Search results for: boundary layer thickness

Authors: Annalakshmi G., Sakthivel Murugan S.

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This paper presents a local directional encoded derivative binary pattern (LDEDBP) feature extraction method that can be applied for the classification of submarine coral reef images. The classification of coral reef images using texture features is difficult due to the dissimilarities in class samples. In coral reef image classification, texture features are extracted using the proposed method called local directional encoded derivative binary pattern (LDEDBP). The proposed approach extracts the complete structural arrangement of the local region using local binary batten (LBP) and also extracts the edge information using local directional pattern (LDP) from the edge response available in a particular region, thereby achieving extra discriminative feature value. Typically the LDP extracts the edge details in all eight directions. The process of integrating edge responses along with the local binary pattern achieves a more robust texture descriptor than the other descriptors used in texture feature extraction methods. Finally, the proposed technique is applied to an extreme learning machine (ELM) method with a meta-heuristic algorithm known as weighted distance grey wolf optimizer (GWO) to optimize the input weight and biases of single-hidden-layer feed-forward neural networks (SLFN). In the empirical results, ELM-WDGWO demonstrated their better performance in terms of accuracy on all coral datasets, namely RSMAS, EILAT, EILAT2, and MLC, compared with other state-of-the-art algorithms. The proposed method achieves the highest overall classification accuracy of 94% compared to the other state of art methods.

Keywords: feature extraction, local directional pattern, ELM classifier, GWO optimization

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Authors: Sunday Oladele, Joseph Oluwagbeja Simeon

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Subsurface exploration, integrating methods of geotechnics and geophysics, of a planned construction site in the coastal city of Lagos, Nigeria has been carried out with the aim of characterizing the soil properties and their implication for the proposed infrastructural development. Six Standard Penetration Tests (SPT), fourteen Dutch Cone Penetrometer Tests (DCPT) and 2D Electrical Resistivity Imaging employing Dipole-dipole and Pole-dipole arrays were implemented on the site. The topsoil (0 - 4m) consists of highly compacted sandy lateritic clay(10 to 5595Ωm) to 1.25m in some parts and dense sand in other parts to 5.50m depth. This topsoil was characterized as a material of very high shear strength (≤ 150kg/m2) and allowable bearing pressure value of 54kN/m2 to 85kN/m2 and a safety factor of 2.5. Soft amorphous peat/peaty clay (0.1 to 11.4Ωm), 3-6m thick, underlays the lateritic clay to about 18m depth. Grey, medium dense to very dense sand (0.37 to 2387Ωm) with occasional gravels underlies the peaty clay down to 30m depth. Within this layer, the freshwater bearing zones are characterized by high resistivity response (83 to 2387Ωm), while the clayey sand/saline water intruded sand produced subdued resistivity output (0.37 to 40Ωm). The overall ground-bearing pressure for the proposed structure would be 225kN/m2. Bored/cast-in-place pile at 18.00m depth with any of these diameters and respective safe working loads 600mm/1,140KN, 800mm/2,010KN and 1000mm/3,150KN is recommended for the proposed multi-story structure.

Keywords: subsurface exploration, Geotechnical properties, resistivity imaging, pile

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Authors: Jithin S. Kumar, Ramesh Kannan Kandasami

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Geomaterials are generally porous in nature due to the presence of discrete particles and interconnected voids. The porosity present in these geomaterials play a critical role in many engineering applications such as CO2 sequestration, well bore strengthening, enhanced oil and hydrocarbon recovery, hydraulic fracturing, and subsurface waste storage. These applications involves solid-fluid interactions, which govern the changes in the porosity which in turn affect the permeability and stiffness of the medium. Injecting fluid into the geomaterials results in permeation which exhibits small or negligible deformation of the soil skeleton followed by cavity expansion/ fingering/ fracturing (different forms of instabilities) due to the large deformation especially when the flow rate is greater than the ability of the medium to permeate the fluid. The complexity of this problem increases as the geomaterial behaves like a solid and fluid under certain conditions. Thus it is important to understand this multiphysics problem where in addition to the permeation, the elastic-plastic deformation of the soil skeleton plays a vital role during fluid injection. The phenomenon of permeation and cavity expansion in porous medium has been studied independently through extensive experimental and analytical/ numerical models. The analytical models generally use Darcy's/ diffusion equations to capture the fluid flow during permeation while elastic-plastic (Mohr-Coulomb and Modified Cam-Clay) models were used to predict the solid deformations. Hitherto, the research generally focused on modelling cavity expansion without considering the effect of injected fluid coming into the medium. Very few studies have considered the effect of injected fluid on the deformation of soil skeleton. However, the porosity changes during the fluid injection and coupled elastic-plastic deformation are not clearly understood. In this study, the phenomenon of permeation and instabilities such as cavity and finger/ fracture formation will be quantified extensively by performing experiments using a novel experimental setup in addition to utilizing image processing techniques. This experimental study will describe the fluid flow and soil deformation characteristics under different boundary conditions. Further, a well refined coupled semi-analytical model will be developed to capture the physics involved in quantifying the deformation behaviour of geomaterial during fluid injection.

Keywords: solid-fluid interaction, permeation, poroelasticity, plasticity, continuum model

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Authors: Ping Ren, Mao Wen, Kan Zhang, Weitao Zheng

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The improvement of comprehensive properties including hardness, toughness, wear, and corrosion resistance in the transition metal carbides/nitrides TMCN films, especially avoiding the trade-off between hardness and toughness, is strongly required to adapt to various applications. Although incorporating ductile metal DM phase into the TMCN via thermally-induced phase separation has been emerged as an effective approach to toughen TMCN-based films, the DM is just limited to some soft ductile metal (i.e. Cu, Ag, Au immiscibility with the TMCN. Moreover, hardness is highly sensitive to soft DM content and can be significantly worsened. Hence, a novel preparation method should be attempted to broaden the DM selection and assemble much more ordered nanocomposite structure for improving the comprehensive properties. Here, we provide a new strategy, by activating solid-state dewetting during layered deposition, to accomplish the self-assembly of ordered TaC@Ta core-shell-like nanocomposite film consisting of TaC nanocrystalline encapsulated with thin pseudocrystal Ta tissue. That results in the superhard (~45.1 GPa) dominated by Orowan strengthening mechanism and high toughness attributed to indenter-induced phase transformation from the pseudocrystal to body-centered cubic Ta, together with the drastically enhanced wear and corrosion resistance. Furthermore, very thin pseudocrystal Ta encapsulated layer (~1.5 nm) in the TaC@Ta core-shell-like structure helps for promoting the formation of lubricious TaOₓ Magnéli phase during sliding, thereby further dropping the coefficient of friction. Apparently, solid-state dewetting may provide a new route to construct ordered TMC(N)@TM core-shell-like nanocomposite capable of combining superhard, high toughness, low friction, superior wear with corrosion resistance.

