Search results for: computational imaging

Authors: Cagri Memis, Muzaffer Kapanoglu

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The school bus routing problem (SBRP) is a variant of the Vehicle Routing Problem (VRP) classified as a location-allocation-routing problem. In this study, the SBRP is decomposed into two sub-problems: (1) bus route generation and (2) bus stop selection to solve large instances of the SBRP in reasonable computational times. To solve the first sub-problem, we propose a genetic algorithm to generate bus routes. Once the routes have been fixed, a sub-problem remains of allocating students to stops considering the capacity of the buses and the walkability constraints of the students. While the exact method solves small-scale problems, treating large-scale problems with the exact method becomes complex due to computational problems, a deficiency that the genetic algorithm can overcome. Results obtained from the proposed approach on 150 instances up to 250 stops show that the matheuristic algorithm provides better solutions in reasonable computational times with respect to benchmark algorithms.

Keywords: genetic algorithm, matheuristic, school bus routing problem, vehicle routing problem

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Authors: Joseph Wolff, Jeffrey Eilbott

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Autism Spectrum Disorders (ASD) are a spectrum of social disorders characterized by deficits in social communication, verbal ability, and interaction that can vary in severity. In recent years, researchers have used magnetic resonance imaging (MRI) to help detect how neural patterns in individuals with ASD differ from those of neurotypical (NT) controls for classification purposes. This study analyzed the classification of ASD within males and females using functional MRI data. Functional connectivity (FC) correlations among brain regions were used as feature inputs for machine learning algorithms. Analysis was performed on 558 cases from the Autism Brain Imaging Data Exchange (ABIDE) I dataset. When trained specifically on females, the algorithm underperformed in classifying the ASD subset of our testing population. Although the subject size was relatively smaller in the female group, the manual matching of both male and female training groups helps explain the algorithm’s bias, indicating the altered sex abnormalities in functional brain networks compared to typically developing peers. These results highlight the importance of taking sex into account when considering how generalizations of findings on males with ASD apply to females.

Keywords: autism spectrum disorder, machine learning, neuroimaging, sex differences

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Authors: Tuba Zahra, Aakash Parekh

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Hyperspectral remote sensing refers to imaging of objects or materials in narrow conspicuous spectral bands. Hyperspectral images (HSI) enable the extraction of spectral signatures for objects or materials observed. These images contain information about the reflectance of each pixel across the electromagnetic spectrum. It enables the acquisition of data simultaneously in hundreds of spectral bands with narrow bandwidths and can provide detailed contiguous spectral curves that traditional multispectral sensors cannot offer. The contiguous, narrow bandwidth of hyperspectral data facilitates the detailed surveying of Earth's surface features. This would otherwise not be possible with the relatively coarse bandwidths acquired by other types of imaging sensors. Hyperspectral imaging provides significantly higher spectral and spatial resolution. There are several use cases that represent the commercial applications of hyperspectral remote sensing. Each use case represents just one of the ways that hyperspectral satellite imagery can support operational efficiency in the respective vertical. There are some use cases that are specific to VNIR bands, while others are specific to SWIR bands. This paper discusses the different commercially viable use cases that are significant for HSI application areas, such as agriculture, mining, oil and gas, defense, environment, and climate, to name a few. Theoretically, there is n number of use cases for each of the application areas, but an attempt has been made to streamline the use cases depending upon economic feasibility and commercial viability and present a review of literature from this perspective. Some of the specific use cases with respect to agriculture are crop species (sub variety) detection, soil health mapping, pre-symptomatic crop disease detection, invasive species detection, crop condition optimization, yield estimation, and supply chain monitoring at scale. Similarly, each of the industry verticals has a specific commercially viable use case that is discussed in the paper in detail.

Keywords: agriculture, mining, oil and gas, defense, environment and climate, hyperspectral, VNIR, SWIR

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Authors: Gabriela Wyszogrodzka, Przemyslaw Dorozynski, Barbara Gil, Maciej Strzempek, Bartosz Marszalek, Piotr Kulinowski, Wladyslaw Piotr Weglarz, Elzbieta Menaszek

