Search results for: somatic sequence mutations

Authors: Yildiray Keskin, Omer Acan, Murat Akkus

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In this paper, the solution of fractional diffusion equations is presented by means of the reduced differential transform method. Fractional partial differential equations have special importance in engineering and sciences. Application of reduced differential transform method to this problem shows the rapid convergence of the sequence constructed by this method to the exact solution. The numerical results show that the approach is easy to implement and accurate when applied to fractional diffusion equations. The method introduces a promising tool for solving many fractional partial differential equations.

Keywords: fractional diffusion equations, Caputo fractional derivative, reduced differential transform method, partial

Procedia PDF Downloads 498

Authors: Aniekan Peter, ECS Naidu, Edidiong Akang, U. Offor, R. Kalhapure, A. A. Chuturgoon, T. Govender, O. O. Azu

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Introduction: Nano-drugs are novel innovations in the management of human immunodeficiency virus (HIV) pandemic, especially resistant strains of the virus in their sanctuary sites: testis and the brain. There are safety concerns to be addressed to achieve the full potential of this new drug delivery system. Aim of study: Our study was designed to investigate toxicity profile of Tenofovir Nanoparticle (TDF-N) synthesized by University of Kwazulu-Natal (UKZN) Nano-team for prevention and treatment of HIV infection. Methodology: Ten adult male Sprague-Dawley rats maintained at the Animal House of the Biomedical Resources Unit UKZN were used for the study. The animals were weighed and divided into two groups of 5 animal each. Control animals (A) were administered with normal saline. Therapeutic dose (4.3 mg/kg) of TDF-N was administered to group B. At the end of four weeks, animals were weighed and sacrificed. Liver and kidney were removed fixed in formal saline, processed and stained using H/E, PAS and MT stains for light microscopy. Serum was obtained for renal function test (RFT), liver function test (LFT) and full blood count (FBC) using appropriate analysers. Cellular measurements were done using ImageJ and Leica software 2.0. Data were analysed using graph pad 6, values < 0.05 were significant. Results: We reported no histological alterations in the liver, kidney, FBC, LFT and RFT between the TDF-N animals and saline control. There were no significant differences in weight, organo-somatic index and histological measurements in the treatment group when compared with saline control. Conclusion/recommendations: TDF-N is not toxic to the liver, kidney and blood cells in our study. More studies using human subjects is recommended.

Keywords: tenofovir nanoparticles, liver, kidney, blood cells

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Authors: Busra Mutlu Ipek, Merve Mutlu, Ahmet Mutlu

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Novel coronavirus COVID-19, which has recently influenced the world, poses a great threat to humanity. In order to overcome this challenging situation, scientists are working on developing effective vaccine against coronavirus. Many experts and researchers have also produced articles and done studies on this highly important subject. In this direction, this special topic was chosen for article to make a contribution to this area. The purpose of this article is to perform RNA sequence analysis of selected virus forms in the Coronaviridae family and predict/classify SARS-CoV-2 (COVID-19) from other selected complete genomes in coronaviridae family using proposed Artificial Neural Network(ANN) algorithm.

Keywords: Coronaviridae family, COVID-19, RNA sequencing, ANN, neural network

Procedia PDF Downloads 127

Authors: Mouad Zouina, Benaceur Outtaj

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The proposed work falls within the context of improving data security for m-commerce systems. In this context we have placed under the light some flaws encountered in HTTPS the most used m-commerce protocol, particularly the man in the middle attack, shortly MITM. The man in the middle attack is an active listening attack. The idea of this attack is to target the handshake phase of the HTTPS protocol which is the transition from a non-secure connection to a secure connection in our case HTTP to HTTPS. This paper proposes a solution to fix those flaws based on the upgrade of HSTS standard handshake sequence using the DNSSEC standard.

Keywords: m-commerce, HTTPS, HSTS, DNSSEC, MITM bootstrap vulnerability

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Authors: Lize Tibiriçá, Ronnie Lee, Samantha Behbahani

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Fibromyalgia (FM) is a musculoskeletal disorder affecting men and women of different ages and cultures. The cause of this disorder is unknown; however, studies suggest an etiology that involves biological and psychosocial factors. Few studies have shown that a personality type such as neuroticism is associated with chronic pain conditions. Past research has explored whether patients with FM present with a specific personality trait. However, studies have used different methods (i.e. Minnesota Multiphasic Personality Inventory (MMPI), Sociotropy and Autonomy Scale (SAS) and Dysfunctional Attitude Scale (DAS), Tridimensional Personality Questionnaire or Temperament and Character Inventory (TCI), Karolinska scale of personality, Big Five Inventory or NEO Personality Inventory) to explore the connection between FM and a personality type. They have identified personality types that present similar characteristics but vary in the name (i.e. high harm avoidance and low novelty seeking, psychasthenia/muscular tension/somatic anxiety, neuroticism). Although Zuckerman-Kuhlman Personality Questionnaire and the Big Five Inventory differ in terms of content and structure, both of them identify neuroticism as the personality type of FM patients, and the former also identifies these patients as having a low sociability personality trait. Previous research also shows a trend of sociotropic personality style with FM patients that also suffer from Major Depressive Disorder. Participants in these studies were, for the most part, adult female and researchers have recognized that as a limitation and whether their findings can be generalized to men and younger patients with FM. Furthermore, most studies reviewed were conducted in Europe (i.e. Spain) and had a cross-sectional design. Future research should replicate past studies in different countries and consider conducting a longitudinal study. Although it is suspected that FM course is modulated by FM patients’ personality, it is not known whether individuals with similar personalities will develop FM. This review sought to explain the differences and similarities between the personality types identified. Limitations in the studies reviewed were addressed, and considerations for future research and treatment were discussed.

