Search results for: gene frequency

Authors: Rim Sghiri, Samia Al Shouli, Hana Benhassine, Nejla Elamri, Zahid Shakoor, Foued Slama, Adel Almogren, Hala Zeglaoui, Elyes Bouajina, Ramzi Zemni

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Objectives: Little is known about genes predisposing to systemic bone loss (SBL) in rheumatoid arthritis (RA). Therefore, we examined the association between SBL and a variant of CD40 gene, which is known to play a critical role in both immune response and bone homeostasis among patients with RA. Methods: CD40 rs48104850 was genotyped in 176 adult RA patients. Bone mineral density (BMD) was measured using dual-energy X-ray absorptiometry (DXA). Results: Low BMD was observed in 116 (65.9%) patients. Among them, 60 (34.1%) had low femoral neck (FN) Z score, 72 (40.9%) had low total femur (TF) Z score, and 105 (59.6%) had low lumbar spine (LS) Z score. CD40 rs4810485 was found to be associated with reduced TF Z score with the CD40 rs4810485 T allele protecting against reduced TF Z score (OR = 0.40, 95% CI = 0.23-0.68, p = 0.0005). This association was confirmed in the multivariate logistic regression analysis (OR=0.31, 95% CI= 0.16-0.59, p=3.84 x 10₋₄). Moreover, median FN BMD was reduced among RA patients with CD40 rs4810485 GG genotype compared to RA patients harbouring CD40 rs4810485 TT and GT genotypes (0.788± 0.136 versus 0.826± 0.146g/cm², p=0.001). Conclusion: This study, for the first time ever, demonstrated an association between a CD40 genetic variant and SBL among patients with RA.

Keywords: rheumatoid arthritis, CD40 gene, bone mineral density, systemic bone loss, rs48104850

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Authors: B.M. Balekwa, D.V.V. Kallon, D.J. Fourie

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Modal analysis is applied to establish the dynamic difference between vibration response of the rails supported on High Density Polyethylene (HDPE) and Hytrel/6358 rail pads. The experiment was conducted to obtain the results in the form of Frequency Response Functions (FRFs) in the vertical and lateral directions. Three antiresonance modes are seen in the vertical direction; one occurs at about 150 Hz when the rail resting on the Hytrel/6358 pad experiences a force mid-span. For the rail resting on this type of rail pad, no antiresonance occurs when the force is applied on the point of the rail that is resting on the pad and directly on top of a sleeper. The two antiresonance modes occur in a frequency range of 250 – 300 Hz in the vertical direction for the rail resting on HDPE pads. At resonance, the rail vibrates with a higher amplitude, but at antiresonance, the rail transmits vibration downwards to the sleepers. When the rail is at antiresonance, the stiffness of the rail pads play a vital role in terms of damping the vertical vibration to protect the sleepers. From the FRFs it is understood that the Hytrel/6358 rail pads perform better than the HDPE in terms of vertical response, given that at a lower frequency range of 0 – 300 Hz only one antiresonance mode was identified for vertical vibration of the rail supported on Hytrel/6358. This means the rail is at antiresonance only once within this frequency range and this is the only time when vibration is transmitted downwards.

Keywords: accelerance, FRF, rail corrugation, rail pad

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Authors: V. Krishna, Shashikumar

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Edible Bananas (Musa spp.) are the major staple food for rural and urban consumers in India and an important source of rural income. The cultivar Musa paradisiaca cv. Karibale Monthan is an endemic cultivar of Malnad region of Karnataka and used as a glomolueroprotective neutraceutical to solve kidney problems. The protocol for mass multiplication of plantlets for this indigenous banana cultivar Karibale Monthan has not yet been standardized so far. In the present study, an attempt has been made to develop high frequency in vitro regeneration protocol and evaluation of morphoagronomic characteristics in the farmyard. The high frequency shoot initiation (93.33 %) was recorded at the synergetic effect of BAP (2 to 8mg/L), TDZ (0.1 to 1.2mg/L) and coconut water (0.1 to 1.2ml/L). It was optimized at the concentration 5 mg/l BAP, 0.5 mg/l TDZ and 0.5 ml/l coconut water with 15.90 ± 1.66 frequency of shoots per propagule. Supplementation of 1.0 mg/l IBA induces 5.33 ± 1.21 numbers of roots with a mean root length of 7.50 ± 1.87 roots. 99% of plantlets with distinct roots and shoots were successfully acclimatized in the green house and transferred to the field to evaluate the agro-morphological variations. The micropropagated plants showed significantly higher morphometric values for height of the plant (16.80±2.17), number of leaves (12.40±1.14), length of the bunch (56.20±2.17), weight of the bunch (13.60±1.14), number of hands in a bunch (11.40±1.14) and girth of the pseudostem (49.80±1.48) when compared with in vivo plants.