Keywords: corrosion, nanocomposite film, solid-state dewetting, tribology

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Authors: Su Chul Han, Seungwoo Park

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As the increasing incidence of cancer, the technology and modality of radiotherapy have advanced and the importance of preclinical model is increasing in the cancer research. Furthermore, the small animal dosimetry is an essential part of the evaluation of the relationship between the absorbed dose in preclinical small animal and biological effect in preclinical study. In this study, we carried out realistic modeling of the preclinical small animal phantom possible to verify irradiated dose using commercial software. The small animal phantom was modeling from 4D Digital Mouse whole body phantom. To manipulate Moby phantom in commercial software (Mimics, Materialise, Leuven, Belgium), we converted Moby phantom to DICOM image file of CT by Matlab and two- dimensional of CT images were converted to the three-dimensional image and it is possible to segment and crop CT image in Sagittal, Coronal and axial view). The CT images of small animals were modeling following process. Based on the profile line value, the thresholding was carried out to make a mask that was connection of all the regions of the equal threshold range. Using thresholding method, we segmented into three part (bone, body (tissue). lung), to separate neighboring pixels between lung and body (tissue), we used region growing function of Mimics software. We acquired 3D object by 3D calculation in the segmented images. The generated 3D object was smoothing by remeshing operation and smoothing operation factor was 0.4, iteration value was 5. The edge mode was selected to perform triangle reduction. The parameters were that tolerance (0.1mm), edge angle (15 degrees) and the number of iteration (5). The image processing 3D object file was converted to an STL file to output with 3D printer. We modified 3D small animal file using 3- Matic research (Materialise, Leuven, Belgium) to make space for radiation dosimetry chips. We acquired 3D object of realistic small animal phantom. The width of small animal phantom was 2.631 cm, thickness was 2.361 cm, and length was 10.817. Mimics software supported efficiency about 3D object generation and usability of conversion to STL file for user. The development of small preclinical animal phantom would increase reliability of verification of absorbed dose in small animal for preclinical study.

Keywords: mimics, preclinical small animal, segmentation, 3D printer

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Authors: Suvorov Vasyl, Filipchuk Viktor

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Developmental Dysplasia of the Hip (DDH) is a frequent pathology in pediatric orthopedist’s practice. Neglected or residual cases of DDH in walking patients are usually treated using pelvic osteotomies. Plastic changes take place in hinge points due to acetabulum reorientation during surgery. Classically described hinge points and a traditional division of pelvic osteotomies on reshaping and reorientation are currently debated. The purpose of this article was to evaluate biomechanical changes during the most commonly used pelvic osteotomies (Salter, Dega, Pemberton) for DDH treatment in pediatric patients. Methods: virtual pelvic models of 2- and 6-years old patients were created, material properties were assigned, pelvic osteotomies were simulated and biomechanical changes were evaluated using finite element analysis (FEA). Results: it was revealed that the patient's age has an impact on pelvic bones and cartilages density (in younger patients the pelvic elements are more pliable - p<0.05). Stress distribution after each of the abovementioned pelvic osteotomy was assessed in 2- and 6-years old patients’ pelvic models; hinge points were evaluated. The new term "restriction point" was introduced, which means a place where restriction of acetabular deformity correction occurs. Pelvic ligaments attachment points were mainly these restriction points. Conclusions: it was found out that there are no purely reshaping and reorientation pelvic osteotomies as previously believed; the pelvic ring acts as a unit in carrying out the applied load. Biomechanical overload of triradiate cartilage during Salter osteotomy in 2-years old patient and in 2- and 6-years old patients during Pemberton osteotomy was revealed; overload of the posterior cortical layer in the greater sciatic notch in 2-years old patient during Dega osteotomy was revealed. Level of Evidence – Level IV, prognostic.

Keywords: developmental dysplasia of the hip, pelvic osteotomy, finite element analysis, hinge point, biomechanics

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Authors: Rajai Al-Rousan

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The repair and strengthening of concrete structures is a big challenge for the concrete industry for both engineers and contractors. Due to increasing economical constraints, the current trend is to repair/upgrade deteriorated and functionally obsolete structures rather than replacing them with new structures. CFRP has been used previously by air space industries regardless of the high costs. The decrease in the costs of the composite materials, as results of the technology improvement, has made CFRP an alternative to conventional materials for many applications. The primary objective of this research is to investigate the flexural behavior of reinforced concrete (RC) beams externally strengthened with CFRP composites exposed for three years for the following conditions: (a) room temperature, (b) cyclic ponding in 15% salt-water solution, (c) hot-water of 65oC, and (d) rapid freeze/thaw cycles. Results indicated that the after three years of various environmental conditions, the bond strength between the concrete beams and CFRP sheets was not affected. No signs of separation or debonding of CFRP sheets were observed before testing. Also, externally strengthening RC beams with CFRP sheets leads to a substantial increase in the ductility of concrete structures. This is a result of forcing the concrete to undergo inelastic deformation, resulting in compression failure of the structure after yielding of steel reinforcement. In addition, exposure to heat water tank for three years reduces the ultimate load by about 11%. This 11% reduction in the ultimate load equates to about 53%, 46% and 68% loss of the gain of the strength attributed to the CFRP of 2/3 Layer, 1 Layers and 2 Layers CFRP Sheets respectively. This mean that with decreasing of number of layers the environmental exposure had an efficient effect on concrete by protection concrete from environmental effect and adverse effect on the bond performance.

Keywords: flexural, behavior, CFRP, composites, environment, conditions

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Authors: Afshan Ejaz, Syed Asim Ali

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The reality is a combination of perception, reconstruction, and interaction. Augmented Reality is the advancement that layer over consistent everyday existence which includes content based interface, voice-based interfaces, voice-based interface and guide based or gesture-based interfaces, so designing augmented reality application interfaces is a difficult task for the maker. Designing a user interface which is not only easy to use and easy to learn but its more interactive and self-explanatory which have high perceived affordability, perceived usefulness, consistency and high discoverability so that the user could easily recognized and understand the design. For this purpose, a lot of interface design principles such as learnability, Affordance, Simplicity, Memorability, Feedback, Visibility, Flexibly and others are introduced but there no such principles which explain the most appropriate interface design principles for designing an Augmented Reality application interfaces. Therefore, the basic goal of introducing design principles for Augmented Reality application interfaces is to match the user efforts and the computer display (‘plot user input onto computer output’) using an appropriate interface action symbol (‘metaphors’) or to make that application easy to use, easy to understand and easy to discover. In this study by observing Augmented reality system and interfaces, few of well-known design principle related to GUI (‘user-centered design’) are identify and through them, few issues are shown which can be determined through the design principles. With the help of multiple studies, our study suggests different interface design principles which makes designing Augmented Reality application interface more easier and more helpful for the maker as these principles make the interface more interactive, learnable and more usable. To accomplish and test our finding, Pokémon Go an Augmented Reality game was selected and all the suggested principles are implement and test on its interface. From the results, our study concludes that our identified principles are most important principles while developing and testing any Augmented Reality application interface.

