Search results for: molecular imaging

Authors: A. Azari, S. S. K. Seyyedi

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One of the unaddressed and open challenges in the nano-networking is the characteristics of noise. The previous analysis, however, has concentrated on end-to-end communication model with no separate modelings for propagation channel and noise. By considering a separate signal propagation and noise model, the design and implementation of an optimum receiver will be much easier. In this paper, we justify consideration of a separate additive Gaussian noise model of a nano-communication system based on the molecular communication channel for which are applicable for MSK and MOSK modulation schemes. The presented noise analysis is based on the Brownian motion process, and advection molecular statistics, where the received random signal has a probability density function whose mean is equal to the mean number of the received molecules. Finally, the justification of received signal magnitude being uncorrelated with additive non-stationary white noise is provided.

Keywords: molecular, noise, diffusion, channel

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Authors: Kolja Them, Johannes Salamon, Harald Ittrich, Michael Kaul, Tobias Knopp

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Superparamagnetic iron oxide nanoparticles (SPIONs) are nanoscale magnets which can be biologically functionalized for biomedical applications. Stem cell therapies to repair damaged tissue, magnetic fluid hyperthermia for cancer therapy and targeted drug delivery based on SPIONs are prominent examples where the visualization of a preferably low concentrated SPION distribution is essential. In 2005 a new method for tomographic SPION imaging has been introduced. The method named magnetic particle imaging (MPI) takes advantage of the nanoparticles magnetization change caused by an oscillating, external magnetic field and allows to directly image the time-dependent nanoparticle distribution. The SPION magnetization can be changed by the electron spin dynamics as well as by a mechanical rotation of the nanoparticle. In this work different calibration methods in MPI are investigated for image reconstruction of magnetically labeled stem cells. It is shown that a calibration using rotationally immobilized SPIONs provides a higher quality of stem cell images with fewer artifacts than a calibration using mobile SPIONs. The enhancement of the image quality and the reduction of artifacts enables the localization and identification of a smaller number of magnetically labeled stem cells. This is important for future medical applications where low concentrations of functionalized SPIONs interacting with biological matter have to be localized.

Keywords: biomedical imaging, iron oxide nanoparticles, magnetic particle imaging, stem cell imaging

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Authors: Cam Nguyen

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Rapid, accurate, and safe sensing and imaging of physical quantities or structures finds many applications and is of significant interest to society. Sensing and imaging using radio-frequency (RF) techniques, particularly, has gone through significant development and subsequently established itself as a unique territory in the sensing world. RF sensing and imaging has played a critical role in providing us many sensing and imaging abilities beyond our human capabilities, benefiting both civilian and military applications - for example, from sensing abnormal conditions underneath some structures’ surfaces to detection and classification of concealed items, hidden activities, and buried objects. We present the developments of several sensing and imaging systems implementing RF technologies like ultra-wide band (UWB), synthetic-pulse, and interferometry. These systems are fabricated completely using RF integrated circuits. The UWB impulse system operates over multiple pulse durations from 450 to 1170 ps with 5.5-GHz RF bandwidth. It performs well through tests of various samples, demonstrating its usefulness for subsurface sensing. The synthetic-pulse system operating from 0.6 to 5.6 GHz can assess accurately subsurface structures. The synthetic-pulse system operating from 29.72-37.7 GHz demonstrates abilities for various surface and near-surface sensing such as profile mapping, liquid-level monitoring, and anti-personnel mine locating. The interferometric system operating at 35.6 GHz demonstrates its multi-functional capability for measurement of displacements and slow velocities. These RF sensors are attractive and useful for various surface and subsurface sensing applications. This paper was made possible by NPRP grant # 6-241-2-102 from the Qatar National Research Fund (a member of Qatar Foundation). The statements made herein are solely the responsibility of the authors.

Keywords: RF sensors, radars, surface sensing, subsurface sensing

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Authors: Syue-Liang Lin, C. Allen Chang

