., ordinary differential equations, statistical methods, and numerical methods– to computational models; e.g., process algebra for modeling behavior and variation in molecular systems. Based on these models, different simulation tools have been developed from mathematical ones to computational ones. Regarding cellular and molecular processes in cancer, its study has also found a valuable support in different simulation tools that, covering a spectrum as mentioned above, have allowed the in silico experimentation of this phenomenon at the cellular and molecular level. In this work, we simulate and explore the complex interaction patterns of intercellular communication in cancer cells using the Cellulat bioinformatics tool, a computational simulation tool developed by us and motivated by two key elements: 1) a biochemically inspired model of self-organizing coordination in tuple spaces, and 2) the Gillespie’s algorithm, a stochastic simulation algorithm typically used to mimic systems of chemical/biochemical reactions in an efficient and accurate way. The main idea behind the Cellulat simulation tool is to provide an in silico experimentation environment that complements and guides in vitro experimentation in intra and intercellular signaling networks. Unlike most of the cell signaling simulation tools, such as E-Cell, BetaWB and Cell Illustrator which provides abstractions to model only intracellular behavior, Cellulat is appropriate for modeling both intracellular signaling and intercellular communication, providing the abstractions required to model –and as a result, simulate– the interaction mechanisms that involve two or more cells, that is essential in the scenario discussed in this work. During the development of this work we made evident the application of our computational simulation tool (Cellulat) for the modeling and simulation of intercellular communication between normal and cancerous cells, and in this way, propose key molecules that may prevent the arrival of malignant signals to the cells that surround the tumor cells. In this manner, we could identify the significant role that has the Wnt/β-catenin signaling pathway in cellular communication, and therefore, in the dissemination of cancer cells. We verified, using in silico experiments, how the inhibition of this signaling pathway prevents that the cells that surround a cancerous cell are transformed.

Keywords: cancer cells, in silico approach, intercellular communication, key molecules, modeling and simulation

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Authors: Sangwoo Oh, Jaewoo Kim, Dongmin Seo, Jaewon Park, Yongha Hwang, Sungkyu Seo

Abstract:

Plasmonics has been regarded one of the most powerful bio-sensing modalities to evaluate bio-molecular interactions in real-time. However, most of the plasmonic sensing methods are based on labeling metallic nanoparticles, e.g. gold or silver, as optical modulation markers, which are non-recyclable and expensive. This plasmonic modulation can be usually achieved through various nano structures, e.g., nano-hole arrays. Among those structures, plasmonic lens has been regarded as a unique plasmonic structure due to its light focusing characteristics. In this study, we introduce a custom designed plasmonic lens array for bio-sensing, which was simulated by finite-difference-time-domain (FDTD) approach and fabricated by top-down approach. In our work, we performed the FDTD simulations of various plasmonic lens designs for bacteria sensor, i.e., Samonella and Hominis. We optimized the design parameters, i.e., radius, shape, and material, of the plasmonic lens. The simulation results showed the change in the peak intensity value with the introduction of each bacteria and antigen i.e., peak intensity 1.8711 a.u. with the introduction of antibody layer of thickness of 15nm. For Salmonella, the peak intensity changed from 1.8711 a.u. to 2.3654 a.u. and for Hominis, the peak intensity changed from 1.8711 a.u. to 3.2355 a.u. This significant shift in the intensity due to the interaction between bacteria and antigen showed a promising sensing capability of the plasmonic lens. With the batch processing and bulk production of this nano scale design, the cost of biological sensing can be significantly reduced, holding great promise in the fields of clinical diagnostics and bio-defense.

Keywords: plasmonic lens, FDTD, fabrication, bacteria sensor, salmonella, hominis

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Authors: Iveta Bryjova

Abstract:

Recording of viscoelastic strain-vs-time curves with the aid of the suction method and a follow-up analysis, resulting into evaluation of standard viscoelastic parameters, is a significant technique for non-invasive contact diagnostics of mechanical properties of skin and assessment of its conditions, particularly in acute burns, hypertrophic scarring (the most common complication of burn trauma) and reconstructive surgery. For elimination of the skin thickness contribution, usable viscoelastic parameters deduced from the strain-vs-time curves are restricted to the relative ones (i.e. those expressed as a ratio of two dimensional parameters), like grosselasticity, net-elasticity, biological elasticity or Qu’s area parameters, in literature and practice conventionally referred to as R2, R5, R6, R7, Q1, Q2, and Q3. With the exception of parameters R2 and Q1, the remaining ones substantially depend on the position of inflection point separating the elastic linear and viscoelastic segments of the strain-vs-time curve. The standard algorithm implemented in commercially available devices relies heavily on the experimental fact that the inflection time comes about 0.1 sec after the suction switch-on/off, which depreciates credibility of parameters thus obtained. Although the Qu’s US 7,556,605 patent suggests a method of improving the precision of the inflection determination, there is still room for nonnegligible improving. In this contribution, a novel method of inflection point determination utilizing the advantageous properties of the Savitzky–Golay filtering is presented. The method allows computation of derivatives of smoothed strain-vs-time curve, more exact location of inflection and consequently more reliable values of aforementioned viscoelastic parameters. An improved applicability of the five inflection-dependent relative viscoelastic parameters is demonstrated by recasting a former study under the new method, and by comparing its results with those provided by the methods that have been used so far.