Keywords: GUI, augmented reality, metaphors, affordance, perception, satisfaction, cognitive burden

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Authors: D. Miroud, H. Mokaddem, M. Tata, N. Foucha

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The body of PDC (polycrystalline diamond compact) drill bit can be manufactured from two different materials, steel and tungsten carbide matrix. Commonly the steel body is produced by machining, thermal spraying a bonding layer and hardfacing of Ni-based matrix reinforced with fused eutectic tungsten carbide (WC/W2C). The matrix body bit is manufactured by infiltrating tungsten carbide particles, with a Copper binary or ternary alloy. By erosion-corrosion mechanisms, the PDC drill bits matrix undergoes severe damage, occurring particularly around the PDC inserts and near injection nozzles. In this study, we investigated the possibility to repair the damaged matrix regions by hardfacing technic. Ni-based hardfacing alloy reinforced with fused eutectic tungsten carbide is deposited on infiltrated WC-W-Ni substrate by oxyacetylene welding (OAW). The microstructure at the hardfacing / matrix interface is characterized by SEM- EDS, XRD and micro hardness Hv0.1. The hardfacing conditions greatly affect the dilution phenomenon and the distribution of carbides at the interface, without formation of transition zone. During OAW welding deposition, interdiffusion of atoms occurs: Cu and Sn diffuse from infiltrated matrix substrate into hardfacing and simultaneously Cr and Si alloy elements from hardfacing diffuse towards the substrate. The dilution zone consists of a nickel-rich phase with a heterogeneous distribution of eutectic spherical (Ni-based hardfacing alloy) and irregular (matrix) WC/W2C carbides and a secondary phase rich in Cr-W-Si. Hardfacing conditions cause the dissolution of banding around both spherical and irregular carbides. The micro-hardness of interface is significantly improved by the presence of secondary phase in the inter-dendritic structure.

Keywords: dilution, dissolution, hardfacing, infiltrated matrix, PDC drill bits

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Authors: Sumaira Zafar, Arjumand Zaidi

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During past few years, several floods have adversely affected the areas along lower Indus River. Besides other climate related anomalies, rapidly increasing urbanization and blockage of natural drains due to siltation or encroachments are two other critical causes that may be responsible for these disasters. Due to flat topography of river Indus plains and blockage of natural waterways, drainage of storm water takes time adversely affecting the crop health and soil properties of the area. Government of Sindh is taking a keen interest in revival of natural drainage network in the province and has initiated this work under Sindh Irrigation and Drainage Authority. In this paper, geospatial techniques are used to analyze landuse/land-cover changes of Larkana district over the past three decades (1980-present) and their impact on natural drainage system. Satellite derived Digital Elevation Model (DEM) and topographic sheets (recent and 1950) are used to delineate natural drainage pattern of the district. The urban landuse map developed in this study is further overlaid on drainage line layer to identify the critical areas where the natural floodwater flows are being inhibited by urbanization. Rainfall and flow data are utilized to identify areas of heavy flow, whereas, satellite data including Landsat 7 and Google Earth are used to map previous floods extent and landuse/cover of the study area. Alternatives to natural drainage systems are also suggested wherever possible. The output maps of natural drainage pattern can be used to develop a decision support system for urban planners, Sindh development authorities and flood mitigation and management agencies.

Keywords: geospatial techniques, satellite data, natural drainage, flood, urbanization

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Authors: Kelum N. Manamendra-Arachchi, Kalangi Rodrigo

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Bones, teeth, and shells have been acknowledged over the last two centuries as evidence of chronology, Palaeo-environment, and human activity. Faunal traces are valid evidence of past situations because they have properties that have not changed over long periods of time. Sri Lanka has been known as an Island, which has a diverse variation of prehistoric occupation among ecological zones. Defining the Paleoecology of the past societies has been an archaeological thought developed in the 1960s. It is mainly concerned with the reconstruction from available geological and biological evidence of past biota, populations, communities, landscapes, environments, and ecosystems. Sri Lanka has dealt with this subject and considerable research has been already undertaken. The fossil and material record of Sri Lanka’s Wet Zone tropical forests continues from c. 38,000–34,000 ybp. This early and persistent human fossil, technical, and cultural florescence, as well as a collection of well-preserved tropical-forest rock shelters with associated ' on-site ' Palaeoenvironmental records, makes Sri Lanka a central and unusual case study to determine the extent and strength of early human tropical forest encounters. Excavations carried out in prehistoric caves in the low country wet zone has shown that in the last 50,000 years, the temperature in the lowland rainforests has not exceeded 5 degrees. Based on Semnopithecus Priam (Gray Langur) remains unearned from wet zone prehistoric caves, it has been argued that periods of momentous climate changes during the LGM and Terminal Pleistocene/Early Holocene boundary, with a recognizable preference for semi-open ‘Intermediate’ rainforest or edges. Continuous Genus Acavus and Oligospira occupation along with uninterrupted horizontal pervasive of Canarium sp. (‘kekuna’ nut) have proven that temperatures in the lowland rain forests have not changed by at least 5 oC over the last 50,000 years. Site Catchment or Territorial analysis cannot be no longer defensible, due to time-distance based factors as well as optimal foraging theory failed as a consequences of prehistoric people were aware of the decrease in cost-benefit ratio and located sites, and generally played out a settlement strategy that minimized the ratio of energy expanded to energy produced.

Keywords: palaeo-environment, prehistory, palaeo-ecology, zooarchaeology

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Authors: Abdul Basit, Shahid Latif, Shah Mehmood

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Lawn fabric was usually prepared from originally of linen but at present chiefly cotton. Lawn fabric is worn in summer. Cotton Lawn is a lightweight pure cloth which is heavier than voile. It is so fine that it is somewhat transparent. It is soft and superb to wear thus it is perfect for summer clothes or for regular wear in hotter climates. Tencel (Lyocell) fiber is considered as the fiber of the future as Tencel fibers are absorbent, soft, and extremely strong when wet or dry, and resistant to wrinkles. Fibers are more absorbent than cotton, softer than silk and cooler than linen. High water absorption and water vapor absorption give more heat capacity and heat balancing effect for thermo-regulation. This thermo-regulation is analogous with the action of phase-change-materials. The thermal wear properties result in cool and dry touch that gives cooling effect in sportswear, and the warmth properties (when used as an insulation layer). These cooling and warming effects are adaptive to the environment giving comfort in a broad range of climatic conditions. In this work, single yarns of Ne 80s were made. Yarns were made from conventional ring spinning. Different yarns of 100% cotton, 100% micro-Tencel and Cotton:micro-Tencel blends (67:33, 50:50:33:67) were made. The mechanical and comfort properties of the woven fabrics were compared. The mechanical properties include the tensile and tear strength, bending length, pilling and abrasion resistance whereas comfort properties include the air permeability, moisture management and thermal resistance. It is found that as the content of the micro-Tencel is increased, the mechanical and comfort properties of the woven fabric are also increased.

