Search results for: gene frequency

Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: Fatemeh Keshavarz

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Background: Schizophrenia is a disease of the nervous system, and immune system disorders can affect its pathogenesis. Activation of microglia, proinflammatory cytokines, disruption of the blood-brain barrier (BBB) due to inflammation, activation of autoreactive B cells, and consequently the production of autoantibodies against system antigens are among the immune processes involved in neurological diseases. interleukin 32 (IL-32) a proinflammatory cytokine that important player in the activation of the innate and adaptive immune responses. This study aimed to measure the serum level of IL-32 as well as the frequency of autoantibody positivity against several nervous system antigens in patients with schizophrenia. Material and Methods: This study was conducted on 40 patients with schizophrenia and 40 healthy individuals in the control group. Serum IL-32 levels were measured by ELISA. The frequency of autoantibodies against Hu, Ri, Yo, Tr, CV2, Amphiphysin, SOX1, Zic4, ITPR1, CARP, GAD, Recoverin, Titin, and Ganglioside antigens were measured by indirect immunofluorescence method. Results: Serum IL-32 levels in patients with schizophrenia were significantly higher compared to the control group. Autoantibodies were positive in 8 patients for GAD antigen and 5 patients for Ri antigen, which showed a significant relationship compared to the control group. Autoantibodies were also positive in 2 patients for CV2, in 1 patient for Hu, and in 1 patient for CARP. Negative results were reported for other antigens. Conclusion: Our findings suggest that elevated the serum IL-32 level and autoantibody positivity against several nervous system antigens may be involved in the pathogenesis of schizophrenia.

Keywords: schizophrenia, microglia, autoantibodies, IL-32

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Authors: Amin Aghatabar Roodbary, Mohammad Hassan Bastani

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One of the defects of stepped frequency radar systems is their sensitivity to target motion. In such systems, target motion causes range cell shift, false peaks, Signal to Noise Ratio (SNR) reduction and range profile spreading because of power spectrum interference of each range cell in adjacent range cells which induces distortion in High Resolution Range Profile (HRRP) and disrupt target recognition process. Thus Target Motion Parameters (TMPs) effects compensation should be employed. In this paper, such a method for estimating TMPs (velocity and acceleration) and consequently eliminating or suppressing the unwanted effects on HRRP based on entropy minimization has been proposed. This method is carried out in two major steps: in the first step, a discrete search method has been utilized over the whole acceleration-velocity lattice network, in a specific interval seeking to find a less-accurate minimum point of the entropy function. Then in the second step, a 1-D search over velocity is done in locus of the minimum for several constant acceleration lines, in order to enhance the accuracy of the minimum point found in the first step. The provided simulation results demonstrate the effectiveness of the proposed method.

Keywords: automatic target recognition (ATR), high resolution range profile (HRRP), motion compensation, stepped frequency waveform technique (SFW), target motion parameters (TMPs)

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Authors: Jakyoung Kim, Sungwook Jang

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The purpose of this study is to examine the research trends of life-long education for people with disabilities using a keyword network analysis. For this purpose, 151 papers were selected from 594 papers retrieved using keywords such as 'people with disabilities' and 'life-long education' in the Korean Education and Research Information Service. The Keyword network analysis was constructed by extracting and coding the keyword used in the title of the selected papers. The frequency of the extracted keywords, the centrality of degree, and betweenness was analyzed by the keyword network. The results of the keyword network analysis are as follows. First, the main keywords that appeared frequently in the study of life-long education for people with disabilities were 'people with disabilities', 'life-long education', 'developmental disabilities', 'current situations', 'development'. The research trends of life-long education for people with disabilities are focused on the current status of the life-long education and the program development. Second, the keyword network analysis and visualization showed that the keywords with high frequency of occurrences also generally have high degree centrality and betweenness centrality. In terms of the keyword network diagram, it was confirmed that research trends of life-long education for people with disabilities are centered on six prominent keywords. Based on these results, it was discussed that life-long education for people with disabilities in the future needs to expand the subjects and the supporting areas of the life-long education, and the research needs to be further expanded into more detailed and specific areas. 

Keywords: life-long education, people with disabilities, research trends, keyword network analysis

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Authors: Taeho Park, Ming Zhou, Sangryul Shim

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With the emergence of the global economy, today’s business environment is getting more competitive than ever in the past. And many supply chain (SC) strategies and operations have significantly been altered over the past decade to overcome more complexities and risks imposed onto the global business. First, offshoring and outsourcing are more adopted as operational strategies. Manufacturing continues to move to better locations for enhancing competitiveness. Second, international operations are a challenge to a company’s SC system. Third, the products traded in the SC system are not just physical goods, but also digital goods (e.g., software, e-books, music, video materials). There are three main flows involved in fulfilling the activities in the SC system: physical flow, information flow, and financial flow. An advance of the Internet and electronic communication technologies has enabled companies to perform the flows of SC activities in electronic formats, resulting in the advent of an electronic supply chain management (e-SCM) system. A SC system for digital goods is somewhat different from the supply chain system for physical goods. However, it involves many similar or identical SC activities and flows. For example, like the production of physical goods, many third parties are also involved in producing digital goods for the production of components and even final products. This research aims at identifying process flows of both physical and digital goods in a SC system, and then investigating all risk elements involved in the physical, information, and financial flows during the fulfilment of SC activities. There are many risks inherent in the e-SCM system. Some risks may have severe impact on a company’s business, and some occur frequently but are not detrimental enough to jeopardize a company. Thus, companies should assess the impact and frequency of those risks, and then prioritize them in terms of their severity, frequency, budget, and time in order to be carefully maintained. We found risks involved in the global trading of physical and digital goods in four different categories: environmental risk, strategic risk, technological risk, and operational risk. And then the significance of those risks was investigated through a survey. The survey asked companies about the frequency and severity of the identified risks. They were also asked whether they had faced those risks in the past. Since the characteristics and supply chain flows of digital goods are varying industry by industry and country by country, it is more meaningful and useful to analyze risks by industry and country. To this end, more data in each industry sector and country should be collected, which could be accomplished in the future research.