Keywords: chronic pain, fibromyalgia, neuroticism, personality type

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Authors: Madhuka G. P. D. Udantha, Gihan V. Dias, Surangika Ranathunga

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Today Websites contain very interesting applications. But there are only few methodologies to analyze User navigations through the Websites and formulating if the Website is put to correct use. The web logs are only used if some major attack or malfunctioning occurs. Web Logs contain lot interesting dealings on users in the system. Analyzing web logs has become a challenge due to the huge log volume. Finding interesting patterns is not as easy as it is due to size, distribution and importance of minor details of each log. Web logs contain very important data of user and site which are not been put to good use. Retrieving interesting information from logs gives an idea of what the users need, group users according to their various needs and improve site to build an effective and efficient site. The model we built is able to detect attacks or malfunctioning of the system and anomaly detection. Logs will be more complex as volume of traffic and the size and complexity of web site grows. Unsupervised techniques are used in this solution which is fully automated. Expert knowledge is only used in validation. In our approach first clean and purify the logs to bring them to a common platform with a standard format and structure. After cleaning module web session builder is executed. It outputs two files, Web Sessions file and Indexed URLs file. The Indexed URLs file contains the list of URLs accessed and their indices. Web Sessions file lists down the indices of each web session. Then DBSCAN and EM Algorithms are used iteratively and recursively to get the best clustering results of the web sessions. Using homogeneity, completeness, V-measure, intra and inter cluster distance and silhouette coefficient as parameters these algorithms self-evaluate themselves to input better parametric values to run the algorithms. If a cluster is found to be too large then micro-clustering is used. Using Cluster Signature Module the clusters are annotated with a unique signature called finger-print. In this module each cluster is fed to Associative Rule Learning Module. If it outputs confidence and support as value 1 for an access sequence it would be a potential signature for the cluster. Then the access sequence occurrences are checked in other clusters. If it is found to be unique for the cluster considered then the cluster is annotated with the signature. These signatures are used in anomaly detection, prevent cyber attacks, real-time dashboards that visualize users, accessing web pages, predict actions of users and various other applications in Finance, University Websites, News and Media Websites etc.

Keywords: anomaly detection, clustering, pattern recognition, web sessions

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Authors: R. R. Billones, N. Lukkahatai, L. N. Saligan

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Mindfulness based interventions (MBIs) have been used in medically unexplained symptoms (MUS). This systematic review describes the literature investigating the general effect of MBIs on MUS and identifies the effects of specific MBIs on specific MUS conditions. The preferred reporting items for systematic reviews and meta-analysis guidelines (PRISMA) and the modified Oxford quality scoring system (JADAD) were applied to the review, yielding an initial 1,556 articles. The search engines included PubMed, ScienceDirect, Web of Science, Scopus, EMBASE, and PsychINFO using the search terms: mindfulness, or mediations, or mindful or MBCT or MBSR and medically unexplained symptoms or MUS or fibromyalgia or FMS. A total of 24 articles were included in the final systematic review. MBIs showed large effects on socialization skills for chronic fatigue syndrome (d=0.65), anger in fibromyalgia (d=0.61), improvement of somatic symptoms (d=1.6) and sleep (d=1.12) for painful conditions, physical health for chronic back pain (d=0.51), and disease intensity for irritable bowel disease/syndrome (d=1.13). A manualized MBI that applies the four fundamental elements present in all types of interventions were critical to efficacy. These elements were psycho-education sessions specific to better understand the medical symptoms, the practice of awareness, the non-judgmental observance of the experience at the moment, and the compassion to ones’ self. The effectiveness of different mindfulness interventions necessitates giving attention to improve the gaps that were identified related to home-based practice monitoring, competency training of mindfulness teachers, and sound psychometric properties to measure the mindfulness practice.

Keywords: mindfulness-based interventions, medically unexplained symptoms, mindfulness-based cognitive therapy, mindfulness-based stress reduction, fibromyalgia, irritable bowel syndrome

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Authors: Kyung Jin Kim, Jiwon Kwak, Jae-Hoon Lee, Soo Suk Lee

