Search results for: atom probe tomography

Authors: Lamla Thungathaa, Conrad Mahlasea, Lisa Ngcebesha

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1,4-Diamino-3,6-dinitropyrazolo[4,3-c]pyrazole (LLM-119) and its structural isomer 3,6-dinitropyrazolo[3,4-c]pyrazole-1,4(6H)-diamine were designed by structural reorientation of the fused pyrazole rings and their respective substituents (-NO2 and -NH2). Structural reorientation involves structural rearrangement which result in different structural isomers, employing this approach, six structural isomers of LLM-119 were achieved. The effect of structural reorientation (isomerisation and derivatives) on the enthalpy of formation, detonation properties, impact sensitivity, and density of these molecules is studied Computationally. The computational method used are detailed in the document and they yielded results that are close to the literature values with a relative error of 2% for enthalpy of formation, 2% for density, 0.05% for detonation velocity, and 4% for detonation pressure. The correlation of the structural reorientation to the calculated thermochemical and detonation properties of the molecules indicated that molecules with a -NO2 group attached to a Carbon atom and -NH2 connected to a Nitrogen atom maximize the enthalpy of formation and detonation velocity. The joining of pyrazole molecules has less effect on these parameters. It was seen that density and detonation pressure improved when both –NO2 or -NH2 functional groups were on the same side of the molecular structure. The structural reorientation gave rise to 3,4-dinitropyrazolo[3,4-c]pyrazole-1,6-diamine which exhibited optimal density and detonation performance compared to other molecules.

Keywords: LLM-119, fused rings, azole, structural isomers, detonation properties

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Authors: Paweł Konieczka, Lech Raczyński, Wojciech Wiślicki, Oleksandr Fedoruk, Konrad Klimaszewski, Przemysław Kopka, Wojciech Krzemień, Roman Shopa, Jakub Baran, Aurélien Coussat, Neha Chug, Catalina Curceanu, Eryk Czerwiński, Meysam Dadgar, Kamil Dulski, Aleksander Gajos, Beatrix C. Hiesmayr, Krzysztof Kacprzak, łukasz Kapłon, Grzegorz Korcyl, Tomasz Kozik, Deepak Kumar, Szymon Niedźwiecki, Dominik Panek, Szymon Parzych, Elena Pérez Del Río, Sushil Sharma, Shivani Shivani, Magdalena Skurzok, Ewa łucja Stępień, Faranak Tayefi, Paweł Moskal

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This paper develops the transformation of non-image data into 2-dimensional matrices, as a preparation stage for classification based on convolutional neural networks (CNNs). In positron emission tomography (PET) studies, CNN may be applied directly to the reconstructed distribution of radioactive tracers injected into the patient's body, as a pattern recognition tool. Nonetheless, much PET data still exists in non-image format and this fact opens a question on whether they can be used for training CNN. In this contribution, the main focus of this paper is the problem of processing vectors with a small number of features in comparison to the number of pixels in the output images. The proposed methodology was applied to the classification of PET coincidence events.

Keywords: convolutional neural network, kernel principal component analysis, medical imaging, positron emission tomography

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Authors: Eva Slaninova, Diana Cernayova, Zuzana Sedrlova, Katerina Mrazova, Petr Sedlacek, Jana Nebesarova, Stanislav Obruca

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Cyanobacteria are gram-negative prokaryotes belonging to a group of photosynthetic bacteria. In comparison with heterotrophic microorganisms, cyanobacteria utilize atmospheric nitrogen and carbon dioxide without any additional substrates. This ability of these microorganisms could be employed in biotechnology for the production of bioplastics, concretely polyhydroxyalkanoates (PHAs) which are primarily accumulated as a storage material in cells in the form of intracellular granules. In this study, there two cyanobacterial cultures from genera Synechocystis were used, namely Synechocystic sp. PCC 6803 and Synechocystis salina CCALA 192. There were optimized and used several various approaches, including microscopic techniques such as cryo-scanning electron microscopy (Cryo-SEM) and transmission electron microscopy (TEM), and fluorescence lifetime imaging microscopy using Nile red as a fluorescent probe (FLIM). Due to these instrumental techniques, the morphology of intracellular space and surface of cells were characterized. The next group of methods which were employed was spectroscopic techniques such as UV-Vis spectroscopy measured in two modes (turbidimetry and integration sphere) and Fourier transform infrared spectroscopy (FTIR). All these diverse techniques were used for the detection and characterization of pigments (chlorophylls, carotenoids, phycocyanin, etc.) and PHAs, in our case poly (3-hydroxybutyrate) (P3HB). To verify results, gas chromatography (GC) was employed concretely for the determination of the amount of P3HB in biomass. Cyanobacteria were also characterized as polyhydroxybutyrate producers by flow cytometer, which could count cells and at the same time distinguish cells including P3HB and without due to fluorescent probe called BODIPY and live/dead fluorescent probe SYTO Blue. Based on results, P3HB content in cyanobacteria cells was determined, as also the overall fitness of the cells. Acknowledgment: Funding: This study was partly funded by the projectGA19-29651L of the Czech Science Foundation (GACR) and partly funded by the Austrian Science Fund (FWF), project I 4082-B25.

