Search results for: structural polymorphism

Authors: Sara A. Al-Jaberi, Salma Ben-Salem, Meriam Messedi, Fatma Ayadi, Lihadh Al-Gazali, Bassam R. Ali

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Background: The chemokine receptor components play crucial roles in the immune system and some of them serve as co-receptors for the HIV virus. Several studies have documented those variants in chemokine receptors are correlated with susceptibility and resistance to infection with HIV virus. For example, mutations in the chemokine receptor 5 gene (CCR5) resulting in loss-of-function (such as the homozygous CCR5Δ32) confer high degree of resistance to HIV infection. Heterozygotes for these variants exhibit slow progression to AIDS. The prevalence of CCR5 polymorphisms varies among ethnic and geographical groups. For example, the CCR5 Δ32 variant is present in 10–15% of north Europeans but is rarely encountered among Africans. This study aims to identify the prevalence of some CCR5 variants in two geographically distant Arab populations (namely Emiratis and Tunisians). Methodology: The prevalence of CCR5 gene variants including CCR5Δ32, FS299, C101X, A29S and C178R has been determined using PCR and direct DNA sequencing. A total of 403 unrelated healthy individuals (253 Emiratis and 150 Tunisians) were genotyped for the CCR5Δ32 variant using PCR amplification and gel electrophoresis. In addition, 200 Emiratis have been screened for other SNPs using Sanger DNA sequencing. Results: Among Emiratis, the allele frequency of the CCR5Δ32 variant has been found to be 0.002. In addition, two variants L55Q and A159 were found at a frequency of 0.002.Moreover, the prevalence of the CCR5Δ32 variant in Tunisians was estimated to be 0.013 which is relatively higher than its frequency in Emiratis but lower than Europeans. Conclusion: We conclude that the allele frequency of the most critical CCR5 polymorphism (Δ32) is extremely low among Emiratis compared to other Arabs and North Europeans. In addition, very low allele frequencies of other CCR5 polymorphisms have been detected among Emiratis.

Keywords: chemokine receptors, CCR5Δ32, CCR5 polymorphisms, Emiratis, Arab populations

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Authors: Mohammad Mokhtari, Gires Usup, Zaidi Che Cob

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Bacteria communities as mediators of the biogeochemical process are the main component of the mangrove ecosystems. Crab burrows by increasing oxic-anoxic interfaces and facilitating the flux rate between sediment and tidal water affect biogeochemical properties of sediments. The effect of fiddler crab burrows on the density and diversity of bacteria were investigated to elucidate the effect of burrow on bacterial distribution. Samples collected from the burrow walls of three species of fiddler crabs including Uca paradussumieri, Uca rosea, and Uca forcipata. Sediment properties including grain size, temperature, Redox potential, pH, chlorophyll, water and organic content were measured from the burrow walls to assess the correlation between environmental variables and bacterial communities. Bacteria were enumerated with epifluorescence microscopy after staining with SYBR green. Bacterial DNA extracted from sediment samples and the community profiles of bacteria were determined with Terminal Restriction Fragment Length Polymorphism (T-RFLP). High endemism was observed among bacterial communities. Among the 152 observed OTU’s, 22 were found only in crab burrows. The highest bacterial density and diversity were recorded in burrow wall. The results of ANOSIM indicated a significant difference between the bacterial communities from the three species of fiddler crab burrows. Only 3% of explained bacteria variability in the constrained ordination model of CCA was contributed to depth, while much of the bacteria’s variability was attributed to coarse sand, pH, and chlorophyll content. Our findings suggest that crab burrows by affecting sediment properties such as redox potential, pH, water, and chlorophyll content induce significant effects on the bacterial communities.

Keywords: bioturbation, canonical corresponding analysis, fiddler crab, microbial ecology

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Authors: Ifeyinwa Orakwe, Ngozi Nwogu, Edward Gobina

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This work presents experimental results relating to the structural characterization of a commercially available alumina membrane. A γ-alumina mesoporous tubular membrane has been used. Nitrogen adsorption-desorption, scanning electron microscopy and gas permeability test has been carried out on the alumina membrane to characterize its structural features. Scanning electron microscopy (SEM) was used to determine the pore size distribution of the membrane. Pore size, specific surface area and pore size distribution were also determined with the use of the Nitrogen adsorption-desorption instrument. Gas permeation tests were carried out on the membrane using a variety of single and mixed gases. The permeabilities at different pressure between 0.05-1 bar and temperature range of 25-200oC were used for the single and mixed gases: nitrogen (N2), helium (He), oxygen (O2), carbon dioxide (CO2), 14%CO₂/N₂, 60%CO₂/N₂, 30%CO₂/CH4 and 21%O₂/N₂. Plots of flow rate verses pressure were obtained. Results got showed the effect of temperature on the permeation rate of the various gases. At 0.5 bar for example, the flow rate for N2 was relatively constant before decreasing with an increase in temperature, while for O2, it continuously decreased with an increase in temperature. In the case of 30%CO₂/CH4 and 14%CO₂/N₂, the flow rate showed an increase then a decrease with increase in temperature. The effect of temperature on the membrane performance of the various gases is presented and the influence of the trans membrane pressure drop will be discussed in this paper.