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MicroRNAs (miRNA) are a class of endogenous, single-stranded, small, and non-protein coding RNA molecules typically 20-25 nucleotides long. They are thought to regulate the expression of other genes in a broad range by binding to 3’- untranslated regions (3’-UTRs) of specific mRNAs. The detection of miRNAs is very important for understanding of the function of these molecules and in the diagnosis of variety of human diseases. However, detection of miRNAs is very challenging because of their short length and high sequence similarities within miRNA families. So, a simple-to-use, low-cost, and highly sensitive method for the detection of miRNAs is desirable. In this study, we demonstrate a novel bi-directional extension (BDE) assay. In the first step, a specific linear RT primer is hybridized to 6-10 base pairs from the 3’-end of a target miRNA molecule and then reverse transcribed to generate a cDNA strand. After reverse transcription, the cDNA was hybridized to the 3’-end which is BDE sequence; it played role as the PCR template. The PCR template was amplified in an SYBR green-based quantitative real-time PCR. To prove the concept, we used human brain total RNA. It could be detected quantitatively in the range of seven orders of magnitude with excellent linearity and reproducibility. To evaluate the performance of BDE assay, we contrasted sensitivity and specificity of the BDE assay against a commercially available poly (A) tailing method using miRNAs for let-7e extracted from A549 human epithelial lung cancer cells. The BDE assay displayed good performance compared with a poly (A) tailing method in terms of specificity and sensitivity; the CT values differed by 2.5 and the melting curve showed a sharper than poly (A) tailing methods. We have demonstrated an innovative, cost-effective BDE assay that allows improved sensitivity and specificity in detection of miRNAs. Dynamic range of the SYBR green-based RT-qPCR for miR-145 could be represented quantitatively over a range of 7 orders of magnitude from 0.1 pg to 1.0 μg of human brain total RNA. Finally, the BDE assay for detection of miRNA species such as let-7e shows good performance compared with a poly (A) tailing method in terms of specificity and sensitivity. Thus BDE proves a simple, low cost, and highly sensitive assay for various miRNAs and should provide significant contributions in research on miRNA biology and application of disease diagnostics with miRNAs as targets.

Keywords: bi-directional extension (BDE), microRNA (miRNA), poly (A) tailing assay, reverse transcription, RT-qPCR

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Authors: Hunmin Jung, Michael Hawkins, Seongmin Lee

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The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively. The exocyclic amines of bases in DNA are hydrogen bond donors, while the carbonyl moiety generated by the base deamination acts as hydrogen bond acceptors, which can alter base pairing properties of the purines. Xanthine is known to base pair with both cytosine and thymine, while hypoxanthine predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA polymerase η (polη) catalyzing across xanthine and hypoxanthine. In the catalytic site of polη, the deaminated guanine (i.e., xanthine) forms three Watson-Crick-like hydrogen bonds with an incoming dCTP, indicating the O2-enol tautomer of xanthine involves in the base pairing. The formation of the enol tautomer appears to be promoted by the minor groove contact by Gln38 of polη. When hypoxanthine is at the templating position, the deaminated adenine uses its O6-keto tautomer to form two Watson-Crick hydrogen bonds with an incoming dCTP, providing the structural basis for the high promutagenicity of hypoxanthine.

Keywords: DNA damage, DNA polymerase, deamination, mutagenesis, tautomerization, translesion synthesis

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Authors: Paula Verdugo-Hernandez, Patricio Cumsille

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We analyze a first-class on the convergence of real number sequences, named hereafter sequences, to foster exploration and discovery of concepts through graphical representations before engaging students in proving. The main goal was to differentiate between sequences and continuous functions-of-a-real-variable and better understand concepts at an initial stage. We applied the analytic frame of mathematical working spaces, which we expect to contribute to extending to sequences since, as far as we know, it has only developed for other objects, and which is relevant to analyze how mathematical work is built systematically by connecting the epistemological and cognitive perspectives, and involving the semiotic, instrumental, and discursive dimensions.

Keywords: convergence, graphical representations, mathematical working spaces, paradigms of real analysis, real number sequences

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Authors: Shalu Jain, Anju Bansal, Anup Kumar, Sunita Saxena

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Objectives: The novel TMPRSS2:ERG gene fusion is a common somatic event in prostate cancer that in some studies is linked with a more aggressive disease phenotype. Thus, this study aims to determine whether clinical variables are associated with the presence of TMPRSS2:ERG-fusion gene transcript in Indian patients of prostate cancer. Methods: We evaluated the clinical variables with presence and absence of TMPRSS2:ERG gene fusion in prostate cancer and BPH association of clinical patients. Patients referred for prostate biopsy because of abnormal DRE or/and elevated sPSA were enrolled for this prospective clinical study. TMPRSS2:ERG mRNA copies in samples were quantified using a Taqman chemistry by real time PCR assay in prostate biopsy samples (N=42). The T2:ERG assay detects the gene fusion mRNA isoform TMPRSS2 exon1 to ERG exon4. Results: Histopathology report has confirmed 25 cases as prostate cancer adenocarcinoma (PCa) and 17 patients as benign prostate hyperplasia (BPH). Out of 25 PCa cases, 16 (64%) were T2: ERG fusion positive. All 17 BPH controls were fusion negative. The T2:ERG fusion transcript was exclusively specific for prostate cancer as no case of BPH was detected having T2:ERG fusion, showing 100% specificity. The positive predictive value of fusion marker for prostate cancer is thus 100% and the negative predictive value is 65.3%. The T2:ERG fusion marker is significantly associated with clinical variables like no. of positive cores in prostate biopsy, Gleason score, serum PSA, perineural invasion, perivascular invasion and periprostatic fat involvement. Conclusions: Prostate cancer is a heterogeneous disease that may be defined by molecular subtypes such as the TMPRSS2:ERG fusion. In the present prospective study, the T2:ERG quantitative assay demonstrated high specificity for predicting biopsy outcome; sensitivity was similar to the prevalence of T2:ERG gene fusions in prostate tumors. These data suggest that further improvement in diagnostic accuracy could be achieved using a nomogram that combines T2:ERG with other markers and risk factors for prostate cancer.