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MOFs (Metal-Organic Frameworks) belong to a new group of porous materials with a hybrid organic-inorganic construction. Their structure is a network consisting of metal cations or clusters (acting as metallic centers, nodes) and the organic linkers between nodes. The interest in MOFs is primarily associated with the use of their well-developed surface and large porous. Possibility to build MOFs of biocompatible components let to use them as potential drug carriers. Furthermore, forming MOFs structure from cations possessing paramagnetic properties (e.g. iron cations) allows to use them as MRI (Magnetic Resonance Imaging) contrast agents. The concept of formation of particles that combine the ability to transfer active substance with imaging properties has been called theranostic (from words combination therapy and diagnostics). By building MOF structure from iron cations it is possible to use them as theranostic agents and monitoring the distribution of the active substance after administration in real time. In the study iron-MOF: Fe-MIL-101-NH2 was chosen, consisting of iron cluster in nodes of the structure and amino-terephthalic acid as a linker. The aim of the study was to investigate the possibility of applying Fe-MIL-101-NH2 as inhalable theranostic particulate system for the first-line anti-tuberculosis antibiotic – isoniazid. The drug content incorporated into Fe-MIL-101-NH2 was evaluated by dissolution study using spectrophotometric method. Results showed isoniazid encapsulation efficiency – ca. 12.5% wt. Possibility of Fe-MIL-101-NH2 application as the MRI contrast agent was demonstrated by magnetic resonance tomography. FeMIL-101-NH2 effectively shortening T1 and T2 relaxation times (increasing R1 and R2 relaxation rates) linearly with the concentrations of suspended material. Images obtained using multi-echo magnetic resonance imaging sequence revealed possibility to use FeMIL-101-NH2 as positive and negative contrasts depending on applied repetition time. MOFs micronization via ultrasound was evaluated by XRD, nitrogen adsorption, FTIR, SEM imaging and did not influence their crystal shape and size. Ultrasonication let to break the aggregates and achieve very homogeneously looking SEM images. MOFs cytotoxicity was evaluated in in vitro test with a highly sensitive resazurin based reagent PrestoBlue™ on L929 fibroblast cell line. After 24h no inhibition of cell proliferation was observed. All results proved potential possibility of application of ironMOFs as an isoniazid carrier and as MRI contrast agent in inhalatory treatment of tuberculosis. Acknowledgments: Authors gratefully acknowledge the National Science Center Poland for providing financial support, grant no 2014/15/B/ST5/04498.

Keywords: imaging agents, metal-organic frameworks, theranostics, tuberculosis

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Authors: Parampal Kaur, Deepak Aggarwal

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In the computational Grid, fault tolerance is an imperative issue to be considered during job scheduling. Due to the widespread use of resources, systems are highly prone to errors and failures. Hence, fault tolerance plays a key role in the grid to avoid the problem of unreliability. Scheduling the task to the appropriate resource is a vital requirement in computational Grid. The fittest resource scheduling algorithm searches for the appropriate resource based on the job requirements, in contrary to the general scheduling algorithms where jobs are scheduled to the resources with best performance factor. The proposed method is to improve the fault tolerance of the fittest resource scheduling algorithm by scheduling the job in coordination with job replication when the resource has low reliability. Based on the reliability index of the resource, the resource is identified as critical. The tasks are scheduled based on the criticality of the resources. Results show that the execution time of the tasks is comparatively reduced with the proposed algorithm using real-time approach rather than a simulator.

Keywords: computational grid, fault tolerance, task replication, job scheduling

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Authors: A. Mohammadi, M. Moghimi, S. Mohammadi

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Engineers need computational methods which could provide solutions less sensitive to the environmental effects, so the techniques should be used which take the uncertainty to account to control and minimize the risk associated with design and operation. In order to consider uncertainty in engineering problem, the optimization problem should be solved for a suitable range of the each uncertain input variable instead of just one estimated point. Using deterministic optimization problem, a large computational burden is required to consider every possible and probable combination of uncertain input variables. Several methods have been reported in the literature to deal with problems under uncertainty. In this paper, different methods presented and analyzed.

Keywords: uncertainty, Monte Carlo simulated, stochastic programming, scenario method

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Authors: Taweechai Nuntawisuttiwong, Natasha Dejdumrong

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Newton-Lagrange Interpolations are widely used in numerical analysis. However, it requires a quadratic computational time for their constructions. In computer aided geometric design (CAGD), there are some polynomial curves: Wang-Ball, DP and Dejdumrong curves, which have linear time complexity algorithms. Thus, the computational time for Newton-Lagrange Interpolations can be reduced by applying the algorithms of Wang-Ball, DP and Dejdumrong curves. In order to use Wang-Ball, DP and Dejdumrong algorithms, first, it is necessary to convert Newton-Lagrange polynomials into Wang-Ball, DP or Dejdumrong polynomials. In this work, the algorithms for converting from both uniform and non-uniform Newton-Lagrange polynomials into Wang-Ball, DP and Dejdumrong polynomials are investigated. Thus, the computational time for representing Newton-Lagrange polynomials can be reduced into linear complexity. In addition, the other utilizations of using CAGD curves to modify the Newton-Lagrange curves can be taken.

Keywords: Lagrange interpolation, linear complexity, monomial matrix, Newton interpolation

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Authors: Reem El Chakik

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The levels of heavy metals in agricultural lands in Lebanon have been witnessing a noticeable increase in the past few years, due to increased anthropogenic pollution sources. Heavy metals pose a serious threat to the environment for being non-biodegradable and persistent, accumulating thus to dangerous levels in the soil. Besides the traditional laboratory and chemical analysis methods, Hyperspectral Imaging (HSI) has proven its efficiency in the rapid detection of HMs contamination. In Lebanon, a continuous environmental monitoring, including the monitoring of levels of HMs in agricultural soils, is lacking. This is due in part to the high cost of analysis. Hence, this proposed research aims at defining the current national status of HMs contamination in agricultural soil, and to evaluate the effectiveness of using HSI in the detection of HM in contaminated agricultural fields. To achieve the two main objectives of this study, soil samples were collected from different areas throughout the country and were analyzed for HMs using Atomic Absorption Spectrophotometry (AAS). The results were compared to those obtained from the HSI technique that was applied using Hyspex SWIR-384 camera. The results showed that the Lebanese agricultural soils contain high contamination levels of Zn, and that the more clayey the soil is, the lower reflectance it has.

