Search results for: LYRM7 gene defect

Authors: Rim Frikha, Nouha Bouayed, Afifa Sellami, Nozha Chakroun, Salima Daoud, Leila Keskes, Tarek Rebai

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Introduction: Recurrent pregnancy loss (RPL) defined as two or more pregnancy losses, is a serious clinical problem. Methylene-tetrahydro-folate-reductase (MTHFR) polymorphisms, commonly the variant C677T is recognized as an inherited thrombophilia which might affect embryonic development and pregnancy success and cause pregnancy complications as RPL. Material and Methods DNA was extracted from peripheral blood samples and PCR-RFLP was performed for the molecular diagnosis of the C677T MTHFR polymorphism among 70 patients (35 couples) with more than 2 fetal losses. Aims and Objective: The aim of this study is to determine the frequency of MTHFR C677T among Tunisian couples with RPL and to critically analyze the available literature on the importance of MTHFR polymorphism testing in the management of RPL. Result and comments: No C677T mutation was detected in the carriers of RPL. This result would be related to sample size and to different criteria (number of abortion), - The association between MTHFR polymorphisms and pregnancy complications has been reported but with controversial results. - A lack of evidence for MTHFR polymorphism testing previously recommended by ACMG (American College of Medical medicine). Our study highlights the importance of screening of MTHFR polymorphism since the real impact of such thrombotic molecular defect on the pregnancy outcome is evident. - Folic supplementation of these patients during pregnancy can prevent such complications and lead to a successful pregnancy outcome.

Keywords: methylenetetrahydrofolate reductase, C677T, recurrent pregnancy loss, genetic testing

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Authors: Sofia Papadimitriou

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INTRODUCTION: The differential diagnosis between acute viral and bacterial infections is an important cost-effectiveness parameter at the stage of the treatment process in order to achieve the maximum benefits in therapeutic intervention by combining the minimum cost to ensure the proper use of antibiotics.The discovery of sensitive and robust molecular diagnostic tests in response to the role of the host in infections has enhanced the accurate diagnosis and differentiation of infections. METHOD: The study used a sample of six independent blood samples (total=756) which are associated with human proteins-proteins, each of which at the transcription stage expresses a different response in the host network between viral and bacterial infections.Τhe individual blood samples are subjected to a sequence of computer filters that identify a gene panel corresponding to an autonomous diagnostic score. The data set and the correspondence of the gene panel to the diagnostic patents a new Bangalore -Viral Bacterial (BL-VB). FINDING: We use a biomarker based on the blood of 10 genes(Panel-VB) that are an important prognostic value for the detection of viruses from bacterial infections with a weighted average AUROC of 0.97(95% CL:0.96-0.99) in eleven independent samples (sets n=898). We discovered a base with a patient score (VB 10 ) according to the table, which is a significant diagnostic value with a weighted average of AUROC 0.94(95% CL: 0.91-0.98) in 2996 patient samples from 56 public sets of data from 19 different countries. We also studied VB 10 in a new cohort of South India (BL-VB,n=56) and found 97% accuracy in confirmed cases of viral and bacterial infections. We found that VB 10 (a)accurately identifies the type of infection even in unspecified cases negative to the culture (b) shows its clinical condition recovery and (c) applies to all age groups, covering a wide range of acute bacterial and viral infectious, including non-specific pathogens. We applied our VB 10 rating to publicly available COVID 19 data and found that our rating diagnosed viral infection in patient samples. RESULTS: Τhe results of the study showed the diagnostic power of the biomarker VB 10 as a diagnostic test for the accurate diagnosis of acute infections in recovery conditions. We look forward to helping you make clinical decisions about prescribing antibiotics and integrating them into your policies management of antibiotic stewardship efforts. CONCLUSIONS: Overall, we are developing a new property of the RNA-based biomarker and a new blood test to differentiate between viral and bacterial infections to assist a physician in designing the optimal treatment regimen to contribute to the proper use of antibiotics and reduce the burden on antimicrobial resistance, AMR.

Keywords: acute infections, antimicrobial resistance, biomarker, blood transcriptome, systems biology, classifier diagnostic score

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Authors: Fuad M. Alkoot

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DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: biometrics, genetic data, identity verification, k nearest neighbor

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Authors: M. Al Huwayz, A. Salhi, S. Alhassan, S. Alotaibi, A. Almalki, M.Almunyif, A. Alhassni, M. Henini

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Recently, there has been much research carried out to investigate quantum dots (QDs) lasers with the aim to increase the gain of quantum well lasers. However, one of the difficulties with these structures is that electrically active defects can lead to serious issues in the performance of these devices. It is therefore essential to fully understand the types of defects introduced during the growth and/or the fabrication process. In this study, the effects of Gamma radiation on the electrically active defects in p-i-n InAs/InGaAsQDs laser structures grown by Molecular Beam Epitaxy (MBE) technique on GaAs substrates were investigated. Deep Level Transient Spectroscopy (DLTS), current-voltage (I-V), and capacitance-voltage (C-V) measurements were performed to explore these effects on the electrical properties of these QDs lasers. I-V measurements showed that as-grown sample had better electrical properties than the irradiated sample. However, DLTS and Laplace DLTS measurements at different reverse biases revealed that the defects in the-region of the p-i-n structures were decreased in the irradiated sample. In both samples, a trap with an activation energy of ~ 0.21 eV was assigned to the well-known defect M1 in GaAs layers

Keywords: quantum dots laser structures, gamma radiation, DLTS, defects, nAs/IngaAs

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Authors: Hamitri-Guerfi Fatiha, Mekimene Lekhder, Madani Khodir, Youyou Ahcene

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Virgin olive oil is appreciated by consumers, the quality of the oil is regulated by the international olive oil council depends on its chemical composition, so, the correct packing conditions are a prerequisite to preserve oil color, flavor, and nutriments, from production to consumption. The contact of food with various materials of packaging, since the production, until their consumption constitutes one of the essential aspects of food safety (directive 76/833/CEE). In Algeria, plastic bottles, although, they are economic and light are largely used at packaging olive oil but not used in other countries. This is due to migration phenomena that can occur from these materials. Thus, the goal of this work is to examine the physicochemical behavior of the couple packaging plastic-oil during their exposure to three temperatures corresponding to the conditions of storage applied in Algeria. Like, it is difficult to compare blowers of bottles which are heavy engineering, it comes out from this study that the effect of heat, the absorption of water, the constraints of storage of acidity, as well as the composition of oil, the PET bottles showed a remarkable structural instability, this defect of quality was confirmed by the analysis of morphology by electronic scan microscopy. These bottles present a total migration significantly higher than the threshold of acceptance. Moreover, a metal contamination of oil by its packaging was confirmed by the spectroscopy of atomic absorption and a microanalysis. The differences observed between the results of the microanalysis applied and the mechanical characterizations of the various bottles are reported, showing the reality of the container-contents exchanges.