Keywords: cyanobacteria, fluorescent probe, microscopic techniques, poly(3hydroxybutyrate), spectroscopy, chromatography

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Authors: H. El-Messiry, M. El-Zainy, D. Abdelkhalek

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Cone-beam computed tomography (CBCT) provides high-quality 3-dimensional images of dental structures because of its high spatial resolution. The study of dental morphology is important in research as it provides information about diversities within a population. Many studies have shown different shapes and numbers of roots canals among different races, especially in molars. The aim of this study was to determine the morphology of root canals of mandibular first and third molars in a sample of Egyptian population using CBCT scanning. Fifty mandibular first Molars (M1) and fifty mandibular third (M3) extracted molars were collected. Thick rectangular molds were made using pink wax to hold the samples. Molars were embedded in the wax mold by aligning them in rows leaving arbitrary 0.5cm space between them. The molds with the samples in were submitted for CBCT scan. The number and morphology of root canals were assessed and classified according to Vertucci's classification. The mesial and the distal roots were examined separately. Finally, data was analyzed using Fisher exact test. The most prevalent mesial root canal frequency in M1 was type IV (60%) and type II (40 %), while M3 showed prevalence of type I (40%) and II (40%). Distal root canal morphology showed prevalence of type I in both M1 (66%) and M3 (86%). So, it can be concluded that CBCT scanning provides supplemental information about the root canal configurations of mandibular molars in a sample of Egyptian population. This study may help clinicians in the root canal treatment of mandibular molars.

Keywords: cone beam computed tomography, mandibular first molar, mandibular third molar, root canal morphology

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Authors: Tieling Xing, Jinqiu Yang, Guoqiang Chen

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It is environmentally friendly to use horseradish peroxidase (HRP) instead of the traditional transition metal catalyst for the catalyst of atom transfer radical polymerization (ATRP). Silk fabrics were successfully grafted with hydroxyl-containing acrylate monomer to improve its crease resistance by HRP-catalyzed ATRP method. Taking grafting yield as the evaluation index, single factor tests revealed that the optimum grafting reaction condition was as follow: monomer mass fraction 120-210%(o.w.f), HRP concentration 360-480U/mL, molar ratio of HRP to NaAsc 1:150, reaction temperature 50-60℃, reaction time 24h. Raman spectra showed hydroxyl-containing acrylate monomer were successfully grafted on silk fabrics. SEM figures indicated the surface of grafted silk became rougher, and graft copolymer was distributed evenly on the surface of silk fiber. The crease-resistant recovery property of grafted silk fabric was greatly improved, especially in wet crease recovery angle. The result showed hydroxyl-containing acrylate monomer can be successfully grafted onto silk fabric based on HRP-catalyzed ATRP method.

Keywords: atom transfer radical polymerization, catalysis, horseradish peroxidase, hydroxyl-containing acrylate monomer

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Authors: Keerthilatha Pai, Sakshi Kamra

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Objectives: Determining the position of the mandibular canal prior to implant placement and surgeries of the posterior mandible are important to avoid the nerve injury. The visibility of the mandibular canal varies according to the imaging modality. Although panoramic radiography is the most common, slowly cone beam computed tomography is replacing it. This study was conducted with an aim to determine and compare the visibility of superior and inferior borders of the mandibular canal in digital panoramic radiograph, reformatted panoramic radiograph and cross-sectional images of cone beam computed tomography. Study design: digital panoramic, reformatted panoramic radiograph and cross sectional CBCT images of 25 human mandibles were evaluated for the visibility of the superior and inferior borders of the mandibular canal according to a 5 point scoring criteria. Also, the canal was evaluated as completely visible, partially visible and not visible. The mean scores and visibility percentage of all the imaging modalities were determined and compared. The interobserver and intraobserver agreement in the visualization of the superior and inferior borders of the mandibular canal were determined. Results: The superior and inferior borders of the mandibular canal were completely visible in 47% of the samples in digital panoramic, 63% in reformatted panoramic and 75.6% in CBCT cross-sectional images. The mandibular canal was invisible in 24% of samples in digital panoramic, 19% in reformatted panoramic and 2% in cross-sectional CBCT images. Maximum visibility was seen in Zone 5 and least visibility in Zone 1. On comparison of all the imaging modalities, CBCT cross-sectional images showed better visibility of superior border in Zones 2,3,4,6 and inferior border in Zones 2,3,4,6. The difference was statistically significant. Conclusion: CBCT cross-sectional images were much superior in the visualization of the mandibular canal in comparison to reformatted and digital panoramic radiographs. The inferior border was better visualized in comparison to the superior border in digital panoramic imaging. The mandibular canal was maximumly visible in posterior one-third region of the mandible and the visibility decreased towards the mental foramen.

Keywords: cone beam computed tomography, mandibular canal, reformatted panoramic radiograph, visualization

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Authors: Mojtaba Mirmontazemi, Habibollah Dadgar

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Bone is the most common metastasis site in some advanced malignancies, such as prostate and breast cancer. Bone metastasis generally indicates fewer prognostic factors in these patients. Different radiological and molecular imaging modalities are used for detecting bone lesions. Molecular imaging including computed tomography, magnetic resonance imaging, planar bone scintigraphy, single-photon emission tomography, and positron emission tomography as noninvasive visualization of the biological occurrences has the potential to exact examination, characterization, risk stratification and comprehension of human being diseases. Also, it is potent to straightly visualize targets, specify clearly cellular pathways and provide precision medicine for molecular targeted therapies. These advantages contribute implement personalized treatment for each patient. Currently, NaF PET/CT has significantly replaced standard bone scintigraphy for the detection of bone metastases. On one hand, 68Ga-PSMA PET/CT has gained high attention for accurate staging of primary prostate cancer and restaging after biochemical recurrence. On the other hand, FDG PET/CT is not commonly used in osseous metastases of prostate and breast cancer as well as its usage is limited to staging patients with aggressive primary tumors or localizing the site of disease. In this article, we examine current studies about FDG, NaF, and PSMA PET/CT images in bone metastases diagnostic utility and assess response to treatment in patients with breast and prostate cancer.