Keywords: agricultural soils in Lebanon, atomic absorption spectrophotometer, hyperspectral imaging., heavy metals contamination

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Authors: Angelis P. Barlampas

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Target: The (SARS-CoV-2) is still a threat. AI software could be useful, categorizing the disease into different severities and indicate the extent of the lesions. Materials and methods: AI is a new revolutionary technique, which uses powered computerized systems, to do what a human being does more rapidly, more easily, as accurate and diagnostically safe as the original medical report and, in certain circumstances, even better, saving time and helping the health system to overcome problems, such as work overload and human fatigue. Results: It will be given an effort to describe to the inexperienced reader (see figures), as simple as possible, how an artificial intelligence system diagnoses computed tomography pictures. First, the computerized machine learns the physiologic motives of lung parenchyma by being feeded with normal structured images of the lung tissue. Having being used to recognizing normal structures, it can then easily indentify the pathologic ones, as their images do not fit to known normal picture motives. It is the same way as when someone spends his free time in reading magazines with quizzes, such as <> and <>. General conclusion: The AI mimics the physiological processes of the human mind, but it does that more efficiently and rapidly and provides results in a few seconds, whereas an experienced radiologist needs many days to do that, or even worse, he is unable to accomplish such a huge task.

Keywords: covid-19, artificial intelligence, automated imaging, CT, chest imaging

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Authors: Hidouri Sami, Aguili Taoufik

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We consider fast and accurate solutions of scattering problems by large perfectly conducting objects (PEC) formulated by an optimization of the Method of Auxiliary Sources (MAS). We present various techniques used to reduce the total computational cost of the scattering problem. The first technique is based on replacing the object by an array of finite number of small (PEC) object with the same shape. The second solution reduces the problem on considering only the half of the object.These two solutions are compared to results from the reference bibliography.

Keywords: method of auxiliary sources, scattering, large object, RCS, computational resources

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Authors: Nabila Jaman, K. E. Hoque, S. Sawall, M. Ferdows

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Coronary artery disease (CAD) is one of the most lethal diseases of the cardiovascular diseases. Coronary arteries stenosis and bifurcation angles closely interact for myocardial infarction. We want to use computer-aided design model coupled with computational hemodynamics (CHD) simulation for detecting several types of coronary artery stenosis with different locations in an idealized model for identifying virtual fractional flow reserve (vFFR). The vFFR provides us the information about the severity of stenosis in the computational models. Another goal is that we want to imitate patient-specific computed tomography coronary artery angiography model for constructing our idealized models with different left anterior descending (LAD) and left circumflex (LCx) bifurcation angles. Further, we want to analyze whether the bifurcation angles has an impact on the creation of narrowness in coronary arteries or not. The numerical simulation provides the CHD parameters such as wall shear stress (WSS), velocity magnitude and pressure gradient (PGD) that allow us the information of stenosis condition in the computational domain.

Keywords: CAD, CHD, vFFR, bifurcation angles, coronary stenosis

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Authors: Hamza Rekab Djabri, Salah Daoud

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The present paper deals with the computational of structural and electronic properties of ThC and ThN compounds using density functional theory within generalized-gradient (GGA) apraximation and local density approximation (LDA). We employ the full potential linear muffin-tin orbitals (FP-LMTO) as implemented in the Lmtart code. We have used to examine structure parameter in eight different structures such as in NaCl (B1), CsCl (B2), ZB (B3), NiAs (B8), PbO (B10), Wurtzite (B4) , HCP (A3) βSn (A5) structures . The equilibrium lattice parameter, bulk modulus, and its pressure derivative were presented for all calculated phases. The calculated ground state properties are in good agreement with available experimental and theoretical results.

Keywords: DFT, GGA, LDA, properties structurales, ThC, ThN

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Authors: Panatda Intanin, Sangutid Thongsawad, Chirapha Tannanonta, Todsaporn Fuangrod