Keywords: alumina membrane, Nitrogen adsorption-desorption, scanning electron microscopy, gas permeation, temperature

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Authors: Ellen Van Den Oord, Julien Marie Jan Ferdinand Van Campen

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This article introduces a computationally efficient method for stacking sequence blending of composite structures. The computational efficiency makes the presented method especially interesting for composite structures with a large number of design regions. Optimization of composite structures with an unequal load distribution may lead to locally optimized thicknesses and ply orientations that are incompatible with one another. Blending constraints can be enforced to achieve structural continuity. In literature, many methods can be found to implement structural continuity by means of stacking sequence blending in one way or another. The complexity of the problem makes the blending of a structure with a large number of adjacent design regions, and thus stacking sequences, prohibitive. In this work the local stacking sequence optimization is preconditioned using a method found in the literature that couples the mechanical behavior of the laminate, in the form of lamination parameters, to blending constraints, yielding near-optimal easy-to-blend designs. The preconditioned design is then fed to the scheme using cellular automata that have been developed by the authors. The method is applied to the benchmark 18-panel horseshoe blending problem to demonstrate its performance. The computational efficiency of the proposed method makes it especially suited for composite structures with a large number of design regions.

Keywords: composite, blending, optimization, lamination parameters

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Authors: Enhui Wang, Qingzhu Ou, Yan Tang, Xiaodong Guo

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As one of most popular polyanionic compounds in lithium-ion cathode materials, Li3V2(PO4)3 has always suffered from the low rate capability especially during 3~4.8V, which is considered to be related with the ion diffusion resistance and structural transformation during the Li+ de/intercalation. Here, as the change of cut-off voltages, cycling numbers and current densities, the process of SEI interfacial film’s formation-growing- destruction-repair on the surface of the cathode, the structural transformation during the charge and discharge, the de/intercalation kinetics reflected by the electrochemical impedance and the diffusion coefficient, have been investigated in detail. Current density, cycle numbers and cut-off voltage impacting on interfacial film and structure was studied specifically. Firstly, the matching between electrolyte and material was investigated, it turned out that the batteries with high voltage electrolyte showed the best electrochemical performance and high voltage electrolyte would be the best electrolyte. Secondly, AC impedance technology was used to study the changes of interface impedance and lithium ion diffusion coefficient, the results showed that current density, cycle numbers and cut-off voltage influenced the interfacial film together and the one who changed the interfacial properties most was the key factor. Scanning electron microscopy (SEM) analysis confirmed that the attenuation of discharge specific capacity was associated with the destruction and repair process of the SEI film. Thirdly, the X-ray diffraction was used to study the changes of structure, which was also impacted by current density, cycle numbers and cut-off voltage. The results indicated that the cell volume of Li3V2 (PO4 )3 increased as the current density increased; cycle numbers merely influenced the structure of material; the cell volume decreased first and moved back gradually after two Li-ion had been deintercalated as the charging cut-off voltage increased, and increased as the intercalation number of Li-ion increased during the discharging process. Then, the results which studied the changes of interface impedance and lithium ion diffusion coefficient turned out that the interface impedance and lithium ion diffusion coefficient increased when the cut-off voltage passed the voltage platforms and decreased when the cut-off voltage was between voltage platforms. Finally, three-electrode system was first adopted to test the activation energy of the system, the results indicated that the activation energy of the three-electrode system (22.385 KJ /mol) was much smaller than that of two-electrode system (40.064 KJ /mol).

Keywords: cut-off voltage, de/intercalation kinetics, solid electrolyte interphase film, structural transformation

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Authors: Tesfay Gebremicheal Reda, K. Samatha, Paul Douglas Sanasi, D. Parajuli

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Nanoparticle technology is fast progressing and is being employed in innumerable medical applications. At this time, the public's health is seriously threatened by the rise of bacterial strains resistant to several medications. Metal nanoparticles are a potential alternate approach for tackling this global concern, and this is the main focus of this study. The citrate precursor sol-gel synthesis method was used to synthesize the Niₓ Co₁₋ₓ Fe₂ O₄, (where x = 0.0:0.2:1.0) nanoparticle. XRD identified the development of the cubic crystal structure to have a preferential orientation along (311), and the average particle size was found to be 29-38 nm. The average crystallizes assessed with ImageJ software and origin 22 of the SEM are nearly identical to the XRD results. In the created NCF NPs, the FT-IR spectroscopy reveals structural examinations and the redistribution of cations between octahedral (505-428 cm⁻¹) and tetrahedral (653-603 cm⁻¹) locales. As the Co²⁺ cation is substituted with Ni²⁺, the coercive fields HC decrease from 2384 Oe to 241.93 Oe. Band gap energy rises as Ni concentration increases, which may be attributed to the fact that the ionic radii of Ni²⁺ ions are smaller than that of Co²⁺ ions, which results in a strong electrostatic interaction. On the contrary, except at x = 0.4, the dielectric constant decreases as the nickel concentration increases. According to the findings of this research work, nanoparticles are composed of Ni₀.₄ Co₀.₆ Fe₂ O₄ have demonstrated a promising value against S. aureus and E. coli, and it suggests a proposed model for their potential use as a source of antibacterial agent.

Keywords: antimicrobial, band gap, citrate precursor, dielectric, nanoparticle

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Authors: Ould Mohamed Cheikh, Mounir Chaik, Hind El Aakib, Mohamed Aggour, Abdelkader Outzourhit

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Zinc sulfide [ZnS] and oxygenated zinc sulfide Zn(O,S) thin films were deposited on glass substrates, by reactive cathodic radio-frequency (RF) sputtering. The substrates power and percentage of oxygen were varied in the range of 100W to 250W and from 5% to 20% respectively. The structural, morphological and optical properties of these thin films were investigated. The optical properties (mainly the refractive index, absorption coefficient and optical band gap) were examined by optical transmission measurements in the ultraviolet-visible-near Infrared wavelength range. XRD analysis indicated that all sputtered ZnS films were a single phase with a preferential orientation along the (111) plane of zinc blend (ZB). The crystallite size was in the range of 19.5 nm to 48.5 nm, the crystallite size varied with RF power reaching a maximum at 200 W. The Zn(O,S) films, on the other hand, were amorphous. UV-Visible, measurements showed that the ZnS film had more than 80% transmittance in the visible wavelength region while that of Zn(O,S is 85%. Moreover, it was observed that the band gap energy of the ZnS films increases slightly from 3.4 to 3.52 eV as the RF power was increased. The optical band gap of Zn(O,S), on the other hand, decreased from 4.2 to 3.89 eV as the oxygen partial pressure is increased in the sputtering atmosphere at a fixed RF-power. Scanning electron microscopy observations revealed smooth surfaces for both type of films. The X-ray reflectometry measurements on the ZnS films showed that the density of the films (3.9 g/cm3) is close that of bulk ZnS.

