Search results for: inverse docking

Authors: Eliska Smidova, Petr Kabele

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This paper describes non-linear finite element simulation of laminated veneer lumber (LVL) under tensile and shear loads that induce cracking along fibers. For this purpose, we use 2D homogeneous orthotropic constitutive model of tensile and shear fracture in timber that has been recently developed and implemented into ATENA® finite element software by the authors. The model captures (i) material orthotropy for small deformations in both linear and non-linear range, (ii) elastic behavior until anisotropic failure criterion is fulfilled, (iii) inelastic behavior after failure criterion is satisfied, (iv) different post-failure response for cracks along and across the grain, (v) unloading/reloading behavior. The post-cracking response is treated by fixed smeared crack model where Reinhardt-Hordijk function is used. The model requires in total 14 input parameters that can be obtained from standard tests, off-axis test results and iterative numerical simulation of compact tension (CT) or compact tension-shear (CTS) test. New engineered timber composites, such as laminated veneer lumber (LVL), offer improved structural parameters compared to sawn timber. LVL is manufactured by laminating 3 mm thick wood veneers aligned in one direction using water-resistant adhesives (e.g. polyurethane). Thus, 3 main grain directions, namely longitudinal (L), tangential (T), and radial (R), are observed within the layered LVL product. The core of this work consists in 3 numerical simulations of experiments where Radiata Pine LVL and Yellow Poplar LVL were involved. The first analysis deals with calibration and validation of the proposed model through off-axis tensile test (at a load-grain angle of 0°, 10°, 45°, and 90°) and CTS test (at a load-grain angle of 30°, 60°, and 90°), both of which were conducted for Radiata Pine LVL. The second finite element simulation reproduces load-CMOD curve of compact tension (CT) test of Yellow Poplar with the aim of obtaining cohesive law parameters to be used as an input in the third finite element analysis. That is four point bending test of small-size arch of 780 mm span that is made of Yellow Poplar LVL. The arch is designed with a through crack between two middle layers in the crown. Curved laminated beams are exposed to high radial tensile stress compared to timber strength in radial tension in the crown area. Let us note that in this case the latter parameter stands for tensile strength in perpendicular direction with respect to the grain. Standard tests deliver most of the relevant input data whereas traction-separation law for crack along the grain can be obtained partly by inverse analysis of compact tension (CT) test or compact tension-shear test (CTS). The initial crack was modeled as a narrow gap separating two layers in the middle the arch crown. Calculated load-deflection curve is in good agreement with the experimental ones. Furthermore, crack pattern given by numerical simulation coincides with the most important observed crack paths.

Keywords: compact tension (CT) test, compact tension shear (CTS) test, fixed smeared crack model, four point bending test, laminated arch, laminated veneer lumber LVL, off-axis test, orthotropic elasticity, orthotropic fracture criterion, Radiata Pine LVL, traction-separation law, yellow poplar LVL, 2D constitutive model

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Authors: Gabrielle Robertson, Matthew Downs, Joseph Dagher

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Iron deposition in the brain has been linked with a host of neurological disorders such as Alzheimer’s, Parkinson’s, and Multiple Sclerosis. While some treatment options exist, there are no objective measurement tools that allow for the monitoring of iron levels in the brain in vivo. An emerging Magnetic Resonance Imaging (MRI) method has been recently proposed to deduce iron concentration through quantitative measurement of magnetic susceptibility. This is a multi-step process that involves repeated modeling of physical processes via approximate numerical solutions. For example, the last two steps of this Quantitative Susceptibility Mapping (QSM) method involve I) mapping magnetic field into magnetic susceptibility and II) mapping magnetic susceptibility into iron concentration. Process I involves solving an ill-posed inverse problem by using regularization via injection of prior belief. The end result from Process II highly depends on the model used to describe the molecular content of each voxel (type of iron, water fraction, etc.) Due to these factors, the accuracy and repeatability of QSM have been an active area of research in the MRI and medical imaging community. This work aims to estimate iron concentration in the brain via a single step. A synthetic numerical model of the human head was created by automatically and manually segmenting the human head on a high-resolution grid (640x640x640, 0.4mm³) yielding detailed structures such as microvasculature and subcortical regions as well as bone, soft tissue, Cerebral Spinal Fluid, sinuses, arteries, and eyes. Each segmented region was then assigned tissue properties such as relaxation rates, proton density, electromagnetic tissue properties and iron concentration. These tissue property values were randomly selected from a Probability Distribution Function derived from a thorough literature review. In addition to having unique tissue property values, different synthetic head realizations also possess unique structural geometry created by morphing the boundary regions of different areas within normal physical constraints. This model of the human brain is then used to create synthetic MRI measurements. This is repeated thousands of times, for different head shapes, volume, tissue properties and noise realizations. Collectively, this constitutes a training-set that is similar to in vivo data, but larger than datasets available from clinical measurements. This 3D convolutional U-Net neural network architecture was used to train data-driven Deep Learning models to solve for iron concentrations from raw MRI measurements. The performance was then tested on both synthetic data not used in training as well as real in vivo data. Results showed that the model trained on synthetic MRI measurements is able to directly learn iron concentrations in areas of interest more effectively than other existing QSM reconstruction methods. For comparison, models trained on random geometric shapes (as proposed in the Deep QSM method) are less effective than models trained on realistic synthetic head models. Such an accurate method for the quantitative measurement of iron deposits in the brain would be of important value in clinical studies aiming to understand the role of iron in neurological disease.