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Luminescence imaging is an important technique used in biomedical research and clinical diagnostic applications in recent years. Concurrently, the development of NIR luminescence probes / imaging contrast agents has helped the understanding of the structural and functional properties of cells and animals. Photodynamic therapy (PDT) is used clinically to treat a wide range of medical conditions, but the therapeutic efficacy of general PDT for deeper tumor was limited by the penetration of excitation source. The tumor targeting biomedical nanomaterials UCNP@PS (upconversion nanoparticle conjugated with photosensitizer) for photodynamic therapy and near-infrared imaging of cancer will be developed in our study. Synthesis and characterization of biomedical nanomaterials were completed in this studies. The spectrum of UCNP was characterized by photoluminescence spectroscopy and the morphology was characterized by Transmission Electron Microscope (TEM). TEM and XRD analyses indicated that these nanoparticles are about 20~50 nm with hexagonal phase. NaYF₄:Ln³⁺ (Ln= Yb, Nd, Er) upconversion nanoparticles (UCNPs) with core / shell structure, synthesized by thermal decomposition method in 300°C, have the ability to emit visible light (upconversion: 540 nm, 660 nm) and near-infrared with longer wavelength (downconversion: NIR: 980 nm, 1525 nm) by absorbing 800 nm NIR laser. The information obtained from these studies would be very useful for applications of these nanomaterials for bio-luminescence imaging and photodynamic therapy of deep tumor tissue in the future.

Keywords: Near Infrared (NIR), lanthanide, core-shell structure, upconversion, theranostics

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Authors: Paweł Stączek, Tomasz Plech, Aleksandra Strzelczyk, Katarzyna Dzitko, Monika Wujec, Edyta Kuśmierz, Piotr Paneth, Agata Paneth

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In this contribution, we will describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile, and molecular modeling evaluation. We have found that one of the tested compounds, 4-benzoyl-1-(2-methyl-furan-3-ylcarbonyl) thiosemicarbazide, remarkably inhibits the activity of S. aureus DNA gyrase with the IC50 below 5 μM. Besides, this compound displays antibacterial activity on Staphylococcus spp. and E. faecalis at non-cytotoxic concentrations in mammalian cells, with minimal inhibitory concentrations (MICs) values at 25 μg/mL. Based on the enzymatic and molecular modeling studies we propose two factors, i.e. geometry of molecule and hydrophobic/hydrophilic balance as important molecular properties for developing thiosemicarbazide derivatives as potent Staphylococcus aureus DNA gyrase inhibitors.

Keywords: bioactivity, drug design, topoisomerase, molecular modeling

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Authors: Hai Hoang, Thanh Xuan Nguyen Thi, Guillaume Galliero

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Coarse-Grained (CG) molecular simulations have shown to be an efficient way to estimate thermophysical (static and dynamic) properties of fluids. Several strategies have been developed and reported in the literature for defining CG molecular models. Among them, those based on a top-down strategy (i.e. CG molecular models related to macroscopic observables), despite being heuristic, have increasingly gained attention. This is probably due to its simplicity in implementation and its ability to provide reasonable results for not only simple but also complex systems. Regarding simple Force-Fields associated with these CG molecular models, it has been found that the four parameters Mie chain model is one of the best compromises to describe thermophysical static properties (e.g. phase diagram, saturation pressure). However, parameterization procedures of these Mie-chain GC molecular models given in literature are generally insufficient to simultaneously provide static and dynamic (e.g. viscosity) properties. To deal with such situations, we have extended the corresponding states by using a quantity associated with the liquid viscosity. Results obtained from molecular simulations have shown that our approach is able to yield good estimates for both static and dynamic thermophysical properties for various real non-associating fluids. In addition, we will show that on simple (e.g. phase diagram, saturation pressure) and complex (e.g. thermodynamic response functions, thermodynamic energy potentials) static properties, results of our scheme generally provides improved results compared to existing approaches.

Keywords: coarse-grained model, mie potential, molecular simulations, thermophysical properties, phase equilibria

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Authors: Alexander Machikhin, Olga Polschikova, Vitold Pozhar, Alina Ramazanova

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White-light quantitative phase imaging is an effective technique for achieving sub-nanometer phase sensitivity. Highly stable interferometers based on common-path geometry have been developed in recent years to solve this task. Some of these methods also apply multispectral approach. The purpose of this research is to suggest a simple and effective interferometer for such systems. We developed a three-lens common-path interferometer, which can be used for quantitative phase imaging with or without multispectral modality. The lens system consists of two components, the first one of which is a compound lens, consisting of two lenses. A pinhole is placed between the components. The lens-in-lens approach enables effective light transmission and high stability of the interferometer. The multispectrality is easily implemented by placing a tunable filter in front of the interferometer. In our work, we used an acousto-optical tunable filter. Some design considerations are discussed and multispectral quantitative phase retrieval is demonstrated.

