Search results for: multilocus sequence typing

Authors: F. Farzan Nasab, H. J. M. Geijselaers, I. Baran, A. De Boer

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A method is introduced for the coupled skin-rib optimization of a wing box where mass minimization is the objective and local buckling is the constraint. The structure is made of composite materials where continuity of plies in multiple adjacent panels (blending) has to be satisfied. Blending guarantees the manufacturability of the structure; however, it is a highly challenging constraint to treat and has been under debate in recent research in the same area. To fulfill design guidelines with respect to symmetry, balance, contiguity, disorientation and percentage rule of the layup, a reference for the stacking sequences (stacking sequence table or SST) is generated first. Then, an innovative fully gradient-based optimization approach in relation to a specific SST is introduced to obtain the optimum thickness distribution all over the structure while blending is fulfilled. The proposed optimization approach aims to turn the discrete optimization problem associated with the integer number of plies into a continuous one. As a result of a wing box deflection, a rib is subjected to load values which vary nonlinearly with the amount of deflection. The bending stiffness of a skin affects the wing box deflection and thus affects the load applied to a rib. This indicates the necessity of a coupled skin-rib optimization approach for a more realistic optimized design. The proposed method is examined with the optimization of the layup of a composite stiffened skin and rib of a wing torsion box subjected to in-plane normal and shear loads. Results show that the method can successfully prescribe a valid design with a significantly cheap computation cost.

Keywords: blending, buckling optimization, composite panels, wing torsion box

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Authors: Stephanie Khater, Ali Chehade, Lamis Chalak

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The progressive replacement of the Lebanese autochthonous grapevine cultivars during the last decade by the imported foreign varieties almost resulted in the genetic erosion of the local germplasm and the confusion with cultivars' names. Hence there is a need to characterize these local cultivars and to assess the possible existing variability at the cultivar level. This work was conducted in an attempt to evaluate the intra-varietal diversity within Lebanese traditional cultivars 'Aswad', 'Maghdoushe', 'Maryame', 'Merweh', 'Meksese' and 'Obeide'. A total of 50 accessions distributed over five main geographical areas in Lebanon were collected and submitted to both ampelographic description and ISSR DNA analysis. A set of 35 ampelographic descriptors previously established by the International Office of Vine and Wine and related to leaf, bunch, berry, and phenological stages, were examined. Variability was observed between accessions within cultivars for blade shape, density of prostrate and erect hairs, teeth shape, berry shape, size and color, cluster shape and size, and flesh juiciness. At the molecular level, nine ISSR (inter-simple sequence repeat) primers, previously developed for grapevine, were used in this study. These primers generated a total of 35 bands, of which 30 (85.7%) were polymorphic. Totally, 29 genetic profiles were differentiated, of which 9 revealed within 'Obeide', 6 for 'Maghdoushe', 5 for 'Merweh', 4 within 'Maryame', 3 for 'Aswad' and 2 within 'Meksese'. Findings of this study indicate the existence of several genotypes that form the basis of the main indigenous cultivars grown in Lebanon and which should be further considered in the establishment of new vineyards and selection programs.

Keywords: ampelography, autochthonous cultivars, ISSR markers, Lebanon, Vitis vinifera L.

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Authors: Prittesh Patel, Rushabh Shah, Krishnamurthy Ramar, Vakulbhushan Bhaskar

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The present research work aims at finding genetic differences in the genomes of sugarcane red rot isolates Colletotrichum falcatum Went using Random Amplified Polymorphic DNA (RAPD) and interspersed simple sequence repeat (ISSR) molecular markers. Ten isolates of C. falcatum isolated from different red rot infected sugarcane cultivars stalk were used in present study. The amplified bands were scored across the lanes obtained in 15 RAPD primes and 21 ISSR primes successfully. The data were analysed using NTSYSpc 2.2 software. The results showed 80.6% and 68.07% polymorphism in RPAD and ISSR analysis respectively. Based on the RAPD analysis, ten genotypes were grouped into two major clusters at a cut-off value of 0.75. Geographically distant C. falcatum isolate cfGAN from south Gujarat had a level of similarity with Coimbatore isolate cf8436 presented on separate clade of bootstrapped dendrograms. First and second cluster consisted of five and three isolates respectively, indicating the close relation among them. The 21 ISSR primers produced 119 distinct and scorable loci in that 38 were monomorphic. The number of scorable loci for each primer varied from 2 (ISSR822) to 8 (ISSR807, ISSR823 and ISSR15) with an average of 5.66 loci per primer. Primer ISSR835 amplified the highest number of bands (57), while only 16 bands were obtained by primers ISSR822. Four primers namely ISSR830, ISSR845, ISSR4 and ISSR15 showed the highest value of percentage of polymorphism (100%). The results indicated that both of the marker systems RAPD and ISSR, individually can be effectively used in determination of genetic relationship among C falcatum accessions collected from different parts of south Gujarat.