Keywords: digital goods, e-SCM, risk analysis, supply chain flows

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Authors: Bineet Kumar

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Many civil engineering infrastructures frequently encounter repetitive loading during their service life. Due to the inherent complexity observed in concrete, like quasi-brittle materials, understanding the fatigue behavior in concrete still posesa challenge. Moreover, the fracture process zone characteristics ahead of the crack tip have been observed to be different in fatigue loading than in the monotonic cases. Therefore, it is crucial to comprehend the energy dissipation associated with the fracture process zone (FPZ) due to repetitive loading. It is well known that stiffness degradation due to cyclic loadingprovides a better understanding of the fracture behavior of concrete. Under repetitive load cycles, concrete members exhibit a two-stage stiffness degradation process. Experimentally it has been observed that the stiffness decreases initially with an increase in crack length and subsequently increases. In this work, an attempt has been made to propose an analytical expression to predict energy dissipation and later the stiffness degradation as a function of crack length. Three-point bend specimens have been considered in the present work to derive the formulations. In this approach, the expression for the resultant stress distribution below the neutral axis has been derived by correlating the bending stress with the cohesive stresses developed ahead of the crack tip due to the existence of the fracture process zone. This resultant stress expression is utilized to estimate the dissipated energydue to crack propagation as a function of crack length. Further, the formulation for the stiffness degradation has been developed by relating the dissipated energy with the work done. It can be used to predict the critical crack length and fatigue life. An attempt has been made to understand the influence of stress amplitude on the damage pattern by using the information on the rate of stiffness degradation. It has been demonstrated that with the increase in the stress amplitude, the damage/FPZ proceeds more in the direction of crack propagation compared to the damage in the direction parallel to the span of the beam, which causes a lesser rate of stiffness degradation for the incremental crack length. Further, the effect of loading frequency has been investigated in terms of stiffness degradation. Under low-frequency loading cases, the damage/FPZ has been found to spread more in the direction parallel to the span, in turn reducing the critical crack length and fatigue life. In such a case, a higher rate of stiffness degradation has been observed in comparison to the high-frequency loading case.

Keywords: fatigue life, fatigue, fracture, concrete

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Authors: Ji Su Kim, Bo Ram Choi, Ju Yeon Cho, Hyukjin Lee

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Epidermal growth factor receptor (EGFR) 19 deletion mutation gene is over-expressed in carcinoma patient. EGFR 19 deletion mutation is known as typical biomarker of non-small cell lung cancer (NSCLC), which one section in the coding exon 19 of EGFR is deleted. Therefore, there have been many attempts over the years to detect EGFR 19 deletion mutation for replacing conventional diagnostic method such as PCR and tissue biopsy. We developed a simple and facile detection platform based on Rolling Circle Amplification (RCA), which provides highly amplified products in isothermal amplification of the ligated DNA template. Limit of detection (~50 nM) and a faster detection time (~30 min) could be achieved by introducing RCA.

Keywords: EGFR19, cancer, diagnosis, rolling circle amplification (RCA), hydrogel

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Authors: Gerhard Gritsch, Ana Skupch, Manfred Hartmann, Wolfgang Frühwirt, Hannes Perko, Dieter Grossegger, Tilmann Kluge

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Rehabilitation of stroke patients is dominated by classical physiotherapy. Nowadays, a field of research is the application of neurofeedback techniques in order to help stroke patients to get rid of their motor impairments. Especially, if a certain limb is completely paralyzed, neurofeedback is often the last option to cure the patient. Certain exercises, like the imagination of the impaired motor function, have to be performed to stimulate the neuroplasticity of the brain, such that in the neighboring parts of the injured cortex the corresponding activity takes place. During the exercises, it is very important to keep the motivation of the patient at a high level. For this reason, the missing natural feedback due to a movement of the effected limb may be replaced by a synthetic feedback based on the motor-related brain function. To generate such a synthetic feedback a system is needed which measures, detects, localizes and visualizes the motor related µ-rhythm. Fast therapeutic success can only be achieved if the feedback features high specificity, comes in real-time and without large delay. We describe such an approach that offers a 3D visualization of µ-rhythms in real time with a delay of 500ms. This is accomplished by combining smart EEG preprocessing in the frequency domain with source localization techniques. The algorithm first selects the EEG channel featuring the most prominent rhythm in the alpha frequency band from a so-called motor channel set (C4, CZ, C3; CP6, CP4, CP2, CP1, CP3, CP5). If the amplitude in the alpha frequency band of this certain electrode exceeds a threshold, a µ-rhythm is detected. To prevent detection of a mixture of posterior alpha activity and µ-activity, the amplitudes in the alpha band outside the motor channel set are not allowed to be in the same range as the main channel. The EEG signal of the main channel is used as template for calculating the spatial distribution of the µ - rhythm over all electrodes. This spatial distribution is the input for a inverse method which provides the 3D distribution of the µ - activity within the brain which is visualized in 3D as color coded activity map. This approach mitigates the influence of lid artifacts on the localization performance. The first results of several healthy subjects show that the system is capable of detecting and localizing the rarely appearing µ-rhythm. In most cases the results match with findings from visual EEG analysis. Frequent eye-lid artifacts have no influence on the system performance. Furthermore, the system will be able to run in real-time. Due to the design of the frequency transformation the processing delay is 500ms. First results are promising and we plan to extend the test data set to further evaluate the performance of the system. The relevance of the system with respect to the therapy of stroke patients has to be shown in studies with real patients after CE certification of the system. This work was performed within the project ‘LiveSolo’ funded by the Austrian Research Promotion Agency (FFG) (project number: 853263).

Keywords: real-time EEG neuroimaging, neurofeedback, stroke, EEG–signal processing, rehabilitation

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Authors: Nazish Badar

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In early 2009, Pandemic type A (H1N1) Influenza virus emerged globally. Since then, it has continued circulation causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in Influenza A (H1N1) pdm09 viruses from 2009-15 and their relevance with the current vaccine viruses. Methods: Respiratory specimens were collected with influenza-like illness and Severe Acute Respiratory Illness. Samples were processed according to CDC protocol. Sequencing and phylogenetic analysis of Haemagglutinin (HA) and neuraminidase (NA) genes was carried out comparing representative isolates from Pakistan viruses. Results: Between Jan2009 - Feb 2016, 1870 (13.2%) samples were positive for influenza A out of 14086. During the pandemic period (2009–10), Influenza A/ H1N1pdm 09 was the dominant strain with 366 (45%) of total influenza positives. In the post-pandemic period (2011–2016), a total of 1066 (59.6%) cases were positive Influenza A/ H1N1pdm 09 with co-circulation of different Influenza A subtypes. Overall, the Pakistan A(H1N1) pdm09 viruses grouped in two genetic clades. Influenza A(H1N1)pdm09 viruses only ascribed to Clade 7 during the pandemic period whereas viruses belong to clade 7 (2011) and clade 6B (2015) during the post-pandemic years. Amino acid analysis of the HA gene revealed mutations at positions S220T, I338V and P100S specially associated with outbreaks in all the analyzed strains. Sequence analyses of post-pandemic A(H1N1)pdm09 viruses showed additional substitutions at antigenic sites; S179N,K180Q (SA), D185N, D239G (CA), S202A (SB) and at receptor binding sites; A13T, S200P when compared with pandemic period. Substitution at Genetic markers; A273T (69%), S200P/T (15%) and D239G (7.6%) associated with severity and E391K (69%) associated with virulence was identified in viruses isolated during 2015. Analysis of NA gene revealed outbreak markers; V106I (23%) among pandemic and N248D (100%) during post-pandemic Pakistan viruses. Additional N-Glycosylation site; HA S179N (23%), NA I23T(7.6%) and N44S (77%) in place of N386K(77%) were only found in post-pandemic viruses. All isolates showed histidine (H) at position 275 in NA indicating sensitivity to neuraminidase inhibitors. Conclusion: This study shows that the Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Certain key substitutions in the receptor binding site and few changes indicative of virulence were also detected in post-pandemic strains. Therefore, it is imperative to continue monitoring of the viruses for early identification of potential variants of high virulence or emergence of drug-resistant variants.