Keywords: banana cv. Karibale Monthan, neutraceutical, high-frequency regeneration, morphometric evaluation

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Authors: Hamid Mustafa, Heather J. Huson, Adeela Ajmal, Kim Euisoo, Tad S. Sonstegard

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In this study, 67 animals, representing six different cattle breeds of Pakistan, were genotyped with the Bovine high density (777K) SNP Beadchip. These include 13 Sahiwal, 09 Red Sindhi, 13 Tharparkar, 08 Achi, 13 Cholistani and 10 Dhanni cattle breeds. Analysis of 500, 939 SNP markers revealed that the mean minor allele frequency (MAF) was 0.21, 0.22, 0.18, 0.23, 0.22 and 0.22 for Sahiwal, Red Sindhi, Tharparkar, Achi, Cholistani and Dhanni respectively. Significant differences of minor allele frequency (MAF) were observed between the indigenous Pakistani cattle population (P<0.001). Across these Pakistani cattle breeds, a common variant MAF (≥0.10 and ≤0.5) accounted for an overall estimated 75.71 % of the 500,939 SNPs and on the average 19.58 % of the markers were monomorphic. Mean observed (HO) and expected (HE) heterozygosities were 0.656 and 0.638, respectively. This primarily study of Pakistani indigenous cattle breeds indicate that this level of SNPs variation can potentially be used for genomic studies for future breeding plans and for farm animal conservation strategies.

Keywords: Pakistan, cattle, minor allele frequency, SNP, variation

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Authors: Vipin Kumar, Girish S. Setlur

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Graphene has been recognized as a promising 2D material with many new properties. However, pristine graphene is gapless which hinders its direct application towards graphene-based semiconducting devices. Graphene is a zero-gapp and linearly dispersing semiconductor. Massless charge carriers (quasi-particles) in graphene obey the relativistic Dirac equation. These Dirac fermions show very unusual physical properties such as electronic, optical and transport. Graphene is analogous to two-level atomic systems and conventional semiconductors. We may expect that graphene-based systems will also exhibit phenomena that are well-known in two-level atomic systems and in conventional semiconductors. Rabi oscillation is a nonlinear optical phenomenon well-known in the context of two-level atomic systems and also in conventional semiconductors. It is the periodic exchange of energy between the system of interest and the electromagnetic field. The present work describes the phenomenon of Rabi oscillations in graphene based systems. Rabi oscillations have already been described theoretically and experimentally in the extensive literature available on this topic. To describe Rabi oscillations they use an approximation known as rotating wave approximation (RWA) well-known in studies of two-level systems. RWA is valid only near conventional resonance (small detuning)- when the frequency of the external field is nearly equal to the particle-hole excitation frequency. The Rabi frequency goes through a minimum close to conventional resonance as a function of detuning. Far from conventional resonance, the RWA becomes rather less useful and we need some other technique to describe the phenomenon of Rabi oscillation. In conventional systems, there is no second minimum - the only minimum is at conventional resonance. But in graphene we find anomalous Rabi oscillations far from conventional resonance where the Rabi frequency goes through a minimum that is much smaller than the conventional Rabi frequency. This is known as anomalous Rabi frequency and is unique to graphene systems. We have shown that this is attributable to the pseudo-spin degree of freedom in graphene systems. A new technique, which is an alternative to RWA called asymptotic RWA (ARWA), has been invoked by our group to discuss the phenomenon of Rabi oscillation. Experimentally accessible current density shows different types of threshold behaviour in frequency domain close to the anomalous Rabi frequency depending on the system chosen. For single layer graphene, the exponent at threshold is equal to 1/2 while in case of bilayer graphene, it is computed to be equal to 1. Bilayer graphene shows harmonic (anomalous) resonances absent in single layer graphene. The effect of asymmetry and trigonal warping (a weak direct inter-layer hopping in bilayer graphene) on these oscillations is also studied in graphene systems. Asymmetry has a remarkable effect only on anomalous Rabi oscillations whereas the Rabi frequency near conventional resonance is not significantly affected by the asymmetry parameter. In presence of asymmetry, these graphene systems show Rabi-like oscillations (offset oscillations) even for vanishingly small applied field strengths (less than the gap parameter). The frequency of offset oscillations may be identified with the asymmetry parameter.