Keywords: Colletotrichum falcatum, ISSR, RAPD, Red Rot

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Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

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Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

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Authors: Salah R. Al Zaidee, Ali S. Mahdi

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Except for simple problems of statically determinate structures, optimum design problems in structural engineering have implicit objective functions where structural analysis and design are essential within each searching loop. With these implicit functions, the structural engineer is usually enforced to write his/her own computer code for analysis, design, and searching for optimum design among many feasible candidates and cannot take advantage of available software for structural analysis, design, and searching for the optimum solution. The meta-model is a regression model used to transform an implicit objective function into objective one and leads in turn to decouple the structural analysis and design processes from the optimum searching process. With the meta-model, well-known software for structural analysis and design can be used in sequence with optimum searching software. In this paper, the meta-model has been used to develop an explicit objective function for plane steel frames subjected to dead, live, and seismic forces. Frame topology is assumed as predefined based on architectural and functional requirements. Columns and beams sections and different connections details are the main design variables in this study. Columns and beams are grouped to reduce the number of design variables and to make the problem similar to that adopted in engineering practice. Data for the implicit objective function have been generated based on analysis and assessment for many design proposals with CSI SAP software. These data have been used later in SPSS software to develop a pure quadratic nonlinear regression model for the explicit objective function. Good correlations with a coefficient, R², in the range from 0.88 to 0.99 have been noted between the original implicit functions and the corresponding explicit functions generated with meta-model.

Keywords: meta-modal, objective function, steel frames, seismic analysis, design

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Authors: Azam Fazelpour, Saeed R. Dehghani, Vlastimil Masek, Yuri S. Muzychka

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The study uses an image analysis technique employing thermal imaging to measure the percentage of areas with various temperatures on a freezing surface. An image segmentation method using threshold values is applied to a sequence of image recording the freezing process. The phenomenon is transient and temperatures vary fast to reach the freezing point and complete the freezing process. Freezing salt water is subjected to the salt rejection that makes the freezing point dynamic and dependent on the salinity at the phase interface. For a specific area of freezing, nucleation starts from one side and end to another side, which causes a dynamic and transient temperature in that area. Thermal cameras are able to reveal a difference in temperature due to their sensitivity to infrared radiance. Using Experimental setup, a video is recorded by a thermal camera to monitor radiance and temperatures during the freezing process. Image processing techniques are applied to all frames to detect and classify temperatures on the surface. Image processing segmentation method is used to find contours with same temperatures on the icing surface. Each segment is obtained using the temperature range appeared in the image and correspond pixel values in the image. Using the contours extracted from image and camera parameters, stratified areas with different temperatures are calculated. To observe temperature contours on the icing surface using the thermal camera, the salt water sample is dropped on a cold surface with the temperature of -20°C. A thermal video is recorded for 2 minutes to observe the temperature field. Examining the results obtained by the method and the experimental observations verifies the accuracy and applicability of the method.

Keywords: ice contour boundary, image processing, image segmentation, salt ice, thermal image

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Alyaa Abdlwahab

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Cutaneous leishmaniasis represents a serious health problem in Syria; this problem has become noticeably aggravated after the civil war in the country. Leishmania tropica parasite is the main cause of cutaneous leishmaniasis in Syria. In order to control the disease, we need an effective vaccine against leishmania parasite. DNA vaccination remains one of the favorable approaches that have been used to face cutaneous leishmaniasis. Ribosomal protein S4 is responsible for important roles in Leishmania parasite life. DNA vaccine based on S4 gene has been used against infections by many species of Leishmania parasite but leishmania tropica parasite, so this gene represents a good candidate for DNA vaccine construction. After proving the existence of ribosomal protein S4 gene in a Syrian strain of Leishmania tropica (LCED Syrian 01), sequencing it and cloning it into pCI plasmid, BALB/C mice were inoculated with pCI-S4 DNA vaccine. The immune response was determined by monitoring the lesion progression in inoculated BALB/C mice for six weeks after challenging mice with Leishmania tropica (LCED Syrian 01) parasites. IL-12, IFN-γ, and IL-4 were quantified in draining lymph nodes (DLNa) of the immunized BALB/C mice by using the RT-qPCR technique. The parasite burden was calculated in the final week for the footpad lesion and the DLNs of the mice. This study proved the existence and the expression of the ribosomal protein S4 gene in Leishmania tropica (LCED Syrian 01) promastigotes. The sequence of ribosomal protein cDNA S4 gene was determined and published in Genbank; the gene size was 822 bp. Expression was also demonstrated at the level of cDNA. Also, this study revealed that pCI-S4 DNA vaccine induces TH1\TH2 response in immunized mice; this response prevents partially developing a dermal lesion of Leishmania.

Keywords: ribosomal protein S4, DNA vaccine, Leishmania tropica, BALB\c

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Authors: Ajmal Hussain

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In Indian music parlance, Rasa denotes a distinct aesthetic experience that builds up in the mind of the listeners while listening to a piece of Indian classical music. The distinction of the experience is rooted in the concept that it gives rise to an enhanced awareness about the Self or God and creates a mental state detached from mundane issues of everyday life. The theory of Rasa was initially proposed in the context of theatre but became a part of Indian musicological discourse roughly two thousand years ago, however, to this day, it remains shrouded in mystery due to its religious associations and connotations. This paper attempts to demystify the theory of Rasa in the light of available scientific knowledge fund particularly in Brain and Mind sciences. The paper initially describes the religious context of the theory of Rasa and then discusses its classical formulations by Bharata and Abhinavagupta including the steps and stages laid down by the latter to explain the creation of musical experience. The classical formulations are then interpreted with reference to the scientific knowledge fund about the human mind and mechanics of perception. The study uses the model of human mind as proposed by Portuguese-American neuroscientist Antonio Damasio in his theory ‘A Nesting Principle’. On the basis of the findings by Damasio, the paper interprets the experience of Rasa from a scientific perspective and clarifies the sequence of steps and stages involved in the making of musical experience. The study concludes that although the classical formulations of Rasa identify key aspects of musical experience, the association of Rasa with religion is misleading. The association with religion does not depend upon musical stimulus but the intellectual orientation of the listener. It further establishes that the function of Rasa is more profound as, from an evolutionary perspective, it can be seen as a catalyst for higher consciousness.