Keywords: acousto-optical tunable filter, common-path interferometry, digital holography, multispectral quantitative phase imaging

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Authors: Manel Boulakoud, Abdelkader Chouaih, Fodil Hamzaoui

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In the present work we are interested in the determination of the Molecular electrostatic potential (MEP) in Z-3N(2-Ethoxyphenyl), 2-N’(2-Ethoxyphenyl) imino thiazolidin-4-one molecule by ab initio and Density Functional Theory (DFT) in the ground state. The MEP is related to the electronic density and is a very useful descriptor in understanding sites for electrophilic attack and nucleophilic reactions as well as hydrogen bonding interactions. First, geometry optimization was carried out using Hartree–Fock (HF) and DFT methods with 6-311G(d,p) basis set. In order to get more information on the molecule, its stability has been analyzed by natural bond orbital (NBO) analysis. Mulliken population analyses have been calculated. Finally, the molecular electrostatic potential (MEP) and HOMO-LUMO energy levels have been performed. The calculated HOMO and LUMO energies show also the charge transfer within the molecule. The energy gap obtained is about 4 eV which explain the stability of the studied compound. The obtained molecular electrostatic potential from the two methods confirms the nature of the electron charge transfer at the molecular shell and locate the electropositive part and the electronegative part in molecular scale of the title compound.

Keywords: DFT, ab initio, HOMO-LUMO, organic compounds

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Authors: Satoshi Nishimura

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Although much information has been garnered from the genomes of humans and mice, it remains difficult to extend that information to explain physiological and pathological phenomena. This is because the processes underlying life are by nature stochastic and fluctuate with time. Thus, we developed novel "in vivo molecular imaging" method based on single and two-photon microscopy. We visualized and analyzed many life phenomena, including common adult diseases. We integrated the knowledge obtained, and established new models that will serve as the basis for new minimally invasive therapeutic approaches.

Keywords: two photon microscope, intravital visualization, thrombus, artery

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Authors: Josef Uher, Jana Boháčová, Richard Kadeřábek

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In this paper, we present a multi-robot imaging and irradiation research platform referred to as Irradion, with full capabilities of portable arbitrary path computed tomography (CT). Irradion is an imaging and irradiation unit entirely based on robotic arms for research on cancer treatment with ion beams on small animals (mice or rats). The platform comprises two subsystems that combine several imaging modalities, such as 2D X-ray imaging, CT, and particle tracking, with precise positioning of a small animal for imaging and irradiation. Computed Tomography: The CT subsystem of the Irradion platform is equipped with two 6-joint robotic arms that position a photon counting detector and an X-ray tube independently and freely around the scanned specimen and allow image acquisition utilizing computed tomography. Irradiation measures nearly all conventional 2D and 3D trajectories of X-ray imaging with precisely calibrated and repeatable geometrical accuracy leading to a spatial resolution of up to 50 µm. In addition, the photon counting detectors allow X-ray photon energy discrimination, which can suppress scattered radiation, thus improving image contrast. It can also measure absorption spectra and recognize different materials (tissue) types. X-ray video recording and real-time imaging options can be applied for studies of dynamic processes, including in vivo specimens. Moreover, Irradion opens the door to exploring new 2D and 3D X-ray imaging approaches. We demonstrate in this publication various novel scan trajectories and their benefits. Proton Imaging and Particle Tracking: The Irradion platform allows combining several imaging modules with any required number of robots. The proton tracking module comprises another two robots, each holding particle tracking detectors with position, energy, and time-sensitive sensors Timepix3. Timepix3 detectors can track particles entering and exiting the specimen and allow accurate guiding of photon/ion beams for irradiation. In addition, quantifying the energy losses before and after the specimen brings essential information for precise irradiation planning and verification. Work on the small animal research platform Irradion involved advanced software and hardware development that will offer researchers a novel way to investigate new approaches in (i) radiotherapy, (ii) spectral CT, (iii) arbitrary path CT, (iv) particle tracking. The robotic platform for imaging and radiation research developed for the project is an entirely new product on the market. Preclinical research systems with precision robotic irradiation with photon/ion beams combined with multimodality high-resolution imaging do not exist currently. The researched technology can potentially cause a significant leap forward compared to the current, first-generation primary devices.

Keywords: arbitrary path CT, robotic CT, modular, multi-robot, small animal imaging

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Authors: Congping Lin

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Intracellular transport in fungi has a number of important roles in, e.g., filamentous fungal growth and cellular metabolism. Two basic mechanisms for intracellular transport are motor-driven trafficking along microtubules (MTs) and diffusion. Mathematical modelling has been actively developed to understand such intracellular transport and provide unique insight into cellular complexity. Based on live-cell imaging data in Ustilago hyphal cells, probabilistic models have been developed to study mechanism underlying spatial organization of molecular motors and organelles. In particular, anther mechanism - stochastic motility of dynein motors along MTs has been found to contribute to half of its accumulation at hyphal tip in order to support early endosome (EE) recycling. The EE trafficking not only facilitates the directed motion of peroxisomes but also enhances their diffusive motion. Considering the importance of spatial organization of early endosomes in supporting peroxisome movement, computational and experimental approaches have been combined to a whole-cell level. Results from this interdisciplinary study promise insights into requirements for other membrane trafficking systems (e.g., in neurons), but also may inform future 'synthetic biology' studies.