Keywords: skeletal metastases, fluorodeoxyglucose, sodium fluoride, molecular imaging, precision medicine, prostate cancer (68Ga-PSMA-11)

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Authors: Bummo Ahn

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Palpation is widely used to measure soft tissue firmness or stiffness in the living condition in order to apply detection, diagnosis, and treatment of tumors, scar tissue, abnormal muscle tone, or muscle spasticity. Since these methods are subjective and depend on the proficiency level, it is concluded that there are other diagnoses depending on the condition of the experts and the results are not objective. The mechanical property obtained by using the elasticity of the tissue is important to calculate a predictive variable for monitoring abnormal tissues. If the mechanical load such as reaction force on the foot increases in the same region under the same conditions, the mechanical property of the tissue is changed. Therefore, objective diagnosis is possible not only for experts but also for patients using this quantitative information. Furthermore, the portable system also allows non-experts to easily diagnose at home, not in hospitals or institutions. In this paper, we introduce a portable palpation system that can be used to measure the mechanical properties of human tissue, which can be applied to monitor diabetic foot ulceration patients with measuring the mechanical property change of foot tissue. The system was designed to be smaller and portable in comparison with the conventional palpation systems. It is consists of the probe, the force sensor, linear actuator, micro control unit, the display module, battery, and housing. Using this system, we performed validation experiments by applying different palpations (3 and 5 mm) to soft tissue (silicone rubber) and measured reaction forces. In addition, we estimated the elastic moduli of the soft tissue against different palpations and compare the estimated elastic moduli that show similar value even if the palpation depths are different.

Keywords: palpation probe, portable, diabetic foot ulceration, monitoring, mechanical property

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Authors: Perumalla Naveen Kumar

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Global Positioning System (GPS) is used for civilian and military user positioning applications. The accuracy of GPS is degrading mainly because of ionospheric error. It is very important to analyze the effects of ionosphere on the performance of satellite systems especially in the low latitude regions. These variations depend on the Total Electron Content (TEC) in the ionosphere. To investigate the variations in the atmosphere, a mini satellite known as YOUTHSAT is launched by India. This is the outcome of the collaboration between India and USSR. One of the YOUTHSAT Indian payload is RaBIT (Radio Beacon for Ionospheric Tomography). In this paper, YOUTHSAT RaBIT payload data for the three typical days of 2011 are considered. The analysis is carried out for four Indian stations. The variations of Slant TEC, elevation angle and azimuth angles are analyzed with respect to local time. The obtained results are encouraging.

Keywords: Global Positioning System (GPS), Total Electron Content (TEC), YOUTHSAT, Radio Beacon for Ionospheric Tomography (RaBIT)

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Authors: Kenan Morani, Esra Kaya Ayana

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This study aimed to develop a novel pipeline for COVID-19 detection using a large and rigorously annotated database of computed tomography (CT) images. The pipeline consists of UNet-based segmentation, lung extraction, and a classification part, with the addition of optional slice removal techniques following the segmentation part. In this work, a batch normalization was added to the original UNet model to produce lighter and better localization, which is then utilized to build a full pipeline for COVID-19 diagnosis. To evaluate the effectiveness of the proposed pipeline, various segmentation methods were compared in terms of their performance and complexity. The proposed segmentation method with batch normalization outperformed traditional methods and other alternatives, resulting in a higher dice score on a publicly available dataset. Moreover, at the slice level, the proposed pipeline demonstrated high validation accuracy, indicating the efficiency of predicting 2D slices. At the patient level, the full approach exhibited higher validation accuracy and macro F1 score compared to other alternatives, surpassing the baseline. The classification component of the proposed pipeline utilizes a convolutional neural network (CNN) to make final diagnosis decisions. The COV19-CT-DB dataset, which contains a large number of CT scans with various types of slices and rigorously annotated for COVID-19 detection, was utilized for classification. The proposed pipeline outperformed many other alternatives on the dataset.

Keywords: classification, computed tomography, lung extraction, macro F1 score, UNet segmentation

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Authors: A. Delimitsou, C. Gouedard, E. Konstanta, A. Koletis, S. Patera, E. Manou, K. Spaho, S. Murray

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Background: There remains a lack of International Standard Control Reference materials for Next Generation Sequencing-based approaches or device calibration. We have designed and validated dsDNA biomimetic reference materials for targeted such approaches incorporating proprietary motifs (patent pending) for device/test calibration. They enable internal single-sample calibration, alleviating sample comparisons to pooled historical population-based data assembly or statistical modelling approaches. We have validated such an approach for BRCA Copy Number Variation analytics using iQRS™-CNVSUITE versus Mixed Ligation-dependent Probe Amplification. Methods: Standard BRCA Copy Number Variation analysis was compared between mixed ligation-dependent probe amplification and next generation sequencing using a cohort of 198 breast/ovarian cancer patients. Next generation sequencing based copy number variation analysis of samples spiked with iQRS™ dsDNA biomimetics were analysed using proprietary CNVSUITE software. Mixed ligation-dependent probe amplification analyses were performed on an ABI-3130 Sequencer and analysed with Coffalyser software. Results: Concordance of BRCA – copy number variation events for mixed ligation-dependent probe amplification and CNVSUITE indicated an overall sensitivity of 99.88% and specificity of 100% for iQRS™-CNVSUITE. The negative predictive value of iQRS-CNVSUITE™ for BRCA was 100%, allowing for accurate exclusion of any event. The positive predictive value was 99.88%, with no discrepancy between mixed ligation-dependent probe amplification and iQRS™-CNVSUITE. For device calibration purposes, precision was 100%, spiking of patient DNA demonstrated linearity to 1% (±2.5%) and range from 100 copies. Traditional training was supplemented by predefining the calibrator to sample cut-off (lock-down) for amplicon gain or loss based upon a relative ratio threshold, following training of iQRS™-CNVSUITE using spiked iQRS™ calibrator and control mocks. BRCA copy number variation analysis using iQRS™-CNVSUITE™ was successfully validated and ISO15189 accredited and now enters CE-IVD performance evaluation. Conclusions: The inclusion of a reference control competitor (iQRS™ dsDNA mimetic) to next generation sequencing-based sequencing offers a more robust sample-independent approach for the assessment of copy number variation events compared to mixed ligation-dependent probe amplification. The approach simplifies data analyses, improves independent sample data analyses, and allows for direct comparison to an internal reference control for sample-specific quantification. Our iQRS™ biomimetic reference materials allow for single sample copy number variation analytics and further decentralisation of diagnostics to single patient sample assessment.