Keywords: aesthetic, consciousness, music, Rasa

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Authors: Yujie Zhou, Hee-Seong Byun, Sang-In Bak, Eui-Joon Kil, Kyung Joo Min, Vivek Chavan, Won Kyong Cho, Sukchan Lee, Seung-Woo Hong, Tae-Sun Park

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Fast neutron irradiation (FNI) can cause mutations on plant genome but, in the most of cases, these irradiated plants have not shown significant characteristics phenotypically. In this study, we utilized RNA-Seq to generate a high-resolution transcriptome map of the tomato (Solanum lycopersicum) genome effected by FNI. To quantify the different transcription levels in tomato irradiated by FNI, tomato seeds were irradiated by using MC-50 cyclotron (KIRAMS, Korea) for 0, 30 and 90 minutes, respectively. To investigate the effects on the pre-soaking condition, experimental groups were divided into dry and soaked seeds, which were soaked for 8 hours before irradiation. There was no noticeable difference in the percentage germination (PG) among dry seeds, while irradiated soaked seeds have about 10 % lower PG compared to the unirradiated control group. Using whole transcriptome sequencing by HiSeq 2000, we analyzed the differential gene expression in response to different time of FNI in dry and soaked seeds. More than 1.4 million base pair reads were mapped onto the tomato reference genome and the expression pattern differences between irradiated and unirradiated seeds were assessed. In 0, 30 and 90 minutes irradiation, 12,135, 28,495 and 28,675 transcripts were generated, respectively. Gene ontology analysis suggested the different enrichment of transcripts involved in response to different FNI. The present study showed that FNI effects on plant gene expression, which can become a new parameters for evaluating the responses against FNI on plants. In addition, the comparative analysis of differentially expressed genes in D and S seeds by FNI will also give us a chance to deep explore novel candidate genes for FNI, which could be a good model system to understand the mechanisms behind the adaption of plant to space biology research.

Keywords: tomato (solanum lycopersicum), fast neutron irradiation, RNA-sequence, transcriptome expression

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Authors: Aouina Nabila Yasmina, Zine El Abidine Chaoui

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Recently, understanding the interactions of electrons with the DNA molecule and its components has attracted considerable interest because DNA is the main site damaged by ionizing radiation. The interactions of radiation with DNA induce a variety of molecular damage such as single-strand breaks, double-strand breaks, basic damage, cross-links between proteins and DNA, and others, or the formation of free radicals, which, by chemical reactions with DNA, can also lead to breakage of the strand. One factor that can contribute significantly to these processes is the effect of water hydration on the formation and reaction of radiation induced by these radicals in and / or around DNA. B-DNA requires about 30% by weight of water to maintain its native conformation in the crystalline state. The transformation depends on various factors such as sequence, ion composition, concentration and water activity. Partial dehydration converts it to DNA-A. The present study shows the results of theoretical calculations for positrons and electrons elastic scattering with DNA medium and water over a broad energy range from 10 eV to 100 keV. Indeed, electron elastic cross sections and elastic mean free paths are calculated using a corrected form of the independent atom method, taking into account the geometry of the biomolecule (SCAR macro). Moreover, the elastic scattering of electrons and positrons by atoms of the biomolecule was evaluated by means of relativistic (Dirac) partial wave analysis. Our calculated results are compared with theoretical data available in the literature in the absence of experimental data, in particular for positron. As a central result, our electron elastic cross sections are in good agreement with existing theoretical data in the range of 10 eV to 1 keV.

Keywords: elastic cross scrion, elastic mean free path, scar macro method, electron collision

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Authors: Tei Kim, Brooklynn McNeil, Kathryn Dunn, Douglas I. Walker

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To better characterize the relationship between complex chemical exposures and disease, our laboratory uses an approach that combines low-cost, polydimethylsiloxane (silicone) wristband samplers that absorb many of the chemicals we are exposed to with untargeted high-resolution mass spectrometry (HRMS) to characterize 1000’s of chemicals at a time. In studies with human populations, these wristbands can provide an important measure of our environment: however, there is a need to use this approach in large cohorts to study exposures associated with the disease. To facilitate the use of silicone samplers in large scale population studies, the goal of this research project was to establish automated sample preparation methods that improve throughput, robustness, and scalability of analytical methods for silicone wristbands. Using the Opentron OT2 automated liquid platform, which provides a low-cost and opensource framework for automated pipetting, we created two separate workflows that translate the manual wristband preparation method to a fully automated protocol that requires minor intervention by the operator. These protocols include a sequence generation step, which defines the location of all plates and labware according to user-specified settings, and a transfer protocol that includes all necessary instrument parameters and instructions for automated solvent extraction of wristband samplers. These protocols were written in Python and uploaded to GitHub for use by others in the research community. Results from this project show it is possible to establish automated and open source methods for the preparation of silicone wristband samplers to support profiling of many environmental exposures. Ongoing studies include deployment in longitudinal cohort studies to investigate the relationship between personal chemical exposure and disease.

