Search results for: okazaki fragments

Authors: Nino Sulava, Brian Gilmour, Nana Rezesidze, Tamar Beridze, Rusudan Chagelishvili

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Studies of ancient metallurgy are a subject of worldwide current interest. Georgia with its famous early metalworking traditions is one of the central parts of in the Caucasus region. The aim of the present study is to introduce the results of archaeometallurgical investigations being undertaken in the mountain region of Colchis, Lechkhumi (the Tsageri Municipality of western Georgia) and establish their place in the existing archaeological context. Lechkhumi (one of the historic provinces of Georgia known from Georgian, Greek, Byzantine and Armenian written sources as Lechkhumi/Skvimnia/Takveri) is the part of the Colchian mountain area. It is one of the important but little known centres of prehistoric metallurgy in the Caucasian region and of Colchian Bronze Age culture. Reconnaissance archaeological expeditions (2011-2015) revealed significant prehistoric metallurgical sites in Lechkhumi. Sites located in the vicinity of Dogurashi Village (Tsageri Municipality) have become the target area for archaeological excavations. During archaeological excavations conducted in 2016-2018 two archaeometallurgical sites – Dogurashi I and Dogurashi II were investigated. As a result of an interdisciplinary (archaeological, geological and geophysical) survey, it has been established that at both prehistoric Dogurashi mountain sites, it was copper that was being smelted and the ore sources are likely to be of local origin. Radiocarbon dating results confirm they were operating between about the 13th and 9th century BC. More recently another similar site has been identified in this area (Dogurashi III), and this is about to undergo detailed investigation. Other prehistoric metallurgical sites are being located and investigated in the Lechkhumi region as well as chance archaeological finds (often in hoards) – copper ingots, metallurgical production debris, slag, fragments of crucibles, tuyeres (air delivery pipes), furnace wall fragments and other related waste debris. Other chance finds being investigated are the many copper, bronze and (some) iron artefacts that have been found over many years. These include copper ingots, copper, bronze and iron artefacts such as tools, jewelry, and decorative items. These show the important but little known or understood the role of Lechkhumi in the late Bronze Age culture of Colchis. It would seem that mining and metallurgical manufacture form part of the local agricultural yearly lifecycle. Colchian ceramics have been found and also evidence for artefact production, small stone mould fragments and encrusted material from the casting of a fylfot (swastika) form of Colchian bronze buckle found in the vicinities of the early settlements of Tskheta and Dekhviri. Excavation and investigation of previously unknown archaeometallurgical sites in Lechkhumi will contribute significantly to the knowledge and understanding of prehistoric Colchian metallurgy in western Georgia (Adjara, Guria, Samegrelo, and Svaneti) and will reveal the importance of this region in the study of ancient metallurgy in Georgia and the Caucasus. Acknowledgment: This work has been supported by the Shota Rustaveli National Science Foundation (grant FR # 217128).

Keywords: archaeometallurgy, Colchis, copper, Lechkhumi

Procedia PDF Downloads 115

Authors: M. Amparo Nunez-Andres, Nieves Lantada

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One of the most harmful geological risks is rockfalls. They cause both economic lost, damaged in buildings and infrastructures, and personal ones. Therefore, in order to estimate the risk of the exposed elements, it is necessary to know the mechanism of this kind of events, since the characteristics of the rock walls, to the propagation of fragments generated by the initial detached rock mass. In the framework of the research RockModels project, several inventories of rockfalls were carried out along the northeast of the Spanish peninsula and the Mallorca island. These inventories have general information about the events, although the important fact is that they contained detailed information about fragmentation. Specifically, the IBSD (Insitu Block Size Distribution) is obtained by photogrammetry from drone or TLS (Terrestrial Laser Scanner) and the RBSD (Rock Block Size Distribution) from the volume of the fragment in the deposit measured by hand. In order to share all this information with other scientists, engineers, members of civil protection, and stakeholders, it is necessary a platform accessible from the internet and following interoperable standards. In all the process, open-software have been used: PostGIS 2.1., Geoserver, and OpenLayers library. In the first step, a spatial database was implemented to manage all the information. We have used the data specifications of INSPIRE for natural risks adding specific and detailed data about fragmentation distribution. The next step was to develop a WMS with Geoserver. A previous phase was the creation of several views in PostGIS to show the information at different scales of visualization and with different degrees of detail. In the first view, the sites are identified with a point, and basic information about the rockfall event is facilitated. In the next level of zoom, at medium scale, the convex hull of the rockfall appears with its real shape and the source of the event and fragments are represented by symbols. The queries at this level offer a major detail about the movement. Eventually, the third level shows all elements: deposit, source, and blocks, in their real size, if it is possible, and in their real localization. The last task was the publication of all information in a web mapping site (www.rockdb.upc.edu) with data classified by levels using libraries in JavaScript as OpenLayers.

Keywords: geological risk, web mapping, WMS, rockfalls

Procedia PDF Downloads 136

Authors: Leonie Bradfield, Stephen Fityus, John Simmons

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The shearing behavior of current and planned coal mine spoil dumps up to 400m in height is studied using large-sample-high-stress direct shear tests performed on a range of spoils common to the coalfields of Eastern Australia. The motivation for the study is to address industry concerns that some constructed spoil dump heights ( > 350m) are exceeding the scale ( ≤ 120m) for which reliable design information exists, and because modern geotechnical laboratories are not equipped to test representative spoil specimens at field-scale stresses. For more than two decades, shear strength estimation for spoil dumps has been based on either infrequent, very small-scale tests where oversize particles are scalped to comply with device specimen size capacity such that the influence of prototype-sized particles on shear strength is not captured; or on published guidelines that provide linear shear strength envelopes derived from small-scale test data and verified in practice by slope performance of dumps up to 120m in height. To date, these published guidelines appear to have been reliable. However, in the field of rockfill dam design there is a broad acceptance of a curvilinear shear strength envelope, and if this is applicable to coal mine spoils, then these industry-accepted guidelines may overestimate the strength and stability of dumps at higher stress levels. The pressing need to rationally define the shearing behavior of more representative spoil specimens at field-scale stresses led to the successful design, construction and operation of a large direct shear machine (LDSM) and its subsequent application to provide reliable design information for current and planned very-high dumps. The LDSM can test at a much larger scale, in terms of combined specimen size (720mm x 720mm x 600mm) and stress (σn up to 4.6MPa), than has ever previously been achieved using a direct shear machine for geotechnical testing of rockfill. The results of an extensive LDSM testing program on a wide range of coal-mine spoils are compared to a published framework that widely accepted by the Australian coal mining industry as the standard for shear strength characterization of mine spoil. A critical outcome is that the LDSM data highlights several non-compliant spoils, and stress-dependent shearing behavior, for which the correct application of the published framework will not provide reliable shear strength parameters for design. Shear strength envelopes developed from the LDSM data are also compared with dam engineering knowledge, where failure envelopes of rockfills are curved in a concave-down manner. The LDSM data indicates that shear strength envelopes for coal-mine spoils abundant with rock fragments are not in fact curved and that the shape of the failure envelope is ultimately determined by the strength of rock fragments. Curvilinear failure envelopes were found to be appropriate for soil-like spoils containing minor or no rock fragments, or hard-soil aggregates.