Keywords: prostate cancer, genetic rearrangement, TMPRSS2:ERG fusion, clinical variables

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Authors: Rajkumar Ghosh

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Jhakri Thrust (JT) coeval of Sarahan Thrust (ST) was later considered to be part of Chaura Thrust (CT). The Main Central Thrust (MCT) delimits the southern extreme of Higher Himalaya, whereas the northern boundary defines by South Tibetan Detachment System (STDS). STDS is parallel set of north dipping extensional faults. The activation timing of MCT and STDS. MCT activated in two parts (MCT-L during 15- 0.7 Ma, and MCT-U during 25-14 Ma). Similarly, STDS triggered in two parts (STDS-L during 24-12 Ma, and STDS-U during 19-14 Ma). The activation ages for MBT and MFT. Besides, the MBT occurred during 11-9 Ma, and MFT followed as <2.5 Ma. There are two mylonitised zones (zone of S-C fabric) found under the microscope. Dynamic and bulging recrystallization and sub-grain formation was documented under the optical microscope from samples collected from these zones. The varieties of crenulated schistosity are shown in photomicrographs. In a rare and uncommon case, crenulation cleavage and sigmoid Muscovite were found together side-by-side. Recrystallized quartzo-feldspathic grains exist in between crenulation cleavages. These thin-section studies allow three possible hypotheses for such variations in crenulation cleavages. S/SE verging meso- and micro-scale box folds around Chaura might be a manifestation of some structural upliftment. Near Chaura, kink folds are visible. Prominent asymmetric shear sense indicators in augen mylonite are missing in meso-scale but dominantly present under the microscope. The main foliation became steepest (range of dip ~ 65 – 80 º) at this place. The aim of this section is to characterize the box fold and its signature in the regional geology of Himachal Himalaya. Grain Boundary Migration (GBM) associated temperature range (400–750 ºC) from microstructural studies in grain scale along Jhakri-Wangtu transect documented. Oriented samples were collected from the Jhakri-Chaura transect at a regular interval of ~ 1km for strain analysis. The Higher Himalayan Out-of-Sequence Thrust (OOST) in Himachal Pradesh is documented a decade ago. The OOST in other parts of the Himalayas is represented as a line in between MCTL and MCTU. But In Himachal Pradesh area, OOST activated the MCTL as well as in between a zone located south of MCTU. The expectations for strain variation near the OOST are very obvious. But multiple sets of OOSTs may produce a zigzag pattern of strain accumulation for this area and figure out the overprinting structures for multiple sets of OOSTs.

Keywords: Chaura Thrust, out-of-sequence thrust, Main Central Thrust, Sarahan Thrust

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Authors: Olomon Wu, Hung Lu, Nick Wilkins, Daniel Kerr, Zekeriya Aliyazicioglu, H. K. Hwang

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Multiple Input Multiple Output (MIMO) radar has received increasing attention in recent years. MIMO radar has many advantages over conventional phased array radar such as target detection, resolution enhancement, and interference suppression. In this paper, the results are presented from a simulation study of MIMO Uniformly-Spaced Linear Array (ULA) antennas. The performance is investigated under varied parameters, including varied array size, Pseudo Random (PN) sequence length, number of snapshots, and Signal to Noise Ratio (SNR). The results of MIMO are compared to a traditional array antenna.

Keywords: MIMO radar, phased array antenna, target detection, radar signal processing

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Authors: Regina R. Gunawan, Indwiani Astuti, H. Raden Danarto

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Cancer is the leading cause of death worldwide. Cancer is caused by mutations that alter the function of normal human genes and give rise to cancer genes. MicroRNA (miRNA) is a small non-coding RNA that regulates the gen through complementary bond towards mRNA target and cause mRNA degradation. miRNA works by either promoting or suppressing cell proliferation. miRNA level expression in cancer may offer another value of miRNA as a biomarker in cancer diagnostic. miRNA-21 is believed to have a role in carcinogenesis by enhancing proliferation, anti-apoptosis, cell cycle progression and invasion of tumor cells. Hsa-miR-21-5p marker has been identified in Prostate Cancer (PCa) and Benign Prostatic Hyperplasia (BPH) patient’s urine. This research planned to explore the diagnostic performance of miR-21 to differentiate PCa and BPH patients. In this study, urine samples were collected from 20 PCa patients and 20 BPH patients. miR-21 relative expression against the reference gene was analyzed and compared between the two. miRNA expression was analyzed using the comparative quantification method to find the fold change. miR-21 validity in identifying PCa patients was performed by quantifying the sensitivity and specificity with the contingency table. miR-21 relative expression against miR-16 in PCa patient and in BPH patient has 12,98 differences in fold change. From a contingency table of Cq expression of miR-21 in identifying PCa patients from BPH patient, Cq miR-21 has 100% sensitivity and 75% specificity. miR-21 relative expression can be used in discriminating PCa from BPH by using a urine sample. Furthermore, the expression of miR-21 has higher sensitivity compared to PSA (Prostate specific antigen), therefore miR-21 has a high potential to be analyzed and developed more.