Keywords: thin films Zn(O, S) properties, Zn(O, S) by Rf-sputtering, ZnS for solar cells, thin films for renewable energy

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Authors: A. T. Al-Isawi, P. E. F. Collins

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The behaviour of structures exposed to fire after an earthquake is not a new area of engineering research, but there remain a number of areas where further work is required. Such areas relate to the way in which seismic excitation is applied to a structure, taking into account the effect of soil-structure interaction (SSI) and the method of analysis, in addition to identifying the excitation load properties. The selection of earthquake data input for use in nonlinear analysis and the method of analysis are still challenging issues. Thus, realistic artificial ground motion input data must be developed to certify that site properties parameters adequately describe the effects of the nonlinear inelastic behaviour of the system and that the characteristics of these parameters are coherent with the characteristics of the target parameters. Conversely, ignoring the significance of some attributes, such as frequency content, soil site properties and earthquake parameters may lead to misleading results, due to the misinterpretation of required input data and the incorrect synthesise of analysis hypothesis. This paper presents a study of the post-earthquake fire (PEF) performance of a multi-storey steel-framed building resting on soft clay, taking into account the effects of the nonlinear inelastic behaviour of the structure and soil, and the soil-structure interaction (SSI). Structures subjected to an earthquake may experience various levels of damage; the geometrical damage, which indicates the change in the initial structure’s geometry due to the residual deformation as a result of plastic behaviour, and the mechanical damage which identifies the degradation of the mechanical properties of the structural elements involved in the plastic range of deformation. Consequently, the structure presumably experiences partial structural damage but is then exposed to fire under its new residual material properties, which may result in building failure caused by a decrease in fire resistance. This scenario would be more complicated if SSI was also considered. Indeed, most earthquake design codes ignore the probability of PEF as well as the effect that SSI has on the behaviour of structures, in order to simplify the analysis procedure. Therefore, the design of structures based on existing codes which neglect the importance of PEF and SSI can create a significant risk of structural failure. In order to examine the criteria for the behaviour of a structure under PEF conditions, a two-dimensional nonlinear elasto-plastic model is developed using ABAQUS software; the effects of SSI are included. Both geometrical and mechanical damages have been taken into account after the earthquake analysis step. For comparison, an identical model is also created, which does not include the effects of soil-structure interaction. It is shown that damage to structural elements is underestimated if SSI is not included in the analysis, and the maximum percentage reduction in fire resistance is detected in the case when SSI is included in the scenario. The results are validated using the literature.

Keywords: Abaqus Software, Finite Element Analysis, post-earthquake fire, seismic analysis, soil-structure interaction

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Authors: H. N. Cheung

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Self-compassion encourages one to accept oneself, reduce self-criticism and self-judgment, and see one’s shortcomings and setbacks in a balanced view. Adolescent self-compassion is a crucial protective factor against mental illness. It is, however, affected by gender. Given the scarcity of self-compassion scales for adolescents, the current study evaluates the Self-Compassion Scale for Youth (SCS-Y) in a large cross-cultural sample and investigates how the subscales of SCS-Y relate to the dimensions of depressive symptoms across gender. Through the internet-based Qualtrics, a total of 2881 teenagers aged 12 to 18 years were recruited from Hong Kong (HK), China, and the United Kingdom. A Multiple Indicator Multiple Cause (MIMIC) model was used to evaluate measurement invariance of the SCS-Y, and differential item functioning (DIF) was checked across gender. Upon the establishment of the best model, a multigroup structural equation model (SEM) was built between factors of SCS-Y and Multidimensional depression assessment scale (MDAS) which assesses four dimensions of depressive symptoms (emotional, cognitive, somatic and interpersonal). The SCS-Y was shown to have good reliability and validity. The MIMIC model produced a good model fit for a hypothetical six-factor model (CFI = 0.980; TLI = 0.974; RMSEA = 0.038) and no item was flagged for DIF across gender. A gender difference was observed between SCS-Y factors and depression dimensions. Conclusions: The SCS-Y exhibits good psychometric characteristics, including measurement invariance across gender. The study also highlights the gender difference between self-compassion factors and depression dimensions.