Keywords: interaction, stability, pet, virgin olive oil

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Authors: Heiko Jessen, Laura Tanus, Slobodan Ruzicic

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Objectives: The efficacy of Stribild®, an integrase strand transfer inhibitor (INSTI) -based STR, has been evaluated in randomized clinical trials and it has demonstrated durable capability in terms of achieving sustained suppression of HIV-1 RNA-levels. However, differences in monitoring frequency, existing selection bias and profile of patients enrolled in the trials, may all result in divergent efficacy of this regimen in routine clinical settings. The aim of this study was to assess the virologic outcomes, safety and tolerability profile of Stribild® in a routine clinical setting. Methods: This was a retrospective monocentric analysis on HIV-1-infected patients, who started with or were switched to Stribild®. Virological failure (VF) was defined as confirmed HIV-RNA>50 copies/ml. The minimum time of follow-up was 24 weeks. The percentage of patients remaining free of therapeutic failure was estimated using the time-to-loss-of-virologic-response (TLOVR) algorithm, by intent-to-treat analysis. Results: We analyzed the data of 197 patients (56 ART-naïve and 141 treatment-experienced patients), who fulfilled the inclusion criteria. Majority (95.9%) of patients were male. The median time of HIV-infection at baseline was 2 months in treatment-naïve and 70 months in treatment-experienced patients. Median time [IQR] under ART in treatment-experienced patients was 37 months. Among the treatment-experienced patients 27.0% had already been treated with a regimen consisting of two NRTIs and one INSTI, whereas 18.4% of them experienced a VF. The median time [IQR] of virological suppression prior to therapy with Stribild® in the treatment-experienced patients was 10 months [0-27]. At the end of follow-up (median 33 months), 87.3% (95% CI, 83.5-91.2) of treatment-naïve and 80.3% (95% CI, 75.8-84.8) of treatment-experienced patients remained free of therapeutic failure. Considering only treatment-experienced patients with baseline VL<50 copies/ml, 83.0% (95% CI, 78.5-87.5) remained free of therapeutic failure. A total of 17 patients stopped treatment with Stribild®, 5.4% (3/56) of them were treatment-naïve and 9.9% (14/141) were treatment-experienced patients. The Stribild® therapy was discontinued in 2 (1.0%) because of VF, loss to follow-up in 4 (2.0%), and drug-drug interactions in 2 (1.0%) patients. Adverse events were in 7 (3.6%) patients the reason to switch from therapy with Stribild® and further 2 (1.0%) patients decided personally to switch. The most frequently observed adverse events were gastrointestinal side effects (20.0%), headache (8%), rash events (7%) and dizziness (6%). In two patients we observed an emergence of novel resistances in integrase-gene. The N155H evolved in one patient and resulted in VF. In another patient S119R evolved either during or shortly upon switch from therapy with Stribild®. In one further patient with VF two novel mutations in the RT-gene were observed when compared to historical genotypic test result (V106I/M and M184V), whereby it is not clear whether they evolved during or already before the switch to Stribild®. Conclusions: Effectiveness of Stribild® for treatment-naïve patients was consistent with data obtained in clinical trials. The safety and tolerability profile as well as resistance development confirmed clinical efficacy of Stribild® in a daily practice setting.

Keywords: ART, HIV, integrase inhibitor, stribild

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Authors: Gunta Resevica, Nikita Zrelovs, Ivars Silamikelis, Ieva Kalnciema, Helvijs Niedra, Gunārs Lācis, Toms Bartulsons, Inga Moročko-Bičevska, Arturs Stalažs, Kristīne Drevinska, Andris Zeltins, Ina Balke

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Newly discovered viruses provide novel knowledge for basic phytovirus research, serve as tools for biotechnology and can be helpful in identification of epidemic outbreaks. Blackcurrant-associated rhabdovirus (BCaRV) have been discovered in USA germplasm collection samples from Russia and France. As it was reported in one accession originating from France it is unclear whether the material was already infected when it entered in the USA or it became infected while in collection in the USA. Due to that BCaRV was definite as non-EU viruses. According to ICTV classification BCaRV is representative of Blackcurrant betanucleorhabdovirus specie in genus Betanucleorhabdovirus (family Rhabdoviridae). Nevertheless, BCaRV impact on the host, transmission mechanisms and vectors are still unknown. In RNA-seq data pool from Ribes plants resistance gene study by high throughput sequencing (HTS) we observed differences between sample group gene transcript heat maps. Additional analysis of the whole data pool (total 393660492 of 150 bp long read pairs) by rnaSPAdes v 3.13.1 resulted into 14424 bases long contig with an average coverage of 684x with shared 99.5% identity to the previously reported first complete genome of BCaRV (MF543022.1) using EMBOSS Needle. This finding proved BCaRV presence in EU and indicated that it might be relevant pathogen. In this study leaf tissue from twelve asymptomatic blackcurrant cv. Mara Eglite plants (negatively tested for blackcurrant reversion virus (BRV)) from Dobele, Latvia (56°36'31.9"N, 23°18'13.6"E) was collected and used for total RNA isolation with RNeasy Plant Mini Kit with minor modifications, followed by plant rRNA removal by a RiboMinus Plant Kit for RNA-Seq. HTS libraries were prepared using MGI Easy RNA Directional Library Prep Set for 16 reactions to obtain 150 bp pair-end reads. Libraries were pooled, circularized and cleaned and sequenced on DNBSEQ-G400 using PE150 flow cell. Additionally, all samples were tested by RT-PCR, and amplicons were directly sequenced by Sanger-based method. The contig representing the genome of BCaRV isolate Mara Eglite was deposited at European Nucleotide Archive under accession number OU015520. Those findings indicate a second evidence on the presence of this particular virus in the EU and further research on BCaRV prevalence in Ribes from other geographical areas should be performed. As there are no information on BCaRV impact on the host this should be investigated, regarding the fact that mixed infections with BRV and nucleorhabdoviruses are reported.