Keywords: validation, diagnostics, oncology, copy number variation, reference material, calibration

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Authors: A. Monika, Manu Sharma, Hong Boo Lee, Richa Dhingra, Neelima Dhingra

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Nuclear factor-κappa B serve as a molecular lynchpin that links persistent infections and chronic inflammation to increased cancer risk. Inflammation has been recognized as a hallmark and cause of cancer. Natural products present a privileged source of inspiration for chemical probe and drug design. Herbal remedies were the first medicines used by humans due to the many pharmacologically active secondary metabolites produced by plants. Some of the metabolites like Lantadene (pentacyclic triterpenoids) from the weed Lantana camara has been known to inhibit cell division and showed anti-antitumor potential. The C-3 aromatic esters of lantadenes were synthesized, characterized and evaluated for cytotoxicity and inhibitory potential against Tumor necrosis factor alpha-induced activation of Nuclear factor-κappa B in lung cancer cell line A549. The 3-methoxybenzoyloxy substituted lead analogue inhibited kinase activity of the inhibitor of nuclear factor-kappa B kinase in a single-digit micromolar concentration. At the same time, the lead compound showed promising cytotoxicity against A549 lung cancer cells with IC50 ( half maximal inhibitory concentration) of 0.98l µM. Further, molecular docking of 3-methoxybenzoyloxy substituted analogue against Inhibitor of nuclear factor-kappa B kinase (Protein data bank ID: 3QA8) showed hydrogen bonding interaction involving oxygen atom of 3-methoxybenzoyloxy with the Arginine-31 and Glutamine-110. Encouraging results indicate the Lantadene’s potential to be developed as anticancer agents.

Keywords: anticancer, lantadenes, pentacyclic triterpenoids, weed

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Authors: Almaz R. Gazizov, Sergey S. Kharintsev, Myakzyum Kh. Salakhov

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This work deals with background signal suppression in tip-enhanced near-field optical microscopy (TENOM). The background appears because an optical signal is detected not only from the subwavelength area beneath the tip but also from a wider diffraction-limited area of laser’s waist that might contain another substance. The background can be reduced by using a taper probe with a grating on its lateral surface where an external illumination causes surface plasmon excitation. It requires the grating with parameters perfectly matched with a given incident light for effective light coupling. This work is devoted to an analysis of the light-grating coupling and a quest of grating parameters to enhance a near-field light beneath the tip apex. The aim of this work is to find the figure of merit of plasmon excitation depending on grating period and location of grating in respect to the apex. In our consideration the metallic grating on the lateral surface of the tapered plasmonic probe is illuminated by a plane wave, the electric field is perpendicular to the sample surface. Theoretical model of efficiency of plasmon excitation and propagation toward the apex is tested by fdtd-based numerical simulation. An electric field of the incident light is enhanced on the grating by every single slit due to lightning rod effect. Hence, grating causes amplitude and phase modulation of the incident field in various ways depending on geometry and material of grating. The phase-modulating grating on the probe is a sort of metasurface that provides manipulation by spatial frequencies of the incident field. The spatial frequency-dependent electric field is found from the angular spectrum decomposition. If one of the components satisfies the phase-matching condition then one can readily calculate the figure of merit of plasmon excitation, defined as a ratio of the intensities of the surface mode and the incident light. During propagation towards the apex, surface wave undergoes losses in probe material, radiation losses, and mode compression. There is an optimal location of the grating in respect to the apex. One finds the value by matching quadratic law of mode compression and the exponential law of light extinction. Finally, performed theoretical analysis and numerical simulations of plasmon excitation demonstrate that various surface waves can be effectively excited by using the overtones of a period of the grating or by phase modulation of the incident field. The gratings with such periods are easy to fabricate. Tapered probe with the grating effectively enhances and localizes the incident field at the sample.

Keywords: angular spectrum decomposition, efficiency, grating, surface plasmon, taper nanoantenna

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Authors: S. Guruprasad, M. Z. Kurian, H. N. Suma

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Medical imaging modalities are becoming life saving components. These modalities are very much essential to doctors for proper diagnosis, treatment planning and follow up. Some modalities provide anatomical information such as Computed Tomography (CT), Magnetic Resonance Imaging (MRI), X-rays and some provides only functional information such as Positron Emission Tomography (PET). Therefore, single modality image does not give complete information. This paper presents the fusion of structural information in CT and functional information present in PET image. This fused image is very much essential in detecting the stages and location of abnormalities and in particular very much needed in oncology for improved diagnosis and treatment. We have implemented and compared image fusion techniques like pyramid, wavelet, and principal components fusion methods along with hybrid method of DWT and PCA. The performances of the algorithms are evaluated quantitatively and qualitatively. The system is implemented and tested by using MATLAB software. Based on the MSE, PSNR and ENTROPY analysis, PCA and DWT-PCA methods showed best results over all experiments.

Keywords: image fusion, pyramid, wavelets, principal component analysis

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Authors: Joanna Maj

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Body machine interfaces (BMIs) afford users a non-invasive way coordinate movement. Vibrotactile stimulation has been incorporated into BMIs to allow feedback in real-time and guide movement control to benefit patients with cognitive deficits, such as stroke survivors. To advance research in this area, we examined vibrational discrimination thresholds at four body locations to determine suitable application sites for future multi-channel BMIs using vibration cues to guide movement planning and control. Twelve healthy adults had a pair of small vibrators (tactors) affixed to the skin at each location: forearm, shoulders, torso, and knee. A "standard" stimulus (186 Hz; 750 ms) and "probe" stimuli (11 levels ranging from 100 Hz to 235 Hz; 750 ms) were delivered. Probe and test stimulus pairs could occur sequentially or simultaneously (timing). Participants verbally indicated which stimulus felt more intense. Stimulus order was counterbalanced across tactors and body locations. Probabilities that probe stimuli felt more intense than the standard stimulus were computed and fit with a cumulative Gaussian function; the discrimination threshold was defined as one standard deviation of the underlying distribution. Threshold magnitudes depended on stimulus timing and location. Discrimination thresholds were better for stimuli applied sequentially vs. simultaneously at the torso as well as the knee. Thresholds were small (better) and relatively insensitive to timing differences for vibrations applied at the shoulder. BMI applications requiring multiple channels of simultaneous vibrotactile stimulation should therefore consider the shoulder as a deployment site for a vibrotactile BMI interface.