Keywords: intracellular transport, stochastic process, molecular motors, spatial organization

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Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

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Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: biological molecular networks, essential genes, graph theory, network subgraphs

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Authors: Hiroki Takiguchi, Masahiro Furuya, Takahiro Arai

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In order to quantitatively comprehend thermal flow for some industrial applications such as nuclear and chemical reactors, detailed measurements for temperature and abundance (concentration) of materials at high temporal and spatial resolution are required. Additionally, rigorous evaluation of the size effect is also important for practical realization. This paper introduces a real-time spectroscopic imaging method in micro scale field, which visualizes temperature and concentration distribution of a liquid or mix liquids with near-infrared (NIR) wavelength region. This imaging principle is based on absorption of pre-selected narrow band from absorption spectrum peak or its dependence property of target liquid in NIR region. For example, water has a positive temperature sensitivity in the wavelength at 1905 nm, therefore the temperature of water can be measured using the wavelength band. In the experiment, the real-time imaging observation of concentration distribution in micro channel was demonstrated to investigate the applicability of micro-scale diffusion coefficient and temperature measurement technique using this proposed method. The effect of thermal diffusion and binary mutual diffusion was evaluated with the time-series visualizations of concentration distribution.

Keywords: near-infrared spectroscopic imaging, micro fluid channel, concentration distribution, diffusion phenomenon

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Authors: Rashmi Yadawad, Disha Narayanan, Ravi Gautam

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Through Wall Radar Imaging is gaining increasing importance now a days in the field of Defense and one of the most important criteria that forms the basis for the image quality obtained is the Cross-Range resolution of the image. In this research paper, the Bilateral Back projection algorithm has been implemented for Through Wall Radar Imaging. The sole purpose is to enhance the resolution in the cross range direction of the obtained Back projection image. Synthetic Data is generated for two targets which are placed at various locations in a room of dimensions 8 m by 6m. Two algorithms namely, simple back projection and Bilateral Back projection have been implemented, images are obtained and the obtained images are compared. Numerical simulations have been coded in MATLAB and experimental results of the two algorithms have been shown. Based on the comparison between the two images, it can be clearly seen that the ringing effect and chess board effect have been heavily reduced in the bilaterally back projected image and hence promising results are obtained giving a relatively sharper image with relatively well defined edges.

Keywords: through wall radar imaging, bilateral back projection, cross range resolution, synthetic data

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Authors: Kwazikwenkosi Sikhakhane, Suvendi Rimer, Mpho Gololo, Khmaies Oahada, Adnan Abu-Mahfouz

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Medical ultrasound imaging is a crucial diagnostic technique due to its affordability and non-invasiveness compared to other imaging methods. However, the presence of speckle noise, which is a form of multiplicative noise, poses a significant obstacle to obtaining clear and accurate images in ultrasound imaging. Speckle noise reduces image quality by decreasing contrast, resolution, and signal-to-noise ratio (SNR). This makes it difficult for medical professionals to interpret ultrasound images accurately. To address this issue, various techniques have been developed to reduce speckle noise in ultrasound images, which improves image quality. This paper aims to review some of these techniques, highlighting the advantages and disadvantages of each algorithm and identifying the scenarios in which they work most effectively.

Keywords: image processing, noise, speckle, ultrasound

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Authors: Ching-Yuan Chen, Lung-Kwang Pan

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Objective: Back pain is a major health problem costing billions of health budgets annually in Taiwan. Thousands of back pain surgeries are performed annually with up to 40% of patients complaining of back pain at time of post-surgery causing failed back surgery syndrome (FBSS), although diagnosis in these patients may be complex. The aim of study is to assess the feasibility of using bone SPECT-CT imaging to localize the active lesions causing persistent, recurrent or new backache after spine surgery. Materials and Methods: Bone SPECT-CT imaging was performed after the intravenous injection of 20 mCi of 99mTc-MDP for all the patients with diagnosis of FBSS. Patients were evaluated using status of subjectively pain relief, functional improvement and degree of satisfaction by reviewing the medical records and questionnaires in a 2 more years’ follow-up. Results: We enrolled a total of 16 patients were surveyed in our hospital from Jan. 2015 to Dec. 2016. Four people on SPEC/CT imaging ensured significant lesions were undergone a revised surgery (surgical treatment group). The mean visual analogue scale (VAS) decreased 5.3 points and mean Oswestry disability index (ODI) improved 38 points in the surgical group. The remaining 12 on SPECT/CT imaging were diagnosed as no significant lesions then received drug treatment (medical treatment group). The mean VAS only decreased 2 .1 point and mean ODI improved 12.6 points in the medical treatment group. In the posttherapeutic evaluation, the pain of the surgical treatment group showed a satisfactory improvement. In the medical treatment group, 10 of the 12 were also satisfied with the symptom relief while the other 2 did not improve significantly. Conclusions: Findings on SPECT-CT imaging appears to be easily explained the patients' pain. We recommended that SPECT/CT imaging was a feasible and useful clinical tool to improve diagnostic confidence or specificity when evaluating patients with FBSS.