Keywords: BCaRV, Betanucleorhabdovirus, Ribes, RNA-seq

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Authors: Ndibarafinia Tobin

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Building defect and failure are common phenomena in the Nigerian construction industry. The activities of the inexperienced labor force in the Nigerian construction industry have tarnished the image of practicing construction professionals in recent past. Defects and collapse can cause unnecessary expenditure, delays, loss of lives, property and left many people injured. They are also generating controversies among parties involved. Also, if this situation is left unanswered and untreated, it will lead to more serious problems in the future upcoming construction projects in Nigeria. Quite a number of factors are responsible for collapse of high-rise, reinforced concrete buildings in Nigeria. Government, professional bodies and stakeholders are asking countless questions as to who should be responsible and how solutions could be proffered. Therefore this study is aimed to identify the contributing factors to high-rise buildings defects and failures in Nigeria, which frequently occur in construction project in order to minimize time and cost and also the roles of professionals and other participants play in the industry in terms of the use of building materials, placement and curing of concrete, modification in the use of a building, collapse of building induced by fire and other causes. The data is collected from questionnaire from various players in construction industry in Nigeria. This study is succeeds in identifying the causes of building failure and also suggesting possible measures to be taken by government and other regulatory bodies in the building industry to avert this and also improve the effectiveness of managing appraisal process of failures and defects in the future.

Keywords: building defects, building failures, Nigerian construction industry, professionals

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Authors: Hamad Almohamadi, Nabeel Alharthi, Majed Alamoudi

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Biphasic electrodes featuring CuSx/NiSx electrodeposited on nickel foam have been investigated for their electrocatalytic activity in water splitting. The study investigates the impacts of an S-vacancy induced biphasic design on the overpotential and Tafel slope. According to the findings, the NiSx/CuSx/NF electrode with S-vacancy defects displays stronger oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) activity with lower overpotential and a steeper Tafel slope than the non-defect sample. NiSx/CuSx/NF exhibits the lowest overpotential value of 212 mV vs reversible hydrogen electrode (RHE) for OER and −109 mV vs RHE for HER at 10 mA cm−2. Tafel slope of 25.4 mV dec−1 for OER and −108 mV dec−1 for OER found of that electrode. The electrochemical surface area (ECSA) and diffusion impedance of the electrode is calculated. The maximum ECSA, lowest series resistance and lowest charge transfer resistance are found in the *NiSx/CuSx/NF sample with S-vacancy defects, showing increased electrical conductivity and quick charge transfer kinetics. The *NiSx/CuSx/NF electrode was found to be stable for 80 hours in pure water splitting and 20 hours in sea-water splitting. The investigation comes to the conclusion that the enhanced water splitting activity and electrical conductivity of the electrode are caused by S-vacancy defects resulting in improved water splitting performance.

Keywords: water splitting, electrocatalyst, biphasic design, electrodeposition

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Authors: Suchao Donpudsa, Anchalee Tassanakajon, Vichien Rimphanitchayakit

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A crustin gene, LV-SWD1, previously found in the hemocyte cDNA library of Litopenaeus vannamei, contains the open reading frames of 288 bp encoding a putative protein of 96 amino acid residues. The putative signal peptides of the LV-SWD1 were identified using the online SignalP 3.0 with predicted cleavage sites between Ala24-Val25, resulting in 72 residue mature protein with calculated molecular mass of 7.4 kDa and predicted pI of 8.5. This crustin contains a Arg-Pro rich region at the amino-terminus and a single whey acidic protein (WAP) domain at the carboxyl-terminus. In order to characterize their properties and biological activities, the recombinant crustin protein was produced in the Escherichia coli expression system. Antimicrobial assays showed that the growth of Bacillus subtilis was inhibited by this recombinant crustin with MIC of about 25-50 µM.

Keywords: crustin, single whey acidic protein, Litopenaeus vannamei, antimicrobial activity

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Authors: Tia Morosin, Marie Shella De Robles

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Rectocele may be associated with symptoms of both obstructed defecation and faecal incontinence. Currently, numerous operative techniques exist to treat patients with rectocele; however, no single technique has emerged as the optimal approach in patients with post-partum faecal incontinence. The purpose of this study was to evaluate the clinical outcome in a consecutive series of patients who underwent transperineal repair of rectocele for patients presenting with faecal incontinence as the predominant symptom. Twenty-three consecutive patients from April 2000 to July 2015 with symptomatic rectocele underwent transperineal repair by a single surgeon. All patients had a history of vaginal delivery, with or without evidence of associated anal sphincter injury at the time. The median age of the cohort was 53 years (range 21 to 90 years). The median operating time and length of hospital stay were 2 hours and 7 days, respectively. Two patients developed urinary retention post-operatively, which required temporary bladder catheterization. One patient had wound dehiscence, which was managed by absorbent dressing applied by the patient and her carer. There was no operative mortality. In all patients with rectocele, there was a concomitant anal sphincter disruption. All patients had satisfactory improvement with regard to faecal incontinence on follow-up. This study suggests this method provides excellent anatomic and physiologic results with minimal morbidity. However, because none of the patients gained full continence postoperatively, pelvic floor rehabilitation might be also needed to achieve better sphincter function in patients with incontinence.