Keywords: combed cotton, comfort properties , mechanical properties, micro-Tencel

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Authors: R. C. Tiwari, N. P. Bhandary, D. B. Thapa Chhetri, R. Yatabe

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The research enlightens the various issues of lake expansion and stability of the moraine dam of Imja lake. The Imja lake considered that the world highest altitude lake (5010m from m.s.l.), located in the Khumbu, Sagarmatha region of Nepal (27.90 N and 86.90 E) was reported as one of the fast growing glacier lakes in the Nepal Himalaya. The research explores a common phenomenon of lake expansion and stability issues of moraine dam to justify the necessity of lake lowering efforts if any in future in other glacier lakes in Nepal Himalaya. For this, we have explored the root causes of rapid lake expansion along with crucial factors responsible for the stability of moraine mass. This research helps to understand the structure of moraine dam and the ice, water and moraine interactions to the strength of moraine dam. The nature of permafrost layer and its effects on moraine dam stability is also studied here. The detail Geo-Technical properties of moraine mass of Imja lake gives a clear picture of the strength of the moraine material and their interactions. The stability analysis of the moraine dam under the consideration of strong ground motion of 7.8Mw 2015 Barpak-Gorkha and its major aftershock 7.3Mw Kodari, Sindhupalchowk-Dolakha border, Nepal earthquakes have also been carried out here to understand the necessity of lake lowering efforts. The lake lowering effort was recently done by Nepal Army by constructing an open channel and lowered 3m. And, it is believed that the entire region is now safe due to continuous draining of lake water by 3m. But, this option does not seem adequate to offer a significant risk reduction to downstream communities in this much amount of volume and depth, lowering as in the 75 million cubic meter water impounded with an average depth of 148.9m.

Keywords: finite element method, glacier, moraine, stability

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Authors: Masaaki Ii, Takashi Saito, Yasuhiko Tabata, Shintaro Nemoto

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Background: Clinical trials of autologous adipose-derived stem cell (AdSC) therapy for ischemic heart diseases (IHD) are now on-going. We have investigated the hypothesis that combination of AdSCs and statin, an agent with pleiotropic effects, could augment the therapeutic effect on myocardial infarction (MI). Methods and Results: Human AdSC functions with different doses of simvastatin-conjugated nanoparticle (STNP) uptake were evaluated by in vitro assays. STNP promoted the migration activity without changing the proliferation activity, and also up-regulated growth factors. Next, MI was induced by LAD ligation in nude mice, and the mice were assigned in the following groups 3 days after MI: 1) PBS (control), 2) NP-AdSCs (50000 cells), 3) STNP, and 4) STNP-AdSCs (50000 cells). Cardiac functional recovery assessed by echocardiography was improved at 4 weeks after surgery in STNP-AdSC group. Masson’s trichrome-stained sections revealed that LV fibrosis length was reduced, and the number of TUNEL-positive cardiomyocytes was less in STNP-AdSC group. Surprisingly, a number of de novo endogenous Nkx-2.5/GATA4 positive immature cardiomyocytes as well as massive vascular formation were observed in outer layer of infarcted myocardium despite of a few recruited/retained transfused STNP-AdSCs 4 weeks after MI in STNP-AdSC group. Finally, massive myocardial regeneration was observed 8 weeks after MI. Conclusions: Intravenously injected small number of statin nanoparticle-loaded hAdSCs exhibited a potent therapeutic effect inducing endogenous cardiac tissue regeneration.

Keywords: statin, drug delivery system, stem cells, cardiac regeneration

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Authors: Pengfei Meng, Shuangcheng Jia, Qian Li

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We proposed a real-time high-precision semantic segmentation network based on a multi-resolution feature fusion module, the auxiliary feature extracting module, upsampling module, and atrous spatial pyramid pooling (ASPP) module. We designed a feature fusion structure, which is integrated with sufficient features of different resolutions. We also studied the effect of side-branch structure on the network and made discoveries. Based on the discoveries about the side-branch of the network structure, we used a side-branch auxiliary feature extraction layer in the network to improve the effectiveness of the network. We also designed upsampling module, which has better results than the original upsampling module. In addition, we also re-considered the locations and number of atrous spatial pyramid pooling (ASPP) modules and modified the network structure according to the experimental results to further improve the effectiveness of the network. The network presented in this paper takes the backbone network of Bisenetv2 as a basic network, based on which we constructed a network structure on which we made improvements. We named this network deep multiple-resolution bilateral networks for real-time, referred to as DMBR-Net. After experimental testing, our proposed DMBR-Net network achieved 81.2% mIoU at 119FPS on the Cityscapes validation dataset, 80.7% mIoU at 109FPS on the CamVid test dataset, 29.9% mIoU at 78FPS on the COCOStuff test dataset. Compared with all lightweight real-time semantic segmentation networks, our network achieves the highest accuracy at an appropriate speed.

Keywords: multi-resolution feature fusion, atrous convolutional, bilateral networks, pyramid pooling

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Authors: Biswajit Pal, Amit Mallik, Anil K. Barik

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Current years have witnessed a phenomenal growth in the research on the rare earth-doped transparent host materials, the essential components in optoelectronics that meet up the increasing demand for fabrication of high quality optical devices especially in telecommunication system. The combination of low phonon energy (because of fluoride environment) and high chemical durability with superior mechanical stability (due to oxide environment) makes the oxyfluoride glass–ceramics the promising and useful materials in optoelectronics. The present work reports on the undoped and doped (1 mol% Pr2O3) glass ceramics of composition 16.52 Al2O3•1.5AlF3• 12.65LaF3•4.33Na2O•64.85 SiO2 (mol%), prepared by melting technique initially that follows annealation at 450 ºC for 1 h. The glass samples so obtained were heat treated at constant 600 ºC with a variation in heat treatment schedule (10- 80 h). TEM techniques were employed to structurally characterize the glass samples. Pr2O3 affects the phase separation in the glass and delays the onset of crystallization in the glass ceramic. The modified crystallization mechanism is established from the analysis of advanced STEM/EDXS results. The phase separated droplets after annealing turn into 10-20 nm of LaF3 nano crystals those upon scrutiny are found to be dotted with the doped Pr3+ ions within the crystals themselves. The EDXS results also suggest that the inner LaF3 crystal core is swallowed by an Al enriched layer that follows a Si enriched surrounding shell as the outer core. This greatly increases the viscosity in the periphery of the crystals that restricts further crystal growth to account for the formation of nano sized crystals.