Keywords: magnetic resonance imaging, MRI, iron deposition, machine learning, quantitative susceptibility mapping

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Authors: Chung-Ming Lo, Chung-Chien Lee

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In many countries, the lifetime prevalence of shoulder pain is up to 70%. In America, the health care system spends 7 billion per year about the healthy issues of shoulder pain. With respect to the origin, up to 70% of shoulder pain is attributed to rotator cuff lesions This study proposed a computer-aided diagnosis (CAD) system to assist radiologists classifying rotator cuff lesions with less operator dependence. Quantitative features were extracted from the shoulder ultrasound images acquired using an ALOKA alpha-6 US scanner (Hitachi-Aloka Medical, Tokyo, Japan) with linear array probe (scan width: 36mm) ranging from 5 to 13 MHz. During examination, the postures of the examined patients are standard sitting position and are followed by the regular routine. After acquisition, the shoulder US images were drawn out from the scanner and stored as 8-bit images with pixel value ranging from 0 to 255. Upon the sonographic appearance, the boundary of each lesion was delineated by a physician to indicate the specific pattern for analysis. The three lesion categories for classification were composed of 20 cases of tendon inflammation, 18 cases of calcific tendonitis, and 18 cases of supraspinatus tear. For each lesion, second-order statistics were quantified in the feature extraction. The second-order statistics were the texture features describing the correlations between adjacent pixels in a lesion. Because echogenicity patterns were expressed via grey-scale. The grey-scale co-occurrence matrixes with four angles of adjacent pixels were used. The texture metrics included the mean and standard deviation of energy, entropy, correlation, inverse different moment, inertia, cluster shade, cluster prominence, and Haralick correlation. Then, the quantitative features were combined in a multinomial logistic regression classifier to generate a prediction model of rotator cuff lesions. Multinomial logistic regression classifier is widely used in the classification of more than two categories such as the three lesion types used in this study. In the classifier, backward elimination was used to select a feature subset which is the most relevant. They were selected from the trained classifier with the lowest error rate. Leave-one-out cross-validation was used to evaluate the performance of the classifier. Each case was left out of the total cases and used to test the trained result by the remaining cases. According to the physician’s assessment, the performance of the proposed CAD system was shown by the accuracy. As a result, the proposed system achieved an accuracy of 86%. A CAD system based on the statistical texture features to interpret echogenicity values in shoulder musculoskeletal ultrasound was established to generate a prediction model for rotator cuff lesions. Clinically, it is difficult to distinguish some kinds of rotator cuff lesions, especially partial-thickness tear of rotator cuff. The shoulder orthopaedic surgeon and musculoskeletal radiologist reported greater diagnostic test accuracy than general radiologist or ultrasonographers based on the available literature. Consequently, the proposed CAD system which was developed according to the experiment of the shoulder orthopaedic surgeon can provide reliable suggestions to general radiologists or ultrasonographers. More quantitative features related to the specific patterns of different lesion types would be investigated in the further study to improve the prediction.