Keywords: anal sphincter defect, faecal incontinence, rectocele, transperineal repair

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Authors: Sachinkumar Patil, Sonali Patil, Shitalkumar Patil

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Nanoparticles played important role in the biomedicine. New advanced methods having great potential apllication in the diagnosis and therapy of cancer. Now a day’s magnetic nanoparticles used in cancer therapy. Cancer is the major disease causes death. Magnetic nanoparticles show response to the magnetic field on the basis of this property they are used in cancer therapy. Cancer treated with hyperthermia by using magnetic nanoparticles it is unconventional but more safe and effective method. Magnetic nanoparticles prepared by using different innovative techniques that makes particles in uniform size and desired effect. Magnetic nanoparticles already used as contrast media in magnetic resonance imaging. A magnetic nanoparticle has been great potential application in cancer diagnosis and treatment as well as in gene therapy. In this review we will discuss the progress in cancer therapy based on magnetic nanoparticles, mainly including magnetic hyperthermia, synthesis and characterization of magnetic nanoparticles, mechanism of magnetic nanoparticles and application of magnetic nanoparticles.

Keywords: magnetic nanoparticles, synthesis, characterization, cancer therapy, hyperthermia, application

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Authors: Blanca Fatela Cantillo, Silvia Iglesias Cerrato, Guadalupe Garrido Ceca

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Purpose: Bleb dysfunction is a late complication following glaucoma filtration surgery. We describe our surgical technique for excision and reconstruction of a hypertrophic bleb complication using bovine pericardium patch graft (Tutopatch®) and amniotic membrane. Material and methods: The case report presents a hypertrophic bleb over the cornea with good intraocular pressure control. The hanging bleb without leak caused dysesthesia and high irregular astigmatism. Bleb reconstruction involved the excision of corneal fibrous material and avascular conjunctiva, preserving the original scleral and tennon. Bovine pericardium patch graft (Tutopatch®) was sited over these with fixed sutures, reinforcing the underlying scleral, and the conjunctiva advanced. The superior epithelium corneal defect was covered using an amniotic membrane. Conclusion: Repair of bleb dysfunction with varied techniques has been reported, including conjunctival advancement, use of scleral patch graft, dural patch graft, or pericardium. Additional use of amniotic membrane promotes epithelialization and exhibits anti-fibrotic and anti-inflammatory features. Reconstruction with bovine pericardium patch graft and amniotic membrane resulted in pain relief, visual rehabilitation, and good aesthetic results, with preservation of bleb function.

Keywords: reconstruction, hypertrophic bleb, bovine pericardium, amniotic membrane, dysesthesia of the bleb

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Authors: Gehan Hussein, Hams Ahmad, Baher Matta, Yasmeen Mansi, Mohamad Fawzi

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Background: Congenital heart disease (CHD) is a common problem worldwide with variable incidence in different countries. The exact etiology is unknown, suggested to be multifactorial. We aimed to study the incidence of various CHD in a neonatal intensive care unit (NICU) in a tertiary care hospital in Egypt and the possible associations with variable risk factors. Methods: Prospective study was conducted over a period of one year (2013 /2014) at NICU KasrAlAini School of Medicine, Cairo University. Questionnaire about possible maternal and/or paternal risk factors for CHD, clinical examination, bedside echocardiography were done. Cases were classified into groups: group 1 without CHD and group 2 with CHD. Results: from 723 neonates admitted to NICU, 180 cases were proved to have CHD, 58 % of them were males. patent ductus arteriosus(PDA) was the most common CHD (70%), followed by an atrial septal defect (ASD8%), while Fallot tetralogy and single ventricle were the least common (0.45 %) for each. CHD was found in 30 % of consanguineous parents Maternal age ≥ 35 years at the time of conception was associated with increased incidence of PDA (p= 0.45 %). Maternal diabetes and insulin intake were significantly associated with cases of CHD (p=0.02 &0.001 respectively), maternal hypertension and hypothyroidism were both associated with VSD, but the difference did not reach statistical significance (P=0.36 &0.44respectively). Maternal passive smoking was significantly associated with PDA (p=0.03). Conclusion: The most frequent CHD in the studied population was PDA, followed by ASD. Maternal conditions as diabetes was associated with VSD occurrence.

Keywords: NICU, risk factors, congenital heart disease, echocardiography

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Authors: Soo Dong Cho, In-Ohk Ouh, Byeong Sul Kang, Seyeon Park, In-Soo Cho, Jae Young Song

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An VP2 gene from the current prevalent CPV (Canine Parvovirus) strain (new CPV-2a) in the Republic of Korea was expressed in a baculovirus expression system. Genomic DNA was extracted from the isolate strain CPV-2a. The recombinant baculovirus, containing the coding sequences of VP2 with the histidine tag at the N-terminus, were generated by using the Bac-to-Bac system. For production of the recombinant VP2 proteins, SF9 cells were transfection into 6 wells. Propagation of recombinant baculoviruses and expression of the VP2 protein were performed in the Sf9 cell line maintained. The proteins were detected to Western blot anlaysis. CPV-2a VP2 was detected by Western blotting the monoclonal antibodies recognized 6x His and the band had a molecular weight of 65 KDa. We demonstrated that recombinant CPV-2a VP2 expression in baculovirus. The recombinant CPV-2a VP2 may able to development of specific diagnostic test and vaccination of against CPV2. This study provides a foundation for application of CPV2 on the development of new CPV2 subunit vaccine.