Keywords: Influenza A (H1N1) pdm09, evolutionary analysis, post pandemic period, Pakistan

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Authors: Yogesh Dalvi, Ruby Varghese, Nibu Varghese, C. K. Krishnan Nair

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Introduction: The Genus Phellinus, locally known as Phansomba is a well-known traditional folk medicine. Especially, in Western Ghats of India, many tribes use several species of Phellinus for various ailments related to teeth, throat, tongue, stomach and even wound healing. It is one of the few mushrooms which play a pivotal role in Ayurvedic Dravyaguna. Aim: The present study focuses on to investigate phytochemical analysis, antioxidant, and antitumor (in vitro and in vivo) potential of Phellinus robinae from South India, Kerala Material and Methods: The present study explores the following: 1. Phellinus samples were collected from Ranni, Pathanamthitta district of Kerala state, India from Artocarpus heterophyllus Lam. and species were identified using rDNA region. 2. The fruiting body was shadow dried, powdered and extracted with 50% alcohol using water bath at 60°C which was further condensed by rotary evaporator and lyophilized at minus 40°C temperature. 3. Secondary metabolites were analyzed by using various phytochemical screening assay (Hager’s Test, Wagner’s Test, Sodium hydroxide Test, Lead acetate Test, Ferric chloride Test, Folin-ciocalteu Test, Foaming Test, Benedict’s test, Fehling’s Test and Lowry’s Test). 4. Antioxidant and free radical scavenging activity were analyzed by DPPH, FRAP and Iron chelating assay. 5. The antitumor potential of Water alcohol extract of Phellinus (PAWE) is evaluated through In vitro condition by Trypan blue dye exclusion method in DLA cell line and In vivo by murine model. Result and Discussion: Preliminary phytochemical screening by various biochemical tests revealed presence of a variety of active secondary molecules like alkaloids, flavanoids, saponins, carbohydrate, protein and phenol. In DPPH and FRAP assay PAWE showed significantly higher antioxidant activity as compared to standard Ascorbic acid. While, in Iron chelating assay, PAWE exhibits similar antioxidant activity that of Butylated Hydroxytoluene (BHT) as standard. Further, in the in vitro study, PAWE showed significant inhibition on DLA cell proliferation in dose dependent manner and showed no toxicity on mice splenocytes, when compared to standard chemotherapy drug doxorubicin. In vivo study, oral administration of PAWE showed dose dependent tumor regression in mice and also raised the immunogenicity by restoring levels of antioxidant enzymes in liver and kidney tissue. In both in vitro and in vivo gene expression studies PAWE up-regulates pro-apoptotic genes (Bax, Caspases 3, 8 and 9) and down- regulates anti-apoptotic genes (Bcl2). PAWE also down regulates inflammatory gene (Cox-2) and angiogenic gene (VEGF). Conclusion: Preliminary phytochemical screening revealed that PAWE contains various secondary metabolites which contribute to its antioxidant and free radical scavenging property as evaluated by DPPH, FRAP and Iron chelating assay. PAWE exhibits anti-proliferative activity by the induction of apoptosis through a signaling cascade of death receptor-mediated extrinsic (Caspase8 and Tnf-α), as well as mitochondria-mediated intrinsic (caspase9) and caspase pathways (Caspase3, 8 and 9) and also by regressing angiogenic factor (VEGF) without any inflammation or adverse side effects. Hence, PAWE serve as a potential antioxidant and antitumor agent.

Keywords: antioxidant, antitumor, Dalton lymphoma ascites (DLA), fungi, Phellinus robinae

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Authors: Ahmed Boutejdar, Bishoy I. Halim, Soumia El Hani, Larbi Bellarbi, Amal Afyf

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In this paper, a planar monopole antenna for multi band applications is proposed. The antenna structure operates at three operating frequencies at 3.7, 6.2, and 13.5 GHz which cover different communication frequency ranges. The antenna consists of a quasi-modified rectangular radiating patch with a partial ground plane and two parasitic elements (open-loop-ring resonators) to serve as coupling-bridges. A stepped cut at lower corners of the radiating patch and the partial ground plane are used, to achieve the multiband features. The proposed antenna is manufactured on the FR4 substrate and is simulated and optimized using High Frequency Simulation System (HFSS). The antenna topology possesses an area of 30.5 x 30 x 1.6 mm³. The measured results demonstrate that the candidate antenna has impedance bandwidths for 10 dB return loss and operates from 3.80 – 3.90 GHz, 4.10 – 5.20 GHz, 11.2 – 11.5 GHz and from 12.5 – 14.0 GHz, which meet the requirements of the wireless local area network (WLAN), worldwide interoperability for microwave access (WiMAX), C- (Uplink) and Ku- (Uplink) band applications. Acceptable agreement is obtained between measurement and simulation results. Experimental results show that the antenna is successfully simulated and measured, and the tri-band antenna can be achieved by adjusting the lengths of the three elements and it gives good gains across all the operation bands.

Keywords: planar monopole antenna, FR4 substrate, HFSS, WLAN, WiMAX, C and Ku

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Authors: Yifu Ding, Vijay Avinash, Malcolm McCulloch

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As the proliferation of decentralized energy systems, the UK power system allows small-scale entities such as microgrids (MGs) to tender multiple energy services including energy arbitrage and frequency responses (FRs). However, its operation requires the balance between the uncertain renewable generations and loads in real-time and has to fulfill their provision requirements of contract services continuously during the time window agreed, otherwise it will be penalized for the under-delivered provision. To hedge against risks due to uncertainties and maximize the economic benefits, we propose a stochastic model predictive control (SMPC) framework to optimize its operation for the multi-service provision. Distinguished from previous works, we include a detailed economic-degradation model of the lithium-ion battery to quantify the costs of different service provisions, as well as accurately describe the changing dynamics of the battery. Considering a branch of load and generation scenarios and the battery aging, we formulate a risk-averse cost function using conditional value at risk (CVaR). It aims to achieve the maximum expected net revenue and avoids severe losses. The framework will be performed on a case study of a PV-battery grid-tied microgrid in the UK with real-life data. To highlight its performance, the framework will be compared with the case without the degradation model and the deterministic formulation.