Keywords: graphene, Bilayer graphene, Rabi oscillations, Dirac fermion systems

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Authors: Vincent Murray

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The chromatin structure at the transcription start sites (TSSs) of genes is very important in the control of gene expression. In order for gene expression to occur, the chromatin structure at the TSS has to be altered so that the transcriptional machinery can be assembled and RNA transcripts can be produced. In particular, the nucleosome structure and positioning around the TSS has to be changed. Bleomycin is utilized as an anti-tumor agent to treat Hodgkin's lymphoma, squamous cell carcinoma, and testicular cancer. Bleomycin produces DNA damage in human cells and DNA strand breaks, especially double-strand breaks, are thought to be responsible for the cancer chemotherapeutic activity of bleomycin. Bleomycin is a large glycopeptide with molecular weight of approximately 1500 Daltons and hence its DNA strand cleavage activity can be utilized as a probe of chromatin structure. In this project, Illumina next-generation DNA sequencing technology was used to determine the position of DNA double-strand breaks at the TSSs of genes in intact cells. In this genome-wide study, it was found that bleomycin cleavage preferentially occurred at the TSSs of actively transcribed human genes in comparison with non-transcribed genes. There was a correlation between the level of enhanced bleomycin cleavage at TSSs and the degree of transcriptional activity. In addition, bleomycin was able to determine the position of nucleosomes at the TSSs of human genes. Bleomycin analogues were also utilized as probes of chromatin structure at the TSSs of human genes. In a similar manner to bleomycin, the bleomycin analogues 6′-deoxy-BLM Z and zorbamycin preferentially cleaved at the TSSs of human genes. Interestingly this degree of enhanced TSS cleavage inversely correlated with the cytotoxicity (IC50 values) of BLM analogues. This indicated that the degree of cleavage by bleomycin analogues at the TSSs of human genes was very important in the cytotoxicity of bleomycin and analogues. It also provided a deeper insight into the mechanism of action of this cancer chemotherapeutic agent since actively transcribed genes were preferentially targeted.

Keywords: anti-cancer activity, chromatin structure, cytotoxicity, gene expression, next-generation DNA sequencing

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Authors: Cheng Yang Kwa, Yoke Rung Wong

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Laminated composite materials are widely employed in automotive, aerospace, and other industries. These materials provide distinct benefits due to their high specific strength, high specific modulus, and ability to be customized for a specific function. However, delamination of laminated composite materials is one of the main defects which can occur during manufacturing, regular operations, or maintenance. Delamination can bring about considerable internal damage, unobservable by visual check, that causes significant loss in strength and stability, leading to composite structure catastrophic failure. Structural health monitoring (SHM) is known to be the automated method for monitoring and evaluating the condition of a monitored object. There are several ways to conduct SHM in aerospace. One of the effective methods is to monitor the natural frequency shift of structure due to the presence of defect. This study investigated the mechanical resonance frequency shift of a multi-layer composite cantilever beam due to interlaminar delamination. ANSYS Workbench® was used to create a 4-plies laminated composite cantilever finite element model with [90/0]s fiber setting. Epoxy Carbon UD (230GPA) Prepreg was chosen, and the thickness was 2.5mm for each ply. The natural frequencies of the finite element model with various degree of delamination were simulated based on modal analysis and then validated by using literature. It was shown that the model without delamination had natural frequency of 40.412 Hz, which was 1.55% different from the calculated result (41.050 Hz). Thereafter, the various degree of delamination was mimicked by changing the frictional conditions at the middle ply-to-ply interface. The results suggested that delamination in the laminated composite cantilever induced a change in its stiffness which alters its mechanical resonance frequency.

Keywords: structural health monitoring, NDT, cantilever, laminate

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Authors: A. Moawad, K. C. Yao, A. Mansour, R. Gautier

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The detecting of an occupied frequency band is a major issue in cognitive radio systems. The detection process becomes difficult if the signal occupying the band of interest has faded amplitude due to multipath effects. These effects make it hard for an occupying user to be detected. This work mitigates the missed-detection problem in the context of cognitive radio in frequency-selective fading channel by proposing blind channel estimation method that is based on scattering transform. By initially applying conventional energy detection, the missed-detection probability is evaluated, and if it is greater than or equal to 50%, channel estimation is applied on the received signal followed by channel equalization to reduce the channel effects. In the proposed channel estimator, we modify the Morlet wavelet by using its first derivative for better frequency resolution. A mathematical description of the modified function and its frequency resolution is formulated in this work. The improved frequency resolution is required to follow the spectral variation of the channel. The channel estimation error is evaluated in the mean-square sense for different channel settings, and energy detection is applied to the equalized received signal. The simulation results show improvement in reducing the missed-detection probability as compared to the detection based on principal component analysis. This improvement is achieved at the expense of increased estimator complexity, which depends on the number of wavelet filters as related to the channel taps. Also, the detection performance shows an improvement in detection probability for low signal-to-noise scenarios over principal component analysis- based energy detection.

Keywords: channel estimation, cognitive radio, scattering transform, spectrum sensing

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Authors: Mondher Labidi, Fethi Choubani

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In this paper, novel miniaturization technique of antenna is proposed using I-slot. Using this technique, gain of antenna can increased for 4dB (antenna only) to 6.6dB for the proposed I-slot antenna and a frequency shift of about 0.45 GHz to 1 GHz is obtained. Also a reduction of the shape size of the antenna is achieved (about 38 %) to operate in the Wi-Fi (2.45 GHz) band.RF Moreover the frequency shift can be controlled by changing the place or the length of the I-slot. Finally the proposed miniature antenna with an improved radiation efficiency and gain was built and tested.