Keywords: coal mine, direct shear test, high dump, large scale, mine spoil, shear strength, spoil dump

Procedia PDF Downloads 143

Authors: V. Agostini, S. Gino, S. Inturri, A. Piccinini

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In cases of corpse identification or parental testing performed on exhumed alleged dead father, usually, we seek and acquire organic samples as bones and/or bone fragments, teeth, nails and muscle’s fragments. The DNA analysis of these cadaveric matrices usually leads to identifying success, but it often happens that the results of the typing are not satisfactory with highly degraded, partial or even non-interpretable genetic profiles. To aggravate the interpretative panorama deriving from the analysis of such 'classical' organic matrices, we must add a long and laborious treatment of the sample that starts from the mechanical fragmentation up to the protracted decalcification phase. These steps greatly increase the chance of sample contamination. In the present work, instead, we want to report the use of 'unusual' cadaveric matrices, demonstrating that their forensic genetics analysis can lead to better results in less time and with lower costs of reagents. We report six case reports, result of on-field experience, in which eyeswabs and cartilage were sampled and analyzed, allowing to obtain clear single genetic profiles, useful for identification purposes. In all cases we used the standard DNA tissue extraction protocols (as reported on the user manuals of the manufacturers such as QIAGEN or Invitrogen- Thermo Fisher Scientific), thus bypassing the long and difficult phases of mechanical fragmentation and decalcification of bones' samples. PCR was carried out using PowerPlex® Fusion System kit (Promega), and capillary electrophoresis was carried out on an ABI PRISM® 310 Genetic Analyzer (Applied Biosystems®), with GeneMapper ID v3.2.1 (Applied Biosystems®) software. The software Familias (version 3.1.3) was employed for kinship analysis. The genetic results achieved have proved to be much better than the analysis of bones or nails, both from the qualitative and quantitative point of view and from the point of view of costs and timing. This way, by using the standard procedure of DNA extraction from tissue, it is possible to obtain, in a shorter time and with maximum efficiency, an excellent genetic profile, which proves to be useful and can be easily decoded for later paternity tests and/or identification of human remains.

Keywords: DNA, eye swabs and cartilage, identification human remains, paternity testing

Procedia PDF Downloads 86

Authors: Abdul Ghaffar Memon, Xiao Hong Zhou, Yunpeng Xing, Ruoyu Wang, Miao He

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Due to deleterious environmental and health effects of the Hg²⁺ ions, various online, detection methods apart from the traditional analytical tools have been developed by researchers. Biosensors especially, label, label-free, colorimetric and optical sensors have advanced with sensitive detection. However, there remains a gap of ultrasensitive quantification as noise interact significantly especially in the AuNP based label-free colorimetry. This study reported an amplification strategy using Exo-III enzyme for target recycling of Hg²⁺ ions in a T-rich hairpin loop metallobase label-free colorimetric nanosensor with an improved sensitivity using unmodified gold nanoparticles (uGNPs) as an indicator. The two T-rich metallobase hairpin loop structures as 5’- CTT TCA TAC ATA GAA AAT GTA TGT TTG -3 (HgS1), and 5’- GGC TTT GAG CGC TAA GAA A TA GCG CTC TTT G -3’ (HgS2) were tested in the study. The thermodynamic properties of HgS1 and HgS2 were calculated using online tools (http://biophysics.idtdna.com/cgi-bin/meltCalculator.cgi). The lab scale synthesized uGNPs were utilized in the analysis. The DNA sequence had T-rich bases on both tails end, which in the presence of Hg²⁺ forms a T-Hg²⁺-T mismatch, promoting the formation of dsDNA. Later, the Exo-III incubation enable the enzyme to cleave stepwise mononucleotides from the 3’ end until the structure become single-stranded. These ssDNA fragments then adsorb on the surface of AuNPs in their presence and protect AuNPs from the induced salt aggregation. The visible change in color from blue (aggregation stage in the absence of Hg²⁺) and pink (dispersion state in the presence of Hg²⁺ and adsorption of ssDNA fragments) can be observed and analyzed through UV spectrometry. An ultrasensitive quantitative nanosensor employing Exo-III assisted target recycling of mercury ions through label-free colorimetry with nanomolar detection using uGNPs have been achieved and is further under the optimization to achieve picomolar range by avoiding the influence of the environmental matrix. The proposed strategy will supplement in the direction of uGNP based ultrasensitive, rapid, onsite, label-free colorimetric detection.

Keywords: colorimetric, Exo-III, gold nanoparticles, Hg²⁺ detection, label-free, signal amplification

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Authors: Hala Obeid

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Among the cities that have been touched by hard events and have been experiencing this polemic of existence, one can quote Beirut. A city that defies and confronts itself for its own existence. Beirut materialized all the social complexity; it has also preserved the memory of a society that has been able to build and reflect a certain unique identity. In spite of its glory, Lebanon’s civil war has marked a turning point in Beirut’s history. It has caused many deaths and opposed religious communities. Once this civil war has ended, the reconstruction of the city center, however, saw the spatial exclusion of manual labor, small local commerce, and middle-class residences. The urban functions that characterized the pre-war center were removed, and the city’s spontaneous evolutions were replaced by a historical urban planning, which neglected the city’s memory and identity. The social and spatial fragmentation that has erupted since the war has led to a breakdown of spatial and social boundaries within the city. The aim of this study is to evaluate the impact of fragmentation and boundaries on the city of Beirut in spatial, social, religious and ethnic terms. The method used in this research is what we call the mixed method which is a combination between the quantitative method and the qualitative one. These two approaches, in this case, do not oppose but complement each other in order to study the city of Beirut physically and socially. The main purpose of the qualitative approach is to describe and analyze the social phenomenon of the fragmentation of the city; this method can be summarized by the field observation and study. While the quantitative approach is based on filling out questionnaires that leads to statistics analyzes. Together, these two approaches will mark the course of the research. As a result, Beirut is not only a divided city but is fragmented spatially into many fragments and socially into many groups. This fragmentation is creating immaterial boundaries between fragments and therefore between groups. These urban and social boundaries are specifically religious and ethnic limits. As a conclusion, one of the most important and discussed boundary in Beirut is a spatial and religious boundary called ‘the green line’ or the demarcation line, a true caesura within the city. It marks the opposition of two urban groups and the aggravated fragmentation between them. This line divided Beirut into two compartments: East Beirut (for Christians) and West Beirut (for Muslims). This green line has become an urban void that holds the past in suspension. Finally, to think of Beirut as an urban unit becomes an insoluble problem.