Keywords: model predictive control (MPC), battery degradation, frequency response, microgrids

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Authors: L. Szymanski, S. Wiak, Z. Kolacinski, G. Raniszewski, L. Pietrzak, Z. Staniszewska

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There exist more than one hundred different types of cancer, and therefore no particular treatment is offered to people struggling with this disease. The character of treatment proposed to a patient will depend on a variety of factors such as type of the cancer diagnosed, advancement of the disease, its location in the body, as well as personal preferences of a patient. None of the commonly known methods of cancer-fighting is recognised as a perfect cure, however great advances in this field have been made over last few decades. Once a patient is diagnosed with cancer, he is in need of medical care and professional treatment for upcoming months, and in most cases even for years. Among the principal modes of treatment offered by medical centres, one can find radiotherapy, chemotherapy, and surgery. All of them can be applied separately or in combination, and the relative contribution of each is usually determined by medical specialist in agreement with a patient. In addition to the conventional treatment option, every day more complementary and alternative therapies are integrated into mainstream care. There is one promising cancer modality - hyperthermia therapy which is based on exposing body tissues to high temperatures. This treatment is still being investigated and is not widely available in hospitals and oncological centres. There are two kinds of hyperthermia therapies with direct and indirect heating. The first is not commonly used due to low efficiency and invasiveness, while the second is deeply investigated and a variety of methods have been developed, including ultrasounds, infrared sauna, induction heating and magnetic hyperthermia. The aim of this work was to examine possibilities of heating magnetic nanoparticles under the influence of electromagnetic field for cancer treatment. For this purpose, multiwalled carbon nanotubes used as nanocarriers for iron particles were investigated for its heating properties. The samples were subjected to an alternating electromagnetic field with frequency range between 110-619 kHz. Moreover, samples with various concentrations of carbon nanotubes were examined. The lowest frequency of 110 kHz and sample containing 10 wt% of carbon nanotubes occurred to influence the most effective heating process. Description of hyperthermia therapy aiming at enhancing currently available cancer treatment was also presented in this paper. Most widely applied conventional cancer modalities such as radiation or chemotherapy were also described. Methods for overcoming the most common obstacles in conventional cancer modalities, such as invasiveness and lack of selectivity, has been presented in magnetic hyperthermia characteristics, which explained the increasing interest of the treatment.

Keywords: hyperthermia, carbon nanotubes, cancer colon cells, ligands

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Authors: N. H. D. P. Fonseka, I. H. Rajapakse, A. S. Dissanayake

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Background: Problem drinking, namely alcohol dependence (AD) and alcohol abuse (AA) are associated with major medical, social and economic adverse consequences. Problem drinking behavior is noted among those admitted to hospitals due to alcohol-related medical/surgical complaints as well as those with unrelated complaints. Literature shows an association between alcohol consumption and depression. Aims of this study were to determine the frequency of problem drinking and depression among males with a history of alcohol consumption tertiary care setting in Southern Sri Lanka. Method: Two-hundred male patients who consumed alcohol, receiving care in medical and surgical wards in Teaching Hospital Galle, were assessed. A validated J12 questionnaire of the Mini International Neuropsychiatric Interview was administered to determine frequency AA and AD. A validated PHQ 9 questionnaire to determine the prevalence and severity of depression. Results: Sixty-three participants (31%) had problem drinking. Of them, 61% had AD, and 39% had AA. Depression was noted in 39 (19%) subjects. In those who reported alcohol consumption not amounting to problem drinking, depression was noted in 23 (16%) participants. Mild depression was seen in 17, moderate in five and moderately severe in one. Among those who had problem drinking, 16 (25%) had depression. Mild depression was seen in four, moderate in seven, moderately severe in three and severe in two. Conclusions: A high proportion alcohol users had problem drinking. Adverse consequences associated with problem drinking places a major strain on the health system especially in a low resource setting where healthcare spending is limited and alcohol cessation support services are not well organised. Thus alcohol consumption and problem drinking behaviour need to be inquired into all medical consultations. Community prevalence of depression in Sri Lanka is approximately 10%. Depression among those consuming alcohol was two times higher compared to the general population. The rates of depression among those with problem drinking were especially high being 2.5 times more common than in the general population. A substantial proportion of these patients with depression had moderately severe or severe depression. When depression coexists with problem drinking, it may increase the tendency to consume alcohol as well as act as a barrier to the success of alcohol cessation interventions. Thus screening all patients who consume alcohol for depression, especially those who are problem drinkers becomes an important step in their clinical evaluation. In addition, in view of the high prevalence of problem drinking and coexistent depression, the need to organize a structured alcohol cessation support service in Sri Lanka as well as the need for increasing access to psychological evaluation and treatment of those with problem drinking are highlighted.

Keywords: alcohol abuse, alcohol, depression, problem drinking

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Authors: Noor Ayuni Che Zakaria, Takashi Komeda, Cheng Yee Low, Kaoru Inoue, Fazah Akhtar Hanapiah

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Previous studies have shown that there are arguments regarding the reliability and validity of the Ashworth and Modified Ashworth Scale towards evaluating patients diagnosed with upper limb disorders. These evaluations depended on the raters’ experiences. This initiated us to develop an upper limb disorder part-task trainer that is able to simulate consistent upper limb disorders, such as spasticity and rigidity signs, based on the Modified Ashworth Scale to improve the variability occurring between raters and intra-raters themselves. By providing consistent signs, novice therapists would be able to increase training frequency and exposure towards various levels of signs. A total of 22 physiotherapists and occupational therapists participated in the study. The majority of the therapists agreed that with current therapy education, they still face problems with inter-raters and intra-raters variability (strongly agree 54%; n = 12/22, agree 27%; n = 6/22) in evaluating patients’ conditions. The therapists strongly agreed (72%; n = 16/22) that therapy trainees needed to increase their frequency of training; therefore believe that our initiative to develop an upper limb disorder training tool will help in improving the clinical education field (strongly agree and agree 63%; n = 14/22).