Keywords: slot antenna, miniaturization, RF, electrical equivalent circuit (EEC)

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Authors: H. Zormati, J. Chebil, J. Bel Hadj Tahar

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Next generation wireless transmission technology (5G) is expected to support the development of channel models for higher frequency bands, so clarification of high frequency bands is the most important issue in radio propagation research for 5G, multiple urban microcellular measurements have been carried out at 60 GHz. In this paper, the collected data is uniformly analyzed with focus on the path loss (PL), the objective is to compare simulation results of some studied channel models with the purpose of testing the performance of each one.

Keywords: 5G, channel model, 60GHz channel, millimeter-wave, urban microcell

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Authors: A. El Hamdouni, J. Zbitou, A. Tajmouati, L. El Abdellaoui, A. Errkik, A. Tribak, M. Latrach

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This paper presents a novel fractal antenna structure proposed for UWB (Ultra – Wideband) applications. The frequency band 3.1-10.6 GHz released by FCC (Federal Communication Commission) as the commercial operation of UWB has been chosen as frequency range for this antenna based on coplanar waveguide (CPW) feed and circular shapes fulfilled according to fractal geometry. The proposed antenna is validated and designed by using an FR4 substrate with overall area of 34 x 43 mm2. The simulated results performed by CST-Microwave Studio and compared by ADS (Advanced Design System) show good matching input impedance with return loss less than -10 dB between 2.9 GHz and 11 GHz.

Keywords: Fractal antenna, Fractal Geometry, CPW Feed, UWB, FCC

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Authors: Sheryl Avendaño, Miguel Ospina, Hebert Montegranario

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Full Wave Inversion (FWI) is a variant of seismic tomography for obtaining velocity profiles by an optimization process that combine forward modelling (or solution of wave equation) with the misfit between synthetic and observed data. In this research we are modelling wave propagation in a visco-acoustic medium in the frequency domain. We apply finite differences for the numerical solution of the wave equation with a mix between usual and rotated grids, where density depends on velocity and there exists a damping function associated to a linear dissipative medium. The velocity profiles are obtained from an initial one and the data have been modeled for a frequency range 0-120 Hz. By an iterative procedure we obtain an estimated velocity profile in which are detailed the remarkable features of the velocity profile from which synthetic data were generated showing promising results for our method.

Keywords: seismic inversion, full wave inversion, visco acoustic wave equation, finite diffrence methods

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Authors: Deepak Kumar, Ravi Rajwanshi, Mohd. Aslam Yusuf, Nisha Kant Pandey, Preeti Singh, Mukesh Saxena, Neera Bhalla Sarin

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Global issues are leading to concerns over food security. These include climate change, urbanization, increase in population subsequently leading to greater energy and water demand. Futuristic approach for crop improvement involves gene pyramiding for agronomic traits that empower the plants to withstand multiple stresses. In an earlier study from the laboratory, the efficacy of overexpressing γ-tocopherol methyl transferase (γ-TMT) gene from the vitamin E biosynthetic pathway has been shown to result in six-fold increase of the most biologically active form, the α-tocopherol in Brassica juncea which resulted in alleviation of salt, heavy metal and osmoticum induced stress by the transgenic plants. The glyoxalase I (gly I) gene from the glyoxalase pathway has also been earlier shown by us to impart tolerance against multiple abioitc stresses by detoxification of the cytotoxic compound methylglyoxal in Brassica juncea. Recently, both the transgenes were pyramided in Brassica juncea lines through sexual crosses involving two stable Brassica juncea lines overexpressing γ-TMT and gly I genes respectively. The transgene integration was confirmed by PCR analysis and their mRNA expression was evident by RT-PCR analysis. Preliminary physiological investigations showed ~55% increased seed germination under 200 mM NaCl stress in the pyramided line and 81% higher seed germination under 200 mM mannitol stress as compared to the WT control plants. The pyramided lines also retained more chlorophyll content when the leaf discs were floated on NaCl (200, 400 and 600 mM) or mannitol (200, 400 and 600 mM) compared to the WT control plants. These plants had higher Relative Water Content and greater solute accumulation under stress compared to the parental plants having γ-TMT or the glyI gene respectively. The studies revealed the synergy of two components from different metabolic pathways in enhancing stress hardiness of the transgenic B. juncea plants. It was concluded that pyramiding of genes (γ-TMT and glyI) from diverse pathways can lead to enhanced tolerance to salt and mannitol stress (simulating drought conditions). This strategy can prove useful in enhancing the crop yields under various abiotic stresses.