Keywords: benign prostate hyperplasia, biomarker, miRNA-21, prostate cancer

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Authors: Hamed Alipour-Banaei, Farhad Mehdizadeh

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We report the design and characterization of ultra high quality factor filter based on one-dimensional photonic-crystal Thue-Morse sequence structure. The behavior of aperiodic array of photonic crystal structure is numerically investigated and we show that by changing the angle of incident wave, desired wavelengths could be tuned and a tunable filter is realized. Also it is shown that high quality factor filter be achieved in the telecommunication window around 1550 nm, with a device based on Thue-Morse structure. Simulation results show that the proposed structure has a quality factor more than 100000 and it is suitable for DWDM communication applications.

Keywords: Thue-Morse, filter, quality factor, photonic

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Authors: Rana Atta Ur Rahman, Daniel Juhre

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Initiation of crack during fatigue of casting alloys are noticed mainly on the basis of experimental results. Crack initiation and strength of fatigue of AA320 are summarized here. Load sequence effect is applied to notify initiation phase life. Crack initiation at notch root and fatigue life is calculated under single & two-step mechanical loading (ML) with and without combined thermal cycling (CTC). An Experimental setup is proposed to create the working temperature as per alloy applications. S-N curves are plotted, and a comparison is made between crack initiation leading to failure under different ML with & without thermal loading (TL).

Keywords: fatigue, initiation, SN curve, alloy

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Authors: Anastasia Papachristou, Anastasia Ntikoudi, Vasileios Saridakis

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The safety and health care needs of refugees have become an increasingly important issue all over the world especially during last few decades. Wars are the primary reason for refugees to leave their countries. Moreover, refugees are frequently exposed to a variety of stressors such as socioeconomic disadvantages, poverty, changes in family structure and functioning, losing social support, difficulty to access education, living in very crowded places, experiencing racism and isolation. This systematic review included research studies published between 2007-2017 from the search databases Medline, Scopus, Cinahl and PubMed, with keywords 'war survivors', 'war trauma', 'psychiatric disorders', 'refugees'. In order to meet the purpose of the systematic review, further research for complementary studies was conducted into the literature references of the research articles included in this study that would meet the criteria. Overall, 14 studies were reviewed and evaluated. The majority of them demonstrated that the most common psychiatric disorders observed among war refugees are post-traumatic stress disorder (PTSD), depression, anxiety and multiple somatic complaints. Moreover, significant relationship was shown between the number of traumatic events experienced by the refugees and sociodemographic features such as gender, age and previous family history of any psychological disorder. War violence is highly traumatic, causing multiple, long-term negative outcomes such as the aforementioned psychiatric disorders. The number of the studies reviewed in this systematic review is not representative of the problem and its significance. The need for care of the survivors and their families is vital. Further research is necessary in order to clarify the role of predictive factors in the development and maintenance of post-traumatic stress and the rest psychiatric disorders following war trauma. In conclusion, it is necessary to have large multicenter studies in the future in order to be able to draw reliable conclusions about the effects of war.

Keywords: psychiatric disorders, refugees, war survivors, war trauma

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Authors: Mostefa Bendouba, Djebli Abdelkader, Abdelkrim Aid, Mohamed Benguediab

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The damage evolution mechanism is one of the important focuses of fatigue behaviour investigation of composite materials and also is the foundation to predict fatigue life of composite structures for engineering application. This paper is dedicated to a damage investigation under two block loading cycle fatigue conditions submitted to composite material. The loading sequence effect and the influence of the cycle ratio of the first stage on the cumulative fatigue life were studied herein. Two loading sequences, i.e., high-to-low and low-to-high cases are considered in this paper. The proposed damage indicator is connected cycle by cycle to the S-N curve and the experimental results are in agreement with model expectations. Some experimental researches are used to validate this proposition.

Keywords: fatigue, damage acumulation, composite, evolution

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Authors: Renata Checiches, Thierry Coche, Nicolas F. Delahaye, Albert Linder, Fernando Ulloa Montoya, Olivier Gruselle, Karen Langfeld, An de Creus, Bart Spiessens, Vincent G. Brichard, Jamila Louahed, Frédéric F. Lehmann

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Background: The RNA-expression levels of cancer-testis antigens MAGE A3 and PRAME were determined in resected tissue from patients with primary non-small-cell lung cancer (NSCLC) and related to clinical outcome. EGFR, KRAS and BRAF mutation status was determined in a subset to investigate associations with MAGE A3 and PRAME expression. Methods: We conducted a single-centre, uncontrolled, retrospective study of 1260 tissue-bank samples from stage IA-III resected NSCLC. The prognostic value of antigen expression (qRT-PCR) was determined by hazard-ratio and Kaplan-Meier curves. Results: Thirty-seven percent (314/844) of tumours expressed MAGE-A3, 66% (723/1092) expressed PRAME and 31% (239/839) expressed both. Respective frequencies in squamous-cell tumours and adenocarcinomas were 43%/30% for MAGE A3 and 80%/44% for PRAME. No correlation with stage, tumour size or patient age was found. Overall, no prognostic value was identified for either antigen. A trend to poorer overall survival was associated with MAGE-A3 in stage IIIB and with PRAME in stage IB. EGFR and KRAS mutations were found in 10.1% (28/311) and 33.8% (97/311) of tumours, respectively. EGFR (but not KRAS) mutation status was negatively associated with PRAME expression. Conclusion: No clear prognostic value for either PRAME or MAGE A3 was observed in the overall population, although some observed trends may warrant further investigation.