Keywords: advanced STEM/EDXS, crystallization mechanism, nano crystals, pr3+ ion doped glass and glass ceramic, structural characterization

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Authors: Tooran Tavangar, Masoud Hosseinpoor, Jeffrey S. Marshall, Ammar Yahia, Kamal Henri Khayat

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In this study, a four-way coupled CFD-DEM methodology was used to simulate the behavior of concrete pipe flow. Fresh concrete, characterized as a biphasic suspension, features aggregates comprising the solid-suspended phase with diverse particle-size distributions (PSD) within a non-Newtonian cement paste/mortar matrix forming the liquid phase. The fluid phase was simulated using CFD, while the aggregates were modeled using DEM. Interaction forces between the fluid and solid particles were considered through CFD-DEM computations. To capture the viscoelastic characteristics of the suspending fluid, a bi-viscous approach was adopted, incorporating a critical shear rate proportional to the yield stress of the mortar. In total, three diphasic suspensions were simulated, each featuring distinct particle size distributions and a concentration of 10% for five subclasses of spherical particles ranging from 1 to 17 mm in a suspending fluid. The adopted bi-viscous approach successfully simulated both un-sheared (plug flow) and sheared zones. Furthermore, shear-induced particle migration (SIPM) was assessed by examining coefficients of variation in particle concentration across the pipe. These SIPM values were then compared with results obtained using CFD-DEM under the Newtonian assumption. The study highlighted the crucial role of yield stress in the mortar phase, revealing that lower yield stress values can lead to increased flow rates and higher SIPM across the pipe.

Keywords: computational fluid dynamics, concrete pumping, coupled CFD-DEM, discrete element method, plug flow, shear-induced particle migration.

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Authors: Ella Sèdé Maforikan

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Sustained water management requires quantitative information and the knowledge of spatiotemporal dynamics of hydrological system within the basin. This can be achieved through the research. Several studies have investigated both surface water and groundwater in Beterou catchment. However, there are few published papers on the application of the SWAT modeling in Beterou catchment. The objective of this study was to evaluate the performance of SWAT to simulate the water balance within the watershed. The inputs data consist of digital elevation model, land use maps, soil map, climatic data and discharge records. The model was calibrated and validated using the Sequential Uncertainty Fitting (SUFI2) approach. The calibrated started from 1989 to 2006 with four years warming up period (1985-1988); and validation was from 2007 to 2020. The goodness of the model was assessed using five indices, i.e., Nash–Sutcliffe efficiency (NSE), the ratio of the root means square error to the standard deviation of measured data (RSR), percent bias (PBIAS), the coefficient of determination (R²), and Kling Gupta efficiency (KGE). Results showed that SWAT model successfully simulated river flow in Beterou catchment with NSE = 0.79, R2 = 0.80 and KGE= 0.83 for the calibration process against validation process that provides NSE = 0.78, R2 = 0.78 and KGE= 0.85 using site-based streamflow data. The relative error (PBIAS) ranges from -12.2% to 3.1%. The parameters runoff curve number (CN2), Moist Bulk Density (SOL_BD), Base Flow Alpha Factor (ALPHA_BF), and the available water capacity of the soil layer (SOL_AWC) were the most sensitive parameter. The study provides further research with uncertainty analysis and recommendations for model improvement and provision of an efficient means to improve rainfall and discharges measurement data.

Keywords: watershed, water balance, SWAT modeling, Beterou

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Authors: K. Drabczyk, Z. Starowicz, S. Maleczek, P. Zieba

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The army, police and fire brigade commonly use dedicated equipment based on special textile materials. The properties of these textiles should ensure human life and health protection. Equally important is the ability to use electronic equipment and this requires access to the source of electricity. Photovoltaic cells integrated with such textiles can be solution for this problem in the most of outdoor circumstances. One idea may be to laminate the cells to textile without changing their properties. The main goal of this work was analyzed lamination quality of special designed semi-flexible solar module with special textile materials as a backsheet. In the first step of investigation, the quality of lamination was determined using device equipped with dynamometer. In this work, the crystalline silicon solar cells 50 x 50 mm and thin chemical tempered glass - 62 x 62 mm and 0.8 mm thick - were used. The obtained results showed the correlation between breaking force and type of textile weave and fiber. The breaking force was in the ranges: 4.5-5.5 N, 15-20 N and 30-33 N depending on the type of wave and fiber type. To verify these observations the microscopic and FTIR analysis of fibers was performed. The studies showed the special textile can be used as a backsheet of semi-flexible solar modules. This work presents a new composition of solar module with special textile layer which, to our best knowledge, has not been published so far. Moreover, the work presents original investigations on adhesion of EVA (ethylene-vinyl acetate) polymer to textile with respect to fiber structure of laminated substrate. This work is realized for the GEKON project (No. GEKON2/O4/268473/23/2016) sponsored by The National Centre for Research and Development and The National Fund for Environmental Protection and Water Management.

Keywords: flexible solar modules, lamination process, solar cells, textile for photovoltaics

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Authors: Shashi Kant Verma, S. L. Sinha, D. K. Chandraker

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Numerical simulations of selected subchannel tracer (Potassium Nitrate) based experiments have been performed to study the capabilities of state-of-the-art of Computational Fluid Dynamics (CFD) codes. The Computational Fluid Dynamics (CFD) methodology can be useful for investigating the spacer effect on turbulent mixing to predict turbulent flow behavior such as Dimensionless mixing scalar distributions, radial velocity and vortices in the nuclear fuel assembly. A Gibson and Launder (GL) Reynolds stress model (RSM) has been selected as the primary turbulence model to be applied for the simulation case as it has been previously found reasonably accurate to predict flows inside rod bundles. As a comparison, the case is also simulated using a standard k-ε turbulence model that is widely used in industry. Despite being an isotropic turbulence model, it has also been used in the modeling of flow in rod bundles and to produce lateral velocities after thorough mixing of coolant fairly. Both these models have been solved numerically to find out fully developed isothermal turbulent flow in a 30º segment of a 54-rod bundle. Numerical simulation has been carried out for the study of natural mixing of a Tracer (Passive scalar) to characterize the growth of turbulent diffusion in an injected sub-channel and, afterwards on, cross-mixing between adjacent sub-channels. The mixing with water has been numerically studied by means of steady state CFD simulations with the commercial code STAR-CCM+. Flow enters into the computational domain through the mass inflow at the three subchannel faces. Turbulence intensity and hydraulic diameter of 1% and 5.9 mm respectively were used for the inlet. A passive scalar (Potassium nitrate) is injected through the mass fraction of 5.536 PPM at subchannel 2 (Upstream of the mixing section). Flow exited the domain through the pressure outlet boundary (0 Pa), and the reference pressure was 1 atm. Simulation results have been extracted at different locations of the mixing zone and downstream zone. The local mass fraction shows uniform mixing. The effect of the applied turbulence model is nearly negligible just before the outlet plane because the distributions look like almost identical and the flow is fully developed. On the other hand, quantitatively the dimensionless mixing scalar distributions change noticeably, which is visible in the different scale of the colour bars.