Keywords: abiotic stress, brassica juncea, glyoxalase I, α-tocopherol

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Authors: Theresa Ukamaka Nwagha, Angela Ogechukwu Ugwu, Martins Nweke

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Background and Objectives: Blood transfusion is an effective and proven treatment for some severe complications of sickle cell disease. Recurrent transfusions have put patients with sickle cell disease at risk of developing antibodies against the various antigens they were exposed to. This study aims to investigate the frequency of red blood cell alloimmunization in patients with sickle disease in Africa. Materials and Methods: This is a systematic review of peer-reviewed literature published in English. The review was conducted consistent with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist. Data sources for the review include MEDLINE, PubMed, CINAHL, and Academic Search Complete. Included in this review are articles that reported the frequency/prevalence of red blood cell alloimmunization in sickle cell disease patients in Africa. Eligible studies were subjected to independent full-text screening and data extraction. Risk of bias assessment was conducted with the aid of the mixed method appraisal tool. We employed a random-effects model of meta-analysis to estimate the pooled prevalence. We computed Cochrane’s Q statistics and I2 and prediction interval to quantify heterogeneity in effect size. Results: The prevalence estimates range from 2.6% to 29%. Pooled prevalence was estimated to be 10.4% (CI 7.7.–13.8); PI = 3.0 – 34.0%), with significant heterogeneity (I2 = 84.62; PI = 2.0-32.0%) and publication bias (Egger’s t-test = 1.744, p = 0.0965). Conclusion: The frequency of red cell alloantibody varies considerably in Africa. The alloantibodies appeared frequent in this order: the Rhesus, Kell, Lewis, Duffy, MNS, and Lutheran

Keywords: frequency, red blood cell, alloimmunization, sickle cell disease, Africa

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Authors: S. Hosseini, M. Ahmadi Najafabadi, M. Akhlaghi

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The health of the journal bearings is very important in preventing unforeseen breakdowns in rotary machines, and poor lubrication is one of the most important factors for producing the bearing failures. Hydrodynamic lubrication (HL), mixed lubrication (ML), and boundary lubrication (BL) are three regimes of a journal bearing lubrication. This paper uses acoustic emission (AE) measurement technique to correlate features of the AE signals to the three lubrication regimes. The transitions from HL to ML based on operating factors such as rotating speed, load, inlet oil pressure by time domain and time-frequency domain signal analysis techniques are detected, and then metal-to-metal contacts between sliding surfaces of the journal and bearing are identified. It is found that there is a significant difference between theoretical and experimental operating values that are obtained for defining the lubrication regions.

Keywords: acoustic emission technique, pressure fed journal bearing, time and frequency signal analysis, metal-to-metal contact

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Authors: Ju-Hyung Kim, Dae-Ho Mun, Hong-Gun Park

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When an impact is applied to a floating floor, noise and vibration response of high-frequency range is reduced effectively, while amplifies the response at low-frequency range. This means floating floor can make worse noise condition when heavy-weight impact is applied. The amplified response is the result of interaction between finishing layer (mortar plate) and concrete slab. Because an impact force is not directly delivered to concrete slab, the impact force waveform or spectrum can be changed. In this paper, the changed impact spectrum was derived from several floating floor vibration tests. Based on the measured data, numerical modeling can describe the floating floor response, especially at low-frequency range. As a result, heavy-weight impact noise can be predicted using modified impact spectrum.

Keywords: floating floor, heavy-weight impact, prediction, vibration

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Authors: Othmane Bouferroum, Malika Boudraa

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In this study, a dual exponential model for CV formant transition is derived from locus theory of speech perception. Then, an algorithm for automatic vowel and consonant’s target formant frequency detection is developed and tested on real speech. The results show that vowels and consonants are detected through transitions rather than their small stable portions. Also, vowel reduction is clearly observed in our data. These results are confirmed by the observations made in perceptual experiments in the literature.

Keywords: acoustic invariance, coarticulation, formant transition, locus equation

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Authors: Seraj Makkawi, Abdulaziz A. Alqarni, Himyan Alghaythee, Suzan Y. Alharbi, Anmar Fatani, Reem Adas, Ahmad R. Abuzinadah

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Amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease, is a neurodegenerative disease that involves both the upper and lower motor neurons. Familial ALS, including superoxide dismutase 1 (SOD1) mutation, accounts for 5-10% of all cases of ALS. Typically, the symptoms of ALS are purely motor, though coexistent sensory symptoms have been reported in rare cases. In this report, we describe the case of a 47- year-old man who presented with progressive bilateral lower limb weakness and numbness for the last four years. A nerve conduction study (NCS) showed evidence of coexistent axonal sensorimotor polyneuropathy in addition to the typical findings of ALS in needle electromyography. Genetic testing confirmed the diagnosis of familial ALS secondary to the SOD1 genetic mutation. This report highlights that the presence of sensory symptoms should not exclude the possibility of ALS in an appropriate clinical setting.