Keywords: MAGE A3, PRAME, cancer-testis gene, NSCLC, survival, EGFR

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Authors: Boutheina Ben Abdelmoumen Mardassi, Salim Chibani, Safa Boujemaa, Amaury Vaysse, Julien Guglielmini, Elhem Yacoub

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Background and aim: Mycoplasma hominis (MH) is a pathogenic bacterium belonging to the Mollicutes class. It causes a wide range of gynecological infections and infertility among adults. Recently, we have explored for the first time the phylodistribution of Tunisian M. hominis clinical strains using an expanded MLST. We have demonstrated their distinction into two pure lineages, which each corresponding to a specific pathotype: genital infections and infertility. The aim of this project is to gain further insight into the evolutionary dynamics and the specific genetic factors that distinguish MH pathotypes Methods: Whole genome sequencing of Mycoplasma hominis clinical strains was performed using illumina Miseq. Denovo assembly was performed using a publicly available in-house pipeline. We used prokka to annotate the genomes, panaroo to generate the gene presence matrix and Jolytree to establish the phylogenetic tree. We used treeWAS to identify genetic loci associated with the pathothype of interest from the presence matrix and phylogenetic tree. Results: Our results revealed a clear categorization of the 62 MH clinical strains into two distinct genetic lineages, with each corresponding to a specific pathotype.; gynecological infections and infertility[AV1] . Genome annotation showed that GC content is ranging between 26 and 27%, which is a known characteristic of Mycoplasma genome. Housekeeping genes belonging to the core genome are highly conserved among our strains. TreeWas identified 4 virulence genes associated with the pathotype gynecological infection. encoding for asparagine--tRNA ligase, restriction endonuclease subunit S, Eco47II restriction endonuclease, and transcription regulator XRE (involved in tolerance to oxidative stress). Five genes have been identified that have a statistical association with infertility, tow lipoprotein, one hypothetical protein, a glycosyl transferase involved in capsule synthesis, and pyruvate kinase involved in biofilm formation. All strains harbored an efflux pomp that belongs to the family of multidrug resistance ABC transporter, which confers resistance to a wide range of antibiotics. Indeed many adhesion factors and lipoproteins (p120, p120', p60, p80, Vaa) have been checked and confirmed in our strains with a relatively 99 % to 96 % conserved domain and hypervariable domain that represent 1 to 4 % of the reference sequence extracted from gene bank. Conclusion: In summary, this study led to the identification of specific genetic loci associated with distinct pathotypes in M hominis.

Keywords: mycoplasma hominis, infertility, gynecological infections, virulence genes, antibiotic resistance

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Authors: Asmaa Zaraq

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In the present work we report X-ray powder diffraction measurements of SrCaCoTeO6 and SrCaNiTeO6, at different temperatures. The crystal structures at room temperature of both compounds are determined; and results showing the existence of high-temperature phase transitions in them are presented. Both compounds have double perovskite structure with 1:1 ordered arrangement of the B site cations. At room temperature their symmetries are described with the P21/n space group, that correspond to the (a+b-b-) tilt system. The evolution with temperature of the structure of both compounds shows the presence of three phase transitions: a continuous one, at 450 and 500 K, a discontinuous one, at 700 and 775 K, and a continuous one at 900 and 950 K for SrCaCoTeO6 and SrCaNiTeO6, respectively with the following phase-transition sequence: P21/n → I2/m → I4/m → Fm-3m.

Keywords: double perovskites, caracterisation DRX, transition de phase

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Authors: Lidia Kowalska, Edward Arseniuk

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Glume and leaf blotch is a disease of wheat caused by necrotrophic fungus Parastagonospora nodorum. It is a serious pathogen in many wheat-growing areas throughout the world. Use of resistant cultivars is the most effective and economical means to control the above-mentioned disease. Plant breeders and pathologists have worked intensively to incorporate resistance to the pathogen in new cultivars. Conventional methods of breeding for resistance can be supported by using the biotechnological ones, i.e., somatic embryogenesis and androgenesis. Therefore, an effort was undertaken to compare genetic variation in P. nodorum resistance among winter wheat somaclones, dihaploids and conventional varieties. For the purpose, a population of 16 somaclonal and 4 dihaploid wheat lines from six crosses were used to assess their resistance to P. nodorum under field conditions. Lines were grown in disease-free (fungicide protected) and inoculated micro plots in 2 replications of a split-plot design in a single environment. The plant leaves were inoculated with a mixture of P. nodorum isolates three times. Spore concentrations were adjusted to 4 x 10⁶ of viable spores per one milliliter. The disease severity was rated on a scale, where > 90% – susceptible, < 10% - resistant. Disease ratings of plant leaves showed statistically significant differences among all lines tested. Higher resistance to P. nodorum was observed more often on leaves of somaclonal lines than on dihaploid ones. On average, disease, severity reached 15% on leaves of somaclones and 30% on leaves of dihaploids. Some of the genotypes were showing low leaf infection, e.g. dihaploid D-33 (disease severity 4%) and a somaclone S-1 (disease severity 2%). The results from this study prove that dihaploid and somaclonal variation might be successfully used as an additional source of wheat resistance to the pathogen and it could be recommended to use in commercial breeding programs. The reported results prove that biotechnological methods may effectively be used in breeding for disease resistance of wheat to fungal necrotrophic pathogens.