Keywords: bioinformatics, automation, opentrons, research

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: D. Kuvshinov, A. Siswanto, W. Zimmerman

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A phorbol-12-myristate-13-acetate (TPA) is a synthetic analogue of phorbol ester (PE), a natural toxic compound of Euphorbiaceae plant. The oil extracted from plants of this family is useful source for primarily biofuel. However this oil can also be used as a food stock due to its significant nutrition content. The limitations for utilizing the oil as a food stock are mainly due to a toxicity of PE. Nowadays a majority of PE detoxification processes are expensive as include multi steps alcohol extraction sequence. Ozone is considered as a strong oxidative agent. It reaction with PE it attacks the carbon double bond of PE. This modification of PE molecular structure results into nontoxic ester with high lipid content. This report presents data on development of simple and cheap PE detoxification process with water application as a buffer and ozone as reactive component. The core of this new technique is a simultaneous application of new microscale plasma unit for ozone production and patented gas oscillation technology. In combination with a reactor design the technology permits ozone injection to the water-TPA mixture in form of microbubbles. The efficacy of a heterogeneous process depends on diffusion coefficient which can be controlled by contact time and interface area. The low velocity of rising microbubbles and high surface to volume ratio allow fast mass transfer to be achieved during the process. Direct injection of ozone is the most efficient process for a highly reactive and short lived chemical. Data on the plasma unit behavior are presented and influence of the gas oscillation technology to the microbubbles production mechanism has been discussed. Data on overall process efficacy for TPA degradation is shown.

Keywords: microbubble, ozonolysis, synthetic phorbol ester, chemical engineering

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Authors: Elsie L. Echeverri-Carroll

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Entrepreneurial ecosystems have become an important concept to explain the birth and sustainability of technology-based entrepreneurship within regions. However, as a theoretical concept, the temporal evolution of entrepreneurship systems remain underdeveloped, making it difficult to understand their dynamic contributions to entrepreneurs. This paper argues that successful technology-based ecosystems go over three cumulative spawning stages: corporate spawning, entrepreneurial spawning, and community spawning. The importance of corporate incubation in vibrant entrepreneurial ecosystems is well documented in the entrepreneurial literature. Similarly, entrepreneurial spawning processes for venture capital-backed startups are well documented in the financial literature. In contrast, there is little understanding of both the third stage of entrepreneurial spawning (when a community of entrepreneurs become a source of firm spawning) and the temporal sequence in which spawning effects occur in a region. We test this three-stage model of entrepreneurial spawning using data from two large databases on firm births—the Secretary of State (160,000 observations) and the National Establishment Time Series (NEST with 150,000 observations)—and information collected from 60 1½-hour interviews with startup founders and representatives of key entrepreneurial organizations. This temporal model is illustrated with case study of Austin, Texas ranked by the Kauffman Foundation as the number one entrepreneurial city in the United States in 2015 and 2016. The 1½-year study founded by the Kauffman Foundation demonstrates the importance of taken into consideration the temporal contributions of both large and entrepreneurial firms in understanding the factors that contribute to the birth and growth of technology-based entrepreneurial regions. More important, these learnings could offer an important road map for regions that pursue to advance their entrepreneurial ecosystems.

Keywords: entrepreneurial ecosystems, entrepreneurial industrial clusters, high-technology, temporal changes

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Authors: M. N. Zelenin, V. S. Mikhailov, R. P. Zhivotovsky

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It is known that residual welding deformations give negative effect to processability and operational quality of welded structures, complicating their assembly and reducing strength. Therefore, selection of optimal technology, ensuring minimum welding deformations, is one of the main goals in developing a technology for manufacturing of welded structures. Through years, JSC SSTC has been developing a theory for estimation of welding deformations and practical activities for reducing and compensating such deformations during welding process. During long time a methodology was used, based on analytic dependence. This methodology allowed defining volumetric changes of metal due to welding heating and subsequent cooling. However, dependences for definition of structures deformations, arising as a result of volumetric changes of metal in the weld area, allowed performing calculations only for simple structures, such as units, flat sections and sections with small curvature. In case of complex 3D structures, estimations on the base of analytic dependences gave significant errors. To eliminate this shortage, it was suggested to use finite elements method for resolving of deformation problem. Here, one shall first calculate volumes of longitudinal and transversal shortenings of welding joints using method of analytic dependences and further, with obtained shortenings, calculate forces, which action is equivalent to the action of active welding stresses. Further, a finite-elements model of the structure is developed and equivalent forces are added to this model. Having results of calculations, an optimal sequence of assembly and welding is selected and special measures to reduce and compensate welding deformations are developed and taken.