Keywords: upper limb disorder, clinical education tool, inter/intra-raters variability, spasticity, modified Ashworth scale

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Authors: B. Neethu, Diptesh Das

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The present study investigates the performance of a semi-active controller using magneto-rheological dampers (MR) for seismic response reduction of a multi-span bridge. The application of structural control to the structures during earthquake excitation involves numerous challenges such as proper formulation and selection of the control strategy, mathematical modeling of the system, uncertainty in system parameters and noisy measurements. These problems, however, need to be tackled in order to design and develop controllers which will efficiently perform in such complex systems. A control algorithm, which can accommodate un-certainty and imprecision compared to all the other algorithms mentioned so far, due to its inherent robustness and ability to cope with the parameter uncertainties and imprecisions, is the sliding mode algorithm. A sliding mode control algorithm is adopted in the present study due to its inherent stability and distinguished robustness to system parameter variation and external disturbances. In general a semi-active control scheme using an MR damper requires two nested controllers: (i) an overall system controller, which derives the control force required to be applied to the structure and (ii) an MR damper voltage controller which determines the voltage required to be supplied to the damper in order to generate the desired control force. In the present study a sliding mode algorithm is used to determine the desired optimal force. The function of the voltage controller is to command the damper to produce the desired force. The clipped optimal algorithm is used to find the command voltage supplied to the MR damper which is regulated by a semi active control law based on sliding mode algorithm. The main objective of the study is to propose a robust semi active control which can effectively control the responses of the bridge under real earthquake ground motions. Lumped mass model of the bridge is developed and time history analysis is carried out by solving the governing equations of motion in the state space form. The effectiveness of MR dampers is studied by analytical simulations by subjecting the bridge to real earthquake records. In this regard, it may also be noted that the performance of controllers depends, to a great extent, on the characteristics of the input ground motions. Therefore, in order to study the robustness of the controller in the present study, the performance of the controllers have been investigated for fourteen different earthquake ground motion records. The earthquakes are chosen in such a way that all possible characteristic variations can be accommodated. Out of these fourteen earthquakes, seven are near-field and seven are far-field. Also, these earthquakes are divided into different frequency contents, viz, low-frequency, medium-frequency, and high-frequency earthquakes. The responses of the controlled bridge are compared with the responses of the corresponding uncontrolled bridge (i.e., the bridge without any control devices). The results of the numerical study show that the sliding mode based semi-active control strategy can substantially reduce the seismic responses of the bridge showing a stable and robust performance for all the earthquakes.

Keywords: bridge, semi active control, sliding mode control, MR damper

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Authors: Hamidreza Akbari

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In this paper, for detection of inclined eccentricity in an induction motor, time–frequency analysis of the stator startup current is carried out. For this purpose, the discrete wavelet transform is used. Data are obtained from simulations, using winding function approach. The results show the validity of the approach for detecting the fault and discriminating with respect to other faults.

Keywords: induction machine, fault, DWT, electric

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Authors: Arash Dara, Mahsa Mokhtari, Nafiseh Zamindar

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The aim of this study was to determine the effect of thermal resistance, temperature, voltage, and pH changes in an ohmic heating system on reducing the logarithmic number of Byssochlamys fulva species (PTCC 5062) in tomato juice water and to investigate the quantitative properties of tomato juice in the ohmic heating pasteurization system. The percentage of thermal degradation by ohmic heating was determined in tomato juice for the kinetics of Byssochlamys fulva in ohmic chamber at the temperatures of 88, 93, and 98°C, with two voltages of 30 and 40 volts and two pH levels of 3.5 and 4.5; this was done using Weibull frequency distribution model. Three different parameters (pH = 3.5, two voltages of 30 and 40, at three temperatures 88, 93, and 98) and (pH = 4.5, two voltages 30 and 40, at three temperatures 88, 93, and 98) in three replications were considered in the ohmic system. Heating time for the temperature of 88°C was 20 minutes once every 2 minutes, while for the temperature of 93°C, it was 10 minutes once every 1 minute. At the temperature of 98°C, the first time was 0.5 minutes, and for other times, sampling was done every 1 minute. In each condition, the qualitative characteristics, including acidity, Brix, and pH, were measured before and after the ohmic process in the tomato juice. This study demonstrates that the differences in pH and voltage due to different temperatures in the ohmic process can greatly affect the inactivation of Byssochlamys fulva fungus and the qualitative characteristics of the tomato juice. This is the first study using the Weibull frequency method to model the inactivation of Byssochlamys fulva in tomato juice. Variation in parameters such as temperature, voltage, and pH can prevent the presence of Byssochlamys fulva in the pasteurized juices.

Keywords: pasteurization, ohmic heating process, Byssochlamys fulva, tomato juice, heat resistance, voltage, pH

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Authors: Xiaobo Rui, Zhoumo Zeng, Yibo Li

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A novel tri-cantilever energy harvester with magnetic oscillator was presented, which could convert the ambient vibration into electrical energy to power the low-power devices such as wireless sensor networks. The most common way to harvest vibration energy is based on the use of linear resonant devices such as cantilever beam, since this structure creates the highest strain for a given force. The highest efficiency will be achieved when the resonance frequency of the harvester matches the vibration frequency. The limitation of the structure is the narrow effective bandwidth. To overcome this limitation, this article introduces a broadband tri-cantilever harvester with nonlinear stiffness. This energy harvester typically consists of three thin cantilever beams vertically arranged with Neodymium Magnets ( NdFeB)magnetics at its free end and a fixed base at the other end. The three cantilevers have different resonant frequencies by designed in different thicknesses. It is obviously that a similar advantage of multiple resonant frequencies as piezoelectric cantilevers array structure is built. To achieve broadband energy harvesting, magnetic interaction is used to introduce the nonlinear system stiffness to tune the resonant frequency to match the excitation. Since the three cantilever tips are all free and the magnetic force is distance dependent, the resonant frequencies will be complexly changed with the vertical vibration of the free end. Both model and experiment are built. The electromechanically coupled lumped-parameter model is presented. An electromechanical formulation and analytical expressions for the coupled nonlinear vibration response and voltage response are given. The entire structure is fabricated and mechanically attached to a electromagnetic shaker as a vibrating body via the fixed base, in order to couple the vibrations to the cantilever. The cantilevers are bonded with piezoelectric macro-fiber composite (MFC) materials (Model: M8514P2). The size of the cantilevers is 120*20mm2 and the thicknesses are separately 1mm, 0.8mm, 0.6mm. The prototype generator has a measured performance of 160.98 mW effective electrical power and 7.93 DC output voltage via the excitation level of 10m/s2. The 130% increase in the operating bandwidth is achieved. This device is promising to support low-power devices, peer-to-peer wireless nodes, and small-scale wireless sensor networks in ambient vibration environment.

Keywords: tri-cantilever, ambient vibration, energy harvesting, magnetic oscillator

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Authors: Nilubon Kurubanjerdjit, Nattakarn Iam-On, Ka-Lok Ng

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MicroRNAs are small non-coding RNA found in many different species. They play crucial roles in cancer such as biological processes of apoptosis and proliferation. The identification of microRNA-target genes can be an essential first step towards to reveal the role of microRNA in various cancer types. In this paper, we predict miRNA-target genes for lung cancer by integrating prediction scores from miRanda and PITA algorithms used as a feature vector of miRNA-target interaction. Then, machine-learning algorithms were implemented for making a final prediction. The approach developed in this study should be of value for future studies into understanding the role of miRNAs in molecular mechanisms enabling lung cancer formation.