Keywords: baculovirus, canine parvovirus 2a, Dog, Korea

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Authors: Igor V. Grigoriev

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Understanding of biological processes encoded in fungi is instrumental in addressing future food, feed, and energy demands of the growing human population. Genomics is a powerful and quickly evolving tool to understand these processes. The Fungal Genomics Program of the US Department of Energy Joint Genome Institute (JGI) partners with researchers around the world to explore fungi in several large scale genomics projects, changing the fungal genomics landscape. The key trends of these changes include: (i) rapidly increasing scale of sequencing and analysis, (ii) developing approaches to go beyond culturable fungi and explore fungal ‘dark matter,’ or unculturables, and (iii) functional genomics and multi-omics data integration. Power of comparative genomics has been recently demonstrated in several JGI projects targeting mycorrhizae, plant pathogens, wood decay fungi, and sugar fermenting yeasts. The largest JGI project ‘1000 Fungal Genomes’ aims at exploring the diversity across the Fungal Tree of Life in order to better understand fungal evolution and to build a catalogue of genes, enzymes, and pathways for biotechnological applications. At this point, at least 65% of over 700 known families have one or more reference genomes sequenced, enabling metagenomics studies of microbial communities and their interactions with plants. For many of the remaining families no representative species are available from culture collections. To sequence genomes of unculturable fungi two approaches have been developed: (a) sequencing DNA from fruiting bodies of ‘macro’ and (b) single cell genomics using fungal spores. The latter has been tested using zoospores from the early diverging fungi and resulted in several near-complete genomes from underexplored branches of the Fungal Tree, including the first genomes of Zoopagomycotina. Genome sequence serves as a reference for transcriptomics studies, the first step towards functional genomics. In the JGI fungal mini-ENCODE project transcriptomes of the model fungus Neurospora crassa grown on a spectrum of carbon sources have been collected to build regulatory gene networks. Epigenomics is another tool to understand gene regulation and recently introduced single molecule sequencing platforms not only provide better genome assemblies but can also detect DNA modifications. For example, 6mC methylome was surveyed across many diverse fungi and the highest among Eukaryota levels of 6mC methylation has been reported. Finally, data production at such scale requires data integration to enable efficient data analysis. Over 700 fungal genomes and other -omes have been integrated in JGI MycoCosm portal and equipped with comparative genomics tools to enable researchers addressing a broad spectrum of biological questions and applications for bioenergy and biotechnology.

Keywords: fungal genomics, single cell genomics, DNA methylation, comparative genomics

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Authors: Benkouiten Imene, Chabli Ouerdia, Boutoutaou Hamid, Kadri Nesrine, Bouledroua Omar

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Algeria is actively enhancing gas productivity by augmenting the supply flow. However, this effort has led to increased internal pressure, posing a potential risk to the pipeline's integrity, particularly in the presence of corrosion defects. Sonatrach relies on a vast network of pipelines spanning 24,000 kilometers for the transportation of gas and oil. The aging of these pipelines raises the likelihood of corrosion both internally and externally, heightening the risk of ruptures. To address this issue, a comprehensive inspection is imperative, utilizing specialized scraping tools. These advanced tools furnish a detailed assessment of all pipeline defects. It is essential to recalculate the pressure parameters to safeguard the corroded pipeline's integrity while ensuring the continuity of production. In this context, Sonatrach employs symbolic pressure limit calculations, such as ASME B31G (2009) and the modified ASME B31G (2012). The aim of this study is to perform a comparative analysis of various limit pressure calculation methods documented in the literature, namely DNV RP F-101, SHELL, P-CORRC, NETTO, and CSA Z662. This comparative assessment will be based on a dataset comprising 329 burst tests published in the literature. Ultimately, we intend to introduce a novel approach grounded in the finite element method, employing ANSYS software.

Keywords: pipeline burst pressure, burst test, corrosion defect, corroded pipeline, finite element method

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Authors: Paula I. Buonfiglio, Carlos David Bruque, Lucia Salatino, Vanesa Lotersztein, Sebastián Menazzi, Paola Plazas, Ana Belén Elgoyhen, Viviana Dalamón

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Hearing loss (HL) is the most prevalent sensorineural disorder affecting about 10% of the global population, with more than half due to genetic causes. About 1 in 500-1000 newborns present congenital HL. Most of the patients are non-syndromic with an autosomal recessive mode of inheritance. To date, more than 100 genes are related to HL. Therefore, the Whole-exome sequencing (WES) technique has become a cost-effective alternative approach for molecular diagnosis. Nevertheless, new challenges arise from the detection of novel variants, in particular missense changes, which can lead to a spectrum of genotype-to-phenotype correlations, which is not always straightforward. In this work, we aimed to identify the genetic causes of HL in isolated and familial cases by designing a multistep approach to analyze target genes related to hearing impairment. Moreover, we performed in silico and in vivo analyses in order to further study the effect of some of the novel variants identified in the hair cell function using the zebrafish model. A total of 650 patients were studied by Sanger Sequencing and Gap-PCR in GJB2 and GJB6 genes, respectively, diagnosing 15.5% of sporadic cases and 36% of familial ones. Overall, 50 different sequence variants were detected. Fifty of the undiagnosed patients with moderate HL were tested for deletions in STRC gene by Multiplex ligation-dependent probe amplification technique (MLPA), leading to 6% of diagnosis. After this initial screening, 50 families were selected to be analyzed by WES, achieving diagnosis in 44% of them. Half of the identified variants were novel. A missense variant in MYO6 gene detected in a family with postlingual HL was selected to be further analyzed. A protein modeling with AlphaFold2 software was performed, proving its pathogenic effect. In order to functionally validate this novel variant, a knockdown phenotype rescue assay in zebrafish was carried out. Injection of wild-type MYO6 mRNA in embryos rescued the phenotype, whereas using the mutant MYO6 mRNA (carrying c.2782C>A variant) had no effect. These results strongly suggest the deleterious effect of this variant on the mobility of stereocilia in zebrafish neuromasts, and hence on the auditory system. In the present work, we demonstrated that our algorithm is suitable for the sequential multigenic approach to HL in our cohort. These results highlight the importance of a combined strategy in order to identify candidate variants as well as the in silico and in vivo studies to analyze and prove their pathogenicity and accomplish a better understanding of the mechanisms underlying the physiopathology of the hearing impairment.