Keywords: electromyography, electromyogram, neuromuscular disorders, biomedical instrumentation, controls engineering

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Authors: P. Sathyathas, H. M. I. S. W. Herath, T. Amalraj, U. J. M. A. L. Jayasinghe

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Over two thirds of medical radiation can now be attributed to Computed Tomography (CT). There is little information on amount of radiation received from multiphase CT scan of abdomen- pelvic region in clinical practice. We sought to estimate the radiation dose and associated exposure parameters in the multiphase abdomen - pelvic scan of Multideteror Computed Tomography (MDCT) studies in clinical practice. This was a retrospective cross sectional studies describing radiation dose associated with main exposure parameters in diagnostic multiphase abdomen - pelvic scans performed on 152 consecutive patients by two different sixteen slice CT scanners. Patient information, exposure parameters of CTDI (volume), DLP, kVp, mAs and pitch were recorded for every phases of abdomen- a pelvic study from dose report of MDCT scanners (MDCTs). Age of patients range from 14 years to 87 years in both MDCT scanners. Overall CTDI (volume) median was 63.8 (±10.4) mGy for a multiphase abdominal-pelvic scan with scanner A while it was 35.4 (±15.6) mGy for scanner B. Patients' effective dose for multiphase abdomen - pelvic CT scan range from 8.2 mSv to 58 mSv. Median effective dose for patients, who underwent multiphase abdomen- pelvis scan with scanner A and B were 38.5 (± 8.2) mSv and 21.3 (± 8.6) mSv respectively. Median value of exposure parameters of mAs, kVp and pitch, were 150 (±29.7), 130 (±15.3) and 1.3 (±0.1) respectively in scanner A. In scanner B; they were 60 (±14.5), 120 and 1. The median effective dose for patients between multiphase abdomen-pelvic scan of both MDCT, a significant different (P<0.05) was observed. Multiphase abdomen – pelvic scan of clinical study shows significant different of effective dose with reference level of phantom studies (8-14mSv) and it depends on the type of vendors.

Keywords: abdomen-pelvic region, computed tomography, exposure parameters, radiation dose

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Authors: Rupesh K. Mishra, Gaëlle Catanante, Akhtar Hayat, Jean-Louis Marty

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Ochratoxins (OTA) are secondary metabolites present in a wide variety of food stuff. They are dangerous by-products mainly produced by several species of storage fungi including the Aspergillus and Penicillium genera. OTA is known to have nephrotoxic, immunotoxic, teratogenic and carcinogenic effects. Thus, needs a special attention for a highly sensitive and selective detection system that can quantify these organic toxins in various matrices such as cocoa beans. This work presents a folding based aptasensors by employing an aptamer conjugated redox probe (methylene blue) specifically designed for OTA. The aptamers were covalently attached to the screen printed carbon electrodes using diazonium grafting. Upon sensing the OTA, it binds with the immobilized aptamer on the electrode surface, which induces the conformational changes of the aptamer, consequently increased in the signal. This conformational change of the aptamer before and after biosensing of target OTA could produce the distinguishable electrochemical signal. The obtained limit of detection was 0.01 ng/ml for OTA samples with recovery of up to 88% in contaminated cocoa samples.

Keywords: ochratoxin A, cocoa, DNA aptamer, labelled probe

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Authors: Jaco Oosthuizen, Nerina C. Van Der Merwe

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The National Health Laboratory Services in Bloemfontien has been the diagnostic testing facility for 1830 patients for familial breast cancer since 1997. From the cohort, 540 were comprehensively screened using High-Resolution Melting Analysis or Next Generation Sequencing for the presence of point mutations and/or indels. Approximately 90% of these patients stil remain undiagnosed as they are BRCA1/2 negative. Multiplex ligation-dependent probe amplification was initially added to screen for copy number variation detection, but with the introduction of next generation sequencing in 2017, was substituted and is currently used as a confirmation assay. The aim was to investigate the viability of utilizing internationally designed copy number variation detection assays based on mostly European/Caucasian genomic data for use within a South African context. The multiplex ligation-dependent probe amplification technique is based on the hybridization and subsequent ligation of multiple probes to a targeted exon. The ligated probes are amplified using conventional polymerase chain reaction, followed by fragment analysis by means of capillary electrophoresis. The experimental design of the assay was performed according to the guidelines of MRC-Holland. For BRCA1 (P002-D1) and BRCA2 (P045-B3), both multiplex assays were validated, and results were confirmed using a secondary probe set for each gene. The next generation sequencing technique is based on target amplification via multiplex polymerase chain reaction, where after the amplicons are sequenced parallel on a semiconductor chip. Amplified read counts are visualized as relative copy numbers to determine the median of the absolute values of all pairwise differences. Various experimental parameters such as DNA quality, quantity, and signal intensity or read depth were verified using positive and negative patients previously tested internationally. DNA quality and quantity proved to be the critical factors during the verification of both assays. The quantity influenced the relative copy number frequency directly whereas the quality of the DNA and its salt concentration influenced denaturation consistency in both assays. Multiplex ligation-dependent probe amplification produced false positives due to ligation failure when ligation was inhibited due to a variant present within the ligation site. Next generation sequencing produced false positives due to read dropout when primer sequences did not meet optimal multiplex binding kinetics due to population variants in the primer binding site. The analytical sensitivity and specificity for the South African population have been proven. Verification resulted in repeatable reactions with regards to the detection of relative copy number differences. Both multiplex ligation-dependent probe amplification and next generation sequencing multiplex panels need to be optimized to accommodate South African polymorphisms present within the genetically diverse ethnic groups to reduce the false copy number variation positive rate and increase performance efficiency.