Keywords: self compassion, gender, depression, structural equation modelling, MIMIC model

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Authors: H. Djaaboube, I. Loucif, Y. Bouachiba, R. Aouati, A. Maameri, A. Taabouche, A. Bouabellou

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

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

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Authors: Munirajulu M, Srikanth Modem

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A large cricket stadium with the capacity to accommodate several thousands of spectators has the seating arena consisting of a two-tier arrangement with an upper and a lower bowl and an intermediate concourse podium level for pedestrian movement to access the bowls. The uniqueness of the stadium is that spectators can have an unobstructed view from all around the podium towards the field of play. Upper and lower bowls are connected by stairs. The stairs landing is a precast slab supported by cantilevered steel beams. These steel beams are fixed to precast columns supporting the stadium structure. The stair slabs are precast concrete supported on a landing slab and cantilevered steel beams. During an event of a fire at podium level between two staircases, fire resistance of steel beams is very critical to life safety. If the steel beam loses its strength due to lack of fire resistance, it will be weak in supporting stair slabs and may lead to a hazard in evacuating occupants from the upper bowl to the lower bowl. In this study, to ascertain fire rating and life safety, a performance-based design using CFD analysis is used to evaluate the steel beams' fire resistance. A fire size of 3.5 MW (convective heat output of fire) with a wind speed of 2.57 m/s is considered for fire and smoke simulation. CFD results show that the smoke temperature near the staircase/ around the staircase does not exceed 1500 C for the fire duration considered. The surface temperature of cantilevered steel beams is found to be less than or equal to 1500 C. Since this temperature is much less than the critical failure temperature of steel (5200 C), it is concluded that the design of structural steel supports on the staircase is adequate and does not need additional fire protection such as fire-resistant coating. CFD analysis provided an engineering basis for the performance-based design of steel structural elements and an opportunity to optimize fire protection requirements. Thus, performance-based design using CFD modeling and simulation of fire and smoke is an innovative way to evaluate fire rating requirements, ascertain life safety and optimize the design with regard to fire protection on structural steel elements.

Keywords: fire resistance, life safety, performance-based design, CFD analysis

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Authors: Annet Namusoke, Annet Namayanja, Peter Wasswa, Shakirah Nampijja

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Common bean cultivar G2333 which offers broad resistance for anthracnose has been widely used as a source of resistance in breeding for anthracnose resistance. The cultivar is pyramided with three genes namely CO-4, CO-5 and CO-7 and of these three genes, the CO-4 gene has been found to offer the broadest resistance. The main aim of this work was to identify and validate easily assayable PCR based co-dominant molecular markers for selection of the CO-4 gene in segregating populations derived from crosses of G2333 with RWR 1946 and RWR 2075, two commercial Andean cultivars highly susceptible to anthracnose. Marker sequences for the study were obtained by blasting the sequence of the COK-4 gene in the Phaseolus gene database. Primer sequence pairs that were not provided from the Phaseolus gene database were designed by the use of Primer3 software. PCR conditions were optimized and the PCR products were run on 6% HPAGE gel. Results of the polymorphism test indicated that out of 18 identified markers, only two markers namely BM588 and BM211 behaved co-dominantly. Phenotypic evaluation for reaction to anthracnose disease was done by inoculating 21days old seedlings of three parents, F1 and F2 populations with race 7 of Colletotrichum lindemuthianum in the humid chamber. DNA testing of the BM588 marker onto the F2 segregating population of the crosses RWR 1946 x G 2333 and RWR 2075 x G2333 further revealed that the marker BM588 co-segregated with disease resistance with co-dominance of two alleles of 200bp and 400bp, fitting the expected segregation ratio of 1:2:1. The BM588 marker was significantly associated with disease resistance and gave promising results for marker assisted selection of the CO-4 gene in the breeding lines. Activities to validate the BM211 marker are also underway.

Keywords: codominant, Colletotrichum lindemuthianum, MAS, Phaseolus vulgaris

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Authors: Aleš Florian, Lenka Ševelová

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Complex sensitivity analysis of stresses in a concrete slab of the real type of rigid pavement made from recycled materials is performed. The computational model of the pavement is designed as a spatial (3D) model, is based on a nonlinear variant of the finite element method that respects the structural nonlinearity, enables to model different arrangements of joints, and the entire model can be loaded by the thermal load. Interaction of adjacent slabs in joints and contact of the slab and the subsequent layer are modeled with the help of special contact elements. Four concrete slabs separated by transverse and longitudinal joints and the additional structural layers and soil to the depth of about 3m are modeled. The thickness of individual layers, physical and mechanical properties of materials, characteristics of joints, and the temperature of the upper and lower surface of slabs are supposed to be random variables. The modern simulation technique Updated Latin Hypercube Sampling with 20 simulations is used. For sensitivity analysis the sensitivity coefficient based on the Spearman rank correlation coefficient is utilized. As a result, the estimates of influence of random variability of individual input variables on the random variability of principal stresses s1 and s3 in 53 points on the upper and lower surface of the concrete slabs are obtained.

Keywords: concrete, FEM, pavement, sensitivity, simulation

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from x-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for x-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across x-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: biomacromolecular structure, coenzyme, electron density discrepancy analysis, x-ray crystallography

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Authors: Eqqab Maree, Habil Jurgen Bast, Zana K. Shakir

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Passive damping, once properly characterized and incorporated into the structure design is an autonomous mechanism. Passive damping can be achieved by applying layers of a polymeric material, called viscoelastic layers (VEM), to the base structure. This type of configuration is known as free or unconstrained layer damping treatment. A shear or constrained damping treatment uses the idea of adding a constraining layer, typically a metal, on top of the polymeric layer. Constrained treatment is a more efficient form of damping than the unconstrained damping treatment. In constrained damping treatment a sandwich is formed with the viscoelastic layer as the core. When the two outer layers experience bending, as they would if the structure was oscillating, they shear the viscoelastic layer and energy is dissipated in the form of heat. This form of energy dissipation allows the structural oscillations to attenuate much faster. The purpose behind this study is to predict damping effects by using two methods of passive viscoelastic constrained layer damping. First method is Euler-Bernoulli beam theory; it is commonly used for predicting the vibratory response of beams. Second method is Finite Element software packages provided in this research were obtained by using two-dimensional solid structural elements in ANSYS14 specifically eight nodded (SOLID183) and the output results from ANSYS 14 (SOLID183) its damped natural frequency values and mode shape for first five modes. This method of passive damping treatment is widely used for structural application in many industries like aerospace, automobile, etc. In this paper, take a steel cantilever sandwich beam with viscoelastic core type 3M-468 by using methods of passive viscoelastic constrained layer damping. Also can proved that, the percentage reduction of modal frequency between undamped and damped steel sandwich cantilever beam 8mm thickness for each mode is very high, this is due to the effect of viscoelastic layer on damped beams. Finally this types of damped sandwich steel cantilever beam with viscoelastic materials core type (3M468) is very appropriate to use in automotive industry and in many mechanical application, because has very high capability to reduce the modal vibration of structures.