Keywords: failed back surgery syndrome, oswestry disability index, SPECT-CT imaging, 99mTc-MDP, visual analogue scale

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Authors: Y. Megrous, A. Chouaih, F. Hamzaoui

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The crystal structure of 4-Methyl-7-(salicylideneamino)coumarin C17H13NO3has been determined using X-ray diffraction to establish the configuration and stereochemistry of the molecule. This crystal is characterized by its nolinear activity. The molecular electron charge density distribution of the title compound is described accurately using the multipolar model of Hansen and Coppens. The net atomic charge and the molecular dipole moment in-crystal have been determined in order to understand the nature of inter-and intramolecular charge transfer. The study present the thermal motion and the structural analysis obtained from the least-square refinement on F2,this study has also allowed us to determine the electrostatic potential and therefore locate the electropositive part and the electronegative part in molecular scale of the title compound.

Keywords: electron charge density, net atomic charge, molecular dipole moment, X-ray diffraction

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Authors: Peter J. Riley

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Medical Imaging students must understand the roles of Photo-electric Absorption (PE) and Compton Scatter (CS) interactions in patients to enable optimal X-ray imaging in clinical practice. A simulator has been developed that shows relative interaction probabilities, color bars for patient dose from PE, % penetration to the detector, and obscuring CS as Peak Kilovoltage (kVp) changes. Additionally, an anthropomorphic chest X-ray image shows the relative tissue contrasts and overlying CS-fog at that kVp, which determine the detectability of a lesion in the image. A series of interactive exercises with MCQs evaluate the student's understanding; the simulation has improved student perception of the need to acquire "sufficient" rather than maximal contrast to enable patient dose reduction at higher kVp.

Keywords: patient dose optimization, radiological physics, simulation, tissue contrast

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Authors: Jurijs Salijevs, Katrina Bolocko

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The integration of artificial intelligence and neural networks has significantly changed full-body imaging and high-resolution 3D mapping systems, and this paper reviews research in these areas. With an emphasis on their use in the early identification of melanoma and other disorders, the goal is to give a wide perspective on the current status and potential future of these medical imaging technologies. Authors also examine methodologies such as machine learning and deep learning, seeking to identify efficient procedures that enhance diagnostic capabilities through the analysis of 3D body scans. This work aims to encourage further research and technological development to harness the full potential of AI in disease diagnosis.

Keywords: artificial intelligence, neural networks, 3D scan, body scan, 3D mapping system, healthcare

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Authors: Anjani Kumar Tiwari, Neelam Kumari, Anil Mishra

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The family of phosphodiesterases (PDEs) plays a critical role in control of the level, localization, and duration of intracellular 3’-5’-cyclic adenosine monophosphate (cAMP) and 3’-5’-cyclic guanosine monophosphate (cGMP) signals by specifically hydrolyzing these cyclic nucleotides. As the involvement of cyclic nucleotide second messengers in cell signaling and homeostasis is established, the regulation of these pathways in the brain by various PDE isoforms is an area of considerable interest, as they are involved in nearly all brain functions and in the etiology of neuropsychiatric diseases. The PDE10A isoform, isolated from different species and characterized regarding structure and function, has received much attention in recent years, particularly in the context of schizophrenia and Huntington’s disease, which are both related to a role of PDE10A in the regulation of striatal dopaminergic neurotransmission. Quinazoline analogue 1-(4-methoxyphenyl)-6,7-dimethoxyquinazoline, was evaluated as specific PET marker for phosphodiesterase (PDE) 10A. Here, we report the radiosynthesis of [11C]2 and the in vitro and in vivo evaluation of [11C]2 as a potential positron emission tomography (PET) radiotracer for imaging PDE10A in the central nervous system (CNS). The radiosynthesis of [11C]2 was achieved by O-methylation of the corresponding des-methyl precursor with [11C]methyl iodide. [11C]2 was obtained with ∼50% radiochemical yield. PET imaging studies in rat brain displayed initial specific uptake with very rapid clearance of [11C]2 from brain. Though [11C]2 is not an ideal radioligand for clinical imaging of PDE10A in the CNS. Modified analogue of quinazoline having a higher potency for inhibiting PDE10A and improved pharmacokinetic properties will be necessary for imaging this enzyme with PET.