Keywords: residual welding deformations, longitudinal and transverse shortenings of welding joints, method of analytic dependences, finite elements method

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Authors: Natascha C. D'Amico, Enzo Grossi, Giovanni Valbusa, Ala Malasevschi, Gianpiero Cardone, Sergio Papa

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Purpose: To characterize, through a radiomic approach, the nature of areas classified PI-RADS (Prostate Imaging Reporting and Data System) 3/5, recognized in multiparametric prostate magnetic resonance with T2-weighted (T2w), diffusion and perfusion sequences with paramagnetic contrast. Methods and Materials: 24 cases undergoing multiparametric prostate MR and biopsy were admitted to this pilot study. Clinical outcome of the PI-RADS 3/5 was found through biopsy, finding 8 malignant tumours. The analysed images were acquired with a Philips achieva 1.5T machine with a CE- T2-weighted sequence in the axial plane. Semi-automatic tumour segmentation was carried out on MR images using 3DSlicer image analysis software. 45 shape-based, intensity-based and texture-based features were extracted and represented the input for preprocessing. An evolutionary algorithm (a TWIST system based on KNN algorithm) was used to subdivide the dataset into training and testing set and select features yielding the maximal amount of information. After this pre-processing 20 input variables were selected and different machine learning systems were used to develop a predictive model based on a training testing crossover procedure. Results: The best machine learning system (three-layers feed-forward neural network) obtained a global accuracy of 90% ( 80 % sensitivity and 100% specificity ) with a ROC of 0.82. Conclusion: Machine learning systems coupled with radiomics show a promising potential in distinguishing benign from malign tumours in PI-RADS 3/5 areas.

Keywords: machine learning, MR prostate, PI-Rads 3, radiomics

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

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Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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Authors: Yujiang Wu

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As electrical machine (e-machine) power density re-querulents become more stringent in vehicle electrification, mounting a temperature sensor for e-machine stator windings becomes increasingly difficult. This can lead to higher manufacturing costs, complicated harnesses, and reduced reliability. In this paper, we propose a deep-learning method for predicting electric machine winding temperature, which can either replace the sensor entirely or serve as a backup to the existing sensor. We compare the performance of our method, the stateful long short-term memory networks (LSTM) with truncated backpropagation through time (TBTT), with that of linear regression, as well as stateless LSTM with/without residual connection. Our results demonstrate the strength of combining stateful LSTM and TBTT in tackling nonlinear time series prediction problems with long sequence lengths. Additionally, in industrial applications, high-temperature region prediction accuracy is more important because winding temperature sensing is typically used for derating machine power when the temperature is high. To evaluate the performance of our algorithm, we developed a temperature-stratified MSE. We propose a simple but effective data preprocessing trick to improve the high-temperature region prediction accuracy. Our experimental results demonstrate the effectiveness of our proposed method in accurately predicting winding temperature, particularly in high-temperature regions, while also reducing manufacturing costs and improving reliability.

Keywords: deep learning, electrical machine, functional safety, long short-term memory networks (LSTM), thermal management, time series prediction

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Authors: Mona Vijayaran, Gurleen Oberoi, Sanjay Mishra

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Introduction: p190 BCR‐ABL1 in CML is often associated with monocytosis. In the case described here, monocytosis is associated with coexisting p210 BCR‐ABL and CMML clones. Mutation analysis using next‐generation sequence (NGS) in our case showed TET2 and SRSF2 mutations. Aims & Objectives: A 75-year male was evaluated for monocytosis and thrombocytopenia. CBC showed Hb-11.8g/dl, TLC-12,060/cmm, Monocytes-35%, Platelets-39,000/cmm. Materials & Methods: Bone marrow examination showed a hypercellular marrow with myeloid series showing sequential maturation up to neutrophils with 30% monocytes. Immunophenotyping by flow cytometry from bone marrow had 3% blasts. Making chronic myelomonocytic leukemia as the likely diagnosis. NGS for myeloid mutation panel had TET2 (48.9%) and SRSF2 (32.5%) mutations. This report further supported the diagnosis of CMML. To fulfil the WHO diagnostic criteria for CMML, a BCR ABL1 by RQ-PCR was sent. The report came positive for p210 (B3A2, B2A2) Major Transcript (M-BCR) % IS of 38.418. Result: The patient was counselled regarding the unique presentation of the presence of 2 clones- P210 CML and CMML. After discussion with an international faculty with vast experience in CMML. It was decided to start this elderly gentleman on Imatinib 200mg and not on azacytidine, as ASXL1 was not present; hence, his chances of progressing to AML would be less and on the other end, if CML is left untreated then chances of progression to blast phase would always be a possibility. After 3 months on Imatinib his platelet count improved to 80,000 to 90,000/cmm, but his monocytosis persists. His 3rd month BCR-ABL1 IS% is 0.004%. Conclusion: After searching the literature, there were no case reports of a coexisting CML p210 with CMML. This case might be the first case report. p190 BCR ABL1 is often associated with monocytosis. There are few case reports of p210 BCR ABL1 positivity in patients with monocytosis but none with coexisting CMML. This case highlights the need for extensively evaluating patients with monocytosis with next-generation sequencing for myeloid mutation panel and BCR-ABL1 by RT-PCR to correctly diagnose and treat them.