Keywords: familial breast cancer, multiplex ligation-dependent probe amplification, next generation sequencing, South Africa

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Authors: Harish Rajak, Preeti Patel

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HDAC inhibitors can reactivate gene expression and inhibit the growth and survival of cancer cells. The 3D-QSAR and Pharmacophore modeling studies were performed to identify important pharmacophoric features and correlate 3D-chemical structure with biological activity. The pharmacophore hypotheses were developed using e-pharmacophore script and phase module. Pharmacophore hypothesis represents the 3D arrangement of molecular features necessary for activity. A series of 55 compounds with well-assigned HDAC inhibitory activity was used for 3D-QSAR model development. Best 3D-QSAR model, which is a five PLS factor model with good statistics and predictive ability, acquired Q2 (0.7293), R2 (0.9811) and standard deviation (0.0952). Molecular docking were performed using Histone Deacetylase protein (PDB ID: 1t69) and prepared series of hydroxamic acid based HDAC inhibitors. Docking study of compound 43 show significant binding interactions Ser 276 and oxygen atom of dioxine cap region, Gly 151 and amino group and Asp 267 with carboxyl group of CONHOH, which are essential for anticancer activity. On docking, most of the compounds exhibited better glide score values between -8 to -10.5. We have established structure activity correlation using docking, energetic based pharmacophore modelling, pharmacophore and atom based 3D QSAR model. The results of these studies were further used for the design and testing of new HDAC analogs.

Keywords: Docking, e-pharmacophore, HDACIs, QSAR, Suberoylanilidehydroxamic acid.

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Authors: A. Abbas, X. Tridon, J. Michelon

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In the electronic or in the photovoltaic industries, components are made from wafers which are stacks of thin film layers of a few nanometers to serval micrometers thickness. Early evaluation of the bounding quality between different layers of a wafer is one of the challenges of these industries to avoid dysfunction of their final products. Traditional pump-probe experiments, which have been developed in the 70’s, give a partial solution to this problematic but with a non-negligible drawback. In fact, on one hand, these setups can generate and detect ultra-high ultrasounds frequencies which can be used to evaluate the adhesion quality of wafer layers. But, on the other hand, because of the quiet long acquisition time they need to perform one measurement, these setups remain shut in punctual measurement to evaluate global sample quality. This last point can lead to bad interpretation of the sample quality parameters, especially in the case of inhomogeneous samples. Asynchronous Optical Sampling (ASOPS) systems can perform sample characterization with picosecond acoustics up to 106 times faster than traditional pump-probe setups. This last point allows picosecond ultrasonic to unlock the acoustic imaging field at the nanometric scale to detect inhomogeneities regarding sample mechanical properties. This fact will be illustrated by presenting an image of the measured acoustical reflection coefficients obtained by mapping, with an ASOPS setup, a 255nm thin-film tungsten layer deposited on a silicone substrate. Interpretation of the coefficient reflection in terms of bounding quality adhesion will also be exposed. Origin of zones which exhibit good and bad quality bounding will be discussed.

Keywords: adhesion, picosecond ultrasonics, pump-probe, thin film

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Authors: Madeleine Anthonisen, M. Hussain Sangji, G. Monserratt Lopez-Ayon, Margaret Magdesian, Peter Grutter

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Advances in micromanipulation techniques and real-time particle tracking with nanometer resolution have enabled biological force measurements at scales relevant to neuron mechanics. An approach to precisely control and maneuver neurite-tethered polystyrene beads is presented. Analogous to an Atomic Force Microscope (AFM), this multi-purpose platform is a force sensor with imaging acquisition and manipulation capabilities. A mechanical probe composed of a micropipette with its tip fixed to a functionalized bead is used to incite the formation of a neurite in a sample of rat hippocampal neurons while simultaneously measuring the tension in said neurite as the sample is pulled away from the beaded tip. With optical imaging methods, a force resolution of 12 pN is achieved. Moreover, the advantages of this technique over alternatives such as AFM, namely ease of manipulation which ultimately allows higher throughput investigation of the mechanical properties of neurons, is demonstrated.

Keywords: axonal growth, axonal guidance, force probe, pipette micromanipulation, neurite tension, neuron mechanics

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Authors: T. Ewetumo, K. D. Adedayo, Festus Ben

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Knowledge of the thermal properties of foods is of fundamental importance in the food industry to establish the design of processing equipment. However, for tropical fruit juice, there is very little information in literature, seriously hampering processing procedures. This research work describes the development of an instrument for automated thermal conductivity and thermal diffusivity measurement of tropical fruit juice using a transient thermal probe technique based on line heat principle. The system consists of two thermocouple sensors, constant current source, heater, thermocouple amplifier, microcontroller, microSD card shield and intelligent liquid crystal. A fixed distance of 6.50mm was maintained between the two probes. When heat is applied, the temperature rise at the heater probe measured with time at time interval of 4s for 240s. The measuring element conforms as closely as possible to an infinite line source of heat in an infinite fluid. Under these conditions, thermal conductivity and thermal diffusivity are simultaneously measured, with thermal conductivity determined from the slope of a plot of the temperature rise of the heating element against the logarithm of time while thermal diffusivity was determined from the time it took the sample to attain a peak temperature and the time duration over a fixed diffusivity distance. A constant current source was designed to apply a power input of 16.33W/m to the probe throughout the experiment. The thermal probe was interfaced with a digital display and data logger by using an application program written in C++. Calibration of the instrument was done by determining the thermal properties of distilled water. Error due to convection was avoided by adding 1.5% agar to the water. The instrument has been used for measurement of thermal properties of banana, orange and watermelon. Thermal conductivity values of 0.593, 0.598, 0.586 W/m^o C and thermal diffusivity values of 1.053 ×〖10〗^(-7), 1.086 ×〖10〗^(-7), and 0.959 ×〖10〗^(-7) 〖m/s〗^2 were obtained for banana, orange and water melon respectively. Measured values were stored in a microSD card. The instrument performed very well as it measured the thermal conductivity and thermal diffusivity of the tropical fruit juice samples with statistical analysis (ANOVA) showing no significant difference (p>0.05) between the literature standards and estimated averages of each sample investigated with the developed instrument.