Keywords: diagnosis, genetics, hearing loss, in silico analysis, in vivo analysis, WES, zebrafish

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Authors: Y. L. Hor, H. S. Chu, V. P. Bui

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Composite material is widely used to replace conventional material, especially in the aerospace industry to reduce the weight of the devices. It is formed by combining reinforced materials together via adhesive bonding to produce a bulk material with alternated macroscopic properties. In bulk composites, degradation may occur in microscopic scale, which is in each individual reinforced fiber layer or especially in its matrix layer such as delamination, inclusion, disbond, void, cracks, and porosity. In this paper, we focus on the detection of defect in matrix layer which the adhesion between the composite plies is in contact but coupled through a weak bond. In fact, the adhesive defects are tested through various nondestructive methods. Among them, pulsed phase thermography (PPT) has shown some advantages providing improved sensitivity, large-area coverage, and high-speed testing. The aim of this work is to develop an efficient numerical model to study the application of PPT to the nondestructive inspection of weak bonding in composite material. The resulting thermal evolution field is comprised of internal reflections between the interfaces of defects and the specimen, and the important key-features of the defects presented in the material can be obtained from the investigation of the thermal evolution of the field distribution. Computational simulation of such inspections has allowed the improvement of the techniques to apply in various inspections, such as materials with high thermal conductivity and more complex structures.

Keywords: pulsed phase thermography, weak bond, composite, CFRP, computational modelling, optimization

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Authors: Keshavamurthy Ganapathy Bhat, Manvinderpal Singh Marwaha

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Background: Coronary artery Disease (CAD) is a common cause of morbidity, mortality and reason for unfitness amongst aircrew. Coronary angioplasty and stenting are the standard of care for CAD. Antiplatelet drugs like Aspirin and Clopidogrel(Dual Antiplatelet therapy) are routinely prescribed post-stenting which are permitted for flying. However, in the recent past, Ticagrelor is being used in place of Clopidogrel as per ACC AHA and ESC guidelines. However Ticagrelor is not permitted for flying. Case Presentation: A 55-year-old pilot suffered Anterior Wall Myocardial Infarction. Angiography showed blockages in Left Anterior Descending Artery(LAD) and Right coronary artery (RCA). He underwent primary angioplasty and stenting LAD and subsequent stenting to RCA. Recovery was uneventful. One year later he was asymptomatic with normal Left ventricular function and no reversible perfusion defect on stress MPI. He had patent stents and coronaries on check angiogram. However, he was not allowed to fly since he was on Ticagrelor. He had to be switched over to Clopidogrel from Ticagrelor one year after stenting to permit him for flying. Similarly, switching had to be done in a 45-year-old pilot. Ticagrelor has been proven to be more effective than clopidogrel and as safe as Clopidogrel in preventing stent thrombosis. If Clopidogrel is being permitted, there is no need to restrict Ticagrelor. Hence "Policy" needs to be changed. Conclusions: Dual Antiplatelet therapy is the standard of care post coronary stenting which has been proved safe and effective. Policy needs to be changed to permit flying with Ticagrelor which is more effective than Clopidogrel and equally safe.

Keywords: antiplatelet drugs, coronary artery disease, stenting, ticagrelor

Procedia PDF Downloads 163

Authors: Swati Srivastava, Mattia Lauriola, Yuval Gilad, Adi Kimchi, Yosef Yarden

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The glucocorticoid receptor (GR) has been proposed to play important, but incompletely understood roles in cancer. Glucocorticoids (GCs) are widely used as co-medication of various carcinomas, due to their ability to reduce the toxicity of chemotherapy. Furthermore, GR antagonism has proven to be a strategy to treat triple negative breast cancer and castration-resistant prostate cancer. These observations suggest differential GR involvement in cancer subtypes. The goal of our study has been to elaborate the current understanding of GR signaling in tumor progression and metastasis. Our study involves two cellular models, non-tumorigenic breast epithelial cells (MCF10A) and Ewing sarcoma cells (CHLA9). In our breast cell model, the results indicated that the GR agonist dexamethasone inhibits EGF-induced mammary cell migration, and this effect was blocked when cells were stimulated with a GR antagonist, namely RU486. Microarray analysis for gene expression revealed that the mechanism underlying inhibition involves dexamenthasone-mediated repression of well-known activators of EGFR signaling, alongside with enhancement of several EGFR’s negative feedback loops. Because GR mainly acts primarily through composite response elements (GREs), or via a tethering mechanism, our next aim has been to find the transcription factors (TFs) which can interact with GR in MCF10A cells.The TF-binding motif overrepresented at the promoter of dexamethasone-regulated genes was predicted by using bioinformatics. To validate the prediction, we performed high-throughput Protein Complementation Assays (PCA). For this, we utilized the Gaussia Luciferase PCA strategy, which enabled analysis of protein-protein interactions between GR and predicted TFs of mammary cells. A library comprising both nuclear receptors (estrogen receptor, mineralocorticoid receptor, GR) and TFs was fused to fragments of GLuc, namely GLuc(1)-X, X-GLuc(1), and X-GLuc(2), where GLuc(1) and GLuc(2) correspond to the N-terminal and C-terminal fragments of the luciferase gene.The resulting library was screened, in human embryonic kidney 293T (HEK293T) cells, for all possible interactions between nuclear receptors and TFs. By screening all of the combinations between TFs and nuclear receptors, we identified several positive interactions, which were strengthened in response to dexamethasone and abolished in response to RU486. Furthermore, the interactions between GR and the candidate TFs were validated by co-immunoprecipitation in MCF10A and in CHLA9 cells. Currently, the roles played by the uncovered interactions are being evaluated in various cellular processes, such as cellular proliferation, migration, and invasion. In conclusion, our assay provides an unbiased network analysis between nuclear receptors and other TFs, which can lead to important insights into transcriptional regulation by nuclear receptors in various diseases, in this case of cancer.