Keywords: PDE10A, PET, radiotracer, quinazoline

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Authors: I-Ling Chang, Jer-An Chen

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The elastic properties and fracture of two-dimensional graphene were calculated purely from the atomic bonding (stretching and bending) based on molecular mechanics method. Considering the representative unit cell of graphene under various loading conditions, the deformations of carbon bonds and the variations of the interlayer distance could be realized numerically under the geometry constraints and minimum energy assumption. In elastic region, it was found that graphene was in-plane isotropic. Meanwhile, the in-plane deformation of the representative unit cell is not uniform along armchair direction due to the discrete and non-uniform distributions of the atoms. The fracture of graphene could be predicted using fracture criteria based on the critical bond length, over which the bond would break. It was noticed that the fracture behavior were directional dependent, which was consistent with molecular dynamics simulation results.

Keywords: energy minimization, fracture, graphene, molecular mechanics

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Authors: Jing Zhao, Yongqing Bai, Qiaofang Shi, Huaihao Zhang

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Advances in software technology enable computational chemistry to be commonly applied in various research fields, especially in pedagogy. Thus, in order to expand and improve experimental instructions of computational chemistry for undergraduates, we designed an introductory experiment—research on acrylamide molecular structure and physicochemical properties. Initially, students construct molecular models of acrylamide and polyacrylamide in Gaussian and Materials Studio software respectively. Then, the infrared spectral data, atomic charge and molecular orbitals of acrylamide as well as solvation effect of polyacrylamide are calculated to predict their physicochemical performance. At last, rheological experiments are used to validate these predictions. Through the combination of molecular simulation (performed on Gaussian, Materials Studio) with experimental verification (rheology experiment), learners have deeply comprehended the chemical nature of acrylamide and polyacrylamide, achieving good learning outcomes.

Keywords: upper-division undergraduate, computer-based learning, laboratory instruction, molecular modeling

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Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

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Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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Authors: Parimalah Velo, Ahmad Zakaria

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Introduction: Monte Carlo simulations of preclinical imaging systems allow opportunity to enable new research that could range from designing hardware up to discovery of new imaging application. The simulation system which could accurately model an imaging modality provides a platform for imaging developments that might be inconvenient in physical experiment systems due to the expense, unnecessary radiation exposures and technological difficulties. The aim of present study is to validate the Monte Carlo simulation of thyroid phantom imaging using Geant4-GATE for Siemen’s e-cam single head gamma camera. Upon the validation of the gamma camera simulation model by comparing physical characteristic such as energy resolution, spatial resolution, sensitivity, and dead time, the GATE simulation of thyroid phantom imaging is carried out. Methods: A thyroid phantom is defined geometrically which comprises of 2 lobes with 80mm in diameter, 1 hot spot, and 3 cold spots. This geometry accurately resembling the actual dimensions of thyroid phantom. A planar image of 500k counts with 128x128 matrix size was acquired using simulation model and in actual experimental setup. Upon image acquisition, quantitative image analysis was performed by investigating the total number of counts in image, the contrast of the image, radioactivity distributions on image and the dimension of hot spot. Algorithm for each quantification is described in detail. The difference in estimated and actual values for both simulation and experimental setup is analyzed for radioactivity distribution and dimension of hot spot. Results: The results show that the difference between contrast level of simulation image and experimental image is within 2%. The difference in the total count between simulation and actual study is 0.4%. The results of activity estimation show that the relative difference between estimated and actual activity for experimental and simulation is 4.62% and 3.03% respectively. The deviation in estimated diameter of hot spot for both simulation and experimental study are similar which is 0.5 pixel. In conclusion, the comparisons show good agreement between the simulation and experimental data.