Keywords: Beirut, boundaries, fragmentation, identity

Procedia PDF Downloads 144

Authors: Christopher Baiyegunhi, Kuiwu Liu, Oswald Gwavava

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Petrography of the sandstones of Ecca Group, Karoo Supergroup in the Eastern Cape Province of South Africa have been investigated on composition, provenance and influence of weathering conditions. Petrographic studies based on quantitative analysis of the detrital minerals revealed that the sandstones are composed mostly of quartz, feldspar and lithic fragments of metamorphic and sedimentary rocks. The sandstones have an average framework composition of 24.3% quartz, 19.3% feldspar, 26.1% rock fragments, and 81.33% of the quartz grains are monocrystalline. These sandstones are generally very fine to fine grained, moderate to well sorted, and subangular to subrounded in shape. In addition, they are compositionally immature and can be classified as feldspathic wacke and lithic wacke. The absence of major petrographically distinctive compositional variations in the sandstones perhaps indicate homogeneity of their source. As a result of this, it is inferred that the transportation distance from the source area was quite short and the main mechanism of transportation was by river systems to the basin. The QFL ternary diagrams revealed dissected and transitional arc provenance pointing to an active margin and uplifted basement preserving the signature of a recycled provenance. This is an indication that the sandstones were derived from a magmatic arc provenance. Since magmatic provenance includes transitional arc and dissected arc, it also shows that the source area of the Ecca sediments had a secondary sedimentary and metasedimentary rocks from a marginal belt that developed as a result of rifting. The weathering diagrams and semi-quantitative weathering index indicate that the Ecca sandstones are mostly from a plutonic source area, with climatic conditions ranging from arid to humid. The compositional immaturity of the sandstones is suggested to be due to weathering or recycling and low relief or short transport from the source area. The detrital modal compositions of these sandstones are related to back arc to island and continental margin arc. The origin and deposition of the Ecca sandstones are due to low-moderate weathering, recycling of pre-existing rocks, erosion and transportation of debris from the orogeny of the Cape Fold Belt.

Keywords: petrography, tectonic setting, provenance, Ecca Group, Karoo Basin

Procedia PDF Downloads 388

Authors: Amy Pullen, Samantha Rodrigues, David Kieser, Brian Shaw

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The aim of the study was to determine if a projectile interacting with the lungs increases the severity of injury in comparison to a projectile interacting with the ribs or intercostal muscle. This comparative study employed a 10% gelatine based model with either porcine ribs or balloons embedded to represent a lung. Four sample groups containing five samples were evaluated; these were control (plain gel), intercostal impact, rib impact, and lung impact. Two ammunition natures were evaluated at a range of 10m; these were 5.56x45mm and 7.62x51mm. Aspects of projectile behavior were quantified including exiting projectile weight, location of yawing, projectile fragmentation and distribution, location and area of the temporary cavity, permanent cavity formation, and overall energy deposition. Major findings included the cavity showing a higher percentage of the projectile weight exit the block than the intercostal and ribs, but similar to the control for the 5.56mm ammunition. However, for the 7.62mm ammunition, the lung was shown to have a higher percentage of the projectile weight exit the block than the control, intercostal and ribs. The total weight of projectile fragments as a function of penetration depth revealed large fluctuations and significant intra-group variation for both ammunition natures. Despite the lack of a clear trend, both plots show that the lung leads to greater projectile fragments exiting the model. The lung was shown to have a later center of the temporary cavity than the control, intercostal and ribs for both ammunition types. It was also shown to have a similar temporary cavity volume to the control, intercostal and ribs for the 5.56mm ammunition and a similar temporary cavity to the intercostal for the 7.62mm ammunition The lung was shown to leave a similar projectile tract than the control, intercostal and ribs for both ammunition types. It was also shown to have larger shear planes than the control and the intercostal, but similar to the ribs for the 5.56mm ammunition, whereas it was shown to have smaller shear planes than the control but similar shear planes to the intercostal and ribs for the 7.62mm ammunition. The lung was shown to have less energy deposited than the control, intercostal and ribs for both ammunition types. This comparative study provides insights into the influence of the lungs on thoracic gunshot trauma. It indicates that the lungs limits projectile deformation and causes a later onset of yawing and subsequently limits the energy deposited along the wound tract creating a deeper and smaller cavity. This suggests that lung impact creates an altered pattern of local energy deposition within the target which will affect the severity of trauma.

Keywords: ballistics, lung, trauma, wounding

Procedia PDF Downloads 141

Authors: Weicheng Luo, Wenzhi Zhao

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Plants growth in desert often suffered from stresses like water deficit, wind erosion and sand burial. Thus, plants in desert always have unique strategies to adapt these stresses. However, data regarding how clonal shrubs withstand wind erosion and sand burial in natural habitats remain relatively scarce. Therefore, we selected a common clonal shrub Calligonum arborescens to study the adaptive strategies of clonal plants to sand dune environment in a transitional zone of desert and Hexi Oasis of China. Our results show that sand burial is one of the essential prerequisites for the survival of C. arborescens rhizome fragments. Both the time and degrees of sand burial and wind erosion had significantly effects on clonal reproduction and growth of C. arborescens. With increasing burial depth, the number of ramets and biomass production significantly decreased. There is same change trend in severe erosion treatments. However, the number of ramets and biomass production significantly increased in moderate erosion treatments. Rhizome severed greatly decreased ramet number and biomass production under both sand burial and severe erosion treatments. That indicated that both sand burial and severe erosion had negative effects on the clonal growth of C. arborescens, but moderate wind erosion had positive effects. And rhizome connections alleviated the negative effects of sand burial and of severe erosion on the growth and performance of C. arborescens. Most fragments of C. arborescens grew in the directions of northeastern and southwestern. Ramet number and biomass, rhizome length and biomass in these two directions were significantly higher than those found in other directions. Interestingly, these directions were perpendicular to the prevailing wind direction. Distribution of C. arborescens differed in different habitats. The total number of individuals was significantly higher in inter-dune areas and on windward slopes than on the top and leeward slopes of dunes; more clonal ramets were produced on the top of dunes than elsewhere, and a few were found on leeward slopes. The mainly reason is that ramets on windward and top of dunes can easily suffered with moderated wind erosion which promoted clonal growth and reproduction of C. arborescens. These results indicated that C. arborescens adapted sand dune environment through directional growth and patchy distribution, and sand-burial and wind erosion were the key factors which led to the directional growth and patchiness of C. arborescens.