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Stereotactic radiosurgery (SRS) is a highly precision delivery technique that requires comprehensive quality assurance (QA) tests prior to treatment delivery. An isocenter of delivery beam plays a critical role that affect the treatment accuracy. The uncertainty of isocenter is traditionally accessed using circular cone equipment, Winston-Lutz (WL) phantom and film. This technique is considered time consuming and highly dependent on the observer. In this work, the development of multileaf collimator (MLC)-based isocenter verification tool using electronic portal imaging device (EPID) was proposed and evaluated. A mechanical isocenter alignment with ball bearing diameter 5 mm and circular cone diameter 10 mm fixed to gantry head defines the radiation field was set as the conventional WL test method. The conventional setup was to compare to the proposed setup; using MLC (10 x 10 mm) to define the radiation filed instead of cone. This represents more realistic delivery field than using circular cone equipment. The acquisition from electronic portal imaging device (EPID) and radiographic film were performed in both experiments. The gantry angles were set as following: 0°, 90°, 180° and 270°. A software tool was in-house developed using MATLAB/SIMULINK programming to determine the centroid of radiation field and shadow of WL phantom automatically. This presents higher accuracy than manual measurement. The deviation between centroid of both cone-based and MLC-based WL tests were quantified. To compare between film and EPID image, the deviation for all gantry angle was 0.26±0.19mm and 0.43±0.30 for cone-based and MLC-based WL tests. For the absolute deviation calculation on EPID images between cone and MLC-based WL test was 0.59±0.28 mm and the absolute deviation on film images was 0.14±0.13 mm. Therefore, the MLC-based isocenter verification using EPID present high sensitivity tool for SRS QA.

Keywords: isocenter verification, quality assurance, EPID, SRS

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Authors: Theresa Slump, Paula Neumeister, Katharina Feldker, Carina Y. Heitmann, Thomas Straube

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A characteristic feature of post-traumatic stress disorder (PTSD) is the automatic processing of disorder-specific stimuli that expresses itself in intrusive symptoms such as intense physical and psychological reactions to trauma-associated stimuli. That automatic processing plays an essential role in the development and maintenance of symptoms. The aim of our study was, therefore, to investigate the behavioral and neural correlates of automatic processing of trauma-related stimuli in PTSD. Although interpersonal traumatization is a form of traumatization that often occurs, it has not yet been sufficiently studied. That is why, in our study, we focused on patients suffering from interpersonal traumatization. While previous imaging studies on PTSD mainly used faces, words, or generally negative visual stimuli, our study presented complex trauma-related and neutral visual scenes. We examined 19 female subjects suffering from PTSD and examined 19 healthy women as a control group. All subjects did a geometric comparison task while lying in a functional-magnetic-resonance-imaging (fMRI) scanner. Trauma-related scenes and neutral visual scenes that were not relevant to the task were presented while the subjects were doing the task. Regarding the behavioral level, there were not any significant differences between the task performance of the two groups. Regarding the neural level, the PTSD patients showed significant hyperactivation of the hippocampus for task-irrelevant trauma-related stimuli versus neutral stimuli when compared with healthy control subjects. Connectivity analyses revealed altered connectivity between the hippocampus and other anxiety-related areas in PTSD patients, too. Overall, those findings suggest that fear-related areas are involved in PTSD patients' processing of trauma-related stimuli even if the stimuli that were used in the study were task-irrelevant.

Keywords: post-traumatic stress disorder, automatic processing, hippocampus, functional magnetic resonance imaging

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Authors: A. Nguyen, K. Nguyen, J. Jackson, E. Manlapig

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With the recent advancement in core imaging systems, a large volume of high resolution drill core images can now be collected rapidly. This paper presents a method for rapid prediction of ore-specific breakage parameters from high resolution mineral classified core images. The aim is to allow for a rapid assessment of the variability in ore hardness within a mineral deposit with reduced amount of physical breakage tests. This method sees its application primarily in project evaluation phase, where proper evaluation of the variability in ore hardness of the orebody normally requires prolong and costly metallurgical test work program. Applying this image-based texture analysis method on mineral classified core images, the ores are classified according to their textural characteristics. A small number of physical tests are performed to produce a dataset used for developing the relationship between texture classes and measured ore hardness. The paper also presents a case study in which this method has been applied on core samples from a copper porphyry deposit to predict the ore-specific breakage A*b parameter, obtained from JKRBT tests.

Keywords: geometallurgy, hyperspectral drill core imaging, process simulation, texture analysis

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Authors: O. J. G. Somsen

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One of the tasks of optical surveillance is to detect anomalies in large amounts of image data. However, if the size of the anomaly is very small, limited information is available to distinguish it from the surrounding environment. Spectral detection provides a useful source of additional information and may help to detect anomalies with a size of a few pixels or less. Unfortunately, spectral cameras are expensive because of the difficulty of separating two spatial in addition to one spectral dimension. We investigate the possibility of modifying a simpler spectral line detector for outdoor detection. This may be especially useful if the area of interest forms a line, such as the horizon. We use a monochrome CCD that also enables detection into the near infrared. A simple camera is attached to the setup to determine which part of the environment is spectrally imaged. Our preliminary results indicate that sensitive detection of very small targets is indeed possible. Spectra could be taken from the various targets by averaging columns in the line image. By imaging a set of lines of various width we found narrow lines that could not be seen in the color image but remained visible in the spectral line image. A simultaneous analysis of the entire spectra can produce better results than visual inspection of the line spectral image. We are presently developing calibration targets for spatial and spectral focusing and alignment with the spatial camera. This will present improved results and more use in outdoor application

Keywords: anomaly detection, spectroscopic line imaging, image analysis, outdoor detection