Keywords: epidermal growth factor, glucocorticoid receptor, protein complementation assay, transcription factor

Procedia PDF Downloads 224

Authors: Janis Zarins, Kristaps Blums, Oskars Radzins, Renars Deksnis, Atis Svare, Santa Salaka

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Wide tumor resection remains the first choice method for tumors of the oral cavity. Nevertheless, remained tissue defect impacts patients functional and aesthetical outcome, which could be improved using microvascular tissue transfers. Mandibular reconstruction is challenging due to the complexity of composite tissue defects and occlusal relationships for normal eating, chewing, and pain free jaw motions. Individual 3-D virtual planning would provide better symmetry and functional outcome. The main goal of preoperative planning is to develop a customized surgical approach with patient specific cutting guides of the mandible, osteotomy guides of the fibula, pre-bended osteosynthesis plates to perform more precise reconstruction, to decrease the surgery time and reach the best outcome. Our study is based on the analysis of 32 patients operated on between 2019 to 2021. All patients underwent mandible reconstruction with vascularized fibula flaps. Patients characteristics, surgery profile, survival, functional outcome, and quality of life was evaluated. Preoperative planning provided a significant decrease of surgery time and the best arrangement of bone closely similar as before the surgery. In cases of bone asymmetry, deformity and malposition, a new mandible was created using 3D planning to restore the appearance of lower jaw anatomy and functionality.

Keywords: mandibular, 3D planning, cutting guides, fibula flap, reconstruction

Procedia PDF Downloads 123

Authors: Soumendu Monia, Vaibhav Jain, Hrishikesh Jugade, Manashi Adhikary, Goutam Mukhopadhyay

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'Rolled in scale' (RIS) and 'Rolled in Scum' (RISc) are two superficial surface defects on cold rolled and annealed steel sheets which affect the aesthetics of surface and thereby that of the end-product. Both the defects are believed to be originating from distinctly different sources having different mechanisms of formation. However, due to their similar physical appearance, RIS and RISc are generally confused with each other and hence attaining the exact root cause for elimination of the defect becomes difficult. RIS appears irregular in shape, sometimes scattered, and always oriented in rolling direction. RISc is generally oval shaped, having identifiable pointed edges and mostly oriented in rolling direction. Visually, RIS appears to be greyish in colour whereas RISc is whitish in colour. Both the defects have quite random occurrence and do not leave any imprints on the reverse-side of the sheet. In the current study, an attempt has been made to differentiate these two similar looking surface defects using various metallographic and characterization techniques. Systematic experiments have been carried out to identify possible mechanisms of formation of these defects. Detailed characterization revealed basic differences between RIS and RISc with respect to their surface morphology. To summarize, RIS was observed as a residue of an otherwise under-pickled scale patch on surface, after it has been subjected to cold rolling and annealing in a batch/continuous furnace. Whereas RISc was found to be a localized rubbing of the surface, at the time of cold rolling itself, resulting in a rough surface texture.

Keywords: annealing, rolled in scale, rolled in scum, skin panel

Procedia PDF Downloads 177

Authors: S. Shankar Bharathi

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Inspection of surface defects on metallic components has always been challenging due to its specular property. Occurrences of defects such as scratches, rust, pitting are very common in metallic surfaces during the manufacturing process. These defects if unchecked can hamper the performance and reduce the life time of such component. Many of the conventional image processing algorithms in detecting the surface defects generally involve segmentation techniques, based on thresholding, edge detection, watershed segmentation and textural segmentation. They later employ other suitable algorithms based on morphology, region growing, shape analysis, neural networks for classification purpose. In this paper the work has been focused only towards detecting scratches. Global and other thresholding techniques were used to extract the defects, but it proved to be inaccurate in extracting the defects alone. However, this paper does not focus on comparison of different segmentation techniques, but rather describes a novel approach towards segmentation combined with hausdorff dilation distance. The proposed algorithm is based on the distribution of the intensity levels, that is, whether a certain gray level is concentrated or evenly distributed. The algorithm is based on extraction of such concentrated pixels. Defective images showed higher level of concentration of some gray level, whereas in non-defective image, there seemed to be no concentration, but were evenly distributed. This formed the basis in detecting the defects in the proposed algorithm. Hausdorff dilation distance based on mathematical morphology was used to strengthen the segmentation of the defects.

Keywords: metallic surface, scratches, segmentation, hausdorff dilation distance, machine vision

Procedia PDF Downloads 420

Authors: R. I. You, C. L. Ho, M. S. Dai, H. M. Hung, S. F. Yen, C. S. Chen, T. Y. Chao

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Neutrophils are the most abundant innate immune cells to against invading microorganisms. Numerous data shown neutrophils have plasticity in response to physiological and pathological conditions. Tumor-associated neutrophils (TAN) exist in distinct types of tumor and play an important role in cancer biology. Different transcriptomic profiles of neutrophils in tumor and non-tumor samples have been identified. Several miRNAs have been recognized as regulators of gene expression in neutrophil, which may have key roles in neutrophil activation. However, the miRNAs expression patterns in TAN are not well known. To address this question, magnetic bead isolated neutrophils from tumor-bearing mice were used in this study. We analyzed production of reactive oxygen species (ROS) by luminol-dependent chemiluminescence assay. The expression of miRNAs targeting NADPH oxidase, ROS generation and autophagy was explored using quantitative real-time polymerase chain reaction. Our data suggest that tumor environment influence neutrophil develop to differential states of activation via miRNAs regulation.

Keywords: tumor-associated neutrophil, miRNAs, neutrophil, ROS

Procedia PDF Downloads 464

Authors: Abdul Manan

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The necessity for efficient and cost-effective energy storage devices to intelligently store the inconsistent energy output from modern renewable energy sources is peaked today. The scientific community is struggling to identify the appropriate material system for energy storage applications. Countless contributions by researchers worldwide have now helped us identify the possible snags and limitations associated with each material/method. Energy storage has attracted great attention for its use in portable electronic devices military field. Different devices, such as dielectric capacitors, supercapacitors, and batteries, are used for energy storage. Of these, dielectric capacitors have high energy output, a long life cycle, fast charging and discharging capabilities, work at high temperatures, and excellent fatigue resistance. The energy storage characteristics have been studied to be highly affected by various factors, such as grain size, optimized compositions, grain orientation, energy band gap, processing techniques, defect engineering, core-shell formation, interface engineering, electronegativity difference, the addition of additives, density, secondary phases, the difference of Pmax-Pr, sample thickness, area of the electrode, testing frequency, and AC/DC conditions. The data regarding these parameters/factors are scattered in the literature, and the aim of this study is to gather the data into a single paper that will be beneficial for new researchers in the field of interest. Furthermore, control over and optimizing these parameters will lead to enhancing the energy storage properties.