Keywords: adaptive strategy, Calligonum arborescens Litv, clonal fragment, desert-oasis transitional zone, sand burial and wind erosion

Procedia PDF Downloads 211

Authors: Marcin Stasiulewicz, Sebastian Filipkowski, Aneta Panuszko

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Background: The hallmark of neurodegenerative diseases, including Alzheimer's and Parkinson's diseases, is an aggregation of the abnormal forms of peptides and proteins. Water is essential to functioning biomolecules, and it is one of the key factors influencing protein folding and misfolding. However, the hydration studies of proteins are complicated due to the complexity of protein systems. The use of model compounds can facilitate the interpretation of results involving larger systems. Objectives: The goal of the research was to characterize the properties of the hydration water surrounding the two three-residue K peptide fragments INS (Isoleucine - Asparagine - Serine) and NSR (Asparagine - Serine - Arginine). Methods: Fourier-transform infrared spectra of aqueous solutions of the tripeptides were recorded on Nicolet 8700 spectrometer (Thermo Electron Co.) Measurements were carried out at 25°C for varying molality of solute. To remove oscillation couplings from water spectra and, consequently, obtain narrow O-D semi-heavy water bands (HDO), the isotopic dilution method of HDO in H₂O was used. The difference spectra method allowed us to isolate the tripeptide-affected HDO spectrum. Results: The structural and energetic properties of water affected by the tripeptides were compared to the properties of pure water. The shift of the values of the gravity center of bands (related to the mean energy of water hydrogen bonds) towards lower values with respect to the ones corresponding to pure water suggests that the energy of hydrogen bonds between water molecules surrounding tripeptides is higher than in pure water. A comparison of the values of the mean oxygen-oxygen distances in water affected by tripeptides and pure water indicates that water-water hydrogen bonds are shorter in the presence of these tripeptides. The analysis of differences in oxygen-oxygen distance distributions between the tripeptide-affected water and pure water indicates that around the tripeptides, the contribution of water molecules with the mean energy of hydrogen bonds decreases, and simultaneously the contribution of strong hydrogen bonds increases. Conclusions: It was found that hydrogen bonds between water molecules in the hydration sphere of tripeptides are shorter and stronger than in pure water. It means that in the presence of the tested tripeptides, the structure of water is strengthened compared to pure water. Moreover, it has been shown that in the vicinity of the Asparagine - Serine - Arginine, water forms stronger and shorter hydrogen bonds. Acknowledgments: This work was funded by the National Science Centre, Poland (grant 2017/26/D/NZ1/00497).

Keywords: amyloids, K-peptide, hydration, FTIR spectroscopy

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Authors: S. Woźniak, J. Rybka, T. Paszkowski, P. Milart

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A 30-year-old patient, who was pregnant for her second 9 weeks, was admitted to the hospital due to a suspected incomplete miscarriage. A fetal egg was found in the uterine cavity near the mouth of the fallopian tube. The patient was qualified for dilatation and curettage. The histopathological examination revealed fragments of the trophoblast. Two months later, the patient was re-admitted to the hospital due to vaginal bleeding and elevated levels of beta-hCG. Additional tests were performed. An intramural pregnancy was suspected. The patient was qualified for embolization of the uterine arteries and then treatment with methotrexate. Three weeks later, during a routine gynecological examination, a detached tumor 4 cm in diameter was found in the vagina. The material was sent for histopathological examination, which showed the presence of trophoblastic cells.

Keywords: ectopic pregnancy, intramural pregnancy, uterine artery embolization, methotrexate

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Authors: Yeimy L. Quintana, Juan G. Zuluaga, Sandra S. Arango

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The comet assay is a method based on electrophoresis that is used to measure DNA damage in cells and has shown important results in the identification of substances with a potential risk to the human population as innumerable physical, chemical and biological agents. With this technique is possible to obtain images like a comet, in which the tail of these refers to damaged fragments of the DNA. One of the main problems is that the image has unequal luminosity caused by the fluorescence microscope and requires different processing to condition it as well as to know how many optimal comets there are per sample and finally to perform the measurements and determine the percentage of DNA damage. In this paper, we propose the design and implementation of software using Image Processing Toolbox-MATLAB that allows the automation of image processing. The software chooses the optimum comets and measuring the necessary parameters to detect the damage.

Keywords: artificial vision, comet assay, DNA damage, image processing

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Authors: Clara Tramuta, Floris Irene, Daniela Manila Bianchi, Monica Pitti, Giulia Federica Cazzaniga, Lucia Decastelli