Keywords: glume and leaf blotch, somaclonal, androgenic variation, wheat, resistance breeding

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Authors: Aminu Bashir Mohammad, Agwu Ezera, Abdulrazaq G. Habib, Garba Iliyasu

Abstract:

Background: Drug resistance tuberculosis (DR-TB) continues to be a challenge in developing countries with poor resources. Routine screening for primary DR-TB before commencing treatment is not done in public hospitals in Nigeria, even with the large body of evidence that shows a high prevalence of primary DR-TB. Data on drug resistance and its genetic determinant among follow up TB patients is lacking in Nigeria. Hence the aim of this study was to determine the prevalence and genetic determinant of drug resistance among follow up TB patients in a tertiary hospital in Nigeria. Methods: This was a cross-sectional laboratory-based study conducted on 384 sputum samples collected from consented follow-up tuberculosis patients. Standard microbiology methods (Zeil-Nielsen staining and microscopy) and PCR (Line Probe Assay)] were used to analyze the samples collected. Person’s Chi-square was used to analyze the data generated. Results: Out of three hundred and eighty-four (384) sputum samples analyzed for mycobacterium tuberculosis (MTB) and DR-TB twenty-five 25 (6.5%) were found to be AFB positive. These samples were subjected to PCR (Line Probe Assay) out of which 18(72%) tested positive for DR-TB. Mutations conferring resistance to rifampicin (rpo B) and isoniazid (katG, and or inhA) were detected in 12/18(66.7%) and 6/18(33.3%), respectively. Transmission dynamic of DR-TB was not significantly (p>0.05) dependent on demographic characteristics. Conclusion: There is a need to strengthened the laboratory capacity for diagnosis of TB and drug resistance testing and make these services available, affordable, and accessible to the patients who need them.

Keywords: drug resistance tuberculosis, genetic determinant, intensive phase, Nigeria

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Authors: Victor Emeli, Akansel Cosgun

Abstract:

This paper explores the navigation among movable obstacles (NAMO) problem and proposes joint path and push planning: which path to take and in what direction the obstacles should be pushed at, given a start and goal position. We present a planning algorithm for selecting a path and the obstacles to be pushed, where a rapidly-exploring random tree (RRT)-based heuristic is employed to calculate a minimal collision path. When it is necessary to apply a pushing force to slide an obstacle out of the way, the planners leverage means-end analysis through a dynamic physics simulation to determine the sequence of linear pushes to clear the necessary space. Simulation experiments show that our approach finds solutions in higher clutter percentages (up to 49%) compared to the straight-line push planner (37%) and RRT without pushing (18%).

Keywords: motion planning, path planning, push planning, robot navigation

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Authors: L. Onal

Abstract:

The aim of this study is to optimize manufacturing process for thermoplastic sandwich composite structures for the pedestrian safety of automobiles subjected to collision condition. In particular, cost-effective manufacturing techniques for sandwich structures with commingled GF/PP skins and low-density foam cores are being investigated. The performance of these structures under bending load is being studied. Samples are manufactured using compression moulding technique. The relationship of this performance to processing parameters such as mould temperature, moulding time, moulding pressure and sequence of the layers during moulding is being investigated. The results of bending tests are discussed in the light of the moulding conditions and conclusions are given regarding optimum set of processing conditions using the compression moulding route

Keywords: twintex, flexural properties, automobile composites, sandwich structures

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Authors: Samira Ghasempourkazemi

Abstract:

In terms of the COVID-19 pandemic, lots of mutations in the urban system, which have systemic impacts, have clearly appeared. COVID-19 not only had a direct impact on health but also caused significant losses to other departments, including the economy, education, tourism, environment and the construction industry. Therefore, the pandemic caused a disruption in the whole urban system. Particularly, today’s large urban areas are not designed in order to be compatible during a pandemic. Hence, cities are more vulnerable to infectious disease threats according to the population density, built environment and socioeconomic aspects. Considering the direct relationship between population and rate of infection, higher rates are given to those individuals located in areas with high-density populations. Population density can be a factor that seems to have a strong impact on the spread of infectious diseases. Thus, the preliminary hypothesis can be related to a densely populated areas which become hotspots for the rapid spread of the pandemic due to high levels of interaction. In addition, some other indicators can be effective in this condition, such as age range, education and socio-economy. To figure out the measure of infectious disease risk in densely populated areas in Istanbul is an objective of this study. Besides, this study intends to figure out Vulnerability Index in the case of COVID-19. In order to achieve the proper result, the considered method can be Analytic Hierarchy Process (AHP) by involving the mentioned variables. In the end, the study represents the COVID Vulnerability of densely populated areas in a metro city and the gaps that need to be identified and plugged for the pandemic-resilience city of tomorrow.