Keywords: Saudi Arabia, polyneuropathy, SOD1 gene mutation, familial amyotrophic lateral sclerosis, amyotrophic lateral sclerosis

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Authors: Titus A. Beu

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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Soultana Konstantinidou, Tiziana Schmidt, Elena Landi, Alessandro De Carli, Giovanni Maltinti, Darius Witt, Alicja Dziadosz, Agnieszka Lindstaedt, Michele Lai, Mauro Pistello, Valentina Cappello, Luciana Dente, Chiara Gabellini, Piotr Barski, Vittoria Raffa

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CRISPR/Cas9 technology has gained the interest of researchers in the field of biotechnology for genome editing. Since its discovery as a microbial adaptive immune defense, this system has been widely adopted and is acknowledged for having a variety of applications. However, critical barriers related to safety and delivery are persisting. Here, we propose a new concept of genome engineering, which is based on a nano-formulation of Cas9. The Cas9 enzyme was conjugated to a gold nanoparticle (AuNP-Cas9). The AuNP-Cas9 maintained its cleavage efficiency in vitro, to the same extent as the ribonucleoprotein, including non-conjugated Cas9 enzyme, and showed high gene editing efficiency in vivo in zebrafish embryos. Since CRISPR/Cas9 technology is extensively used in cancer research, melanoma was selected as a validation target. Cell studies were performed in A375 human melanoma cells. Particles per se had no impact on cell metabolism and proliferation. Intriguingly, the AuNP-Cas9 internalized spontaneously in cells and localized as a single particle in the cytoplasm and organelles. More importantly, the AuNP-Cas9 showed a high nuclear localization signal. The AuNP-Cas9, overcoming the delivery difficulties of Cas9, could be used in cellular biology and localization studies. Taking advantage of the plasmonic properties of gold nanoparticles, this technology could potentially be a bio-tool for combining gene editing and photothermal therapy in cancer cells. Further work will be focused on intracellular interactions of the nano-formulation and characterization of the optical properties.

Keywords: CRISPR/Cas9, gene editing, gold nanoparticles, nanotechnology

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Authors: Shuenn-Yih Chang, Chiu-LI Huang, Ngoc-Cuong Tran

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A new family of structure-dependent integration methods, whose coefficients of the difference equation for displacement increment are functions of the initial structural properties and the step size for time integration, is proposed in this work. This family method can simultaneously integrate the controllable numerical dissipation, explicit formulation and unconditional stability together. In general, its numerical dissipation can be continuously controlled by a parameter and it is possible to achieve zero damping. In addition, it can have high-frequency damping to suppress or even remove the spurious oscillations high frequency modes. Whereas, the low frequency modes can be very accurately integrated due to the almost zero damping for these low frequency modes. It is shown herein that the proposed family method can have exactly the same numerical properties as those of HHT-α method for linear elastic systems. In addition, it still preserves the most important property of a structure-dependent integration method, which is an explicit formulation for each time step. Consequently, it can save a huge computational efforts in solving inertial problems when compared to the HHT-α method. In fact, it is revealed by numerical experiments that the CPU time consumed by the proposed family method is only about 1.6% of that consumed by the HHT-α method for the 125-DOF system while it reduces to be 0.16% for the 1000-DOF system. Apparently, the saving of computational efforts is very significant.

Keywords: structure-dependent integration method, nonlinear dynamic analysis, unconditional stability, numerical dissipation, accuracy

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Authors: Kamila Weissova, Jitka Skrabalova, Katerina Skalova, Jana Koprivova, Zdenka Bendova

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Any Arctic visitor has to deal with extreme conditions, including constant light during the summer season or constant darkness during winter time. Light/dark cycle is the most powerful synchronizing signal for biological clock and the absence of daily dark period during the polar day can significantly alter the functional state of the internal clock. However, the inner clock can be synchronized by other zeitgebers such as physical activity, food intake or social interactions. Here, we investigated the effect of polar day on circadian clock of 10 researchers attending the polar base station in the Svalbard region during July. The data obtained on Svalbard were compared with the data obtained before the researchers left for the expedition (in the Czech Republic). To determine the state of circadian clock we used wrist actigraphy followed by sleep diaries, saliva, and buccal mucosa samples, both collected every 4 hours during 24h-interval to detect melatonin by radioimmunoassay and clock gene (PER1, BMAL1, NR1D1, DBP) mRNA levels by RT-qPCR. The clock gene expression was analyzed using cosinor analysis. From our results, it is apparent that the constant sunlight delayed melatonin onset and postponed the physical activity in the same order. Nevertheless, the clock gene expression displayed higher amplitude on Svalbard compared to the amplitude detected in the Czech Republic. These results have suggested that the common daily schedule at the Svalbard expedition can strengthen circadian rhythm in the environment that is lacking light/dark cycle. In conclusion, the constant sunlight delays melatonin onset, but it still maintains its rhythmic secretion. The effect of constant sunlight on circadian clock can be minimalized by common daily scheduled activity.