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This work presents the results obtained by the Regional Reference Centre for Salmonella Typing (CeRTiS) in a retrospective study aimed to investigate, through Pulsed-field Gel Electrophoresis (PFGE) analysis, the genetic relatedness of emerging Salmonella serotypes of human origin circulating in North-West of Italy. Furthermore, the goal of this work was to create a Regional database to facilitate foodborne outbreak investigation and to monitor them at an earlier stage. A total of 112 strains, isolated from 2016 to 2018 in hospital laboratories, were included in this study. The isolates were previously identified as Salmonella according to standard microbiological techniques and serotyping was performed according to ISO 6579-3 and the Kaufmann-White scheme using O and H antisera (Statens Serum Institut®). All strains were characterized by PFGE: analysis was conducted according to a standardized PulseNet protocol. The restriction enzyme XbaI was used to generate several distinguishable genomic fragments on the agarose gel. PFGE was performed on a CHEF Mapper system, separating large fragments and generating comparable genetic patterns. The agarose gel was then stained with GelRed® and photographed under ultraviolet transillumination. The PFGE patterns obtained from the 112 strains were compared using Bionumerics version 7.6 software with the Dice coefficient with 2% band tolerance and 2% optimization. For each serotype, the data obtained with the PFGE were compared according to the geographical origin and the year in which they were isolated. Salmonella strains were identified as follow: S. Derby n. 34; S. Infantis n. 38; S. Napoli n. 40. All the isolates had appreciable restricted digestion patterns ranging from approximately 40 to 1100 kb. In general, a fairly heterogeneous distribution of pulsotypes has emerged in the different provinces. Cluster analysis indicated high genetic similarity (≥ 83%) among strains of S. Derby (n. 30; 88%), S. Infantis (n. 36; 95%) and S. Napoli (n. 38; 95%) circulating in north-western Italy. The study underlines the genomic similarities shared by the emerging Salmonella strains in Northwest Italy and allowed to create a database to detect outbreaks in an early stage. Therefore, the results confirmed that PFGE is a powerful and discriminatory tool to investigate the genetic relationships among strains in order to monitoring and control Salmonellosis outbreak spread. Pulsed-field gel electrophoresis (PFGE) still represents one of the most suitable approaches to characterize strains, in particular for the laboratories for which NGS techniques are not available.

Keywords: emerging Salmonella serotypes, genetic characterization, human strains, PFGE

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Authors: Atsuko Okazaki, Jurg Ott

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Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

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Authors: Palwinder Singh

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Beyond the conventional mode of working with anti-inflammatory agents through enzyme inhibition, herein, an alternate substrate of cyclooxygenase-2 was developed. Proline centered pentapeptide iso-conformational to arachidonic acid exhibited appreciable selectivity for COX-2 overcoming acetic acid and formalin induced pain in rats to almost 80% and was treated as a substrate by the enzyme. Remarkably, COX-2 metabolized the pentapeptide into small fragments consisting mainly of di- and tri-peptides that ensured the safe breakdown of the peptide under in-vivo conditions. The kinetic parameter Kcat/Km for COX-2 mediated metabolism of peptide 6.3 x 105 M-1 s-1 was quite similar to 9.5 x 105 M-1 s-1 for arachidonic acid. Evidenced by the dynamic molecular studies and the use of Y385F COX-2, it was observed that the breakage of the pentapeptide has probably taken place through H-bond activation of the peptide bond by the side chains of Y385 and S530.

Keywords: small peptides, anti-inflammatory agents, cyclooxygenase-2, unnatural substrates

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Authors: P. Karalis, E. Dotsika, A. Godelitsas, M. Tassi, D. Ignatiadou

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Glass artefacts originated from Northern Greece, dated between 1st and 6th AC, were analyzed for their oxygen isotopic and chemical compositions in order to identify their raw materials provenance. The chemical composition of these glasses is rather heterogeneous although they are all obtained with natron as flux, having both K₂O and MgO contents lower than 1.5 wt%. The majority of these samples have a homogeneous oxygen isotopic composition (𝛿18O= 16‰,), which is equal to or very close to the mean value of “Roman” glass (from about 15‰ to 16.0‰). The rest of the samples present heavily enriched 𝛿18O values that indicate that their raw materials differ from those normally used in Roman and Medieval glass production, and this matches with the possibility of the different origins of these materials. So, all these fragments are soda-lime-silica natron-glass produced from natron, possibly coming from more than one source.

Keywords: ancient glass, provenance of raw materials of ancient glass, roman glass, oxygen isotope analysis in glass

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Authors: Natia Jalagonia, Jimsher Maisuradze, Karlo Barbakadze, Tinatin Kuchukhidze

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At present intensive scientific researches of ceramics, cermets and metal alloys have been conducted for improving materials physical-mechanical characteristics. In purpose of increasing impact strength of ceramics based on alumina, simple method of graphene homogenization was developed. Homogeneous distribution of graphene (homogenization) in pressing composite became possible through the connection of functional groups of graphene oxide (-OH, -COOH, -O-O- and others) and alumina superficial OH groups with aluminum organic compounds. These two components connect with each other with -O-Al–O- bonds, and by their thermal treatment (300–500°C), graphene and alumina phase are transformed. Thus, choosing of aluminum organic compounds for modification is stipulated by the following opinion: aluminum organic compounds fragments fixed on graphene and alumina finally are transformed into an integral part of the matrix. By using of other elements as modifier on the matrix surface (Al2O3) other phases are transformed, which change sharply physical-mechanical properties of ceramic composites, for this reason, effect caused by the inclusion of graphene will be unknown. Fixing graphene fragments on alumina surface by alumoorganic compounds result in new type graphene-alumina complex, in which these two components are connected by C-O-Al bonds. Part of carbon atoms in graphene oxide are in sp3 hybrid state, so functional groups (-OH, -COOH) are located on both sides of graphene oxide layer. Aluminum organic compound reacts with graphene oxide at the room temperature, and modified graphene oxide is obtained: R2Al-O-[graphene]–COOAlR2. Remaining Al–C bonds also reacts rapidly with surface OH groups of alumina. In a result of these process, pressing powdery composite [Al2O3]-O-Al-O-[graphene]–COO–Al–O–[Al2O3] is obtained. For the purpose, graphene oxide suspension in dry toluene have added alumoorganic compound Al(iC4H9)3 in toluene with equimolecular ratio. Obtained suspension has put in the flask and removed solution in a rotary evaporate presence nitrogen atmosphere. Obtained powdery have been researched and used to consolidation of ceramic materials based on alumina. Ceramic composites are obtained in high temperature vacuum furnace with different temperature and pressure conditions. Received ceramics do not have open pores and their density reaches 99.5 % of TD. During the work, the following devices have been used: High temperature vacuum furnace OXY-GON Industries Inc (USA), device of spark-plasma synthesis, induction furnace, Electronic Scanning Microscopes Nikon Eclipse LV 150, Optical Microscope NMM-800TRF, Planetary mill Pulverisette 7 premium line, Shimadzu Dynamic Ultra Micro Hardness Tester DUH-211S, Analysette 12 Dynasizer and others.