Keywords: single-phase flow, turbulent mixing, tracer, sub channel analysis

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Authors: Martin Botz, Michael Kraus, Geralt Siebert

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The use of laminated glass gains increasing importance in structural engineering. For safety reasons, at least two glass panes are laminated together with a polymeric interlayer. In case of breakage of one or all of the glass panes, the glass fragments are still connected to the interlayer due to adhesion forces and a certain residual load-bearing capacity is left in the system. Polymer interlayers used in the laminated glass show a viscoelastic material behavior, e.g. stresses and strains in the interlayer are dependent on load duration and temperature. In the intact stage only small strains appear in the interlayer, thus the material can be described in a linear way. In the broken stage, large strains can appear and a non-linear viscoelasticity material theory is necessary. Relaxation tests on two different types of polymeric interlayers are performed at different temperatures and strain amplitudes to determine the border to the non-linear material regime. Based on the small-scale specimen results further tests on broken laminated glass panes are conducted. So-called ‘through-crack-bending’ (TCB) tests are performed, in which the laminated glass has a defined crack pattern. The test set-up is realized in a way that one glass layer is still able to transfer compressive stresses but tensile stresses have to be transferred by the interlayer solely. The TCB-tests are also conducted under different temperatures but constant force (creep test). Aims of these experiments are to elaborate if the results of small-scale tests on the interlayer are transferable to a laminated glass system in the broken stage. In this study, limits of the applicability of linear-viscoelasticity are established in the context of two commercially available polymer-interlayers. Furthermore, it is shown that the results of small-scale tests agree to a certain degree to the results of the TCB large-scale experiments. In a future step, the results can be used to develop material models for the post breakage performance of laminated glass.

Keywords: glass breakage, laminated glass, relaxation test, viscoelasticity

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Authors: Weirong Wang, Shenghong Huang, Xisheng Luo, Zhenyu Li

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Material mixing process and related dynamic issues at extreme compressing conditions have gained more and more concerns in last ten years because of the engineering appealings in inertial confinement fusion (ICF) and hypervelocity aircraft developments. However, there lacks models and methods that can handle fully coupled turbulent material mixing and complex fluid evolution under conditions of high energy density regime up to now. In aspects of macro hydrodynamics, three numerical methods such as direct numerical simulation (DNS), large eddy simulation (LES) and Reynolds-averaged Navier–Stokes equations (RANS) has obtained relative acceptable consensus under the conditions of low energy density regime. However, under the conditions of high energy density regime, they can not be applied directly due to occurrence of dissociation, ionization, dramatic change of equation of state, thermodynamic properties etc., which may make the governing equations invalid in some coupled situations. However, in view of micro/meso scale regime, the methods based on Molecular Dynamics (MD) as well as Monte Carlo (MC) model are proved to be promising and effective ways to investigate such issues. In this study, both classical MD and first-principle based electron force field MD (eFF-MD) methods are applied to investigate Richtmyer-Meshkov Instability of metal Lithium and gas Hydrogen (Li-H2) interface mixing at different shock loading speed ranging from 3 km/s to 30 km/s. It is found that: 1) Classical MD method based on predefined potential functions has some limits in application to extreme conditions, since it cannot simulate the ionization process and its potential functions are not suitable to all conditions, while the eFF-MD method can correctly simulate the ionization process due to its ‘ab initio’ feature; 2) Due to computational cost, the eFF-MD results are also influenced by simulation domain dimensions, boundary conditions and relaxation time choices, etc., in computations. Series of tests have been conducted to determine the optimized parameters. 3) Ionization induced by strong shock compression has important effects on Li-H2 interface evolutions of RMI, indicating a new micromechanism of RMI under conditions of high energy density regime.

Keywords: first-principle, ionization, molecular dynamics, material mixture, Richtmyer-Meshkov instability

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Authors: Zainab Algharibi, Julie McAdam, Catherine Fagan

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The purpose of this paper is to shed light on how Omani children in the first grade experience their needs during their transition to primary school. Theoretically, the paper was built on two perspectives: Dewey's concept of continuity of experience and the boundary objects introduced by Vygotsky (CHAT). The methodology of the study is based on the crucial role of children’s agency which is a very important activity as an educational tool to enhance the child’s participation in the learning process and develop their ability to face various issues in their life. Thus, the data were obtained from 45 children in grade one from 4 different primary schools using drawing and visual narrative activities, in addition to researcher observations during the start of the first weeks of the academic year for the first grade. As the study dealt with children, all of the necessary ethical laws were followed. This paper is considered original since it seeks to deal with the issue of children's transition from kindergarten to primary school in Oman, if not in the Arab region. Therefore, it is expected to fill an important gap in this field and present a proposal that will be a door for researchers to enter this research field later. The analysis of drawing and visual narrative was performed according to the social semiotics approach in two phases. The first is to read out the surface message “denotation,” while the second is to go in-depth via the symbolism obtained from children while they talked and drew letters and signs. This stage is known as “signified”; a video was recorded of each child talking about their drawing and expressing themself. Then, the data were organised and classified according to a cross-data network. Regarding the researcher observation analyses, the collected data were analysed according to the model was developed for the "grounded theory". It is based on comparing the recent data collected from observations with data previously encoded by other methods in which children were drawing alongside the visual narrative in the current study, in order to identify the similarities and differences, and also to clarify the meaning of the accessed categories and to identify sub-categories of them with a description of possible links between them. This is a kind of triangulation in data collection. The study came up with a set of findings, the most vital being that the children's greatest interest goes to their social and psychological needs, such as friends, their teacher, and playing. Also, their biggest fears are a new place, a new teacher, and not having friends, while they showed less concern for their need for educational knowledge and skills.