Keywords: actighraph, clock genes, human, melatonin, polar day

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Authors: B. G. Ayantunji, B. Musa, H. Mai-Unguwa, L. A. Sunmonu, A. S. Adewumi, L. Sa'ad, A. Kado

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For achieving reliable and efficient communication system, both terrestrial and satellite communication, surface refractivity is critical in planning and design of radio links. This study analyzed the impact of atmospheric parameters on Ultra High Frequency (UHF) signal strength over Gusau, North West, Nigeria. The analysis exploited meteorological data measured simultaneously with UHF signal strength for the month of June 2017 using a Davis Vantage Pro2 automatic weather station and UHF signal strength measuring devices respectively. The instruments were situated at the premise of Federal University, Gusau (6° 78' N, 12° 13' E). The refractivity values were computed using ITU-R model. The result shows that the refractivity value attained the highest value of 366.28 at 2200hr and a minimum value of 350.66 at 2100hr local time. The correlation between signal strength and refractivity is 0.350; Humidity is 0.532 and a negative correlation of -0.515 for temperature.

Keywords: refractivity, UHF (ultra high frequency) signal strength, free space, automatic weather station

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Authors: Anna D. Kotrova, Alexandr N. Shishkin, Elena I. Ermolenko

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The aim. To study the quantitative and qualitative colon bacteria ratio from patients with metabolic syndrome. Materials and methods. Fecal samples from patients of 2 groups were identified and analyzed: the first group was formed by patients with metabolic syndrome, the second one - by healthy individuals. The metagenomics method was used with the analysis of 16S rRNA gene sequences. The libraries of the variable sites (V3 and V4) gene 16S RNA were analyzed using the MiSeq device (Illumina). To prepare the libraries was used the standard recommended by Illumina, a method based on two rounds of PCR. Results. At the phylum level in the microbiota of patients with metabolic syndrome compared to healthy individuals, the proportion of Tenericutes was reduced, the proportion of Actinobacteria was increased. At the genus level, in the group with metabolic syndrome, relative to the second group was increased the proportion of Lachnospira. Conclusion. Changes in the colon bacteria ratio in the gut microbiota of patients with metabolic syndrome were found both at the type and the genus level. In the metabolic syndrome group, there is a decrease in the proportion of bacteria that do not have a cell wall. To confirm the revealed microbiota features in patients with metabolic syndrome, further study with a larger number of samples is required.

Keywords: gut microbiota, metabolic syndrome, metagenomics, tenericutes

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Authors: Vladimir Mantsevich, Natalya Maslova, Petr Arseyev

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We investigated the tunneling current peculiarities in the system of two coupled by means of the external field quantum dots (QDs) weakly connected to the electrodes in the presence of Coulomb correlations between localized electrons by means of Heisenberg equations for pseudo operators with constraint. Special role of multi-electronic states was demonstrated. Various single-electron levels location relative to the sample Fermi level and to the applied bias value in symmetric tunneling contact were investigated. Rabi frequency tuning results in the single-electron energy levels spacing. We revealed the appearance of negative tunneling conductivity and demonstrated multiple switching "on" and "off" of the tunneling current depending on the Coulomb correlations value, Rabi frequency amplitude and energy levels spacing. We proved that Coulomb correlations strongly influence the system behavior. We demonstrated the presence of multi-stability in the coupled QDs with Coulomb correlations when single value of the tunneling current amplitude corresponds to the two values of Rabi frequency in the case when both single-electron energy levels are located slightly above eV and are close to each other. This effect disappears when the single-electron energy levels spacing increases.

Keywords: Coulomb correlations, negative tunneling conductivity, quantum dots, rabi frequency

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Authors: Haruka Ito, Toru Maruyama, Michihiro Ito, Chuya Shinzato, Hiroyuki Fujimura, Yoshikatsu Nakano, Shoichiro Suda, Sachiyo Aburatani, Haruko Takeyama

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Clarifying symbiotic relationships is one of the most important theme for understanding the marine eco-system. Coral reef has been regarded as an important environmental resource. Coral holobiont composed by coral, symbiotic microalgae zooxanthellae, and bacteria have complexed relationship. Zooxanthellae mainly supply organic matter to the host corals through their photosynthetic activity. The symbiotic relationship is indispensable for corals but may easily collapses due to the rise of seawater temperature. However, the molecular mechanism how seawater temperature influences their relationships still remain unclear. In this study, the transcriptomic analysis has applied to elucidate the coral-zooxanthellae relationships under high seawater temperature stress. To observe reactions of corals and zooxanthellae against the rise of seawater temperature, meta-gene expression in coral have been analyzed. The branches from six different colonies of a stony coral, Acropora tenuis, were sampled at nine times by 2016 at two locations, Ishikawabaru and South of Sesoko Island, Okinawa, Japan. The mRNAs extracted from the branches including zooxanthellae were sequenced by illumina HiSeq. Gene Set Enrichment Analysis (GSEA) based on hyper geometric distribution was performed. The seawater temperature at 2016 summer was unusually high, which was caused by El Niño event, and the number of zooxanthellae in coral was decreased in August. GSEA derived the several specific genes expressed in A. tenuis under heat stress conditions. The upregulated genes under heat stress highly related with infection immunity. The downregulated genes significantly contained cell cycle related genes. Thu, it is considered that heat stress cause disorder in cell metabolism of A. tenuis, resulting in serious influence to coral holobiont.