Keywords: graphene oxide, alumo-organic, ceramic

Procedia PDF Downloads 286

Authors: Swati Srivastava, Mattia Lauriola, Yuval Gilad, Adi Kimchi, Yosef Yarden

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The glucocorticoid receptor (GR) has been proposed to play important, but incompletely understood roles in cancer. Glucocorticoids (GCs) are widely used as co-medication of various carcinomas, due to their ability to reduce the toxicity of chemotherapy. Furthermore, GR antagonism has proven to be a strategy to treat triple negative breast cancer and castration-resistant prostate cancer. These observations suggest differential GR involvement in cancer subtypes. The goal of our study has been to elaborate the current understanding of GR signaling in tumor progression and metastasis. Our study involves two cellular models, non-tumorigenic breast epithelial cells (MCF10A) and Ewing sarcoma cells (CHLA9). In our breast cell model, the results indicated that the GR agonist dexamethasone inhibits EGF-induced mammary cell migration, and this effect was blocked when cells were stimulated with a GR antagonist, namely RU486. Microarray analysis for gene expression revealed that the mechanism underlying inhibition involves dexamenthasone-mediated repression of well-known activators of EGFR signaling, alongside with enhancement of several EGFR’s negative feedback loops. Because GR mainly acts primarily through composite response elements (GREs), or via a tethering mechanism, our next aim has been to find the transcription factors (TFs) which can interact with GR in MCF10A cells.The TF-binding motif overrepresented at the promoter of dexamethasone-regulated genes was predicted by using bioinformatics. To validate the prediction, we performed high-throughput Protein Complementation Assays (PCA). For this, we utilized the Gaussia Luciferase PCA strategy, which enabled analysis of protein-protein interactions between GR and predicted TFs of mammary cells. A library comprising both nuclear receptors (estrogen receptor, mineralocorticoid receptor, GR) and TFs was fused to fragments of GLuc, namely GLuc(1)-X, X-GLuc(1), and X-GLuc(2), where GLuc(1) and GLuc(2) correspond to the N-terminal and C-terminal fragments of the luciferase gene.The resulting library was screened, in human embryonic kidney 293T (HEK293T) cells, for all possible interactions between nuclear receptors and TFs. By screening all of the combinations between TFs and nuclear receptors, we identified several positive interactions, which were strengthened in response to dexamethasone and abolished in response to RU486. Furthermore, the interactions between GR and the candidate TFs were validated by co-immunoprecipitation in MCF10A and in CHLA9 cells. Currently, the roles played by the uncovered interactions are being evaluated in various cellular processes, such as cellular proliferation, migration, and invasion. In conclusion, our assay provides an unbiased network analysis between nuclear receptors and other TFs, which can lead to important insights into transcriptional regulation by nuclear receptors in various diseases, in this case of cancer.

Keywords: epidermal growth factor, glucocorticoid receptor, protein complementation assay, transcription factor

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Authors: Nadjib Drouiche, Abdenour Lami, Salaheddine Aoudj, Tarik Ouslimane

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Although solar cells manufacturing is a conservative industry, economics drivers continue to encourage innovation, feedstock savings and cost reduction. Kerf slurry waste is a complex product containing both valuable substances as well as contaminants. The valuable substances are: i) high purity silicon, ii) polyethylene glycol, and iii) silicon carbide. The contaminants mainly include metal fragments and organics. Therefore, recycling of the kerf slurry waste is an important subject not only from the treatment of waste but also from the recovery of valuable products. The present paper relates to processes for the recovery of valuable products from the kerf slurry waste in which they are contained, such products comprising nanoparticles, polyethylene glycol, high purity silicon, and silicon carbide.

Keywords: photovoltaic cell, Kerf slurry waste, recycling, silicon carbide

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Authors: Veronika Antoniou, Rene Carraz, Yiorgos Hadjichristou

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The Green Urban Lab took the form of public installations that were placed at various locations in four cities in Cyprus. These installations - through which a series of events, activities, workshops and research took place - were the main tools in regenerating a series of urban public spaces in Cyprus. The purpose of this project was to identify issues and opportunities related to public space and to offer guidelines on how design and participatory democracy improvements could strengthen civil society, while raising the quality of the urban public scene. Giant inflatable structures were injected in important urban fragments in order to accommodate series of events. The design and playful installation generated a wide community engagement. The fluid presence of the installations acted as a catalyst for social interaction. They were accessed and viewed effortlessly and surprisingly, creating opportunities to rediscover public spaces.

Keywords: bottom-up initiatives, creativity, public space, social innovation, urban environments

Procedia PDF Downloads 492

Authors: Keping Zuo, Jia Yin Chia, Gideon Praveen Kumar Vijayakumar, Foad Kabinejadian, Fangsen Cui, Pei Ho, Hwa Liang Leo

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Carotid artery is the major vessel supplying blood to the brain. Carotid artery stenosis is one of the three major causes of stroke and the stroke is the fourth leading cause of death and the first leading cause of disability in most developed countries. Although there is an increasing interest in carotid artery stenting for treatment of cervical carotid artery bifurcation therosclerotic disease, currently available bare metal stents cannot provide an adequate protection against the detachment of the plaque fragments over diseased carotid artery, which could result in the formation of micro-emboli and subsequent stroke. Our research group has recently developed a novel preferential covered-stent for carotid artery aims to prevent friable fragments of atherosclerotic plaques from flowing into the cerebral circulation, and yet retaining the ability to preserve the flow of the external carotid artery. The preliminary animal studies have demonstrated the potential of this novel covered-stent design for the treatment of carotid therosclerotic stenosis. The purpose of this study is to evaluate the biomechanical property of PU membrane of different concentration configurations in order to refine the stent coating technique and enhance the clinical performance of our novel carotid covered stent. Results from this study also provide necessary material property information crucial for accurate simulation analysis for our stents. Method: Medical grade Polyurethane (ChronoFlex AR) was used to prepare PU membrane specimens. Different PU membrane configurations were subjected to uniaxial test: 22%, 16%, and 11% PU solution were made by mixing the original solution with proper amount of the Dimethylacetamide (DMAC). The specimens were then immersed in physiological saline solution for 24 hours before test. All specimens were moistened with saline solution before mounting and subsequent uniaxial testing. The specimens were preconditioned by loading the PU membrane sample to a peak stress of 5.5 Mpa for 10 consecutive cycles at a rate of 50 mm/min. The specimens were then stretched to failure at the same loading rate. Result: The results showed that the stress-strain response curves of all PU membrane samples exhibited nonlinear characteristic. For the ultimate failure stress, 22% PU membrane was significantly higher than 16% (p<0.05). In general, our preliminary results showed that lower concentration PU membrane is stiffer than the higher concentration one. From the perspective of mechanical properties, 22% PU membrane is a better choice for the covered stent. Interestingly, the hyperelastic Ogden model is able to accurately capture the nonlinear, isotropic stress-strain behavior of PU membrane with R2 of 0.9977 ± 0.00172. This result will be useful for future biomechanical analysis of our stent designs and will play an important role for computational modeling of our covered stent fatigue study.