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Authors: Kenneth A. Rostowsky, Alexander S. Maher, Nahian F. Chowdhury, Andrei Irimia

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The clinical significance of cerebral microbleeds (CMBs) due to mild traumatic brain injury (mTBI) remains unclear. Here we use magnetic resonance imaging (MRI), diffusion tensor imaging (DTI) and connectomic analysis to investigate the statistical association between mTBI-related CMBs, post-TBI changes to the human connectome and neurological/cognitive deficits. This study was undertaken in agreement with US federal law (45 CFR 46) and was approved by the Institutional Review Board (IRB) of the University of Southern California (USC). Two groups, one consisting of 26 (13 females) mTBI victims and another comprising 26 (13 females) healthy control (HC) volunteers were recruited through IRB-approved procedures. The acute Glasgow Coma Scale (GCS) score was available for each mTBI victim (mean µ = 13.2; standard deviation σ = 0.4). Each HC volunteer was assigned a GCS of 15 to indicate the absence of head trauma at the time of enrollment in our study. Volunteers in the HC and mTBI groups were matched according to their sex and age (HC: µ = 67.2 years, σ = 5.62 years; mTBI: µ = 66.8 years, σ = 5.93 years). MRI [including T1- and T2-weighted volumes, gradient recalled echo (GRE)/susceptibility weighted imaging (SWI)] and gradient echo (GE) DWI volumes were acquired using the same MRI scanner type (Trio TIM, Siemens Corp.). Skull-stripping and eddy current correction were implemented. DWI volumes were processed in TrackVis (http://trackvis.org) and 3D Slicer (http://www.slicer.org). Tensors were fit to DWI data to perform DTI, and tractography streamlines were then reconstructed using deterministic tractography. A voxel classifier was used to identify image features as CMB candidates using Microbleed Anatomic Rating Scale (MARS) guidelines. For each peri-lesional DTI streamline bundle, the null hypothesis was formulated as the statement that there was no neurological or cognitive deficit associated with between-scan differences in the mean FA of DTI streamlines within each bundle. The statistical significance of each hypothesis test was calculated at the α = 0.05 level, subject to the family-wise error rate (FWER) correction for multiple comparisons. Results: In HC volunteers, the along-track analysis failed to identify statistically significant differences in the mean FA of DTI streamline bundles. In the mTBI group, significant differences in the mean FA of peri-lesional streamline bundles were found in 21 out of 26 volunteers. In those volunteers where significant differences had been found, these differences were associated with an average of ~47% of all identified CMBs (σ = 21%). In 12 out of the 21 volunteers exhibiting significant FA changes, cognitive functions (memory acquisition and retrieval, top-down control of attention, planning, judgment, cognitive aspects of decision-making) were found to have deteriorated over the six months following injury (r = -0.32, p < 0.001). Our preliminary results suggest that acute post-TBI CMBs may be associated with cognitive decline in some mTBI patients. Future research should attempt to identify mTBI patients at high risk for cognitive sequelae.

Keywords: traumatic brain injury, magnetic resonance imaging, diffusion tensor imaging, connectomics

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Authors: Jay L. Fu

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Patients with Alzheimer's disease progressively lose their memory and thinking skills and, eventually, the ability to carry out simple daily tasks. The disease is irreversible, but early detection and treatment can slow down the disease progression. In this research, publicly available MRI data and demographic data from 373 MRI imaging sessions were utilized to build models to predict dementia. Various machine learning models, including logistic regression, k-nearest neighbor, support vector machine, random forest, and neural network, were developed. Data were divided into training and testing sets, where training sets were used to build the predictive model, and testing sets were used to assess the accuracy of prediction. Key risk factors were identified, and various models were compared to come forward with the best prediction model. Among these models, the random forest model appeared to be the best model with an accuracy of 90.34%. MMSE, nWBV, and gender were the three most important contributing factors to the detection of Alzheimer’s. Among all the models used, the percent in which at least 4 of the 5 models shared the same diagnosis for a testing input was 90.42%. These machine learning models allow early detection of Alzheimer’s with good accuracy, which ultimately leads to early treatment of these patients.

Keywords: Alzheimer's disease, clinical diagnosis, magnetic resonance imaging, machine learning prediction

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Authors: O. T. Oluriz, O. D. Akinyemi, J. A.Olowofela, O. A. Idowu, S. A. Ganiyu

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This study was carried out using aeromagnetic data which record variation in the magnitude of the earth magnetic field in order to detect local changes in the properties of the underlying geology. The aeromagnetic data (Sheet No. 261) was acquired from the archives of Nigeria Geological Survey Agency of Nigeria, obtained in 2009. The study present estimation of source parameters within an area of about 3,025 square kilometers on geographic latitude to and longitude to within Ibadan and it’s environs in Oyo State, southwestern Nigeria. The area under study belongs to part of basement complex in southwestern Nigeria. Estimation of source parameters of aeromagnetic data was achieve through the application of source imaging parameters (SPI) techniques that provide delineation, depth, dip contact, susceptibility contrast and mineral potentials of magnetic signatures within the region. The depth to the magnetic sources in the area ranges from 0.675 km to 4.48 km. The estimated depth limit to shallow sources is 0.695 km and depth to deep sources is 4.48 km. The apparent susceptibility values of the entire study area obtained ranges from 0.01 to 0.005 [SI]. This study has shown that the magnetic susceptibility within study area is controlled mainly by super paramagnetic minerals.