Keywords: steel cantilever, sandwich beam, viscoelastic materials core type (3M468), ANSYS14, Euler-Bernoulli beam theory

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Authors: C. A. Ologunde

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Escherichia coli have been a major microorganisms associated with, and isolated from feacal samples either in adult or children all over the world. Strains of these organisms are resistant to cephalosporins and fluoroquinolone (FQ) antimicrobial agents among hospitalized patients and FQs are the most frequently prescribed antimicrobial class in hospitals, and the level of resistant of E. coli to these antimicrobial agents is a risk factor that should be assessed. Hence, this study was conducted to determine the prevalence and risk factors for colonization with fluoroquinolone (FQ)-resistant E. coli in hospitalized patients in Ado-Ekiti. Rectal swabs were obtained from patients in hospitals in the study area and FQ-resistant E. coli were isolated and identified by means of Nalidixic acid multi-disk and a 1-step screening procedure. Species identification and FQ resistance were confirmed by automated testing (Vitek, bioMerieux, USA). Individual colonies were subjected to pulse-field gel electrophoresis (PAGE) to determine macro-restriction polymorphism after digestion of chromosomal DNA. FQ-resistant E. coli was detected in the stool sample of 37(62%) hospitalized patient. With multivariable analyses, the use of FQ before hospitalization was the only independent risk factor for FQ-resistant E. coli carriage and was consistent for FQ exposures for the 3-12 months of study. Pulsed-field gel electrophoresis of FQ-resistant E. coli identified conal spread of 1(one) strain among 18 patients. Loss (9 patients) or acquisition (10 residents) of FQ-resistant E. coli was documented and was associated with de novo colonization with genetically distinct strains. It was concluded that FQ-resistant E. coli carriage was associated with clonal spread. The differential effects of individual fluoroquinolone on antimicrobial drug resistance are an important area for future study, as hospitals manipulate their formularies with regard to use of individual fluoroquinolone, often for economic reasons.

Keywords: E. coli, fluoroquinolone, risk factors, feacal carriage, hospitalized patients, Ado-Ekiti

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Authors: Vallence Ngabo M., Leonard Atuhaire, Peter Clever Rutayisire

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The main aim of this study was to establish the differences in both the determinants of stunting and the causal mechanism through which the identified determinants influence stunting amongst male and female under-fives in Uganda. Literature shows that male children below the age of five years are at a higher risk of being stunted than their female counterparts. Specifically, studies in Uganda indicate that being a male child is positively associated with stunting, while being a female is negatively associated with stunting. Data for 904 males and 829 females under-fives was extracted form UDHS-2016 survey dataset. Key variables for this study were identified and used in generating relevant models and paths. Structural equation modeling techniques were used in their generalized form (GSEM). The generalized nature necessitated specifying both the family and link functions for each response variable in the system of the model. The sex of the child (b4) was used as a grouping factor and the height for age (HAZ) scores were used to construct the status for stunting of under-fives. The estimated models and path clearly indicated that the set of underlying factors that influence male and female under-fives respectively was different and the path through which they influence stunting was different. However, some of the determinants that influenced stunting amongst male under-fives also influenced stunting amongst the female under-fives. To reduce the stunting problem to the desirable state, it is important to consider the multifaceted and complex nature of the risk factors that influence stunting amongst the under-fives but, more importantly, consider the different sex-specific factors and their causal mechanism or paths through which they influence stunting.

Keywords: stunting, underfives, sex of the child, GSEM, causal mechanism

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Authors: M. Hosseini, N. Ghorbani Amirabad, M. Zhian

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Seismic design codes accept structural and nonstructural damages after the sever earthquakes (provided that the building is prevented from collapse), so that in many cases demolishing and reconstruction of the building is inevitable, and this is usually very difficult, costly and time consuming. Therefore, designing and constructing of buildings in such a way that they can be easily repaired after earthquakes, even major ones, is quite desired. For this purpose giving the possibility of rocking or see-saw motion to the building structure, partially or as a whole, has been used by some researchers in recent decade .the central support which has a main role in creating the possibility of see-saw motion in the building’s structural system. In this paper, paying more attention to the key role of the central fuse and support, an innovative energy dissipater which can act as the central fuse and support of the building with seesaw motion is introduced, and the process of reaching an optimal geometry for that by using finite element analysis is presented. Several geometric shapes were considered for the proposed central fuse and support. In each case the hysteresis moment rotation behavior of the considered fuse were obtained under simultaneous effect of vertical and horizontal loads, by nonlinear finite element analyses. To find the optimal geometric shape, the maximum plastic strain value in the fuse body was considered as the main parameter. The rotational stiffness of the fuse under the effect of acting moments is another important parameter for finding the optimum shape. The proposed fuse and support can be called Yielding Curved Bars and Clipped Hemisphere Core (YCB&CHC or more briefly YCB) energy dissipater. Based on extensive nonlinear finite element analyses it was found out the using rectangular section for the curved bars gives more reliable results. Then, the YCB energy dissipater with the optimal shape was used in a structural model of a 12 story regular building as its central fuse and support to give it the possibility of seesaw motion, and its seismic responses were compared to those of a the building in the fixed based conditions, subjected to three-components acceleration of several selected earthquakes including Loma Prieta, Northridge, and Park Field. In building with see-saw motion some simple yielding-plate energy dissipaters were also used under circumferential columns.The results indicated that equipping the buildings with central and circumferential fuses result in remarkable reduction of seismic responses of the building, including the base shear, inter story drift, and roof acceleration. In fact by using the proposed technique the plastic deformations are concentrated in the fuses in the lowest story of the building, so that the main body of the building structure remains basically elastic, and therefore, the building can be easily repaired after earthquake.