Keywords: carotid artery, covered stent, nonlinear, hyperelastic, stress, strain

Procedia PDF Downloads 282

Authors: P. M. Ikonić, T. A. Tasić, L. S. Petrović, S. B. Škaljac, M. R. Jokanović, V. M. Tomović, B. V. Šojić, N. R. Džinić, A. M. Torbica, B. B. Ikonić

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The aim of the study was to determine how different ripening processes (traditional vs. industrial) influenced the proteolysis in traditional Serbian dry-fermented sausage Petrovská klobása. The obtained results indicated more intensive pH decline (0.7 units after 9 days) in industrially ripened products (I), what had a positive impact on drying process and proteolytic changes in these samples. Thus, moisture content in I sausages was lower at each sampling time, amounting 24.7% at the end of production period (90 days). Likewise, the process of proteolysis was more pronounced in I samples, resulting in higher contents of non-protein nitrogen (NPN) and free amino acids nitrogen (FAAN), as well as in faster and more intensive degradation of myosin (≈220 kDa), actin (≈45 kDa) and other polypeptides during processing. Consequently, the appearance and accumulation of several protein fragments were registered.

Keywords: dry-fermented sausage, Petrovská klobása, proteolysis, ripening process

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Authors: Aliyu Adamu, Fahrul Huyop, Roswanira Abdul Wahab, Mohd Shahir Shamsir

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Halogenated organic compounds occur in huge amount in biosphere. This is attributable to the diverse use of halogen-based compounds in the synthesis of various industrially important products. Halogenated compound is toxic and may persist in the environment, thereby causing serious health and environmental pollution problems. L-2-haloacid dehalogenases (EC 3.8.1.2) catalyse the specific cleavage of carbon-halogen bond in L-isomers of halogenated compounds, which consequently reverse the effects of environmental halogen-associated pollution. To enhance the efficiency and utility of these enzymes, this study investigates the catalytic amino acid residues and the molecular functional mechanism of DehL, by classical molecular dynamic simulations, MM-PBSA and ab initio fragments molecular orbital (FMO) calculations. The results of the study will serve as the basis for the molecular engineering of the enzyme.

Keywords: DehL, Functional mechanism, Catalytic residues, L-2-haloacid dehalogenase

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Authors: Elissandro Voigt Beier, Cristiano Poleto

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The main objective of the research is to assess the loss through the quantification of material culture (archaeological fragments) in rural areas, sites explored economically by machining on seasonal crops, and also permanent, in a hydrographic subsystem Camaquã River in the state of Rio Grande do Sul, Brazil. The study area consists of different micro basins and differs in area, ranging between 1,000 m² and 10,000 m², respectively the largest and the smallest, all with a large number of occurrences and outcrop locations of archaeological material and high density in intense farm environment. In the first stage of the research aimed to identify the dispersion of points of archaeological material through field survey through plot points by the Global Positioning System (GPS), within each river basin, was made use of concise bibliography on the topic in the region, helping theoretically in understanding the old landscaping with preferences of occupation for reasons of ancient historical people through the settlements relating to the practice observed in the field. The mapping was followed by the cartographic development in the region through the development of cartographic products of the land elevation, consequently were created cartographic products were to contribute to the understanding of the distribution of the absolute materials; the definition and scope of the material dispersed; and as a result of human activities the development of revolving letter by mechanization of in situ material, it was also necessary for the preparation of materials found density maps, linking natural environments conducive to ancient historical occupation with the current human occupation. The third stage of the project it is for the systematic collection of archaeological material without alteration or interference in the subsurface of the indigenous settlements, thus, the material was prepared and treated in the laboratory to remove soil excesses, cleaning through previous communication methodology, measurement and quantification. Approximately 15,000 were identified archaeological fragments belonging to different periods of ancient history of the region, all collected outside of its environmental and historical context and it also has quite changed and modified. The material was identified and cataloged considering features such as object weight, size, type of material (lithic, ceramic, bone, Historical porcelain and their true association with the ancient history) and it was disregarded its principles as individual lithology of the object and functionality same. As observed preliminary results, we can point out the change of materials by heavy mechanization and consequent soil disturbance processes, and these processes generate loading of archaeological materials. Therefore, as a next step will be sought, an estimate of potential losses through a mathematical model. It is expected by this process, to reach a reliable model of high accuracy which can be applied to an archeological site of lower density without encountering a significant error.

Keywords: degradation of heritage, quantification in archaeology, watershed, use and occupation of land

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Authors: Lilia M. Fernando, Matthew K. Vasher, Evangelyn C. Alocilja

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This paper describes the development of a DNA-based nanobiosensor to detect the dengue virus in mosquito using electrically active magnetic (EAM) nanoparticles as the concentrator and electrochemical transducer. The biosensor detection encompasses two sets of oligonucleotide probes that are specific to the dengue virus: the detector probe labeled with the EAM nanoparticles and the biotinylated capture probe. The DNA targets are double hybridized to the detector and the capture probes and concentrated from nonspecific DNA fragments by applying a magnetic field. Subsequently, the DNA sandwiched targets (EAM-detector probe–DNA target–capture probe-biotin) are captured on streptavidin modified screen printed carbon electrodes through the biotinylated capture probes. Detection is achieved electrochemically by measuring the oxidation–reduction signal of the EAM nanoparticles. Results indicate that the biosensor is able to detect the redox signal of the EAM nanoparticles at dengue DNA concentrations as low as 10 ng/ul.