Keywords: infectious disease, COVID-19, urban system, densely populated area

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Authors: Boukerch Haroun, Luo Qing Sheng, Li Hua Shi, Boukraa Sebti

Abstract:

In this paper we present the design and the implementation of a target tracking system where the target is set to be a moving person in a video sequence. The system can be applied easily as a vision system for mobile robot. The system is composed of two major parts the first is the detection of the person in the video frame using the SVM learning machine based on the “HOG” descriptors. The second part is the tracking of a moving person it’s done by using a combination of the Kalman filter and a modified version of the Camshift tracking algorithm by adding the target motion feature to the color feature, the experimental results had shown that the new algorithm had overcame the traditional Camshift algorithm in robustness and in case of occlusion.

Keywords: camshift algorithm, computer vision, Kalman filter, object tracking

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Authors: Hisyam Hidayatullah

Abstract:

This world events consciously or not realize everything has a pattern, until the events of the universe according to the Big Bang theory of the solar system which makes so regular in the rotation. The author would like to create a results curve area between the quadratic function y=kx2 and line y=ka2 using GeoGebra application version 4.2. This paper can provide a series that is no less interesting with Fourier series, so that will add new material about the series can be calculated with sigma notation. In addition, the ranks of the unique natural numbers of extensive changes in established areas. Finally, this paper provides analytical and geometric proof of the vast area in between the lines and curves that give the area is formed by y=ka2 dan kurva y=kx2, x-axis, line x=√a and x=-√a make a series of numbers for k=1 and a ∈ original numbers. ∑_(i=0)^n=(4n√n)/3=0+4/3+(8√2)/3+4√3+⋯+(4n√n)/3. The author calls the series “H154M”.

Keywords: sequence, series, sigma notation, application GeoGebra

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Authors: Yanyan Wang

Abstract:

This paper on second language teaching and learning uses conversation analysis (CA) approach and focuses on how second language learners of Chinese do repair when making clarification requests. In order to demonstrate their behavior in interaction, a comparison was made to study the differences between native speakers of Chinese with non-native speakers of Chinese. The significance of the research is to make second language teachers and learners aware of repair and how to seek clarification. Utilizing the methodology of CA, the research involved two sets of naturally occurring recordings, one of native speaker students and the other of non-native speaker students. Both sets of recording were telephone talks between students and teachers. There were 50 native speaker students and 50 non-native speaker students. From multiple listening to the recordings, the parts with repairs for clarification were selected for analysis which included the moments in the talk when students had problems in understanding or hearing the speaker and had to seek clarification. For example, ‘Sorry, I do not understand ‘and ‘Can you repeat the question? ‘were the parts as repair to make clarification requests. In the data, there were 43 such cases from native speaker students and 88 cases from non-native speaker students. The non-native speaker students were more likely to use repair to seek clarification. Analysis on how the students make clarification requests during their conversation was carried out by investigating how the students initiated problems and how the teachers repaired the problems. In CA term, it is called other-initiated self-repair (OISR), which refers to student-initiated teacher-repair in this research. The findings show that, in initiating repair, native speaker students pay more attention to mutual understanding (inter-subjectivity) while non-native speaker students, due to their lack of language proficiency, pay more attention to their status of knowledge (epistemic) switch. There are three major differences: 1, native Chinese students more often initiate closed-class OISR (seeking specific information in the request) such as repeating a word or phrases from the previous turn while non-native students more frequently initiate open-class OISR (not specifying clarification) such as ‘sorry, I don’t understand ‘. 2, native speakers’ clarification requests are treated by the teacher as understanding of the content while non-native learners’ clarification requests are treated by teacher as language proficiency problem. 3, native speakers don’t see repair as knowledge issue and there is no third position in the repair sequences to close repair while non-native learners take repair sequence as a time to adjust their knowledge. There is clear closing third position token such as ‘oh ‘ to close repair sequence so that the topic can go back. In conclusion, this paper uses conversation analysis approach to compare differences between native Chinese speakers and non-native Chinese learners in their ways of conducting repair when making clarification requests. The findings are useful in future Chinese language teaching and learning, especially in teaching pragmatics such as requests.

Keywords: conversation analysis (CA), clarification request, second language (L2), teaching implication

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Authors: Aravind Mohan Krishnan

Abstract:

This paper identifies a research gap in the literature on tourism entrepreneurship in Malawi, Africa, and investigates how entrepreneurs from the Malawian tourism sector discover and exploit business opportunities. In particular, the importance of prior experience and business networks in the opportunity development process is debated. Another area of empirical research examined here is the opportunity recognition-venture creation sequence. While Malawi presents fruitful business opportunities, exploiting these opportunities into fully realized business ideas is a real challenge due to the country’s difficult business environment and poor promotional and marketing efforts. The study concludes by calling for further research in Sub-Saharan Africa in order to develop our understanding of entrepreneurship in this (African) context.

Keywords: entrepreneurship, Malawi, opportunities, tourism

Procedia PDF Downloads 311