Keywords: children’s academic needs, children’s social needs, transition, primary school

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Authors: Ariadna Manresa, Ines Ferrer

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Introduction: Ultrasonic moulding process (USM) is a recent injection technology used to manufacture micro components. It is able to melt small amounts of material so the waste of material is certainly reduced comparing to microinjection molding. This is an important advantage when the materials are expensive like medical biopolymers. Micro-scaled components are involved in a variety of uses, such as biomedical applications. It is required replication fidelity so it is important to stabilize the process and minimize the variability of the responses. The aim of this research is to investigate the influence of the main process parameters on the filling behaviour, the dimensional accuracy and the cavity pressure when a micro-plate is manufactured by biomaterials such as PLA and PCL. Methodology or Experimental Procedure: The specimens are manufactured using a Sonorus 1G Ultrasound Micro Molding Machine. The used geometry is a rectangular micro-plate of 15x5mm and 1mm of thickness. The materials used for the investigation are PLA and PCL due to biocompatible and degradation properties. The experimentation is divided into two phases. Firstly, the influence of process parameters (vibration amplitude, sonotrodo velocity, ultrasound time and compaction force) on filling behavior is analysed, in Phase 1. Next, when filling cavity is assured, the influence of both cooling time and force compaction on the cavity pressure, part temperature and dimensional accuracy is instigated, which is done in Phase. Results and Discussion: Filling behavior depends on sonotrodo velocity and vibration amplitude. When the ultrasonic time is higher, more ultrasonic energy is applied and the polymer temperature increases. Depending on the cooling time, it is possible that when mold is opened, the micro-plate temperature is too warm. Consequently, the polymer relieve its stored internal energy (ultrasonic and thermal) expanding through the easier direction. This fact is reflected on dimensional accuracy, causing micro-plates thicker than the mold. It has also been observed the most important fact that affects cavity pressure is the compaction configuration during the manufacturing cycle. Conclusions: This research demonstrated the influence of process parameters on the final micro-plated manufactured. Future works will be focused in manufacturing other geometries and analysing the mechanical properties of the specimens.

Keywords: biomaterial, biopolymer, micro injection molding, ultrasound

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Authors: H. M. N. L. Handagiripathira

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The distributions of naturally occurring and anthropogenic radioactive materials were determined in surface sediments taken at 27 different locations along the bank of Negombo Lagoon in Sri Lanka. Hydrographic parameters of lagoon water and the grain size analyses of the sediment samples were also carried out for this study. The conductivity of the adjacent water was varied from 13.6 mS/cm to 55.4 mS/cm near to the southern end and the northern end of the lagoon, respectively, and equally salinity levels varied from 7.2 psu to 32.1 psu. The average pH in the water was 7.6 and average water temperature was 28.7 °C. The grain size analysis emphasized the mass fractions of the samples as sand (60.9%), fine sand (30.6%) and fine silt+clay (1.3%) in the sampling locations. The surface sediment samples of wet weight, 1 kg each from upper 5-10 cm layer, were oven dried at 105 °C for 24 hours to get a constant weight, homogenized and sieved through a 2 mm sieve (IAEA technical series no. 295). The radioactivity concentrations were determined using gamma spectrometry technique. Ultra Low Background Broad Energy High Purity Ge Detector, BEGe (Model BE5030, Canberra) was used for radioactivity measurement with Canberra Industries' Laboratory Source-less Calibration Software (LabSOCS) mathematical efficiency calibration approach and Geometry composer software. The mean activity concentration was found to be 24 ± 4, 67 ± 9, 181 ± 10, 59 ± 8, 3.5 ± 0.4 and 0.47 ± 0.08 Bq/kg for 238U, 232Th, 40K, 210Pb, 235U and 137Cs respectively. The mean absorbed dose rate in air, radium equivalent activity, external hazard index, annual gonadal dose equivalent and annual effective dose equivalent were 60.8 nGy/h, 137.3 Bq/kg, 0.4, 425.3 mSv/year and 74.6 mSv/year, respectively. The results of this study will provide baseline information on the natural and artificial radioactive isotopes and environmental pollution associated with information on radiological risk.

Keywords: gamma spectrometry, lagoon, radioactivity, sediments

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Authors: S. Gariani, I. Shyha

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Cutting titanium alloys are usually accompanied with low productivity, poor surface quality, short tool life and high machining costs. This is due to the excessive generation of heat at the cutting zone and difficulties in heat dissipation due to relatively low heat conductivity of this metal. The cooling applications in machining processes are crucial as many operations cannot be performed efficiently without cooling. Improving machinability, increasing productivity, enhancing surface integrity and part accuracy are the main advantages of cutting fluids. Conventional fluids such as mineral oil-based, synthetic and semi-synthetic are the most common cutting fluids in the machining industry. Although, these cutting fluids are beneficial in the industries, they pose a great threat to human health and ecosystem. Vegetable oils (VOs) are being investigated as a potential source of environmentally favourable lubricants, due to a combination of biodegradability, good lubricous properties, low toxicity, high flash points, low volatility, high viscosity indices and thermal stability. Fatty acids of vegetable oils are known to provide thick, strong, and durable lubricant films. These strong lubricating films give the vegetable oil base stock a greater capability to absorb pressure and high load carrying capacity. This paper details preliminary experimental results when turning Ti-6Al-4V. The impact of various VO-based cutting fluids, cutting tool materials, working conditions was investigated. The full factorial experimental design was employed involving 24 tests to evaluate the influence of process variables on average surface roughness (Ra), tool wear and chip formation. In general, Ra varied between 0.5 and 1.56 µm and Vasco1000 cutting fluid presented comparable performance with other fluids in terms of surface roughness while uncoated coarse grain WC carbide tool achieved lower flank wear at all cutting speeds. On the other hand, all tools tips were subjected to uniform flank wear during whole cutting trails. Additionally, formed chip thickness ranged between 0.1 and 0.14 mm with a noticeable decrease in chip size when higher cutting speed was used.

Keywords: cutting fluids, turning, Ti-6Al-4V, vegetable oils, working conditions

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Authors: Naveeda Akhtar Qureshi, Wajiha

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Coccidiosis is a protozoan parasitic disease of genus Eimeria. It is an avian infection causing a great economic loss of 3 billion USD per year globally. A number of anticoccidial drugs are in use however many of them have side effects and cost effective. With increase in poultry demand throughout the world there is a need of more drugs and vaccines against coccidiosis. The present study is based upon the use of F. racemosa a medicinal plant to be a potential source of anticoccidial agents. The methanolic leaves extract was fractionated by column and thin layer chromatography and got nineteen fractions. Each fraction different concentrations was evaluated for its anticoccidial properties in an invitro experiment against E. tenella, E. necatrix and E. mitis. The anticoccidial active fractions were further characterized by spectroscopy (UV-Vis, FTIR) and GC-MS analysis. The in silico molecular docking of active fractions identified compounds were carried out. Among all fractions significantly maximum sporulation inhibition efficacy was shown by F-19 (67.11±2.18) followed by F-15 (65.21±1.34) at concentration of 30mg/ml against E. tenella. The significantly highest sporozoites viability inhibition was shown by F-19 (69.23±2.11) followed by F-15 (67.14±1.52) against E. necatrix at concentration 30mg/ml. Anticoccidial active fractions 15 and 19 showed peak spectrum at 207 and 202nm respectively by UV analysis. Their FTIR analysis confirmed the presence of carboxylic acid, amines, phenols, etc. Anticoccidial active compounds like Cyclododecane methanol, oleic acid, Octadecanoic acid, etc were identified by GC-MS analysis. Identified compounds in silico molecular docking study showed that cyclododecane methanol of F-19 and oleic acid of F-15 showed highest binding affinity with target S-Adenosylmethionine synthase. Hence for further authentication in vivo anticoccidial studies are recommended.