Keywords: coral, symbiosis, thermal stress response, transcriptome analysis

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Authors: Abdullah Alnutayfat, Alexander Sutin, Dong Liu

Abstract:

Wind turbine has become one of the most popular energy productions. However, failure of blades and maintenance costs evolve into significant issues in the wind power industry, so it is essential to detect the initial blade defects to avoid the collapse of the blades and structure. This paper aims to apply modulation of high-frequency blade vibrations by low-frequency blade rotation, which is close to the known Vibro-Acoustic Modulation (VAM) method. The high-frequency wideband blade vibration is produced by the interaction of the surface blades with the environment air turbulence, and the low-frequency modulation is produced by alternating bending stress due to gravity. The low-frequency load of rotational wind turbine blades ranges between 0.2-0.4 Hz and can reach up to 2 Hz for strong wind. The main difference between this study and previous ones on VAM methods is the use of a wideband vibration signal from the blade's natural vibrations. Different features of the vibroacoustic modulation are considered using a simple model of breathing crack. This model considers the simple mechanical oscillator, where the parameters of the oscillator are varied due to low-frequency blade rotation. During the blade's operation, the internal stress caused by the weight of the blade modifies the crack's elasticity and damping. The laboratory experiment using steel samples demonstrates the possibility of VAM using a probe wideband noise signal. A cycle load with a small amplitude was used as a pump wave to damage the tested sample, and a small transducer generated a wideband probe wave. The received signal demodulation was conducted using the Detecting of Envelope Modulation on Noise (DEMON) approach. In addition, the experimental results were compared with the modulation index (MI) technique regarding the harmonic pump wave. The wideband and traditional VAM methods demonstrated similar sensitivity for earlier detection of invisible cracks. Importantly, employing a wideband probe signal with the DEMON approach speeds up and simplifies testing since it eliminates the need to conduct tests repeatedly for various harmonic probe frequencies and to adjust the probe frequency.

Keywords: vibro-acoustic modulation, detecting of envelope modulation on noise, damage, turbine blades

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Authors: Wesam Ali

Abstract:

This paper provides useful guidelines to the circuit designers on the magnitude of fabrication errors in multilayer millimeter-wave components that are acceptable and presents data not previously reported in the literature. A particularly significant error that was quantified was that of skew between conductors on different layers, where it was found that a skew angle of only 0.1° resulted in very significant changes in bandwidth and insertion loss. The work was supported by a detailed investigation on a 35GHz, multilayer edge-coupled band-pass filter, which was fabricated on alumina substrates using photoimageable thick film process.

Keywords: fabrication errors, multilayer, high frequency band, photoimagable technology

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Authors: Jose Ramon Calvo-Ferrer

Abstract:

Video games have been extensively employed in educational contexts to teach contents and skills, upon the premise that they engage students and provide instant feedback, which makes them adequate tools in the field of education and training. Term frequency, along with metacognition and implicit corrective feedback, has often been identified as powerful variables in the learning of vocabulary in a foreign language. This study analyses the learning of L2 mobile operating system terminology by a group of students and uses the data collected by the video game The Conference Interpreter to identify the predictive strength of term frequency (times a term is shown), positive metacognition (times a right answer is provided), and negative metacognition (times a term is shown as wrong) regarding L2 vocabulary learning and perceived learning outcomes. The regression analysis shows that the factor ‘positive metacognition’ is a positive predictor of both dependent variables, whereas the other factors seem to have no statistical effect on any of them.

Keywords: digital game-based learning, feedback, metacognition, frequency, video games

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Authors: Rim Frikha, Maha Ben Jema, Moez Elloumi, Tarek Rebai

Abstract:

Background: Acute lymphoblastic leukemia (ALL); a common blood cancer characterized by the interaction between genetic and environmental factors. Methylenetetrahydrofolate reductase (MTHFR) is an essential folate metabolic enzyme in the processes of DNA synthesis and methylation. A common functional variant of the MTHFR gene, the A1298C, which induces disturbances in folate metabolism, may affect susceptibility to ALL. Objective: The present study aimed to assess the prevalence of MTHFR polymorphism A1298 > C in Tunisian children with ALL. Materials and Methods: A total of 28 Tunisian ALL children were enrolled in this study. Genomic DNA was extracted from whole venous blood collected in ethylenediaminetetraacetic acid (EDTA). Genotyping was carried out with restriction fragment length polymorphism (RFLP) using MboII restriction enzyme. Genotype distribution and allele frequency of MTHFR A1298C was calculated in ALL patients. Results: The A1298C variant of MTHFR was found in 11(19.6%) heterozygous and one homozygous patient (3.5%). Conclusions: This result highlights that A1298C polymorphism of MTHFR is common in Tunisian childhood ALL and suggests that this variant may have a potential role in leukemogenesis. Genotyping of large samples and different ethnicities are required to validate these findings.

Keywords: methylenetetrahydrofolate reductase, acute lymphoblastic leukemia, A1298C variant, prevalence

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