Keywords: gamma camera, Geant4 application of tomographic emission (GATE), Monte Carlo, thyroid imaging

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Authors: Bryce R. Jolley, Michael Uchic

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This study presents initial results toward the correlative characterization of inherent defects of Ti-6Al-4V additive manufacture (AM). X-Ray Computed Tomography (CT) defect data are compared and correlated with microscopic photographs obtained via automated serial sectioning. The metal AM specimen was manufactured out of Ti-6Al-4V virgin powder to specified dimensions. A post-contour was applied during the fabrication process with a speed of 1050 mm/s, power of 260 W, and a width of 140 µm. The specimen was stress relief heat-treated at 16°F for 3 hours. Microfocus CT imaging was accomplished on the specimen within a predetermined region of the build. Microfocus CT imaging was conducted with parameters optimized for Ti-6Al-4V additive manufacture. After CT imaging, a modified RoboMet. 3D version 2 was employed for serial sectioning and optical microscopy characterization of the same predetermined region. Automated montage capture with sub-micron resolution, bright-field reflection, 12-bit monochrome optical images were performed in an automated fashion. These optical images were post-processed to produce 2D and 3D data sets. This processing included thresholding and segmentation to improve visualization of defect features. The defects observed from optical imaging were compared and correlated with the defects observed from CT imaging over the same predetermined region of the specimen. Quantitative results of area fraction and equivalent pore diameters obtained via each method are presented for this correlation. It is shown that Microfocus CT imaging does not capture all inherent defects within this Ti-6Al-4V AM sample. Best practices for this correlative effort are also presented as well as the future direction of research resultant from this current study.

Keywords: additive manufacture, automated serial sectioning, computed tomography, nondestructive evaluation

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Authors: Guoqiang Yu, Mehrana Mohtasebi, Jinghong Sun, Thomas Pittman

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Malignant glioma (MG) is the most common type of primary malignant brain tumor. Surgical resection of MG remains the cornerstone of therapy, and the extent of resection correlates with patient survival. A limiting factor for resection, however, is the difficulty in differentiating the tumor from normal tissue during surgery. Fluorescence imaging is an emerging technique for real-time intraoperative visualization of MGs and their boundaries. However, most clinical-grade neurosurgical operative microscopes with fluorescence imaging ability are hampered by low adoption rates due to high cost, limited portability, limited operation flexibility, and lack of skilled professionals with technical knowledge. To overcome the limitations, we innovatively integrated miniaturized light sources, flippable filters, and a recording camera to the surgical eye loupes to generate a wearable fluorescence eye loupe (FLoupe) device for intraoperative imaging of fluorescent MGs. Two FLoupe prototypes were constructed for imaging of Fluorescein and 5-aminolevulinic acid (5-ALA), respectively. The wearable FLoupe devices were tested on tumor-simulating phantoms and patients with MGs. Comparable results were observed against the standard neurosurgical operative microscope (PENTERO® 900) with fluorescence kits. The affordable and wearable FLoupe devices enable visualization of both color and fluorescence images with the same quality as the large and expensive stationary operative microscopes. The wearable FLoupe device allows for a greater range of movement, less obstruction, and faster/easier operation. Thus, it reduces surgery time and is more easily adapted to the surgical environment than unwieldy neurosurgical operative microscopes.

Keywords: fluorescence guided surgery, malignant glioma, neurosurgical operative microscope, wearable fluorescence imaging device

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Authors: Bimali Sanjeevani Weerakoon, Toshiaki Osuga, Takehisa Konishi

Abstract:

Magnetic Resonance Imaging Contrast Agents (MRI-CM) are significant in the clinical and biological imaging as they have the ability to alter the normal tissue contrast, thereby affecting the signal intensity to enhance the visibility and detectability of images. Superparamagnetic Iron Oxide (SPIO) nanoparticles, coated with dextran or carboxydextran are currently available for clinical MR imaging of the liver. Most SPIO contrast agents are T2 shortening agents and Resovist (Ferucarbotran) is one of a clinically tested, organ-specific, SPIO agent which has a low molecular carboxydextran coating. The enhancement effect of Resovist depends on its relaxivity which in turn depends on factors like magnetic field strength, concentrations, nanoparticle properties, pH and temperature. Therefore, this study was conducted to investigate the impact of field strength and different contrast concentrations on enhancement effects of Resovist. The study explored the MRI signal intensity of Resovist in the physiological range of plasma from T2-weighted spin echo sequence at three magnetic field strengths: 0.47 T (r1=15, r2=101), 1.5 T (r1=7.4, r2=95), and 3 T (r1=3.3, r2=160) and the range of contrast concentrations by a mathematical simulation. Relaxivities of r1 and r2 (L mmol-1 Sec-1) were obtained from a previous study and the selected concentrations were 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0, and 3.0 mmol/L. T2-weighted images were simulated using TR/TE ratio as 2000 ms /100 ms. According to the reference literature, with increasing magnetic field strengths, the r1 relaxivity tends to decrease while the r2 did not show any systematic relationship with the selected field strengths. In parallel, this study results revealed that the signal intensity of Resovist at lower concentrations tends to increase than the higher concentrations. The highest reported signal intensity was observed in the low field strength of 0.47 T. The maximum signal intensities for 0.47 T, 1.5 T and 3 T were found at the concentration levels of 0.05, 0.06 and 0.05 mmol/L, respectively. Furthermore, it was revealed that, the concentrations higher than the above, the signal intensity was decreased exponentially. An inverse relationship can be found between the field strength and T2 relaxation time, whereas, the field strength was increased, T2 relaxation time was decreased accordingly. However, resulted T2 relaxation time was not significantly different between 0.47 T and 1.5 T in this study. Moreover, a linear correlation of transverse relaxation rates (1/T2, s–1) with the concentrations of Resovist can be observed. According to these results, it can conclude that the concentration of SPIO nanoparticle contrast agents and the field strengths of MRI are two important parameters which can affect the signal intensity of T2-weighted SE sequence. Therefore, when MR imaging those two parameters should be considered prudently.