Keywords: ficus racemosa, cluster fig, column chromatography, anticoccidial fractions, GC-MS, molecular docking., s-adenosylmethionine synthase

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Authors: Sindhu Govardhan, Kenneth G. Crowther

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Modernisation of the water sector is leading to increased connectivity and integration of emerging technologies with traditional ones, leading to new security risks. The convergence of Information Technology (IT) with Operation Technology (OT) results in solutions that are spread across larger geographic areas, increasingly consist of interconnected Industrial Internet of Things (IIOT) devices and software, rely on the integration of legacy with modern technologies, use of complex supply chain components leading to complex architectures and communication paths. The result is that multiple parties collectively own and operate these emergent technologies, threat actors find new paths to exploit, and traditional cybersecurity controls are inadequate. Our approach is to explicitly identify and draw data flows that cross trust boundaries between owners and operators of various aspects of these emerging and interconnected technologies. On these data flows, we layer potential attack vectors to create a frame of reference for evaluating possible risks against connected technologies. Finally, we identify where existing controls, mitigations, and other remediations exist across industry partners (e.g., suppliers, product vendors, integrators, water utilities, and regulators). From these, we are able to understand potential gaps in security, the roles in the supply chain that are most likely to effectively remediate those security gaps, and test cases to evaluate and strengthen security across these partners. This informs a “shared responsibility” solution that recognises that security is multi-layered and requires collaboration to be successful. This shared responsibility security framework improves visibility, understanding, and control across the entire supply chain, and particularly for those water utilities that are accountable for safe and continuous operations.

Keywords: cyber security, shared responsibility, IIOT, threat modelling

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Authors: Nur Farah Ain Zainee, Ahmad Ismail, Nazlina Ibrahim, Asmida Ismail

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The study of genus Halimeda in Malaysia is in the early stage due to less specific study on its taxonomy. Most of the previous research tend to choose other genus such as Caulerpa and Gracilaria because of the potential of being utilized. The identification of Halimeda is complex by the high morphological variation within individual species due to different types of habitat and the changes in composition of seawater. The study was completed to study the diversity and distribution of Halimeda in Malaysia and to identify the morphological and anatomical differences between Halimeda species. The methods which have been used for this study are collection of Halimeda and seawater, preservation of specimen, identification of the specimen including the preparation of the temporary slide and decalcification of the calcium layer by using diluted hydrochloric acid. The specimen were processed in laboratory and kept as herbarium specimen in Algae Herbarium, Universiti Kebangsaan Malaysia. Environmental parameters were tested by using YSI multiparameter probe and the recorded data were temperature, salinity, pH and dissolved oxygen. The nutrient content of seawater such as nitrate and phosphate were analysed by using Hach kit model DR 2000. In the present study, out of 330 herbarium specimen, ten species were identified as Halimeda cuneata, H. discoidea, H. macroloba, H. macrophysa, H. opuntia, H. simulans, H. stuposa, H. taenicola, H. tuna and H. velasquezii. Of these, five species were new record to Malaysia. They are Halimeda cuneata, H. macrophysa, H. stuposa, H. taenicola and H. velasquezii. H. opuntia was found as the most abundance species with wide distribution in Malaysia coastal area. Meanwhile, from the study of their distribution, two localities in which Pulau Balak Balak, Kudat and Pulau Langkawi, Kedah, were noted having high number of Halimeda species. As a conclusion, this study has successfully identified ten species of Halimeda of Malaysia with full description of morphological characteristics that may assist further researcher to differentiate and identify Halimeda.

Keywords: Distribution, diversity, Halimeda, morphological, taxonomy

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Authors: Agnieszka Krzemińska, Katarzyna Świderek, Vicente Molinier, Piotr Paneth

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In order to understand in details the interactions between ligands and the enzyme isotope effects were studied between clinically used drugs that bind in the active site of Human Immunodeficiency Virus Reverse Transcriptase, HIV-1 RT, as well as triazole-based inhibitor that binds in the allosteric pocket of this enzyme. The magnitudes and origins of the resulting binding isotope effects were analyzed. Subsequently, binding isotope effect of the same triazole-based inhibitor bound in the active site were analyzed and compared. Together, these results show differences in binding origins in two sites of the enzyme and allow to analyze binding mode and place of newly synthesized inhibitors. Typical protocol is described below on the example of triazole ligand in the allosteric pocket. Triazole was docked into allosteric cavity of HIV-1 RT with Glide using extra-precision mode as implemented in Schroedinger software. The structure of HIV-1 RT was obtained from Protein Data Bank as structure of PDB ID 2RKI. The pKa for titratable amino acids was calculated using PROPKA software, and in order to neutralize the system 15 Cl- were added using tLEaP package implemented in AMBERTools ver.1.5. Also N-terminals and C-terminals were build using tLEaP. The system was placed in 144x160x144Å3 orthorhombic box of water molecules using NAMD program. Missing parameters for triazole were obtained at the AM1 level using Antechamber software implemented in AMBERTools. The energy minimizations were carried out by means of a conjugate gradient algorithm using NAMD. Then system was heated from 0 to 300 K with temperature increment 0.001 K. Subsequently 2 ns Langevin−Verlet (NVT) MM MD simulation with AMBER force field implemented in NAMD was carried out. Periodic Boundary Conditions and cut-offs for the nonbonding interactions, range radius from 14.5 to 16 Å, are used. After 2 ns relaxation 200 ps of QM/MM MD at 300 K were simulated. The triazole was treated quantum mechanically at the AM1 level, protein was described using AMBER and water molecules were described using TIP3P, as implemented in fDynamo library. Molecules 20 Å apart from the triazole were kept frozen, with cut-offs established on range radius from 14.5 to 16 Å. In order to describe interactions between triazole and RT free energy of binding using Free Energy Perturbation method was done. The change in frequencies from ligand in solution to ligand bounded in enzyme was used to calculate binding isotope effects.

Keywords: binding isotope effects, molecular dynamics, HIV, reverse transcriptase

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