Keywords: strategies, ceramics, energy storage, capacitors

Procedia PDF Downloads 70

Authors: Marcus Klein, Martina GrießBach, Richard Kupke

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The current advances in the research and manufacturing of large area graphene layers are promising towards the introduction of this exciting material in the display industry and other applications that benefit from excellent electrical and optical characteristics. New production technologies in the fabrication of flexible displays, touch screens or printed electronics apply graphene layers on non-metal substrates and bring new challenges to the required metrology. Traditional measurement concepts of layer thickness, sheet resistance, and layer uniformity, are difficult to apply to graphene production processes and are often harmful to the product layer. New non-contact sensor concepts are required to adapt to the challenges and even the foreseeable inline production of large area graphene. Dedicated non-contact measurement sensors are a pioneering method to leverage these issues in a large variety of applications, while significantly lowering the costs of development and process setup. Transferred and printed graphene layers can be characterized with high accuracy in a huge measurement range using a very high resolution. Large area graphene mappings are applied for process optimization and for efficient quality control for transfer, doping, annealing and stacking processes. Examples of doped, defected and excellent Graphene are presented as quality images and implications for manufacturers are explained.

Keywords: graphene, doping and defect testing, non-contact sheet resistance measurement, inline metrology

Procedia PDF Downloads 305

Authors: Yu-Shan Wu, Po-Liang Lai, I-Ming Chu

Abstract:

Poly(methylmethacrylate)(PMMA) is the most frequently used bone void filler for vertebral augmentation in osteoporotic fracture. PMMA bone cement not only exhibits strong mechanical properties but also can fabricate according to the shape of bone defect. However, the adhesion between the PMMA-based cement and the adjacent bone is usually weak and as PMMA bone cement is inherently bioinert. The combination of bioceramics and polymers as composites may increase cell adhesion and improve biocompatibility. The nano-hydroxyapatite(HAP) not only plays a significant role in maintaining the properties of the natural bone but also offers a favorable environment for osteoconduction, protein adhesion, and osteoblast proliferation. However, defects and cracks can form at the polymer/ceramics interface, resulting in uneven distribution of stress and subsequent inferior mechanical strength. Surface-modified HAP nano-crystals were prepared by chemically grafting poly(ε-caprolactone)(PCL) on surface-modified nano-HAP surface to increase the affinity of polymer/ceramic phases .Thus, incorporation of surface-modified nano-hydroxyapatite (EC-HAP) may not only improve the interfacial adhesion between cement and bone and between nanoparticles and cement, but also increase biocompatibility. In this research, PMMA mixing with 0, 5, 10, 15, 20, 25 and 30 wt% EC-HAP were examined. MC3T3-E1 cells were used for the biological evaluation of the response to the cements in vitro. Morphology was observed using scanning electron microscopy (SEM). Mechanical properties of HAP/PMMA and EC-HAP/PMMA cement were investigated by compression test. Surface wettability of the cements was measured by contact angles.

Keywords: bone cement, biocompatibility, nano-hydroxyapatite, polycaprolactone, PMMA, surface grafting

Procedia PDF Downloads 393

Authors: Anurag Niranjan, Michael Fitzpatrick, Yin Jin Janin, Jazeel Chukkan, Niall Smyth

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Fillet welds are used in joining longitudinal stiffeners in ship structures. Welding residual stresses in fillet welds are generally distributed in a non-uniform manner, as shown in previous research the residual stress redistribution occurs under the cyclic loading that is experienced by such joints during service, and the combination of the initial residual stress, local constraints, and loading can alter the stress field in ways that are extremely difficult to predict. As the residual stress influences the crack propagation originating from the toe of the fillet welds, full understanding of the residual stress field and how it evolves is very important for structural integrity calculations. Knowledge of the residual stress redistribution in the presence of a flaw is therefore required for better fatigue life prediction. Moreover, defect assessment procedures such as BS7910 offer very limited guidance for flaw acceptance and the associated residual stress redistribution in the assessment of fillet welds. Therefore the objective of this work is to study a surface-breaking flaw at the weld toe region in a fillet weld under cyclic load, in conjunction with residual stress measurement at pre-defined crack depths. This work will provide details of residual stress redistribution under cyclic load in the presence of a crack. The outcome of this project will inform integrity assessment with respect to the treatment of residual stress in fillet welds. Knowledge of the residual stress evolution for this weld geometry will be greatly beneficial for flaw tolerance assessments (BS 7910, API 591).

Keywords: fillet weld, fatigue, residual stress, structure integrity

Procedia PDF Downloads 134

Authors: Meysam Naeimi, Zili Li, Roumen Petrov, Rolf Dollevoet, Jilt Sietsma, Jun Wu

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The substantial similarity of fatigue mechanism in a new test rig for rolling contact fatigue (RCF) has been investigated. A new reduced-scale test rig is designed to perform controlled RCF tests in wheel-rail materials. The fatigue mechanism of the rig is evaluated in this study using a combined finite element-fatigue prediction approach. The influences of loading conditions on fatigue crack initiation have been studied. Furthermore, the effects of some artificial defects (squat-shape) on fatigue lives are examined. To simulate the vehicle-track interaction by means of the test rig, a three-dimensional finite element (FE) model is built up. The nonlinear material behaviour of the rail steel is modelled in the contact interface. The results of FE simulations are combined with the critical plane concept to determine the material points with the greatest possibility of fatigue failure. Based on the stress-strain responses, by employing of previously postulated criteria for fatigue crack initiation (plastic shakedown and ratchetting), fatigue life analysis is carried out. The results are reported for various loading conditions and different defect sizes. Afterward, the cyclic mechanism of the test rig is evaluated from the operational viewpoint. The results of fatigue life predictions are compared with the expected number of cycles of the test rig by its cyclic nature. Finally, the estimative duration of the experiments until fatigue crack initiation is roughly determined.

Keywords: fatigue, test rig, crack initiation, life, rail, squats

Procedia PDF Downloads 507