Keywords: shoulder ultrasound, rotator cuff lesions, texture, computer-aided diagnosis

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Authors: H. K. Esfahani, B. Datta

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Groundwater is one of the most important natural resources in many parts of the world; however it is widely polluted due to human activities. Currently, effective and reliable groundwater management and remediation strategies are obtained using characterization of groundwater pollution sources, where the measured data in monitoring locations are utilized to estimate the unknown pollutant source location and magnitude. However, accurately identifying characteristics of contaminant sources is a challenging task due to uncertainties in terms of predicting source flux injection, hydro-geological and geo-chemical parameters, and the concentration field measurement. Reactive transport of chemical species in contaminated groundwater systems, especially with multiple species, is a complex and highly non-linear geochemical process. Although sufficient concentration measurement data is essential to accurately identify sources characteristics, available data are often sparse and limited in quantity. Therefore, this inverse problem-solving method for characterizing unknown groundwater pollution sources is often considered ill-posed, complex and non- unique. Different methods have been utilized to identify pollution sources; however, the linked simulation-optimization approach is one effective method to obtain acceptable results under uncertainties in complex real life scenarios. With this approach, the numerical flow and contaminant transport simulation models are externally linked to an optimization algorithm, with the objective of minimizing the difference between measured concentration and estimated pollutant concentration at observation locations. Concentration measurement data are very important to accurately estimate pollution source properties; therefore, optimal design of the monitoring network is essential to gather adequate measured data at desired times and locations. Due to budget and physical restrictions, an efficient and effective approach for groundwater pollutant source characterization is to design an optimal monitoring network, especially when only inadequate and arbitrary concentration measurement data are initially available. In this approach, preliminary concentration observation data are utilized for preliminary source location, magnitude and duration of source activity identification, and these results are utilized for monitoring network design. Further, feedback information from the monitoring network is used as inputs for sequential monitoring network design, to improve the identification of unknown source characteristics. To design an effective monitoring network of observation wells, optimization and interpolation techniques are used. A simulation model should be utilized to accurately describe the aquifer properties in terms of hydro-geochemical parameters and boundary conditions. However, the simulation of the transport processes becomes complex when the pollutants are chemically reactive. Three dimensional transient flow and reactive contaminant transport process is considered. The proposed methodology uses HYDROGEOCHEM 5.0 (HGCH) as the simulation model for flow and transport processes with chemically multiple reactive species. Adaptive Simulated Annealing (ASA) is used as optimization algorithm in linked simulation-optimization methodology to identify the unknown source characteristics. Therefore, the aim of the present study is to develop a methodology to optimally design an effective monitoring network for pollution source characterization with reactive species in polluted aquifers. The performance of the developed methodology will be evaluated for an illustrative polluted aquifer sites, for example an abandoned mine site in Queensland, Australia.

Keywords: monitoring network design, source characterization, chemical reactive transport process, contaminated mine site

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Authors: Simone Dell'Agnello

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There are laser retroreflectors on the Moon and no laser retroreflectors on Mars. Here we describe the design, construction, qualification and imminent deployment of next-generation, optimized laser retroreflectors on the Moon and on Mars (where they will be the first ones). These instruments are positioned by time-of-flight measurements of short laser pulses, the so-called 'laser ranging' technique. Data analysis is carried out with PEP, the Planetary Ephemeris Program of CfA (Center for Astrophysics). Since 1969 Lunar Laser Ranging (LLR) to Apollo/Lunokhod laser retro-reflector (CCR) arrays supplied accurate tests of General Relativity (GR) and new gravitational physics: possible changes of the gravitational constant Gdot/G, weak and strong equivalence principle, gravitational self-energy (Parametrized Post Newtonian parameter beta), geodetic precession, inverse-square force-law; it can also constraint gravitomagnetism. Some of these measurements also allowed for testing extensions of GR, including spacetime torsion, non-minimally coupled gravity. LLR has also provides significant information on the composition of the deep interior of the Moon. In fact, LLR first provided evidence of the existence of a fluid component of the deep lunar interior. In 1969 CCR arrays contributed a negligible fraction of the LLR error budget. Since laser station range accuracy improved by more than a factor 100, now, because of lunar librations, current array dominate the error due to their multi-CCR geometry. We developed a next-generation, single, large CCR, MoonLIGHT (Moon Laser Instrumentation for General relativity high-accuracy test) unaffected by librations that supports an improvement of the space segment of the LLR accuracy up to a factor 100. INFN also developed INRRI (INstrument for landing-Roving laser Retro-reflector Investigations), a microreflector to be laser-ranged by orbiters. Their performance is characterized at the SCF_Lab (Satellite/lunar laser ranging Characterization Facilities Lab, INFN-LNF, Frascati, Italy) for their deployment on the lunar surface or the cislunar space. They will be used to accurately position landers, rovers, hoppers, orbiters of Google Lunar X Prize and space agency missions, thanks to LLR observations from station of the International Laser Ranging Service in the USA, in France and in Italy. INRRI was launched in 2016 with the ESA mission ExoMars (Exobiology on Mars) EDM (Entry, descent and landing Demonstration Module), deployed on the Schiaparelli lander and is proposed for the ExoMars 2020 Rover. Based on an agreement between NASA and ASI (Agenzia Spaziale Italiana), another microreflector, LaRRI (Laser Retro-Reflector for InSight), was delivered to JPL (Jet Propulsion Laboratory) and integrated on NASA’s InSight Mars Lander in August 2017 (launch scheduled in May 2018). Another microreflector, LaRA (Laser Retro-reflector Array) will be delivered to JPL for deployment on the NASA Mars 2020 Rover. The first lunar landing opportunities will be from early 2018 (with TeamIndus) to late 2018 with commercial missions, followed by opportunities with space agency missions, including the proposed deployment of MoonLIGHT and INRRI on NASA’s Resource Prospectors and its evolutions. In conclusion, we will extend significantly the CCR Lunar Geophysical Network and populate the Mars Geophysical Network. These networks will enable very significantly improved tests of GR.