Keywords: CMML, NGS, p190 CML, Imatinib

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Authors: Adriana M. Duquette, Derek P. Bornath

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Reaction Time (RT) and Movement Time (MT) are important components of everyday life that have an effect on the way in which we move about our environment. These measures become even more crucial when an event can be caused (or avoided) in a fraction of a second, such as the RT and MT required while driving. The purpose of this study was to develop a more simple method of testing RT and MT during simulated driving with or without text messaging, in a university-aged population (n = 170). In the control condition, a randomly-delayed red light stimulus flashed on a computer interface after the participant began pressing the ‘gas’ pedal on a foot switch mat. Simple RT was defined as the time between the presentation of the light stimulus and the initiation of lifting the foot from the switch mat ‘gas’ pedal; while MT was defined as the time after the initiation of lifting the foot, to the initiation of depressing the switch mat ‘brake’ pedal. In the texting condition, upon pressing the ‘gas’ pedal, a ‘text message’ appeared on the computer interface in a dialog box that the participant typed on their cell phone while waiting for the light stimulus to turn red. In both conditions, the sequence was repeated 10 times, and an average RT (seconds) and average MT (seconds) were recorded. Condition significantly (p = .000) impacted overall RTs, as the texting condition (0.47 s) took longer than the no-texting (control) condition (0.34 s). Longer MTs were also recorded during the texting condition (0.28 s) than in the control condition (0.23 s), p = .001. Overall increases in Response Time (RT + MT) of 189 ms during the texting condition would equate to an additional 4.2 meters (to react to the stimulus and begin braking) if the participant had been driving an automobile at 80 km per hour. In conclusion, increasing task complexity due to the dual-task demand of text messaging during simulated driving caused significant increases in RT (41%), MT (23%) and Response Time (34%), thus further strengthening the mounting evidence against text messaging while driving.

Keywords: simulated driving, text messaging, reaction time, movement time

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Authors: Jeelka Ray

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Survey of the papers revealed that there is no practical design available for packaging machine based on Embedded system, so the need arose for the development of the prototype model. In this paper, author has worked on the development of an ARM7 based Embedded Controller for controlling the sequence of packaging machine. The unit is made user friendly with TFT and Touch Screen implementing human machine interface (HMI). The different system components are briefly discussed, followed by a description of the overall design. The major functions which involve bag forming, sealing temperature control, fault detection, alarm, animated view on the home screen when the machine is working as per different parameters set makes the machine performance more successful. LPC2478 ARM 7 Embedded Microcontroller controls the coordination of individual control function modules. In back gone days, these machines were manufactured with mechanical fittings. Later on, the electronic system replaced them. With the help of ongoing technologies, these mechanical systems were controlled electronically using Microprocessors. These became the backbone of the system which became a cause for the updating technologies in which the control was handed over to the Microcontrollers with Servo drives for accurate positioning of the material. This helped to maintain the quality of the products. Including all, RS 485 MODBUS Communication technology is used for synchronizing AC Drive & Servo Drive. These all concepts are operated either manually or through a Graphical User Interface. Automatic tuning of heaters, sealers and their temperature is controlled using Proportional, Integral and Derivation loops. In the upcoming latest technological world, the practical implementation of the above mentioned concepts is really important to be in the user friendly environment. Real time model is implemented and tested on the actual machine and received fruitful results.

Keywords: packaging machine, embedded system, ARM 7, micro controller, HMI, TFT, touch screen, PID

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Authors: Helen K. Buteme, Rebecca Axelsson-Robertson, Moses L. Joloba, Henry W. Boom, Gunilla Kallenius, Markus Maeurer

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Background: The Ugandan population is heavily affected by infectious diseases and Human leukocyte antigen (HLA) diversity plays a crucial role in the host-pathogen interaction and affects the rates of disease acquisition and outcome. The identification of HLA class 1 alleles and determining which alleles are associated with tuberculosis (TB) outcomes would help in screening individuals in TB endemic areas for susceptibility to TB and to predict resistance or progression to TB which would inevitably lead to better clinical management of TB. Aims: To be able to determine the HLA class 1 phenotype distribution in a Ugandan TB cohort and to establish the relationship between these phenotypes and active and latent TB. Methods: Blood samples were drawn from 32 HIV negative individuals with active TB and 45 HIV negative individuals with latent MTB infection. DNA was extracted from the blood samples and the DNA samples HLA typed by the polymerase chain reaction-sequence specific primer method. The allelic frequencies were determined by direct count. Results: HLA-A*02, A*01, A*74, A*30, B*15, B*58, C*07, C*03 and C*04 were the dominant phenotypes in this Ugandan cohort. There were differences in the distribution of HLA types between the individuals with active TB and the individuals with LTBI with only HLA-A*03 allele showing a statistically significant difference (p=0.0136). However, after FDR computation the corresponding q-value is above the expected proportion of false discoveries (q-value 0.2176). Key findings: We identified a number of HLA class I alleles in a population from Central Uganda which will enable us to carry out a functional characterization of CD8+ T-cell mediated immune responses to MTB. Our results also suggest that there may be a positive association between the HLA-A*03 allele and TB implying that individuals with the HLA-A*03 allele are at a higher risk of developing active TB.