Keywords: rocking mechanism, see-saw motion, finite element analysis, hysteretic behavior

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Authors: Taimur Khan, Zakirullah, Muhammad Shahab

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The SARS-CoV-2 variant BA.2.86 (Omicron) has emerged with unique mutations that may increase its transmission and infectivity. This study investigates how these mutations alter the Omicron receptor-binding domain's interaction network and dynamic properties (RBD) compared to the wild-type virus, focusing on its binding affinity to the human ACE2 (hACE2) receptor. Protein-protein docking and all-atom molecular dynamics simulations were used to analyze structural and dynamic differences. Despite the structural similarity to the wild-type virus, the Omicron variant exhibits a distinct interaction network involving new residues that enhance its binding capacity. The dynamic analysis reveals increased flexibility in the RBD, particularly in loop regions crucial for hACE2 interaction. Mutations significantly alter the secondary structure, leading to greater flexibility and conformational adaptability compared to the wild type. Binding free energy calculations confirm that the Omicron RBD has a higher binding affinity (-70.47 kcal/mol) to hACE2 than the wild-type RBD (-61.38 kcal/mol). These results suggest that the altered interaction network and enhanced dynamics of the Omicron variant contribute to its increased infectivity, providing insights for the development of targeted therapeutics and vaccines.

Keywords: SARS-CoV-2, molecular dynamic simulation, receptor binding domain, vaccine

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Authors: Sakiru Badmos, David R. Cole, Alberto Striolo

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It is known that confinement in nm-size pores affects many structural and transport properties of water and co-existing volatile species. Of particular interest for fluids in sub-surface systems, in catalysis, and in separations are reports that confinement can enhance the solubility of gases in water. Equilibrium molecular dynamics simulations were performed for aqueous H₂S confined in slit-shaped silica pores at 313K. The effect of pore width on the H₂S solubility in water was investigated. Other properties of interest include the molecular distribution of the various fluid molecules within the pores, the hydration structure for solvated H₂S molecules, and the dynamical properties of the confined fluids. The simulation results demonstrate that confinement reduces the H₂S solubility in water and that the solubility increases with pore size. Analysis of spatial distribution functions suggests that these results are due to perturbations on the coordination of water molecules around H₂S due to confinement. Confinement is found to dampen the dynamical properties of aqueous H₂S as well. Comparing the results obtained for aqueous H₂S to those reported elsewhere for aqueous CH₄, it can be concluded that H₂S permeates hydrated slit-shaped silica nano-pores faster than CH₄. In addition to contributing to better understanding the behavior of fluids in subsurface formations, these observations could also have important implications for developing new natural gas sweetening technologies.

Keywords: confinement, interfacial properties, molecular dynamic simulation, sub-surface formations

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Authors: Amira Abdelhafez, Rufus Brunt

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Geothermal energy in Egypt represents a significant untapped renewable resource that can reduce reliance on conventional power generation. Exploiting these geothermal resources depends on depth, temperature range, and geological characteristics. The intracontinental rift setting of the Gulf of Suez (GoS)-Red Sea rift is a favourable tectonic setting for convection-dominated geothermal plays. The geothermal gradient across the GoS ranges from 24.9 to 86.66 °C/km, with a heat flow of 31-127.2 mW/m². Surface expressions of convective heat loss emerge along the gulf flanks as hot springs (e.g., Hammam Faraun) accompanying deeper geothermal resources. These thermal anomalies are driven mainly by the local tectonic configuration. Characterizing the structural framework of major faults and their control on reservoir properties and subsurface hydrothermal fluid circulation is vital for geothermal applications in the gulf. The geothermal play systems of the GoS depend on structural and lithological properties that contribute to heat storage and vertical transport. Potential geothermal reservoirs include the Nubia sandstones, which, due to their thickness, continuity, and contact with hot basement rocks at a mean depth of 3 km, create an extensive reservoir for geothermal fluids. To develop these geothermal resources for energy production, defining the permeability anisotropy of the reservoir due to faults and facies variation is a crucial step in our study, particularly the evaluation of influence on thermal breakthrough and production rates.

Keywords: geothermal, October field, site specific study, reservoir modelling

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Authors: Mebarek Boukelkoul, Abdelhalim Haroun

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By means of the first principle calculation, we have investigated the structural, magnetic and magneto-optical properties of the ultra-thin films of Fen/Cu(001) with (n=1, 2, 3). We adopted a relativistic approach using DFT theorem with local spin density approximation (LSDA). The electronic structure is performed within the framework of the Spin-Polarized Relativistic (SPR) Linear Muffin-Tin Orbitals (LMTO) with the Atomic Sphere Approximation (ASA) method. During the variational principle, the crystal wave function is expressed as a linear combination of the Bloch sums of the so-called relativistic muffin-tin orbitals centered on the atomic sites. The crystalline structure is calculated after an atomic relaxation process using the optimization of the total energy with respect to the atomic interplane distance. A body-centered tetragonal (BCT) pseudomorphic crystalline structure with a tetragonality ratio c/a larger than unity is found. The magnetic behaviour is characterized by an enhanced magnetic moment and a ferromagnetic interplane coupling. The polar magneto-optical Kerr effect spectra are given over a photon energy range extended to 15eV and the microscopic origin of the most interesting features are interpreted by interband transitions. Unlike thin layers, the anisotropy in the ultra-thin films is characterized by a perpendicular magnetization which is perpendicular to the film plane.