Keywords: aeromagnetic, basement complex, meta-sediment, precambrian

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Authors: Marcela de Oliveira, Guilherme Giacomini, Allan Felipe Fattori Alves, Ana Luiza Menegatti Pavan, Maria Eugenia Dela Rosa, Fernando Antonio Bacchim Neto, Diana Rodrigues de Pina

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It is estimated that each year one death every 10 seconds (about 2 million deaths) in the world is attributed to tuberculosis (TB). Even after effective treatment, TB leaves sequelae such as, for example, pulmonary fibrosis, compromising the quality of life of patients. Evaluations of the aforementioned sequel are usually performed subjectively by radiology specialists. Subjective evaluation may indicate variations inter and intra observers. The examination of x-rays is the diagnostic imaging method most accomplished in the monitoring of patients diagnosed with TB and of least cost to the institution. The application of computational algorithms is of utmost importance to make a more objective quantification of pulmonary impairment in individuals with tuberculosis. The purpose of this research is the use of computer algorithms to quantify the pulmonary impairment pre and post-treatment of patients with pulmonary TB. The x-ray images of 10 patients with TB diagnosis confirmed by examination of sputum smears were studied. Initially the segmentation of the total lung area was performed (posteroanterior and lateral views) then targeted to the compromised region by pulmonary sequel. Through morphological operators and the application of signal noise tool, it was possible to determine the compromised lung volume. The largest difference found pre- and post-treatment was 85.85% and the smallest was 54.08%.

Keywords: algorithm, radiology, tuberculosis, x-rays exam

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Authors: Habib Alah Dadgar, Nasim Norouzbeigi

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The precise definition margin of high and low-grade gliomas is crucial for treatment. We aimed to assess the feasibility of assessment of the resection legions with post-operative positron emission tomography (PET) using [18F]O-(2-[18F]-fluoroethyl)-L-tyrosine ([18F]FET). Four patients with the suspicion of high and low-grade were enrolled. Patients underwent post-operative [18F]FET-PET, pre-operative magnetic resonance imaging (MRI) and CT for clinical evaluations. In our study, three patients had negative response to recurrence and progression and one patient indicated positive response after surgery. [18F]FET-PET revealed a legion of increased radiotracer uptake in the dura in the craniotomy site for patient 1. Corresponding to the patient history, the study was negative for recurrence of brain tumor. For patient 2, there was a lesion in the right parieto-temporal with slightly increased uptake in its posterior part with SUVmax = 3.79, so the study was negative for recurrence evaluation. In patient 3 there was no abnormal uptake with negative result for recurrence of brain tumor. Intense radiotracer uptake in the left parietal lobe where in the MRI there was a lesion with no change in enhancement in the post-contrast image is indicated in patient 4. Assessment of the resection legions in high and low-grade gliomas with [18F]FET-PET seems to be useful.

Keywords: FET-PET, CT, glioma, MRI

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Authors: Muhammad Qasim, Dolors Puigjaner, Josep Maria López, Joan Herrero, Carme Olivé, Gerard Fortuny

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Computational modeling of the human pelvis using the finite element (FE) method has become extremely important to understand the mechanics of prostate motion and deformation when transrectal ultrasound (TRUS) guided biopsy is performed. The number of reliable and validated hyperelastic constitutive FE models of the male pelvis region is limited, and given models did not precisely describe the anatomical behavior of pelvis organs, mainly of the prostate and its neoplasms location. The motion and deformation of the prostate during TRUS-guided biopsy makes it difficult to know the location of potential lesions in advance. When using this procedure, practitioners can only provide roughly estimations for the lesions locations. Consequently, multiple biopsy samples are required to target one single lesion. In this study, the whole pelvis model (comprised of the rectum, bladder, pelvic muscles, prostate transitional zone (TZ), and peripheral zone (PZ)) is used for the simulation results. An isotropic hyperelastic approach (Signorini model) was used for all the soft tissues except the vesical muscles. The vesical muscles are assumed to have a linear elastic behavior due to the lack of experimental data to determine the constants involved in hyperelastic models. The tissues and organ geometry is taken from the existing literature for 3D meshes. Then the biomechanical parameters were obtained under different testing techniques described in the literature. The acquired parametric values for uniaxial stress/strain data are used in the Signorini model to see the anatomical behavior of the pelvis model. The five mesh nodes in terms of small prostate lesions are selected prior to biopsy and each lesion’s final position is targeted when TRUS probe force of 30 N is applied at the inside rectum wall. Code_Aster open-source software is used for numerical simulations. Moreover, the overall effects of pelvis organ deformation were demonstrated when TRUS–guided biopsy is induced. The deformation of the prostate and neoplasms displacement showed that the appropriate material properties to organs altered the resulting lesion's migration parametrically. As a result, the distance traveled by these lesions ranged between 3.77 and 9.42 mm. The lesion displacement and organ deformation are compared and analyzed with our previous study in which we used linear elastic properties for all pelvic organs. Furthermore, the visual comparison of axial and sagittal slices are also compared, which is taken for Magnetic Resource Imaging (MRI) and TRUS images with our preliminary study.