Keywords: HLA, phenotype, tuberculosis, Uganda

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Authors: Yixin Yan, Miao Yan, Irini Angelidaki, Ioannis Fotidis

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Ammonia, which derives from the degradation of urea and protein-substrates, is the major toxicant of the commercial anaerobic digestion reactors causing loses of up to 1/3 of their practical biogas production, which reflects directly on the overall revenue of the plants. The current experimental work is aiming to alleviate the ammonia inhibition in anaerobic digestion (AD) process by developing an innovative bioaugmentation method of ammonia tolerant methanogenic consortia. The ammonia tolerant consortia were cultured in batch reactors and immobilized together with biochar in agar (customized inocula). Three continuous stirred-tank reactors (CSTR), fed with the organic fraction of municipal solid waste at a hydraulic retention time of 15 days and operated at thermophilic (55°C) conditions were assessed. After an ammonia shock of 4 g NH4+-N L-1, the customized inocula were bioaugmented into the CSTR reactors to alleviate ammonia toxicity effect on AD process. Recovery rate of methane production and methanogenic activity will be assessed to evaluate the bioaugmentation performance, while 16s rRNA gene sequence will be used to reveal the difference of microbial community changes through bioaugmentation. At the microbial level, the microbial community structures of the four reactors will be analysed to find the mechanism of bioaugmentation. Changes in hydrogen formation potential will be used to predict direct interspecies electron transfer (DIET) between ammonia tolerant methanogens and syntrophic bacteria. This experimental work is expected to create bioaugmentation inocula that will be easy to obtain, transport, handled and bioaugment in AD reactors to efficiently alleviate the ammonia toxicity, without alternating any of the other operational parameters including the ammonia-rich feedstocks.

Keywords: artisanal fishing waste, acidogenesis, volatile fatty acids, pH, inoculum/substrate ratio

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Authors: Arthi Ganapathy, Rati Tandon, Saroj Kaler

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Introduction: A thorough knowledge of variations in lung anatomy is of prime significance during surgical procedures like lobectomy, pneumonectomy, and segmentectomy of lungs. The arrangement of structures in the lung hilum act as a guide in performing such procedures. The normal pattern of arrangement of hilar structures in the right lung is eparterial bronchus, pulmonary artery, hyparterial bronchus and pulmonary veins from above downwards. In the left lung, it is pulmonary artery, principal bronchus and pulmonary vein from above downwards. The arrangement of hilar structures from anterior to posterior in both the lungs is pulmonary vein, pulmonary artery, and principal bronchus. The bronchial arteries are very small and usually the posterior most structures in the hilum of lungs. Aim: The present study aims at reporting the variations in hilar anatomy (arrangement and number) of lungs. Methodology: 75 adult formalin fixed cadaveric lungs from the department of Anatomy AIIMS New Delhi were observed for variations in the lobar anatomy. Arrangement of pulmonary hilar structures was meticulously observed, and any deviation in the pattern of presentation was recorded. Results: Among the 75 adult lung specimens observed 36 specimens were of right lung and the rest of left lung. Seven right lung specimens showed only 2 lobes with an oblique fissure dividing them and one left lung showed 3 lobes. The normal pattern of arrangement of hilar structures was seen in 22 right lungs and 23 left lungs. Rest of the lung specimens (14 right and 16 left) showed a varied pattern of arrangement of hilar structures. Some of them showed alterations in the sequence of arrangement of pulmonary artery, pulmonary veins, bronchus, and others in the number of these structures. Conclusion: Alterations in the pattern of arrangement of structures in the lung hilum are quite frequent. A compromise in knowledge of such variations will result in inadvertent complications like intraoperative bleeding during surgical procedures.

Keywords: fissures, hilum, lobes, pulmonary

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Authors: Pragathi Gurumurthy, Christina Hagen, Patricia Ulloa, Martin A. Koch, Thorsten M. Buzug

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Obstructive sleep apnea (OSA) is a sleep disorder where the patient suffers a disturbed airflow during sleep due to partial or complete occlusion of the pharyngeal airway. Recently, numerical simulations have been used to better understand the mechanism of pharyngeal collapse. However, to gain confidence in the solutions so obtained, an experimental validation is required. Therefore, in this study an experimental validation of computational fluid dynamics (CFD) used for the study of human pharyngeal flow patterns during OSA is performed. A stationary incompressible Navier-Stokes equation solved using the finite element method was used to numerically study the flow patterns in a computed tomography-based human pharynx model. The inlet flow rate was set to 250 ml/s and such that a flat profile was maintained at the inlet. The outlet pressure was set to 0 Pa. The experimental technique used for the validation of CFD of fluid flow patterns is phase contrast-MRI (PC-MRI). Using the same computed tomography data of the human pharynx as in the simulations, a phantom for the experiment was 3 D printed. Glycerol (55.27% weight) in water was used as a test fluid at 25°C. Inflow conditions similar to the CFD study were simulated using an MRI compatible flow pump (CardioFlow-5000MR, Shelley Medical Imaging Technologies). The entire experiment was done on a 3 T MR system (Ingenia, Philips) with 108 channel body coil using an RF-spoiled, gradient echo sequence. A comparison of the axial velocity obtained in the pharynx from the numerical simulations and PC-MRI shows good agreement. The region of jet impingement and recirculation also coincide, therefore validating the numerical simulations. Hence, the experimental validation proves the reliability and correctness of the numerical simulations.