Keywords: microRNA, miRNAs, lung cancer, machine learning, Naïve Bayes, SVM

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Authors: E. Didaskalou, C. Roussi-Vergou, E. Andreou, G. Skrzypiec, P. Slee

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There has been growing interest lately, in the study of victimization among adolescent students in Greece and elsewhere with a view to improve school policies concerning anti-bullying practices. Researchers have recently focused on investigating the relationships between the extent of students’ victimization and the distinct mechanisms that they employ for coping with this particular problem. In particular, the emphasis has been placed on exploring the relationship between the coping strategies students use to counteract bullying, their sense of belonging at school, and extent of their victimization. Methods: Within the research framework outlined above, we set out to: a) examine the frequency of self-reported victimization among secondary school students, b) investigate the coping strategies employed by students when confronted with school bullying and c) explore any differences between bullied and non-bullied students with regard to coping strategies and school belongingness. The sample consisted of 860 from fifteen secondary public schools in central Greece. The schools were typical Greek secondary schools and the principals volunteered to participate in this study. Participants’ age ranged from 12 to 16 years. Measures: a) Exposure to Victimization: The frequency of victimization was directly located by asking students the question: ‘Over the last term, how often have you been bullied or harassed by a student or students at this high school?’ b) Coping Strategies: The ‘Living and Learning at School: Bullying at School’ was administered to students, c) School belongingness was assessed by the Psychological Sense of School Membership Scale, that students completed. Results: Regarding the frequency of self-reported victimization, 1.5% of the students reported being victimized every day, 2.8% most days of the week, 2.1% one or more days a week, 2.9% about once a week, 22.6% less than once a week and 68.1% never. The coping strategies that the participants employed for terminating their victimization included: a) adult support seeking, b) emotional coping/keep away from school, c) keeping healthy and fit, d) demonstrating a positive attitude towards the bully, d) peer support seeking, e) emotional out bursting, f) wishful thinking and self-blaming, g) pretending as if it is not happening, h) displaying assertive behaviors and i) getting away from the bullies. Bullied from non-bullied children did not differ as much in coping, as in feelings of being rejected in school. Discussion: The findings are in accordance with accumulated research evidence which points to a strong relationship between student perceptions of school belongingness and their involvement in bullying behaviors. We agree with the view that a positive school climate is likely to serve as a buffer that mitigates wider adverse societal influences and institutional attitudes which favor violence and harassment among peers.

Keywords: school bullying, school belonging, student coping strategies, victimization

Procedia PDF Downloads 245

Authors: Sophio Kobauri, Temur Kantaria, Nina Kulikova, David Tugushi, Ramaz Katsarava

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The elaboration of effective drug delivery vehicles is still topical nowadays since targeted drug delivery is one of the most important challenges of the modern nanomedicine. The last decade has witnessed enormous research focused on synthetic cationic polymers (CPs) due to their flexible properties, in particular as non-viral gene delivery systems, facile synthesis, robustness, not oncogenic and proven gene delivery efficiency. However, the toxicity is still an obstacle to the application in pharmacotherapy. For overcoming the problem, creation of new cationic compounds including the polymeric nano-size particles – nano-containers (NCs) loading with different pharmaceuticals and biologicals is still relevant. In this regard, a variety of NCs-based drug delivery systems have been developed. We have found that amino acid-based biodegradable polymers called as pseudo-proteins (PPs), which can be cleared from the body after the fulfillment of their function are highly suitable for designing pharmaceutical NCs. Among them, one of the most promising are NCs made of biodegradable Cationic PPs (CPPs). For preparing new cationic NCs (CNCs), we used CPPs composed of positively charged amino acid L-arginine (R). The CNCs were fabricated by two approaches using: (1) R-based homo-CPPs; (2) Blends of R-based CPPs with regular (neutral) PPs. According to the first approach NCs we prepared from CPPs 8R3 (composed of R, sebacic acid and 1,3-propanediol) and 8R6 (composed of R, sebacic acid and 1,6-hexanediol). The NCs prepared from these CPPs were 72-101 nm in size with zeta potential within +30 ÷ +35 mV at a concentration 6 mg/mL. According to the second approach, CPPs 8R6 was blended in organic phase with neutral PPs 8L6 (composed of leucine, sebacic acid and 1,6-hexanediol). The NCs prepared from the blends were 130-140 nm in size with zeta potential within +20 ÷ +28 mV depending on 8R6/8L6 ratio. The stability studies of fabricated NCs showed that no substantial change of the particle size and distribution and no big particles’ formation is observed after three months storage. In vitro biocompatibility study of the obtained NPs with four different stable cell lines: A549 (human), U-937 (human), RAW264.7 (murine), Hepa 1-6 (murine) showed both type cathionic NCs are biocompatible. The obtained data allow concluding that the obtained CNCs are promising for the application as biodegradable drug delivery vehicles. This work was supported by the joint grant from the Science and Technology Center in Ukraine and Shota Rustaveli National Science Foundation of Georgia #6298 'New biodegradable cationic polymers composed of arginine and spermine-versatile biomaterials for various biomedical applications'.

Keywords: biodegradable polymers, cationic pseudo-proteins, nano-containers, drug delivery vehicles

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Authors: Jinee Gogoi, Som K. Sharma, Kalyan Bhuyan

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The atmospheric layers are coupled to each other with the different dynamical, electrical, radiative and chemical processes. A large scale thermodynamical phenomenon in winter polar regions which affects the middle atmosphere vigorously is Sudden Stratospheric Warming (SSW). Two major SSW events were occurred during 1998-1999; one in December 1998 which is associated with vortex displacement and another in February- March 1999 associated with vortex splitting. Lidar study of these two major events from Mt. Abu (24.36⁰N, 72.45⁰E, ~1670 m amsl) has shown that though SSWs are mostly observed over high and mid latitudes, their effects can also be seen over India. We have studied ionospheric variations (primarily fₒF₂, h’F and hpF₂) over Ahmedabad (23.1⁰N, 72.58⁰E) during these events. Ionospheric disturbances have been found after four-five days of peak temperature. An increase (decrease) in critical frequency (fₒF₂) during morning (afternoon) has been noticed which may be in response to the updrift (down drift). Effects are stronger during displacement event (1998) than during the splitting event (1999). We have also studied some recent events occurred during 2006 (January), 2009 (January) and 2013 (January) using temperature data from Sounding of Atmosphere using Broadband Emission Radiometry (SABER) satellite. Though some modeling work supports the hypothesis that planetary waves are responsible for atmosphere-ionosphere coupling, there is still more significant works to do to understand how exactly the coupling can take place.