Keywords: ultrathin films, magnetism, magneto-optics, pseudomorphic structure

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Authors: Yahya Toyin Muritala, Nonglaksana Kama, Ahmad Yani

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The aim of the paper is to investigate various linguistic techniques in enhancing and facilitating the acquisition of the practical knowledge of Arabic grammatical structuring among non-Arab learners of the standard classical Arabic language in non-Arabic speaking academic settings in the course of the current growth of the internationalism and cultural integration in some higher institutions. As the nature of the project requires standard investigations into the unique principal features of Arabic structurings and implications, the findings of the research work suggest some principles to follow in solving the problems faced by learners while acquiring grammatical aspects of Arabic language. The work also concentrates on the the structural features of the language in terms of inflection/parsing, structural arrangement order, functional particles, morphological formation and conformity etc. Therefore, grammatical aspect of Arabic which has gone through major stages in its early evolution of the classical stages up to the era of stagnation, development and modern stage of revitalization is a main subject matter of the paper as it is globally connected with communication and religion of Islam practiced by millions of Arabs and non-Arabs nowadays. The conclusion of the work shows new findings, through the descriptive and analytical methods, in terms of teaching language for the purpose of effective global communication with focus on methods of second language acquisitions by application.

Keywords: language structure, Arabic grammar, classical Arabic, intercultural communication, non-Arabic speaking environment and prospects

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Authors: Elham Sharif, Nasser Rizk, Sirin Abu Aqel, Ofelia Masoud

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Background: Previous studies have investigated the association of rs1544410, rs7975232 and rs731236 polymorphisms in vitamin D receptor gene and its impact on diseases such as cancer, diabetes and hypertension in different ethnic backgrounds. Aim: The aim of this study is to investigate the association between VDR polymorphisms using three SNP’s (rs1544410, rs7975232 and rs731236) and the severity of the significant lesion in coronary arteries among angiographically diagnosed CAD. Methods: A prospective-retrospective study was conducted on 192 CAD patients enrolled from the cardiology department-Heart Hospital HMC, grouped in 96 subjects with significant stenosis and 96 with non-significant stenosis with a mean age between 30 and 75 years old. Genotyping was performed for the following SNPs rs1544410, rs7975232 and rs731236 using TaqMan assay by the Real Time PCR, ABI 7500 in Health Sciences Labs at Qatar University Biomedical Research Center. Results: The results showed that both groups have matched age and gender distribution but patients with the significant stenosis have significantly higher; BMI (p=0.047); smoking status (p=0.039); FBS (p= 0.031); CK-MB (p=0.025) and Troponin (p=0.002) than the patients with non–significant lesion. Among the traditional risk factors, smoking increases the odds of the severe stenotic lesion in CAD patients by 1.984, with 95% CI between 1.024 – 7.063, with p= 0.042.HWE showed deviations of the rs1544410 and rs731236 among the study subjects. The most frequent genotype in distribution of rs7975232 is the AA among the significant stenosis patients, while the heterozygous AC was the frequent genotype in distribution among the non-significant stenosis group. The carriers of CC genotype in rs7975232 increased the risk of having significant coronary arteries stenotic lesion by 1.83 with 95% CI (1.020 – 3.280), p=0.043. No association was found between the rs7975232 with vitamin D and VDBP. Conclusion: There is a significant association between rs7975232 and the severity of CAD lesion. The carrier of CC genotype in rs7975232 increased the risk of having significant coronary arteries atherosclerotic lesion especially in patients with smoking history independent of vitamin D.

Keywords: vitamin D, vitamin D receptor, polymorphism, coronary harat disease

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Authors: Seyed Abdolreza Mosavi, Alireza Babakhan, Elham Sadat Hoseinifard

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Knowledge-based firms need to design mechanisms for continuous absorptive and creation of knowledge in order to ensure their survival in the competitive arena and to follow the path of development. Considering the project-oriented nature of product development activities in knowledge-based firms on the one hand and the importance of analyzing the factors affecting knowledge absorptive capacity in these firms on the other, the purpose of this study is to identify and classify the factors affecting project management practices on absorptive knowledge capacity. For this purpose, we have studied and reviewed the theoretical literature in the field of project management and absorptive knowledge capacity so as to clarify its dimensions and indexes. Then, using the ISM method, the relationship between them has been studied. To collect data, 21 questionnaires were distributed in project-oriented knowledge-based companies. The results of the ISM method analysis provide a model for the relationship between project management activities and knowledge absorptive capacity, which includes knowledge acquisition capacity, scope management, time management, cost management, quality management, human resource management, communications management, procurement management, risk management, stakeholders management and integration management. Having conducted the MICMAC analysis, we divided the variables into three groups of independent, relational and dependent variables and came up with no variables to be included in the group of autonomous variables.

Keywords: knowledge absorptive capacity, project management practices, knowledge-based firms, interpretive structural modeling

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Authors: Whitehead-Clarke T., Beynon V., Banks J., Karanjia R., Mudera V., Windsor A., Kureshi A.