Keywords: thermal conductivity, thermal diffusivity, tropical fruit juice, diffusion equation

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Authors: Ali Pour Yazdanpanah, Farideh Foroozandeh Shahraki, Emma Regentova

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The reconstruction from sparse-view projections is one of important problems in computed tomography (CT) limited by the availability or feasibility of obtaining of a large number of projections. Traditionally, convex regularizers have been exploited to improve the reconstruction quality in sparse-view CT, and the convex constraint in those problems leads to an easy optimization process. However, convex regularizers often result in a biased approximation and inaccurate reconstruction in CT problems. Here, we present a nonconvex, Lipschitz continuous and non-smooth regularization model. The CT reconstruction is formulated as a nonconvex constrained L1 − L2 minimization problem and solved through a difference of convex algorithm and alternating direction of multiplier method which generates a better result than L0 or L1 regularizers in the CT reconstruction. We compare our method with previously reported high performance methods which use convex regularizers such as TV, wavelet, curvelet, and curvelet+TV (CTV) on the test phantom images. The results show that there are benefits in using the nonconvex regularizer in the sparse-view CT reconstruction.

Keywords: computed tomography, non-convex, sparse-view reconstruction, L1-L2 minimization, difference of convex functions

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Authors: Viyango Pandian, Kumaresh Athiyappan

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Pelvic congestion Syndrome (PCS) is usually seen in multiparous women who give history of chronic dull-aching pelvic pain. We report a case of a 17 year old unmarried female, who presented with acute onset of chronic dull-aching abdominal pain in the left iliac fossa, which particularly increased during menstruation and was finally diagnosed to be pelvic congestion syndrome. On ultrasonography, multiple tortuous and dilated veins were observed in the left adnexa. Both ovaries appeared normal in size, volume and echotexture. Computed tomography (CT) angiography was performed to precisely delineate the venous pathway and to assess any associated abnormality; which showed a dilated and tortuous left ovarian vein with an anomalous course around the left kidney and draining into the left renal vein. Clinical parameters and hormonal levels were within normal limits. This is a rare case of anomalous course of left ovarian vein associated with pelvic congestion syndrome.

Keywords: anomalous course of ovarian vein, computed tomography, pelvic congestion syndrome, ultrasonography

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Authors: Ajit Brindhaban

Abstract:

Background and Purpose: Computed Tomography (CT) scans have become the largest source of radiation in radiological imaging. The purpose of this study was to compare the quality of pediatric Computed Tomography (CT) images reconstructed using Filtered Back Projection (FBP) with images reconstructed using different strengths of Iterative Reconstruction (IR) technique, and to perform a feasibility study to assess the use of IR techniques as a dose reduction tool. Materials and Methods: An anthropomorphic phantom representing a 5-year old child was scanned, in two stages, using a Siemens Somatom CT unit. In stage one, scans of the head, chest and abdomen were performed using standard protocols recommended by the scanner manufacturer. Images were reconstructed using FBP and 5 different strengths of IR. Contrast-to-Noise Ratios (CNR) were calculated from average CT number and its standard deviation measured in regions of interest created in the lungs, bone, and soft tissues regions of the phantom. Paired t-test and the one-way ANOVA were used to compare the CNR from FBP images with IR images, at p = 0.05 level. The lowest strength value of IR that produced the highest CNR was identified. In the second stage, scans of the head was performed with decreased mA(s) values relative to the increase in CNR compared to the standard FBP protocol. CNR values were compared in this stage using Paired t-test at p = 0.05 level. Results: Images reconstructed using IR technique had higher CNR values (p < 0.01.) in all regions compared to the FBP images, at all strengths of IR. The CNR increased with increasing IR strength of up to 3, in the head and chest images. Increases beyond this strength were insignificant. In abdomen images, CNR continued to increase up to strength 5. The results also indicated that, IR techniques improve CNR by a up to factor of 1.5. Based on the CNR values at strength 3 of IR images and CNR values of FBP images, a reduction in mA(s) of about 20% was identified. The images of the head acquired at 20% reduced mA(s) and reconstructed using IR at strength 3, had similar CNR as FBP images at standard mA(s). In the head scans of the phantom used in this study, it was demonstrated that similar CNR can be achieved even when the mA(s) is reduced by about 20% if IR technique with strength of 3 is used for reconstruction. Conclusions: The IR technique produced better image quality at all strengths of IR in comparison to FBP. IR technique can provide approximately 20% dose reduction in pediatric head CT while maintaining the same image quality as FBP technique.