Keywords: Savitzky–Golay filter, scarring, skin, viscoelasticity

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Authors: Sara Herrero Jaén, José María Santamaría García, María Lourdes Jiménez Rodríguez, Jorge Luis Gómez González, Adriana Cercas Duque, Alexandra González Aguna

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Background: Health concept has evolved throughout history. The health level is determined by the own individual perception. It is a dynamic process over time so that you can see variations from one moment to the next. In this way, knowing the health of the patients you care for, will facilitate decision making in the treatment of care. Objective: To design a technological tool that calculates the people health level in a sequential way over time. Material and Methods: Deductive methodology through text analysis, extraction and logical knowledge formalization and education with expert group. Studying time: September 2015- actually. Results: A computational tool for the use of health personnel has been designed. It has 11 variables. Each variable can be given a value from 1 to 5, with 1 being the minimum value and 5 being the maximum value. By adding the result of the 11 variables we obtain a magnitude in a certain time, the health level of the person. The health calculator allows to represent people health level at a time, establishing temporal cuts being useful to determine the evolution of the individual over time. Conclusion: The Information and Communication Technologies (ICT) allow training and help in various disciplinary areas. It is important to highlight their relevance in the field of health. Based on the health formalization, care acts can be directed towards some of the propositional elements of the concept above. The care acts will modify the people health level. The health calculator allows the prioritization and prediction of different strategies of health care in hospital units.

Keywords: calculator, care, eHealth, health

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Authors: Xiuguo Zhao, He Li, Alireza Yazdani, Xiaoning Zheng, Xinxi Xu

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Wound infected poses a serious threat to the surgery on the patient during the process of surgery. Understanding the bacteria-carrying particles (BCPs) transportation and deposition in the open surgical wound model play essential role in protecting wound against being infected. Therefore BCPs transportation and deposition in the surgical wound model were investigated using force-coupling method (FCM) based computational fluid dynamics. The BCPs deposition in the wound was strongly associated with BCPs diameter and concentration. The results showed that the rise on the BCPs deposition was increasing not only with the increase of BCPs diameters but also with the increase of the BCPs concentration. BCPs deposition morphology was impacted by the combination of size distribution, airflow patterns and model geometry. The deposition morphology exhibited the characteristic with BCPs deposition on the sidewall in wound model and no BCPs deposition on the bottom of the wound model mainly because the airflow movement in one direction from up to down and then side created by laminar system constructing airflow patterns and then made BCPs hard deposit in the bottom of the wound model due to wound geometry limit. It was also observed that inertial impact becomes a main mechanism of the BCPs deposition. This work may contribute to next study in BCPs deposition limit, as well as wound infected estimation in surgical-site infections.

Keywords: BCPs deposition, computational fluid dynamics, force-coupling method (FCM), numerical simulation, open surgical wound model

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Authors: A. M. Tiara, Sudipto Chakraborty, S. K. Pal

Abstract:

Impinging jets and their different configurations are important from the viewpoint of the fluid flow characteristics and their influence on heat transfer from metal surfaces due to their complex flow characteristics. Such flow characteristics results in highly variable heat transfer from the surface, resulting in varying cooling rates which affects the mechanical properties including hardness and strength. The overall objective of the current research is to conduct a fundamental investigation of the heat transfer mechanisms for an impinging coolant jet. Numerical simulation of the cooling process gives a detailed analysis of the different parameters involved even though employing Computational Fluid Dynamics (CFD) to simulate the real time process, being a relatively new research area, poses many challenges. The heat transfer mechanism in the current research is actuated by jet cooling. The computational tool used in the ongoing research for simulation of the cooling process is ANSYS Workbench software. The temperature and heat flux distribution along the steel strip with the effect of various flow parameters on the heat transfer rate can be observed in addition to determination of the jet impingement patterns, which is the major aim of the present analysis. Modelling both jet and air atomized cooling techniques using CFD methodology and validating with those obtained experimentally- including trial and error with different models and comparison of cooling rates from both the techniques have been included in this work. Finally some concluding remarks are made that identify some gaps in the available literature that have influenced the path of the current investigation.

Keywords: CFD, heat transfer, impinging jets, numerical simulation

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Authors: Pooja Verma, Sumana Ghosh

Abstract:

There is a growing need for alternative way of power generation worldwide. The reason can be attributed to limited resources of fossil fuels, environmental pollution, increasing cost of conventional fuels, and lower efficiency of conversion of energy in existing systems. In this context, one of the potential alternatives for power generation is wave energy. However, it is difficult to estimate the amount of electrical energy generation in an irregular sea condition by experiment and or analytical methods. Therefore in this work, a numerical wave tank is developed using the computational fluid dynamics software Open FOAM. In this software a specific utility known as waves2Foam utility is being used to carry out the simulation work. The computational domain is a tank of dimension: 5m*1.5m*1m with a floating object of dimension: 0.5m*0.2m*0.2m. Regular waves are generated at the inlet of the wave tank according to Stokes second order theory. The main objective of the present study is to validate the numerical model against existing experimental data. It shows a good matching with the existing experimental data of floater displacement. Later the model is exploited to estimate energy extraction due to the movement of such a point absorber in real sea conditions. Scale down the wave properties like wave height, wave length, etc. are used as input parameters. Seasonal variations are also considered.

Keywords: OpenFOAM, numerical wave tank, regular waves, floating object, point absorber

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