Keywords: code-aster, magnetic resonance imaging, neoplasms, transrectal ultrasound, TRUS-guided biopsy

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Authors: Keaghan Brown

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The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

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Authors: Natasha Goh, Sebastian Brown

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Purpose: This case report describes an unusual presentation of uveal melanoma. Method: Case notes, imaging, and histopathological specimen were reviewed for this case report. Result: The patient is a 62-year-old lady of Chinese heritage who had been receiving follow-up at the eye clinic of a tertiary hospital. She had a longstanding history of poor vision in her right eye after sustaining trauma to the eye at age 3. She was found to have a carotid-cavernous sinus fistula in the right eye in 2009 and underwent stenting in China. Unfortunately, this was unsuccessful and resulted in a painful blind eye. She had represented with headaches, worsening eye pain, and ptosis in Sydney in 2016. Her CT angiogram showed a calcified vascular structure in the orbit and globe, and she was offered a digital subtraction angiography by the neurosurgical team, which she ultimately declined. She had since been followed up at the eye clinic for the pthisical eye. Due to chronic ocular pain and recurrent conjunctivitis, the decision was made for an evisceration in 2021. The specimen was sent for routine histopathological examination and returned positive for uveal melanoma. The patient was subsequently referred to a melanoma center for further follow-up, which comprised serial imaging and radiotherapy treatment. Conclusion: Clinicians should bear in mind that uveal melanomas may present in a longstanding phthisical eye and in patients with no or little apparent risk factors.

Keywords: uveal melanoma, pthisical eye, carotid cavernous fistula, uveal melanoma risk factors

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Authors: Sohini Manna, Jong Woo Kim, Oleg Shpyrko, Eric E. Fullerton

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CVD techniques have emerged as a promising approach in the formation of a broad range of nanostructured materials. The realization of many practical applications will require efficient and economical synthesis techniques that preferably avoid the need for templates or costly single-crystal substrates and also afford process adaptability. Towards this end, we have developed a single-step route for the reduction-type synthesis of nanostructured Ni materials using a thermal CVD method. By tuning the CVD growth parameters, we can synthesize morphologically dissimilar nanostructures including single-crystal cubes and Au nanostructures which form atop untreated amorphous SiO2||Si substrates. An understanding of the new properties that emerge in these nanostructures materials and their relationship to function will lead to for a broad range of magnetostrictive devices as well as other catalysis, fuel cell, sensor, and battery applications based on high-surface-area transition-metal nanostructures. We use coherent X-ray diffraction imaging technique to obtain 3-D image and strain maps of individual nanocrystals. Coherent x-ray diffractive imaging (CXDI) is a technique that provides the overall shape of a nanostructure and the lattice distortion based on the combination of highly brilliant coherent x-ray sources and phase retrieval algorithm. We observe a fine interplay of reduction of surface energy vs internal stress, which plays an important role in the morphology of nano-crystals. The strain distribution is influenced by the metal-substrate interface and metal-air interface, which arise due to differences in their thermal expansion. We find the lattice strain at the surface of the octahedral gold nanocrystal agrees well with the predictions of the Young-Laplace equation quantitatively, but exhibits a discrepancy near the nanocrystal-substrate interface resulting from the interface. The strain in the bottom side of the Ni nanocube, which is contacted on the substrate surface is compressive. This is caused by dissimilar thermal expansion coefficients between Ni nanocube and Si substrate. Research at UCSD support by NSF DMR Award # 1411335.

Keywords: CVD, nanostructures, strain, CXRD

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Authors: Diane Vassallo., Leonard Busuttil

Abstract:

Recent educational developments have seen increasing attention attributed to Computational Thinking (CT) and its integration into primary and secondary school curricula. CT is more than simply being able to use technology but encompasses fundamental Computer Science concepts which are deemed to be very important in developing the correct mindset for our future digital citizens. The case study presented in this article explores the journey of a Maltese secondary school teacher in his efforts to plan, develop and integrate CT within the context of a local classroom. The teacher participant was recruited from the Malta EU Code week summer school, a pilot initiative that stemmed from the EU Code week Team’s Train the Trainer program. The qualitative methodology involved interviews with the participant teacher as well as an analysis of the artefacts created by the students during the lessons. The results shed light on the numerous challenges and obstacles that the teacher encountered in his integration of CT, as well as portray some brilliant examples of good practices which can substantially inform further research and practice around the integration of CT in classroom practice.