Keywords: sudden stratospheric warming (SSW), polar vortex, ionosphere, critical frequency

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Authors: Kumud Singh, Janvin Itteera, Priti Ukarde, Sanjay Malhotra, P. PMarathe, Ayan Bandyopadhay, Rakesh Meena, Vikram Rawat, L. M. Joshi

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Application of Permanent magnet technology to high frequency miniature klystron tubes to be utilized for space applications improves the efficiency and operational reliability of these tubes. But nevertheless the task of generating magnetic focusing forces to eliminate beam divergence once the beam crosses the electrostatic focusing regime and enters the drift region in the RF section of the tube throws several challenges. Building a high quality magnet focusing lens to meet beam optics requirement in cathode gun and RF interaction region is considered to be one of the critical issues for these high frequency miniature tubes. In this paper, electromagnetic design and particle trajectory studies in combined electric and magnetic field for optimizing the magnetic circuit using 3D finite element method (FEM) analysis software is presented. A rectangular configuration of the magnet was constructed to accommodate apertures for input and output waveguide sections and facilitate coupling of electromagnetic fields into the input klystron cavity and out from output klystron cavity through coupling loops. Prototype lenses have been built and have been tested after integration with the klystron tube. We discuss the design requirements and challenges, and the results from beam transmission of the prototype lens.

Keywords: beam transmission, Brillouin, confined flow, miniature klystron

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Authors: B.S. Roopa

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Objectives: To investigate the prevalence of concomitant use of GPDs in patients treated with NSAIDs and GPDs in recommended dose and frequency as prophylaxis. And also to know the association between risk factors and prescription of GPDs in patients treated with NSAIDs. Methods: Study was a prospective, observational, cross-sectional survey. Data from patients with prescription of NSAIDs at the out-patient departments of secondary care Hospital, Nilgiris, India were collected in a specially designed proforma for a period of 45 days. Analysis using χ2 tests for discrete variables. Factors that might be associated with prescription of GPD with NSIADs were assessed in multiple logistic regression models. Results: Three hundred and three patients were included in this study, and the rate of GPD prescription was 89.1%. Most of the patients received H2-receptor antagonist, and, to a lesser degree, antacid and proton pump inhibitor. Patients with history of GI ulcer/bleeding were much more likely to be co-prescribed GPD than those who had no history of GI disorders .Compared with patients who were managed in general outpatient clinic, those managed in Secondary care hospital in Nilgrisis, India were more likely to receive GPD. Conclusions: The prescription rate of GPD with NSAIDs is high. Patients were prescribed with H2RA with dose of 150mg twice daily, which are not effective in reducing the risk of NSAIDs induced gastric ulcer. Only the frequency of NSAIDs prescription was considered significant determinant for the co-prescription with GPAs in patients who are < 65 years and ≥ 65 years old.

Keywords: gastro protective agents, non steridol anti inlfammatory agents

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Authors: Somya Ranjan Patro, Abhigna Bhatt, Arnab Banerjee

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Inertial amplifier has recently gained increasing attention as a new mechanism for vibration control of structures. Currently, theoretical investigations are undertaken by researchers to reveal its fundamentals and to understand its underline principles in altering the structural response of structures against dynamic loadings. This paper investigates experimental and analytical studies on the dynamic characteristics of hybrid beam inertial amplifier (HBIA). The analytical formulation of the HBIA has been derived by implementing the spectral element method and rigid body dynamics. This formulation gives the relation between dynamic force and the response of the structure in the frequency domain. Further, for validation of the proposed HBIA, the experiments have been performed. The experimental setup consists of a 3D printed HBIA of polylactic acid (PLA) material screwed at the base plate of the shaker system. Two numbers of accelerometers are used to study the response, one at the base plate of the shaker second one placed at the top of the inertial amplifier. A force transducer is also placed in between the base plate and the inertial amplifier to calculate the total amount of load transferred from the base plate to the inertial amplifier. The obtained time domain response from the accelerometers have been converted into the frequency domain using the Fast Fourier Transform (FFT) algorithm. The experimental transmittance values are successfully validated with the analytical results, providing us essential confidence in our proposed methodology.

Keywords: inertial amplifier, fast fourier transform, natural frequencies, polylactic acid, transmittance, vibration absorbers

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Authors: R. R. Galiev, I. I. Lykov, A. E. Shitikov, I. A. Bilenko

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Dual-comb interferometry is based on the mixing of two optical frequency combs with slightly different lines spacing which results in the mapping of the optical spectrum into the radio-frequency domain for future digitizing and numerical processing. The dual-comb approach enables diverse applications, including metrology, fast high-precision spectroscopy, and distance range. Ordinary frequency-modulated continuous-wave (FMCW) laser-based Light Identification Detection and Ranging systems (LIDARs) suffer from two main disadvantages: slow and unreliable mechanical, spatial scan and a rather wide linewidth of conventional lasers, which limits speed measurement resolution. Dual-comb distance measurements with Allan deviations down to 12 nanometers at averaging times of 13 microseconds, along with ultrafast ranging at acquisition rates of 100 megahertz, allowing for an in-flight sampling of gun projectiles moving at 150 meters per second, was previously demonstrated. Nevertheless, pump lasers with EDFA amplifiers made the device bulky and expensive. An alternative approach is a direct coupling of the laser to a reference microring cavity. Backscattering can tune the laser to the eigenfrequency of the cavity via the so-called self-injection locked (SIL) effect. Moreover, the nonlinearity of the cavity allows a solitonic frequency comb generation in the very same cavity. In this work, we developed a fully integrated, power-efficient, electrically driven dual-micro comb source based on the semiconductor lasers SIL to high-quality integrated Si3N4 microresonators. We managed to obtain robust 1400-1700 nm combs generation with a 150 GHz or 1 THz lines spacing and measure less than a 1 kHz Lorentzian withs of stable, MHz spaced beat notes in a GHz band using two separated chips, each pumped by its own, self-injection locked laser. A deep investigation of the SIL dynamic allows us to find out the turn-key operation regime even for affordable Fabry-Perot multifrequency lasers used as a pump. It is important that such lasers are usually more powerful than DFB ones, which were also tested in our experiments. In order to test the advantages of the proposed techniques, we experimentally measured a minimum detectable speed of a reflective object. It has been shown that the narrow line of the laser locked to the microresonator provides markedly better velocity accuracy, showing velocity resolution down to 16 nm/s, while the no-SIL diode laser only allowed 160 nm/s with good accuracy. The results obtained are in agreement with the estimations and open up ways to develop LIDARs based on compact and cheap lasers. Our implementation uses affordable components, including semiconductor laser diodes and commercially available silicon nitride photonic circuits with microresonators.