Keywords: filtered back projection, image quality, iterative reconstruction, pediatric computed tomography 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: H. Djaaboube, I. Loucif, Y. Bouachiba, R. Aouati, A. Maameri, A. Taabouche, A. Bouabellou

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Thin films of pure and barium-doped zinc oxide (ZnO) were prepared using a spray pyrolysis process. The films were deposited on glass substrates at 450°C. The different samples are characterized by X-ray diffraction (XRD) and UV-Vis spectroscopy. X-ray diffraction patterns reveal the formation of a single ZnO Wurtzite structure and the good crystallinity of the films. The substitution of Ba ions influences the texture of the layers and makes the (002) plane a preferential growth plane. At concentrations below 6% Ba, the hexagonal structure of ZnO undergoes compressive stresses due to barium ions which have a radius twice of the Zn ions. This result leads to the decrees of a and c parameters and, therefore, the volume of the unit cell. This result is confirmed by the decrease in the number of crystallites and the increase in the size of the crystallites. At concentrations above 6%, barium substitutes the zinc atom and modifies the structural parameters of the thin layers. The bandgap of ZnO films decreased with increasing doping; this decrease is probably due to the 4d orbitals of the Ba atom due to the sp-d spin-exchange interactions between the band electrons and the localized d-electrons of the substituted Ba ion. Although, the Urbache energy undergoes an increase which implies the creation of energy levels below the conduction band and decreases the band gap width. The photocatalytic activity of ZnO doped 9% Ba was evaluated by the photodegradation of methylene blue under UV irradiation.

Keywords: barium, doping, photodegradation, spray pyrolysis, ZnO

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Authors: Sajid Abas, Jon Pyo Hong, Jung-Ryun Le, Seungryong Cho

Abstract:

Computed tomography and laminography are heavily investigated in a compressive sensing based image reconstruction framework to reduce the dose to the patients as well as to the radiosensitive devices such as multilayer microelectronic circuit boards. Nowadays researchers are actively working on optimizing the compressive sensing based iterative image reconstruction algorithm to obtain better quality images. However, the effects of the sampled data’s properties on reconstructed the image’s quality, particularly in an insufficient sampled data conditions have not been explored in computed laminography. In this paper, we investigated the effects of two data properties i.e. sampling density and data incoherence on the reconstructed image obtained by conventional computed laminography and a recently proposed method called spherical sinusoidal scanning scheme. We have found that in a compressive sensing based image reconstruction framework, the image quality mainly depends upon the data incoherence when the data is uniformly sampled.

Keywords: computed tomography, computed laminography, compressive sending, low-dose

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Authors: Jonathan Galvan-Colin, Ariel Valladares, Renela Valladares, Alexander Valladares

Abstract:

Both porous materials and bulk metallic glasses have been studied due to their potential applications and their exceptional physical and chemical properties. However, each material presents certain drawbacks which have been thought to be overcome by generating bulk metallic glass foams (BMGF). Although some experimental reports have been performed on multicomponent BMGF, still no ab initio works have been published, as far as we know. We present an approach based on the expanding lattice (EL) method to generate binary amorphous nanoporous Cu64Zr36. Starting from two different configurations: a 108-atom crystalline cubic supercell (cCu64Zr36) and a 108-atom amorphous supercell (aCu64Zr36), both with an initial density of 8.06 g/cm3, we applied EL method to halve the density and to get 50% of porosity. After the lattice expansion the supercells were subject to ab initio molecular dynamics for 500 steps at constant room temperature. Then, the samples were geometry-optimized and characterized with the pair and radial distribution functions, bond-angle distributions and a coordination number analysis. We found that pores appeared along specific spatial directions different from one to another and that they differed in size and form as well, which we think is related to the initial structure. Due to the lack of experimental counterparts our results should be considered predictive and further studies are needed in order to handle a larger number of atoms and its implication on pore topology.

Keywords: ab initio molecular dynamics, bulk mettalic glass, porous alloy

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Authors: Paola Causin, Andrea Aspri, Alessandro Benfenati

Abstract:

Diffuse Optical Tomography (DOT) is an emergent medical imaging technique which employs NIR light to estimate the spatial distribution of optical coefficients in biological tissues for diagnostic purposes, in a noninvasive and non-ionizing manner. DOT reconstruction is a severely ill-conditioned problem due to prevalent scattering of light in the tissue. In this contribution, we present our research in adopting hybrid knowledgedriven/data-driven approaches which exploit the existence of well assessed physical models and build upon them neural networks integrating the availability of data. Namely, since in this context regularization procedures are mandatory to obtain a reasonable reconstruction [1], we explore the use of neural networks as tools to include prior information on the solution. 2. Materials and Methods The idea underlying our approach is to leverage neural networks to solve PDE-constrained inverse problems of the form 𝒒 ∗ = 𝒂𝒓𝒈 𝒎𝒊𝒏𝒒 𝐃(𝒚, 𝒚̃), (1) where D is a loss function which typically contains a discrepancy measure (or data fidelity) term plus other possible ad-hoc designed terms enforcing specific constraints. In the context of inverse problems like (1), one seeks the optimal set of physical parameters q, given the set of observations y. Moreover, 𝑦̃ is the computable approximation of y, which may be as well obtained from a neural network but also in a classic way via the resolution of a PDE with given input coefficients (forward problem, Fig.1 box ). Due to the severe ill conditioning of the reconstruction problem, we adopt a two-fold approach: i) we restrict the solutions (optical coefficients) to lie in a lower-dimensional subspace generated by auto-decoder type networks. This procedure forms priors of the solution (Fig.1 box ); ii) we use regularization procedures of type 𝒒̂ ∗ = 𝒂𝒓𝒈𝒎𝒊𝒏𝒒 𝐃(𝒚, 𝒚̃)+ 𝑹(𝒒), where 𝑹(𝒒) is a regularization functional depending on regularization parameters which can be fixed a-priori or learned via a neural network in a data-driven modality. To further improve the generalizability of the proposed framework, we also infuse physics knowledge via soft penalty constraints (Fig.1 box ) in the overall optimization procedure (Fig.1 box ). 3. Discussion and Conclusion DOT reconstruction is severely hindered by ill-conditioning. The combined use of data-driven and knowledgedriven elements is beneficial and allows to obtain improved results, especially with a restricted dataset and in presence of variable sources of noise.

Keywords: inverse problem in tomography, deep learning, diffuse optical tomography, regularization

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