Keywords: computational thinking, digital citizens, digital literacy, technology integration

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Authors: Sedat Yayla, Mehmet Oruc, Shakhwan Yaseen

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Cavitation phenomena might rigorously impair machine parts such as pumps, propellers and impellers or devices as the pressure in the fluid declines under the liquid's saturation pressure. To evaluate the influence of cavitation, in this research two-dimensional computational fluid dynamics (CFD) venturi models with variety of inlet pressure values, throat lengths and vapor fluid contents were applied. In this research three different vapor contents (0%, 5% 10%), four inlet pressures (2, 4, 6, 8 and 10 atm) and two venturi models were employed at different throat lengths ( 5, 10, 15 and 20 mm) for discovering the impact of each parameter on the cavitation number. It is uncovered that there is a positive correlation between pressure inlet and vapor fluid content and cavitation number. Furthermore, it is unveiled that velocity remains almost constant at the inlet pressures of 6, 8,10atm, nevertheless increasing the length of throat results in the substantial escalation in the velocity of the throat at inlet pressures of 2 and 4 atm. Furthermore, velocity and cavitation number were negatively correlated. The results of the cavitation number varied between 0.092 and 0.495 depending upon the velocity values of the throat.

Keywords: cavitation number, computational fluid dynamics, mixture of fluid, two-phase flow, velocity of throat

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Authors: Muzna Tariq, Ihtzaz Qamar

Abstract:

In most engineering cases, the working temperatures inside a combustion chamber are high enough that they lie beyond the operational range of thermocouples. Furthermore, design and manufacturing limitations restrict the use of internal thermocouples in many applications. Heat transfer inside a combustion chamber is caused due to interaction of the post-combustion hot fluid with the chamber wall. Heat transfer that involves an interaction between the fluid and solid is categorized as Conjugate Heat Transfer (CHT). Therefore, to satisfy the needs of CHT, CHT Analysis is performed by using ANSYS CFD tool to estimate theoretically precise thermocouple positions at the combustion chamber wall where excessive temperatures (beyond thermocouple range) can be avoided. In accordance with these Computational Fluid Dynamics (CFD) results, a combustion chamber is designed, and a prototype is manufactured with multiple thermocouple ports positioned at the specified distances so that the temperature of hot gases can be measured on the chamber wall where the temperatures do not exceed the thermocouple working range.

Keywords: computational fluid dynamics, conduction, conjugate heat transfer, convection, fluid flow, thermocouples

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Authors: Abdelrahman Mohamed Abdelrahman

Abstract:

Canopic jars are one of the vessels of funerary nature used by the ancient Egyptian in mummification process that were used to save the viscera of the mummified body after being extracted from the body and treated. Canopic jars are made of several types of materials like Limestone, Alabaster, and Pottery. The studied canopic jar dates back to Late period, located in the Grand Egyptian Museum (GEM), Giza, Egypt. This jar carved from limestone with carved hieroglyphic inscriptions, and it filled and closed by mortar from inside. Some aspects of damage appeared in the jar, such as dust, dirts, classification, wide crack, weakness of limestone. In this study, we used documentation and investigation modern techniques to document and examine the jar. 3D scanning and X-ray Radiography imaging used in applied study. X-ray imaging showed that the mortar was placed at a time when the jar contained probably viscera where the mortar appeared that not reach up to the base of the inner jar. Through the three-dimensional photography, the jar was documented, and we have 3D model of the jar, and now we have the ability through the computer to see any part of the jar in all its details. After that, conservation procedures have been applied with high accuracy to conserve the jar, including mechanical, wet, and chemical cleaning, filling wide crack in the body of the jar using mortar consisting of calcium carbonate powder mixing with primal E330 S, and consolidation, so the limestone became strong after using paraloid B72 2% concentrate as a consolidate material.

Keywords: vessel, limestone, canopic jar, mortar, 3D scanning, X-ray radiography

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Authors: Dhurgham Al-Karawi, Nisreen Polus, Shakir Al-Zaidi, Sabah Jassim

Abstract:

The management of COVID-19 patients based on chest imaging is emerging as an essential tool for evaluating the spread of the pandemic which has gripped the global community. It has already been used to monitor the situation of COVID-19 patients who have issues in respiratory status. There has been increase to use chest imaging for medical triage of patients who are showing moderate-severe clinical COVID-19 features, this is due to the fast dispersal of the pandemic to all continents and communities. This article demonstrates the development of machine learning techniques for the test of COVID-19 patients using Chest X-Ray (CXR) images in nearly real-time, to distinguish the COVID-19 infection with a significantly high level of accuracy. The testing performance has covered a combination of different datasets of CXR images of positive COVID-19 patients, patients with viral and bacterial infections, also, people with a clear chest. The proposed AI scheme successfully distinguishes CXR scans of COVID-19 infected patients from CXR scans of viral and bacterial based pneumonia as well as normal cases with an average accuracy of 94.43%, sensitivity 95%, and specificity 93.86%. Predicted decisions would be supported by visual evidence to help clinicians speed up the initial assessment process of new suspected cases, especially in a resource-constrained environment.

Keywords: COVID-19, chest x-ray scan, artificial intelligence, texture analysis, local binary pattern transform, Gabor filter

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