Keywords: Concentration, resovist, field strength, relaxivity, signal intensity

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Authors: Salem El-Tohami Ashoor

Abstract:

Here we show that the reduction of [Cr(ArN(CH2)3NAr)2Cl2] (1) where (Ar = 2,6-Pri2C6H3) and in presence of NaCp (2) (Cp= C5H5 = cyclopentadien), with a center coordination η5 interaction between Cp as co-ligand and chromium metal center, this was optimization by using density functional theory (DFT) and then was comparing with experimental data, also other possibility of Cp interacted with ion metal were tested like η1 ,η2 ,η3 and η4 under optimization system. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP ( Becke)( Lee–Yang–Parr ) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [Cr(ArN(CH2)3NAr)2(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of chromium cyclopentadienyl. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Chromium(III) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Abhishek Sharma, Amit Gupta, Manish Singhal

Abstract:

Background: The management of patients with penetrating neck injuries in the prehospital setting and in the emergency department has evolved with regard to the use of multidetector computed tomographic (MDCT) imaging. Hence, there is a shift in the management of neck injuries from mandatory exploration in certain anatomic areas to more conservative approach using imaging and so-called “no zone approach”. Objective: To study the no zone approach in the management of penetrating neck injury using routine imaging in all stable patients. Methods: 137 patients with penetrating neck injury attending emergency department of level 1 trauma centre at AIIMS between 2008–2014 were retrospectively analysed. All hemodynamically stable patients were evaluated using CT scanning. Results: Stab injury is most common (55.91%) mode of pni in civilian population followed by gunshot(18.33%). The majority of patients could be managed with imaging and close observation. 39 patients (28.46%) required operative intervention. The most common indication for operative intervention was vascular followed by airway injury manifesting as hemodynamic destabilisation.There was no statistical difference between the zonal distribution of injuries in patients managed conservatively and those taken to OR. Conclusions: Study shows that patients with penetrating neck trauma who are haemodynamically stable and exhibit no “hard signs” of vascular injury or airway injury may be evaluated initially by MDCT imaging even when platysma violation is present. “No Zone” policy may be superior to traditional zone wise management.

Keywords: penetrating neck injury, zone approach, CT scanning, multidetector computed tomographic (MDCT)

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Authors: Kalthoum Riahi, Max T. Rietberg, Javier Perez y Perez, Corné Dijkstra, Bennie ten Haken, Lejla Alic

Abstract:

Magnetic nanoparticles (MNPs) are widely used to facilitate magnetic particle imaging (MPI) which has the potential to become the leading diagnostic instrument for biomedical imaging. This comparative study assesses the effects of changing iron content and excitation frequency on point-spread function (PSF) representing the effect of magnetization reversal. PSF is quantified by features of interest for MPI: i.e., drive field amplitude and full-width-at-half-maximum (FWHM). A superparamagnetic quantifier (SPaQ) is used to assess differential magnetic susceptibility of two commercially available MNPs: Synomag®-D50 and Synomag®-D70. For both MNPs, the signal output depends on increase in drive field frequency and amount of iron-oxide, which might be hampering the sensitivity of MPI systems that perform on higher frequencies. Nevertheless, there is a clear potential of Synomag®-D for a stable MPI resolution, especially in case of 70 nm version, that is independent of either drive field frequency or amount of iron-oxide.

Keywords: magnetic nanoparticles, MNPs, differential magnetic susceptibility, DMS, magnetic particle imaging, MPI, magnetic relaxation, Synomag®-D

Procedia PDF Downloads 109