Keywords: dual-comb spectroscopy, LIDAR, optical microresonator, self-injection locking

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Authors: Diala Bitar, Emmanuel Gourdon, Claude H. Lamarque, Manuel Collet

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Acoustic absorber devices play an important role reducing the noise at the propagation and reception paths. An electroacoustic absorber consists of a loudspeaker coupled to an electric shunt circuit, where the membrane is playing the role of an absorber/reflector of sound. Although the use of linear shunt resistors at the transducer terminals, has shown to improve the performances of the dynamical absorbers, it is nearly efficient in a narrow frequency band. Therefore, and since nonlinear phenomena are promising for their ability to absorb the vibrations and sound on a larger frequency range, we propose to couple a nonlinear electric shunt circuit at the loudspeaker terminals. Then, the equivalent model can be described by a 2 degrees of freedom system, consisting of a primary linear oscillator describing the dynamics of the loudspeaker membrane, linearly coupled to a cubic nonlinear energy sink (NES). The system is analytically treated for the case of 1:1 resonance, using an invariant manifold approach at different time scales. The proposed methodology enables us to detect the equilibrium points and fold singularities at the first slow time scales, providing a predictive tool to design the nonlinear circuit shunt during the energy exchange process. The preliminary results are promising; a significant improvement of acoustic absorption performances are obtained.

Keywords: electroacoustic absorber, multiple-time-scale with small finite parameter, nonlinear energy sink, nonlinear passive shunt

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Authors: K. A. Gladkova, N. P. Babushkina, E. Y. Bragina

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Purpose: Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the major public health problems worldwide. It is clear that the immune response to M. tuberculosis infection is a relationship between inflammatory and anti-inflammatory responses in which Tumour Necrosis Factor-α (TNF-α) plays key roles as a pro-inflammatory cytokine. TNF-α involved in various cell immune responses via binding to its two types of membrane-bound receptors, TNFRSF1A and TNFRSF1B. Importantly, some variants of the TNFRSF1B gene have been considered as possible markers of host susceptibility to TB. However, the possible impact of such TNF-α and its receptor genes polymorphism on TB cases in Tomsk is missing. Thus, the purpose of our study was to investigate polymorphism of TNF-α (rs1800629) and its receptor TNFRSF1B (rs652625 and rs525891) genes in population of Tomsk and to evaluate their possible association with the development of pulmonary TB. Materials and Methods: The population distribution features of genes polymorphisms were investigated and made case-control study based on group of people from Tomsk. Human blood was collected during routine patients examination at Tomsk Regional TB Dispensary. Altogether, 234 TB-positive patients (80 women, 154 men, average age is 28 years old) and 205 health-controls (153 women, 52 men, average age is 47 years old) were investigated. DNA was extracted from blood plasma by phenol-chloroform method. Genotyping was carried out by a single-nucleotide-specific real-time PCR assay. Results: First, interpopulational comparison was carried out between healthy individuals from Tomsk and available data from the 1000 Genomes project. It was found that polymorphism rs1800629 region demonstrated that Tomsk population was significantly different from Japanese (P = 0.0007), but it was similar with the following Europeans subpopulations: Italians (P = 0.052), Finns (P = 0.124) and British (P = 0.910). Polymorphism rs525891 clear demonstrated that group from Tomsk was significantly different from population of South Africa (P = 0.019). However, rs652625 demonstrated significant differences from Asian population: Chinese (P = 0.03) and Japanese (P = 0.004). Next, we have compared healthy individuals versus patients with TB. It was detected that no association between rs1800629, rs652625 polymorphisms, and positive TB cases. Importantly, AT genotype of polymorphism rs525891 was significantly associated with resistance to TB (odds ratio (OR) = 0.61; 95% confidence interval (CI): 0.41-0.9; P < 0.05). Conclusion: To the best of our knowledge, the polymorphism of TNFRSF1B (rs525891) was associated with TB, while genotype AT is protective [OR = 0.61] in Tomsk population. In contrast, no significant correlation was detected between polymorphism TNF-α (rs1800629) and TNFRSF1B (rs652625) genes and alveolar TB cases among population of Tomsk. In conclusion, our data expands the molecular particularities associated with TB. The study was supported by the grant of the Russia for Basic Research #15-04-05852.

Keywords: polymorphism, tuberculosis, TNF-α, TNFRSF1B gene

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Authors: Yana Posmitnaya, Galina Rudnitskaya, Tatyana Lukashenko, Anton Bukatin, Anatoly Evstrapov

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An important area of biological and medical research is the study of genetic mutations and polymorphisms that can alter gene function and cause inherited diseases and other diseases. The following methods to analyse DNA fragments are used: capillary electrophoresis and electrophoresis on microfluidic chip (MFC), mass spectrometry with electrophoresis on MFC, hybridization assay on microarray. Electrophoresis on MFC allows to analyse small volumes of samples with high speed and throughput. A soft lithography in polydimethylsiloxane (PDMS) was chosen for operative fabrication of MFCs. A master-form from silicon and photoresist SU-8 2025 (MicroChem Corp.) was created for the formation of micro-sized structures in PDMS. A universal topology which combines T-injector and simple cross was selected for the electrophoretic separation of the sample. Glass K8 and PDMS Sylgard® 184 (Dow Corning Corp.) were used for fabrication of MFCs. Electroosmotic flow (EOF) plays an important role in the electrophoretic separation of the sample. Therefore, the estimate of the quantity of EOF and the ways of its regulation are of interest for the development of the new methods of the electrophoretic separation of biomolecules. The following methods of surface modification were chosen to change EOF: high-frequency (13.56 MHz) plasma treatment in oxygen and argon at low pressure (1 mbar); 1% aqueous solution of polyvinyl alcohol; 3% aqueous solution of Kolliphor® P 188 (Sigma-Aldrich Corp.). The electroosmotic mobility was evaluated by the method of Huang X. et al., wherein the borate buffer was used. The influence of physical and chemical methods of treatment on the wetting properties of the PDMS surface was controlled by the sessile drop method. The most effective way of surface modification of MFCs, from the standpoint of obtaining the smallest value of the contact angle and the smallest value of the EOF, was the processing with aqueous solution of Kolliphor® P 188. This method of modification has been selected for the treatment of channels of MFCs, which are used for the separation of mixture of oligonucleotides fluorescently labeled with the length of chain with 10, 20, 30, 40 and 50 nucleotides. Electrophoresis was performed on the device MFAS-01 (IAI RAS, Russia) at the separation voltage of 1500 V. 6% solution of polydimethylacrylamide with the addition of 7M carbamide was used as the separation medium. The separation time of components of the mixture was determined from electropherograms. The time for untreated MFC was ~275 s, and for the ones treated with solution of Kolliphor® P 188 – ~ 220 s. Research of physical-chemical methods of surface modification of MFCs allowed to choose the most effective way for reducing EOF – the modification with aqueous solution of Kolliphor® P 188. In this case, the separation time of the mixture of oligonucleotides decreased about 20%. The further optimization of method of modification of channels of MFCs will allow decreasing the separation time of sample and increasing the throughput of analysis.

Keywords: electrophoresis, microfluidic chip, modification, nucleic acid, polydimethylsiloxane, soft lithography

Procedia PDF Downloads 405