Keywords: general relativity, laser retroreflectors, lunar laser ranging, Mars geodesy

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Authors: Dmitriy Berillo, Areej K. A. Al-Jwaid, Jonathan L. Caplin, Andrew Cundy, Irina Savina

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Chlorophenols (CPs) are used as a precursor in the production of higher CPs and dyestuffs, and as a preservative. Contamination by CPs of the ground water is located in the range from 0.15-100mg/L. The EU has set maximum concentration limits for pesticides and their degradation products of 0.1μg/L and 0.5μg/L, respectively. People working in industries which produce textiles, leather products, domestic preservatives, and petrochemicals are most heavily exposed to CPs. The International Agency for Research on Cancers categorized CPs as potential human carcinogens. Existing multistep water purification processes for CPs such as hydrogenation, ion exchange, liquid-liquid extraction, adsorption by activated carbon, forward and inverse osmosis, electrolysis, sonochemistry, UV irradiation, and chemical oxidation are not always cost effective and can cause the formation of even more toxic or mutagenic derivatives. Bioremediation of CPs derivatives utilizing microorganisms results in 60 to 100% decontamination efficiency and the process is more environmentally-friendly compared with existing physico-chemical methods. Microorganisms immobilized onto a substrate show many advantages over free bacteria systems, such as higher biomass density, higher metabolic activity, and resistance to toxic chemicals. They also enable continuous operation, avoiding the requirement for biomass-liquid separation. The immobilized bacteria can be reused several times, which opens the opportunity for developing cost-effective processes for wastewater treatment. In this study, we develop a bioremediation system for CPs based on macroporous materials, which can be efficiently used for wastewater treatment. Conditions for the preparation of the macroporous material from specific bacterial strains (Pseudomonas mendocina and Rhodococus koreensis) were optimized. The concentration of bacterial cells was kept constant; the difference was only the type of cross-linking agents used e.g. glutaraldehyde, novel polymers, which were utilized at concentrations of 0.5 to 1.5%. SEM images and rheology analysis of the material indicated a monolithic macroporous structure. Phenol was chosen as a model system to optimize the function of the cryogel material and to estimate its enzymatic activity, since it is relatively less toxic and harmful compared to CPs. Several types of macroporous systems comprising live bacteria were prepared. The viability of the cross-linked bacteria was checked using Live/Dead BacLight kit and Laser Scanning Confocal Microscopy, which revealed the presence of viable bacteria with the novel cross-linkers, whereas the control material cross-linked with glutaraldehyde(GA), contained mostly dead cells. The bioreactors based on bacteria were used for phenol degradation in batch mode at an initial concentration of 50mg/L, pH 7.5 and a temperature of 30°C. Bacterial strains cross-linked with GA showed insignificant ability to degrade phenol and for one week only, but a combination of cross-linking agents illustrated higher stability, viability and the possibility to be reused for at least five weeks. Furthermore, conditions for CPs degradation will be optimized, and the chlorophenol degradation rates will be compared to those for phenol. This is a cutting-edge bioremediation approach, which allows the purification of waste water from sustainable compounds without a separation step to remove free planktonic bacteria. Acknowledgments: Dr. Berillo D. A. is very grateful to Individual Fellowship Marie Curie Program for funding of the research.