Keywords: computational fluid dynamics, experimental validation, phase contrast-MRI, obstructive sleep apnea

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Authors: Waqas Shafqat Chattha, Muhammad Iqbal, Amir Shakeel

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Transcriptional factors are proteins that play a vital role in regulating the transcription of target genes in different biological processes and are being widely studied in different plant species. In the current era of genomics, plant genomes sequencing has directed to the genome-wide identification, analyses and categorization of diverse transcription factor families and hence provide key insights into their structural as well as functional diversity. The DNA-binding with One Finger (DOF) proteins belongs to C2-C2-type zinc finger protein family. DOF proteins are plant-specific transcription factors implicated in diverse functions including seed maturation and germination, phytohormone signalling, light-mediated gene regulation, cotton-fiber elongation and responses of the plant to biotic as well as abiotic stresses. In this context, a genome-wide in-silico analysis of DOF TF family in diploid cotton species i.e. Gossypium raimondii has enabled us to identify 55 non-redundant genes encoding DOF proteins renamed as GrDofs (Gossypium raimondii Dof). Gene distribution studies have shown that all of the GrDof genes are unevenly distributed across 12 out of 13 G. raimondii chromosomes. The gene structure analysis illustrated that 34 out of 55 GrDof genes are intron-less while remaining 21 genes have a single intron. Protein sequence-based phylogenetic analysis of putative 55 GrDOFs has divided these proteins into 5 major groups with various paralogous gene pairs. Molecular evolutionary studies aided with the conserved domain as well as gene structure analysis suggested that segmental duplications were the principal contributors for the expansion of Dof genes in G. raimondii.

Keywords: diploid cotton , G. raimondii, phylogenetic analysis, transcription factor

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Authors: Ebru Dural, M. Zulfu Asık

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Laminated glass is a kind of safety glass, which is made by 'sandwiching' two glass sheets and a polyvinyl butyral (PVB) interlayer in between them. When the glass is broken, the interlayer in between the glass sheets can stick them together. Because of this property, the hazards of sharp projectiles during natural and man-made disasters reduces. They can be widely applied in building, architecture, automotive, transport industries. Laminated glass can easily undergo large displacements even under their own weight. In order to explain their true behavior, they should be analyzed by using large deflection theory to represent nonlinear behavior. In this study, a nonlinear mathematical model is developed for the analysis of laminated glass cylindrical shell which is free in radial directions and restrained in axial directions. The results will be verified by using the results of the experiment, carried out on laminated glass cylindrical shells. The behavior of laminated composite cylindrical shell can be represented by five partial differential equations. Four of the five equations are used to represent axial displacements and radial displacements and the fifth one for the transverse deflection of the unit. Governing partial differential equations are derived by employing variational principles and minimum potential energy concept. Finite difference method is employed to solve the coupled differential equations. First, they are converted into a system of matrix equations and then iterative procedure is employed. Iterative procedure is necessary since equations are coupled. Problems occurred in getting convergent sequence generated by the employed procedure are overcome by employing variable underrelaxation factor. The procedure developed to solve the differential equations provides not only less storage but also less calculation time, which is a substantial advantage in computational mechanics problems.

Keywords: laminated glass, mathematical model, nonlinear behavior, PVB

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Authors: Fereshteh M. Haskouei, Habib Alimohammadian

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Magnetic susceptibility (χ) is operational to identify of late quaternary glacial-interglacial cycles in loess-paleosol sequences. It is well accepted that many loess-paleosol sequences bear witness to cold-dry/warm-humid periods, well known as glacial-interglacial cycles, respectively. For this study, loess-paleosol sequence of north-east of Iran was magnetically investigated. The study area is situated at about 8 km away of Neka city, on the main road of Sari-Behshahr, in Mazandaran Province, north of Iran. The youngest deposits of study area are the late Quaternary wind-blown accumulations. In this study, the total number of 117 samples was collected from loess-paleosols units. After that, the natural remnant magnetization (NRM) and magnetic susceptibility (MS) of the samples were measured. Variation of MS of more than 110 loess samples was plotted to reveal the correlation of the MS and paleoclimatic changes. This study aims reconstruction of climatic changes (glacial-interglacial and stadials-interstadials cycles). To confirm our results we compared MS (χ) and the curves of other investigations in paleoclimatology. This correspondence abled us to recognize worldly events in the study area such as: Younger Dryas, the Last Glacial Maximum (LGM), deglaciation of Northern Hemisphere etc. The obtained magnetic data indicate that during almost 50 ka, at least two glacial-interglacial periods occurred in north-east of Iran. Further, variation of χ values revealed short period of climatically cycles known as stadials-interstadials. We recognized 4 stadials and a single stadial as colder sub-periods for S₀ (recently soil-paleosol) and S₂ (lower paleosol), respectively, Moreover, we recognized 6 warmer sub-periods (interstadials) for L₁ (upper loess) and one interstadial L₂ (lower loess).

Keywords: glacial-interglacial cycles, Iran, last glacial maximum (LGM), loess, magnetic susceptibility (χ), Neka, stadials-interstadials sub-periods, younger dryas

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