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Introduction: Mesh implants are regularly used to help repair both hiatus hernias (HH) and diaphragmatic hernias (DH). In vivo studies are used to test not only mesh safety but increasingly comparative efficacy. Our work examines the field of in vivo mesh testing for HH and DH models to establish current practices and standards. Method: This systematic review was registered with PROSPERO. Medline and Embase databases were searched for relevant in vivo studies. 44 articles were identified and underwent abstract review, where 22 were excluded. 4 further studies were excluded after full text review – leaving 18 to undergo data extraction. Results: Of 18 studies identified, 9 used an in vivo HH model and 9 a DH model. 5 studies undertook mechanical testing on tissue samples – all uniaxial in nature. Testing strip widths ranged from 1-20mm (median 3mm). Testing speeds varied from 1.5-60mm/minute. Upon histology, the most commonly assessed structural and cellular factors were neovascularization and macrophages, respectively (n=9 each). Structural analysis was mostly qualitative, where cellular analysis was equally likely to be quantitative. 11 studies assessed adhesion formation, of which 8 used one of four scoring systems. 8 studies measured mesh shrinkage. Discussion: In vivo studies assessing mesh for HH and DH repair are uncommon. Within this relatively young field, we encourage surgical and materials testing institutions to discuss its standardisation.

Keywords: hiatus, diaphragmatic, hernia, mesh, materials testing, in vivo

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Authors: Marco Sewald

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Comparing present to past the numbers of Americans expatriating U. S. citizenship have risen. Even though these numbers are small compared to the immigrants, U. S. citizens expatriations have historically been much lower, making the uptick worrisome. In addition, the published lists and numbers from the U.S. government seems incomplete, with many not counted. Different branches of the U. S. government report different numbers and no one seems to know exactly how big the real number is, even though the IRS and the FBI both track and/or publish numbers of Americans who renounce. Since there is no single explanation, anecdotal evidence suggests this uptick is caused by global tax law and increased compliance burdens imposed by the U.S. lawmakers on U.S. citizens abroad. Within a research project the question arose about the reasons why a constant growing number of U.S. citizens are expatriating – the answers are believed helping to explain the underlying governmental policy rational, leading to such activities. While it is impossible to locate former U.S. citizens to conduct a survey on the reasons and the U.S. government is not commenting on the reasons given within the process of expatriation, the chosen methodology is Structural Equation Modeling (SEM), in the first step by re-using current surveys conducted by different researchers within the population of U. S. citizens residing abroad during the last years. Surveys questioning the personal situation in the context of tax, compliance, citizenship and likelihood to repatriate to the U. S. In general SEM allows: (1) Representing, estimating and validating a theoretical model with linear (unidirectional or not) relationships. (2) Modeling causal relationships between multiple predictors (exogenous) and multiple dependent variables (endogenous). (3) Including unobservable latent variables. (4) Modeling measurement error: the degree to which observable variables describe latent variables. Moreover SEM seems very appealing since the results can be represented either by matrix equations or graphically. Results: the observed variables (items) of the construct are caused by various latent variables. The given surveys delivered a high correlation and it is therefore impossible to identify the distinct effect of each indicator on the latent variable – which was one desired result. Since every SEM comprises two parts: (1) measurement model (outer model) and (2) structural model (inner model), it seems necessary to extend the given data by conducting additional research and surveys to validate the outer model to gain the desired results.

Keywords: expatriation of U. S. citizens, SEM, structural equation modeling, validating

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Authors: Mona Zaryoun, Mahmood Hosseini, Seyed Mohammad Hassan Khalkhali, Haniyeh Okhovat

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Zegalli houses in Guilan province, northern Iran, are a type of vernacular houses which their foundation, skeleton and walls all have been made of wood. The only houses which could survive the major Manjil-Rudbar earthquake of 1990 with a magnitude of 7.2 were these houses. Regarding this fact, some researchers started thinking of this type of foundations used in these houses to benefit from rocking-wise behavior. On the one hand, the relatively light weight of the houses, have helped these houses to withstand well against seismic excitations. In this paper at first a brief description of Zegalli houses and their architectural features, with emphasis on their foundation is presented. in the next stage foundation of one of these houses is modeled as a sample by a using a computer program, which has been developed in MATLAB environment, and by using the horizontal and vertical accelerograms of a set of selected site compatible earthquakes, a series of time history analysis (THA) are carried out to investigate the behavior of this type of houses against earthquake. Based on numerical results of THA it can be said that even without no sliding at the foundation timbers, only due to the rocking which occurs in various levels of the foundation the seismic response of the house is significantly reduced., which results in their stability subjected to earthquakes with peak ground acceleration of around 0.35g. Therefore, it can be recommended the Zegalli houses are considered as sustainable Iranian vernacular architecture, and it can be recommended that the use of these houses and their architecture and their structural merits are reconsidered by architects as well as civil and structural engineers.

Keywords: MATLAB software, rocking behavior, time history analysis, Zegalli houses

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Authors: Omnia F. Kharoob, Nashwa M. Yossef

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Concrete-filled double skin steel tubular (CFDST) columns could be utilized in structures such as bridges, high-rise buildings, viaducts, and electricity transmission towers due to its great structural performance. Alternatively, lean duplex stainless steel has recently gained significant interest for its high structural performance, similar corrosion resistance and lower cost compared to the austenitic steel grade. Hence, this paper presents the nonlinear finite element (FE) analysis, behaviour and design of rectangular outer lean duplex stainless steel (EN 1.4162) CFDST short columns under compression. All classes of the outer rectangular hollow section according to the depth-to-thickness (D/t) ratios were considered. The results showed that the axial ultimate strength of rectangular CFDST short columns increased linearly by increasing the concrete compressive strength, while it does not influence when changing the hollow ratios. Finally, the axial capacities were compared with the available design methods, and recommendations were conducted for the design strength of this type of column.

Keywords: concrete-filled double skin columns, compressive strength, finite element analysis, lean duplex stainless steel, ultimate axial strength, short columns

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