Keywords: bioremediation, cross-linking agents, cross-linked microbial cell, chlorophenol degradation

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Authors: Mohammadjavad Sotoudeheian, Navid Farahmandian

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Cardiac hypertrophy arises in response to persistent increases in hemodynamic loads. In comparison, diabetic cardiomyopathy is defined by an abnormal myocardial changes without other cardiac-related risk factors. Pathological cardiac hypertrophy and myocardial remodeling are hallmarks of cardiovascular diseases and are risk factors for heart failure. The transcription factor forkhead box class O (FOXOs) can protect heart tissue by hostile oxidative stress and stimulating apoptosis and autophagy. FOXO proteins, as sensitive elements and mediators in response to environmental changes, have been revealed to prevent and inverse cardiac hypertrophy. FOXOs are inhibited by insulin and are critical mediators of insulin action. Insulin deficiency and uncontrolled diabetes lead to a catabolic state. FOXO1 acts downstream of the insulin-dependent pathways, which are dysregulated in diabetes. It regulates cardiomyocyte hypertrophy downstream of IGF1R/PI3K/Akt activation, which are critical regulators of cardiac hypertrophy. The complex network of signaling pathways comprising insulin/IGF-1 signaling, AMPK, JNK, and Sirtuins regulate the development of cardiovascular dysfunction by modulating the activity of FOXOs. Insulin receptors and IGF1R act via the PI3k/Akt and the MAPK/ERK pathways. Activation of Akt in response to insulin or IGF-1 induces phosphorylation of FOXOs. Increased protein synthesis induced by activation of the IGF-I/Akt/mTOR signaling pathway leads to hypertrophy. This pathway and the myostatin/Smad pathway are potent negative muscle development regulators. In cardiac muscle, insulin receptor substrates (IRS)-1 or IRS-2 activates the Akt signaling pathway and inactivate FOXO1. Under metabolic stress, p38 MAPK promotes degradation of IRS-1 and IRS-2 in cardiac myocytes and activates FOXO1, leading to cardiomyopathy. Sirt1 and FOXO1 interaction play an essential role in starvation-induced autophagy in cardiac metabolism. Inhibition of Angiotensin-II induced cardiomyocyte hypertrophy is associated with reduced FOXO1 acetylation and activation of Sirt1. The NF-κB, ERK, and FOXOs are de-acetylated by SIRT1. De-acetylation of FOXO1 induces the expression of genes involved in autophagy and stimulates autophagy flux. Therefore, under metabolic stress, FOXO1 can cause diabetic cardiomyopathy. The overexpression of FOXO1 leads to decreased cardiomyocyte size and suppresses cardiac hypertrophy through inhibition of the calcineurin–NFAT pathway. Diabetes mellitus is associated with elevation of O-GlcNAcylation. Some of its binding partners regulate the substrate selectivity of O-GlcNAc transferase (OGT). O-GlcNAcylation of essential contractile proteins may inhibit protein-protein interactions, reduce calcium sensitivity, and modulate contractile function. Uridine diphosphate (UDP)-GlcNAc is the obligatory substrate of OGT, which catalyzes a reversible post-translational protein modification. The increase of O-GlcNAcylation is accompanied by impaired cardiac hypertrophy in diabetic hearts. Inhibition of O-GlcNAcylation blocks activation of ERK1/2 and hypertrophic growth. O-GlcNAc modification on NFAT is required for its translocation from the cytosol to the nucleus, where NFAT stimulates the transcription of various hypertrophic genes. Inhibition of O-GlcNAcylation dampens NFAT-induced cardiac hypertrophic growth. Transcriptional activity of FOXO1 is enriched by improved O-GlcNAcylation upon high glucose stimulation or OGT overexpression. In diabetic conditions, the modification of FOXO1 by O-GlcNAc is promoted in cardiac troponin I and myosin light chain 2. Therefore targeting O-GlcNAcylation represents a potential therapeutic option to prevent hypertrophy in the diabetic heart.

Keywords: diabetes, cardiac hypertrophy, O-GlcNAcylation, FOXO1, Akt, PI3K, AMPK, insulin

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