Keywords: dengue, magnetic nanoparticles, mosquito, nanobiosensor

Procedia PDF Downloads 332

Authors: Tammy Shel (Aboody)

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The integration of philosophy with ethnography, i.e., ethno-philosophy, or any qualitative method, is multi-dimensional. It is, thus, vital to the discourse on caring in the philosophy of education, and in therapy. These two significant dimensions are focal in this proposal’s discussion. The integration of grounded data with philosophy can shed light on cultural, gender, socio-economic and political diversities in the relationships and interactions between and among individuals and societies. This approach can explain miscommunication and, eventually, violent conflicts. The ethno-philosophy study in this proposal focuses on the term caring, through case studies of 5 non-white male and female elementary school teachers in Los Angeles County. The study examined the teachers’ views on caring and, consequently, the implications on their pedagogy. Subsequently, this method turned out to also be a caring approach in therapy. Ethnographic data was juxtaposed with western philosophy. Research discussion unraveled transformable gaps between western patriarchal and feminist philosophy on caring, and that of the teachers. Multiple interpretations and practices of caring were found due to cultural, gender, and socio-economic-political differences. Likewise, two dominant categories emerged. The first is inclusive caring, which is perceived as an ideal, as the compass of humanity that aims towards emancipation from the shackles of inner and external violence. The second is tribal caring, which illuminates the inherently dialectical substantial diversity in the interpretations and praxes of caring. Such angles are absent or minor in traditional western literature. Both categories teach of the incessant dynamic definition of caring, and its subliminal and repressed mechanisms. The multi-cultural aspects can teach us, however, that despite the inclusive common ground we share on caring, and despite personal and social awareness of cultural and gender differences, the hegemonic ruling-class governs the standardized conventional interpretation of caring. Second is the dimension of therapy in ethno-philosophy. Each patient is like a case study per se, and is a self-ethnographer. Thus, the patient is the self-observer and data collector, and the therapist is the philosopher who helps deconstruct into fragments the consciousness that comprises our well-being and self-esteem and acceptance. Together, they both identify and confront hurdles that hinder the pursuit of a more composed attitude towards ourselves and others. Together, they study and re-organize these fragments into a more comprehensible and composed self-acceptance. Therefore, the ethno-philosophy method, which stems from a caring approach, confronts the internal and external conflicts that govern our relationships with others. It sheds light on the dark and subliminal spots in our minds and hearts that operate us. Unveiling the hidden spots helps identify a shared ground that can supersede miscommunication and conflicts among and between people. The juxtaposition of ethnography with philosophy, as a caring approach in education and therapy, emphasizes that planet earth is like a web. Hence, despite the common mechanism that stimulates a caring approach towards the other, ethno-philosophy can help undermine the ruling patriarchal oppressive forces that define and standardize caring relationships, and to subsequently bridge gaps between people.

Keywords: caring, philosophy of education, ethnography, therapy, research

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Authors: Harsha B. R., K. S. Anil Kumar

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A profile was dug at the University of Agricultural Sciences, Bangalore, where grapes were intensively cultivated for 25 years on the dimension of 1.5 × 1.5 × 1.5 m. Demarcation was done on the basis of texture, structure, colour, and the details like depth, texture, colour, consistency, rock fragments, presence of mottles, and structure were recorded and studied according to standard performa of soil profile description. Horizons noticed were Ap, Bt1, Bt2, Bt3, Bt4C, Bt5C and BC with respective depths of 0-13, 13-37, 37-60, 60-78, 78-104, 104-130 and 130-151+ cm. The reddish-brown colour was noticed in Ap, Bt1, and Bt2 horizons. The sub-angular blocky structure was observed in all the layers with slightly acid in reaction. Clear and abrupt smooth boundaries were present between two respective layers with clayey texture in all the horizons except the Ap horizon, which was clay loam in texture. Variegated soil colours and iron concretions were observed in Bt4, Bt5, and BC horizons. Clay skins were observed in Bt and BC horizons. Soils were of highly friable consistency for grapes cultivation.

Keywords: soil morphology, horizons, clay skins, consistency, vineyards

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Authors: Aliyu Isah Agaie, Masrah Azrifah Azmi Murad, Nurfadhlina Mohd Sharef, Aida Mustapha

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Natural Language Interfaces typically support a restricted language and also have scopes and limitations that naïve users are unaware of, resulting in errors when the users attempt to retrieve information from ontologies. To overcome this challenge, an auto-suggest feature is introduced into the querying process where users are guided through the querying process using interactive query construction system. Guiding users to formulate their queries, while providing them with an unconstrained (or almost unconstrained) way to query the ontology results in better interpretation of the query and ultimately lead to an effective search. The approach described in this paper is unobtrusive and subtly guides the users, so that they have a choice of either selecting from the suggestion list or typing in full. The user is not coerced into accepting system suggestions and can express himself using fragments or full sentences.

Keywords: auto-suggest, expressiveness, habitability, natural language interface, query interpretation, user guidance

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Authors: A. T. Adetunji, F. B. Lewu, R. Mundembe

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Plants require nitrogen (N) to support desired production levels. Nitrogen is available to plants in the form of nitrate or ammonium, which are transported into the cell with the aid of various transport proteins. Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which nitrogen is preferentially absorbed by plants. Solanum tuberosum AMT1 (StAMT1) was characterized using molecular biology and bioinformatics methods. Nucleotide database sequences were used to design AMT1-specific primers which were used to amplify the AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned StAMT1 to the AMT1 family. The deduced amino acid sequences showed that StAMT1 is 92%, 83% and 76% similar to Solanum lycopersicum LeAMT1.1, Lotus japonicus LjAMT1.1 and Solanum lycopersicum LeAMT1.2 respectively. StAMT1 fragments were shown to correspond to the 5th - 10th trans-membrane domains. Residue StAMT1 D15 is predicted to be essential for ammonium transport, while mutations of StAMT1 S76A may further enhance ammonium transport.

Keywords: ammonium transporter, bioinformatics, nitrogen, primers, Solanum tuberosum

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Authors: Aptin Rahnavard, Ghavamaldin Asadian, Khalil Pourshamsian, Mariamalsadat Taghavi

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Dog rose is one of the important rose species in Iran that the distant past had been considered due to nutritional value and medicinal. Despite its long history of use, due to poor information on the genetic modification of plants has been done resources inheritance. In this study was to assess the genetic diversity. Total of 30 genotypes Dog rose from areas of northern Iran in the Caspian region (provinces of Guilan and Mazandaran) were evaluated using 25 RAPD primers. The number of bands produced total of 202 and for each primer were measured in a bands with an average 8-band .The number of polymorphic bands per primer ranged from 1 to 13 and the bands were in the range of 300 to 3000 bp. Based on the results OPA-04 primer with 13 bands and PRA-1, E-09 and A-04 with 5-band were created maximum and minimum number of amplified fragments. Molecular marker genotypes showed a high degree of polymorphism. Studied genotypes based on RAPD results were divided into 2 groups and 2 subgroups. Most similar in subgroups A2 and B group was the lowest.

Keywords: rosa canina spp., RAPD marker, genetic variation, caspian climate

Procedia PDF Downloads 543